Bottom trawling fishing boats have caused extensive damage to many cold water coral reefs along the margin of the North East Atlantic Ocean. But now, researchers have uncovered a glimmer of hope for these important biodiversity hotspots in the form of cliffhanging coral colonies. These colonies, 1350 metres below the surface of the Bay of Biscay, cover several hundred square metres of cliff face belonging to the vertical and overhanging sides of submarine canyons. The scientists believe that these newly-discovered habitats could help repair the areas damaged by the trawlers heavily-weighted nets.

Miller's grizzled langur, a breed of large monkey so rare that it was thought to be extinct, has been captured on film by researchers who set up camera traps in Borneo. Scientists were baffled by the discovery as the monkeys showed up well outside of their previously recorded home range. With virtually no existing photographs of the monkeys available, the scientists faced a considerable challenge while trying to identify the species to confirm their suspicions, eventually forcing them to compare their photographs with museum sketches.

Extraordinarily cold temperatures in the winter of 2010/ 2011 was the cause of unprecedented damage to the ozone layer above the Arctic, a new study reports. Researchers from the KIT Institute of Meteorology and Climate Research (IMK) analysed measurements of the chemical composition of the atmosphere and found that a further decrease in temperatures by just 1C would be sufficient to cause a nearly complete destruction of the Arctic ozone layer in some areas. Observations over the past thirty years indicate that the stratosphere in cold Arctic winters cooled down by about 1C per decade and that, whilst a further increase in carbon dioxide and other greenhouse gasses will warm up the bottom air layers near the ground due to reflection, they will also result in a cooling of the air layers in the stratosphere above, where the ozone is located.

Be it skydiving, performing a karaoke number or swimming with sharks, why do we often plan to take risks but back down when the moment of truth arrives? For scientists, this “illusion of courage” is just one example of an “empathy gap” - otherwise known as our inability to imagine how we will behave in future emotional situations. According to the empathy gap theory, when that moment of truth is in the future, we’re not feeling, and are thus not in touch with the fear we’ll experience when it’s time to jump. A recent study undertaken at Carnegie Mellon University has demonstrated how this illusion of courage can be reduced by putting people in touch with the fear they would experience.

A NASA study has found 2011 to be the ninth-warmest year on record. The finding marks the continuation of a trend in which nine of the ten warmest years in the modern meteorological record have occurred since the year 2000. The data compares temperatures across the planet in 2011 to the average global temperature from the mid-20th century. The average temperature around the globe in 2011 was 0.51 celcius warmer than this mid-20th century baseline. The team further underlined how temperatures have climbed alongside the rising levels of greenhouse gas emissions from energy production, industry and vehicles, most notably since the 1970s.

What is a leap second? And why are some people intent on getting rid of it? Take a look at this video to find out why a decision on abolishing the occasional, extra second added to the world’s time has been delayed until 2015.
 

 The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks (at) researchgate.net

Chris Austin, of Louisiana State University, has discovered the world’s smallest known vertebrate in the form of a frog found in New Guinea. Averaging only 7.7 millimetres in size, Paedophryne amauensis takes the title away from Paedocypris progenetica, an Indonesian fish averaging just over 8 millimetres. "The size limit of vertebrates, or creatures with backbones, is of considerable interest to biologists because little is understood about the functional constraints that come with extreme body size, whether large or small," said Austin.

Researchers at the University of Missouri have pioneered advanced 3D microscopic imaging that is helping scientists identify and monitor proteins involved in stiffening arteries - a major factor in cardiovascular disease. The new technology could eventually accelerate our understanding and treatment of the disease and help to combat a leading cause of death in the US as it contributes to the circulatory in disorders such as high blood pressure and diabetes. Furthermore, the team hope that the study’s findings may also be useful in future efforts to develop artificial vascular structures to improve tissue replacement.

A NASA statistical study based on six years worth of observations estimates that there are at least 100 billion planets located in our Milky Way galaxy. The technique employed, known as microlensing, uses one star as a magnifying lens, brightening the light from a background star. If planets are indeed orbiting the foreground star, the background star’s light further brightens, revealing the presence of planets that are too faint to be seen. Cool, right?

Preliminary research released by a team in China has found that adolescents with internet addiction disorder showed changes in the structure of white matter in the brain. Using MRI scanners the team compared images of the brains of 17 adolescents aged between 14 and 21 with internet addiction disorder and 16 without. By highlighting the fact that the changes affected the part of the brain associated with emotions, attention and decision making, the team sought to underline how this addiction may share psychological and neural mechanisms with other forms of substance addiction. The team now hopes to expand the sample size in order to further investigate these findings.

We may be one step closer to time travel... Researchers from Cornell University have managed to create a time or temporal cloak, albeit on a small scale, that effectively makes an event vanish by transporting information via a beam of light. The researchers hope that their findings might allow inserting an emergency signal without interrupting the main data screen, or multitasking operations in a photonic computer, where light beams on a chip replace wires.

Researchers from the University of California Los Angeles have set out to uncover the evolutionary background of the many species of New World monkeys. This BBC slide show celebrates the their varying, colourful and complex faces.  

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks (at) researchgate.net

Graphite may prove to be the key to a stronger and longer-lasting hip implant. New research released by Northwestern University focused on what is known as the tribological layer, the lubricating layer that forms on metallic joints as a result of friction. Until now, researchers were unsure as to how this layer formed and what it was composed of. But using a number of analytical tools, including electron and optical microscopes, the team successfully identified the chemical fingerprint of graphitic carbon. The team now hope develop graphitic surfaces that can be used to replace the traditional metal implants.

A recent study of 26 wealthy nations suggests that obesity may be an unintended side effect of free market economic policies. The research, released by the University of Michigan, found that countries with a high density of fast food restaurants per capita exhibited high levels of obesity. The team chose one fast food restaurant to use as a proxy measure for the amount of fast food restaurants present per 100,000 people. The teams calculations revealed that there are 7.52 fast food restaurants per 100,000 people in the United States, alongside obesity rates of 31.3% for men and 33.2% for women. For Japan, the figures showed 0.13 fast food restaurants per 100,000 people, alongside obesity rates of 2.9% for men and 3.3% for women. Furthermore, when comparing their data with figures charting the evolution of trade liberalisation policies, the team found a direct correlation between the two.

Steve Kawaler, professor of physics at Iowa State University, has assisted an international team of astronomers in analysing data collected by the Kepler space telescope to confirm that two Earth-sized planets have survived getting caught in the red-giant expansion of their host star. Kawaler, also a leader of the Kepler Asteroseismic Investigation, was able to verify that variations of light from a star were actually caused by two planets of that star. The findings, published in the journal Nature, allow astronomers a glimpse into what our own solar system may look like after several billion more years of evolution.

The BBC’s new six-part series takes viewers on a breathtaking journey across six continents from the perspective of migrating birds. This Guardian slide show gives you a behind the scenes look at the filming process and reveals some of cutting edge technology used to capture the soaring birds’ view.

The world was baffled when the once-deemed-impossible quasicrystals were found by geologists in rocks from Russia’s Koryak Mountains. First described by Nobel prize winner Daniel Schechtman in the 1980s, Quasicrystals have a most unusual structure which lies halfway between crystal and glass. However, a new study by researchers from Princeton University has found evidence to suggest that the Russian mineral may have extra-terrestrial origins, having arrived on Earth via meteorites.

Zebedee, a lone zebra shark living in Dubai’s Burj aAl Arab hotel aquarium has managed to lay healthy eggs for the fourth year in a row without ever being exposed to a male. In this BBC report, Phillip Hampsheir looks at some of the possible reasons behind this apparent ‘virgin birth.’ [Video]

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks (at) researchgate.net

The Hilbert book model

This model is a simple model of physics that is strictly based on the axioms of quantum logic. Quantum logic is very similar to classical logic, but one of the axioms of quantum logic is weaker than the corresponding axiom of classical logic. This concerns the modular law. The direct result of this weakening is that quantum logic has a lot more complicated structure than classical logic. Where classical logic can be displayed with a simple representation consisting of Venn diagrams, will quantum logic correspond to a complicated mathematical model that has the same lattice structure. This model consists of the set of the closed subspaces of an infinite dimensional separable Hilbert space. Hence that quantum physics is usually carried out within the framework of a Hilbert space. However, because also other types of Hilbert spaces exist, not always a separable Hilbert space is used for that purpose. An example is quantum field theory. This derogation can lead to contradictions that must be solved by a renormalization of the solution thus obtained. But, there are better ways to address fields that keep the direct relation with quantum logic intact. Such a different approach is applied in the Hilbert book model.
The Hilbert book model uses the broadest choices that can be made for this separable Hilbert space. The most important freedom of choice that still exists is the number system with the help of which the inner product between Hilbert vectors can be defined. This number system may consist of real numbers, complex numbers or quaternions. This last one is the widest choice and offers the most flexible opportunities. For this reason, the Hilbert book model also allows quaternions as eigenvalues of operators and as the values of fields and coordinates.
Both quantum logic and the corresponding separable Hilbert space offer no place for fields and can only offer a static representation. Neither quantum logic nor the separable Hilbert space can adapt the equivalent of local time. In addition the operators that work in separable Hilbert space do not possess eigenspaces that have the properties of a continuum. The eigenspaces of these operators have a countable number of eigenvalues. It is not possible to use these ingredients in order to form continuous equations of motion. So it is no wonder that physicists look to the capabilities of other Hilbert spaces. That happens especially in quantum field theories. Such a step breaks the direct relationship with quantum logic. However, there are other solutions to this dilemma.
Every separable Hilbert space is part of a Gelfand triple. This construct features operators that possess eigenspaces with the structure of a continuum. For that reason the Gelfand triple is also falsely called a "rigged Hilbert space". However, it is not a real Hilbert space. It's a sandwich, where a separable Hilbert space is part of.
The next step is that the eigenvalues of operators in the separable Hilbert space link to the continuum background eigenspace of corresponding operators in the Gelfand triple. This link will not be one on one. We allow the link to be inaccurate in a stochastic way. In other words, a probability distribution is added that for the eigenvector of the operator in the separable Hilbert space selects an exact value that at a test event is taken from the continuum background eigenspace.
Instead of directly applying a probability density distribution we use a quaternionic probability amplitude distribution. However, the square of the modulus of this distribution is a probability density distribution.
We can separate the amplitude distribution into a charge density distribution and a current density distribution. For a while the interpretation of these charges and currents will be left in the middle. In the described way we achieve several goals at one blow. It opens the possibility to apply continuity equations. Continuity equations are also called balance equations. The equations of motion of the charge-bearing quanta are in fact continuity equations. By using this approach, we have created the possibility to analyze the movement of these quanta, whatever those quanta may be.
This interpretation also determines the kind of operator that is involved. It is an operator that delivers an observable, which changes dynamically in the realm of a background continuum space.
We now have a powerful weapon in the hands to describe the behavior of quanta. Unfortunately, neither the separable Hilbert space that is extended with quaternionic probability amplitude distributions, nor the similarly extended quantum logic can represent anything else than a static status quo. Since the charge distributions and flow distributions are known in the form of probability distributions at least something is known about how the following static status quo will look. Thus, the somewhat extended model is still a static model and not a dynamic model.
The solution is obvious. It consists of an ordered sequence of consecutive static models. Each static model consists of a sandwich in the form of a Gelfand triple and the stochastic but static links that exist between the separable Hilbert space and the Gelfand triple. The picture that emerges is that of a book where the consecutive pages represent successive sandwiches. The page number acts as a progress counter. It is a global working counter. It adds a parameter that represents the Hilbert space wide progress to each Hilbert space in the Hilbert book model. So this parameter is not our common notion of time, but the progression counter has certainly much relation with it.
This model shows that no direct relationship exists between the progression parameter and the position of a quantum. The progression is represented by a Hilbert space wide parameter. The position is an eigenvalue of a corresponding operator. Only when the quantum moves, a relationship emerges between these quantities. A uniform movement can be described by a Galileo transformation or, when a maximum speed exists, by a Lorentz transformation.
We now have a dynamic model that can display the movement of quanta and can describe the behavior of related fields.
The beauty of this model is that it is literally based on pure logic. Only mathematics is used in order to extend that foundation. The main extra ingredient is the stochastic link between eigenvalues in the separable Hilbert space and eigenspaces in the Gelfand triple.
For more details see: Http://www.crypts-of-physics.eu/OntheoriginofdynamicsBoek2.pdf

Essentials of quantum movement

For an introduction, see: Essentials of the Hilbert book model.
The movements of quanta can be described by continuity equations. Dirac was the first to put the equation of motion of free electrons in the form of a continuity equation. However, he used a complex format and he used spinors and Dirac matrices in order to represent the quaternionic behavior of fields. Majorana followed him with a similar equation for Majorana particles. Both equations can be converted into quaternionic format and then they become a much easier interpretable form. It appears that the continuity equation contains a source/drain term that contains another quaternion flavor of the main transported field.
The general format of the equation that describes the free movement of quanta appears to be:
∇ψˣ = m ψʸ
Here the quaternionic nabla operator is the transporter. ψˣ is the transported quaternionic field flavor. ψʸ is the coupled quaternionic field flavor and m is the coupling factor.
The ordered pair {ψˣ, ψʸ} identifies a quantum type.
Two independent switch operations together determine four field flavors. The local coordinate system acts as a reference.
The first switch operation ψ⟹ψ* switches the sign of all three imaginary base vectors of the quaternion values. In imaginary quaternion space this operation works isotropic.
The second switch operation ψ⟹ψ¹ switches the sign of only one imaginary base vector of the quaternion values. In imaginary quaternion space this operation works anisotropic.
Both switch operations switch the handedness of the quaternion external vector product.
The four flavors differ in the sign of one, two or three imaginary base vectors. Two of the field flavors are right handed, the other two are left handed.
The flavor of the nabla operator equals the flavor of the local coordinate system of which the values act as parameters for the distributions that form the considered fields.
With each quantum that fulfills this scheme exists an anti-quantum.
That anti-quantum is formed by the pair {ψˣ*, ψʸ*} and obeys the equation of movement:
∇*ψˣ* = m ψʸ*
The real part of ψˣ represents a “charge” density distribution. The imaginary part of ψˣ represents a “current” density distribution. The “charge” for which the dynamics is described by the continuity equation stands for the switch event ψˣ⟹ψʸ in case of the quantum and stands for the switch event ψˣ*⟹ψʸ* in case of the anti-quantum.
If in a switch event the handedness is switched, then this involves an electrical charge. The strength of the charge and its sign is determined by the number of imaginary base vectors that switch and on the direction in which this switch takes place. This result in a variety of electrical charges (±e, ± ⅔ e, ± ⅓ e and 0.). Apart from electrical charges the quanta can be afflicted with color charge. This characteristic relates to the direction of the anisotropic switch.
Quanta exist for which coupling factor is zero. They obey different equations of motion.
If the transported field ψˣ is isotropic and the coupling factor not equal to zero, then the quantum concerns a fermion. Otherwise, it's a boson.
From the equation of motion another equation can be derived, from which via integration the coupling factor m can be calculated from the fields.
∫˯ (ψʸ*∇ψˣ) dV = m ∫˯ (ψʸ* ψʸ) dV= m ∫˯ |ψʸ|² dV = mg

g is a real constant g>0.
This equation shows that m is a property of the pair {ψˣ, ψʸ}, which defines the corresponding quantum.
In this way important properties, equations of motion and coupling factors for electrons, neutrinos, quarks, W bosons, Z bosons and their anti quanta can be derived.
Since photons and gluons are not coupled, apply to them other equations.
This schema determines important characteristics for all known particles from the standard model. It is also contains open places for not yet observed particles.
More details can be found in: http://www.crypts-of-physics.eu/Quaternionic_continuity_equation_for_charges.pdf

The cause of gravitation

The cause of the gravitational field is almost invariably seen as a single mass or a group of mass carriers which have a common center of gravity. We are faced with the gravity field because things have weight or due the fact that acceleration confronts us with inertia. From deeper knowledge, we learn that the gravitational field is associated with the curvature of the space that surrounds us. In our immediate environment the effects of curvature(other than weight) are barely noticeable, but there are places in the universe where the curvature is much stronger and causes significant effects.
From these experiences the false idea may emerge that the gravitational field acts as the cause of curvature. However, that is a reversal of affairs. The gravitational field is no more and no less than the accurate administrator of the curvature of the local space. Therefore the value of the gravitational field is not a simple number. It is a tensor that exactly represents the local curvature by using a matrix of characterizing numbers. This matrix can vary from place to place.
We can go a step further and argue that the gravitational field designates the points on which the cause of the curvature seems anchored. Actually, these point-shaped mass carriers do not need to exist. It means that there may also be other causes to be coined for the curvature. An example is formed by an anomaly in the local geometry that is surrounded by a different structure of the normal curvature.
A black hole can be considered as such a geometric abnormality. A black hole is surrounded by a very strong curvature field such that information can no longer pass the skin of the hole. Therefore the hole can as well be completely empty. What happens to the material that is sucked up by the black hole? Well, that will be ripped apart into its smallest possible parts. Part of the debris is used to widen the skin of the hole. The other part escapes from the absorption process and is reflected back. The hole gets bigger, but that only becomes visible via the enlargement of the skin. The surface of the skin gives an indication of the mass, which the hole represents. The curvature around the black hole is in correspondence with this mass. However, the hole itself is empty.
If this picture is correct, then nature might perform this trick more often. What to say of the idea that all elementary particles that have a mass, contain in their inner a small geometric abnormality that is responsible for the gravitational field of the particle.
The question results of what causes this abnormality. The physical fields that belong to a particle determine what is present in the domain of that quantum. These fields are quaternion valued probability amplitude distributions. The square of the modulus of these distributions is a probability density distribution of the presence of the quanta considered. At places where nothing is allowed to be present, in fact a geometric abnormality emerges in the form of a hole. The hole represents the mass of the particle.
The gravity field is thus a very different type of field than the fields that belong to the quanta.
What about inertia? This effect is caused by the collaboration of all geometric abnormalities. The most distant abnormalities play the largest role. Further away, the influence of a single abnormality falls off quickly with distance, but the number of participating abnormalities increases much faster with that same distance. Moreover, the influence of differences level out due to averaging over an increasing number of contributions. It looks as if a uniform background attracts the local object from every direction. Because the forces come in equal size from all directions nothing happens. In a similar way nothing will happen as long as the object moves in a uniform manner. If the object accelerates, then according to field theory, this goes hand in hand with the presence of an additional gravitational field that counteracts the acceleration.
So it is not surprising that physicists cannot reconcile the electromagnetic fields and the weak and strong binding fields with the gravitational field. Apparently the gravitational field is a field that is caused by the other fields. All other fields are quaternionic probability amplitude distributions that belong to quanta.

According to research from the Carnegie Institution for Science, the properties exhibited by iron oxide change depending on its composition and where it is located within the Earth, with experiments pointing towards a new kind of metallization occurring. By subjecting iron oxide to conditions similar to those found at the depth where our planet’s innermost two layers meet, the researchers found that the metal changed to such a degree that it conducted electricity. The most remarkable finding is perhaps that this all happened without the metal altering its structure, meaning that depending on only pressure and temperature, iron oxide can be either an insulator or a conductor. The findings may help us to further understand just how the Earth’s interior produces our planet’s magnetic field.

A new drug developed by scientists at the Salk Institute for Biological Studies may be the first capable of halting the mental decline of Alzheimer’s disease. When tested on mice, the drug, known as J147, led to improved memory and prevented the loss of synaptic connections associated with the disease. In order to synthesise the compound, the researchers focused on the biological pathways involved in the formation of amyloid plaques. Although the team do not yet know whether the compound will prove to be safe for and effective in humans, their research suggests that this could be the first drug to offer a treatment for one of the top ten causes of death.

Recent findings released by Johns Hopkins University have thrown up some intriguing insights into how babies perceive the world around them. The study suggests that whilst infants are unable to remember the details of objects that were shown to them and then hidden, they do retain a notion that what they saw remains in existence. By displaying and hiding a series of shapes, the team found that a baby’s brain possesses a set of built in ‘pointers’ that are able to pick out the objects in the world the they want to keep track of, without remembering what they are. The team believes the study sheds new light on the brain mechanisms that support memory in infancy and beyond.

A new study reveals how the genome of 138 stem cell lines of diverse ethnic backgrounds changed when the cells were grown in laboratories. The findings have led to concern from scientists that over time the cells can acquire genetic mutations which may compromise their usefulness for cell therapy. The study, which was the largest of its kind, was carried out by researchers from the University of Sheffield who analysed the pattern of genes expressed in 127 HES cell lines and 11 iPS cell lines from ethnically diverse backgrounds. After a prolonged culture about 20 percent of the cell lines acquired amplifications of a specific region in chromosomes 20.

An international group of researchers has set a new world record for data transfer, helping to usher in the next generation of high-speed network technology. Led by the California Institute of Technology (Caltech), the scientists succeeded in transferring data in opposite directions at a combined rate of 186 gigabytes per second (Gbps) in a wide-area network circuit. This rate is equivalent to moving two million gigabytes per day and fast enough to transfer nearly 100,000 full Blu-ray disks - each with a complete movie and extras - in a day. As well as providing the research community with an improved way to share information, a key motive behind the findings is to enable scientists everywhere in the world to work on the LHC data, allowing the best minds to work on the mysteries of the universe together.

A team of scientists from Fauna and Flora International, the Zoological Society of London and the Forestry Development Authority of Liberia has been using camera traps to study the endangered pygmy hippo in its natural habitat - they released this footage. [Video]

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks (at) researchgate.net

A massive star spinning around its axis at 600 kilometres per second has been discovered by researchers from the University of California, Santa Barbara. The rotational velocity, which is the fastest ever recorded, is so high that the star is almost being torn apart by centrifugal forces. Located some 160,000 light years from Earth in the Tarantula Nebula, the star is hot and luminous, shining 100,000 times more brightly than our sun. The astrophysicists behind the discovery believe stars such as this one to be responsible for gamma-ray bursts, some of the brightest explosions in the universe.

A new study has shown that so-called ‘Frankenstein’ viruses can be safely used for gene therapy. ‘Frankenstein’ viruses, commonly known as chimeric viruses, are created by cutting two different viruses up and sticking them together, often with the aim of creating a vehicle for gene therapy. A recent clinical trial saw such a virus successfully used as a delivery system for an essential muscle protein in patients with muscular dystrophy. The team believe that the trial “demonstrates that gene therapy is no longer limited by the viruses we find in nature, and should usher in the next generation of viral delivery systems for human gene transfer”.

Did you know that arranging warm and cold sausages alternatively in the pattern of a grill and then placing your hand on them can cause you to feel pain? Well it can: known as the thermal grill illusion, feeling harmless levels of cold and warm all at once in a grill-like pattern can cause humans to experience a burning cold pain. One group of scientists decided to use an fMRI scanner to figure out what this might look like in our brains. Their findings showed that those who experienced the pain had a rather busy thalamus, a part of the brain’s pain matrix which acts as a relay station for sensory impulses to pass through. The team hopes to use the data to locate exactly where the brain transforms the perception of temperature into pain.

New findings published in the journal Cancer Cell shed light on exactly how cancer tumours can grow at exponential rates. It seems that cancer cells gain the nutrients they need by producing proteins that create their own blood vessels, helping to deliver oxygen and sugars to the tumour. Scientists at the University of Bristol discovered that mutations in one specific cancer gene control how these blood vessels are created and balanced by allowing a ‘master switch’ in the cell to be turned on. By using new cancer drugs the scientists were able to block this master switch in experimental models, thereby successfully preventing the tumour from growing. The discovery marks an exciting new phase in the development of cancer drugs that might one day stop tumour growth at its source.

New research by scientists at the University of Toronto has uncovered how the intestinal tract influences a key component of the immune system to prevent infection. The findings clear up some long-standing confusion and mystery surrounding the complex balance between beneficial and harmful bacteria in the gut. The researchers discovered that some B cells - a type of white blood cell that produces antibodies - take on functions that allow them to neutralise pathogens only when within the gut. The findings highlight the importance of the gut in fighting infection and provide potential clues to the cause of autoimmune disorders like rheumatoid arthritis and multiple sclerosis.

Electric vehicles might be gaining in popularity, but, because they are almost silent, safety concerns continue to be raised. In this video, the BBC takes a look at how the music industry is playing a part in sorting the motor industry out with some new sounds.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks (at) researchgate.net

Rejoice! Earth may have found its long-lost twin, Kepler 22-b. The exoplanet is located around 600 light years away from Earth and has been identified as having many similarities to our own - making it the latest potential target for life. Housed in what is known as the Goldilocks Zone, Keplar is 2.4 times bigger than Earth, maintains a cosy average temperature of 22C and orbits a star not unlike our sun. However, before we pack our bags and call NASA for a reservation on the Kepler express, astronomers have yet to work out whether the planet is made mostly of rock, gas or liquid. Regardless, the discovery of Kepler 22-b is a milestone in NASA’s continued mission to learn more about our place in the universe.

A study has found a direct relationship between violent video games and changes in areas of the brain associated with cognitive function and emotional control. The experiment, carried out by researchers at Indiana University, saw 28 men aged 18 to 29 split into two groups: one group played a shooting game at home for 10 hours for a week, the other did not. fMRI analysis found that those who had played the game showed less activation in areas of the brain responsible for controlling emotion and aggressive behaviour than those who had not. The team believe that over an extended period of time, these games might translate into behavioural changes.

Two gigantic black holes with masses around 10 billion times that of our sun have been discovered by an international team of astronomers. The team used several telescopes to measure the speed of planets orbiting the galaxies concerned, thereby measuring the gravitational pull the black holes exert. The most astounding statistic? Each of their masses is more than 50 percent greater than all previously measured black holes.

Computer simulations have provided NASA scientists with a greater understanding of how solar storms affect our moon. According to the simulations, solar storms and Coronal Mass Ejections (CMEs) effectively ‘sandblast’ the moon, significantly eroding the lunar surface. Firstly drawing attention to the the large amount of material these storms remove from the moon’s surface, the team went on to highlight how this could lead to atmospheric loss for planets that are not protected by a global magnetic field, such as Mars.

NASA’s Dawn spacecraft has compiled a rainbow-coloured image of Asteroid Vesta’s southern hemisphere. The image centres on the Rheasilvia formation, an impact basin measuring some 467 kilometres in diameter with a central mound reaching around 23 kilometres high.

Over the past decade, around three quarters of UK butterfly species have declined in abundance - this BBC video takes a look at why this might be.  

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks (at) researchgate.net

Researchers at Texas A&M University are close to developing a topical gel that prevents the transmission of HIV by dissolving the virus on contact. The synthetic compound contained within the gel, PD 404,182, acts by breaking the virus open and exposing its RNA, thereby rendering it non-infectious. In simple terms, the compound rips open the virus before it is able to inject its genetic material into a human cell. The compound achieves this by acting on something within the virus other than its viral envelope protein; the team believe this to be a cellular material common to all lentiviruses. Most impressive is perhaps the fact that the process prohibits the virus from altering its proteins, meaning that it is unable to boost its resistance. The team now hope to develop and test a gel that could be applied to the vaginal canal.

The U.S. Department of Energy’s Joint BioEnergy Institute has reached a milestone in the development of advanced biofuels. Researchers from the department have engineered strains of Escherichia coli (E. coli bacteria) that are capable of digesting a certain form of bunchgrass and synthesising its sugars into gasoline, diesel and jet fuel. The process begins with pretreated switchgrass, native to North America, and sees the cellulose and hemicellulose contained within turned into sugars, which are then fermented into fuels - and it all takes place in one single step. Unlike ethanol, the fuels created during the process can replace gasoline on a gallon-for-gallon basis and, what’s more, they can be used in existing engines and infrastructures.

Scientists Worcester Polytechnic Institute are offering new hope for people suffering from major muscle trauma. As part of their work on new technologies and therapies for those who suffer serious wounds and limb loss, the team successfully regenerated functional muscle tissue in mice. Mature human muscle cells were first coaxed into a stem cell-like state and then grown on biopolymer microthreads. The team then removed a large section of leg muscle from a mouse and replaced it with the microthreads. Over time, the threads and cells were able to restore near-normal function to the muscle. The team believes these surprisingly successful results will open the door to new therapies and technologies.

An international team of scientists from Leicester and Monash universities have announced a breakthrough in the fight against malaria which could lead to the development of drugs capable of stopping the deadly disease in its tracks. Malaria currently affects more than 225 million people worldwide and accounts for nearly 800,000 deaths a year. The researchers have discovered that malaria parasites survive in the human blood stream by way of a group of enzymes called protein kinases. The team are now looking into identifying drugs that halt the production of protein kinases. Despite these optimistic findings, the researchers warn that the malaria parasite is notoriously good at building up resistance to drug treatments. The team hope that their work will provide a plausible avenue toward the successful treatment of the disease.

What’s the best way to suppress fire in space? That’s exactly the question NASA’s FLEX (Flame Extinguishing Experiment) is trying to answer. Since it’s inception in 2009, the FLEX team have conducted more than 200 experiments to better understand the fundamentals of flames. In space, flames burn with a lower temperature, at a lower rate and with less oxygen. The research can be classified as two-fold: exploration-driven fire safety research and more fundamental science research into the physics of combustion.

By using a mixture of fossil and bio fuels, the Mexican aviation industry is hoping to pioneer a greener way to fly. Though the new fuel may seem to promise prosperity, some experts warn that in reality the initiative could have the opposite effect. [video]

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks (at) researchgate.net

A multidisciplinary team of researchers has developed the world’s lightest material. With a density of 0.9 mg/cc, the new material is around 100 times lighter than Styrofoam. The unique micro-lattice cellular architecture consists of interconnected hollow tubes with a wall thickness 1,000 times thinner than a human hair. Originally intended for defense projects, there are hopes that the material could now be used in battery electrodes and acoustic, vibration and shock energy absorption.

A new strain of yeast developed by researchers at the University of Georgia is able to ferment ethanol from pretreated pine. The pine, one of the most common trees found in the USA, is a notoriously resistant to fermentation. To get around these problems, the team created a process which sees the wood pretreated with heat and chemicals and then fermented with the new yeast. As the so-called ‘super strain’ of yeast can withstand the chemicals used in the process, it can successfully convert the sugars released from the wood into ethanol. The ‘super strain’, an adaptation of Saccharomyces cerevisiae, brings us one step closer to replacing gasoline with biofuels.

A breakthrough in the search for effective cancer treatments was announced after chemists at Rice University found a way to load 2 million tiny gold particles into a single cancer cell. The particles, known as nanorods, are around the size of a small virus and are able to convert light into heat. The team hopes the nanorods, which are activated by a laser, could be used to cook tumours from inside a cell. Take a look at the video to see how the process works.

A University of Oregon study has found that the domestication of soybeans occurred much earlier than thought: previously pegged at 3,000 years ago, domestication of the legume is now believed to have taken place around 5,500 years ago. A comparison of 949 charred soybean samples from 22 sites in northern China, Japan and South Korea allowed the researchers to take a closer look at the effect carbonization has had on the size of the bean. The study will afford archaeologists, crop scientists and plant geneticists a greater understanding of cultural contributions, which may lead to better soybean characteristics.

Can time be reversed? In this interview, Dr Giles Barr, a physicist at Oxford University, explains that if neutrinos can travel faster than light, time could effectively be “reversed”.

This week’s video comes courtesy of Duke University and shows us how an invisible octopus defends itself by changing from clear to red, all in the blink of an eye.  

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks (at) researchgate.net

NASA’s Hubble Space Telescope has peered 9 billion years back in time and uncovered 18 young dwarf galaxies filled with forming stars. The galaxies, all of which are on average a hundred times smaller than the Milky Way, appear to produce stars at such a phenomenal pace that their stellar content would double in a mere 10 million years. By comparison, the Milky Way would take a thousand times longer to double its star population. The data, acquired using Hubble’s near-infrared vision, could push astronomers to readdress their understanding of the way in which galaxies form.

Scientists from Brown University recently determined the structure of p38alpha:HePTP, an enzyme complex that plays a key role in regulating cell functions. Whilst it was known that the disregulation of these types of complexes can be associated with diseases such as cancer and Alzheimer’s, little was known about the structures themselves. By combining techniques such as nuclear magnetic resonance spectroscopy and small-angle X-ray scattering, the team have been able to provide the clearest picture yet of a MAP kinase complex. The findings provide drug developers with a new target in their efforts to find new treatments for a variety of diseases.

Little is know about the long-term effects cognitive-enhancing drugs can have on the brains of healthy people; even less is known about the impact these drugs have on society. Commonly prescribed to treat medical conditions, ‘smart drugs’ are increasingly being bought over the internet by a seemingly broad demographic. In this piece, the BBC’s Susan Watts looks at what these drugs are, how they work and who is using them.

A University of Florida study has shown that it is possible for Salmonella to enter tomatoes through the plant’s leaves. Previously, food-safety experts believed Salmonella was only able to enter the fruit through wounds in the stem or the fruit itself. The researcher behind the findings, Ariena van Bruggen, has however stressed that the risk of this happening is so low that consumers have no need to worry - you’re more likely to catch it by not washing your hands...

In this video, Professor Michael Shattock delves into the make-up of the human heart, or more precisely, of a single heartbeat, giving us an insight into what it takes to pump blood to every part of the body.

2011 saw the number of migrating whales reach a 50-year high. The 5,000km round trip sees the whales leave Antarctica to give birth off the coast of Australia, before heading back to their main feeding grounds, only to do it all again the following year. Be sure to check out this video on the whole process.  

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks (at) researchgate.net

Human skin detects light in much the same way as the eye, according to a recent study. Researchers from Brown University discovered that skin cells known as melanocytes contain rhodopsin, a photosensitive receptor the eye uses to detect light. When we step out into the sun these skin cells release calcium ion signals that trigger the production of melanin, which in turn absorbs incoming radiation from UVB rays - all in a bid to prevent damage to DNA. Sunscreen is still very much advised...

The ferocious roars of lions and tigers have at long last been attributed to the somewhat unconventional shape of their vocal cords. Researchers from the University of Utah found that the king of the jungle has square-shaped vocal cords, as opposed to the more traditional triangular shape most species possess. The study details how square-shaped vocal cords, which are able to withstand a high degree of stretching and sheering, make it easier for the tissue to respond to the passing airflow. All of this means that lions and tigers are able to produce louder roars at lower lung pressure. The findings will help scientists to better understand the structure of vocal folds, which could in turn help surgeons to more effectively repair damaged vocal fold tissue in humans.

Using the green marker that causes jellyfish to glow, researchers of Monash University in Melbourne have found a way to isolate heart cells by turning them green. As a result, the scientists discovered that heart cells can be infinitely produced, thereby providing a potentially inexhaustible source for research and drug testing. The findings are incredibly significant since, up until now, the development of drugs to treat heart disease has been hampered by the lack of a dependable supply of heart cells for experimentation.

A clinical trial carried out by researchers at Haukeland University Hospital in Bergen shows hope for sufferers of Chronic Fatigue Syndrome, also known as ME. The study details how the disease, for which there is currently no cure, could be caused by a wayward immune system attacking the body. The researchers found that patients who were administered two doses of Rituximab, a cancer drug that eliminates a type of white blood cell, reported a 67% decrease in fatigue as opposed to 13% in the placebo group. Although these are very encouraging results, the authors of the study stress that they are years away from a major breakthrough.

The mysteries of the human brain have eluded even our greatest scientists - and quite rightly so. In this piece, the BBC have been debunking some of the myths surrounding this most complex of organs.

A 400 m (1,300 ft) asteroid will pass Earth tonight. In this NASA video, Lance Benner of JPL gives us all the necessary details including a word of reassurance that it will pose no danger to earth.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks (at) researchgate.net

Strawberries are good for you! A pan-European team of researchers has shown that eating strawberries reduces the damage alcohol causes to the stomach’s mucous membrane. By giving ethanol to laboratory rats, the team found that the stomachs of those who had eaten strawberry extract suffered less damage than those who had not. The research further showed that the positive effects of strawberries are not only linked to their antioxidant capacity and high levels of phenolic compounds, but also to the fact that they activate antioxidant defences and enzymes occurring naturally in the body. In the study, the team set out how the antioxidant properties found in strawberries could be used to prevent some gastric illnesses and improve the treatments currently available for stomach ulcers.

Grapefruit, a fruit long off-limits to many patients, may soon be making a return to the menu. For years, doctors have advised patients on certain medications, including those designed to lower cholesterol, to steer clear of the grapefruit - and grapefruit juice - as it can change the way the drugs are absorbed into the bloodstream. Researchers at the University of Florida now believe they will soon be able to release a grapefruit-pummelo hybrid that will contain no furanocoumarin, a chemical found naturally in certain fruits and vegetables and which is responsible for this adverse effect.

A study by researchers at McMaster and McGill University suggests those who are genetically susceptible to heart disease could considerably lower the risk of developing it by eating five or more portions of raw fruit and vegetables daily. The research indicates that somebody with a high-risk version of the 9p21 gene who consumed a large amount of fresh produce would only be as likely to suffer a heart attack as somebody with a low-risk variant of the same gene. The results are a testament to the ‘Five-A-Day’ campaign and reminds us that while both lifestyle and genes can increase the risk of heart disease, the way they interact with each other is also of great importance.    

The remarkable plasticity of the brain has once again been highlighted, this time thanks to a study released by the California Institute of Technology. Researchers showed that those born without a link between the brain’s right and left hemispheres, around one in 4,000 of us, still exhibit surprisingly normal communication across the gap. The condition results from the lack of a corpus callosum - a ‘c’-shaped structure containing some 200 million connections - and leads to a radical rewiring of the connections between the two hemispheres. What the team found to be most surprising is that despite the lack of coupling, the brain was able to maintain synchronised activity on both sides.

The world’s population has officially reached seven billion, and continues to grow by a further 200,000 each day. This week’s video takes a look at what this all means and this graph might help you to understand where you fit into the story of life on Earth.

October has been a good month for those seeking to capture snap some photographs of space. So here’s another selection of some of this month’s best images, including one particularly stunning auroral display (no. 23).

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks (at) researchgate.net

A team of scientists from the Medical Research Council have found a potential alternative treatment for ‘Glue ear’, a common condition in children that prevents oxygen from reaching the middle ear. Currently the only treatment is grommet surgery, which involves inserting tiny plastic tubes into the eardrum to improve ventilation during a short operation under general anaesthetic. The possible new cure is non-invasive and will aim to re-purpose existing cancer drugs known as VEGF inhibitors, delivering them directly to the area of inflammation. Although still in very early stages, the research has been deemed ‘groundbreaking’ and will hopefully contribute to a greater understanding of deafness while giving families greater choices in treatment and support.

New York University and University of Iowa biologists have identified a key mechanism controlling the early embryonic development that is critical in determining how structures, such as arms and legs in humans, grow in the right place at the right time. The lead authors found that a protein named Zelda is responsible for switching on groups of genes essential to development in a remarkably coordinated fashion. The researchers used fruit flies to investigate regulatory networks and discovered that when Zelda is absent, activation of the genes is delayed causing a drastic change in body plan such that many tissues and organs are not formed properly, if at all.

The Herschel Space Observatory has provided astronomers with evidence that enough water “to fill thousands Earth oceans” is to be found some 175 light-years away in the Hydra constellation. Using HIFI (Herschel’s Heterodyne Instrument for the Far-Infrared), scientists were able to detect a young star surrounded by a water-logged disk. The existence of the disk, which looks set to become a solar system, suggests that water-covered planets like Earth may be commonplace in the universe.

Scientists at the University of Leeds have identified a method by which the brain is able to protect itself when its energy supply runs low. Many regions of the brain constantly consume as much energy as legs muscles require during marathon running. When the energy supply from the blood vessels feeding the brain becomes compromised, the brain is able to trigger a protein that reduces the frequency of electrical impulses. The study could lead to new treatments for those at a high risk of stroke due to problems with these blood vessels.

Saturn’s moons, ice caps on Mars, a planet with two suns, the Southern Lights - The Guardian has taken a look back at some of the best images of space from the past month.

In this video, Professor Mark Post of Maastricht University discusses the future of meat production and his efforts to grow meat from stem cells in the laboratory. Professor Post hopes that his research will help to make factory produced meat a reality, thereby reducing the environmental impact of rearing animals for food production.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks (at) researchgate.net

Using a piece of software known as Eureqa, researchers from Cornell University have demonstrated that a computer can analyse data from biological systems and turn it into mathematical equations - these equations describe precisely how a system operates. The team used the software to study glycolysis, specifically, the manner in which yeast cells control fluctuations in the chemical compounds the process produces. When the team fed the data into Eureqa, the computer produced a series of equations almost identical to the known equations. It is hoped the software could now be used to solve a multitude of problems.

