Category Archives: News

All the news from around the world in the various scientific fields

Biotech for all – taking science back to it’s roots?

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This morning I came across a very interesting TED talk by Ellen Jorgensen entitled “Biohacking — you can do it, too” (http://on.ted.com/gaqM). The basic premise is to make biotech accessible to all, by setting up community labs, where anyone can learn to genetically engineer an organism, or sequence a genome. This might seem like a very risky venture from an ethical point of view, but actually she makes a good argument for the project being at least as ethically sound than your average lab. With the worldwide community of ‘biohackers’ having agreed not only to abide by all local laws and regulations, but drawing up its own code of ethics.

So what potential does this movement have as a whole? One thing it’s unlikely to lead to is bioterrorism, an idea that the media like to infer when they report on the project. The biohacker labs don’t have access to pathogens, and it’s very difficult to make a harmless microbe into a malicious one without access to at least the protein coding DNA of a pathogen. Unfortunately, the example she gives of what biohacking *has* done is rather frivolous, with a story of how a German man identified the dog that had been fouling in his street by DNA testing. However, she does give other examples of how the labs could be used, from discovering your ancestry to creating a yeast biosensor. This rings of another biotech project called iGem (igem.org), where teams of undergraduate students work over the summer to create some sort of functional biotech (sensors are a popular option) from a list of ‘biological parts’.

image

The Cambridge 2010 iGem team made a range of colours of bioluminescent (glowing!) E.coli as part of their project.

My view is that Jorgensen’s biohacker project might actually have some potential to do great things. Professional scientists in the present day do important work, but are often limited by bureaucracy and funding issues – making it very difficult to do science for the sake of science. Every grant proposal has to have a clear benefit for humanity, or in the private sector for the company’s wallet, which isn’t really how science works. The scientists of times gone by were often rich and curious people, who made discoveries by tinkering and questioning the world around them, and even if they did have a particular aim in mind they weren’t constricted to that by the agendas of companies and funding bodies. Biohacking seems to bring the best of both worlds, a space with safety regulations and a moral code that allows anyone to do science for whatever off-the-wall or seemingly inconsequential project that takes their fancy – taking science back to the age of freedom and curiosity.

Discreet Meat Deceit

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As you’re probably aware, horse meat has been found in many of the UK’s cheaper ‘beef’ products. This led to an investigation which discovered that this is happening all over Europe, including Sweden, Switzerland, Germany and France. Personally, I don’t mind, but a lot of people are creating a lot of noise about it, so it must be pretty important. I think maybe its the fact that people have been mislead. But how was the horse meat initially discovered in these products?

Horse head on cow body

Corse or How?

Some of the products tested showed a positive result for equine DNA – but if DNA is, at the end of the day, made of exactly the same building blocks in every living species on earth, how can you identify horse DNA from cow DNA from human DNA? Every individual living thing on the earth has their own unique DNA sequence (except identical twins) otherwise we’d all be clones of each other, and there are certain genes that must be present in each species in order to make them look how they do. An example would be the genes that give horses a single hoof and cows a cloven hoof on each foot, or the genes that give the horse one stomach chamber but the cow four.

The DNA sequences of many, many animals have been catalogued, and so if a sample of meat is subjected to a DNA test, you can compare the genetic material in the meat to the ‘generic’ horse genome, and if horse meat is present, you know you have it in your sample!

DNA

DNA

So, what are the implications of having horse meat in our burgers, lasagnes, etc? Horse meat is cheaper than beef in some countries, so using it can drive the price of products down. Horses are also fed a drug called bute as an anti-inflammatory, but it is actually lethal to humans at high enough concentrations, but you’d have to have a lot of it to kill you (it is still used as a last resort for extreme cases of spinal arthritis in humans – but only a last resort as the side effects are quite serious).

My opinion is that horse meat is leaner, apparently more succulent than beef, and is considered a delicacy in many countries, so maybe we should start too? Original post and personal blog at http://danthechemist.wordpress.com/2013/03/03/discreet-meat-deceit/

 

Neuroscientists Make Declaration On Animal Consciousness

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Scientists have officially acknowledged that birds have consciousness, and can experience emotions.

On 7/7/2012 a group of prominent neuroscientists signed a declaration supporting the view that non-human animals experience consciousness. The statement claims to be a ‘re-evaluation of previously held preconceptions’. It states that:

‘Convergent evidence indicates that non-human animals have the neuroanatomical, neurochemical and neurophysiologial substrates of conscious states, along with the capacity to exhibit intentional behaviours‘.