New research from Cornell University claims that around 96 percent of vertebrates, humans included, descend from a common ancestor. The species, most probably a predatory marine fish, is thought to have lived some 500 million years ago and would appear to have possessed a sixth sense: electroreception, the biological ability to perceive natural electrical stimuli. Researchers hope the findings will help us better understand the origin and evolution of many organ systems, including the brain.

Researchers from Carnegie Mellon University developed an MRI-based technique that allowed them to non-invasively follow stem cells in vivo. Until now, scientists have only been able to study neuronal stem cells by looking at slices of the brain under a microscope. The team tagged the cells with ferritin, a metalloprotein that harvests and stores iron, which caused the cells to draw in even more iron. The cells thus became nanomagnets that an MRI scan can detect. The technique could be used to develop treatments for brain injuries caused by trauma, stroke and, amongst others, Parkinson’s disease.

NASA’s Mars Rover captured 309 images at the end of each drive during it’s Opportunity trek from Victoria Crater to Endeavor crater. Although sadly no extraterrestrial life was found, the images of this three-year journey provide a captivating glimpse of the red planet.

In partnership with NASA’s Terra spacecraft instrument ASTRA, the Japanese Advanced Spaceborne Thermal Emission and Reflection Readiometer has released a significantly improved version of the most complete digital topographic map of the Earth. Known as a global digital elevation model, the map adds 260,000 additional stereo-pair images, improved spatial resolution and heightened vertical and horizontal accuracy to the original map, which was released in 2009. The data covers 99 percent of Earth’s landmass and spans 83 degrees north latitude to 83 degrees south. The map provides civilian users with the highest-resolution topography data available and is available online at no cost.  

Dark matter, the mysterious substance holding together stars within the Milky Way, has come under scrutiny following a study conducted by Astrophysicists at Harvard and Cambridge University. The standard model assumes that dark matter should be densely packed in the centres of galaxies. Instead, new measurements of two dwarf galaxies show that they contain a smooth distribution of dark matter, suggesting that the traditional cosmological model may be wrong. The research team measured the locations, speeds and basic chemical composition of 1500-2500 stars in the Fornax and Sculptor galaxies to reach their findings.  

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks (at) researchgate.net

Astronomers have found a new cosmic source for the same kind of water that appeared on Earth billions of years ago and created our planet’s oceans. New measurements from the Herschel Space Observatory show that comet Hartley 2, which originates in the distant Kuiper Belt, over 30 to 50 times as far away as the distance between the earth and sun, contains water with the same chemical signature as Earth’s oceans. The findings may help explain how the Earth’s surface ended up covered in water.  

A study carried out by researchers at the University of Warwick has found that depression can lead to the brain’s ‘hate circuit’ coming ‘unplugged’. The team used MRI scans to highlight the impact depression has on several areas of the brain, including those associated with risk and action responses, reward and emotion, attention and memory processing. Jianfeng Feng, a professor of computer science at the university, believes that the uncoupling of the ‘hate circuit’ could be associated with an impaired ability to control and learn from social or other situations that “provoke feelings of hate towards self or others”.

Researchers from Rutgers have identified the structure of a protein that is the first line of defence against viral infections, including influenza, hepatitis C, West Nile, rabies and measles. RIG-I is a receptor protein able to recognise differences in molecular patterns in order to differentiate between viral RNA, a double-stranded structure, and cellular RNA, a single-stranded structure. The findings could lead to new drugs to fight viruses or control inflammation.

An international team led by the SRON Netherlands Institute for Space Research, has discovered an extremely hot ‘converter’ corona hovering above one of the brightest supermassive blackholes known to exist. The ‘monster’ hole, which is located in a distant galaxy known as Markarian 509 and boasts a mass 300 times greater than the sun also features cold gas ‘bullets’ in hotter diffuse gas, speeding away from the hole at 700 km/s. The discovery allows astronomers to locate outflowing matter, and shows that not all matter surrounding black holes is swallowed up.  

Researchers in France have documented colossal aggregations of the Wels catfish in the Rhone River. A native of Eastern Europe, the catfish is considered an alien species in this part of the world; the researchers were therefore interested in studying the impact large aggregations of alien species can have on a local ecosystem. The fish formed dense groups of 15 to 44 individuals, corresponding to a biomass density of 14 to 40 kilograms per square metre. The team calculated that the fish could excrete extremely large amounts of phosphorus and nitrogen, creating the highest biogeochemical hotspots reported in freshwater ecosystems.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks (at) researchgate.net

Researchers at John Hopkins University have used a patients’ stem cells to correct the genetic defect that causes sickle cell disease, a disorder that occurs mainly in African Americas. The disease is caused by a single DNA change in the gene for adult hemoglobin and can lead to clogged blood vessels, fatigue, pain, infections, organ damage and premature death. Although years away from becoming a treatment used on regular patients, the research team successfully coaxed the corrected stem cells into becoming immature red blood cells which then developed into a normal version of the gene, providing new hope for effective therapies for sickle cell and a variety of other blood diseases.

Better sleep may be helpful in reducing the risk of Alzheimer’s disease, a new study published in Archives of Neurology suggests. The research shows that the normal highs and lows of amyloid beta, a byproduct of brain activity, begin to flatten out in older adults when deep sleep is often shorter and prone to disruption. In Alzheimer’s patients the ebb and flow is almost eradicated and amyloid beta levels are close to constant. More research is to go into the hypothesis that sleep might be linked to this effect, though scientists are already hopeful that they have a strong case.     

Astrophysicists from the University of Leeds have identified one of our galaxy’s largest and rarest stars. IRAS 17163-3907 is what is known as a yellow hypergiant, one of only three such stars in the Milky Way. Half a million times brighter than our Sun, and possessing a volume one billion times larger, the hypergiant will allow for a detailed look into stellar evolution and insights into the way in which massive stars can influence the shape of a galaxy.

Fermilab’s Tevatron collider, the world’s first high-energy superconducting accelerator, has smashed together high-energy protons and anti-protons for the last time. For 25 years the Tevatron was the highest energy collider in the world and laid the groundwork the work now being carried out at the LHC. Particle physics experiments aim to discover the phenomena predicted by a particular theory - with more than 1000 papers associated with its name, the Tevatron was able to achieve this to a degree as yet unmatched by any other facility.

A NASA-led study, involving scientists from 19 different institutions, has documented an unprecedented depletion of the Earth’s ozone layer above the Arctic. The depletion, which occurred over the course of last winter and spring, was caused by an unusually long period of extremely low temperatures in the stratosphere, with some altitudes seeing cold periods lasting 30 days longer than any previously studied. Although smaller than its Antarctic counterpart, the Arctic ozone hole is more mobile, therefore posing a greater threat to the planet’s densely populated northern regions.

The Alma telescope, found in Chile’s Atacama desert, recently began its quest to view the formation of the Universe’s first stars. This week’s video takes a look at the world’s most powerful radio telescope.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks (at) researchgate.net

The news that neutrinos might travel faster than light, and thus violate the speed limit of the universe, this week caused an audible stir in the scientific community. The CERN experiment, which employed highly precise GPS positioning and timing measurements, was designed to measure how neutrinos change their properties as they travel. Instead, the data appeared to show neutrinos travelling from Geneva and arriving in Gran Sasso, Italy, faster than light itself. The data, which has been released in the hope that researchers might be able to shed some light on the findings, has the potential to rewrite the physics rulebook. Follow the discussion in the ResearchGate Physics Topic.

Researchers from Stanford University combined ‘deep sequencing’ with a host of other techniques from genetics, computer science and statistics to identify a gene fusion present in cases of ovarian cancer. The team found that ESRRA breaks and fuses with a neighbouring gene, known as C11orf20, in around 15 percent of serious ovarian cancer cases. The findings could help medics identify these cancers early in their development.

A group of scientists from some of England’s leading universities have discovered five new genes that affect the risk of developing coronary artery disease (CAD). One of the variants was close to the area of the genome coding for interleukin-5 (IL-5), which is linked to inflammation. If confirmed, this could be the first case of a gene linked to heart disease working through inflammation. This very large study - which involved around 80,000 patients - could signal a new era in the understanding of heart disease.

The recent conversion of adult stem cells from mice into antigen-specific T cells may pave the way for a more efficient way of using the body’s immune system to fight cancer. Researchers from Penn State believe that they have come closer to generating T cells in the lab that could be used to target cancer cells in the body. The technique, known as adoptive T cell immunotherapy, saw altered induced pluripotent stem cells being turned into stem cells that were then able to provide an unlimited source of the cells required for the therapy.

A computational approach has allowed scientists at Virginia Tech to predict numerous human proteins that the HIV virus requires to replicate itself. As human proteins develop at a much slower rate than the virus, the research aims to find ways in which the proteins can be targeted in the fight against the virus.

20 years after its launch, NASA’s decommissioned Upper Atmosphere Research Satellite (UARS) fell back to Earth between 11:23 p.m. EDT Friday, Sept. 23 and 1:09 a.m. Sept. 24. The satellite was able to provide some of the first long-term records of the chemicals that make up our atmosphere. Data showed that, during re-entry, the satellite passed over the east coast of Africa, the Indian Ocean, the Pacific Ocean, northern Canada and finally over western Africa. It is believed that most of the debris landed in the Pacific Ocean, far off the U.S. coast.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks (at) researchgate.net

 In the famous Monty Python "Dead Parrot" sketch, John Cleese returns to a pet shop where he has just bought a parrot and asks for his money back.  The reason being that the parrot is in fact dead.

This seems to be a not unreasonable request on the part of the purchaser - on buying a parrot, there is a reasonable expectation that it might be alive.

However, true to Monty Python form, the owner of the pet shop disagrees and goes to extreme lengths to try to suggest that the parrot is not in fact dead, merely sleeping.

I cannot go through the sketch, you will have to take a look for yourself below, however, this sketch reminds me of those scientists who are still trying to support the notion of the Tree of Life.

The Tree of Life is the phrase used for the hypothesis that the evolution of life on the planet can be adequately accounted for by drawing a single phylogenetic tree depicting the relationships of all the evolving entities on the planet.

Darwin thought this was a neat idea and one of the iconic Darwin images is his drawing of a tree.

Darwin, however, did not know anything about plasmids, viruses or horizontal gene transfer.  Therefore, he made no comments on how these might affect tree-like representations of life on the planet.

Everything went swimmingly for the ToL hypothesis for zoologists and botanists for pretty much all of the 20th century.  Even with the advent of molecular sequence data, there was no real objection to the hypothesis.

However, microbiologists could not seem to get their part of the tree organised.  Depending on what kind of character you used - morphology, motility, biochemistry - you got a different tree.  The characters did not tend agree with one another.  Microbiology faltered a little as a discipline and suffered from not having the kind of all-encompassing systematic footing as zoology and botany.

By the 1950s, microbiologists had largely given up on the microbial tree and focussed instead on what bugs did, rather than how they were related.

Carl Woese led the charge to change this and proposed that because all cells had ribosomal RNA sequences, this could be used as a proxy tree and everybody seemed happy with that.

Then genomes came along and we were right back where we started - different gene trees tended not to agree with each other completely.  They did agree a little bit and sometimes a lot.  But they tended to disagree in significant ways.

However, rather than say that the tree of life hypothesis is now dead - no single unifying tree could be constructed that encompassed all life - the tree-thinkers kept insisting that the parrot tree was not dead, it was simply sleeping.

For some of us this was not good enough.  If it ain't a tree, then it ain't a tree.

Some people like Eugene Koonin and Pere Puigbo have looked at statistical trends among phylogenetic trees and have seen how there is a single trend that is to be found in "nearly universal trees" - genes that are widespread in nature - and that as a consequence, this is the "statistical tree of life".  Unfortunately, for me, any graph that represents only about 1.6% of all the data is really only a tiddler of a graph (no offence).

We have recently published a manuscript that advocates that we take all current ideas about the existence of a great "Tree of Life" and we finally let them go.  We say "they are no more", they are dead parrots.

Let's just imagine that genes are 'goods', like air or water or screws or wheels.  We know that these goods can be passed around, we know that they can be put together in new combinations (a chair can be made of steel and foam and wood, or just wood or tin and plastic) and when looked at objectively, we can see that genes or bits of genes can be considered to be goods.

So, right there things are different.  We don't start with a tree and then try to explain everything with reference to the tree.  We start with the molecules.  We allow them to be recombined together - as happens all the time in nature.  We don't force them to be in cells - thereby accommodating plasmids, phage, viruses etc.

We then interpret the similarity of gene trees by simply looking at how these goods are inherited - vertically and horizontally.  

What is the consequence of these two mechanisms of inheritance? Well, genes that are inherited together should have similar gene trees.

Genes that tend to be passed around through horizontal transfer on their own will have a different evolutionary history to other genes.

...and this is the pattern that we see.

The public goods hypothesis also immediately suggests categories of genes and these categories (public, private, club or common goods) immediately suggest a larger influence of ecology in evolution.  Selection modifies how a gene is inherited and who inherits it.  The tree of life hypothesis had little to do with environment and selection.

In our view, we don't think Darwin was wrong - the Tree of Life hypothesis is simply a 'regionalized' hypothesis. It explains some things, but doesn't explain everything.

Goods-thinking should replace tree-thinking, but I guess we will only know this retrospectively.

Here is the dead parrot sketch.

Researchers at the University of Warwick have developed a crystal able to deliver highly accurate temperature readings, ranging from -120 to +680 degrees centigrade. The team’s work employs what is known as a ‘birefringent’ crystal, which splits the light passing through it into two separate rays. The device is designed to measure temperatures in environments where interference makes other sensors unreliable, such as near MRI machines.

Doctors this week reached a milestone in the fight against ovarian cancer as ten women underwent fluorescence-guided surgery. This novel technique saw the women injected with a liquid that contained fluorescent dye attached to a chemical known as folate. As ovarian tumors contain more folate receptors than healthy cells they ‘lit up’. Ovarian cancer is notoriously difficult to spot; this new form of surgery enabled surgeons to find clusters as small as one tenth of a millimetre across, compared with the norm of around 3mm using visual and manual inspections.

NASA’s Kepler mission has discovered a world orbiting two stars, also known as a circumbinary planet - meaning that it has a double sunset. The planet is located 200 light years away from earth and is believed to be cold, gaseous and unable to harbour life. Kepler discovered the planet by observing the transits and monitoring the brightness patterns of parent stars. Principal investigator William Borucki hopes that this discovery will increase the chances of discovering planets that could harbour life, since life is more likely to be present if a planet forms around more than one star. 

A study released by researchers from Uppsala University has found that the planet’s most successful bacteria are to be found in our oceans and belong to the group SAR11. The bacteria, which make up 30-40 percent of all bacteria cells in the oceans, also play host to a previously unknown relative of mitochondria. SAR11 bacteria have a small cell volume; in an environment poor in nutrients, this allows them to maximise the concentration of nutrients they store. The study may provide new insights into our basic understanding of the global carbon cycle and of life on Earth.

Researchers from Imperial College London and Oxford University have seen the inner workings of white blood cells at the highest resolution ever documented. The team first used optical laser tweezers to immobilise the cell and then employed a super high-resolution microscope to watch how it goes on to rearrange the scaffolding of actin proteins on the inside of its membrane - the resulting hole is used to deliver enzyme-filled granules that target diseased tissue. The technique is providing new ways of observing the dynamic molecular processes taking place in live cells.

A new study led by Nick Orr of the Breakthrough Breast Cancer Research Centre at the ICR in London shows how the genes that cause breast cancer in men are similar to those known to cause it in women. The research looked at 433 cases of male breast cancer and studied the twelve most common genes that contribute to the risk of breast cancer in females. The team found that five of these genes significantly affect men too, but in varying extents to their female counterparts. Dr Orr hopes that these discoveries could lead to tailored treatments for male breast cancer patients while simultaneously improving knowledge of female breast cancer.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net

New research by scientists at Stanford University indicates that the 22,000 pieces of debris orbiting around the earth do less damage to spacecrafts and satellites than the minuscule particles weighing roughly a billionth of a gram or less. The initial findings by the Stanford team show that radio frequency emissions are indeed produced when a particle weighing less than a billionth of a gram and traveling upward of 20 kilometers per second smacks into a spacecraft and produces ionization.

Researchers at Germany’s Bremen university have uncovered some shocking statistics using daily satellite sea-ice maps of the Arctic sea. The rate at which ice is now melting in the region has more than doubled since 1972, meaning that the Arctic may be ice-free in as little as 30 years. Researchers are certain that this is a direct result of human-induced global warning, which is particularly pronounced in the Arctic due to the albedo effect. The last time the Arctic was incontestably free of summertime ice was 125,000 years ago, at the height of the last major interglacial period, known as the Eemian.

Researchers at the University of Bradford may revolutionise chemotherapy, drastically reducing the negative side-effects such as hair loss, nausea and suppression of the immune system . Based on a modified version of colchicine (an already existing drug), the new therapy, known as ‘smart-bomb chemotherapy’, can isolate and destroy tumours without damaging healthy cells. Although the drug is in early development, the initial lab tests have had promising results, with mice responding favourably to the treatment.

Scientists have pinpointed a correlation between the sex hormones present during early embryonic development and finger length. A team of developmental biologists at the University of Florida found that digit development is controlled directly by androgen and estrogen receptor activity: men’s ring fingers tend to be longer than their index fingers; the opposite being true for women. The research provides a genetic explanation for studies that link finger proportions with traits such as sperm counts, musical ability, sexual orientation, depression and even certain cancers.

A team of researchers from Spain and France have shown how a synthetic cannabinoid can prevent the brain damage associated with ethanol withdrawal. The administration of the synthetic cannabinoid agonist HU-210 was shown to protect neurons against the cell death caused by the hyperexcitability patients develop during alcohol withdrawal.

This week’s must-listen: Dr Ed Moses, director of the National Ignition Facility in California, and Sir Peter Knight, president of the Institute of Physics, explain how nuclear fusion “will work” and how it will “change the geopolitics of energy worldwide”.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net

Researchers from the University of California, Davis have begun to uncover why some obesity sufferers develop chronic diseases such as diabetes and heart disease, while others do not. The researchers specifically studied the body fat of people with metabolic syndrome - a condition characterized by increased blood pressure, high fasting blood-sugar levels, excess abdominal fat and abnormal cholesterol levels. The results of their study show that not all forms of obesity are the same and that some body fat could actually be toxic. This study is the first to pinpoint fat as a contributing source of the biomarkers associated with insulin resistance and chronic inflammation.

Researchers from Michigan State University’s computer and plant science departments have teamed up to try and decipher when certain plant genes activate and deactivate in order to cope with extreme weather conditions. The research focused specifically on Arabidopsis thaliana, a plant with more than 25,000 genes. Using a myriad of computer queries, the scientists were able to figure out the exact conditions in which the plant ‘turned on’ different genes. The researchers hope that their work will contribute to improving crops in the face of environmental changes and climate change.

Scientists have reportedly reached a major milestone in the understanding of - and fight against - the malaria parasite. According to the team from the University of California and Stanford Medical School, the parasite survives and proliferates in the human bloodstream due to a chemical it is able to produce internally. The chemical, known as isopentenyl pyrophosphate (IPP), is a binding block used by the parasite to produce other molecules. By growing the parasite in the lab and treating it with drugs designed to eliminate its ability to produce IPP, the team believe they may be able to develop a vaccine against the disease.

A team of British researchers have uncovered the unique way coral shields itself against harmful UV rays. They hope their discovery could pave the way for a sunscreen revolution in tablet form that protects both skin and eyes. The scientists have found that the algae living within the coral makes a compound that is transported to the coral, which then modifies it into a sunscreen beneficial for both the algae and the coral. The researchers hope that once they determine how this compound is created and passed on, they could biosynthetically develop it in a laboratory to create a sunscreen for human use within the next five years.

The world’s first clinical trial of brain stem cells to treat strokes is currently taking place in Glasgow, Scotland. An independent assessment of the trial recently concluded that the three patients who had stem cells injected into their brain had suffered no adverse effects. Researchers hope to use the stem cells to repair the damaged brain tissue resulting from strokes. Ready to move into its next stage, the trial will be expanded to a further nine patients who will receive progressively higher doses of the stem cells.

Astronomers have discovered the first pair of supermassive black holes in a spiral galaxy similar to the Milky Way. Greatly obscured by dust and gas, pairs of black holes are notoriously difficult to detect and separate. Using data from NASA’s Chandra X-ray Observatory, the team from the Harvard-Smithsonian Center for Astrophysics theorised that the pair are the result of the merger of two galaxies of unequal mass some billion years ago.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net  

Brazilian scientists have discovered a new river in the Amazon basin - around 4km beneath the Amazon river. Named the Rio Hamza, it flows, like the Amazon, from west to east and is also around 6000km in length. Ranging from 200km to 400km wide, the Hamza is hundreds of times wider than the Amazon, which measures between 1km and 100km. However the Amazon, which flows at around 5 metres per second, moves a great deal faster than the Hamza, which flows at less than a millimetre per hour. The team used a mathematical model based on temperature changes in wells in the Amazon to predict the presence of the underground river.

The discovery of a 160-million-year-old Chinese fossil has shed new light on the evolution of mammals on Earth. The shrew-like creature, termed Juramaia sinensis by the team, is the earliest known example of a eutherian, an animal that provides nourishment to its unborn through a placenta. The palaeontologists, led by Zhe-Xi Luo of the Carnegie Museum of Natural History, Pittsburgh, have shown how the fossil has brought us closer to understanding the evolution of mammals and also explained how this evidence corroborates what we already knew from genetics.

According to a recent study, human beings are just one of the 8.7 million species that make up the planet Earth - and up to 90% of these species are yet to be discovered. The study estimates that there are 6.5 million species to be found on land and 2.2 million to be found in the world’s oceans. The new figure, believed to be the most accurate yet, is based on a cross-validated analytical method which takes into account mathematical models, the rate of species discovery and data pertaining to all known species.

Astronomers from the University of California, Berkeley, discovered a supernova closer to Earth than any other of its kind in a generation. The supernova, believed to have been caught within hours of its explosion, represents such a rare opportunity for study that it has sent the entire astronomical community to telescopes. Situated in the Pinwheel Galaxy, part of the Ursa Major constellation, the supernova, PTF 11kly, is situated some 21 million light-years form Earth and continues to get brighter - it may soon be visible with a good pair of binoculars.

A crew member aboard the International Space Station was able to capture some footage of Tropical Storm Irene as it moved over the east coast of the United States.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net  

A new design for prosthetic legs looks set to make it easier for amputees to walk, sit, stand and climb. The device, designed by engineers from Vanderbilt University, is the first to include powered knee and ankle joints that are able to move in unison, helping the user to walk without the gait often associated with prosthetic limbs. The device is moreover able to record the user’s motions, use the data to predict the movements the wearer is attempting to accomplish and to then facilitate them.

A new method is being used by scientists from Stanford and Harvard universities to develop fast, durable organic semiconductors with which the team hope to create flexible displays - imagine an iPad you could roll up. The semiconductors take so long to make that the team decided to adopt a computational predictive approach to narrow the number of candidate materials to test. In total it took a year and a half to synthesise a very small amount of a material which turned out to be 30 times faster than the silicon currently used in liquid crystal displays.

Researchers at the University of Birmingham have created a modified version of ecstasy that could help to fight blood cancers such as leukemia. Professor John Gordon stated in an interview that the team tweaked the drug, already known to fight some cancers, to make it more effective, but that they believe treatment to be a long way off yet.

Fossils that date back to 3.4 billion years have been discovered in a slab of rock in Western Australia. The fossils were found in Strelley Pool, one of the first known stretches of beach.  The researchers hope that understanding the nature of the world's oldest organisms will help them  to not only understand the initial phases of life on Earth, but will also aid the search for life elsewhere.

An international team of researchers from the University of Missouri, the University of Hong Kong, Academia Sinica in Taiwan and Imperial College London have uncovered exactly how a human egg captures an incoming sperm. Their findings show that a sugar molecule that makes the outer egg ‘sticky’ is vital for enabling the sperm and egg to bind together. The authors of the study hope that their discovery could help infertile couples conceive and spur the development of new, natural contraceptive agents.

Using a spacecraft situated far from Earth, NASA was for the first time able to watch a solar storm engulf our planet. Solar physicists say the findings and the accompanying video could lead to important advances in space weather forecasting.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net  

Engineers have developed an electronic device with physical properties similar to those of skin. The skin patch, which has been likened to a temporary tattoo, could mean that patients will no longer be hooked up to wires and monitors - and it could also find applications in the field of human-computer interfacing. The team, led by John A. Rogers of the University of Illinois, developed methods to create bendable versions of superconductors that can twist and stretch whilst still maintaining their functionality. The work represents a key milestone in the marrying of electronics and biology.

A team of researchers from Imperial College London found that blocking sensory nerve functions can prevent late asthmatic response in mice and rats. Unblocked, the nerves set off a chain reaction which causes airways to narrow by releasing the neurotransmitter acetylcholine. If the findings translate to humans, the researchers hope to develop the drug anticholinergics, which could be used to treat asthma patients who suffer from delayed attacks that cannot be treated with steroids.

Significant differences in the metabolites of men and women have led German scientists to conclude that there is a need for gender-specific therapies. The team from Helmholtz Zentrum München studied 3000 men and women and found differences in 101 of the 131 metabolites they looked at. The study could lead to more tailored forms of treatment for progressive diseases such as diabetes.

Researchers at MIT’s Lincoln Center may have finally discovered a cure for the common cold and a host of other viral infections including influenza and deadly hemorrhagic fevers such as Ebola. The drug, entitled DRACO, works by targeting a type of RNA produced only in cells that have been infected by viruses and was developed by combining a dsRNA-binding protein with another protein that induces cells to undergo apoptosis (programmed cell suicide). As the technology is so broad-spectrum, authors of the study hope it could potentially be used to prevent the outbreak and spread of new viruses, such as the 2003 SARS epidemic.  

The Necklace Nebula, located 15,000 light-years from Earth in the constellation Sagitta, is the glowing remnants of a Sun-like star. The nebula, studded with bright knots of gas and likened to a diamond necklace, was recently photographed by NASA - this image is not to be missed.

After studying the Axial Seamount for 13 years, scientists from Oregon State University were able to make the first successful prediction of an underwater volcanic eruption. The team have released footage of lava which was released from a vent and spread 2km across the ocean floor.
 

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net  

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net  

Observations made by NASA’s Mars Reconnaissance Orbiter have revealed signs that water could be flowing on the red planet during its warmest months. The data showed a great number of long, dark tendrils that appear to run down some of the planet’s mountains - so far, the best explanation is that water flows within them. The finger-like features can be seen from late spring and throughout summer, after which they fade during the winter only to return the following spring. The discoveries are yet another sign that the planet may harbour forms of life.

The most abundant source of antimatter near the Earth has been discovered by scientists working with the Pamela satellite. The thin band of antimatter, in this case antiprotons, envelops the entire planet and lies between the Van Allen belts of trapped ‘normal’ matter. While the research confirms previous predictions, the team hopes to use the particles to fuel future spacecrafts.

Researchers from New Jersey have developed a blood test able to diagnose Alzheimer’s disease in its earliest stages. Using human protein microarrays, the test can detect the presence of specific antibodies in the blood with unprecedented accuracy. The technique marks a significant milestone in the history of the disease as, up until now, it was only possible to conclusively diagnose by examining a patients’ brain tissue after death.

Scientists from Vanderbilt University have shown that a diet rich in folate may reduce the chances of developing breast cancer. Whilst the study could not confirm the amount of folate required to prevent the onset of the disease, it did show that women with a high intake of folate had a 40 percent reduced risk of developing it. Folate is a water-soluble B vitamin found in leafy green vegetables, fruits and dried beans and peas.

A new gene-based test developed by researchers at Johns Hopkins University may eventually help patients avoid unnecessary and potentially risky surgery. The test analysed precancerous cysts from 19 patients and searched for mutations in the KRAS gene, commonly found in pancreatic cancers, and the GNAS gene, which had not previously been associated with pancreatic cancer. The result was that both genes were not found in benign cysts. Although more research needs to be conducted with a larger test group, the scientists hope their findings could mean the end of painful and invasive procedures such as unnecessary cyst fluid removal.

Over the summer holidays, thousands of people will crowd theme parks seeking an adrenaline rush from large roller coasters and rides. This report by the BBC asks whether or not screaming is a vital part of the experience and what happens when we don’t allow ourselves to verbally express these extreme sensations.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net

Using an acoustic diode researchers at the California Institute of Technology have managed to demonstrate the one-way transmission of sound in an audible frequency range for the first time. The diode is a component that allows a current to pass in one direction while blocking the current in the opposite direction. Authors of the study believe their findings could be important for architectural acoustics, or the science and engineering of sound control within buildings.

Researchers at the California Institute of Technology are hoping to kickstart an area of our brains that springs to life when we exercise self-control throughout our decision-making process. Known as the dorsolateral prefrontal cortex, or dlPFC, this section of the brain helps us to take more than two factors - like health benefits and taste - into account when assessing the value of a particular food. Following an experiment with over 33 volunteers, the researchers found that external cues can influence how much self-control we exercise. Authors of the study hope that the findings could be applicable to other health warnings, such as supporting the current changes to cigarette packaging.

New research from the Spanish National Cancer Research Centre has shown that progressive telomere shortening is characteristic of hereditary breast cancer. The telomeres of peripheral blood cells were found to be significantly shorter in patients suffering from breast cancers that run in a family than those found in the rest of the population. The research also found evidence of telomere shortening leading to the earlier onset of breast cancer down generations.

Florian Beutler, a PhD student from The International Centre for Radio Astronomy Research, has produced one of the most accurate measurements ever made of how fast the universe is expanding. By using a measurement of the clustering of more than 125,000 galaxies, Beutler was able to calculate the Hubble constant to within 5%. This new method will allow researchers to verify future measurements using an entirely independent method.

Be sure to check out this stunning selection of images of the earth taken from space by European Space Agency and NASA satellites.

This week’s video provides a history of the first ever weather forecast - and it makes for very interesting viewing.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net

New research from the University of California found that human sperm quality and quantity has little or nothing to do with whether a man is fertile or not. Instead, the research shows that the absence of the DEFB126 protein could be responsible for a significant amount of male infertility. The protein acts as a cloaking device, allowing sperm to swim through mucus and avoid the immune system in order to reach the egg. If the study is successfully developed into a test, researchers hope that couples could be treated by sperm injection, avoiding a great deal of added expenses.

Prof. Yoav Gothilf of Tel Aviv University's Department of Neurobiology is looking to the zebrafish to learn more about how the human circadian system -the natural cycle that dictates our biological processes over a 24-hour period- functions. Zebrafish make successful test candidates for research as, like human beings, they are diurnal - awake during the day and asleep at night. This provides an opportunity to manipulate the circadian clock, testing different therapies and medications to advance our understanding of the circadian system and how disruptions, whether caused by biology or lifestyle, can best be treated.

A study into yeast chromosomes could help to shed light on the process of cell replication and division which takes place when cancerous cells form. A team from Trinity College Dublin looked at how yeast evolves by studying the telomeres - the ends - of their chromosomes. They found that in eight out of nine cases, chromosome loss was due to telomere-to-telomere fusion. The exception was found to have evolved when the breakage of a chromosome caused the fusion of the two broken ends to two different chromosome ends. As yeasts are simple organisms and have a lot in common with mammalian cells, the team believe their findings can now be used to provide a greater understanding of the way in which cancers form.

Scientists from St. Jude Children’s Research Hospital have identified a signalling molecule responsible for ensuring the right mixture of T cells is available to fight infections and guard against autoimmune disease. The molecule, Phosphatase MKP-1, was also shown to be an important regulator of immune balance as it serves as a bridge between the body’s innate immune response and the adaptive immune response which follows.

Astronomers from the California Institute of Technology discovered the largest and farthest body of water in the universe. Situated some 30 billion trillion miles away in the heart of a quasar, the reservoir of water vapour consists of at least 140 trillion times that of all the water in the world’s oceans - and it’s around 100,000 times larger than the sun. The discovery of water vapour is in itself unsurprising, but it nevertheless provides insight into the nature of the quasar, which is already believed to be one of the most violent objects in the universe.

Chile's Atacama desert, the world's driest, is home to some of the world's biggest telescopes. The incredibly clear skies over the area means the conditions are perfect for observing space. This video gives you an inside look into the telescopes and control room of the Paranal observatory high up in the Andes mountains.  

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net

Neptune last week arrived at the same location in space where it was discovered 165 years ago and, by way of celebration, the Hubble Space Telescope released some anniversary pictures of our solar system’s most distant planet. Take a look at what NASA had to say about Neptune and be sure to check out the video compiled from Hubble’s latest images.

Researchers at the University of California have identified a protein which could be used to diagnose and treat lymphoma in both humans and dogs. The findings suggest that a gene known as RNPC1, an RNA-binding protein, may play a vital role in the onset of lymphoma as it appears to inactivate the p53 gene, which plays an important role in the suppression of cancer.

A team from the Institute of Human Genetics in Munich has identified two more genetic regions associated with restless leg syndrome (RLS), bringing the number of known regions implicated in RLS to six. One of the regions, TOX3, is also known to regulate brain activity. These findings could now help scientists to develop new treatments for those suffering from this neurological disorder, which is thought to effect 10% of people over 65.

A joint British and Norwegian study has revealed how many dementia patients being prescribed antipsychotic drugs could be better treated with painkillers. The study’s authors believe around 150,000 patients in the UK are being unnecessarily prescribed antipsychotic drugs when proper pain management would suffice. Antipsychotics, known for their powerful sedative effects, can in fact worsen dementia symptoms, and increase the risk of stroke or death.

New findings released by researchers at Mount Sinai School of Medicine have found that the natural antioxidants found in grape seed polyphenols could prevent the generation of β-amyloid (Aβ) peptide, a substance in the brain that can lead to the neurotoxicity associated with the onset and progression of Alzheimer's disease. The leader of the study Dr. Pasinetti hopes that since polyphenols are both readily available and have little to no adverse effects even after prolonged treatment, the new findings could hold significant promise as a preventive method or treatment.

A new plastic, nano-structured surface for growing stem cells has been developed by Glasgow and Southampton universities as an improvement to the standard surfaces which have proven limited for retaining large numbers of stem cells. Created using a similar technique to that used when manufacturing Blue-Ray discs, the new surface could be used to effectively culture mesencyhmal stem cells, taken from sources such as bone marrow, which can then be put to use in musculoskeletal, orthopaedic and connective tissues.

As high as the potential of web 2.0 for the communication among scientists might be, any kind of widespread use is nowhere to be seen. Academia mostly reacts hesitantly at best to the new technological opportunities. The discussions in our recent international workshop, however, also revealed that "Science 2.0" is no closer to becoming mainstream as "Journalism 2.0", since hardly any science or innovation journalists seem to be earnestly using the new platforms yet to identify topics or experts. The reluctance among scientists when it comes to interactive media has just been confirmed by my colleagues (see project "Interactive Science"):

3 out of 4 scientists still use the good old "mailing lists" to keep up to date with calls for papers or conference announcements. However the usage is mainly passive.

Less than one out of ten scientists use blogs at all. And those who use them use them mainly passively (68%). Any kind of intended collaborative use, therefore, is still the exception.

The bottom line also from our own studies is:

• Web 2.0 is still underdeveloped, both in science and in science journalism
• There are very few cutting edge researchers and institutions experimenting extensively with the new opportunities, which inevitably results in a significant divide
• The old systems in both research and publishing prove to be more resistant to change than many online evangelists originally had anticipated, so that refereed publications and classic media formats prevail
• Scientists and their institutions, as well as science journalists, increasingly demand orientation when it comes to the paradigmatic changes allegedly on the verge of a breakthrough.

Youtube recording of our workshop.

What has happened so far... (as in the sequels)

First, the good-old "peer review" system as an increasingly criticised means of assuring quality and relevance has given way to new approaches like Open Access, where we see a "public peer review" nowadays as an open discussion with the community. Once the first scientists had discovered that interactive media means much more than just to blog or tweet, the first science-specific online platforms and software tools appeared, claiming to make scientific practice more efficient and transparent. Instead of stockpiling publications on the institute's web site, researchers could now share them with their peers and get automated or even personal recommendations for related material. Hundreds of thousands of scientists worldwide meanwhile discuss on platforms like BiomedExperts, NatureNetwork or ResearchGate, thereby cultivating an increasingly collaborative research practice which often brings about new trans-disciplinary knowledge networks. Whether these figures, however, are a lot or a little, is hard to answer. In our workshop we showed how connections between scientists or even citation cartels today can be analysed and visualised within seconds. Researchers now have "followers" publicly showing their "impact points" as if that was their personal golf handicap. Some university chairs service their own TV channels on iTunes and live out the new opportunities of public science as far as possible. While the experts are still debating potential impact falsifications of scientific publishing through academic search engine optimisation, some scientists are already making intensive use of the new ways of pushing their publications up in the rankings and search results. There is a widening gap between the masses of "ordinary" scientists and the very few cutting edge researchers and (mostly large and renowned) institutions experimenting extensively with the new opportunities. Therefore it will be a major challenge for us in science communication (research) to come up with appropriate advice and practical orientation for every interested scientist and science journalist to apply. Please feel free to watch an amateur recording (mostly with good audio quality) of our workshop at Youtube:

Introduction by myself
[09:33 min.]

Video statement by Dr. med. Soenke Bartling,
radiologist and researcher in molecular imaging, German Cancer Research Center
[11:39 min.]

Video statement by Dr. Ijad Madisch,
M.D. PhD, founder and CEO, ResearchGate
[09:20 min.]

Video statement by Lou Woodley,
Community Specialist, Nature Publishing
[01:36 min.] More statements later in the discussion

Video statement by Ian Mulvany,
Vice President New Product Development, Mendeley
[07:16 min.]

Discussion (in 8 parts)
[ca. 100 min.]

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net 

Surgeons in Sweden this week reached an important milestone in regenerative medicine after a cancer patient received the world’s first synthetic organ transplant. The operation saw the implantation of a trachea grown from the patient’s own stem cells. The cells, once placed onto an artificial scaffold, took only two days to grow into tracheal cells ready for transplantation.

Researchers at the University of Pennsylvania have successfully reprogrammed brain cells to become heart cells. The team placed heart cell mRNAs directly into brain cells, causing the host nucleus to change the cell’s RNA populations, which in turn changed the phenotype of the host cell. The findings are unique in that they directly reprogrammed cells using RNA without an intermediate step.

X-ray crystallography has been employed by scientists to decipher an important part of Mediator, a sizable molecular machine that regulates the transcription of DNA. The team from Indiana University believe that their findings will help to map mutations that affect the transcription process, leading to a new generation of drugs that target these multi-protein complexes to treat disease.

The effectiveness of anti-HIV drugs looks set to greatly increase after researchers used a mathematical modelling technique known as elastic network modelling to help predict the location of the mutations that lead to resistance to protease inhibitor drugs. These drugs have dramatically reduced the number of AIDS related deaths by halting the protease enzyme, but the virus eventually mutates and develops resistance during the course of treatment. The new research could improve the quality of life for the estimated 34 million people living with HIV worldwide.

Foxp2, a gene already known for its role in speech and language, has been shown to play an important role in the networks of genes responsible for the wiring of the brain. A team from the University of Oxford demonstrated how the gene acts as a genetic dimmer switch, able to regulate the amount of protein product made by nerve cells. The study of neurodevelopmental genes such as Foxp2 is providing science with a much greater understanding of the brain itself.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net 

A new class of antiangiogenesis drugs was discovered by researchers from Massachusetts General Hospital. The team demonstrated how a compound derived from a tree native to Argentina and Brazil was able to interfere with the formation of blood vessels in animal models of normal development, wound healing and tumour growth. The research could lead to new treatments for cancer and other diseases which feature abnormal blood vessels.

With the help of NASA's Spitzer Space Telescope, Astronomers have found that contrary to popular belief, galaxies in the early universe continuously ingested the fuel required for the formation of stars over long periods of time. Scientists previously thought that galaxies consumed fuel in a violently voracious manner when they merged with other galaxies. The new findings also indicated high levels of H alpha, which would have made the skies a place of bright stars and frequent supernova explosions.

A team of European researchers has shown how the adaptation of fat cells to obesity could lead to the development of inflammatory disease. The expansion of adipose tissue (where excess fat is stored) leads to the failure to properly store lipid, resulting in a build-up of lipid in organs such as the liver and muscle.

Researchers from the UK believe that the drugs used in IVF may increase the risk of having a baby with Down's syndrome, especially for older women. The error, pinpointed in fertilised eggs, often resulted in an extra copy of chromosome 21, the chromosome behind the syndrome. More work is now needed to confirm the findings and their long-term implications.

According to research from UCLA, hydrogen peroxide plays an important role in wound healing: the chemical, released by wounded skin cells, was shown to promote the regeneration of sensory axons.

Research undertaken by Erich Karkoschka (University of Arizona) was able to determine precisely how long a day lasts on the planet Neptune. Using data gathered over the last 20 years, Karkoschka calculated that one day on the gas giant lasts exactly 15 hours, 57 minutes and 59 seconds. The findings have lead him to conclude that the planet's mass must be closer to the centre than previously thought and could now pave the way for a better understanding of giant gas planets in general.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net 

New research from Northwestern University has demonstrated how ICU mortality rates can be cut when physicians are prompted to address items on a checklist. Curtis Weiss noted that the prompting, carried out by a physician not involved in the patients’ care, caused the mortality rate to decrease by 50 percent over a three-month period.

Scientists in Switzerland have engineered genes that can be ‘switched on’ with pulses of blue light. By modifying kidney cells with light-sensitive molecules from the eye, the team were able to make them produce proteins on demand. The discovery looks set to improve to quality of life for patients suffering from diseases such as diabetes.

Nanotechnology has been used to create sand that is able to purify water more efficiently. By coating coarse grains of sand with graphite oxide, researchers from Rice University developed a material that is effectively able to sequester water-soluble contaminants.

Researchers at San Raffaele Institute in Milan and the CNR Institute of Neuroscience in Pisa have created a mouse model for the rare and painful Familial Migraine type 2 (FHM2), in order to come closer to treatment for those suffering from this severe migraine subtype. The in vivo analysis of the FHM2 model indicates an increased cortical spreading depression (CSD), which the authors hypothesize is caused by inefficient glutamate clearance. 

Science has come closer to preventing the onset of Huntington’s disease after researchers from Johns Hopkins identified a natural mechanism that is able to block the expression of the mutated gene linked to the neurodegenerative disorder. The team believe the research could one day lead to drugs that manipulate a natural ‘brake’ known to slow the production of the toxic huntingtin protein.

Video: A new technique pioneered by researchers from UCLA uses saliva to determine one’s age to within five years. The method, which measures the degree of methylation in certain areas of the genome, could find applications in both health care and law enforcement.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net 

A massive black hole (MBH) situated in a galaxy some four billion light-years away has ripped apart a sun-like star. Taking place around once every million years, for the black hole, this is certainly a rather rare occurrence. Astronomers from the University of California became aware of the phenomenon after they noticed an emission of powerful radiation moving towards earth over a period of months.

Living cells have been genetically engineered to produce laser light. Scientists from the Wellman Center for Photomedicine engineered human kidney cells to produce a protein known as GFP that is commonly found in jellyfish. The green fluorescent protein could lead to developments in light-based therapeutics, diagnosis and imaging, as it is able to deliver an emission from an external laser source deep into tissue. 

Three years worth of research undertaken in New York and Barcelona that focused on proteins known as Smads has brought the medical world one step closer to clinical treatments for cancer. The study shed light on the life cycle of the proteins and the way in which they react to mutations.

Researchers from France have uncovered how enzymes work on a macromolecular level. The research, which looked closely at substrate binding, could be used to develop or improve drugs such as antibiotics.

The quality of life for patients managing the effects of multiple sclerosis, cerebral palsy and stroke looks set to improve after researchers from the University of California identified some important factors relating to cells in the brain known as oligodendrocytes. Building upon this research, scientists could one day develop drugs or stem cell therapies that could eventually be used to harness the regenerative power of the brain.

This week’s video: GOES-13, the Geostationary Operational Environmental Satellite, has been continually documenting a Chilean volcano from its vantage point since it began erupting on June 4.

 The undergraduate education in India is booming (Nature, vol 472, 24 – 26, 2011) and the government is increasing investment towards research and higher education. However, lack of quality education as well as proper policy remains a major concern. Accordingly, Indian science is lagging behind not just developed nations, but also recently industrialized countries such as China.

Publications in high impact journals often indicate a high quality of research. According to a recent scientometric analysis (Curr. Sci. vol 99 no 5 577 – 587, 2010) the number of publications from Indian institutions in higher impact journals like Nature, Science, Cell etc is very poor. Almost all top Asian universities have published more than the Indian institutions.

Lack of proper policy for higher education and research is one of the major concerns in India. University Grants Commission, the controlling body of Indian universities recently launched an academic performance indicator (API) based system for recruiting and promoting professors in colleges and universities [http://www.ugc.ac.in/policy/englishgazette.pdf]. The API score for papers in referred journal would be augmented as follows: (i) indexed journals – 5 points (ii) paper with impact factor (IF) between 1 & 2 by 10 points (iii) paper with IF between 2 & 5 by 15 points (iii) paper with IF between 5 & 10 by 25 points (iv) for paper in non referred journal API score is 10. The API for joint publications will have to be divided. One can earn an API score of 10 by presenting a paper in a seminar. This in turn will discourage collaborative research, as it will cause a division of API scores. Also the corresponding author and first author will share maximum points. For example: suppose there are 4 authors publishing a paper in a journal with IF 9. Then total API score = 25. Out of which first author and corresponding author will share 60% = 15. The remaining two authors will have an API score of 5 each. So publishing a paper in a high impact (IF=9) journal, the 3 rd and 4th author will get 5 API points. Whereas publishing a paper in a non referred journal (with only ISSN/ISBN), a single author can receive 10 points. Even attending a national conference one can receive an API score of 7.5. Now a day's seminars are almost like a picnic, lots of seminars are being organized and there is hardly any quality control except for the top 1-2% of total seminars/conferences held. As a result people are trying to attend more seminars and publish more papers in non referred journals to earn the maximum score.

Therefore in order to fulfill the dream of becoming a developed nation, India should frame and implement a proper policy to boost the quality of research and higher education in universities and institutions. Otherwise quantity will continue to reign over quality. In this regard, India should adopt proper research policies that have proved successful in other countries.

References:

1. A. Nayar, Nature, vol 472, 24 – 26, 2011

2. K. P. Raghuraman, R. Chander, G. Madras, Curr. Sci. vol 99 no 5 577 – 587, 2010

3. “The Gazette of India, September 18, 2010 (Bhadra 27, 1932) [Part III – Sec. 4] http://www.ugc.ac.in/policy/englishgazette.pdf

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net

A study released by the Translational Genomics Research Institute reported that deadly bacteria might be developing resistance to antibiotics by mimicking human proteins, a process known as molecular mimicry. The study might go some way to explaining the reasons behind some of the public health threats that have emerged in recent years.

Scientists from the University of Adelaide developed a potential treatment for E. coli over a decade ago. It did not however go forward into clinical trials due to a lack of commercial interest. The probiotic bacterium, designed to bind the toxin produced by E. coli, could have been used to prevent the deaths caused by the most recent outbreak of the disease.

Researchers at the University of Finland have shown how effective strategies for managing forests have in fact increased the amount of carbon stored by the world’s trees. After looking at forestry data from 68 nations, the team demonstrated that a higher density is key to creating larger carbon sinks. 

A piece of open-source software looks set to change the way biologists analyse genomes. Whereas data was previously sent to information specialists for analysis, GenPlay offers a user-friendly platform where scientists can visualise their data, are provided with feedback and are offered a greater level of control over the analysis itself.

Sunspots are not just a form of visual candy: they are points where convection occurs on the surface of the sun. Swedish scientists were able to observe a sunspot from 2010 and found that hot plasma rises from below, radiates away heat and then sinks back into the sun as it cools. It looks pretty cool too.

The sun produced quite a superb solar flare this week. This video is not to be missed.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net

The World Health Organisation yesterday announced that the strain of E. coli behind the current outbreak has in fact never before been found in humans. Scientists are hurriedly attempting to sequence the entire genome of the bacterium after discovering that it is what is commonly known as a chimera, a mutant form consisting of multiple strains.

Researchers from the University of Florida have shed new light on the effects which common viruses can have on the health of patients in intensive care units. By analysing the role of viruses in the health outcomes of more than 200,000 patients, the team was able to conclude that viral infections greatly influence the amount of recovery time necessary.

A new study released by the Oregon Health & Science University has revealed that a high-fat diet can have an adverse effect on pregnancy: these types of diets decrease the blood flow from the mother to the placenta, and thereby increase the risk of stillbirth.

New findings by a German research group stationed in Antarctica have shown that, for Emperor penguins, huddling is crucial to ensuring the survival of their eggs during Antarctica’s brutal winter. The tightly packed penguins collectively shuffle every 30 to 60 seconds, reordering themselves so that each individual and their egg get their moment in the warmth.

A new study published in the latest issue of Emotion, found that when humans see the colour red, their reactions become (involuntarily and unconsciously) both faster and more forceful. The reason? Red enhances our physical reactions because humans see it as a danger cue.

Robert LaMotte, professor of anesthesiology and neurobiology at Yale University, has discovered the basis for the pricking, stinging and burning that is inherent in chronic itchiness and immune to antihistamines and topical creams.  The peptide BAM8-22 was tested on 15 healthy volunteers and evoked scratching in all of them. LaMotte is hoping that the discovery could open avenues for the development of anti-itch treatments.

This week’s video comes from NASA and features the upcoming solar collisions for June. Well worth a watch.

Introduction

Fitness landscape theory is becoming to use for answering the search of developing species which desire to reach highest peak on the potential gene space in the field of evolutionary biology (Wright, 1932; Gillespie, 1984). Development of the cost landscapes in related solution space is used as an approach to combinatorial optimization problems’ solutions (Holland, 1975; Kirkpatrick et al., 1983; Palmer, 1988) in computer engineering and operations research fields.

In recent years, different approaches are used in various fields of social sciences like organizational change (Beinhocker, 1999; McKelvey, 1999; Reuf, 1997), evolution of social structures (Levinthal, 1996), innovation networks (Frenken, 2000 and 2006), selection of appropriate technology (McCarthy and Tan, 2000; McCarthy, 2003), economic structures (Kauffman, 1993) and political systems (Kollman et al., 1992).

Introducing perspective with NK model which is simplify using fitness landscape theory in various fields is devoted to be possible in global optimum searching on a stochastic but easily controllable fitness landscape that composed of possible fitness values.

Local optimum points besides global optimums are also important in fitness landscapes (see for detailed information: Ilter, 2007; Ilter, 2008). Local optimum points can be seen peak points which isn’t allow for changing possible fitness values even if alternatives of selection are changed. After all, firms can terminate their search for global or local optimum value(s) because of sub-optimal value(s) are accepted as best value(s) for them. “Why does the firm generally terminate their search on the fitness landscape before finding the local optimum value yet?” is still an unanswered question in social sciences.

Decisions on information systems, technology and innovation have a different place in firms’ decision mechanism in terms of some aspects. There are various factors seems to be important which affect the selection of technological structures (production technology, information technology, etc.) in firms and the decision behaviors of decision makers in making decision related to these technologies. These behaviors can be revealed by affecting the optimality of firm’s final decision and the inner-fitness of decision maker in a large extent. It is possible to say that organization properties and factors in organization hierarchy effect decisions about information systems, technology and innovation management which can be concluded as a part of complex systems. Decisions except optimal ones (sub-optimal decisions) couldn’t recognized while design of decision mechanism in organization targets the optimal decision in some conditions.

Method

In this article, we try to determine some important dynamics that may cause of termination of firms’ searching action of optimality even if they couldn't reach the local optimum value.  These dynamics are considered together with some factors of organizational decision-making models and then supported with simulation results to reveal sub-optimality conditions.

Various scenarios have reviewed by using NK fitness landscape theory for determining sub-optimality conditions that could be in decisions which are related to information systems, technology and innovation. Scenarios are developed as some conditions which are include one decision maker, various numbers of subordinates and various numbers of decisions (Table 1). The state of optimality divergence and the state of sub-optimality toleration of decision maker emphasized in this article are supported by simulations’ results after statistically acceptable number of runs. As an example, scenario L07 is reflecting a case which includes two subordinates (subordinate A has to make a decision and subordinate B has to make three decisions) and a passive decision maker (has to make a decision of subordinates’ decision combination).

Several runs of various scenarios are inspected with using NK fitness theory for determining sub-optimality states of decisions which are related to information systems, technology and innovation. 

Results

In simulation, global optimum points that on the fitness landscape (space of decision alternatives) are determined by generation of a landscape which includes fitness values of each scenario. Probability of achieving global optimum in final decision of the decision maker after evaluation of decision alternatives can be defined as the term of “Probability of Optimality”. Sub-optimality is appeared if decision’s probability of optimality descents below 100%. Relationship between fitness value of the final decision of the decision maker and global optimum value on the fitness landscape can be defined as “Fitness Rate” and it can be recognized as of success factor of decision maker’s final decision. Successes of decisions can be determined by inspection on global optimum-decision’s fitness value bias for the decision that can’t achieve optimality but sub-optimality. (Figure 1)

Figure 1: Relationship Between Probability of Optimality and Fitness Rate in Various Scenarios

Conclusion

Probabilities of optimality and fitness values of each scenario are correlated each other during the analysis of simulation results. These correlations show that decisions of active decision makers (scenario code in light color) are more efficient than decisions of passive decision makers (scenario code in dark color) in terms of the fitness value. On the other hand, there are no optimal values for each of all decisions and noticed that these decisions are not optimal but sub-optimal. Addition to this determination, decisions of active decision makers have higher values than decisions of passive decision makers in terms of the probability of optimality. Success of decision maker is limited from the point of view of the probability of optimality in despite of these two settings are stated that the active decision makers are more successful than passive decision makers.

Bibliography

Beinhocker, E. D., 1999. Robust adaptive strategies, Sloan Management Review, 40/3, 95-106.

Frenken, K., 2000. A complexity approach to innovation networks, Research Policy, 29, 257-272.

Frenken, K., 2006. A fitness landscape approach to technological complexity, modularity, and vertical disintegration, Structural Change and Economic Dynamics, 17, 288-305.

Gillespie, J.H., 1984. Molecular evolution over the mutational landscape, Evolution, 38, 1116-1129.

Holland, J., 1975. Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence. University of Michigan Press: Ann Arbor.

Ilter, H.K., 2007. Optimality in the Technological Fitness Landscapes: Conceptual Viewpoint of Searching for Summit, Proceedings of 27. National Operations Research and Industrial Engineering Congress, 2-4 July, Izmir, Turkey.

Ilter, H.K. 2008. Research on Information Technology Strategies in terms of Fitness Landscape Theory, Journal of Economics and Administrative Sciences (Hacettepe University), 26/2, 163-182.

Kauffman, S. A., 1993. The Origins of Order: Self Organization and Selection in Evolution, Oxford University Press, New York, NY.

Kirkpatrick, S.; Gelatt, Jr., C.D. ve Vecchi, M.P., 1983. Optimization by simulated annealing. Science, 220, 671–680.

Levinthal, D., 1996. Learning and Schumpeterian dynamics, Malerba, G.D. (Ed.), Organization and Strategy in The Evolution of The Enterprise, Macmillan Press Ltd, Basingstoke.

McCarthy, I. P., 2003. Technology management – A complex adaptive systems approach, International Journal of Technology Management, 25/8, 728-745.

McCarthy, I. P. ve Tan, Y. K., 2000. Manufacturing competitiveness and fitness landscape theory, Journal of Materials Processing Technology, 107/1-3, 347-352.

McKelvey, B., 1999. Self-Organization, complexity, catastrophe, and microstate models at the edge of chaos, Baum, J.A.C. ve McKelvey, B. (Ed), Variations in Organization Science, Sage Publications, Thousand Oaks, CA, 279-307.

Palmer, R., 1988. Statistical mechanics approaches to complex optimization problems, Anderson, P.W.; Arrow, K.J.; Pines D., (Ed.), The Economy as an Evolving Complex System, Addison-Wesley: Reading.

Reuf, M., 1997. Assessing organizational fitness on a dynamic landscape: An empirical test of the relative inertia thesis, Strategic Management Journal, 18/11, 837-853.

Wright, S., 1932. The roles of mutation, inbreeding, crossbreeding and selection in evolution, Proceedings of the Sixth International Congress of Genetics, 356-366.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net

We all know that black holes have a rather unfortunate tendency to suck everything in their paths into oblivion. But have you ever heard of white holes? It would seem that they do rather much the opposite; ejecting a great deal of gamma rays into the rest of the universe. The phenomenon, observed in 2005, is akin to the Big Bang itself, so much so that one group of scientists decided to call them 'Small Bangs'.

A new biomaterial created by nanoengineers at the University of California, San Diego is able to mimic the properties of human tissue: it doesn't wrinkle when stretched. The material, a significant leap forward for medicine, might also find applications in defence, energy and communications.

New research from Michigan State University has shown that precision-tinted lenses are able to attenuate the pain associated with migraines by correcting the activity in the brain's visual cortex.

A new study by researchers at the Queensland University of Technology, Australia indicates that polysaccaropeptide (PSP), which is extracted from the turkey tail mushroom, is able to target cancer stem cells and suppress the formation of tumours in mice. Lead researcher Patrick Ling hopes that the results will be an important step towards fighting the disease.

A team of NASA-funded scientists from Brown University demonstrated that some parts of the lunar mantle contain as much water as the Earth's upper mantle. Their findings uncovered around 100 times more water than previous studies had suggested, thereby raising a great deal of questions about how the moon actually formed.

Video-fluoroscopy recordings of a dog lapping up liquid have shown that both cats and dogs use their tongues to draw columns of water into their open jaws, disproving published accounts that dogs scoop liquid with a spoon-shaped cavity.

Researchers at Imperial College London have found that the electron is a perfect sphere to within one billionth of a billionth of a billionth of a centimetre. The findings could shed light on unknown particles that may exist in nature, and even explain why matter won out over antimatter.

The Internet has already had a huge impact on how we communicate with each other, do business, and maintain our personal relationships - and it’s now starting to change to face of how we do research. Whether you’re a graduate student straight out of University wondering what to do next with your degree, or you’re working towards your PhD with your sights already firmly set on a career in academic research, the Internet offers many opportunities to help you on the way to a successful career in research. Here are some tips on how to use the internet to its best advantage as a young researcher.

Manage your online reputation. Making an impact on the world of research is not always just down to how hard you work and the amazing new discoveries that you’ve made – it’s about making yourself, and your work, known to the wider research community. Without being able to clearly communicate your research and its implications to others you risk all your hard work going unnoticed. One of the easiest ways to make your presence known is to build up an online research portfolio. ResearchGate, for example, offers members the opportunity to create a personal profile which summarises research interests, experience, and education all in one place. Increase the visibility of your research by self-archiving your publications on your profile to make your work more accessible to a larger audience of researchers and scientists. Another great way to use social media to raise your profile is by starting a blog – use it to keep a record of how your research is going, to publish your thoughts and encourage discussion. Keep posts interesting and of a high quality, and you can even use them as another point of interest that you can present to potential supervisors or employers. In addition to blogging you can participate in academic discussions by commenting on publications (for example, through PLoS) or other blogs. And if you’re particularly keen on developing your science writing skills, find a small online magazine covering the subject you’re interested in and pitch an article to them that you can write. 

Market yourself - having an active internet presence can be an excellent way of selling your skills to the growing community of scientists and researchers online, but remember to exercise caution with the information you make available. Take care to manage your online profile and always be aware of your potential audience!

Build up your professional network. Networking plays an essential role in ensuring your progress as a successful researcher. Building up a strong network of contacts in the world of research - be they professors, students or your co-workers - means that you have people to discuss your ideas with and get advice from when most needed. Online networking makes the whole process a lot easier, enabling you to maintain existing relationships with your colleagues whilst also offering you the opportunity to make new ones – without having to attend countless conferences.

Use professional networking sites such as ResearchGate and LinkedIn to expand your network, collaborate with researchers from all over the world and to develop your research ideas further. Follow major researchers in your field using Twitter or ResearchGate – it’s an easy way to keep up to date on what they’re reading, thinking about, or even who they themselves follow! When you do make a new contact, make sure to follow up by sending an email shortly afterwards to say it was nice to meet them, or ask them a question about something you discussed – researchers love talking about their research!  Think about having a simple business card made up with your name, email address and a link to your blog or online profile and adding this to your email signature – you could also use the ResearchGate profile share button for an easy way of making your information available to others at the click of a button! Above all, keep all correspondence professional, especially if you want to use it to get ahead and make useful, long-lasting contacts. 

Remember to use the internet to aid, rather than replace, more traditional face-to-face networking opportunities. For example, find lectures or conferences on the subjects that you’re interested in and don’t be afraid to approach speakers with questions or to seek advice! Also keep an eye out for invited lecture series’ run by universities which are usually open to the public and free to attend.

Take the first step towards your career in research.  If you’re passionate about your subject and ready to pursue your interests further, a master’s degree could be the perfect route into the world of academic research. Doing a master’s can be a great way to specialise in the topic areas that you enjoyed most during your first degree and to gain the necessary skills and confidence needed to kick-start your career in research. But how do you decide on the right course for you? There are many important factors to consider when making your decision, but a good starting point is to take a look at University websites. Faculty webpages now tend to offer comprehensive advice about the main departmental research themes and the range of postgraduate courses available to you as well as other information that may play a role in your decision-making process such as departmental research assessment performance, the destinations of recent graduates in your field and detailed information on how you can apply for a particular position. Get more inside information by reaching out to people who are already working in the labs you’re interested in – ask questions about their research and the day-to-day running of the lab. If you’re still unsure, consider a position as a research assistant to get critical lab experience, or just to see if a certain field is really for you. 

Another key point to think about when considering postgraduate study is funding. As student loans are no longer available to you as a postgraduate student and funded courses are few and far between, research into alternative sources of funding is essential - use the internet to search for funding opportunities offered by the UK Research Council, grants from educational trusts and professional and career development loans.

Although a master’s degree can be good starting point, remember that they are not always a prerequisite for a career in research - many students decide to go straight on to a PhD after they graduate. The internet contains a wealth of information and advice on how to do this - do your research to find out which PhD is for you and what qualifications you need to do it. Most institutes advertise departmental studentships on their own pages, but expand your search further and take a look at websites such as ResearchGate which advertise PhD studentships from Institutions all over the world - you never know what you might find!

Find a job. Careers in research and development require people from all types of academic backgrounds and researchers at any stage of their career can find jobs in a variety of places on the internet. If you’re an undergraduate considering a career in research, find out what it really means to be a researcher and build up your practical skills by offering to do unpaid internships with a lab or supervisor whose work you’re interested in.  This is not only a great way for young researchers to gain a better understanding of the field, but it can also give you a real edge when later applying for postgraduate positions. If you’re a graduate student, find work as a research assistant to help focus your research interests and build up your relevant work experience. But what’s the best way of seeking out these posts? The first step is to identify labs conducting active research in an area that interests you. Take a look at their websites to find an outline of the research they conduct, their recently published papers and whether they have any advertised vacancies for positions within their lab. You can also keep up to date on the lasted advertised job vacancies with ease by using the ResearchGate Research Jobs board, which has hundreds of listings for positions in research and academia.

With a large number of jobs also going unadvertised, don’t forget the importance of making speculative applications. Think beyond just applying for positions that are advertised and contact supervisors directly – make your own opportunities!

Get organised. As a young researcher, you are probably already aware of the importance of getting your research published in order to increase the visibility of your own findings, but it’s also essential to keep up with the work of other researchers in your field. After all, you don’t want to find out that after spending all of your waking hours in the lab for six months, trying to perfect that one experiment, that someone else has already beaten you to it! The best way to ensure that doesn’t happen to you is by making sure you keep on top of the latest research published by your peers. 

The internet offers a number of advanced literature search engines, making finding the publications that you need quicker and easier than ever. ResearchGate’s powerful semantic search engine focuses your search results and helps you to discover articles related to your research from a range of different sources on the internet, making your search more efficient and helping you to keep up to date with advancements in your field. Another way to start off your career on the right track is to keep a record of all the papers relevant to your research right from the word go using one of the many available reference management tools - Endnote is considered the industry standard software for keeping your references in order whilst for Mac users, Apple’s Papers application is seen as the way to best organise your research. Using these tools you can organise your papers, generate bibliographies and manage your citations without any of the usual stress!

To sum up, the Internet is seeing in a whole new generation of sharing and communicating ideas online and is proving to be an invaluable collaboration tool for researchers today. Use these tips to learn how you can get the most out of it to help you on your way towards becoming a happy, successful researcher! 

Most infectious diseases that have put heavy burdens on humans came from animal viruses. The examples of such influential diseases are the 1918 influenza pandemic, also known as the 'Spanish Flu' pandemic, that killed 20 – 50 million people worldwide; the short-lasting global outbreak of the previously unrecognized severe acute respiratory syndrome-associated Coronavirus (SARS CoV) infections in humans, which sickened 8098 people and caused 774 fatalities during November 2002 – July 2003, but generated a huge economic loss due to the fear of having the next devastating pandemic; and the human immunodeficiency virus-1 (HIV-1), against which humans have not had vaccines to prevent the development of the acquired immune disease syndrome (AIDS), even nearly 40 years after the discovery of the virus (Gallo & Montagnier 2003, p. 2283; CDC 2005, p. 2; Taubenberger & Morens 2006, p. 15). The 1918 strain of influenza virus A/H1N1 initially came from waterfowl and then entered the swine population before infecting humans (Reid et al., 1999, p 1654; Reid & Taubenberger 2003, p. 2289; Taubenberger & Morens 2006, 18). The natural reservoir of SARS CoV is bats; it could enter humans after adapting in palm civets (Paguma larvata) (Cyranoski 2003). The HIV-1 evolved from a simian immunodeficiency virus, whose natural reservoir is chimpanzees, and gained access to humans approximately 100 years ago (Pennisi 2008). How animal viruses pass into humans is not complicated; for example, the viruses can enter the blood circulation through accidental wounds resulting from animal bites, butchering, and vector bites – e.g. mosquitoes or ticks. Sometimes the case is trivial, such as when humans contracted the deadly Hantavirus pulmonary syndrome (HPS) after having contact with infected rodents (deer mouse – Peromyscus maniculatis) or their urine and droppings (Morens et al. 2004, p. 243). Indeed, humans and viruses share the same world and it is only a matter of the right moment when they come into contact with each other. Fortunately, the viruses do not always directly cause diseases when they first enter human bodies; mostly they need to adjust their structure before entering human cells, in a long-term evolutionary process. Therefore, if the viruses are identified at the point they are just entering humans; the birth of a new pandemic may be aborted because researchers would have time to develop diagnostic tests, effective treatments, future plans for disease surveillance, and even antiviral and vaccines important for defending against the most severe threats. Understanding the origins of human viruses, therefore, is an important key in controlling infectious diseases, in terms of predicting the next event of a pandemic.

An animal virus can only use humans as their new hosts after going through an evolutionary process. The emergence of a new disease in humans is determined first by the increasing opportunities for the virus to enter a human population, then its adaptation to growth within humans, and lastly its acquisition of effective human-to-human transmission. In fact, the evolutionary process is the period for an animal virus to adopt the ability to efficiently infect the appropriate cells, in which host barriers at different levels, such as receptor binding, fusion and entry, making use of biochemical resources within the cells, genome replication, and gene expression must be passed. The process is highly vulnerable to the influences of many external factors, such as ecological changes related to climate condition and the social structure of human populations. Wolfe et al. (2007, p. 280) theorized there are five evolutionary stages during the process of how animal viruses ‘jump’ to humans. Stage 1 is where animal viruses maintain closed circulation in the animal reservoir without having any contact with humans. Stage 2 is where an animal virus occasionally infects humans, but does not maintain human-to-human transmission. Stage 3 is where an animal virus has occasional human-to-human transmission and can generate limited outbreaks. Stage 4 is when an animal pathogen has a sylvatic (natural) cycle in an animal reservoir, but can also maintain long-term human-to-human transmission without involving the animal hosts. The last stage, stage 5, is where a virus has completely switched its host into humans. On the other hand, Parrish et al. (2008, p. 457) and Daszak (2009, pp. 253 – 254) simplified the five stages into three phases (pre-emergence, spillovers, and pandemic). Pre-emergence represents stages 1 and 2, where an animal virus maintains a long-term circulation in animal reservoir and occasionally enters a human population without subsequent transmission. Spillover represents stage 3, where an animal virus enters a human reservoir and causes “single cases, small clusters of cases, or localized outbreaks”. A pandemic represents stages 4 and 5, which is when an animal virus is either adapting or has adapted to a human population so that it establishes human-to human transmission. The two different schools emerge because Wolfe et al. (2007, pp. 279 – 281) based their observation on infectious diseases that have caused the highest mortality and morbidity in the past, while Parrish et al. (2008, p. 458) and Daszak (2009, p. 252 – 257) lay an emphasis on the recent emerging infectious diseases, whose emergences are highly influenced by ecological changes related to the nature as well the social structure of modern human society. They reasoned that factors such as international travel, natural disasters, drug resistance, or wars could strongly interfere with the evolutionary process so that certain stages that occur solely due to viral evolution are bypassed.

There are remarkable patterns of disease emergences in humans, which are the result of infection by animal viruses. These patterns are very obvious, in terms of geographical and animal origins of viruses infecting humans and the distinguishing rates of emergences between established and emerging infectious diseases. In the past, viruses causing high mortality and morbidity rates had mostly come from domestic animals and primates (Wolfe et al. 2007, p. 281). In temperate regions, the rise of agriculture forced humans to domesticate animals, mostly the Old World's mammals, for their meat, milk, or leather; therefore, frequent contact between them had exposed humans to these animals' disease, such as smallpox in cows or influenza in pigs or poultry. On the other hand, the hunter-gatherers of tropical regions encountered primates in the wild. Primates have the closest evolutionary distance to humans; therefore, viruses originating from them more easily adapted to human cells and in doing so, had a higher probability to establish a disease in humans. A prominent example of this would be the human immunodeficiency virus 1 (HIV-1) that evolved from a simian immunodeficiency virus (SIV), whose natural host is chimpanzees (Pan troglodytes) (Sharp et al., p. 339). Nowadays, emerging infectious diseases are increasing rapidly in numbers as a result of the modified settings of human population density and the ecological landscape. In just 10 years, from 1993 to 2003, previously unrecognized outbreaks emerged all around the globe for various reasons. In 1993, the epidemic of Hantavirus pulmonary syndrome (HPS) emerged in the United States because the natural reservoir of the virus, the deer mouse (Peromyscus maniculatis), proliferated abundantly after climatic changes increased their food sources (CDC 2006, p. 1). This situation created a greater opportunity for mice to have contact with humans, who contracted the disease after being exposed to their urine and droppings. In 1994, three previously unidentified human cases of Hendra virus were reported in Australia; two of them were fatal cases (CDC 2007, pp. 1 – 2). The natural reservoir of the virus is thought to be flying foxes (Pteropus sp.); the virus causes respiratory and neurologic disease in horses, from which humans were infected after having been exposed to body fluids and excretions of infected horses. In 1999, an outbreak of Nipah-virus-associated encephalitis emerged in Malaysia after the host population, the fruit bats' (Pteropus sp.), increased sharply in association with increased mangoes farmed near pig farming (Daszak 2009, pp. 257 – 260). The bats created virus spillovers to the pig population, which in turn acted as a mediating host of the virus to humans. The outbreak caused more than 100 fatalities without human-to-human transmission at all. The 2003 global outbreak of SARS-CoV was initiated from human contact with infected palm civets. Although it had never been identified in humans previously, the respiratory virus could be transmitted between humans. Based on these patterns of disease emergence, it can be concluded that the contact rate between animal viruses and humans is the major determiner of cross-species virus transmission.

The scientists believe that early identification of the increase in contact-rate can be used as an early warning of future emerging infectious diseases. Previously, the scientists had successfully revealed the cause of two emerging infectious diseases, the Nipah virus (NiV) encephalitis and Hantavirus pulmonary syndrome (HPS), by identifying factors that cause the contact-rate increase. In the case of NiV, the increased contact rate was between bats and pigs, then pigs to humans. Why bats gained closer access to a large number of pigs was related to the increased production of mangoes planted near pig farms, which made use of the pig manure as fertilizer. In the case of HPS, the increased number of mice was caused by the abundance of food sources, which in turn led to a more frequent encounter between humans and mice. The success in analyzing the causes of the two cases provides knowledge for analyzing the future cross transmission of an animal virus to humans. The most suitable condition for initiating a new disease emergence involves an increase in the food supply of an animal host, which was the initial trigger for their prolific proliferation and subsequently led to a more frequent contact with humans; the related factors would include the route of virus transmission, the density of human population, and the climatic condition, to mention a few. An initial recognition of such appropriate settings will generate an early warning for a possible emergence of unknown disease in humans. Presently, in accordance with currently available resources, efforts to minimize the risk of disease emergence are emphasized in a generation of reliable data, particularly those that provide the evidence of increased contact rates (Morens et al. 2004, p. 247 – 248; Wolfe et al. 2007, p. 282 – 283; Parrish et al. 2008, p.466 – 467; Daszak 2009, p. 261 – 266). Early detection of virus transmission from animals to humans can inhibit the potential risks of emerging infectious diseases in the future; therefore, it may significantly reduce the cost of vaccination as one of the currently most effective interventions to limit virus spread.

Infectious diseases in humans are mostly caused by animal viruses. Until recently, there has been no method to obstruct the transfer; however, based on the knowledge of the virus carriers and factors that increase the contact rates between the carriers and / or the viruses and humans, scientists have found a way to predict the next event of disease outbreak. This prediction helps minimizing the risk of an emerging infectious disease at a very early stage.

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Morens, D.M, Folkers, G.K., & Fauci. A.S 2004. 'The challenge of emerging and re-emerging infectious diseases', Nature, vol. 430, pp. 242-49.

Parrish, C.R., Holmes, E.C., Morens, D.M., Eun-Chung Park, Burke, D.S., Calisher, C.H., Laughlin, C.A., Saif, L.J., & Daszak, P. 2008. 'Cross-species virus transmission and the emergence of new epidemic diseases', Microbiology and Molecular Biology Reviews, vol. 72, no. 3, retrieved 1 April 2010, <http://mmbr.asm.org/cgi/reprint/72/3/457>.

Pennisi, E. 2008, Revising HIV’s Origin, ScienceNOW, retrieved 25 April 2010, < http://news.sciencemag.org/sciencenow/2008/06/25-01.html>.

Reid, A.H., Fanning, T.G., Hultin, J.V, & Taubenberger, J.K. 1999. 'Origin and evolution of the 1918 “Spanish” influenza virus hemagglutinin gene', Proc. Natl. Acad. Sci. USA, vol. 96, retrieved 25 April 2010, <http://www.pnas.org/content/96/4/1651.full.pdf+html>.

Reid, A.H. & Taubenberger, J.K. 2003. ‘The origin of the 1918 pandemic influenza virus: a continuing enigma’. Journal of General Virology, vol. 84, retrieved 25 April 2010, <http://vir.sgmjournals.org/cgi/content/short/84/9/2285.pdf>.

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The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net

Science has come closer to new treatments for obesity, heart disease and diabetes after a team of researchers from across the world found that a gene previously linked to type 2 diabetes and cholesterol levels is in fact a 'master regulator' gene for many other genes.

New Scientist reporter submits herself to intimate fMRI scanner to explore the pathways of pleasure and pain in aid of Barry Komisaruk from Rutgers University in Newark. Komisaruk is trying to find a treatment for the 5-10% of women who are anorgasmic – unable to orgasm at all.

Researchers believe they might soon be able to block the neurodegenerative proteins responsible for disorders such as Alzheimer's disease by using sharp-edged nanoparticles. 

A new study by Vivien Cheung of the Howard Hughes Medical Institute has disproved the widely accepted theory that RNA identically matches corresponding DNA sequences. This has the potential to bring about further significant scientific discoveries.

New research from Spain has shown that cannabis use in patients suffering from fibromyalgia, a chronic pain syndrome, can alleviate not only the physical pain involved but almost all associated symptoms.

This week's watch: Andrei Ninu of German prosthetics company Otto Bock talks through the latest innovations in bionic hands with BBC reporter Neil Bowdler.

A 3D stereoscopic movie of a representative protein kinase in complex with staurosporine. The cyan, orange, and purple bar can be used to guide an inhibitor design based on staurosporine's prefered interaction.

The figure above can be viewed on Chrome with 3D glasses on Zalman stereoscopic monitor.  It shows how various distances in the kinase pockets influence the binding affinity to staurosporine. A protein kinase which contains bulgy hydrophobic residues along the orange bar, maintains the cyan bar distance, and also can force the closure of the pocket along the purple bar directions should result in tighter binding to staurosporine. 

Reference:

Tanramluk D, Schreyer A, Pitt WR, Blundell TL (2009) On the origins of enzyme inhibitor selectivity and promiscuity: a case study of protein kinase binding to staurosporine. Chem Biol Drug Des 74(1): 16-24

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net

According to a study released by the United States National Institutes of Health, anti-retroviral drugs could help reduce the transmission of HIV.  The team found that the risk of spreading the virus to an uninfected partner can be cut by 96% if an HIV-positive person commences a course of anti-retroviral drugs immediately after diagnosis.

Doctors might soon be able to diagnose cancer earlier than ever before after researchers from Cincinnati used a genetically modified herpes virus to prompt cancers to secrete a biomarker, thereby giving away their presence.

A study by researchers at the University of Rochester may lead to a new treatment for people with irregular heart rhythms, possibly preventing sudden death. Researchers studied the most common genetic mutation, Long QT syndrome type 1, and its effects on the ion channels in 390 patients to reach their findings.

Researchers from UT Southwestern Medical Center believe they could one day prevent cancer cells from spreading by blocking Rasip1, a protein central to the formation of new blood vessels.

Vampire bat saliva is being used to develop a drug designed to break up the blood clots in the brain that cause strokes.  And it's called Draculin.

A radical new science series by British television channel Channel 4, will broadcast volunteers taking class A drugs such as Ecstasy and LSD live in a clinical environment. The series aims to clear up some of the confusion surrounding drug use by demonstrating the actual effects in scientific detail.

NASA's Dawn spacecraft has captured its first image of the giant asteroid Vesta from a distance of around 1.2 million kilometres.  The asteroid reflects so much light that its size is greatly exaggerated at this exposure.

A powerful new insect repellent, a thousand times more effective than DEET, has been created by scientists at Vanderbilt University. The new substance (VUAA1) affects mosquitoes' odorant receptors, leaving them unable to find blood.

A reassessment of data from Nasa's Galileo probe has come closer to discovering why Jupiter's moon, Io, produces 100 times more lava each year than Earth. The answer could lie in its blisteringly hot, giant magma ocean which lies under its crust and is some 50km (30 miles) thick.

Some impressive footage has been released of Sicily's Mount Etna sending clouds of ash into the air during an eruption in the early hours of Thursday.

GMOs - Risk Assessment

During the 1990s the commercialization of transgenic plants started and the paradigm of a linear “one gene - one protein” was at the basis of the risk assessment. Regulation of genes is far more complex and epigenetic mechanisms have a central and major role in that. Whereas sequence specific consequences of genetic transformation in GMOs are common part of the risk assessment of GMOs. Consequences for epigenetic regulation of gene-expression is poorly understood and not aspect of risk assessment procedures. The present work aims to determine mechanisms where genetic modification of plants might result in changes with relevance for safety. Both, the principle of substantial equivalence in the US, and the precautionary principle in the EU are not combined with a feedback mechanism that could be used to evaluate the principles [21]. Therefore an adequate labelling and monitoring for GMOs should be established worldwide to allow analysis of unintended effects or missevaluated data and enhance future methods of risk assessment [9].

Sequence specific effects

Unintended effects arise due to the gene transfer techniques. The integration of foreign DNA is more or less random. Not only single-gene transfer methods have to deal with that fact, also conventional breeding programs spend efforts to eradicate unintended and undesirable traits by backcrossing. The amount of unintended effects is not connected to the number of introduced genes, the contrary is the case, single-gene products might interact more efficiently with other pathways [25].