Unfortunately the declaration doesn’t define clearly what exactly the ‘consciousness’ they are referring to is. Instead the text switches between referring to different elements of conscious experience, such as arousal (e.g. levels of sleep and attentiveness), conscious decision making, perceptual distortions (e.g. hallucinations) and the experience of emotional states. As the concept of consciousness is a notoriously difficult one to define, the lack of an operational definition makes the declaration somewhat difficult to interpret.

A further peculiarity of the declaration is that it states something which I suspect the vast majority of scientists working in the fields of neuroscience, psychology and animal behaviour have believed for some time. Indeed I suspect a significant proportion of the ‘general public’ would accept that most animals have some level of conscious understanding, especially mammals. The declaration isn’t therefore heralding a breakthrough in scientific understanding, even if it does contradict certain religious and philosophical standpoints that propose consciousness as a uniquely human characteristic.

Despite these reservations, the declaration may prove to be of importance. It focuses on the commonalities between different animals in the neural structures supporting various conscious experiences, and discusses the implications this may have for understanding the development of consciousness through evolution. It represents an official acknowledgement that a larger range of animals experience consciousness that many may have previously believed, based off the proposition that absence of a cerebral cortex does not preclude conscious thought. Those animals considered ‘conscious’ can therefore include non-mammalian creatures such as insects and cephalopods. The declaration may hopefully lead to greater discussion of both the nature of consciousness, and the relationship between humans and other animals.  More importantly it may facilitate political changes to ensure the more humane treatment of animals.

A full text of the declaration can be found at http://fcmconference.org/img/CambridgeDeclarationOnConsciousness.pdf

A New Moon Has Been Discovered Orbiting Pluto

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By Maria Panagiotidi

A fifth moon was discovered orbiting Pluto by a team of astronomers using NASA’s Hubble space Telescope.

The icy dwarf planet Pluto has four other known moons, the largest being Charon which was discovered in 1978 at the United States Naval Observatory in Washington, D.C. Hubble observations in 2006 uncovered two additional small moons, Nix and Hydra. Pluto’s fourth moon, which is provisionally named “P4″, was discovered almost a year ago.

Hubble Discovers a Fifth Moon Orbiting Pluto

This image, taken by NASA's Hubble Space Telescope, shows five moons orbiting the distant, icy dwarf planet Pluto. The green circle marks the newly discovered moon, designated P5, as photographed by Hubble's Wide Field Camera 3 on July 7. (Source: Hubblesite.org)

Pluto’s fifth moon  was provisionally named P5 and was detected in nine separate sets of images taken by Hubble’s Wide Field Camera 3 on 26, 27 and 29 June, and 7 and 9 July 2012. It is estimated to be irregular in shape and 6 to 15 miles across. P5 is in a 58,000-mile-diameter circular orbit around Pluto that is assumed to lie in the same plane as Pluto’s other known moons.

Scientists are intrigued that such a small planet (Pluto is smaller than our moon) can have such a complex collection of satellites.

“The discovery of so many small moons indirectly tells us that there must be lots of small particles lurking unseen in the Pluto system,” said Harold Weaver of the Johns Hopkins University Applied Physics Laboratory in Laurel, Md.

The new discovery provides additional clues about  the formation and evolution of the Pluto system. The most popular theory suggests that all the moons are relics of a collision between Pluto and another large Kuiper belt object billions of years ago. The Kuiper belt refers to a region of the Solar System that consists mainly of small icy bodies.

The new detection will allow scientists navigate NASA’s New Horizons spacecraft through the Pluto system in 2015, when it is expected to make an historic and long-awaited high-speed flyby of the distant world.  New Horizons will return the first ever detailed images of the Pluto system.

 

Official NASA announcement here: http://www.nasa.gov/mission_pages/hubble/science/new-pluto-moon.html

 

Particle Consistent with the Higgs Boson Discovered at the LHC

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By Stephen Sadler

On Wednesday, in a seminar watched live on the Internet all around the world, scientists from the two main detectors at CERN’s Large Hadron Collider (LHC) in Geneva announced the discovery of a new particle whose properties are consistent with the long sought-after Higgs boson.

The Higgs is the fundamental particle responsible for providing all other particles with mass, and represents the final missing piece of the Standard Model of particle physics. Its existence was proposed in 1964 by three groups independently: Peter Higgs; Robert Brout and Francois Englert; and Gerald Guralnik, C.R. Hagen and Tom Kibble, and in 2010 the six physicists were jointly awarded the J.J. Sakurai Prize for Theoretical Particle Physics for their work.

Candidate Higgs event recorded by the CMS detector in May 2012. This event exhibits the characteristics expected from a Standard Model Higgs (not seen) decaying into two photons (yellow dashes and green bars).

In Wednesday’s seminar, CMS spokesman Joe Incandela and ATLAS spokeswoman Fabiola Gianotti announced that both of their experiments had detected a new particle with a significance of 5 sigma, which corresponds to a 1 in 3.5 million chance that the result is in fact a statistical fluke. This is the benchmark in the field for claiming the discovery of a new particle.