Transgene DNA integrated into the plant genome could modify their expression pattern. The transgene could be expressed in an unexpected manner through interactions with various epigenetic mechanism with the result in production of unintended gene products [10]. In the case of “stacked events” unintended effects are measurable; e.g. the expression of GM maize CRY proteins was found to be higher in MON863 x MON810 than CRY expression in parental GM events [26].

Epigenetic effects in plants

Epigenetic mechanisms

In plants DNA methylation, histone modification, chromatin structure and RNAi are in the focus of epigenetic inheritance mechanisms. DNA methylation involves the addition of a methyl group to a DNA domain by different enzymes. The targets are cytosines and there is evidence for methylated adenines [24]. This domain is no more accessible to the RNA polymerase and is so called silenced. Plants maintain the methylation marks during gametogenesis and embryogenesis, accumulate during life and are transmitted to the next generation [1, 3]. These marks are not static and vastly linked to developmental and environmental circumstances [6]. The ability to downregulate gene expression due to methylations is more potent in promoter regions than in other DNA regions [35]. It was found that DNA methylation polymorphisms in soybean are enriched during the domestication process, and that this epigenetic variation is mostly uncoupled from genetic polymorphism [36]. Hypomethylation is an efficient way in response to stresses or a defense mechanism for regulating gene expression accurately [19], suggesting that plants itself create new possibilities to deal with the changed environmental condition by exhausting the possibilities given in the DNA.

Histones are octameric and exhibit notable sequence conservation in eukaryotes. The core histones are more or less globular except the N-tails, that protrudes from the central complex, are unstructured. At least eight different posttranslational processes modify histones. The appearance of a modification depends on the signaling conditions in the cell [17]. Two modification mechanisms are characterized. One is the disruption of the nucleosomal contacts in order to “unravel” chromatin. The other is the recruitment of nonhistone proteins with enzymatic activity that further modify chromatin [17]. Chromatin structure alterations can be caused by histone modification or physical remodeling like ATP-dependent chromatin remodeling enzymes [12, 15]. Findings suggest this to be important for gene regulation in response to environmental cues, not long-term adaption in expression [18].

Posttranscriptional gene silencing (PTGS) or RNAi is important in processes including development, transgene silencing, and plant response to the environment [30]. In this process RNA is transcribed, but then degraded before translation. RNA polymerase families have been identified in the RNA-directed heritable silencing to direct DNA methylations via siRNAs [23, 28].

Interactions

It is clear that there is significant cross-talk, redundancy, and interdependence among these molecular mechanisms with the objective to strengthen the heritability and help to preserve this epigenetic information following DNA replication and cell division [27]. A model that links histone modifications, histone variants and chromatin structure to nucleosome stability was recently proposed by Henikoff [11]. The presented interactions are just examples.

Deficient in DNA Methylation 1 (DDM1) is an ATP-dependent chromatin remodelling protein of Arabidopsis thaliana, similar to SWI2/SNF2-like proteins. DDM1 may change chromatin structure to direct certain sequences to the methylation machinery or to facilitate the methylation of genomic substrates [14]. DDM1 is required for maintenance of histone H3 methylation patterns [8].

Alterations in DNA methylation patterns affect the histone methylation patterns and vice versa. It was suggested that the two epigenetic pathways, H3K4me and DNA methylation, may not directly interfere with each other in Arabidopsis, they rather interact through transcription [34].

The SET domain is a highly conserved, approximately 150-amino acid motif implicated in the modulation of chromatin structure. This gene encodes a histone methyltransferase. It links the DNA and histone methylation [“Entrez Genes: 9869”]. Several of the plant H3K9 methyltransferases contain an SET- and RING-associated (SRA) domain which exhibit methyl-DNA specific binding activities [16, 31].

Plant Evidence, examples

Imprinting is a form of epigenetic regulation in which the maternal and paternal alleles exhibit altered expression in the following generation. At an imprinted locus, there are two alleles with identical, or nearly identical sequences in the same nucleus. These two alleles exhibit differential expression. To date, all examples of imprinting in plants occur in endosperm tissue. There is evidence that the imprinting mechanism involves DNA methylation and histone modification [13]. Paramutation is a form of epigenetic inheritance that involves the communication of two alleles. Paramutable alleles can be heritably altered by being exposed to a paramutagenic allele in a heterozygote [7]. This mechanism involves RNAi and chromatin remodelling [2].

Ribosomal RNA genes in plants are highly repeated but only a portion of these genes are normally expressed in any cell, and the silenced portion is in a contiguous strech indicating a mechanism to simultaneously silence megabase segments of DNA. The insertion of multiple ribosomal gene clusters into an organism by hybridization leads to the phenomena of nucleolar dominance. Nucleolar dominance is achieved during an interaction of gene clusters on different chromosomes in which an entire cluster on one chromosome is silenced and the other ramains active. The mechanism underlying this
process is still being characterized [27].

Polyploidy involves an alteration in gene dosage (autopolyploidy) or a fusion of two complete genomes (allopolyploidy). In both situations the majority of genes are redundant and new expression patterns are possible. Newly formed polyploids often show substantial genomic instability. Sequence elimination was noticed in wheat and Tragogon polyploids, chromosomal translocation and transposon insertion in Brassica polyploids; and in Arabidopsis and cotton, gene expression changes were observed [27].

Consequences for Risk assessment

The first steps in any risk assessment are hazard identification and characterization and the inserted genetic material construct needs to undergo an extensive molecular characterization. An integrated toxicological evaluation will combine all of the information with relation to the food safety of the GMO-derived food [10]. In a long term reproduction study of NK603 x MON810 fed mice, differences in gene expression were identified in a number of biological processes and pathways between the GM and non-genetically modified diets and the reproduction of mice was affected in the RACB trial [29], but no evidences for epigenetic consequences of gene expression from gene modification have been reported until now. However, usual risk assessment did carefully look for sequence-specific changes but not of epigenetic changes. The present analyses from literature suggest that such changes could feasible achieve from the interaction of inserted prokaryotic DNA which is recognized as foreign because of its generally high CpG content and/or because it cannot be packed properly with eukaryotic proteins [20], like histones, which could lead to a changed chromatin structure with altered gene expression.

As known from the plant immune system, several defense mechanisms against pathogens are are known. Microbe-associated molecular patterns (MAMPs) are recognized by cells of the innate immune in plants and mammals. Results show that bacterial DNA stimulates the plant immune system, leading to the generation of reactive oxygen species, deposition of callose, and activation of flg22-induced receptor-like kinase 1 promoter. This immune response might take place intracellular, in the endosomes, but the mechanisms during this interaction are not fully understood, but it is clear that the result is a plant defense response [32]. That will cause stress that might change epigenetic pattern due to hypomethylation. These epigenetic changes may also affect the metabolism leading to a modified composition of ingredients. Food and feed containing bacterial DNA like the BT vector could induce immune responses. Interactions of unmethylated CpG islands with the Toll-like Receptor 9 (TLR9) in mammals are a risk to be analyzed. TLRs play a major role in the innate immune system. They are one of the most important mechanisms of the immune system to distinguish self from non-self. The immuno-modulating activity of TLRs is used in recently developed adjuvants [5]. In chicken the TLR21 acts as a functional homologue to mammalian TLR9 in the recognition of CpG oligodeoxynucleotides [4].

CpG-motifs were shown to promote prostate cancer progression and metastasis through the TRL9 pathway, and generally lead to inflammatory response [22]. Vectors with bacterial origin in GMOs, are rich in unmethylated CpG motifs. The strongest TLR9 activation is seen with dsDNA fragments containing “optimal” CpG motifs (purine-purine- CpG-pyrimidine-pyrimidine) that are common in microbial DNA [33]. E.g. the cry3 ds gene that codes for a BT insecticidal crystal protein (2832bp) [GenBank: AY572010.1] contains 2.75% of this “optimal CpG” motif (6bp).
This evaluation does not want to raise specific concerns from GMO safety because of epigenetic effects, but addresses mechanisms which should be explored because of scientific interest.

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The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net

Science has come closer to a greater understanding of fundamental physics after a team of researchers at CERN were able to trap antimatter for 1000 seconds.  The team now intend to cool a small lump of antihydrogen, which is certainly not a common occurrence in our part of the universe, to see how it interacts with gravity: will it fall or will it rise?

The face of the ecosystem is changing: record numbers of humpback whales have been observed in the Western Antarctic Peninsula.  Putting the numbers down to climate change, the researchers from Duke University fear that such changes could rapidly alter this already unstable ecosystem.

The untimely death of a Marsican brown bear has brought this subspecies a step closer to extinction.  The remaining bears, thought to number around 50, can be found in only two of Italy's national parks; they are now sadly 'below the threshold of survival'.

Researchers from Cambridge University have added yet another layer of complexity to an already complex question: a recent study found that female-to-male transsexual people exhibit a higher than average number of autistic traits.  The findings could now help people to better understand what they are going through and to make more informed decisions about possible treatments.

Did you know that tortoises don't yawn when other tortoises yawn?

Getting the short end of the stick. Literally. Jan-Emmanuel De Neve, a researcher at the London School of Economics and Political Science makes steps towards discovering the biological reason behind why some are naturally happier than others. His findings show that people who possess a longer version of the 5-HTT gene (partly responsible for the transport of serotonin) tend to be happier and more positive than those with shorter 5-HTT.

Seven women at the forefront of science, engineering and technology were honoured last night at the Royal Academy of Engineering in London. Among the recipients of the UKRC awards were President of Young Engineers Kate Bellingham, CEO and founder of Mydeo.com Cary Marsh and head of Cambridge's engineering department Dame Ann Dowling.

Babies do in fact wake up taller. A new study by Michelle Lampl, professor of anthropology at Emory University shows that irregular sleep behaviour is a normal part of growth development. She collected real time data on 23 infants over a four to 17 month span as part of her research.

Did you know that your eyes actually form at the side of your head? A unique time lapse video showing the exact formation process of the human face has been created based on footage of embryo development provided by universities and hospitals. Fascinating stuff!

Anders Garm of the University of Copenhagen has found that jellyfish have a total of 24 eyes, four of which are permanently fixed on the sky, therefore allowing them a 180 degree view of the stars above.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net

Royal wedding fever gripped the world and all waited with bated breath for William to kiss his Kate. In keeping with the festive mood of the royal nuptials, the Guardian's science blog has asked their favourite chemistry professor to talk them through the scientific properties of Kate's sapphire engagement ring. Fascinating stuff!

A brave photographer spent a night on the rim of an erupting volcano and lived.  He released some rather impressive footage too.

Ever feel like you're half alseep? Chances are small sections of your brain are actually switching to 'offline' status, following periods of sleep deprivation, in order to achieve a state of 'local sleep'.

Did you know that ants can walk on water?  I most certainly didn't.

The Health Halo Effect: new research released by Cornell University has shown that an organic label can have a significant influence over how we perceive food. 

Social networks are continuing to play a sizeable role in the advancement of medical science after researchers from Boston implemented an online diabetes network where patients were able to upload and share their health data.

Life scientists from UCLA believe that they might one day be able to help people overcome traumatic events by erasing the memory of the event itself: they discovered that preventing the activation of a specific protein kinase in the brain of the marine snail can dramatically alter their long-term memory.

A German biologist stumbled upon a whole new order of species whilst stopping for gas.  I don't know about you but I’m sure I’ve come across some interesting species at dirty rest stops too… 

Proteins!  They help people build muscle and plants to get up and grow. New research by Alison DeLong of Brown University finds that an intricate network of proteins regulates plant growth to enable seedlings to push past the surface of the soil.

Expect the unexpected: more than 30 years after leaving Earth, NASA's twin Voyager probes are about to enter interstellar space.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net

New hope has been offered to people infected with HIV after researchers were able to unlock the mechanism behind a protein found in monkeys: TRIM5 prevents the HIV virus from multiplying once it infects a cell.  This breakthrough could lead to a better quality of life for the 33 million people living with HIV worldwide.

I'd be embarrassed if I had a pregenual anterior cingulate cortex as big as yours!  Scientists from the University of California have found that the size of the brain region responsible for embarrassment is directly related to how embarrassed you feel.

Researchers from New York have demonstrated how a change in diet can reverse the gene expression associated with kidney damage in patients suffering from diabetes.  The team believe that the ketogenic diet (high-fat, moderate protein and low-carbohydrate) could also be used to treat some neurological diseases. 

What's your gut type?  Scientists from the University of Copenhagen have uncovered a new form of biological fingerprint: your intestinal bacteria.  The study could lead to a greater understanding of our diet and to the advent of medication designed for each type of gastrointestinal tract.

To celebrate Hubble's 21st birthday, NASA had the telescope look at a 'rose' of galaxies: the outcome is particularly beautiful.  

A new study by the University of Iowa's Experimental Psychology department shows that Pigeons are capable of recognizing varying facial expressions and, by extension, emotions. The researchers involved hope that our feathered friends may prompt scientists to reassess the accepted notion that perceptual and cognitive processes are unique to humans.

Coastal areas in the US and around the world are about to become a lot safer. New research by atmospheric scientists at the University of Illinois hopes to predict the impact of hurricanes and tropical storms through satellites, allowing for speedy evacuation in the case of rapidly intensifying weather conditions.

Breath tests may take on a whole new meaning. Researchers at Technion - Israel Institute of Technology - are hoping to revolutionise the way cancer is diagnosed through a device called the nano artificial nose. A preliminary study of the prototype uses chemicals to spot patterns of molecules in the breath, hopefully allowing GPs to one day instantly diagnose difficult to spot head-and-neck cancer.

Imagine in life in 1D: A radical new theory proposed by physicist Dejan Stojkovic and colleagues at the University at Buffalo hypothesises that the universe may have been one dimensional. They suggest that the universe, which was once considerably smaller, expanded to include two and eventually three dimensions to form the world we live in today. If valid, the theory could resolve a number of inconsistencies in particle physics.

This week's appropriately Easter-themed video: eggsperimenting with eggstraction.

The 'Weekly Science Digest' is a compilation of science news from around the world. News suggestions are always welcome: mark.howardbanks@researchgate.net

Tell me: where do you buy your Manuka?  A study has shown that honey may be an effective anti-bacterial agent for small wounds.

Change is afoot: for those who suffer from trypanophobia (needle phobia), there may soon be a viable alternative in the form of nasal vaccinations.

A team of scientists from across America have made headway in understanding schizophrenia on a biological level: recent advances in pluripotent stem cells meant that the researchers were able to work with brain cells in Petri dishes, thereby studying them away from any possible environmental effects.

This week’s watch: the story of the forbidden (genetically modified) fruit.

It’s all about the growing conditions: a recent study has shown that algal biofuel has the potential to replace 17% of US oil imports.

The authors of a study on the 2010 cholera outbreak in Haiti hope that society can once again learn from its mistakes: the team from Seattle have shown how a combination of vaccination and effective sanitation could have greatly reduced the final death toll.

Just because you can’t see herpes, it doesn’t mean that it isn’t there.

Scientists at the Gran Sasso National Laboratory in Italy have been stood up: after 100 days, their dark matter date failed to show; we might have to wait a little longer to learn the secrets of the universe.

A recent study has cast doubt on the belief that the brain is the driving force behind language; the authors believe that languages formed because of cultural evolution, and not due to a set of universal laws applied to language by the brain.

Humpback whales have got soul: a recent study has found that, much like humans, whales share their tunes with each other.

The 'Weekly Science Digest' is a compilation of science news from around the world.  News suggestions are always welcome: mark.howardbanks@researchgate.net

Just what the doctor ordered: researchers at the Federal University of São Paulo, Brazil, have found that, when it comes to Restless Leg Syndrome, an orgasm a day can keep the doctor away.

Patients undergoing chemotherapy look set to benefit from a better quality of life after researchers from Philadelphia were able to regenerate human taste cells in a dish, thereby proving false the belief that taste cells must be attached to a nerve in order to function. 

It seems that a fat tax just won’t cut the mustard in Alberta: a recent study found that the best way to dissuade people from buying unhealthy foods was to place a warning label on the packaging.

Researchers from the University of Buffalo have shown that insulin has the potential to be used as a therapeutic agent for Alzheimer’s disease.

Evidence of liquid water inside a comet is causing scientists to rethink their understanding of how these ‘dirty snowballs’ came to be.

Chimpanzees yawn because they care: researchers from the Yerkes National Primate Research Center have discovered that chimpanzees yawn out of empathy for their fellow primates.

After finding that our caffeine intake is linked to our genes, science might be coming close to clearing up that age-old question: is coffee good or bad for you? 

Regenerative medicine continues to move forward: microRNAs are now being used to create stem cells.

Brain implants could be the key to helping people who are unable to speak to communicate: previous experiments having focused on the areas of the brain responsible for movement, as part of a new study, patients were this time able to control a cursor on a computer screen with the areas of the brain that control speech.

New research has shed more light on neuroplasticity by showing that virtual reality gaming can improve motor function in stroke patients.

This week’s video: you were destined to be a musical star!

The 'Weekly Science Digest' is a compilation of science news from around the world.  News suggestions are always welcome: mark.howardbanks@researchgate.net

After twenty years, scientists have put their minds over matter and come up with… more matter.

I'll stand by this one: some of us are just more susceptible to addiction than others.  It's in our genes.

Researchers from Johns Hopkins University have demonstrated how harvesting organs from HIV-infected deceased donors could attenuate the current organ shortage experienced by patients living with HIV.

If you can't see something, how do you know that it's there?

The age of fossil fuel dependency is finite: scientists have found that preventing carbon dioxide fixation in bacteria increases the production of biofuel.

Science listening for the week: The Guardian Science Podcast featuring popular physicist, Brian Cox.

Immunity against fertility looks set to become a reality after scientists from Weill Cornell Medical College were able to successfully control the fertility of some mammals through immunisation.

NASA has released some stunning images from Mercury's long-awaited close-up.

Lowering your cholesterol is not just beneficial to your general health; it could also help you to fight off infection.

Researchers have unravelled the riddle of the ribbon in our heliosphere, shedding light on how it protects our solar system from galactic cosmic rays.

The introduction of a strain of influenza virus A that has a new variety of the hemagglutinin gene to human population has been recorded in several outbreaks. The new hemagglutinin gene is typically acquired from other species, such as birds or swine, through a process called interspecies transmission (Mims, 1987, Neumann et al., 2009, Zimmer, 2009). The hemagglutinin protein functions in the binding of virus to host cell receptors, during the entry of virus into host cells, and fusion of virus envelope with endosomal membranes, during the release of virus ribonucleoprotein, which can result in changes of the pathogenicity and infectivity of the virus (Neumann et al., 2009). The altered degree of pathogenicity and infectivity may subsequently trigger an outbreak; that is, the incidence of a particular disease in a population that outnumbers the common expectancy due to either accidental or on-purpose causes (Gordis, 2009). In short, interspecies transmission causes outbreaks through the alteration of the hemagglutinin structure, which affects the binding, fusion, and disease features in sequence.

Firstly, the change in hemagglutinin structure affects the disease features by evading neutralization during the binding between virus and host cells. Hemagglutinin is the surface protein of influenza virus that binds to specific receptor in the epithelial cells (Mims, 1987, Neumann et al., 2009). The important receptor types are SAα2,6 Gal, which is located in the human respiratory tract, and SAα2,3 Gal, which is located in the avian intestinal tract; both types are found in the respiratory tract of pigs as well (Neumann et al., 2009). On the other hand, the virus has unique determinants to bind specifically to human or avian cells, which lie in the receptor-binding pocket of hemagglutinin. For example, in the hemagglutinin of the H1N1 subtype, the determinants are amino acid number 190 and 225: in humans they are both aspartic acid while in avian they are glutamic acid and glycine (Neumann et al., 2009). The hemagglutinin of a human influenza virus must recognize human type receptor in order to infect humans, and so must the hemagglutinin of an avian influenza virus to infect birds; however, changes in the receptor-binding specificity may generate an avian influenza virus that can recognize human type receptor. As a result, the avian virus enters human cells, replicates abundantly, and in doing so, causes a distinguished feature of influenza disease compared to the usual seasonal influenza disease. The features are, for example, a higher mortality rate, particularly for young adults, in the 1918 H1N1 ‘Spanish flu’, that exceed 2.5% in comparison to less than 0.1% of seasonal influenza virus and the use of lower respiratory tract of humans as the main replication site of the highly pathogenic avian influenza (HPAI) H5N1 virus compared to the seasonal H3N2 and H1N1 influenza virus, which mainly replicate in the upper respiratory tract (Neumann et al., 2009). Briefly, an avian influenza virus can infect humans after undergoing interspecies transmission, which takes place in the following process.

As the genome of influenza virus consists of eight gene-encoding RNA segments, when an avian and / or a human and / or a swine influenza virus infect a similar cell, which particularly is in a pig, the new copies of those genes can recombine during assembly of new viruses (Neumann et al., 2009, Zimmer, 2009). The newly formed viruses evolve a matched receptor binding specificity to human, and in doing so, they gain the ability to enter human cells (Neumann et al., 2009, Zimmer, 2009). Inside the human body, an infecting influenza virus is supposedly bound by antibody specific to its antigen, which is hemagglutinin, in order to prevent the attachment to the cell receptor (Mims, 1987, Neumann et al., 2009). An antibody has partial reactivity to an antigen that is closely related to the one that stimulated its production such that the closely related strains of seasonal influenza virus commonly receive partial neutralization from the pre-existing antibody (Mims, 1987). However, on the first introduction of a new virus, the production of a specific antibody takes several days (Mims, 1987). Because there is an absence of neutralization by the human immune system and the newly formed virus possesses the ability to recognize human type receptor, infection occurs pervasively in susceptible cells and the disease often develops more severely. In addition to causing neutralization evasion, the alteration of hemagglutinin structure changes disease features by affecting the fusion between virus envelope and host cell endosomal membrane during the release of viral ribonucleoprotein (vRNP) into the cytoplasm (Neumann et al., 2009). The hemagglutinin functions in mediating the fusion between virus envelope and endosomal membrane of host cell, which subsequently determines the virus capability to infect and replicate inside the host cells. The fusion process requires the exposure of amino terminus of HA2 fragment, which is obtained from the cleavage of hemagglutinin into HA1 and HA2 fragments by host cell protease, after the virus enter host cell. Such cleavability is governed by specific amino acid motif in the cleavage site of hemagglutinin, which is recognized only by specific host cell protease. A single arginine residue at the cleavage site can be recognized by protease in the human respiratory organs or avian intestinal organs; hence, cleavage and virus replication are restricted locally in the respiratory or intestinal tracts. On the other hand, multi-basic amino acid residues at the cleavage site can be recognized by protease found almost everywhere in the body; further, this recognition can lead to systemic infections. For example, the highly pathogenic avian influenza (HPAI) H5 possesses the multi-basic motif while low pathogenic avian influenza (LPAI) and non-avian influenza viruses possess single arginine residue at the cleavage site. As a result, the infection by LPAI tends to be asymptomatic in the natural reservoir of influenza virus, the waterfowl, while the infection by HPAI causes deaths in waterfowl population (Neumann et al., 2009)  

As such, interspecies transmission generates a new distinctive feature of influenza disease by introducing a new hemagglutinin gene to the existing strains of human influenza virus. Because the new hemagglutinin can evade neutralization by pre-existing antibody or facilitate virus infection in various organs, different manifestation of infection by the newly formed strain other than by the common seasonal strains can arise (Mims, 1987, Neumann et al., 2009). The introduction of the new hemagglutinin gene occurs after various strains of influenza virus from different species infect similar cells: their copies of genes recombine, and the newly formed virus subsequently evolves the specificity to bind to human type receptor (Neumann et al., 2009, Zimmer, 2009). Interspecies transmission occurs frequently, particularly in regions where humans, poultry, and pigs live in a close proximity, such as South East Asia. Therefore, continuous surveillance of hemagglutinin gene is important to prepare preventive attempts, such as vaccine or antiviral drugs, for protection against potential outbreaks that are posed by influenza virus having a new hemagglutinin type.

References:

GORDIS, L. 2009. Epidemiology, Philadelphia, PA, Saunders.

MIMS, C. A. 1987. The pathogenesis of disease, Orlando, FL, Academic Press Inc.

NEUMANN, G., NODA, T. & KAWAOKA, Y. 2009. Emergence and pandemic potential of swine-origin H1N1 influenza virus. Nature, 459, 931-939.

ZIMMER, C. 2009. 10 genes, furiously evolving. 5 May 2009 ed.: The New York Times.  

The 'Weekly Science Digest' is a compilation of science news from around the world.  News suggestions are always welcome: mark.howardbanks@researchgate.net

Genes off!  Get ready to stretch.

Scientists at the University of Nottingham have shown that people suffering from Tourette syndrome actually demonstrate a higher level of cognitive motor control, leading to theories that ‘brain training’ could help patients with neurological diseases to control their respective symptoms.

Researchers have found that when emotions run high at the football, they also run high at home, leading to increased reports of domestic violence.

Does religion make you fat?

Hope has been offered to patients suffering from schizophrenia after researchers discovered that oestrogen facilitates a quicker recovery from psychotic symptoms.

A great many patients stand to benefit from the development of a safer and more effective form of morphine.

Is this the coolest dwarf in the galaxy?

Sign language is beginning to be recognised as a real language after researchers at Penn State demonstrated that a signer processes words and signs in much the same way as a bilingual person processes languages: the study revealed that both languages appear to be active on a cognitive level even when only one is in use.

Which is more harmful: heroin or methadone?

Yet more damning evidence has revealed that acupuncture is not only an ineffective form of pain relief but, moreover, a potentially fatal one.

The 'Weekly Science Digest' is a compilation of science news from around the world.  News suggestions are always welcome: mark.howardbanks@researchgate.net

Scientists have come closer to understanding the plasticity of the brain after neuropsychologists from Montreal found that the parts used to process vision are able to rewire themselves to process sound.

Also in brain plasticity: by suppressing genes in the brains of mice, researchers showed how the brain reorganises itself to compensate for the lack of key functions.

Wording matters: do you believe in global warming or climate change?

New research has revealed that cell-cell communication in plants takes place in much the same way as it does in animals; these findings could lead to fresh insights into a whole host of neurodegenerative diseases.

In an attempt to help smokers kick the habit, researchers in Finland have developed a drug designed to prevent the withdrawal symptoms associated with stopping smoking.

How determined are you to be free?

Worth a watch this week: a BBC report on how technology is helping us to deal with the aftermath of a disaster.

The advent of a new phylogenetic tree could shed light on how human beings have evolved.

Scientists at Yale University feel they might now be able to explain why racism is proving so difficult to eradicate.

The world can once again sleep easily: the genetic makeup of bedbugs has been revealed.  

The 'Weekly Science Digest' is a compilation of science news from around the world.  News suggestions are always welcome: mark.howardbanks@researchgate.net

• New hope has been offered to patients suffering from Parkinson's disease after a team from the University of Colorado found that it is possible to turn on a protective gene in the brain.

• Scientists have discovered that it is possible to prevent the development of malaria by using human antibodies to alter the genetic make-up of a fungus that infects mosquitoes.

• There might just be a link between the penis and the brain after all.

• An iPad app developed by physicists at the University of Glasgow allows scientists to move microscopic objects at a swipe of the fingers.

• Fancy an interplanetary pint?

• Researchers at the University of California at Berkeley have engineered the bacteria E. coli to produce large amounts of biofuel.

• New research has revealed how exercise could help people to quit smoking cannabis.

• More light has been shed on the potential of cell-based therapies after researchers used patients' own cells to grow urethras for five young boys suffering from tissue damage.

• Now everybody can be a researcher! Power of Research is an entertaining way to interest children in science: pretty cool.

• A team of designers from Oslo have produced some beautiful images of the invisible Wi-Fi signals that surround us.

The 'Weekly Science Digest' is a compilation of science news from around the world.  News suggestions are always welcome: mark.howardbanks@researchgate.net

Researchers at the University of Arkansas have created fuel by cleaning up lakes and rivers.

The quality of life for patients suffering from spinal cord injuries looks set to be greatly improved after research teams from Colorado and Rochester were able to use human stem cells to help rats regain locomotor function. 

A study published in the British Medical Journal has found that using cannabis in one's younger years increases the risk of experiencing psychotic symptoms and that continued use may increase the risk of the onset of a psychotic disorder in later years.

Footage has been released of the final Discovery spacewalk: the shuttle is due to complete its 39th and final mission within the next week.

In a bid to save the pearl mussel, scientists have implanted mussel larvae into the gills of salmon and trout.  The team from Northumberland hopes that this will help boost the mussel population.

New research has suggested that amyotrophic lateral sclerosis (ALS) could be caused by a retrovirus that infected our ancestors a long time ago.

Researchers in Jerusalem have shown that bacteria can communicate through nanotubes; a better understanding of these tubes on a molecular level could lead to new methods to fight pathogenic bacteria.

Technology developed and used by NASA in plant growth experiments in space has been used to reduce some of the painful side effects experienced by cancer patients.

Want to know what 44,000,000 horsepower looks like?  Wait for the separation at 2:25.

The Little Atoms team have once again produced a great podcast: science journalist Henry Nicholls joins them to talk about his latest book.  This is definitely a podcast to add to your weekly science listening list.

Protease Mapping

Purpose
 

Tagged proteins are attached to a resin, and a partial protease digest is done. Unbound fragments are washed away, and the bound fragments are eluted and run on a gel. This method has many applications, including domain mapping (as in Devos et al, PLoS 2004). The following protocol assumes that you’ are starting with already-purified protein. You can also start from yeast lysate, in which case pick up this protocol after you have done your pullout, bound your  protein to the beads and washed them.

Reagents

Proteases:
a) endoproteinase Asp-N (Roche, 1 420 488 or 1 054 589),
b) endoproteinase Lys-C (Roche, 1 420 429 or 1 047 825),
c) trypsin (Roche 1 521 187 or 1 418 025)

Preparation of proteinases

Asp-N (1:200):
2ug in 50 µl = 40ng/µl (stock solution).
For 3 µg of protein need 15 ng of proteinase (1/200).
Dilute stock solution 2.5 times with 1x reaction buffer.
Use 1 µl of 16ng/µl solution in reaction
Asp-N reaction buffer: 50mM sodium phospate buffer, pH8, 0.01%SDS
Prepare 10 ml of 10x buffer. Filter.

Lys-C (1:200):
5µg in 50 µl = 100ng/µl (stock solution)
For 3 µg of protein need 15ng of proteinase (1/200).
Dilute stock solution 6.5 times with 1x reaction buffer.
Use 1 µl of 15.3ng/µl solution in reaction

Lys-C reaction buffer:
 25mM Tris, pH8.5 buffer, pH8.5, 1mMEDTA, 0.01%SDS
Prepare 10 ml of 10x buffer. Filter.

Trypsin (1:200):
25 µg in 50µl = 500ng/µl
For 3 µg of protein need 15ng of proteinase (1/200).
Dilute stock solution 33 times with water.
Use 1 µl of 15.15ng/µl solution in reaction

Lys-C reaction buffer:
100mM Tris, pH8.5 buffer, pH8.5, 0.01%SDS
Prepare 10 ml of 10x buffer. Filter.

Gel sample buffer:
Solution A = 0.5M Tris base, 5% SDS
Solution B (50mL) = 37.5ml glycerol, 12.5mL ddH2O, 960mg DTT, 0.05% bromophenol blue

Procedure

A. Transfer 25µl (1mg) of Dynabeads to each of 5 microcentrifuge tubes. The Dynabeads are conjugated with the appropriate binding partner to the tagged protein. (We have done this successfully with PrA, GFP, and 6xhis tagged proteins).

B. Add 700µl binding/wash buffer (as appropriate to your tag), and vortex to equilibrate beads. Apply to magnet and aspirate off supernatant. Repeat wash once.

C. Resuspend beads in 100µl binding/wash buffer. Add at least 2-3ug tagged protein to the tubes, and bring volume up to 700µl with binding/wash buffer.

D. Incubate on nutator 10 minutes at room temperature to bind protein to beads.

E. Place tubes on magnet, and aspirate off supernatant.

F. Wash beads 4x 700µl binding/wash buffer. Each wash add buffer, vortex, put beads on magnet, and aspirate off supernatant.

G. Meanwhile, make 1ng/µl dilution of your protease in the appropriate buffer (see below).

H. To each tube of beads, add the appropriate amount of diluted protease (you will have to do test runs to see how much enzyme gives a good ladder). Bring to 50µl with buffer. Add 50µl buffer alone to the control.

I. Incubate digests on the TOMY shaker in the 37 degree C incubator for the appropriate times (we have used times ranging from 1 second to 75 minutes). After that time, put the tube on the magnet, and aspirate off supernatant. Wash the beads with 700µl binding/wash buffer. Vortex, put on magnet, and aspirate off supernatant. For the 1 second time point, do this immediately after adding the protease. (5 tubes including the control gives four time points).

J. Elute the protein. This can be done in many ways. Two suggestions follow:

a. This method was used for his-tagged proteins on Dynabeads TALON: Add 60µl 2x Morris buffer to each of the Dynabead tubes after the wash. Vortex, and heat 10 minutes at 95°C. (keep the control tube without protease at 37°C for the full 30 minutes). Store on ice until ready to run gel.

b. This method was used for PrA and GFP tagged proteins on antibody-conjugated Dynabeads: Wash Dynabeads with 0.1M NH40Ac, 0.1mMMgCl2 0.02% Tween 20.(Make fresh and filter). Add 1ml, incubate on nutator 5 min-Vortex-Place on magnetic bar. Take off supernatant. Elute bound protein with 1mL of 0.5M NH4OH 0.5mMEDTA (pH ~10.9), incubate on nutator 30 minutes at room temperature. Place beads on magnetic bar, and transfer supernatant to a fresh tube. Flash freeze elution in liquid nitrogen, and allow to evaporate in Speedvac overnight. Resuspend pellet in gel sample buffer (10µl solution A, sonicate, 10µl solution B). Heat 10 minutes to 95°C. Store on ice until ready to run gel.
 

Immunofluorescence Protocol

Purpose

Immunofluorescence is a technique used in genetic engineering to label antibodies or antigens with fluorescent dyes. Immunostaining is often used to visualize the subcellular distribution of biomolecules in fluorescent-labeled tissue sections or cultures.

Reagents

PBS, methanol, 3.5% paraformaldehyde in PBS, PBS containing 30 mM glycine, PBS + 0.1% Triton X-100,  4% paraformaldehyde, 0.5% saponin, 0.1% sodium borohydride/ 0.1% saponin, antibody steps must contain 0.1% saponin, 3% BSA in PBS, primary antibody should be diluted in PBS-BSA, DAPI (1:5000 in PBS if required), Mowiol

1. Methanol fixation

A. Wash cell in PBS.

B. Fix at –20°C for 4 minutes with cold methanol (the methanol is kept in the freezer and cells are also fixed in the freezer itself – it is important to maintain everything at –20°C for optimal fixation). Wash PBS to remove all traces of methanol and proceed to immunofluorescence staining.

2. Paraformaldehyde fixation and Triton X-100 permeabilization

A. Wash cells in PBS.

B. Fix in 3.5% paraformaldehyde in PBS.

C. Quench with a 5 minute incubation in PBS containing 30 mM glycine.

D. Permeabilise with a 5 minute incubation in PBS + 0.1% Triton X-100.

E. Wash in PBS and proceed to immunofluorescence staining.

3. Paraformaldehyde fixation and saponin permeabilization

A. Wash x1 PBS Fix for 15min in fresh 4% paraformaldehyde Wash x1 PBS Permeabilise with 0.5% saponin for 5 min Wash x1 PBS Treat 5-10min with fresh 0.1% sodium borohydride/ 0.1% saponin Wash x3 PBS

B. Make up PFA as for Fixation 1. All solutions are in PBS. Saponin permeabilisation is reversible and so all subsequent antibody steps must contain 0.1% saponin.

4. Immunostaining

A. Coverslips are blocked and washed in 6-well plates. Antibody staining is done on flattened sheets of parafilm (in a humidified atmosphere – wet tissue under a plastic box). Live cell dishes are stained intact.

B. Block non-specific antibody binding with 3% BSA in PBS (PBS-BSA) for 30 minutes.

C. Incubate in primary antibody for 1 hour (primary antibody should be diluted in PBS-BSA).

D. Wash cells 3x 5 minutes in PBS.

E. Incubate in secondary antibody diluted in PBS-BSA for 1 hour.

F. Wash 3x 10 minutes in PBS. Counter stain with DAPI (1:5000 in PBS if required).

G. Mount coverslips on slides with Mowiol where required. Live cell dishes can be left in PBS as long as images are acquired within 24h of immunostaining.
 

The 'Weekly Science Digest' is a compilation of science news from around the world.  News suggestions are always welcome: mark.howardbanks@researchgate.net

The discovery of a gene mutation linked to schizophrenia may lead to the emergence of new antipsychotic drugs to help treat this disorder.

Scientists at MIT have engineered a nanoparticle that could potentially be used to deliver vaccines for HIV, malaria and cancer.

Researchers in Canada have discovered that THC, the active ingredient in cannabis, can help cancer patients to regain their appetite and sense of taste: a healthy diet is essential to treating the disease.

A study carried out amongst America’s TV meteorologists found that ‘Climategate’ made them more likely to doubt global warming.

An experiment carried out in Sweden has revealed how the brain can be duped into believing it has a supernumerary limb: three hands to you and me.

A nanomembrane developed by researchers at the University of Buffalo could hold the key to solving the world’s water problem: the material allows water molecules to pass through whilst preventing the larger bacteria from coming through with them.

A team of computer scientists has created photos that the blind can see: the new software takes an existing photo and renders it into a tactile form.

Chandra, NASA’s X-ray Observatory, has produced evidence for the existence of a superfluid in the heart of a neutron star.  The data moves science a step closer to understanding the nuclear reactions in the densest known matter that we can observe.

New research has shown how bilingual people are better able to work on many tasks at once: the study revealed that possessing the mental agility required to operate in two languages can help people to edit and sort information.

Have you ever wondered how explosives can be used to prevent floods?

This TED Talk is a postmortem on the defeat of two human Jeopardy! champions by Watson, an IBM natural language-processing computer. Of interest to me (beyond the fascination of potentially moving closer to Ray Kurzweil's singularity) is the discussion of medical applications of this technology. If Watson can assist a physician in reaching a diagnosis (e.g., by scanning for the patient's complaints in hospital records and the medical literature, then using algorithms to arrive at the most likely possibility), could a clinical psychologist or psychiatrist also benefit from this kind of assistance?

The answer is "yes," obviously. But since mental health has stickier problems of subjectivity to contend with, it would be very interesting to see how Watson's programmers would handle the following issues:

1) Diagnostic criteria. Definitions of mental disorders change over time and space. Would only one source of diagnostic criteria be used, e.g., the DSM, or could many different sources be cross-referenced? Would including non-Western sources like Chinese Traditional Medicine be helpful in some cases? Finally, if Watson is attempting a tricky differential diagnosis, could it prompt for more information in real time?

2) Cultural/ethnic background. In the diagnostic manuals, clinicians are exhorted to take culture into account. If a particular experience or behavior is sanctioned by the individual's culture, it affects whether it should be considered a sign of illness or not. Yet Western doctors struggle and sometimes fail to incorporate cultural considerations in mental health diagnoses. Would Watson do better?

3) Race. Some severe mental disorders (e.g., schizophrenia) are diagnosed at higher rates in minority populations, and there is a concern that this base rate information self-perpetuates. Clinicians may be using the statistic to inform a diagnosis, which then contributes to the statistic. Could Watson help address this by intentionally leaving race out of the diagnostic algorithm (but still including socioeconomic status and other relevant risk factors)? Would that help or hurt the accuracy of the diagnosis?

4) Treatment recommendations. Beyond pharmacology, how would Watson go about ranking various evidence-based/empirically supported psychotherapy treatments? How would it deal with comorbidity, since most evidence-based treatments are designed for one disorder only? Could it use the availability and skills of local therapists to make practical recommendations?

Overall I believe a Watson-type assistant would be of tremendous benefit to mental health settings. I will be very curious to see (and participate in?) research comparing human-only diganosis to Watson-assisted diagnosis. Because real-time human decision-making is limited, the most parsimonious explanation usually wins. But the simple answer is not always the right answer, and this limitation has served to drown out inherently more complicated contextual approaches. Ultimately, Watson's massive processing power and relatively bias-free diagnostic ability might provide more culturally sensitive diagnoses and treatment recommendations than a typical mental health professional would be able to consider.

The 'Weekly Science Digest' is a compilation of science news from around the world.  News suggestions are always welcome: mark.howardbanks@researchgate.net

By using skin cells to generate stem cells, researchers from Stanford University were able to create beating heart cells: the study could lead to new treatments for heart disease.

New footage has documented advances in thought-controlled devices that could help improve the quality of life for people living with disabilities.

A new study of ecstasy has cast doubts on the belief that using the drug leads to an increased level of cognitive impairment.  Researchers highlighted the methodological errors of previous studies in order to obtain more reliable results.

Researchers believe they may finally be able to explain why autism is more common in males than it is in females: the discovery of a gene that is sensitive to sex hormones could provide an insight into the biology of the disease.

A stress-blocking chemical could open the door to new research into human hair loss.

A recent study of America’s classrooms has revealed a high level of reluctance amongst teachers to endorse evolution.

The Wellcome Trust has underlined how a more open access approach to research could enable us to use our knowledge of the human genome to deliver improvements in the health and wellbeing of the world’s populations. 

Scientists at the Herschel Space Observatory have calculated how much dark matter is required to form a new galaxy.  And it’s a lot.

During a recent study of the circadian clock, researchers were able to identify round 120,000 uncharacterised compounds, one of which has the potential to eliminate the effects of jet lag.

Plants which change colour in response to specific substances could provide a new means of checking our surroundings for potentially dangerous substances.

The 'Weekly Science Digest' is a compilation of science news from around the world.  News suggestions are welcome: mark.howardbanks@researchgate.net

New evidence has emerged in the study of HIV after scientists were for the first time able to eliminate a similar virus in mice without the use of anti-viral drugs. 

Sick worms could help scientists to understand the interaction between a virus and its host, shedding light on how organisms respond to viral infections.

Hubble has once again found the farthest galaxy from Earth, a mere 0.1 billion light-years further than the previous record holder.

Easing stress has been shown to help the healing process after new research found that stress management could improve postoperative biological functioning. 

A study of songbirds in the Netherlands demonstrated how changing climate conditions are influencing the rate at which a species responds to selection.

Research involving mirrors and heat has shed light on how humans perceive pain.  Scientists at UCL found that changing the manner in which we see our body alters the way in which we feel pain.

The development of one atom thick nanosheets has opened the door to myriad potential applications for this very promising material.  The future could see this technology helping to drastically diminish the amount of waste heat our power plants produce.

The Pacific Walrus has been placed on the endangered species short list due to the changing conditions of its habitat; the U.S. Fish and Wildlife Service will henceforth keep a close eye on the species and submit a yearly review of the situation.

NASA has released some wonderful footage of volcanoes erupting in Japan and Russia.

In his annual letter, Bill Gates outlined the motivation behind his endeavor to eradicate polio by 2012; the program is to focus on the last few remaining countries where efforts have been unable to put an end to transmission of the virus.

‘To win these big important fights, partnerships, money, science, politics, and delivery in developing countries have to come together on a global scale.’ 

Bill Gates

The Institute of Technology Assessment (ITA) of the Austrian Academy of Sciences just published a research report on the potential of social network sites for science and academia in the framework of the project "Interactive Science":

Nentwich, M. und König, R., 2011, Wissenschaft und Social Network Sites. Steckbrief 5 im Rahmen des Projekts Interactive Science. ITA-Reports Nr. a52-5, hrsg. v. Institut für Technikfolgen-Abschätzung (ITA), Wien: ITA http://epub.oeaw.ac.at/ita/ita-projektberichte/d2-2a52-5.pdf

The report is in German language - here is the abstract in English:

This report deals with the numerous social network sites (SNS) that have spread successfully in the Internet over recent years and sheds light on their potential for scholarly communication and cooperation. SNS like the well known Facebook are special Internet platforms designed for representing and maintaining existing social networks and building up new ones. These activities are supported by a specialised, mostly web-based infrastructure.

To begin with, we address the issue of the vague term SNS and its various definitions and the present different types of SNS. We then present an overview of the common business models of these services and a timeline of the development of the numerous platforms. This shows that alongside the general SNS such as the above-mentioned Facebook, platforms specializing in academic uses have also been established since 2004. With a view to the following asessment, we provide a detailed description and systematization of the various technical functions and instruments provided by the different SNS with varying coverage.

In a next step we focus on SNS in the scholarly context. Based on a comparison of typical academic activities and the services’ functions previously described, we identify their high theoretical potential. In addition, we map the empirically observable coverage and user practices within general and scholarly SNS. The empirical basis for this assessment is previous studies and our own qualitative observations. One key result is that many academics have already begun to use SNS – but we are far from being able to speak of a comprehensive coverage of the scholarly communities. Furthermore, scholars do not exploit all potential usage opportunities.

Against the background of the theoretically conceivable and empirically observable usage, we finally assess the potential and possible impact of an increased or even comprehensive use of SNS in academia. We analyse possible network effects, the role of informal communication, of anonymity and the protection of privacy as well as the challenge that results from the multiplication of communication channels in every day office life of scientists and researchers.

We come to the conclusion that only a limited assessment is possible given the particularly dynamic development of the field. While the concrete usage practices would be very important for such an assessment, they are still under-researched. Nevertheless, academics are also increasingly using SNS and the figures are partly impressive, but usage seems still rather experimental and scarcely institutionalised; without mobilisation, however, the theoretical potentia is hardly likely to be realised (lack of network effects). A number of obstacles impede academic use of SNS, in particular the need for additional time, which is accompanied by benefits that are not immediately visible for the individual. In contrast we stress that SNS may indeed be functional for
academic communication and cooperation.

Science, for the most part, is unaware of the existence of Web 2.0. Instead, a "legacy gap” exists. Modern research policies, laws, culture and impact measurement methods deter scientists from adopting Web 2.0.  This in turn prevents scientists from utilizing the complete benefits of the internet and the open-minded ideology that evolves with it.

Here are four pillars / key concepts identified that - once realized – will unleash numerous opportunities to overcome this - legacy gap and ensure the future of science – Science 2.0 – to the benefit of us all !

By

Dr. Sönke Bartling

Ronald The, M.A.

Introduction

What the heck is Science 2.0?: Simply, Science 2.0 (Ref. 1-4) is a revolution in the world of scientific communication and publishing. On a broad scale, it is a cultural and ideological movement set in motion by the use of Web 2.0.  It will change the way scientist think about authorship, data, copyright and content, all in sync with Web 2.0. This is monumental as science is vital to our well-being and for that reason we all share a common interest in its advancement.

(For different conceptions of the term Science 2.0 see Ref. 5)

So, yes, I know what Web 2.0 is... Web 2.0 does not mark a distinct development or a new feature, but instead a transition from static content presentation that is received by a passive internet user, to a more dynamic, interactive internet experience (Ref. 6). These types of exchanges have already and continue to have a profound impact on society.  Many believe that we are just at the start of this evolution.

At the same token, any massive change is not without risk, and society, the public and private decision-makers are often overwhelmed by these developments and their potential implications. However, as awareness of the benefits and our knowledge of the concept increases, more and more people will actively contribute to Web 2.0 and hence Science 2.0. Eventually Web 2.0 will be a new culture which will question the current copyrights and philosophies with regard to content.

But what about Science?: Currently science, predominantly, advances in isolation of Web 2.0.  Despite acceptance of recent innovations as online social networks, open access journals, dynamic lab books, science remains moored in Web 1.0. However, it is almost certain that at some point in the future we will be able to look back and realize that science – as all parts of our life - are largely influenced by Web 2.0 and its associated philosophies. The question that remains is when this transition will take place? How? What for?, By whom and to whose advantage?

Transitions take time.  It’s an involved cultural, political and structural process. Let’s call this phenomenon the "legacy gap". 

Publications within modern day science are an excellent example of the legacy gap. The time delay to adopt new publications that are enabled, but do not yet play a relevant role within science vividly demonstrates this point (Fig. 1). 

Figure 1: The legacy gap between availability of web 2.0 methods and its adaptation within science - demonstrated using a key feature of science – publishing.

Let´s face it, we are in the gap.  Let´s find a way out of it! Below are four key concepts identified within Science 2.0. All of them must evolve simultaneously and are essential for the future of radically improved science communication that enables the features of Web 2.0 to be fully available and viable for scientists.

Obviously, in this transition process, observers and critics from both inside and outside of science are very important and key to helping science identify critical roadblocks, dangers and pitfalls. However, criticism should not preclude adaptation and should never cause blind conservatism. All who are involved in science and scientific publishing need to collaborate to drive this development in a direction that would be best for science.

The authors gained knowledge of Science 2.0 through discussions via blogs and tweets.  They gained understanding through participation in meetings and by reviewing the current literature extensively. Both like to purpose how Science 2.0 may influence science, science publications, scientist´s communication, patenting, and founding of science and science politics.

Four pillars of Science 2.0

There are four key concepts within Science 2.0 (Fig. 2). While they all have already been described, their interdependency has only been partially eluted to.  Their interaction and co integration is key to the successful development of Science 2.0.  In seclusion, one of the four pillars is of no value. Furthermore, for the sake of the clarity of this publication, current implementations with their special procedural advantages and disadvantages will not be discussed.

Figure 2: Four key concepts of Science 2.0. All four have to be realized more or less simultaneously, because one pillar is only useful if all three others are available.

I. Unique Research Identifier

A unique research identity is the most basic concept of the four pillars. By moving away from standard publications towards Science 2.0, it is essential to have a means of identifying a researcher non-ambiguously (Ref. 7). Currently, names alone are vague and can lead to confusion. A unique research identifier could be used to “sign” all  publications, regardless whether they are tweets, blogs, classic static publications, comments, discussions or publications 2.0.  Further, it can be used to gather publications inclusively for a particular researcher and can be used to assess his or her impact on research, including novel impact measurement methods. A unique researcher identifier represents the researcher and his or her credibility within the scientific community.

II. Online Profile

An online profile of a researcher (e.g. as in an online social network for scientists) serves to portray the researcher online. This is where you can find information pertaining to the researcher, including research activity, publications, comments, etc. which will be easily accessible. The online profile is connected with the research identifier as well links to publications, CV and impact metrics. Connections to fellow researchers and their ongoing work are also provided.

III. Publication 2.0: Blogs, dynamic publication formats and open data

Publications 1.0 within Science 1.0 are papers, abstracts, talks, books (Fig. 4). Common to all these forms of publications is that scientists publish their research only in a rich, “final” version (Fig. 3) at the end or near the end of a project. Before that time usually nothing is publicly available and significant effort is made to protect and guard the data until is has been released. The consequence of doing so is that the research and updates are not presented to the interested audience in a timely manner.  In addition, collaboration beyond the research group is difficult if not impossible. New results, potential ideas, and input from the scientific community is delayed until a final published abstract or a full paper is available. If the results are negative often no publication is written since the effort to write a paper is high and in case of negative results it is often not worthwhile.

Figure 3: Publication culture in Science 1.0 and Science 2.0. In Science 1.0 publication threshold is high, which causes lots of unpublished data (loss) and publication delay.

In Science 1.0 there are fundamental reasons for this behavior. Early publications in any form less than a final publication usually destroys the novelty of a research finding and with it the chance to publish research in an accepted and credited way. Similarly, ideas, sparks, small findings, additions to publications, remarks and so on usually have no adequate and honored way to become published.  Therefore scientists usually keep ideas or comments for themselves rather than contributing to the potential success of a colleague scientist, always afraid of not being appropriately acknowledged.

Figure 4: Publications 1.0 in Science 1.0. A high publication threshold exists, because publications have to be “complete” and “final”.

In Science 2.0 a variety of forms of publications are accepted and can contribute to the reputation of a scientist (Fig. 5). The scientist is in a safe haven where he/she can share research results, ideas and conclusion as they occur, knowing that the time, name of the researcher and potential impact is forever associated with it. This promotes collaboration and increases the productivity of science as a whole. These Science 2.0 publications will co-exist with established publication forms as well.

Figure 5: Publication 1 & 2 in Science 2.0: The Web 2.0 enabled lots of new, low threshold fast and dynamic publication methods.

The Publication 2.0 form is free and thought-provoking. It includes updates to wikis or comments to publication 1.0. as well as contributions to databases as the genome or chemical structure databases  (Open data). Obviously small blogs, tweets or discussions are not a concise publication form and therefore full publications (papers, books, abstracts) still have an important role in Science 2.0.

So the following statements apply to Publications 2.0:

·      Ideas that have been published in form of tweets might be referenced to in later, full paper publications.

·      Final papers may be written online, open viewable for all scientists as the research results occur – clearly, writings can be marked as preliminary.

·      Recent versions of Publications 2.0 will be accessible through the history function in wikis. Besides historical relevance they have to be available for impact measurement of earlier research.

·      Negative research results may remain published in less structured format with concluding remarks in e.g. a blog. At least - in contrast to Science 1.0 - they are published, and other scientists may find ways to overcome the issues.

It can be assumed that novel publication formats will reduce the amount of unpublished data, the amount of repeated experiments and will facilitate the interaction of scientists. The impact on science is endless.

IV. New impact factor measurements

Measuring the scientific impact of research is very difficult and even more so when career decisions and research funding is dependent on it. Impact measurement methods weigh vary largely within the scientific disciplines. There exists a tendency to employ quantifiable impact measurements based on hard metrics.

Currently, the most famous of these instruments is the journal impact factor and its derivatives. The journal impact factor assigns an impact factor to a journal and every publication that is published within the journal is accounted with that impact factor. The journal impact factor is in contrast to publication based impact factors, which is calculated for every single publication. The assumed advantage of a journal based impact factor is that is has a fore-seen quality. Meaning, research published in a high-ranked journal will most likely have a great impact on research – a doubtable conclusion.

Currently, a privately owned company calculates the journal impact factor and keeps the copyright on calculated impact factors. If all research publications were open, many different providers could easily calculate impact factors.

The journal impact factor developed around traditional publication concepts. It is certainly not a method that can be used to assess the quality of Publications 2.0. In Science 2.0 many different impact quality measurements need to be established and calculated (Ref. 8). It is important to understand that there is no fundamental reason whatsoever to adhere to a journal impact factor system. E.g. its fore-seeing quality can easily be simulated by online “journals” – certain publications can be grouped to simulate an edition of a journal – selection of the articles can be done by experienced scientists which resemble a current editorial board including reviewers.

Besides citations, which are the basis for current impact factor calculations, many different measurements may be the basis for new impact measurements. The advantages and disadvantages of new impact measurements have to be discussed openly and have to evolve with the past experiences. Also Science 2.0 impact factor measurements allow for manipulations and limitations similar to the current journal impact factors. However, Science 2.0 existing as a vivid culture of discussion and criticism  will lead to the eventual development of meaningful impact measurements.  This is in contrast to a monolithic, fixed system that prevails in Science 1.0.

Conclusions

So what ? Yes, Science 2.0 will happen. The legacy gap will be bridged one day. The question remains : How fast we want to make this happen, and how fast can we make this happen? The four pillars as discussed will be the foundation of Science 2.0. This decade could become the decade of Science 2.0 (Ref. 9).

Get started!

Acknowledgement:

Thanx to Vershalee Shukla & Nick Trautmann for very fruitful discussions.

References:

1. Science 2.0 (change will happen...)

2. Science 2.0: Great New Tool, or Great Risk?: Scientific American.

3. Science 2.0 « O'Really?

4. Science 2.0/Brainstorming - OpenWetWare.

5. MSCI 2010 W.

6. What Is Web 2.0 - O'Reilly Media.

7. Lang, A. & Lang, E. Do we need a Unique Scientist ID for publications in biomedicine? Biomedical Digital Libraries 2,  (2005).

8. Scientometrics 2.0.

9. Twitter / Science 2.0: This is the decade of Science 2.0

This work is licensed under a Creative Commons Attribution 3.0 Unported License

All infographics can be found powerpoint ready in the file section of the group Science 2.0 & Publication 2.0

Are you using Google Scholar? For finding scientific literature? For obtaining citation counts and publication lists of researchers? Have you ever thought about how trustworthy the information is you get on Google Scholar? 

My colleague and I performed several tests with Google Scholar and found out that it is really easy to fool Google Scholar. You can easily increase citation counts of articles and therefore increase the article's rankings. You can easily add invisible keywords to articles and make the article appear relevant for searches it actually isn't. You can also create complete non-sensical articles with the paper generator SciGen and make Google Scholar index them. And you can place any kind of advertisement in manipulated articles and make users of Google Scholar downloading them.

Of course, our results do not mean that you cannot trust Google Scholar at all or shouldn't use it at all. Despite our results I am using Google Scholar frequently - imho it's still the best academic search engine on the market. However, as with all other search engines you should be aware that there might be spam and manipulated information and you should really be carefully using citation counts from Google Scholar. Maybe there are no, or little, manipulations right now. But the more citation counts from Google Scholar are used for performance evaluations, the higher the incentive for researchers to manipulate them (and, as said, it's really easy).

What I am interested in now is: What's you opinion on this subject? Have you every found something on Google Scholar that was suspicious?

 If you are interested in more information read the full article, titled "Academic Search Engine Spam and Google Scholar’s Resilience Against it",  here. 

Someone has truly said that 3 things are always changing, "Time, Temperature and Technology.”  New technologies are the breathing a new life into this present Era.  Very Small DNA is responsible for formation of giant Blue Whale. Every reaction, physiology is encrypted in these small components of cell. Whole process is just like computer program or electronics algorithms.

So why cannot we use this system to solve our complex mathematical problems? We can use RNA interference in human kidney cells to construct a molecular computing core that implements general Boolean logic to make decisions based on endogenous molecular inputs. These molecular inputs may be mRNA, siRNA or any other factor which is used in protein synthesis and output will be particular protein which is responsible for fluorescence or colored colonies of bacteria. We can design numerous electronic systems which are more effective and efficient than conventional technology. These genetic circuits can be designed for solving many complex problems in mathematics like the famous Hamiltonian Path Problem which can be solved using Hin recombinations.

Programming bacteria to compute solutions to difficult problems could offer the same advantage of parallel processing that DNA computing brings. Bacterial systems are autonomous, eliminating the need for human intervention, Bacterial computers can adapt to changing conditions, evolving to meet the challenges of a problem, and the exponential growth of bacteria continuously increases the number of processors working on a problem. This technology at present is limited to laboratories, but as we know “necessity is the mother of invention”, with growing needs this technology will lead us into a new era of emerging Biological Electronics that is Biotronics.

Synthetic Biology is the growing technology and has various applications in different fields of science. Cancer treatment can be easier through this technology. There are many treatments for Cancer like Chemotherapy, Radiation therapy, anti Cancer Drugs etc. But Cancers in advance stages are difficult to treat with such traditional approaches. Gene Therapies like Adenovirus treatment are more effective and efficient. It is because of very high affinity of adenovirus towards tumor cells. Hence it plays very efficient role as vector for transferring various engineered genes circuits or DNA strings into tumor cells. Such engineered vectors selectively penetrate tumor cells and perform oncolysis. In general Adenovirus therapy use serotype 5 and success of such therapy is depends upon coxsackie-adenovirus receptor (CAR) expression. But specificity decreases as expression level decreases. Hence we are aiming to create such genetic circuits which are highly specific to Cancer Cells as well as perform oncolyses . We are also considering Tissue specific promoters, various surface markers as well as ligands domains. Some of the examples are SLPI, MSLN, Cox-2, VEGF, Midkine, Survivin etc. We are concentrating on p53 protein network and other related protein pathways. We have designed gene circuit which will express only in tumor cells. Expression leads to production of different proteins which are responsible for lyses of that tumor cell. For this purpose we have used various stimulations and designing software. This Synthetic Biology technique can also be used in many different types of diseases. Even we have given idea about the AIDS treatment through Synthetic Biology Techniques.

J is a high-level, general purpose programming language, though it is mostly suited to mathematical and statistical applications. The system comprises an interpreter, a number of package utilities, labs and documentation. J supports a number of Unix systems including Linux, Solaris, AIX, FreeBSD, NetBSD and OS X; as well as Windows and Windows CE. It is also available on 32 and 64 bit architectures.

While J is not open source, the licence is free. J uses natural language nomenclature, for example, functions are called verbs and data elements are called nouns. Adverbs and conjunctions are used to alter the behaviour of verbs. New verbs are written by combining sequences of existing verbs as phrases. J’s rules of composition govern how verb sequences combine and interact. In this article we will introduce some of the basic concepts of J and how to programme in it.

Most of the built-in verbs (functions) in J are denoted by punctuation characters (though a few use alphabetic characters). Some just use a single characer (such as the basic arithmetic operators) others are represented by a dygraph: a character followed by a period . or a colon :. The basic arithmetic operators (verbs) are: + (addition), - (subtraction), * (multiplication), % (division) and ˆ (power). The best way to illustrate the features of J is with a few simple examples:

   5 * 3 + 1 NB. which is not the same as below

20   

   (5 * 3) + 1 NB. equivalent to 5 * (3 + 1)

16

The first thing to note is the J prompt is a three space indentation (where non-indented lines are the resultant output). Be aware of operator precedence, given that the interpreter parses right to left. Finally, the NB. directive indicates a comment. Instead of the traditional forward slash (/), the division operator is the percent character (%):

   1 - 3 % 2

_0.5

Negative numbers are denoted by a preceeding underscore: _ and not by a hyphen: -. There is a subtle difference between _1 which is the value minus one, and -1 which is negation function applied to (positive) one. The expression below results in a divide by zero, however, instead of an error, J returns infinity (denoted by an underscore _):

   2 % 6 - 2 * 3 NB. divide by zero = infinity

_

J returns a complex number for the square root of a negative value:

   3 + (1 - 5) ˆ 0.5 NB. results in complex number

3j2

Complex numbers in J are represented by a real and imaginary component delimited by a j. J can also handle higher dimensional objects. In the example below a list of integer values are assigned to variables x and y:

  ]x =: i. 6 NB. assign and display x

0 1 2 3 4 5

  ]y =: (2*x) - 3 NB. assign and display y

_3 _1 1 3 5 7

  yˆ2

9 1 1 9 25 49

The integers verb i. generates n integers from 0 to n − 1, where n is the value of its argument. The right verb ] returns the right argument (and [ returns the left argument), and is used here as a convenient way of displaying the result of an assignment. This next examples show array arithmetic. The i. verb is used to generate a 3 × 3 array:

   ]X =: i. 3 3

0 1 2

3 4 5

6 7 8

Add a literal (in this case 2) from each element of the array:

  X+2

 2 3 4

 5 6 7

8 9 10

Define a three element list Y and find the product of X and Y:

   Y =: _1 0 2

   X * Y

0 _1 _2 0 0 0 12 14 16

Notice that the list is applied to each column of the array, this is determined by the rank of the verb. The rank of a verb can be altered with the rank conjunction ". To multiply along the rows, use the expression:

  X *"1 Y

0 0 4 _3 0 10 _6 0 16

J has many other built-in verbs in addition to the basic arithmetic operators, a few are shown below:

   +: i.6 NB. double

0 2 4 6 8 10

   -: i.6 NB. halve

0 0.5 1 1.5 2 2.5  

   %: i.6 NB. square root

0 1 1.41421 1.73205 2 2.23607

   *: i.6 5 NB. square

0 1 4 9 16 25

   >: i.6 NB. increment

1 2 3 45 6

   <: i.6 NB. decrement

_1 0 1 2 3 4

  # i.6 NB. tally (number of elements)

6

J is a powerful analytical tool which can be used in many disciplines: mathematics, economics, finance and engineering to name but a few. It is a somewhat terse langauge, but this can be advantage if you programming on a PDA for example, with only a touch screen and stylus pen for input.

Dr. HUANG Sui at the University of Calgary has spent the last few years exemplifying and improving the State Space & Attractor theory of gene regulatory networks (GRN), which was initially proposed by Prof. Stuart KAUFFMAN from 1960’s. Incorporating the original concept of epigenetics (Waddington 1942) and methodology of systems biology, the theory seems surprisingly simple to be understood and, in my opinion,  a promising framework for future stem cell and cancer researches.

Assuming each gene has two alternative states (ON or OFF), a genome containing N genes will have 2^N possible states, composing the so-called high-dimensional State Space. However, due to the mutual interactions between all the genes within a genome, some positions in the space are impossible to occur, and the realistic positions of the genome expression profile are limited to the space surrounding some lines, or ‘trajectories’. In the whole life of a cell, its genome expression profile is like ‘walking’ through these trajectories within the presumed state space.

What’s more, there are ‘attractors’ on the way of the trajectories. This means some positions in the state space are the most likely to occur to a cell; they are like black holes in the cosmos and any walking-by cells will be attracted towards them. If we were given a known genome and the information about all the interactions between the genes involved, we could be able to determine what the trajectories look like and where the attractors are located within the state space.

Unsurprisingly, these attractors could correspond to different cell types (or cell fates) in terms of cell development. In an analogy from Huang and Kauffman, a cell as a pluripotent progenitor is like to be at a mountain top, and its daughter cells will just ‘fall’ into surrounding valleys driven by the imaginary ‘potential energy’. Each valley is literally an attractor, and cells ‘falling’ into different valleys will turn to be different types of cells. This is not only an analogy now because it is already well formulated and supported by data from Huang and other scientists’ studies. (See Figure 1 from Huang 2009.)

Figure 1. A diagram of the 'mountain and valley' analogy (from Huang 2009)

It remains a question whether genome expression profile can solely and exhaustively explain cell differentiation, I think. Anyway, case studies of a simple system were able to show that the expression profile of a pair of cross-inhibiting genes (GATA1 and PU.1) can sufficiently decide whether a colony of progenitor blood cells will develop to be red or white blood cells.

The theory seems an exciting blueprint from which a plural of more specific inferences can be derived, perhaps at first in the area of induced Pluripotent Stem (iPS) cells. Imagine if Dr. YAMANAKA Shinya could benefit from special ‘trajectories’ from this theory, he would be able to develop more efficient ways of cell induction and quality control, rather than just overexpressing some candidate genes and checking them in the culture media, and shortly he will be able to move those procedures from bench to factory.

Huang himself says that he aims at building up a unifying theory of multi-cellularity. I really appreciate his ambition. And again I agree that good works in basic (or pure) science never went against application research.

However, the present theory is still steps away from its final success. Several questions have to be answered to make it more rigorous and applicable.

1) The first question is how pluri/multipotency is maintained (and escaped) as the status of stem cells and all levels of progenitor cells.

 Huang gave a possible explanation by providing a model in which auto-stimulation of cross-inhibiting genes leads to a ‘meta-stable’ state, which serves as an attractor as well. As shown in Figure 1, there is an assumed 'lake' on the mountaintop where the stem/pluri/multipotent cells are supposed to locate.  But even if the pluripotent status is not an attractor, i.e., the 'lake' does not exist, we can still go on looking for mechanisms keeping cells there and driving them out of it.

2) The second question is how the imaginary ‘walking’ of cells along the trajectories is coupling with cell division. Are the ‘walking’ potential and the proliferation potential correlated with each other?

 Considering the imaginary ‘potential energy’ in the ‘mountain and valley’ analogy, there is a possibility that the non-attractor status or the height of the mountain indeed provides a driving force for cell proliferation. If so, the ‘potential energy’ will turn out a realistic energy, not only an mathematical derivative in the abstract model. However, things are not so easy to be tackled. Extremely clever minds are needed to define this energy, if it does exist.

 A specific question derived here is whether the cell ‘walking’ is discrete or continuous when the overall trajectory is divided into cell generations. To answer this question, the very recent techniques of single cell profiling are needed.

3) A mechanistic question is how the rules of interaction between genes/regulators can be elaborated in molecular terms.

 Referring to the belief that functions are determined by structures, we may have to go back to those trivial things like miRNAs, DNA methylation, histone modification, etc. But this time we will look into them from a brand new perspective and towards a more comprehensive understanding.

4) An even deeper and basic question is how the rules in question 3) and the all the mechanisms had evolved when multi-cellular organisms emerged in the world.

 This should be part of Huang’s final goal in constructing his theory. I am very interested in this question, but I think it may not be solved within one or two decades. Anyway, one could be more optimistic because we are living in an accelerated era and we all can expect miracles.

Literatures:

Huang, S. (2010). Cell Lineage Determination in State Space: A Systems View Brings Flexibility to Dogmatic Canonical Rules. PLoS Biology, 8(5), e1000380. doi: 10.1371/journal.pbio.1000380

Huang, S. (2009). Reprogramming cell fates: reconciling rarity with robustness. BioEssays, 31(5), 546-560. doi: 10.1002/bies.200800189

Huang, S., Guo, Y.-P., May, G., & Enver, T. (2007). Bifurcation dynamics in lineage-commitment in bipotent progenitor cells. Developmental Biology, 305(2), 695-713. doi: 10.1016/j.ydbio.2007.02.036

Huang, S., Eichler, G., Bar-Yam, Y., & Ingber, D. (2005). Cell Fates as High-Dimensional Attractor States of a Complex Gene Regulatory Network. Physical Review Letters, 94(12), 1-4. doi: 10.1103/PhysRevLett.94.128701

Informational crowdsourcing is growing in popularity to answer questions of all kinds. David Pogue gives a brief overview and discussion on crowdsourciing approaches in the TechnoFiles section of the latest Scientific American issue (Question Time, Sci. Am. Oct. 2010, page 38). As to whether one will get satisfying answers, depends on the question type such as look-up and how-to questions.

For chemical and materials research, a large array of digital bibliographies, archives, databases and specialized services are available, open-source and otherwise. A human being in the crowd may just use those tools and services to answer a a look-up question or even prepare a proposal for a how-to question. 

Having answered many chemistry-related questions myself, not so much as a crowd member but as a research scientist, I am going to conclude that most questions are deeply context dependent (and often of the non-disclosure type) that crowdsourcing provides a limited perspective. In addition, whether relying on the crowd or the surrounding team, the art of formulating a chemical question is still in its infancy when it comes to efficient and concise description of complex molecular structures, assembles and nanodevice architextures.

The Shaw Prize in Mathematical Science has been awarded to Jean Bourgain (Institute for Advanced Study, Princeton, USA) for his profound work in mathematical analysis and its application to partial differential equations, mathematical physics, combinatorics, number theory, ergodic theory and theoretical computer science. 

A brief CV for Jean Bourgain.

Jean Bourgain’s work touches on many central topics of mathematical analysis: the geometry of Banach spaces, harmonic analysis, ergodic theory, spectral problems, and nonlinear partial differential equations from mathematical physics. His contributions solved longstanding problems in convexity theory and harmonic analysis such as Mahler’s conjecture and the lambda-p set problem. His work also had important consequences in theoretical computer science and on exponential sums in analytic number theory. In Hamiltonian dynamics, he developed the theory of invariant Gibbs measures and quasi-periodicity for the Schrödinger equation.

• Vrije Universiteit Brussel, Ph.D. 1977, Habilitation 1979
• National Fund for Scientific Research, Belgium, Research Fellow 1975–81
• Vrije Universiteit Brussel, Professor 1981–85;
• University of Illinois, J. L. Doob Professor of Mathematics 1985–2006;
• Institut des Hautes Études Scientifiques, Professor 1985–95;
• Institute for Advanced Study, Professor 1994–;
• Academia Europaea, Foreign Member; Académie des Sciences, Institut de France, Foreign Member; Polish Academy of Sciences, Foreign Member; Swedish Academy of Sciences, Foreign Member; National Fund for Scientific Research, Belgium, Empain Prize 1983,
• A. De Leeuw-Damry-Bourlart Prize 1985;
• Académie des Sciences, Institut de France, Langevin Prize 1985,
• Élie Cartan Prize 1990;
• Ostrowski Prize 1991;
• Fields Medal 1994;
• Ukraine Academy of Sciences, Vernadsky Gold Medal 2010;
• Shaw Prize in Mathematics 2010

In his famous book Laws of Form, George Spencer Brown tries to construct the world from the most simple. He begins with a simple distinction, a circle on a structureless plane for example. He does not say that this is the only way to begin, but makes the reader simply do it and see what is developing. In addition, he gives more handling instructions, which reduces the most possible to the least possible.

I focus on his beginnings – the distinction – and the way how this is interpreted by him (indeed): ”… every duality implies triplicity: what the thing is, what it isn’t, and the boundary between them.” By this the world is digitalized. Subsequently, he examines extensions (“… to recross [the boundary] is not to cross [the boundary]”) and reductions (“What a thing is and what it is not are identical in form”). In any case, the boundary remains only boundary, i.e. distinction.

However, the boundary has been created just by crossing itself: It only exists by changing the sides. If I stand still on one side, all vanishes.

But when I change the side, I must change to another. Therefore, both sides are never identical in distinction, because then the crossing, the alternation, that creates them, would vanish.

If we reduce everything to distinction (“form”) as such, as Spencer Brown sometimes does, the distinction still must be perceived as such. This means, the alternation condenses. And this it does (without changing everything) only in the middle. So the boundary is unity in extreme, moment of identity of both sides. The alternation then takes place between the center of identity and periphery, which leads to infinitesimality structure.

What Spencer Brown wants to rationalize out of existence, therefore, is alternation itself – the prerequisite of his whole operation! By that he simplifies (identifies) more than he says. And he does not say all that is important.

If one follows his instructions, no contradiction results. But who says, that one has to restrict oneself in this manner?

As for the extension “to recross is not to cross”: It shows that identity always points beyond itself, since strictly speaking it came into being by recrossing – there is no closed operation, the unlimited world is connected. With this even the extension of the Brownian principles is justified.

Decades ago a fortunate experimental condition was discovered in the anatomy of the C57BL/10J  inbred mouse, where a purely endogenous origin of "natural" antibody production could be demonstrated (1,2,3). The first time a so called classical "natural" antibody was here unmasked as an autoantibody and a growth process already postulated (2). While this was in contrast to the predominant concepts of an environmental origin, in particular concerning the much discussed antibodies within the common ABH (blood group) antigen system (4, 5, 6, 7), the ovary of unfertilized females was clearly identified as an autologous source of a "natural" anti-A antibody induction (1, 2, 3).  So the appearance  of the respective hemagglutinin and complement-dependent hemolysin, both of not yet determined protein and/or immunoglobulin classes, was stopped by early ovariectomy, which together with the organ completely removes the A-like autoantigenic power (1).  

The murine“natural”  hemagglutinin and hemolysin activities, reacting strongly with human blood group A erythrocytes, were inhibited exclusively by autologous, water-soluble A-like glycosphingolipids detected in the ovary, and the respective measurements were saved at statistically significant levels using multiple comparisons with the other male and female  tissues (1, 8).  Binding specifically the lectins of Helix pomatia and Dolichos biflorus (2), they exhibit N-acetyl-D-galactosamine in a terminal linkage but are not yet analyzed on a current chemical and genetical basis.  Markedly age -dependent, they reach their peak of activity at the onset of puberty (1, 2) and did not show any A-like expression at birth. Their production always precedes the appearance of their corresponding antibody, which was demonstrated at extremely low levels, if at all, in early ovariectomized animals.  Its auto-reactive hemagglutinin and hemolysin specificities were shown to be distinct from a human anti-A antibody, which discovers growth-dependently xeno-reactive A-like structures in several other murine tissues,  and it is not a Forssman antibody (9). Moreover, there is no comparable murine anti-B antibody of endogenous origin (10). While an anti-B can be exogenously induced in the C57BL/10J inbred mouse by the B-reactive lipopolysaccharide of Escherichia coli O86, it is always associated with a cross-reactive immune anti-A, which together with the immune anti-B can be absorbed by the microbial antigen and separated from the “natural” anti-A (11).  

Today “natural" antibodies are known to reflect various origins (11) and believed to be produced also without any exogenous stimulation, but nevertheless are polyreactive with exogenous and endogenous structures and so are always auto-antibodies as well (13, 14)). Their appearance in healthy man and animals excludes autoimmune diseases and perhaps displays self control procedures of autologous cell growth under physiological and pathological conditions (15). 

The particular association, or even cooperation of specific surface receptors with their corresponding (auto) antibody, apparently controlled not by the thymus but peripheral mechanisms, as demonstrated for anti-A as anti-B (auto) antibodies in normal human sera, independently from the phenotype (16), may raise again the intriguing question, how the genetic background, when identified by cell surface properties, could be of significance in disease and survival, i.e. evolutionary advantage. Cancer biology here is a large field of discussion, blood groups as genetic markers always played a role. The molecular structures of the histo-blood type ABH, Lewis, Tn - and related systems, residing from fishes to mammals, in a long-term evolution of the CAZY glycosyltransferase 6 (ABO) gene family (17), were a long matter of extensive experiments (18). And the discovery of the A-related Tn structures and derivatives as diagnostic markers and vaccines in tumor therapy and prophylaxis was one of the first important results (19).  

But statistics about a direct correlation between cancer and blood groups were up to now not satisfying. While earlier reports appeared to reveal a modest predominance for malignant growth in people with the expression of blood group A, especially concerning certain organs such as the ovary and intestinal tract,  meanwhile too many discrepant results do not permit final statistical inferences (data not shown). And the latest prospective study, considering epithelial ovarian cancer, demonstrated even a predominance of “B” instead of “A” (20).  Moreover, in an earlier report on blood group A patients, suffering from non-small-cell cancer of the lung, the preservation or appearance of A-like structures in the tumor cells was shown to be a favorable factor in prognosis (21).  

However, although a disadvantage for the expression of the histo-blood group A phenotype, undergoing several structurally and serologically defined changes during maturation (22), could up to now not be verified, on the other hand, some predominance of common evolutionary A-specific potentials for growth processes per se might exist, independently from species or blood groups. Such potentials should be reflected by appearance of the "inappropriate" A-specific ovarian glycosphingolipids in the growing unfertilized  C57BL/10J female and by neo expressions of “inappropriate” A-specific structures, observed in malignant tumors of non reproductice tissues in other animals (23), as well as in man, occasionally in tumors of blood group O ( 24, 25, 26, 27 ) or blood group B people ( 26 ), while there is up to now only one report on an “inappropriate”  B-specific structure, which however, occurred in cholangitis ( 28 ). The classical phenotypes, genetically clearly distinct from each other, are structurally closely related and experimentally convertible. But although neo expressions are relatively rare in comparison with many epitope deletions, observed on malignant cell surfaces (22), the permanent blood group independent production of “natural” anti-A (auto) antibodies in any human serum (16) strongly suggests respective activities and a steady response to invisible autologous “inappropriate” A-like growth.    

In fact, the histo-blood group A-gene exhibits some biological predominance in the growing C57BL/10J inbred female mouse. While a murine equivalent of the human ABO gene as a cis-AB gene encodes a glycosyltransferase with both A and B transferase activities, and prevails in mouse populations (29), in the C57BL/10J female A-activities alone arise or escape during maturation, without any trace of B-activity.  And the great polymorphism of the common, species independent (blood group) antigen A complex, a complete structure of the human ABH blood group system was presented by a single inbred organism which distinguishes between xeno- and auto-reactive A-like activities and their related Forssman type specificity.  The growth dependent appearance of the “inappropriate” A-like activity in the ovaries of unfertilized females strongly suggest a genetical polymorphism due to parthenogenetic developmental processes in their eggs. And the binding of the lectin from Dolichos biflorus to the ovarian glycosphingolipids suggests “A” determining N-acetyl-D-galactosamine epitopes on the surface of active embryogenic stem cells (30).    

The reproductive pressure of inbreeding apparently promotes parthenogenesis (31). Increased developmental potentials were already observed after pharmacological or hormonal manipulations respectively, particularly in inbred mice (32). And even viable chimaeras were already produced from normal and parthogenetic mouse embryos (33)). They perhaps also explain the observations in the C57/BL10J female mouse, as the distribution of its xeno- and auto-reactive structures could reflect the developmental process during tissue maturation.  

In man parthenogenetic potentials were recognized to be essential in stem cell research (34, 35, 36) and may be of significance in “natural” immunity as well. But they are neither restricted to germinal tissue nor always concentrated or over-expressed as in the ovary of the C57/BL10J inbred mouse, discovered as experimental tool (1, 2, 8). During maturation various potentials are preserved to some somatic cells, which dependent from the tissue, display different amounts.

The human pluripotent self-renewing cell dictates the developmental procedures in non reproductive tissues, and undergoes genetical polymorphisms involving aberrant glycotransferase specificities i.e. production of “inappropriate” neo antigens such as “A”.  It is so hypothesized that both, the murine and the human “natural” anti-A antibody represent a to be analyzed polyclonal control of a common, species-independent polymorphic structure, which is encoded by an evolutionary glycosyltransferase  (ABO) gene family (17), and arises or escapes by some biological predominance from the genetical polymorphism of developmental processes.