“We observe in our data clear signs of a new particle, at the level of 5 sigma, in the mass region around 126 GeV. The outstanding performance of the LHC and ATLAS and the huge efforts of many people have brought us to this exciting stage,” said Gianotti.

Scientists at the University of Sheffield have played a key role in both engineering and data analysis for the ATLAS detector, as well as providing supercomputers for the worldwide particle physics computing network known as the Grid.

CERN Director General Rolf Heuer had this to say about the new discovery:

“We have reached a milestone in our understanding of nature. The discovery of a particle consistent with the Higgs boson opens the way to more detailed studies, requiring larger statistics, which will pin down the new particle’s properties, and is likely to shed light on other mysteries of our universe.”

Scientists discover bees that can reverse brain aging

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By Maria Panagiotidi

Scientists at Arizona State University have discovered that older honey bees can reverse brain aging when they take on nest responsibilities typically handled by much younger bees.

This finding could provide alternative interventions for the treatment of age-related dementia. Current research focuses mainly on potential new drug treatments.

The study was published in the scientific journal Experimental Gerontology by a team of scientists from ASU and the Norwegian University of Life Sciences, led by Gro Amdam. The researchers found that tricking older, foraging bees into doing social tasks inside the nest causes changes in the molecular structure of their brains.

Previous research on honey bees has found that bees that stay in the nest and take care of larvae – the baby bees – remain mentally competent. However, after a period of nursing, bees fly out looking for food and begin aging very quickly. The effects of aging are visible after two weeks in the appearance of the foraging bees (worn wings, hairless bodies) and more importantly, in their brain function. Specifically, these bees lose the ability to learn new things.

Influenced by recent studies on brain plasticity, Amdam and colleagues wanted to see what would happen if the foraging bees returned to the nest and took care of the larval babies again.

The results of the experiment were fascinating. After 10 days, about 50 percent of the older bees caring for the nest and larvae had significantly improved their ability to learn new things.

The change observed in the older bees was not just behavioural but also physiological; Amdam and colleagues discovered a change in proteins in the bees’ brains. After comparing the brains of the bees that improved to those that did not, they found that two proteins had noticeably changed: Prx6 and “chaperone” protein. Both proteins have been previously found to protect the brain against diseases such as Alzheimer’s.

This finding could lead to the development of a drug that could help older people maintain brain function. However, many years of basic research and trials will be needed before such a drug becomes commercially available.

For now, Amdam and colleagues propose that social interventions might help our brains stay younger. Since the proteins being researched in people are the same as those found in bees, it is possible that these proteins may be able to respond to specific social experiences. Further research is needed on mammals in order to confirm that the same molecular changes occur on other species’ brains.

 

Reference

Nicholas Baker, Florian Wolschin, Gro V. Amdam. Age-related learning deficits can be reversible in honeybees Apis mellifera. Experimental Gerontology, 2012; DOI: 10.1016/j.exger.2012.05.011

First Steps Toward Emergence of Life Theory

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By Stephen Sadler

What turned a primordial mixture of amino acids and proteins into the first organized, self-replicating unit? What was it that breathed the vital breath into a collection of inanimate chemical building blocks, giving rise to an unbroken chain of evolution stretching three and a half billion years into the future and culminating in us?

For many years Kauffman has studied the mathematics behind groups of molecules known as ‘autocatalytic sets’. These sets of molecules and their associated chemical reactions are special because they form self-sustaining systems which, given a ‘food source’ of simple molecules, are able to form more complex molecules which themselves catalyse, or speed up, reactions which give rise to other molecules in the set. In this way, they form “functionally closed” structures (see Figure 1) that speed up the production of the members of the set, promoting the existence of the set as a whole.

Figure 1: an example of an autocatalytic set. Black dots represent molecules in the set, whilst white boxes represent reactions. Solid arrows stand for reaction inputs and outputs, and dashed arrows indicate catalysis. Because each arrow ends on a molecule in the group, the group is said to be “functionally closed”.

To see what all this has to do with life, we must define what we mean by “life”. Whilst definitions vary, most share some common themes, for example: self-organisation, self-replication, and the ability to evolve with successive generations. Kauffman himself has defined a living organism as “an autonomous agent or a multi-agent system capable of reproducing itself or themselves, and of completing at least one thermodynamic work cycle” [1].

So could autocatalytic sets fulfil these criteria? Almost by definition their existence promotes the proliferation of their constituents, which sounds remarkably like self-replication. Their closed structure and well-defined flow of reactants and catalysts through reactions also sounds like it might fulfil the self-organisation criterion. But can they evolve? It is this question that Kauffman’s latest work addresses.