                                               References

1. Arend, P. and Nissen, J.: Z Immunitatsforsch  Immunobiol. 1977 (153) 74-84.
2. Arend, P. and Nijssen, J.: Nature 1977, (269) 255-257. 
3.  Rocher, J.: Diplome,  Ecole Pratiqu des Hautes Etudes (Sciences de la Vie et de la Terre),  Nantes 2005. 
4. Eisler, M. : Z Immunitatsforsch.1930,  (67) 38 - 49.
5. Landsteiner, K.: Science 1931, (73) 403-409.
6. Springer, G.F.et al.: J Exp Med 1961, (113)) 1077-1093.
7. Springer, G. F. and Horton, R. E.:  J Clin Invest 1969, (7) 1280–1291. 
8. Arend, P. and Njissen,  J.: J Immunogenet. 1976, (6) 373-82. .  
9. Arend, P.: Immunobiology 1979, (156) 410-417.
10. Néron, S. and Lemieu, R..  Vox Sang 1994, (67) 68–74.
11. Arend, P.: Eur J Immunol 1971, (5) 398-402.
12. Casali, P. and Schettino, E.W.: Curr Top Microbiol Immunol 1996 (210) 167-179.
13. Baumgarth, N. et al. : Springer Semin Immunopathol 2005 (4) 347-362
14. Duk, M. et al.: Glycobiology 2003, (13) 279-284.
15. Wang, H. and Chow, D.A.: Immunology 2000, (4) 456-467.
16. Spalter, S.: Blood 1999, (93) 4418-4424.  
17. Turcot-Dubois, A.L. et al : Glycobiology  2007, (17) 516–528, 2007.  
18. Hakomori, S.: Cancer Res 1985, (45) 2405-2414. 
19. Lo-Man, R.. et al.: J Immunol 2001, (166) 2849-2854
20. Gates, M.A. et al.: Int J Cancer 2010, March 22 .
21. Lee, J.S. et al.:  N Engl J Med 1991, (324) 1084-1090.
22. Hakomori, S.: Biochim Biophys Acta 1999, (1473) 247-266
23. Hirota, M., Pour, P. M., Tempero,  Margaret A. and Chaney, W.G.: Cancerogenesis 1992, (13) 1829-1833.
24. Clausen, H., Hakomori, S., Graem, N. and Dabelsteen  E.:  J Immunol 1986, (136) 326-330
25. Okada, Y.J. et al. : J Natl Cancer Inst 1987, (1) 19-28.
26. Metoki,R., Kakudo, K., Tsuji,Y., Clausen, H., Hakomori, S.:  J Natl Cancer Inst. 1989, (15) 1151-7.
27. David, Leonor et al : Cancer Research 1993, (53) 494-55OO.
28. Bloom, S., Heryet, A., Fleming, K. and Chapman, R.W.: Gut 1993, (34) 977-983.
29. Yamamoto, M , et al.: J Biol Chem  2001, ( 276) 13701-13708.
30. Nash, R. et al. Stem Cells. 2007, (4) 974-82.
31. Uyenoyama,  Marcy. K. : Evolution 1985, (39) 1194-1206.
32. Downs, S.: Biol Reprod 1990, (43) 427-436.
33. Leroy, C. et al.: Nature 1977, (269) 515- 517.
34. Isaev, D.A. et al. : Russian Journal of Developmental Biology 2001, (32) 292-297.
35. Kim, K., et al.: Cell Stem Cell 2007, (1) 346-352.
36. Polak de Fried, Ester et al.: Fertil Steril 2008, (89) 943-947.                   

Internet, which is considered to be the treasure house of knowledge orthe information superhighway, makes a huge difference as far as dissemination of information is concerned. But unfortunately in India the Internet penetration is too low. The Indian population could be classified as the people who have access to internet and those who don’t have access to it. There are many reasons to this disparity. The most important are the infrastructure bottlenecks (low bandwidth) and the economic status.  Those who have access to this vital source of knowledge are able to make rapid progress and grab the opportunities leaving their less fortunate brethren behind. In some developed countries, they made access to Internet a fundamental right. In US where around 75% of the people have access to this treasure house, have set an ambitious target for themselves to provide all their citizens with high speed Internet by 2020. They think that it is one of the ways they can maintain their technological and economic superiority. They also started taking measures to effectively counter the cyber attacks and protect their information networks.

Internet has become an essential source for acquiring knowledge. In fact it is a very fascinating thing. Take the example of a newspaper. Every morning you get a hard copy of the newspaper delivered at your doorsteps. We eagerly grab it and start reading as it has something new to offer. Humans by nature seek new things everyday. Research findings revealed that not more than 10% of the readers read beyond first chapter after they buy a book. So it is obvious that the remaining people, after reading some more pages or chapters shelve it because it has become old and it no longer attracts their attention. But in case of a newspaper every morning we get a new copy and that is why we get fascinated by it. But take Internet. It has something new to show us every minute in fact every second. So when I sit in front of my networked computer I rarely turn my eyes from it. It has got every thing I want. I can not only access information but even share the information with others. 

So to improve the educational standards in our country we need to device a plan to provide every school going child with a networked laptop. In fact there is a program called One Laptop per Child started by MIT labs. This laptop is very sturdy and runs on open source LINUX based software called Sugar.

OLPC Project has made a start in India with a pilot deployment in a rural village at Khairat near Navi Mumbai where laptops have been deployed and every child carries one laptop home.

Just imagine a teacher teaching Geography lesson and the students in the classroom use Google Earth to locate the countries, water bodies and observe the terrain of different locations. How effective the teaching-learning process would be!

Note: For full version visit  (http://www.teachingenglish.org.uk/blogs/eggheadedram/bridging-digital-divide-india-create-equal-opportunities)

Till Steffen, Senator of Justice of the City of Hamburg, tabled a motion to the Bundesrat, the German second chamber, proposing new provisions in regard to Google Street View and similar services. It is Hamburg's Data Protection Officer Johannes Caspar that investigated for violations of German privacy law by Google Street View (and also Facebook) recently.

The bill contains the following main provisions:

• If a photo is taken under circumvention of a visual protection, it shall not to be considered publicly available data;
• An obligation to inform the competent authorities and the public, for anyone who wants to take photos of the public systematically, referenced to geographical data;
• An obligation to blur faces and license plates not only for display purposes, but for the raw data;
• A right for anyone to request to disable access to photos of his/her house.

The bill would limit the "Freedom of Panorama" in German law, that allows anyone to take, publish and distribute pictures of the public. Already now, that freedom can be limited by the individual rights of persons displayed. The bill is clearly limited to systematically geo-referenced images, and thus does not affect ordinary press photos.

One of the most fundamental concepts of ecology is an ecosystem. The traditional definition was proposed in the 1930s. A new, modern definition is needed (PDF).

The relatively recent definition that was proposed in the paper (S. A. Ostroumov, “New Definitions of the Concepts and Terms Ecosystem and Biogeocenosis” Doklady Biological Sciences, 383 (2002): 141–143. Translated from Doklady Akademii Nauk, 383, no. 4 (2002): 571–573), was often cited by other authors. The definition is:

An “ecosystem is the complex of interconnected living organisms inhabiting particular area or unit of space, together with their environment and all their interrelationships and relationships with the environment. An ecosystem is characterized by the description of populations; the abundance of individual species; interspecies relationships; activity of organisms; physical and chemical characteristics of environment; flows of matter, energy, and information; and description of changes of these parameters with time.”

Comment of an independent expert:

Shehla Rais,  Oct 7, 2010 1:23 am

  Congratulations. One of the most comprehensive definitions of ecosystems from an ecology student's perspective.

An example of a paper that cited and used this definition, with the reference to the abovementioned article: 

Community Resilience: A function of resources and adaptability. (WHITE PAPER)

Patricia H. Longstaff, Nicholas J. Armstrong, Keli A. Perrin, Whitney May Parker, Matthew Hidek (JUNE 2010; INSCT.SYR.EDU)

Executive Summary: This white paper is intended for people who must help communities prepare for surprises. It assumes that no community can protect itself from every conceivable threat, but can increase its ability to be resilient or ‘bounce back.’ The resilience approach described below is written in plain language and as culturally-neutral as possible in order to make it globally applicable across a broad range of communities. We recommend that communities assess their resources and adaptive capacity for a variety of community systems: ecological, economic, civil society, government, and infrastructure in order to find the balance that achieves the degree of resilience most appropriate for them. This approach also requires attention to the intersections and overlaps of these systems. The ideas presented here are consistent with the most current efforts at defining and assessing resilience, even if the terminology varies. The paper concludes by outlining the next steps for concept refinement and validation through case-based research and development of assessment tools for practitioners.

The full text of the paper is accessible in PDF.

The full text of the English paper with the new definiton of ecosystem:
http://b23.ru/n68y

The Institute of Technology Assessment (ITA) of the Austrian Academy of Sciences just published a research report on the role of Google, Google Scholar and Google Books for science, in the framework of the project "Interactive Science":

König, R., Nentwich, M., 2010, Google, Google Scholar und Google Books in der Wissenschaft. Steckbrief III im Rahmen des Projekts Interactive Science. ITA-Reports, Nr. a52-3 hrsg. v. Institut für Technikfolgen-Abschätzung, Wien: ITA (PDF)

The 69-pages report is in German language - here is the abstract in English:

In this report we examine three Google services that can be used for textual searches and assess their impact on (primarily internal) scholarly communication: The universal web search engine Google, the academic search engine Google Scholar and the book search Google Books.

Firstly, we present basic information about the company Google Inc. and its roots. We then introduce each service by outlining important functional principles, namely the searchable databases, the way content is delivered and the available options for users. Starting with Google web search, we also describe some general aspects of search engines.

We found that all three services have effects on (internal) scholarly communication. They seem to be relevant especially with regard to searches for academic information. Since the observed platforms follow functional principles that differ from traditional information systems (e.g. libraries), possible changes are outlined and discussed. We also focus on various other aspects of the specific services, such as the effects of the Google web search on public relations, Google Scholar’s citation analysis functionality, or the legal problems that arise from the Google Books project.

We conclude that despite the preliminary character of this assessment, which results from the dynamics in the field observed, certain aspects seem striking and almost certainly persistent. Due to Google’s market power and popularity and the fact that it shares some goals with academics (gathering and organizing information), it will probably continue to have major effects on scholarly communication. While some of them can be dealt with in the academic system itself, others raise fundamental questions that require a wider perspective.

Malaria is a vector borne parasitic disease caused by the genus Plasmodium, affecting over 100 countries of the tropical and subtropical regions of the world.

Four different Plasmodium species infect humans and cause distinct disease patterns:

• P. falciparum (malaria tropica),
• P. vivax (malaria tertiana),
• P. malariae (malaria tertiana) and
• P. ovale (malaria quartana) 

P. falciparum and P. vivax account for 95% of malaria infections. Of these two parasites, P. falciparum is the most deadly one, causing cerebral malaria which, if remain untreated, leads to coma and ultimately death of the patient. 40% of the world populations live in areas with the risk of malaria.

Around 300-500 million clinical cases of malaria are reported every year, of which more than a million die of severe and complicated cases of malaria. Malaria is known to kill one child every 30 sec, 3000 children per day under the age of 5 years.

Malaria ranks third among the major infectious diseases in causing deaths after pneumococcal acute respiratory infections and tuberculosis, and accounts for approximately 2.6% of the total disease burden of the world.

Although malaria has been widely eradicated in many parts of the world, the global number of cases continues to rise. The most important reason for this alarming situation is the rapid spread of malaria parasites that are resistant to antimalarial drugs.

In 1967, the Chinese government launched a program to discover new antimalarial drugs from indigenous plants. The first written record of the antipyretic activity of tea-brewed leaves of Artemisia annua was described in "The Handbook of Prescriptions for Emergency Treatments" written by Ge Hong (281-340 A.D.).    

In 1971, Chinese researchers isolated, by extraction at low temperature from A. annua (Sweet wormwood), a stable easily crystallizable compound that they named Qinghaosu and later on named artemisinin . 

In the past 36 years, out of all antimalarial drugs discovered during this period, artemisinin was the only natural product whose medicinal properties were known for more than 2000 years. The only one synthetic antimalarial drug, mefloquine, has been discovered during this period.

Since its discovery, artemisinin has distinguished itself as a rapidly acting plasmodial agent against the blood phase of P. falciparum, and  is potent against both chloroquine-sensitive and chloroquine-resistant strains of the parasite in vitro,in vivo animal studies, and most importantly, in humans. 1,2,4-trioxane is the basic pharmacophore responsible for antimalarial activity. 

Owing to the fact that the peroxy linkage is essential for the antimalarial activity of artemisinin activity of artemisine and its derivatives, many 1,2,4-trioxane have been synthesized in different laboratory from inexpensive and readily available starting material. 

References

• http://malaria.who.int/
• Qinghaosu Antimalarial Coordinating Research Group. Chin. Med. J. 1979, 92, 811.
• Meshnick, S. R.; Taylor, T. E.; Kamchonwongpaisan, S. Microbiol. Rev. 1996, 60, 301. 

Worldology is a term I coined back in 1984 during my first year as a graduate student in the Department of Sociology at Princeton University. Back then there was really no pressing need to speak of globalization regardless of the fact that the process was well under way. Worldology was to be the name of a newly emerging social science discipline; it would follow the hierarchical tradition of naming disciplines based on the unit of measurement that they collected data upon for empirical investigation.

Psychology deals with and collects data at the level of the individual, Social Psychology deals with the behavior of individuals as they interact as groups and Sociology deals with the investigation of human institutions, the largest of which are presently nations and religions. Worldology would deal with the newly emerging unit of the whole “world” as its unit of measurement.  

Global consciousness would be the ultimate unit of organization possible for the human race. A journey that began some 100,000 years ago with the possibilities born from the evolution of the language organ giving us the ability to form progressively complex and increasingly encompassing social dimensions. After over a 100 millennium of ebb and flow, we stand at the verge of the possibility of a world unite. Social systems of reciprocally predictable behavior, which began with tiny groups of isolated humans towards its ultimate capacity of the complete world, have evolved to a point where today we stand at the threshold of our final human frontier of global consciousness.    

Generation from here on in will be faced with the daunting task of human organization at a scale that was neither possible nor that can be exceeded. Worldology is conceived of as a social scientific discipline that acts as a platform for the evaluation, investigation and facilitation of this newly emerging opportunity. An opportunity to preserve the biodiversity of our planet in all its forms and to work together toward global awareness and a world at peace, cognizant that we all live in one ecologically whole unit. There is only one world; the boundaries that we have drawn are mere blots of ink, meaningful only to the minds of one creature, humans. Boundaries have come and gone and they will for ever transform as we realign our allegiances and paradigms of co-existence.    

The idea of Worldology came to me after writing a final paper for my MA degree in Social Psychology at Bogazici University (Istanbul, Turkey). In the paper which was titled "Critical Review of Social Psychological Theories" one of the dimensions that I compared various theories upon was -how universally appropriate the theories were. In other words, were theoretical findings universally applicable cross culturally. I had concluded that most theorists agreed that when social psychological theories were reduced beyond social attribution of meaning that they lost their usefulness, and that meaning was anchored in language.  

Having grown up nearly symmetrically bicultural between Swissvale, a small suburb of Pittsburgh Pennsylvania, and Istanbul a megalopolis of the East, I was well aware of the impact and importance of language and culture on perception. It dawned on me that for social psychological theories to be universally applicable that all people would need to be speaking the same language and thus be referring to the same source of extracting meaning.  

The next question was, would, at some point in time, everyone in the world speak the same language and truly understand each other, and if so how quickly would such a global reciprocity of awareness develop. Back in 1984 the globalization craze was just beginning to unfold as new technologies emancipated the individual with increasingly more power. Individuals were being bombarded with new opportunities to participate in novel situations and expand their perceptions beyond the boundaries of their own nations. The flattening of the world, to use Thomas Friedman's term, was just beginning to compress cultures into one big playing field.  

Globalization was well on its way but to speak of a global consciousness was still the stuff of musical imagination. The real world seemed to be launched into a spiral of polarization rather than moving toward world peace. The concept of Worldology was more of a deduction from the relationship between language and behavior rather than an observation induced by reality.  For years it was hard to discuss the concept with anyone other than a close group of academic friends.  But those days are past and after some 25 years, it's time to discuss how this process will unfold and nurture the emergence of a discipline that will work on behalf of the needs of the world as one ecologically diverse whole. 

Some remarks on the Neoplatonic One, in connection with a book review of mine: 

 George Lekkas, Plotinus. Towards an ontology of mode, Editions Papazisi, Athens 2009, 134 pp. in Critica - A Greek Online Journal of Philosophical Reviews (in Greek)  

This is a corpus of studies, which cast new light on the interpretation of Enneads, striving to reveal the relations, the Neoplatonic hypostases develop in their articulation. Particularly focusing on the mode itself as exegetical tool, examines the mode of existence or the existence of the mode. This is an original approach, introducing the existential factor of relation, of which the inherent indeterminacy is combined with the metaphysical potentiality.  

Emanation  

According to Neoplatonism the whole universe, in its material and metaphysical aspects, is a product of the first hypostasis, the One. Through the process of emanation, the hierarchy of hypostases, One-Intelligence-Soul, ends at the non being of the region of matter. The intelligibles, being inside the hypostasis of Intelligence, form and embellish everything exists under them, of which nothing is considered without having a part of it inside the third hypostasis, the Soul. Human bodies, as being material, are also inside the hypostasis of Soul, by their individual souls. The river of creative and generative power of One flows into the dark region of non being, watering it. Everything is under the influence of this immense power, including matter, which is only a privation of good.    

The kind of relations between the hypostases guarantees the overflowing of power. Nothing exists for itself; even the Intelligence and the Soul need the dependence on the first hypostasis, the One, as they need themselves. Since the first hypostasis stands beyond everything, beyond being, this means that nothing owes its existence to the existence itself.  

Return 

 But the opposite course of ascend through the hypostases is to be accomplished, which comes right after every ensouled being realizes its destiny and of what is made of.  

 The mode of Soul’s existence gives rise to the question: of what special and general characteristics is that mode, since there is always in relation to itself and to the other? The answer is that the mode of psychic existence tends always to become intelligible, in order to find something it hasn’t. If the mode of the ensouled being presupposes the way of being intelligible, then what means to be intelligible? The answer to this, brings to mind that the higher destination of Intelligence is to cease being in itself. The only way the Intelligence has of not being in itself, is to succeed the complete unification with the One. Oness for some people looks very simple, and in reality it is as simple as it is the simplicity itself (πάντῃ ἁπλοῦν).

In fact the Soul and the Intelligence are related to the One by various ways, but always the ascending course for approaching the higher level of hypostases, is a return to the source of being, life and reason. Nevertheless, the extremely unapproachable nature and knowledge of the One make It a resident of beyond being. In final analysis the One isn’t related to anything; they are not humans those who find It, bud godlike and blessed men.  

Rest  

The mode of being hasn't only a single meaning. But when we come at the One, there is no meaning other than being One, as we exist as nothing and everything, as no one and as all. This ambiguity characterizes the absolute hypostasis not due to the lack of being, but due to the superabundance of being; its ambiguity is not common: it is a fundamental ambiguity. In reverse, if any kind of certainty exists, this is to be found where no one can really look: at the One Itself. The contradictions and the apophatic language is only our insufficient way to understand what the mystical union would be, when someone experiences it. In reality it is an inexpressible situation.  

By determining and generating the Being, the One resides at the same time at the heart of everything, as the absolute otherness to Being and the complete identity to Itself. If the One tries only a little to make everything similar to It, this is not why it doesn't care, but because everything and everybody must earn the kind of freedom which exists inside It. In any case, the name Absolute (ἀπολλελυμένον), which fits for the One, means "the free", "the without bond". The final rest inside One is an achievement of freedom, because by coming to this abode means to leave everything behind. The experience of mystical union (Unio Mystica), the ecstasy, is accomplished in this world and life as a flight to our real fatherland that is God or Good or One.    

The existence of the One everywhere, doesn't mean that Its absence isn't felt sometimes somewhere. If the One is the biggest attraction for everything, this is because everything yearns for unity, beauty and goodness. The union with the One becomes the most secret and valuable hope for mankind, having take through the course of history various forms, in every field of activity. In reality, nature and history cannot be considered and viewed otherwise, without being connected with what constantly makes them coherent, including any particularity and totality may constitute.         

Fogal et al (2010) found that the p32 gene (on human chromosome 17q13.3), which was overexpressed in some cancer cells, had actually promoted the level of oxidative phosphorylation (OXPHOS) in mitochondria. The knockdown of p32 in an experiment then lead to a lower level of complexes III, IV and V composing the electron transport chain (ETC) of OXPHOS, thus making a shift in ATP synthesis from OXPHOS to glycolysis in tumor cells, but meanwhile causing a lower level of tumor growth than before. 

This is contradictory with the well known Warburg Effect (Warburg 1924), i.e. an elevated level of glycolysis and glucose consumption as a hallmark of tumor growth, hypothesized to provide a growth advantage for the tumor cells.

However, another gene p53 (on human chromosome 17p13.1), also promoting OXPHOS, is a well known tumor suppressor. p53 could inhance expression of Cytochrome c Oxidase II (also a part of complex IV of ETC), which is essential for OXPHOS in mitochondria. p53 is found to have mutated in many cancer cells, causing a shift from OXPHOS to glycolysis (Matoba 2006) during tumor growth. This is in turn consistent with Warburg Effect.

As the result we see two genes located on the same chromosome regulating the balance between OXPHOS and glycolysis in the same way. However, they seem to play opposite roles in carcinogenesis. So why are they so different?

One possible reason may lie in their roles in inducing apoptosis. Over-expression of p32 could induce apoptosis only when p53 functions in normal status (Itahana & Zhang 2008). So once p53 is disfunctional in cancer cells as said above, the overexpression of p32 won't cause apoptosis alone, and thus won't give any disadvantage against the tumor cells. On the other hand, overexpression of p32 could produce ATPs for tumor cells in a higher efficiency. In such a hypothesis p32 would not be an oncogene, but is only overexpressed as a consequence of carcinogenesis. And in such a case, the Warburg Effect is not rejected but irrelevant to the mechanisms here.

Anyway, the Warburg Effect has been questioned more than once (Weinhouse et al 1956; Zu & Guppy 2004; Dang 2010). Although the inhibition of OXPHOS and promotion of glycolysis have been correlated to carcinogenesis either as a cause or as a consequence in numerous studies throughout the last 80 years (too many literatures), the underlying mechanisms seem still unsolved. And it is still possible to answer the above question in the context of metabolism regulation based on the framework raised by Warburg.

Many studies have been proposing an evolutionary perspective onto the correlation between ATP synthesis and carcinogenesis (e.g. Gatenby & Vincent 2003; Pfeiffer & Schuster 2005; Vincent 2006), by considering the tumor/normal cells within the same tissue/organ as a population, in which individual cells compete with each other in a series of cell generations within the life span of the human body. Such a micro-evolution process could be investigated with methods from population genetics, adaptation dynamics, theories of competition and coexistence, etc. These Darwinist have provided interesting viewpoints and they never forgot about the important roles of mitochondrial functions and mtDNA mutations in tumor growth. However, they seldom considered the cooperation between the mitochondrial genome and the nuclear genome, as de Bivort et al (2007) did in their effort to correlate such an coevolutionary force behind ATP synthesis with the progression of some mitochondrial diseases.

It is known that many proteins and enzymes involved in mitochondrial functions, including complexes I, III, IV and V of the ETC, are composed of both mtDNA-encoded and nDNA-encoded subunits (Wallace 2005). Interestingly, both p32 and p53 could regulate complex IV, but not complex II, which is encoded solely by nDNA. Considering that the two genomes belong to different hierarchies of life forms, some delicate cooperation mechanisms may have evolved to keep them match in a cell. Such mechanisms could be vulnerable to novel influences in the modern world, either environmental or physical, causing cyto-nuclear conflict. It is worth including such cyto-nuclear mismatch/incompatibility patterns when constructing an evolutionary model to answer the above question.

Vital references

• Fogal, V., Richardson, A. D., Karmali, P. P., Scheffler, I. E., Smith, J. W., & Ruoslahti, E. 2010. Mitochondrial p32 protein is a critical regulator of tumor metabolism via maintenance of oxidative phosphorylation. Molecular and Cellular Biology 30: 1303-1318.
• Matoba, S., Kang, J., Patino, W. D., Wragg, A., Boehm, M., Gavrilova, O., Hurley, P. J., Bunz, F., & Hwang, P. M. 2006. p53 regulates mitochondrial respiration. Science 312: 1650-1653.
• de Bivort, B. L., Chen, C., Perretti, F., Negro, G., Philip, T. M., & Bar-Yam, Y. 2007. Metabolic implications for the mechanism of mitochondrial endosymbiosis and human hereditary disorders. Journal of Theoretical Biology 248: 26-36.

A full understanding of the genetics of schizophrenia, autism, dyslexia, attention deficit hyperactivity disorder (ADHD), alzheimer and a large number of neurodegenerative diseases seems to be impossible without reckoning with IQ as a major confounding variable. Nobody will obtain clearcut results in the genetics of neurodegenerative diseases as long as the genetic background of general intelligence remains unknown. Despite this in many samples IQ variation is not controlled by collecting data on years of education and social status of probands which provide good surrogates of IQ estimates, at least in industrialized countries.

Until now, more than 1 million of SNPs have already been investigated for an association with IQ by Plomin, Deary et al. and others. No major effect has been discovered which could explain the high heritability of general cognitive ability and the known pattern of Mendelian segregation of IQ in the normal range of variation. Plomin et al. found only very small and mostly non-replicable effects. Therefore, our mind should be open for a broader outlook and new hypotheses. 

MicroRNAs as regulatory factors in gene expression renders them attractive candidates for harbouring genetic variants with effects on IQ. There is already ample evidence that miRNA-mediated gene regulation plays an important role in a number of neurodegenerative diseases. MiRNAs bind to complementary sequences in the three prime untranslated regions (3' UTRs) of target messenger RNA transcripts. MiRNA genes are found in intergenic regions or in anti-sense orientation to genes and contain their own miRNA gene promoter and regulatory units. As much as 40% of miRNA genes may lie in the near-gene introns of protein and non-protein coding genes or even in exons. 

Our first example:

Harold, D. et al. have found out and replicated compelling evidence that rs3851179 of the PICALM gene is associated with alzheimer. The homozygotes and heterozygotes of the rare allele A of rs3851179 have a 0,86x decreased risk for alzheimer. Since many years I am looking for such findings, because we should expect that probands of high general intelligence (high IQ) have a later onset of alzheimer and a decreased risk. Surprisingly, the allele frequencies not only of rs3851179, but even more of rs669556 and of at least 30 other SNPs in this near gene region exhibit the frequencies of a hypothetical major gene locus of general intelligence, see http://www.v-weiss.de/majgenes.html and http://knol.google.com/k/national-iq-means.

As it seems, at the moment, nobody has an explanation why the non-coding SNP rs3851179 is associated with Alzheimer and why in a large chunk of DNA with copy number variation a high number of SNPs exhibits similar allele frequencies in all the populations of the HapMap project. In which way could such a phenomenon have been stabilized by natural selection? Could this region be coding for miRNA or be its binding target?

The second example:

By checking routinely the bibliographical details of paper published together with A. Payton et al. on "Investigation of a functional quinine oxireductase (NQO2) polymorphism and cognitive decline" in  Neurobiol. Aging 31 (2010) 351, I became aware of a publication on "Genetic variant of glutathione peroxidase 1 in autism" Brain Dev. 32 (2010) 105.

Since 1982 I did collect evidence on a relationship between glutathione peroxidase activity, general cognitive ability (IQ) and social status. I quote in the following from an editorial published by me 1994 in the journal "Intelligence":

"In 1982 I became aware of a paper published by Sinet, Lejeune & Jerome (1979) in which a correlation of .58 between IQ and erythrocyte glutathione peroxidase activity (GSHPx, now GPX1) was reported for 50 trisomy 21 patients. None of the other enzymes studied correlated with IQ. Sinet et al. thought the correlation to be trisomy-specific, because an increase of about 50% in the superoxide dismutase activity (SOD-1) can be observed in cells from trisomy 21 patients. There is a feedback control of GSHPx concentration by the amount of superoxide, which explains the elevated activity of GSHPx in cells of trisomy 21 patients. However, Fraser and Sadovnick (1976) had found that the correlations of IQ between trisomy 21 probands with their fathers, mothers and sibs are about .50, consequently of the same size as with healthy  children despite the mean IQ of trisomy 21 probands being about 70 points lower. Therefore already Lenz (1978) had concluded that individual differences in trisomy-IQ have generally the same biochemical background as in normal persons. And Brugge et al. (1992) confirmed a correlation of .73 between erythrocyte GSHPxactivity anda short-term memory score. ...  By Gerli et al. (1984) GSHPx was assayed in families and the results support the existence of two Mendelian alleles.” 

In the following years I instigated a number of colleagues from all over the world to discover the underlying genetic cause of the cited correlations, but nearly completely in vain. We investigated SNPs of GST transferases, NQO and many, many others. Therefore I came to the conclusion that the major contribution to the correlation between lipid peroxidation and IQ could or should be the effect of a gene with copy number variations and repeat polymorphisms for which data are still not available or incomplete.
 

In April 2010, at the present state of knowledge, GPX1 is such a gene for which at least 4 common frameshift polymorphisms are already known. The arguments in favor of a relationship between trinucleotide repeat polymorphisms of GPX1 and general cognitive ability are holding for GCLC and its repeat polymorphisms, too.  Glutamate-cysteine ligase (GCL) is the rate limiting enzyme in glutathione synthesis. GCLC repeat polymorphisms are located in the 3' UTR and 5’UTR regions and therefore a likely binding target of miRNA. In view of the claimed relationship of GSH/GSSG redox status with schizophrenia and other neurodegenerative diseases, we should be eager to see whether a correlation between GCLC and its trinucleotide repeats and IQ can be confirmed or not. For the GLCL GAG-repeat status ethnic differences of allele frequencies are known.

As I see, new publications and reviews on the relationship between glutathione status and brain function are not aware of some older publications. In the appendix „Memory as a Macroscopic Ordered State by Entrainment and Resonance in Energy Pathways”, pp. 201-221, of the monograph “Psychogenetik der Intelligenz”. Dortmund. Verlag Modernes Lernen 1986, I wrote on p. 210ff:

“It would defy the most fundamental laws of thermodynamics, when individual differences in brain power would not find their counterpart in individual differences of brain energy metabolism. … Reactions involving S-S or S-H groups of proteins may readily account for the apparently opposite effects of the same control mechanism.  … . At this point we direct attention to the correlation (.58) between IQ and glutathione peroxidase (GSHPx, now GPX) activity (SINET et. 1979) … In modulating the GSH/GSSG ratio, GSHPx not only contributes to the regulation of glycolysis (GILBERT 1984) but consequently also the adenylate energy charge (REHNCRONA et al. 1980) and the NADP/NADPH ratio (GRIMM 1978) are prefectly correlated (r = 1.00!) with glutathione status. Thus the fundamental chemical needs of a living cell, high-energy phosphate stores (ATP) and reducing power (NADPH) depend upon the cortical concentration of glutathione, and the dynamic behavior of a complex system can be reduced to the molecular properties of a master enzyme in an energy pathway.”

The combination of autozygosity mapping and microarray RNA expression analysis has led to the discovery of new genetic polymorphisms underlying nonsyndromic mental retardation with autosomal-recessive inheritance, see Medical News Today and Cell.  

Conclusion

We can be convinced that the application of similar methods to consanguineous families with several members in the high IQ range will lead to the discovery of gene polymorphisms underlying variability of IQ in the upper and normal range of the distribution.  Sites where miRNA are coded or binding and those are especially regions with trinucleotid repeats in the UTRs as in the case of GCLC should be investigated as soon as possible. Until now, all known cases of a causal relationship between copy number variation of trinucleotid repeats and disease have been neurodegenerative diseases and are associated with different degrees of  mental retardation . Therefore the idea, that also the hitherto unknown genetic variation underlying the normal range of IQ could have similar causes (see Tam et al,  Anthony et al, and Barbato et al) , seems not be far fetched.

On the drive to work today I listened to an interview on CSPAN's Washington Journal with a doctor based in Texas and actor Dennis Quaid.  Nearly a year ago, Quaid and his wife Kimberly were in the room when their newborn twins were given a dose of heparin that was 1,000 times the appropriate dose.  At 1:00 today Quaid and the doctor were to speak here in Washington at the National Press Club, in order to call attention to the release of a 500-page report on accumulated best practices in the avoidance of catastrophes.  A few themes that should be very familiar to HRO researchers:

1. It's not bad people, it's bad systems.  Quaid and the doctor were very good at praising performers within the systems and emphasizing that the 98,000 deaths per year identified by the Institute on Medical Organizations report from 1999 were a product of flawed systems, not evil people.
2. There are cross-industry lessons to be learned.  Quaid and the doctor referred several times to the fact that their friendship and their work was accelerated by the fact that they are both pilots.  They called for a National Transportation Safety Board for medicine. They noted that the nurses' "Five Rights" -- right patient, right prescription, right dosage, right time, and right method -- was a low-cost and helpful checklist that can reduce errors.  I kept waiting for them to recognize Chris Hart's "near-miss" data set as one of the things that could be transferred between industry contexts, but didn't hear that mentioned.
3. Awareness is important. They talked frequently about how little people care about medical errors until it affects them directly, and Quaid's twins' experience -- and his celebrity -- put "wind in the sails" of the project.  I suppose that Katie Couric will be talking about Quaid's project in a couple of hours on the evening news, and USA Today might have an article on the event tomorrow morning -- and it's a little sad that the American public has the attention span of a baby monkey -- but perhaps we can learn to leverage celebrity in the service of high-reliability better than we have in the past.

If I ever get an intern to help me with this blog, this would be a good place to put a link to the CSPAN video on Washington Journal on April 12, 2010, this would be a good place to put a link to the National Press Club event on April 12, 2010; and this would be a good place to put a link to media coverage of the event.  Quick core dump on HRO and medical error:

1. Kathie Sutcliffe co-edited a book with the title Medical Error several years' ago.
2. George Washington University doctoral student Kip Rollins is finishing a strong dissertation on team-based cardio surgical teams and the structuring actitivities that take place in them.
3. I'm a huge fan, recently, of a Katherine Klein et al. article in Administrative Science Quarterly on Trauma Resuscitation Units and the process of "dynamic delegation." 
4. And Amy Edmondson's research on cardio surgical teams learning to collaborate even more tightly than before due to a new surgical procedure is very impressive at driving home the importance of "psychological safety" in team cultures.
5. Finally, for now, Jenny Rudolph's dissertation data on anaesthesiology residents' leadership of teams in response to a complex 25-minute simulation convinces me that individuals do not have the cognitive bandwidth to solve wickedly complex problems, and teams can be built to be smart enough to accomplish those tasks.

Please feel free to leave a comment if you know the diagnosis.

On June 23-24, 2010, an international conference with the title ‘Ecosystems, Organisms, Innovations – 12’  will take place in Moscow, Russian Federation. The conference is hosted by Moscow State University together with several other national and international organizations and institutions, including the Moscow Chapter of Eco-Ethics International Union, Environmental Leadership Institution, and others. An excerpt from the conference website:

“What is unique about the conference and make it an attractive option to submit your work:

• the registration/publication fee is very reasonable;
• a distant participation is possible, no need to attend in person;
• the proceedings are published as a series that is included  in the international Ulrich’s databases of reviewed serial editions; the reference to the proceedings has a format of a reviewed journal;
• the event is widely covered by mass media…"

This is the 12th of the series of International Poster Session Conferences started in 1999.  Abstracts of the conferences are published.

SCIENCE DISCIPLINES: Biological Sciences, Environmental Sciences, Earth Sciences, Geography Science, Chemical Science, Agricultural Science, Biotechnology, Education, Other.

ORGANIZERS: Independent organizing committee, including scientists and representatives of Moscow State University, Russian Academy of Sciences (RAS), Hydrobiological Society (associated with RAS), SIL, EcoEthics International Union (EEIU), and other national and international scientific organizations; the permanent organizing committee started in 1999, and organized 11 conferences of this series.

DEADLINES: May 11, 2010 for  registration fees; May 20 (17:00 Moscow time), 2010  for the abstracts (by e-mail),  June 2 for posters (by paper mail). We also accept the materials and the fee after the deadline, but in that case the registration fee increases for all categories of participants. Sending preliminary information on your intention to submit an abstract/poster is strongly encouraged.

DETAILS: No personal attendance is needed. The posters sent by mail will be displayed/exhibited by organizers on behalf of the authors. Non-attendees can receive some feedback from other participants by e-mail. The best posters presented by students (including those sent by mail) will receive honorary diplomas.

PUBLICATION OF PROCEEDINGS: in the next volume  (No. 16) of the serial ‘Ecological Studies, Hazards, Solutions’, which is included in the authoritative international Ulrich’s databases of reviewed serial editions; the reference to your work will have the format: J. Smith. Discovery of a new phenomenon in biology and environmental science. -  Ecological Studies, Hazards, Solutions, 2010, vol. 16, p. 21.

COVERAGE OF THE CONFERENCE BY MASS MEDIA. The conference is regularly covered by several editions, including journals and newspapers. Some examples.

Also, we invite nominations for candidates to receive the honorary titles of Aquatic Ecologist of the Year and Ecologist of the Year, with your rationale for your nomination. The process of nomination and selection of the finalists will be finished at the conference.

More information is available here. 

Robert M.Wald in The Arrow of Time and the Initial Conditions of the Universe (Enrico Fermi Institute and Department of Physics University of Chicago, arXiv:gr-qc/050709 vl 21 Jul 2005) writes:

“There is no question that our present universe displays a thermodynamic arrow of time: We all have observed phenomena in our everyday lives where entropy is seen to increase significantly, but no one has ever reliably reported an observation of entropy decrease in a macroscopic system.”

We can have a different approach. After the Big Bang all visible matter undergoes temperature decrease and its entropy is changing due to dS=dQ/T=mcdT/T, where m - mass, c - the heat capacity. After integrating we get the entropy change  ΔS=mc lnT/T0, where T0 – the temperature at which all molecules of matter have zero kinetic energy.

Besides we have step-by-step entropy decreases due to phase changes: radiation – atoms – molecules – gas – liquid – solid.

Some say that after the heat deaf the entropy of the Universe is maximal. It depends on approach, depends on POV, or on distribution we look at. At heat deaf the atoms and molecules are maintained, so is the information originated at their formation. Robert Ayres in his book “Information, Entropy and Progress”  names it the ‘morphological information’.

The Second Law was formulated by observations on Earth: by all physical processes where labor or heat is exchanged entropy increases. For example, Earth radiates the heat dQ into the environment. Earth’s entropy change dS=–dQ/300 (when heat is received, it is designated by +dQ, when heat is given away, it is designated by –dQ), environment receives the radiated heat, its entropy changes dS= +dQ/2,7. The system’s ‘Earth-environment’ total entropy changes dS =dQ/2,7–dQ/300 is positive.

What is ‘the environment’? Vacuum + photons (I don’t discuss dark matter). On a cosmic scale all the photons emitted by stars get redshifted due to expansion of the Universe. Does their entropy get decreased too?

It seems that we are not forced always to say that there is a global increase of entropy due to the Second Law. It seems that we can reliably report “an observation of entropy decrease in a macroscopic system.”   

Several studies have found that people living with the human immunodeficiency virus (HIV) suffer from posttraumatic stress disorder (PTSD) at a higher rate than that of the general population (Gore-Felton et al., 2001; Kimerling et al., 1999; Martinez et al., 2002; Mellins, Ehrardt, & Grant, 1997).  In addition, people are living longer with the disease as a result of medical treatment advances, and a fast-growing population of individuals infected with HIV is coping with complex psychosocial demands of this life-threatening illness.  I will review the research that currently exists with regard to HIV and PTSD.  Further, it is important to determine to what extent psychological treatment should be integrated with the medical treatment of people living with HIV and AIDS.  My aim is to evaluate the recent developments in the field regarding PTSD as a viable psychological diagnosis for individuals living with HIV.  

Also, I discuss the accumulating literature addressing the importance of assessment and treatment of PTSD in patients recently diagnosed with HIV, and the push for this becoming standard practice in primary care settings.  Another aim is to consider whether patients for whom the HIV diagnosis is the primary or sole traumatic event differ from patients who have experienced a significant number of traumatic events prior to HIV diagnosis.

Posttraumatic Stress Disorder

In the Diagnostic and Statistical Manual of Mental Disorders, 4th edition, text revision (DSM-IV-TR; American Psychiatric Association, 2000a), the defining characteristic of a traumatic stressor is presence of a life-threat or threat to one’s physical integrity where the individual’s response is great fear, horror or helplessness.  Traumatic stressors are generally thought of as involvement or proximity to war combat, witnessing or being subjected to violent acts, torture, and natural or man-made disaster.  Individuals may have intrusive thoughts about these past experiences, or avoidant/numbing reactions to them.  While this may be true of receiving a diagnosis for a life-threatening medical illness or disease, additional circumstances specific to living with the medical condition warrant consideration as contributing to continued trauma.

The biological aspects of trauma were explored as well as the psychological effects of traumatic stressors.  For example, the use of functional magnetic resonance imaging (fMRI) and positron emission tomography (PET) has led to evidence of alteration in brain neurocircuitry in response to trauma.  Specifically, patients with PTSD show greater activation of the amygdala and insula and lesser activation in the anterior cingulate cortex (ACC) and ventromedial prefrontal cortex (Friedman & Pitman, 2007; Shin et al., 2007).  Chronically applied stress can inhibit development of hippocampal neurons, cause certain neurons of the hippocampus to atrophy, and elevate cortisol levels.  These effects of stress could have detrimental effects on the optimal functioning of the immune system (Sapolsky, 2004).

Posttraumatic Stress Disorder and Medical Illness as Trauma

There are a number of research studies examining coexistence of PTSD and life-threatening medical illnesses and diagnoses.  The subject of medical events as traumatic stressors has gained considerable interest, and is becoming a focus of research.  Medical diagnoses and events surrounding medical illness have been found to result in extreme fear, helplessness, or horror (Baum & Mundy, 2004).  In fact, in the Diagnostic and Statistical Manual, 4th edition (DSM-IV; American Psychiatric Association, 1995), it was recognized that PTSD may be precipitated by life-threatening medical illness or diagnosis.

Much research on PTSD in the medical population began with adult cancer patients, noting incidence of cancer-related PTSD ranging from 0% to 32%. A cancer diagnosis and treatment effects may also produce trauma and stress, although rates of distress in this population are low and patients seem to cope effectively overall.  Nonetheless, traumatic stress syndrome has been observed (Kangas, Henry, & Bryant, 2002).  Research on PTSD following medical diagnosis and treatment were reviewed in the areas of cardiac medicine, vascular medicine, obstetrics, gynecology, and HIV.  Studies also included patient awareness under anesthesia and the experience of intensive care treatment.  The purpose of reviewing the literature was to determine whether the experience of severe physical illness, an event internal to the individual, satisfied the traumatic stress criterion for PTSD (Tedstone & Tarrier, 2003).  As research on psychological trauma continues, issues surrounding the differences between medical stressors and more traditional sources of trauma are being highlighted.  There is advocacy and disagreement on the application of PTSD to those diagnosed with medical disease or illness (Mundy & Baum, 2004).

Experiencing a subjective sense of life-threat as a result of some event is vital for the development of PTSD.  Medical diagnoses and events, including myocardial infarction, a cancer diagnosis and the severe effects of treatment, and HIV with its chronic course, have been found to result in extreme fear, helplessness, or horror.  The intrusions and re-experiencing symptoms that occur as part of posttraumatic stress experienced by those receiving life-threatening medical diagnoses, however, may be of a different type than those experienced by individuals exposed to traditional traumas (Mundy & Baum, 2004).

Tedstone and Tarrier (2003) examined the occurrence of PTSD in adults with medical conditions by identifying studies from a search of relevant articles in the Medline and PsychINFO databases between 1985 to 2003.  It was concluded that PTSD prevalence rates were highest in patients who had been in a life-threatening medical situation or received the diagnosis of a terminal illness in comparison to the general population.  One possible explanation of this is knowledge about disease recurrence and progression can produce greater PTSD symptoms compared to the initial diagnosis, if the degree of life threat is perceived as more intense.

Posttraumatic Stress Disorder and HIV Disease

Understanding PTSD in people living with HIV or AIDS is necessary, as mental health impacts overall HIV treatment, health-related behaviors, and quality of life.  Given the uncertainty and disruption in every area of life for individuals living with HIV, anxiety and PTSD is not a surprising facet of life with HIV/AIDS.  Some research exists on anxiety disorders resulting from HIV infection, and coping mechanisms or self-management strategies by those living with HIV.  Phillips and Morrow (1998) emphasized that anxiety is a universal problem for patients with HIV/AIDS because the disease creates uncertainty and disruption in every aspect of patients’ lives.  Although many anxiety-proving factors are similar across groups, it may vary by degree and type for some.  In other words, gay men, women and children may experience anxiety-provoking factors specific to them.  The growing body of research suggests that rates of probable anxiety disorders are roughly two to three times higher in persons with HIV/AIDS as compared to the general population (Kaplan et al., 1997; Perretta et al., 1996).

While prevalence rates of PTSD in HIV/AIDS have ranged from 30% to 64% (Botha, 1996; Kelly et al., 1998; Martinez et al., 2002), studying the nature of this relationship and assessing the impact of the HIV/AIDS diagnosis on mental health has been problematic.  PTSD may be particularly relevant to HIV/AIDS due to the traumatic impact of being infected (Kelly et al., 1998), which consists of various “crisis points” such as learning one’s seropositive status, receiving the diagnosis of AIDS, beginning new treatment, discontinuing treatment, appearance of new symptoms, recurrence and relapse and terminal illness (Flaskerud, 1995).

The future-oriented aspect of HIV disease requires those patients to confront and re-experience the trauma over and over again with each doctor’s visit, blood draw, discussion or disclosure of the condition, changes in drug treatment, anticipated treatment failure, and disease stage.  Mundy and Baum noted that in addition to flashbacks or intrusive thoughts of receiving the initial diagnosis, re-experiencing occurs in thoughts about future-oriented events and may cause significant distress.  (e.g., Will I live to watch my child graduate or get married?  Will I have excruciating pain once the disease takes me?  Will my family be cared for after I am gone?)  Thus, the focus of threat to life is not only based on a past event for medical patients but also on the future.  Of course, the question arises – if these events are future-oriented, is this still PTSD?

The Current Issues

Olley, Zeier, Seedat, and Stein (2005) conducted exploratory research to examine the prevalence of and factors associated with posttraumatic stress disorder in 149 recently diagnosed HIV/AIDS patients in South Africa (mean time since diagnosis = 5.8 months,SD = 4.1).  Multivariate analysis was used to investigate the discriminating factors for a positive history of PTSD.  Independent variables were derived from sociodemographic characteristics, medical status and disability, stressful life events and social support, coping styles and risky sexual behaviors.  Researchers used the MINI International Neuropsychiatric Interview (MINI; Sheehan et al., 1998), a 42-item clinician-administered checklist measuring stressful life events and degree of impact during brief structured diagnostic interviews for major psychiatric disorders.

The findings of the study indicate that 22 patients (14.8%) met criteria for current PTSD.  In eight patients, the index trauma was knowledge of the diagnosis of HIV/AIDS.  The study concluded that those patients with HIV-related PTSD did not differ significantly from other patients with non-HIV related PTSD on demographic or clinical features.  Similar to the findings of Hutton and colleagues (2001), results suggest that “many features of PTSD in HIV/AIDS are similar to those reported in PTSD patients in general” (Olley et. al, 2005). 

The HIV/PTSD+ patients’ mean time since diagnosis (6.2 months, SD = 4.6) suggests that while trauma resulting from the initial HIV diagnosis was assessed, little else regarding the experience of living with HIV was explored.  Given the progressive nature of HIV/AIDS, there are various “crisis points” (Flaskerud, 1995) associated with PTSD symptoms.  Olley et al. concluded that for eight HIV/PTSD+ patients, the HIV diagnosis was the single most traumatic time point, but did not evaluate whether any PTSD symptoms such as intrusions were future oriented.  When determining what is measured as the criterion, observational research and qualitative analyses of intrusive thoughts experienced by patients, in addition to categorizing those experiences as being future or past event oriented, are critical to the overall understanding of medical disorders as a cause of psychological trauma (Mundy & Baum, 2004).  In the sample as a whole, Olley et al. reported that the majority of the participants were asymptomatic, but none were receiving antiretroviral drug treatment for the HIV despite a mean CD4 count of 397.0 (SD = 294.9).  Additionally, there is no discussion about the stage of disease progression for any of the participants at the time of initial diagnosis other than CD4 counts.  Even years later, a diagnosis with a life-threatening disease such as HIV can result in significant PTSD symptomatology (Delahanty, Bogart & Figler, 2004).

The research concedes that the relationship between HIV/AIDS and PTSD remains unclear.  Also, prior traumatic events in the HIV patient population impact the severity of PTSD.  Nonetheless, PTSD patients reported significantly more work impairment and poor coping skills, such as the abuse of substances (Olley et al., 2005).  This research adds to the growing body of knowledge about the HIV population being burdened with significant stressors surrounding their medical condition.

Safren, Gershuny and Hendriksen (2003) examined the frequency and correlates of self-reported symptoms of posttraumatic stress among patients with HIV and self-reported medication adherence problems.  The sample consisted of 59 men and 16 women with HIV infection, the majority being white or African American, who were using the services of a community health center serving primarily lesbian, gay, bisexual, and transgendered individuals.  98% of the men in the sample indicated their sexual orientation (29% heterosexual, 7% bisexual, 64% gay) as did 94% of the women (80% heterosexual, 13% bisexual, 7% lesbian).  Safren and colleagues used the Posttraumatic Diagnostic Scale (PDS) and substituted “the trauma” in the original measure with “being diagnosed with/having HIV.”

Safren and colleagues found that more than half (n = 48/75 = 64%) of the sample met criteria for a diagnosis of PTSD related to the diagnosis of and living with HIV.  Using a series of multiple regression analyses, the researchers found that death anxiety was uniquely associated with total PTSD severity scores, contributing unique variance over and above the other predictor variables of depression and satisfaction with social support.  They also concluded that comprehensive psychosocial screening as a part of the medical care of patients with HIV is needed, especially because many individuals with HIV are disenfranchised in some way before their diagnosis.

The use of self-report instruments, a narrow sample of patients with HIV, and the missing assessment of additional traumatic events in addition to the HIV diagnosis were considered limitations to the study.  Safren and colleagues suggested further research that examines whether patients with HIV reporting PTSD related to the diagnosis have additional traumatic stressors prior the HIV diagnosis, and if diagnosis constitutes a “retraumatizing experience.”

There is growing debate about PTSD being the appropriate model to represent the psychological distress experienced by those diagnosed with medical conditions such as HIV.  Some urge that a new diagnosis may need to be formulated surrounding medical life-threatening illness and disease (Kagee, 2008; Mundy & Baum, 2004).  In a recent article published in the Journal of Health Psychology, Kagee (2008) questioned the appropriateness of a PTSD diagnosis for people living with HIV and AIDS.  He argued that “neither the experience of being HIV positive nor living with AIDS is traumatic in DSM-IV-TR sense” (p.1010).  Patients with HIV have an abundance of future-oriented concerns, but the “anchoring event” for PTSD must be the “receipt of notification” of one’s HIV status in order for there to be a PTSD diagnosis (p.1009).  Kagee argues that the anxiety, fear of physical decline and death because of having HIV does not qualify as a valid PTSD symptom.  Essentially, for there to be a valid PTSD diagnosis, one must suffer recurrent and intrusive recollections, dreams, or physiological reactivity from cues about the informer, and being informed of (e.g., place, time, etc.) the HIV positive status.

In response to Kagee's assertion that medical diagnoses do not fit well with criterion A1, it is important to make clear that the DSM-IV-TR states “a threat to the physical integrityof self or others” (emphasis added) and that there is no reference to time and place.  Not only does the individual experience the ambit of receiving a diagnosis of HIV for which no cure is available, but also, having HIV can be considered a threat to the individual’s physical integrity where fear and helplessness are common reactions to the initial diagnosis and ongoing treatment with aggressive antiretroviral medications.  Kagee (2008) argued that conceptualizing an HIV+ patient’s psychological status in terms of PTSD nosology is likely inaccurate.  However, it is important for the psychologist or future researcher to carefully define the construct being measured.  Advocacy of current conceptual and methodological approaches to PTSD and stressful medical conditions is beneficial to the research community despite differences that may be seen in the medical population and the traditional population being assessed for PTSD (Mundy & Baum, 2004).

Is PTSD an Appropriate Diagnosis for People with HIV?

It is an assumption that the assessment of psychopathology in patients diagnosed with HIV or AIDS is paramount to their overall treatment plan.  However, questions have arisen regarding the appropriateness of PTSD as a mental health diagnosis given the specific nature of medical disease or illness.  Is generalized anxiety disorder more appropriate, or should an anxiety disorder more specific to this population be considered in the publication of the DSM-V.

What important differences exist between “knowledge of the HIV diagnosis” and “initial notification of the HIV diagnosis?”  "Knowledge of" is an ongoing state, yet trauma was defined in this way by the Olley et al. study.  Similarly, trauma was defined as “being diagnosed with HIV” and “having HIV” in the Safren et al. study.  Yet, others would argue that a much narrower definition of the trauma is required.  For example, there must be intrusive recollections of the health care worker who informed the patient about the diagnosis, and the experience of being informed. Yet, do all of these concepts of trauma surrounding HIV have similar impacts on people with HIV?

Relatively little is known about the course of symptoms over time following trauma exposure (Orcutt, Erickson & Wolfe, 2005; Perkonigg, Pfister, Stein, Hofler, Lieb, Maercker, & Wittchen, 2005).  There is general agreement that a growing number of studies are demonstrating HIV diagnosis as a traumatic stressor often leading to PTSD.  Also, people living with HIV tend to present with a significant number of traumatic events prior to HIV diagnosis.  Does this then require an alteration in the approach to psychological and possibly medical treatment?  Indeed, not all persons experiencing traumatic medical events get PTSD.  However, help with effective coping tools and with the psychological distress that ensues following an HIV or AIDS diagnosis is instrumental.  Medical and mental health professionals must recognize and intervene as necessary to help patients cope with stigma surrounding HIV disease and the disenfranchisement that tends to plague people with HIV.  Better HIV treatment adherence and outcomes correlate with primary care physicians screening patients for PTSD, anxiety and depression.  (Olley et al., 2005; Safren et al., 2003; Phillips & Morrow, 1998; Delahanty, Bogart & Figler, 2004).  Yet, the literature suggests that medical patients are rarely screened routinely for PTSD (Tedstone & Tarrier, 2003; Olley et al.).

Conclusions

One must wonder whether it is important at all to determine whether the PTSD symptoms arise from the HIV diagnosis, or if simply knowing that a patient with HIV also suffers with PTSD, regardless of the traumatic event(s), is enough so long as some treatment is sought.  It seems that non-HIV-related PTSD has a similar effect on biology and psychosocial functioning of the individual as does HIV-related PTSD.  However, for patients without prior history of PTSD or trauma, it is important to know whether a diagnosis of HIV can cause PTSD.  Having the best model for exploring the effects of a life-threatening diagnosis or terminal illness is paramount to moving forward with best treatment practices.

Based on a review of all of the research articles discussed, an accurate definition of the construct “trauma” is required to correctly determine the impact of HIV on mental health aside from other traumatic events.  Whether the PTSD model can accommodate the differences that exist with medical traumas (e.g., future-oriented events) is a worthy topic for further exploration.  It is true that there is the single anchoring event, as referred to by some researchers.  However, these future-oriented events can retraumatize some patients, returning them to the experience of being initially diagnosed with HIV.  How should those individuals be best treated in their mental health care to ensure successful medical treatment?  How does an individual’s appraisal of stress and coping mechanisms hinder or complement HIV medical treatment?  Further research could explore these issues, as well as whether this population differs significantly from patients with prior traumas, thus warranting a different mental health treatment approach.

Some gaps in the research are noted.  There is a tremendous need for further research into this area with the Latino and Asian population.  Also, given the fact that women have unique stressors and suffer from PTSD at a disproportionately higher rate, more research on women with HIV is needed.  Other suggestions for research include outcome studies of medical settings serving individuals being diagnosed with and treated for HIV disease.  Research should assess the differences in a patient’s overall treatment success in medical settings where ongoing mental health treatment is integrated compared to those medical settings without a mental health component.

References

• American Psychiatric Association. (1995). Diagnostic and statistical manual of mental disorders. (4th ed.).     Washington, D.C.: Author.
• Baum, A. & Mundy, E. (2004). Medical disorders as a cause of psychological trauma and posttraumatic stress disorder. Current Opinion in Psychiatry, 17, 123-128.
• Delahanty, D. L., Bogart, L. M., & Figler, J. L. (2004). Posttraumatic stress disorder symptoms, salivary cortisol, medication adherence, and CD4 levels in HIV-positive individuals. AIDS Care, 16, 247-260.
• Flaskerud, J. H. (1995). Psychosocial and psychiatric aspects. In J. H. Flaskerud & P. J. Ungvarski (Eds.), HIV/AIDS: A guide to nursing care (3rd ed.). Philadelphia, PA: Saunders.
• Friedman, M. J., & Pitman, R. K., (2007). New findings on the neurobiology of posttraumatic stress disorder. Journal of Traumatic Stress, 20, 653-655.
• Gore-Felton, C., Koopman, C., & Spiegel, D. (2001). The influence of traumatic stress responses in HIV risk behavior. Presentation from the 22nd Annual Scientific Conference of the Society of Behavioral Medicine, Seattle, Washington.
• Hutton, H. E., Treisman, G. J., Hunt, W. R., Fishman, M., Kendig, N., Swetz, A., & Lyketsos, C.G. (2001). HIV risk behaviors and their relationship to post-traumatic stress disorder among women prisoners. Psychiatric Services, 52, 508-513.
• Kagee, A. (2008). Application of the DSM-IV criteria to the experience of living with AIDS: some concerns. Journal of Health Psychology. 13, 1008-1011.
• Kangas, M., Henry, J., & Bryant, R. (2002). Posttraumatic stress disorder following cancer: A conceptual and empirical review. Clinical Psychology Review, 22, 499-524.
• Kimerling, R., Calhoun, K. S., Forehand, R., Armistead, L., Morse, E., Morse, P., Clark, R., & Clark, L. (1999). Traumatic stress in HIV-infected women. AIDS Education and Prevention, 11, 321-330.
• Martinez, A., Israelski, D., Walker, C., & Koopman, C. (2002). Posttraumatic stress disorder in women attending human immunodeficiency virus outpatient clinics. AIDS Patient Care and STDs, 16, 283-291.
• Mellins, C. A., Ehrardt, A. A., & Grant, W. F. (1997). Psychiatric symptomatology and psychological functioning in HIV-infected mothers. AIDS Behavior, 1, 233-245.
• Olley, B. O., Zeier, M. D., Seedat, S., & Stein, D. J. (2005). Post-traumatic stress disorder among recently diagnosed patients with HIV/AIDS in South Africa. AIDS Care, 17, 550-557.
• Orcutt, H., Erickson, D. J., & Wolfe, J. (2005). The course of PTSD symptoms among Gulf War veterans: A growth mixture modeling approach. Journal of Traumatic Stress.17, 195-202.
• Perkonigg, A., Pfister, H., Stein, M., Hofler, M., Lieb, R., Maercker, A., & Wittchen, H. (2005). Longitudinal course of posttraumatic stress disorder and posttraumatic stress disorder symptoms in a community sample of adolescents and young adults. Am J Psychiatry, 162, 1320-1327.
• Phillips, K. D., & Morrow, J. H. (1998). Nursing management of anxiety in HIV infection. Issues in Mental Health Nursing, 19, 375-397.
• Sapolsky, R. M. (2004). Why zebras don’t get ulcers: The acclaimed guide to stress, stress-related diseases, and coping. New York: Henry Holt and Company.
• Shin, L. M., Bush, G., Whalen, P. J., Handwerger, K., Cannistraro, P. A., Wright, C. I., et al. (2007). Dorsal anterior cingulated function in posttraumatic stress disorder. Journal of Traumatic Stress, 20, 701-712.
• Tedstone, J., & Tarrier, N. (2003). Posttraumatic stress disorder following medical illness and treatment. Clinical Psychology Review, 23, 409-448.

An inert foreign body placed in the subcutaneous tissue induces new tissue that encapsulates the foreign body (called granulation tissue). In a new study published in the journal Translational Research, Dr. Jilpa Patel and her group at the Cook County Hospital and Hektoen Institute of Medicine in Chicago have isolated and characterized adult stem cells from granulation tissue in rats.

These stem cells called granulation-tissue stem cells (GTSC) can be multiplied infinitely outside the body, and are rich in growth and other stem cell factors. GTSC readily differentiated to bone, cartilage and fat cells when cultured in specialized media, an important property of multi-potent stem cells. When injected into the body with an injured organ, GTSC recognized and engrafted only to the injured organ and not to normal organs. It was possible to freeze GTSC for long-term storage without loss of potency. Because GTSC can be easily obtained from the patient’s own body and can be stored long-term, it can serve as an excellent source of stem cells for use in repair of damaged organs.

Stem cells are by and large categorized as either

• a) embryonic stem cells, that are obtained from the inner cell mass of an embryo or
• b) adult stem cells, those that are derived from adult tissues.

The use of embryonic stem cells is controversial as it is hampered by ethical, political and safety concerns. In contrast, the use of adult tissue derived stem cells (bone marrow cells being the commonest of adult stem cells) is free of such concerns and therefore of immediate utility.  Adult stem cells have been obtained from many tissue including bone marrow, adipose tissue, skin, hair, dental pulp, and omentum. Because granulation tissue derived stem cells described by Dr. Jilpa Patel in this study are obtained from a rapidly regenerating granulation tissue, they are activated stem cells, and therefore they could prove to be more potent than other adult tissue-derived stem cells.  Presently, the authors are conducting further studies to assess the utility of GTSC in kidney disease, liver disease and osteoarthritis.

This article is based on the manuscript ‘Foreign body-induced granulation tissue is a source of adult stem cells’ published in the journal Translational Research. (Citation: doi: 10.1016/j.trsl.2009.08.010)

While there are more and more entries published in the MasterBlog, ResearchGATE was featured in the New York Times. An excerpt from the report in which founder Dr. Ijad Madisch describes how ResearchGATE was launched:

"...Enter ResearchGATE, which its founder Dr. Ijad Madisch (pictured) fairly describes as “Facebook for scientists.” In close to two years of operation, ResearchGate has built a social network of more than 250,000 researchers from 196 countries. Over 1,000 subgroups have been formed for specific disciplines, and 60,000 research documents have been uploaded for sharing with others on the site. These guys aren’t pretending they’re farmers.

“People ask a question, presenting an issue they have in the lab, and anyone can answer the question. This is happening on a daily basis,” said Madisch, who was in Silicon Valley this week drumming up support for ResearchGATE from researchers at universities and private research labs, while also networking with potential investors, although he added the company is currently “well funded.”

Introduction

Genetic algorithm is an artificial intelligence (AI) algorithm used to solve problems that can't be solved with a mathematic formula.

It is inspired by the theory of evolution which uses genes and chromosomes to evolve. The generations that evolve are your solutions to the problem. To understand how this algorithm works, it is good if you have some knowledge about evolution and DNA and how the 'mom' and 'dad' pass their DNA to their children.

Values

Genes: A string of binary numbers (0 and 1).
Chromosomes: A group of genes.
Population/Generation: A group of chromosomes.

To setup your values, you must first look at your problem and find what are the values required. Let's take a simple example, we want to find what equation gives us the number 30. What we need here are numbers and operators and let's say we want to have an equation with 3 numbers in it. We would setup our genes like this (note that you can give them the value you want):

0000 = 0
0001 = 1
0010 = 2
0011 = 3
0100 = 4
0101 = 5
0110 = 6
0111 = 7
1000 = 8
1001 = 9
1010 = +
1011 = -
1100 = *
1101 = /

These are our genes. To generate a chromosome, we need to choose random genes and put them together. When you generate a chromosome, you can make it completely random which could give something like "1+-+3" or make it generate valid equation from the beginning like "1+2+3". Now, we need 5 genes (3 numbers + 2 operators), so we would have a chromosome like:

00111100011110101001 <- which is 3 * 7 + 9

You can see the genes as values in the DNA, every pair of bits have their own value. We generate a population using the same function. The population can have as many chromosomes as you want. In this example, you can generate 100 chromosomes, it would be enough. To save your chromosomes you can create a string and consider every 0 and 1 as a character, or save it in an array of short (8 bits) /int (32 bits depending on your OS) which will take less memory.

Analysis

Once you have your generation, loop through every generated chromosomes and see if one of them gives you the solution you seek (in this case, 30). For every chromosome, set a fitness score which is a value that specifies how far the chromosome is to the solution. An example of a fitness score for our problem would be:

01011010011110110111 <- we will calculate the fitness score of this chromosome, which is 5 + 7 - 7
5 + 7 - 7 = 5
1/(30-5) = 0.04 <- this is the fitness score of our chromosome, in our case, the closer it is to 1, the closer it is to the solution.

If you don't find the solution, you need to generate a new generation by creating babies.

Generate New Population

There are many ways to generate a new population. We will use the one called 'Crossover Rate'. First you need to choose 2 chromosomes at random (this is where the fitness score comes handy, if you match 2 chromosomes that are near your solution, it increases the chance to find the solution) and generate a random number between 1 and the length of your chromosomes (in this case, 20). Take the 2 chromosomes and switch each parts:

1. 00111100 011110101001
2. 01011010 011110110111
---------------------------------
1. 00111100 011110110111
2. 01011010 011110101001

You can see here the random number was 8 and we switched every parts (before and after 8) and created 2 babies using their parents' DNA. Do the same until you made babies with all the chromosomes. You will now have a population of 200 chromosomes.

You can set a mutation rate for every gene, which should be at a very low level, such as 1%. If a gene mutates, you need to change it to a random gene, which can go better or worse.

Invalid Chromosomes

You can either keep them or kill them. I prefer to kill them as when they are invalid they become very useless, but you can make a function that fixes an invalid chromosome.

Conclusion

This is the very basic of the algorithm. Using this algo, you can solve many problems such as where can we fit the biggest circle in a given GUI or how many boxes can fit in a containers. It is an algo that you must program yourself to understand it well, so open your IDE and start coding!

My "favorite gene" is on human chromosome 3q27. It encodes a moderate-sized phosphorylated glycoprotein (yes!) which is secreted at a high rate from hepatocytes, into the bloodstream. The gene is called AHSG (in H. sapiens), Ahsg (mouse), or sometimes fetuin-A. The protein was discovered as the first fetal protein (yes!) in 1944 in Sweden, and published in Nature:

Pedersen, K.O. (1944). Fetuin, a New Globulin Isolated from Serum. Nature 154, 575.

We became interested in this gene in 1991 when we cloned the human cDNA using a homologous rat probe, and expressed the human ORF in insect cells. The cells produced a phosphorylated glycoprotein which strongly blunted the tyrosine kinase (TK) activity of the insulin-activated insulin receptor (IR). The glycoprotein does not bind to the insulin site on the IR, but to the extracellular portion of the beta subunit of the IR. It binds 5 times better to insulin-activated IR than to insulin-naive IR. We think it thus "picks out" the 1% of cell surface IR which are in functional complexes, and selects them for blunting. When blunted, the TK is down-regulated, and instead there is SER phosphorylation of IRS-1 and -2 which acts to confound insulin's sharp edge.

In 2002, we showed that a mouse null for both alleles of Ahsg was quite the opposite of type 2 diabetes: it was super-sensitive to insulin! and the mouse failed to gain weight on a prolonged high-fat (HF) diet:

Mathews, S.T., Singh, G.P., Ranalletta, M., Cintron, V.J., Qiang, X., Goustin, A.S., Jen, K.L., Charron, M.J., Jahnen-Dechent, W., and Grunberger, G. (2002). Improved insulin sensitivity and resistance to weight gain in mice null for the Ahsg gene. Diabetes 51, 2450-2458.

Many clinical groups have now looked at AHSG gene function, and corroborated our prediction that this gene helps to underly insulin resistance and obesity, including:

Lavebratt, C., Wahlqvist, S., Nordfors, L., Hoffstedt, J., and Arner, P. (2005). AHSG gene variant is associated with leanness among Swedish men. Hum Genet 117, 54-60.

On March 17-18, 2010, an international conference with the title Commons, Users, Service Providers - Internet (Self-) Regulation and Copyright will take place in Hannover. The conference is hosted by Prof Dr Axel Metzger (Leibniz Universität Hannover, Institute for Legal Informatics) together with Prof Dr Thomas Dreier (Karlsruhe Institute of Technology) and Prof Dr Gerald Spindler (Georg-August-Universität Göttingen). An excerpt from the conference website:

"Self-regulation of the internet has been controversial from the very beginning. Liberal voices have emphasized the positive effects of a truly global medium of unrestricted communication where new ways of collaboration amongst creators, users and providers may be implemented. For conservatives, the internet provides a biotope for all types of illegal activity including copyright ‘piracy’. However,state-driven regulation is hardly ever effective due to the decentralized architecture of the internet andthe territorially restricted sovereignty of states.

The conference highlights three different models of regulation for copyright issues; the self-regulation of free software and content communities, the de-regulation of ISP‘s liability and the strict regulation of personal and other privileged use by copyright limitations and exceptions."

Those three models will be discussed in three conference sessions, each with very well renommed speakers, including, for example, Prof Eben Moglen (Columbia University, New York City), who played a vital role in the process of drafting the General Public Licence (GPL) version 3.

More information is available at the conference website.

Recent research has shown that facilitation follows attention in the Cerebral Cortex.

In order to understand why this might be, it is important to recognize the fact that the 40 hertz signal noted in a recent article on anesthesia, and Facilitation might be connected. What the anesthetist discovered, was a link between the 40 hertz signal, and Long-term Implicit Memory.

One model of Cerebral Plasticity, suggests that the Facilitation effect, is just as much a trigger of cerebral plasticity, as LTP is a trigger of Hippocampal Plasticity. To understand how this might work, we need to look at the nature of the biochemical pathway that links synapses to the DNA, something that is well characterized for the hippocampal neurons and the NMDA ion channel.

The Facilitation effect, which reverses almost instantly cellular habituation, is triggered by the S synapse, which is a Calcium synapse that pumps calcium into the cell. The primary difference between this and the NMDA synapse, is the fact that the S synapse does not also, pump Potasium out of the cell, potentiating the cell.

What facilitation makes possible is strings of activation of the same cell. Habituation would attenuate the firing of the cell, as Calcium content dropped in the Axial Buds. This is thought to be because Calcium makes it practical for NeuroTransmitter Vessicles to bond to the Presynaptic surface so that they can secrete the NeuroTransmitter into the synaptic gap.

A shortage of calcium, due to a supply shortage, would therefore result in a gradual attenuation of the signal, as the same neuron fires multiple times. This effect called habituation will reverse as soon as a calcium supply hits the axion buds.

The Facilitative effect is therefore a result of an increase in supply of Calcium to the Axion.

However this is not all that is happening when the S synapse fires. The calcium reacts with other chemicals in the cell, causing the formation of a secondary messenger called cAMP The combination of increased calcium, and a supply of cAMP causes a number of chemical pathways to operate, which trigger eventually DNA expression, that triggers the growth of new Synaptic Spikes, and new Neural processes such as dendrites, and Axions.

The link between the 40 hertz signal and implicit memory probably happens because of activation of the S synpase.

The link to Attention however that is suggested by the new work linking Facilitation to Attention, probably lies in the direction of the 40 hertz signal during pre-activation of cortex areas by the Thalamus in the bottom-up attention system. 

Other blog entries written by Graeme Smith:

• Phosphorylation, the link between Bipolar and Schizophrenia
• A possible role for the anterior cingulate cortex in hypnosis

The open access "movement" has existed for decades, but with the coming of the digital age in the 90's it truly bloomed as the distribution cost of electronic media dropped to essentially nothing. Some groups completely embraced the paradigm-shifting potential of the internet; open-source software and piracy being the main examples which come to mind. And while individual scientific disciplines took advantage of the new, more efficient way of searching for and distributing journal articles, the science community as a whole has still not tapped in to the full potential offered by the near limitlessly connected world in which we now live.

I am personally a big fan of the concept of a truly open scientific community that shares findings and raw data via the internet in a melting-pot of consilience. I'm aware that such a vision is extremely naive, not least because of the strangle-hold the big journals currently hold on what is perceived as "proper publishing" and the financial motivators so often required to secure funding for good science. None the less, websites such as ReasearchGATE demonstrate the possibilities which can be unlocked by simply linking together people and ideas. And open access journals do exist and can be made to work. However what impact does making a research paper open access have?

A 2008 paper, "Open access publishing, article downloads, and citations: randomised controlled trial" (Davis et al) took a suitably scientific approach to this question by randomly assigning 247 articles published in 11 journals of the American Physiological Society to open access status between January and April 2007. The control group of 1372 articles was articles available via subscription, the traditional access model for the American Physiological Society’s journals for the first year of an articles life. The researchers looked at a number of related variables- the number of abstract and full article downloads, and the number of times a given article was cited in the year following its publication.

Unsurprisingly removing subscription restriction lead to a significant increase in full text downloads (89% higher for open access articles compared to subscription articles). Interestingly, however, despite the increased number of downloads this did not translate into an increased level of citation. While 59% of the open access articles were cited a year later, 63% of the subscription articles were cited. The authors concluded that open access to articles in fact reduced the chance of the article being cited (although not significantly) compared to subscription articles, and that "open access increases the readership of articles but has no effect on the number of citations in the first year after publication."

The main issues with these findings, however, is that the researchers made the articles open access at random, when in fact there is nothing random about the articles made available in the real world. Indeed a number of studies have shown that open access articles are consistently cited more often than subscription ones (an interesting look at the issue here), with the suggestion being that it is this very non-random nature of article availability which drives the perceived benefit of making a paper open access. In other words, there is self-selection bias in open access papers, in that only the "best" papers are made available this way, and hence they inevitably will be cited more. 

However a paper from the start of this year, "Self-Selected or Mandated, Open Access Increases Citation Impact for Higher Quality Research" (Gargouri et al, 2010) has questioned this very assumption, by comparing the impact of self-selective self-archiving (i.e. researchers choosing to make their articles freely available), with that of mandated open access (i.e. research institutions forcing their staff to make all research freely available as it is produced) for 27,197 articles published between 2002-2006 in 1,984 journals. As expected, when controlling for a number of other variables linked to citation, open access articles were cited significantly more than non-open access articles.

Most interesting however was the finding that it didn't matter whether the article had been chosen to be make open access, or was merely made available due to institution policy, the open access citation advantage was still found. The authors concluded that it is "highly unlikely that the OA advantage is either entirely or mostly the result of an author bias toward selectively self-archiving higher quality – hence higher citeability – articles." Higher quality articles were cited more, but this was independent of whether the author had chosen to make the article available themselves.

Making your research open access gets it cited more. Is there anything more a scientist could ask for? The dissemination of knowledge is one of the core tenets of science and should be, in my opinion, one of the core principles of any society. As an added bonus, with original research freely available online anyone making dodgy claims, such as poor media reporting, could be fact checked far more easily by members of the public. It's win-win in my eyes.

I have just completed my personal profile for membership of the proposed psychoneuroimmunology discussion group within ResearchGATE. This interdisciplinary science which emerged from the field of psychosomatic research, was founded by such pioneers as the late Professor George Solomon M.D. with whom I had the privelege of  working during the early 1980's as a member of the Biopsychosocial AIDS Project at the University of California, San Francisco, USA. Professors Solomon, Klaus Bahnson, George Engel and others, including myself had previously worked in the field now known as psycho-oncology and with other immunologically mediated and resisted disease, including autoimmune disorders and infections.

Engel (1977) had published a seminal paper titled "The need for a new medical model: a challenge for biomedicine" Science, 196, pages 129-36 as one of the figurative chorus of researchers who had perceived Kuhnian anomalies in biomedical research and hence the need for a paradigm shift in the scientific understanding of disease. The proposed paradigm shift implied multifactorial concepts of causality in which psychosocial and mental factors, including such unconscious variables as ego-defences and affects would be encompassed in the derivation of robust and useful scientific predictions of illness morbidity and mortality.

The biological mediators of the impact of psychosocial and mental factors would need to be included in research studies which would move the psychosomatic and psychoneuroimmunological fields beyond mere correlations without necessarily implying causality. In the HIV/AIDS field, the simultaneous analysis of psychosocial factors, biological mediators including neuroendocrine, cytokine and immune system variables and HIV progression still remains an important issue for future psychoneuroimmunological research. Perhaps partly because of funding priorities in HIV related research.

My recent paper "Unconscious Mental Factors in HIV Infection", published in the journal "Mind and Matter", Volume 6, Issue 2, (2009) explores the history of psychoneuroimmunology while suggesting a new paradigm of scientific understanding due to Kuhnian anomalies (such as multiple drug resistance and rapid mutation) with the traditional medical and Jenner/Pasteur models of infectious disease. The traditional medical model is neither multifactorial nor biopsychosocial in its understanding of the determinants of disease onset, morbidity and mortaity.

I would value comments.

Peter B. Todd 

In my memory model, the anterior cingulate cortex (ACC) is connected to many areas in the cerebral cortex, by a backbone network that seems to extend down both sides of the central fissure, as referenced in recent works on connectomics.

It's role, seems to be the selective suppression of processing in areas that are not of current interest to the brain. What this means, is that when the brain is idling, there is significant processing going on, but it is unselective, and chaotic in nature. Work such as David LaBerges Triangular Circuit theory of Attention, has suggested that it is the attention mechanism that limits processing and that therefore the ACC is an important part of the Attention system. As a proponent of Weak Attention, the idea that attention actually is used to guide information between processing centers to improve the signal to noise ratio, and the author of a Model, of memory that involves both bottom-up attention and Top-down attention at even the lowest levels of memory processing, I believe I understand a plausible mechanism for attention to direct processing in the implicit memory which lies at the bottom of the cerebral cortex circuits. If so the way that the ACC works, is likely to be in conjunction with other centers in the PFC, that direct it what clusters of inputs are best NOT to suppress, probably via some link to the Synchronous Activity in the cerebral cortex. Essentially, each process, is tagged with a different frequency, and the ventro-lateral PFC is thought to be sensitive to the frequencies, so that it can help the ACC decide which clusters are most likely to be useful, possibly in conjunction with the executive processes that are also thought to cluster in the PFC.

Recent MRI studies done on Hypnotism seem to suggest that the Idling processes of the brain are suppressed during Hypnotic states. This seems to suggest, that Hypnosis is a form of Attention, which involves significant activity in the ACC, (In order to suppress the natual idling processes) This should be visible if a comparative study, is done using an fMRI.

In my Memory Model, I have proposed a concept I call complicit attention, where the direction of processing in some centers of the brain, forms the equivalent of a processing command. I have also noted the utility of the cerebellum, for offering pseudo-sequences of these commands, in much the same way it produces pseudo-sequences of actions in Skill Memory. This being the basis of Automation and eventually what is sometimes called Intention, sub-conscious processing that is thought to determine what is consciously processed from 7 seconds before it is actually processed, to 500 milliseconds before it is processed depending on which model of sub-conscious processing you use.

What is important to realize is that this supports the idea that Consciousness is a control mechanism, rather than an executive function. What hypnosis seems to do is suppress the control mechanism of consciousness in order to replace it with default sub-conscious processing, during the trance.

The Idling processes are probably related to spontaneous attempts for the brain to make sense of ambiguities in the environment, and involves some conscious processing. The ACC is the location in the brain where ambiguities are isolated, so it makes sense that the ACC is controlling not only the data flowing into consciousness, but also the amount of conscious processing that occurs. If we train the ACC to shut down the speculative processing, it also throttles down consciousness, and with it the more abstract processes that act as barriers to suggestion. A clue that defenses against suggestion are in fact a form of abstract processing is suggested by the lateness in the development of the brain, to the susceptibility to hypnotism. It has been suggested that children before about 7 years of age, are not capable of supporting hypnotic trance states. This indicates to me that about the time of the development of an advanced theory of mind, people build defenses against suggestion.

Although there is still growth in the brain at this piont, I suggest that it is growth in the multi-modal Associative areas, that are the targets for my Complicit Attention, and as a result, the ACC can selectively suppress activity in these areas if the PFC is motivated to indicate it should. This might explain the apparrent conflict between the Hypnotic Communities statement that "You will not do anything that you do not want to" while under the influence, and the seemingly ethically questionable influence that the Mind Control sub-community of the hypnotic community has, in that it suggests that the YOU that decides is about as sophisticated as a 5 year old child, because it has suppressed the abstract defenses that are linked to Ethics and an advanced theory of mind.

The role of biodiversity in benefiting stability of ecosystems is a matter of  a hot dispute.The matter of stability  of ecosystems is very important as it is a part of stability of the biosphere at the time of hazards of global change.  Not much is known on whether biodiversity is instrumental for increasing stability of AQUATIC ecosystems. A research project was done that is filling the gap in knowledge on this controversial issue.

A paper was published that provides a fresh analysis and new vision of how biodiversity helps towards better stability of aquatic habitats, i.e. water quality.  To my mind, the paper mentioned below is a contribution to better understanding of the positive role of biodiversity in increasing stability of aquatic habitats and by doing so, to increasing the stability of aquatic ecosystem as a whole. I will be happy to know the opinion of other members of the network.

Biodiversity protection and quality of water: the role of feedbacks in ecosystems.- Doklady Biological Sciences. Volume 382, Numbers 1-6, p.18-21.; ISSN0012-4966 (Print) 1608-3105 (Online). DOI 10.1023/A:1014465220673]. Springerlink and Google Sites

The Institute of Technology Assessment (ITA) of the Austrian Academy of Sciences just published a research report on the potential of microblogging for science, with a focus on Twitter, in the framework of the project "Interactive Science":

Herwig, J., Kittenberger, A., Nentwich, M. und Schmirmund, J., 2009, Microblogging und die Wissenschaft. Das Beispiel Twitter. Steckbrief 4 im Rahmen des Projekts "Interactive Science". ITA-Reports, Nr. a52-4 hrsg. v. Institut für Technikfolgen-Abschätzung, Wien: ITA
http://epub.oeaw.ac.at/ita/ita-projektberichte/d2-2a52-4.pdf

The report is in German language - here is the abstract in English:

This report investigates the potentials of microblogging in an academic context, drawing on the example of Twitter. In the introductory chapter we present the basics of Twitter in connection with the principles of blogs and social network services (SNS). As a sort of condensed form of blogging Twitter allows the writing of public, log-like entries; as a variation of a SNS it enables the communication between users and maps their relationships. Apart from introducing the basic functions with relation to communication, interaction, publication and archiving, we discuss the demographics and growth tendencies as well as alternative platforms.

In the main part we ask the question how microblogging is already being used in the academic realm and what the potential is for its use. Twitter is not only used for answering the question given by Twitter, namely what one is doing or what is just happening, but for a number of further communicative purposes. In particular, researchers refer to scientific events and publications, ask questions and coordinate their activities. Furthermore, Twitter shows a potential for informal communication and hence as a substitute for the “Café” among scientists who are not co-present. In the framework of scientific conferences, microblogging is used both as a feedback channel and as an organizational tool, hence establishing an additional informal communication layer among those participating locally or at distance at the conference. With a view to external science communication or public relations we need to consider whether microblogging is only one more publication channel or whether it should serve as a means to enter into dialogue with the public. In the latter case, separation between the professional and personal spheres is non-trivial, if individual scholars act for their research institutions or if this is expected. In a digression we present the preliminary results of an empirical study of current Twitter activities of a few researchers. Inter alia, these results confirm the difficulty of the above-mentioned separation and show that professional exceeds non-professional content. Finally, we illustrate the individual attempts to adopt Twitter in teaching. This shows that one needs to be aware of the sensitive change between a non-public and a more or less public communication situation.

Finally, we ask what microblogging is able to deliver for scientific practices and what major application opportunities there are, and conclude with a forecast. The major results of this study are: Microblogging is used by a growing number of scientists for a growing diversity of purposes. As far as one can tell at this early stage, it seems to be used for academic practices, whereby individual usage patterns and cultural (e.g. subject-related) factors play an important role. So far there are no classical incentive systems for using microblogging, but a number of indirect factors, e.g. that users may potentially acquire reputation or that the information exchange is extremely easy and swift. The main application fields for microblogging in science are consequently in the field of context-augmented searching and publishing and with a view to reputation management; also in teaching and at conferences, microblogging may become established as a parallel communication channel; and the social components of open and informal communication may gain importance. In the end we conclude that microblogging is still a dynamic and fast developing new communication medium, which is not only offered by the market champion Twitter but is also increasingly embedded in other social media platforms. Consequently we reckon that microblogging will continue to function as a platform-independent communication principle, not least in academia.

Further blogposts:

• digiom: Unsert Twitter-Steckbrief ist da!

• J_SCH: Microblogging und die Wissenschaft und Glossar

• axkibe: Microblogging und die Wissenschaft
• textundblog: Wann erkennt die Wissenschaft die Bedeutung der Digitalen Medien?
  

   

When people think of Circadian Rhythms, they think of sleep cycles, or those silly Bio-rhythm horoscopes in the newspaper. Recently however science has shown that even cyanobacteria have clock-like systems in their cells. A recent article on CAIK in cyanobacteria noted that it was involved in the phosphorylation reactions in the bacteria, and created a multi-level timing system that regulated the cell bio-chemistry.

Phosphorylation is important because the cellular energy chemicals AMP, ADP, ATP, GMP, GDP, GTP all operate by attaching a phosphate group, to a reactive substrate, thus releasing the energy of the phosphate bond, which increases the likelihood of related chemical reactions.

Normally these energy chemicals, are protected from reaction by negative charges, but enzymes can increase the speed of a reaction to one of these chemicals, using stereo-chemistry to overcome the static repulsion.

One such enzyme is Adenosine Cyclase. Of interest to human health, is the link between PACAP, a pituitary secretion, and phosphorylation. Both Bipolar populations and Schizophrenic populations have vulnerability to PACAP based risk factors.

In PACAP knock out mice, researchers have found evidence of:

1. Energy level changes
2. Sleep disorders
3. An increase in Anxiety/Depression

The energy level changes, are of course linked to regulation of energy within the cell, The sleep disorders and anxiety are not however as easily explained, unless you accept a cellular circadian rhythm model, based on Phosphorylation

If PACAP's job is to advance phosphorylation, as it's name implies, then there is probably another enzyme that acts to slow phosphorylation. It is the nature of these regulatory chemicals, that true health can only be achieved when there is a balance between the two enzymes. This balance must be struck in such a way that the body stabilizes in a pattern associated with the day/night rhythm.

Failure to regulate the cellular circadian rhythm, results in inefficient bio-chemistry in the cell, and either hyperactivity, or hypoactivity. However, the cellular bio-chemical rhythms, are just one of the factors that is important to health. Evidence of sleep disturbances, in PACAP knockout mice, indicates that regulation of sleep is also affected by this same enzymic balance.

Those silly bio-rhyth horoscopes, are also based on the fact that the body has distinctive rhythms, and that at least 5 major rhythms have been found. These bio-rhythms, are simply cyclical processes in the body such as intellectual, sexual, cycles etc. What is important to note is that when these rhythms are in sync with the environment, the individual is relatively healthy. However consider that some of these rhythms are interdependent, and have other health risks associated with them. When the day/night rhythm of the bio-chemistry of the brain changes, so do these longer cycles, and they increase the risk of disorders related to the longer cycles.

This is why the pituitary tries to regulate the phosphorylation of the brain.

The link to Bipolar and Schizophrenia, lies in the fact that sometimes due to genetic, environmental, or other factors, the complex bio-chemical pathways that regulate these cyclic systems, break down. Like a clock, they often fail by running fast or slow. In essence creating an advanced phase, or a delayed phase, which have sometimes been called early phase or late phase error.

When this happens each cyclic system that fails to synchronize with the environment adds a stress factor on top of their inefficiencies, partly created by the inefficiencies, and partly created by inverse phase, situation where the bio-rhythms effect is to promote an inappropriate response, such as increasing the amount of sweat produced in the winter-time, or increasing the energy level during normal sleep periods.

Bipolar disorder is a periodic disorder that affects mood, The periodicity of the disorder is a clue that it is linked to circadian rhythms. However, people who have had this disorder untreated, or who's treatments have failed, tend to slowly become schizophrenic. Schizo-Affective Disorder is a case in point.

Many people question the connection between Schizophrenia and Bipolar disorder, since schizophrenics are less likely to report depression, than psychotic conditions. However there is a connection, and that connection has to do with the stress the body is under due to circadian rhythms.

Stress itself affects sleep, so there is a chicken and an egg problem that science finds it difficult to resolve, a low grade of sleep disorder does not seem dangerous, so it would not be seen to be germane in a study of major stressors. Psychotic episodes happen only at major stress peaks, so environmental factors might play a role, but if we factor into account the cumulative stress associated with bio-chemical inefficiencies, at multiple levels in the organism, it makes sense that a circadian upset, might trigger periodic stress peaks in the cumulative stress wave. If these stress peaks happen in an otherwise healthy individual, we don't notice the minor sleep disturbance associated with them, so we assume that they are based on some life stress, instead of a genetic anomaly, and relatively minor sleep disturbance.

However finding the PACAP gene as a risk factor in both Bipolar and Schizophrenic populations indicates that the speed of phosphorylation is critical to mental health.

Proponents of Green Revolution or high inputs chemical farming system (HICFS) generally argue that developing countries should opt for an agro-industrial model that relies on standardized technologies and ever-increasing chemical fertilizer and pesticide use to provide additional food supplies for growing populations and economies. In contrast, a growing number of farmers, I/NGOs, academia and analysts propose that instead of this capital- and input-intensive approach, developing countries should favor an agro-ecological model, which emphasizes biodiversity conservation; recycling of nutrients; synergy among crops, animals, soils, and other biological components; and regeneration and conservation of resources. The concept of bio-intensive farming (BIF) system is based on agro-ecological principles. In other words, the concept and approaches of BIF system is based on holistic system of sustainable management of natural resources in a given agro-ecosystem with specific cultural and knowledge base.  

The principles of BIF system include the following:  

1. Scientific crop rotation
2. Mixed farming systems
3. Optimization of organic recycling 
4. Participatory and sustainable management of natural resources
5. Participatory research, extension and advocacy
6. Networking and cooperation
7. Attainment of high degree of self-reliance of farm households.  

Features of bio-intensive farming system: The participants are provided with insight about the features on BIF system. Leader farmers (LF) and Technical Assistants share their experiences with other local farmers about a number of these features. The characteristic features of BIF system within the framework of its principles are as follows:

1. Empowerment of people and their independent democratic organizations
2. Conservation and utilization of biodiversity
3. Eco- and health-friendly biologically intensive production systems
4. Equitable access to natural productive resources and public services
5. Sustainable technologies  

Approaches of BIF system  

Some clarity is given to the participants on the approaches of BIF system programme that has been implemented in Udayapur for the last eight years and Siraha district for the last 5 years. The approaches include:

1. Participatory approach
2. Holistic system approach focusing on experiential learning and knowledge generation
3. Collective empowerment and self-reliance building  

Implementation strategies and components of BIFS  

BIF system ensures access of marginalised/small farmers and women to resources, information, technology, and market. More specifically, in the process of planning and implementation of the BIF system, the local farmers' groups /cooperatives and networks address and do advocacy on the following issues.  

1. Ensuring women's leadership role in agricultural cooperatives, extension and marketing
2. Issues of land rights of the marginalized farmers and women
3. Issues of food security and sustainability of rural enterprises
4. Issues of conservation of diversity (biological, social, environmental)
5. Issues of women’s and marginalised household's role and access to and control over resources   Farmer's groups (FG) or cooperatives/ farmer's networks (FN), Model Demonstration Farms (MDF) cum Farmer’s Field School (FFS) are the major components of BIF system. FGs are the main implementing communities at local level. Their cooperatives and FNs are engaged in extension, marketing and advocacy activities. MDF of BIF system is a component developed by Dr B P Rajbhandari in 1992 and was first implemented in Nuwakot district. It is a space for participatory action research, farmer-to-farmer extension and promotion/development of new technologies. It also serves as a FFS where local farmers learn from the active engagement and experience of LFs.  

Major achievements  

1. Farmer's groups/cooperatives/networks strengthened
2. FG/FN doing advocacy
3. MDF/FFS attain success in meeting its goal
4. Farm households socio-economic status upgraded
5. Soil fertility and local bio-diversity conserved/improved
6. Food insecurity level declining substantially        

NASA and the Arab Youth Venture Foundation in Dubai, United Arab Emirates (UAE) have partnered to provide three to 12 UAE engineering students each year the opportunity to work with U.S. students, scientists, and engineers on NASA missions. The program's goal is to engage outstanding college students from the UAE in fields of science, technology, engineering and aerospace. Statement of Joyce Winterton, assistant administrator for education at NASA Headquarters:

"The space program has a unique ability to inspire students to pursue excellence in disciplines that drive science and technology innovation." "With this Space Act Agreement, NASA will engage outstanding students in the UAE to continue their development in the critical skills of science, technology, engineering and mathematics."

From January, 2010,  under this program, UAE students will join U.S. students in a research project administered by the Education Associates Program at NASA's Ames Research Center in Mountain View, Calif. This new partnership and NASA's many other education programs play a key role in preparing students in the critical disciplines of science, technology, engineering and mathematics.

Read more on NASA.gov...

When Lindsay Kallis and me wrote our first entries for the official blog of ResearchGATE, we were really excited and also a bit worried because we knew well how hard it is to start a new blog and provide relevant, quality entries. An excerpt from my introduction:

"Today we start streaming the best content produced by the ResearchGATE community here by sharing selected blog entries and microarticles. Blog entries will cover a wide variety of topics from all disciplines while microarticles are a summary of a peer-reviewed publication in 300 characters or less. We hope you find this blog useful and if you are a researcher, academic, journalist, or someone who uses research, we encourage you to join our community."

But now there is nothing to worry about. You only have to check some of the best blog entries of November and you hopefully will write your own ones for December.

• 200 repetative vulnerabilities in the Human Genome
• Why do we still use adenoviral type 5 backbones for Gene Therapy?
• My Phd Study
• Social Networking
• Did we make any significant in-roads into the health effects research of non-ionizing radiation?
• Teaching Artificial Intelligence

See you on ResearchBLOG (BQ27EW3WA5MG).

On Monday, 23 Nov 2009, another "Forum IT Law" took place at the Institute for Legal Informatics (IRI) of Leibniz Universität Hannover. This time, the forum was about "Used Software", meaning trade with pre-owned software licenses. The legal questions are very current ones, there has been some recent jurisdiction and one case has just been accepted by the German Federal Supreme Court (BGH) for appeal.

Benno Barnitzke, who is Alumnus of IRI's masters programme EULISP and presented the forum, gave a short introduction to the legal issues: Secondary Exploitation is mainly a question of exhaustion of copyright, and this again depends on the way the software is distributed: For software distrubuted on a physical medium, the distribution right of the coyright holder clearly exhausts. But disputes start when it comes to volume licenses that are distributed with "master media" and later re-bundled by the secondary distrubutor, and how to deal with software that is distributed without any physical media by internet download is again another question.

Dr Reiner Hirschberg, who is CTO and head of license management of UsedSoft AG, presented the view of a secondary distributor and their business model. He showed that his company buys software licenses that are not needed any longer by other companies, mainly due to insolvency, dismissals, mergers, and technical or organisational restructuring. Usedsoft's customers again can safe money not only on the license fees, but also on hardware and training, especially if older software is used that is not on sale by the publisher any longer (such as Windows 2000, Office 2003...).

Andreas Kammholz, attorney-at-law in Berlin and specialised on intellectutal property and competition law, and mandated by UsedSoft, presented his point of view on the exhaustion of distribution rights in respect to distribution without physical media. He admitted that the wording of § 69c UrhG (German copyright act) is clear and requires distribution of physical media for exhaustion. But he sees room for an anology, as the legislator had not taken distribution by download into consideration, and the relation of interests of the first purchaser and the primary distributor/copyright holder are the same, especially considering that exhaustion limits the copyright holders' control over distribution, which is an interest of the first purchaser and alsoa common interest, as merchantibility of pre-owned software licenses is an economic benefit.

Dr Andreas Wiebe, Professor on a chair for intellectual propery and competition law at Georg August Universität Göttingen, presented his view and took a counter-position. Wiebe argued that, de lege lata,  the legislator did consider this form of distribution, which was visible in the reasons of some EC directives. Furthermore, the interests were not the same as for physical distribution, as the interest of the copyright holder were more in danger.

Thomas Feil, who is attorney-at-law in Hannover and specialised on IT law, showed the relevance of the issues for the consultation practice of lawyers. The legal obstacles and uncertainties prevent careful companies from using the business model to sell unused licenses aswell as to buy pre-owned licenses, Feil reported. He also mentioned that major software labels make use of this uncertainties to take legal actions against secondary distributors, in order to intimidate them.

After the presentation, a lively debate with the audience came up. If there was a common point, it was probably that there is a lack of clear legislation or jurisdiction in this field. The legislator should clearify the situation of pre-owned licenses without physical media soon, in the one or other direction.

I worked for several years in adenoviral research. My main research focus was to understand the evolution of adenoviruses and to understand how recombination events of adenoviruses effects the emergence of new adenoviruses. Adenoviruses are widely known as THE gene vector for gene therapy. For example, in HIV clinical vaccination trials (September 2007, STEP trial) human adenovirus Type 5 was used as a vector for a vaccine (HIV-1 gag/pol/nef) from Merck & Co Inc, but it was halted at the first interim analysis because the vaccine demonstrated no positive impact on virus acquisition or virus load following infection (see a comprehensive review here: Bradac et al.)

I want to share some thoughts and ideas in the following paragraphs on  C5 backbone gene therapy vectors:

It is well known that Loop1 and Loop2 of the adenoviral hexon gene is responsible for antibody binding and for subsequently neutralizing the adenovirus. Most vectors today are based on an adenoviral Type 5 (species C) backbone. The obvious problem is that most humans have antibodies against this type as there is a high probability of becoming infected with a wild type C5 in a lifetime. Loop1 and Loop2 - located in the hexon gene - are very important for the structure of human adenoviruses. However, knocking these genes out is also not a solution. In my opinion, it is not understandable why Merck is starting a large trial with a virus as a backbone (Type 5 species C), where the probability is relatively high that the vaccine will be destroyed by preformed antibodies.

Just recently a PNAS paper demonstrated the following:"This suggests that adenoviral-based vaccination against HIV-1 in individuals with pre-existing immunity against Ad5 results in preferential expansion of HIV-susceptible activated CD4 T cells that home to mucosal tissues, increases the number of virus targets, and leads to a higher susceptibility to HIV acquisition." This paper is extensive and it underlines my findings.

I suggested in my papers (this and this) published in Journal of Virology in 2005  and 2007  that we should use adenoviral vector therapy backbones from either bovine adenoviruses or adenoviruses from species D, or at least swap the hexon gene.

I also demonstrated in my research (Analysis of a unique adenoviral prime strain, p'17H30, Madisch et al.) that our immune systems are building antibodies against the penton protein and fiber gene, which may also affect the efficiency of an adenoviral vector. I recently co-authored a paper published in PLoS One, where we detected a new adenoviral type: This type was interesting because the backbone of the adenovirus does not usually induce disease, but this virus recombinated in a specific way and the virus acquired a pathogen. This virus was "created" by nature and we should look more closely at these naturally occuring recombinated adenoviruses, which give us bold insights into how we should structure adenoviral vectors for gene therapy.

As a conclusion, I want to make the point that we have to move away from the adenoviral 5 backbones to other backbones or swap the antibody neutralization determinants.

I invite you to visit my paper, Oral sources, bridge analysis implicit theories of university's technology convergence by Horacio Guevara Cross University, online:

IV Congress of Cybersociety 2009, Analog crisis, digital future is the only conference dedicated to virtual Internet that takes place in the Hispanic area, and specifically based virtual (virtual platform), as a meeting of participants in reading and discussion of communications in different formats.

CyberSociety Congress is the most important event of reflection on new technologies in the Hispanic environment, but with participation of people around the world.

In this fourth edition, over 400 communications were presented, from places like Finland, England, Japan and Portugal. These communications (conferences online) will be discussed online from 12 to 29 November.

Oral sources, bridge analysis implicit theories of university's technology convergence.

The paper identifies the oral history as a major element in the analysis of cognitive representations of academics in their implementation through the implicit theories in technology integration, technology integration in education has not yet been able to consolidate or has only been achieved in some sectors of society which is far away from the overall vision of the so-called "information age". It is through the recovery of the protagonists of education and no political speeches will be known as representations, beliefs and concepts that can facilitate the process of inclusion of information technology to educational practice.

The human genome has the capability to code for literally thousands of different protiens. It will be years, working our way through the genome linking it to biochemical processes in the body, and learning from them what the mechanisms are for the many diseases of the body. However recent breakthroughs in psychicatric medicine at both Stanford and MIT, suggest that some of the most puzzling of psychiatric disorders, might be related to regulatory protein syntheis being unbalanced by genetic errors that either are notable in the families with the dieases, and are caused by sloppy copying of these important regulatory protiens DNA codes.

Research at Stanford has implicated the repetitive sections as being important for the regulation of protein synthesis, and has developed the disease model, where both deletions in these segments of DNA and Duplications within these segments can cause disease. This has been used to propose a disease model for two types of Autism, for which drugs are in trial, or soon to be in trial. In one case a deletion of a segment of repetitive DNA can cause a reduction in a protein that regulates a process within the cell, and in another case a duplication of a segment of DNA can cause an up-regulation in the supply of a protein that regulates a process in the cell. When this happens, the effect, is to destroy the regulation of the process.

Now, because the net effect of both errors is to deregulate a process, similar symptoms may appear in both genetic populations, if they deregulate the same process. A case was described of one family where each generation one more repetition of a sequence was removed, causing the symptoms to appear earlier each generation.. Stanfords success at building it's disease model of two types of Autism, is based on simple chemical interventions that are associated within sub-populations of the Autism diagnosis, where the particular symptoms made genetic analysis more directed Fragile X, and Rett's Syndrome. Most Autism is yet undifferentiated, but a possible role of multiple proteins in the same biochemical pathway, suggests that there might be a spectrum of diseases that in different ways have an impact on that pathway, and that the disease is related to the disruption of the pathway.

MIT however is working on a different disease, that is just as difficult, the relationship between bipolar and schizophrenic diseases. They too have found, a spectrum of possible genetic disorders at least some of which are coding for regulatory proteins that regulate a pathway within the biochemistry of the cell. What they say, is that there are only 200 sites in the human genome where there are repetitive codes, that seem to be vulnerable to these duplication and deletion errors. because they involve long sequences of repetitive codes If each of these sites is one of a number of regulatory proteins, then evaluating these sites will probably result in disease models similar to those found by first Stanford and now MIT. Once such a model is available knock-out mice can probably be designed that show the symptoms of the disease, helping in determining what disesases are likely to be most prevalent as spectrum type diseases.

If both the autism spectrum and the bipolar-schizophrenic spectrum are caused by regulatory failure in protein synthesis for specific pathways in the cell, then it makes sense that other diseases may also be related to such failures.

Twenty years ago I published a little known review paper titled "Effects of microwave radiation on the eye: the occupational health perspective" (A. Cutz, Lens and Eye Toxicity Research. 01/02/1989; 6(1-2): 379-86).

Today I ask you ... "Did we make any significant in-roads into the health effects research of non-ionizing radiation"?

Back in 1989 after spending about 7-years monitoring information flow on this contentious public health topic, I concluded in frustration that it would take a genius to make a meaningful breakthrough as we continue to gain greater understanding of the non-linear phenomena in physics and biological sciences. One should ponder could "Chaos Theory" apply at the molecular, cellular levels in complex biological systems?  

Having an occasional ‘peak’ at the NIR (non-ionizing radiation) discussions these days, it remains obvious to me that we tend to be going in "circles" with our health effects research dollars and continue to reinvent the wheel.  The 17th century Descartes rationalism translated into the “dose and effect” approach in the scientific milieu continues to rule our thinking, as do the lawmakers and lawyers dating their foundations back to 13th century the Magna Carta.  

For example listen to the cross examination of the evidence by the U.S. Senator Arlene Specter as presented before the September 14, 2009 U.S Senate Hearing on 'Health Effects of Cell Phone Use'

It must make one think of the "Spanish Inquisition"!

Sincerely,

Andrew Cutz, CIH
Markham, Ontario, Canada

Albeit the title relates to Philosophy actually it deals with Mankind Behaviorism: 'Why very few Men can easily prospect (un)known fields and really grasp (deep researching) innovative solutions derived from newer standpoints while most of them could only express astonishments - skepticisms or full engagements?"

In spite of the general philosophical hope that we all are equal while also not adhering to 1984 (George Orwell's landmark book) surely there are people that are a little bit ahead of the crowd. What is the technical foundation that entitles a person to hold such skills? If any?

After several years prospecting scientists, politicians (front and rear row), famous criminals, philosophers and other prominent people whose personal data was available while deep scrutinizing & researching it at an energized Philosophical Temple an answer was timely gathered and it did match those Men whose main skills on their fields were (badly) remarkable for mankind.

Some facts depend on their birth hour, others on life grown-up experiences and finally the surviving challenges shared with some others. Obviously a good academic background is always a must!

On the other hand in trying to compare with the front row one's a cross reference was also handled with most recent great disasters promoters in order to due balance it and taking out those whose main task was exactly to promote a disaster (no one could deny that without World War II deep suffering and scientific breakthroughs we would have not reach nowadays 6.5 billionth people and more than 70 years of life on average) a confirmation gathered by opposites results was also obtained.

There is an old motto: "You may say a person is stupid, just don't prove it".

This is a technical basic truth in case you need to hire a responsible and yet trustee person or to appoint some other one to hold a position of decision and/or command. From now on no one could say: "I didn't know!"

Cogito - Ergo Sum! A famous phrase of Rene Descartes. Always keep in mind that philosophy standpoints are clearly Philosophical Orders Temples outcomes transliterated into discussions; allegories; lineages and the like.

In the last couple of years, the implications of Neural Network have been the subject of research along with its application. However, the training aspect of this most promising technique is not taken so seriously, and thus as a result most of the students find it a troublesome corner to touch.

The thing we need to do is to simplify the concept and to provide an example application with adequate program, so that the learners can put it to experiment and learn, since students have a common tendency to learn faster by experimenting...lots of bookish learning create boredom for them.

This is the responsibility of teachers and researchers to:

1. Simplify the technology, and
2. Provide the practicle aspects of the technology in an experimental way. 

What we want now is to make the students properly prepared to take up the task independently in hand the moment they finish their study, and for this they must be practically oriented before they drop down to the real job assignment.

All the members of scientific community must think together and to spare some moments for the generation to follow. We all need to be in constant communication to each other to perform this greatest task.

The camel plays a pivotal role in the life of the pastoral people, browse scanty vegetation and produce where other livestock species cannot survive. The camel is used for milk, meat, draught, riding, racing, recreation, wool, hides and prestige in Pakistan. Out of one million camels Balochistan province has the largest proportion (46%) followed by Punjab (23%), placing the majority in north eastern and south western zones of Balochistan and Punjab respectively. The low precipitation, water & feed scarcity, diseases and migrations provoked the pastoral people to develop the breeds which can cope with those conditions. The camel breeds are important local animal genetic resource, well adapted to the harsh and hostile ecology of those areas. The dromedary camel was originally domesticated for milk production in the harsh and arid areas of the world. After a period of use as beast of burden, the capacity of milk production was again realized and hence many studies have been conducted in many parts of the world. The myth of camel milk as stated by the pastoral people in their folk stories has been approved by many scientists.

Image: Neil Carey on Flickr

Even more important in Future

Water and feed scarcity is one of the major challenges in the arid and semi arid lands. The globe is already changed and warmed. The camel has no way to meet the cabinet meeting under the water of ocean like the Maldives cabinet, but the camel scientists can realize. Desertification is continuing and the UN has alarmed the world that millions of acres of land is engulfing by the desert each year. Camel can tolerate a temperature up to 55 c easily. It even absorbs the surrounding temperature in the hot time of the day and dissipates in the cool period of the night. The model of commercial and intensive livestock is in competition with man on the use of cereals, camel doesn’t need that. The disease register of camel is too short and few diseases are fatal to camel health. Camel is resistant to the notorious zoonotic diseases like swine flu, avian influenza, mad cow disease and FMD. Also the land is shrinking of agro pastoral purposes because of the creeping urbanization and the fertile lands are converting in the jungle of concrete and sements.

Humps under threat

The camel is the animal of poor and neglected populace, hence it is seldom considered in research and development policies of the country. Camels catch good prices but their products cannot reach to the markets; therefore, earning of camel herders is quite low. The herders in the country earn modest as compared to other parts of the world where value addition to camel milk is practiced. The camel herders are poor, illiterate and unable to find markets for their products. They live in poverty and cannot financially invest in their camels, which results in low production and low economic returns.
The camels catch high prices offered by merchants from Iran and other countries. The camels are then transported to those countries and never return to its homelands unfortunately. This sad state of situation create social problems like the young boys escaping from the camel production systems and are being attracted by the war seeking groups in the region.
 

Can we keep the humps viable?

No doubt, camel can be a tool to combat the future challenges of draught, environmental changes, global warming and threats of new disease etc. Camel is the animal of future, i.e. everlasting threat to the environment, global warming, creeping desertification and competition on feed & water resources are the future challenges which can be beat by camel only.
Camel has a good potential as meat export to the rich Gulf courtiers. Only the harvested animals are slaughtered in the country and interest from Pakistani consumers is limited, therefore, camel beef is mixed with other meats or minced. Fattening units and feed lots can obtain a growth of 1.5 kg/day. Camel meat is produced organically and is free of zoonotic diseases like mad cow disease, swine flu and avian influenza etc.

Value addition is a tool to make camel production profitable i.e. Kurth, Sorain, ice cream, chocolates and other products can be made from it. With the collaboration of WHO the milk products can be made available for the school goings to fight with malnutrition on one hand and to support camel herders on the other hand. Camel milk can also be used as a tool for poverty elevation.

Niche products exploitation is another tool, being used by many small breeders for the conservation of the breeds in many parts of the world. Eco-tourism (racing, safaris) is one more avenue for fortifying camel production. Camel fairs and safaris are attracting thousands of people from around the world.

 

My study focuses on an aspect of NHS Connecting for Health Electronic Health Record system.  The study builds upon a collaboration between NHS Connecting for Health (CFH), the developers of the NHS Electronic Health Record (EHR) and the University of Huddersfield.  The existing work has developed electronic discharge report exemplars based on clinical information drawn from anonymised patient case records. The development to date now requires refinement in order to ensure the meanings (semantics), context and intentions (pragmatics) contained in discharge summary reports will be captured by the information technology system. 

The research will use a qualitative case study approach.  Anonymised patient case records will be used by participating volunteer clinicians to generate discharge summary reports (DSR). Case records from a number of specialities ranging from uncomplicated clinical care to those of increasing complexity will be selected. Volunteer clinician participants will be asked to create a DSR based on a patient case using a template (Royal College of Physicians [RCP]) designed to standardise content.

Subsequently, they will be interviewed to discuss the semantic and pragmatic aspects contained in the report. The unit of study is the template based DSR, the original DSR from the anonymised case records and the interview transcript. All data will be analysed thematically to identify the relationships between the expressions in the reports and their underlying semantic and pragmatic aspects. The template DSR will then be translated (coded) into an electronic version.

The translation process will allow the evaluation of capabilities and limitations of current health information technology and standards to capture the semantic and pragmatic aspects of this form of clinical communication. The study will contribute to a better understanding of the semantic and pragmatic aspects of clinical communication and inform how current health information technology and standards can be improved

It never ceased to amaze me how many social networking programs have developed in the last few years.

Everything from Facebook to Youtube, Wikipedia, and many other networking programs to many to mention have developed to keep people in touch with one another on a daily and hourly basis. I used to think it was cute when a friend IMed me in the middle or doing a report on Word. Now I consider it an intrusion and breaks the cycle of getting things done on time.

The day will soon arrive I predict when the US Government will have it's own IRS social networking software where the IRS will contact you to remind you to get your taxes in on time or to ask you where you spent the entertainment money in your recent tax return? When will the Senate and Assembly start their own social network software keeping you informed on a daily basis what the Senate or Assembly is doing? When will it all end? When we run out of memory on our computers.

The other day I saw the first tera-byte backup portable storage device for only $80.00.  A tera-byte is a lot of memory, a real lot. It is the kind of extra memory you would find in a server. Memory storage makes it possible to store movies, social network e-mails and on and on until our computers are completely junked up with the massive triva of society.

Is it possible for us to over communicate? Perhaps it is time to go to an island with no WAN or wireless access? 

Dr. Pelham Mead, Director of NYCOM Faculty Development, Old Westbury, NY

Dr. Cédric Sueur, working at the Department of Ecology and Evolutionary Biology at Princeton University, was awarded by Le Monde for his work on primates during his PhD thesis research.

Each year, the French newspaper Le Monde gives a prize to the five best theses in science and allows the winners to write an article on their work in the newspaper.  Cédric Sueur's article, published the 15th of October, explained how macaques are able to vote and live in democracy. Macaques live in groups like many animal species. In order to stay cohesive, animals have to take collective decisions, reach consensus and move collectively. Sometimes, however, individuals have different motivations and want to go in different directions at the same time. One solution to stay together and satisfy the majority of group members is to vote.

This process was found in macaques: some individuals advance and displayed unique behaviors in one direction, some other individuals do these behaviors in the other direction but at one moment, all individuals decide to go in only one direction, the one the majority decided. Macaques count the number of individuals in each direction, wait for a quorum, i.e. a minimum number of participants and then choose one direction when this quorum is reached.

However, some scientist may suggest that primates use insights, manipulations or intentions in this voting process but this is not the case. Macaques respond to a sequence of simple rules found in ants, bees and fishes. It seems that general principles underlie collective decision making in animals, whatever the species.

This work was supervised by Dr. Odile Petit from Strasbourg University, president of the French Society for the Study of Animal Behavior and Prof. Jean-Louis Deneubourg from the Free University of Brussels, a member of the Royal Academy of Sciences of Belgium.

Jerry Fodor, published a book called The Mind Doesn't Work That Way! in around 2000 or thereabouts in which he published some discussion on the scope and limitations of Computational Psychology. In it he suggested that Neural Network architectures had certain constraints that meant that it was difficult to store and retrieve discrete memories using them.

Working from these constraints, creates a need for architectural conventinos that would not be required in a computer or analog electronic circuit. As such, it puts a particular stress on the nature of the tissue that makes up the brain, and how it is organized. Further it suggests that how the tissue is organized, might be particularly important to understanding how the brain works, and how it evolved.

My work suggests that the Allocortical (Three Layer) Cortex Tissue acts as an implicit memory, and that in order to address that tissue so that discrete memories can be accessed, requires Isocortical Tissues, such as the 6 layer tissues commonly found in the neo-cortex, 5 layer agranular tissue such as is found in certain other areas of the neo-cortex, and even 9 layer tissues such as found in the Occipital Cortex.

Current Information Theory, has suggested that there are really only two types of memory, Place Code memory, which is suitable for addressing discrete memories, and Content Addressable Memory, which is accessed by content. If this is true, then implicit memory must be a form of Content Addresable Memory, because it does not lend itself to addressing discrete memories, unless accessed by at least two more layers of neurons. (The difference between Allocortical and Agranular cortex tissues.)

Interpreting the Micro-Architecture of brain tissues, becomes more important when we realize that constraints such as these, will affect the psychology, by limiting the functions that cortex tissues can achieve. It suggests that Allocortical Tissues are precursors to Isocortical Tissues, and that animals with primarily allocortical memories are incapable of accessing discrete memories. It also calls into question the assumption that consciousness is a universal phenomena, and that all animals are conscious, since the ability to address discrete memories is considered highly important in perception.

A recent Nature letters paper by Mancuso et al details the use of a recombinant adeno-associated virus (rAAV) in gene delivery to restore the function of photo-pigments in squirrel monkeys. The male monkeys, red-green color-blind from birth, obtained the ability to process red-green color information via the delivery of the L-opsin gene into the retina. 

While this research opens the door for further hope of gene therapy involved in human eye conditions, including blindness, it also raises some interesting questions. It was previously thought that the brain of adult monkeys would be too "hard-wired" to gain a beneficial effect from the restoration of deficient pathways. The recent paper proves that gene therapy can be utilized in "middle aged" monkeys, and is not solely an avenue to be pursued during early development. This adds a lot of significance to work already begun in human patients, to restore an enzyme involved in a type of hereditary blindness.

Original Article:

Gene therapy for red-green colour blindness in adult primates

Katherine Mancuso, William W. Hauswirth, Qiuhong Li, Thomas B. Connor, James A. Kuchenbecker, Matthew C. Mauck, Jay Neitz & Maureen Neitz

A recent Nature letters paper by Ge et al examines the discovery of Single Nucleotide Polymorphisms (SNPs) in and around the IL28B gene, that correlates with clearance of Hepatitis C Virus (HCV) after treatment. The IL28B gene encodes IFN-3, similar in activity to IFN-, the same cytokine currently used for treatment of HCV. The genetic lesion was identified from examination of two independent Genome Wide Association Studies (GWAS) by Suppiah et al and Tanaka et al, covering 1,137 patients infected with HCV. The advantageous variant of the allele allowed clearance of the virus in 80% of patients after treatment with IFN. The paper also discussed the natural variation of the allele with 90% of chinese and japanese people carrying the advantageous allele - compared with only 30-50% of sub-saharan africans carrying the allele. The paper summarizes a clear study of freely available patient data and identifies a gene clearly implicated in the clearance of HCV from the body following treatment (and potentially before treatment).

In an interesting twist, Michael Katze and Shawn Iadonato discuss the result in the News and Views article in the same issue of Nature. They comment on the usefulness of data collected in this way and the application of the results to research resulting in treatments. They cite the disease of Cystic Fibrosis as an example, where researchers have known for 20 years that a mutation on the CFTR gene is the sole cause of the disease. Even after twenty years of research, no suitable treatment option has been released based upon this knowledge. The two new drug treatments soon available did not rely on research involving this genetic mutation, yet show more promise than the failed gene delivery experiments resulting in Leukemia. They highlight the inefficiency of genetics as a tool for drug discovery.

Despite this gloomy outlook, scientists remain hopeful that genetic discoveries such as this will provide a tool for new research hopefully resulting in new clinical treatment options.

Original Article:

Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance

Dongliang Ge, Jacques Fellay, Alexander J. Thompson, Jason S. Simon, Kevin V. Shianna, Thomas J. Urban, Erin L. Heinzen, Ping Qiu, Arthur H. Bertelsen, Andrew J. Muir, Mark Sulkowski, John G. McHutchison & David B. Goldstein

Nature 461, 399-401 (17 September 2009) | doi:10.1038/nature08309;

News and Views:

Genomics: Hepatitis C virus gets personal

Shawn P. Iadonato & Michael G. Katze

Science is changing. Collective knowledge has expanded to the point where it is both being shaped by and is shaping the technological tools and applications we use. Designed by researchers, ResearchGATE is an innovative platform that was developed to utilize web technology for science: semantic literature search of a custom built meta-database, professional networking, personalized paper recommendations, collaboration tools, discussion groups, self-archiving, reference management, and now, a blog platform.

The internet has witnessed a tipping point: users have moved from the passive role of consumers, to the active role of producers and publishers. This change is fostering dynamic interaction within and between communities. It is a positive thing for progression in science to have technologies that are both dynamic and accessible.

Publishing allows us to share theories, results, and engage in constructive debate. It also serves to preserve the work in a way that is archivable and retrievable. But the traditional model of scientific publishing has been relatively static and restrictive since its inception nearly 400 years ago. Open access and self-archiving movements are making positive ground in challenging this model, and reputable, citable, high-quality science communicated through blogs is proving to be another component in facilitating a scientific publishing revolution.

Like science, this blog is produced by a community, and here at ResearchBLOG we are looking forward to facilitating the community in changing how science is communicated and built upon. We welcome your suggestions and comments as we embark on this endeavour.