The group studied the mathematical properties of autocatalytic sets and made the remarkable discovery that any given set can be decomposed into so-called ‘irreducible autocatalytic sets’. What’s more, the number of irreducible autocatalytic sets that any larger autocatalytic set can be decomposed into rises exponentially with the size of the larger set. Since these sets overlap to some degree, they can be said to be mutually dependent, and it is not too much of a leap of faith to imagine them beginning to behave as the elements of a ‘meta autocatalytic set’.

“In other words, self-sustaining, functionally closed structures can arise at a higher level (an autocatalytic set of autocatalytic sets), i.e., true emergence,” the group say.

The combining and splitting of these functionally-closed, self-replicating entities can, according to the group’s paper, give rise to inheritance, mutation and competition. In other words: evolvability.

However, the authors don’t stop there. Is it too far fetched, they ask, to “consider a complete cell as an (emergent) autocatalytic set?” And if not, then why not think “of the collection of bacterial species in your gut (several hundreds of them) as one big autocatalytic set”? Going one step further, could the theory not be applied to ecology to describe any mutually dependent set of organisms, they ask? Could the economy not be viewed as an autocatalytic set, with its processes (reactions) assembling complex structures out of more simple ones (reactants), facilitated by tools, factory production lines and humans (catalysts)?

These are big ideas and, by the authors’ own admission, rather speculative, but with the tantalising possibility of a single theory to explain the phenomena of emergence, functional organisation and the origin of life, it seems difficult to disagree with them when they conclude: “we believe that these ideas are worth pursuing and developing further”.

A preprint version of the group’s paper can be found at http://arxiv.org/abs/1205.0584

[1] 2004, “Autonomous Agents”, in John D. Barrow, P.C.W. Davies, and C.L. Harper Jr., eds., Science and Ultimate Reality: Quantum Theory, Cosmology, and Complexity, Cambridge University Press.

 

Coffee consumption associated with lower risk of death in older adults

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By Maria Panagiotidi

Older adults who drank coffee — caffeinated or decaffeinated — had a lower risk of death overall than others who did not drink coffee, according a study by researchers from the National Cancer Institute (NCI), part of the National Institutes of Health, and AARP. The  results of the study were published in the May 17, 2012 edition of the New England Journal of Medicine.

Coffee is one of the most widely consumed beverages worldwide, but the association between coffee consumption and the risk of death remains unclear. Neal Freedman and his colleagues examined this relationship in 229,119 men and 173,141 women who participated in the NIH-AARP Diet and Health Study. The ages of the participants varied from 50 to 71.

 

After adjusting for tobacco-smoking, alcohol consumption, and other potential confounders, the researchers found that coffee drinkers were less likely to die from heart disease, respiratory disease, stroke, injuries and accidents, diabetes, and infections. No difference was found in the case of cancer. Heavier coffee intake among men was associated with increased risk of cancer death. The association, however, was only marginally statistically significant.

The researchers found that the association between coffee and reduction in risk of death increased with the amount of coffee consumed. The participants who consumed three or more cups of coffee per day had approximately a 10 percent lower risk of death. The findings were similar for caffeinated and decaffeinated coffee consumption.

It should be noted that the current study does not allow us to infer a causal relationship between coffee drinking and lower risk of death. Examining the exact nature of this relationship will be the subject of future studies.

 

Reference

Neal D. Freedman, Yikyung Park, Christian C. Abnet, Albert R. Hollenbeck, Rashmi Sinha. Association of Coffee Drinking with Total and Cause-Specific Mortality. New England Journal of Medicine, 2012; 366 (20): 1891 DOI:10.1056/NEJMoa1112010

Scientists Implant Biofuel Cell in Living Snail

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By Maria Panagiotidi

Researchers led by Evgeny Katz, the Milton Kerker Chaired Professor of Colloid Science at Clarkson University, have implanted a biofuel cell in a living snail. Their findings were published in the Journal of The American Chemical Society.

Researchers led by Evgeny Katz, the Milton Kerker Chaired Professor of Colloid Science at Clarkson University, have implanted a biofuel cell in a living snail. This is the first incidence of an implanted biofuel cell continuously operating in a snail and producing electrical power over a long period of time using the snail’s physiologically produced glucose as a fuel. (Credit: Image courtesy of Clarkson University)

The “implanted battery” can generate electrical power for several months driven by glucose, which is produced by the snail.

This is the first reported incident of an implanted biofuel cell operating in a snail and producing electrical power over a long period of time using as fuel the glucose that is physiologically generated by its host.

Implantable biofuel cells have been suggested as sustainable micropower sources operating in living organisms, but such systems are still very challenging to design. In the future, implanted fuel cells that are driven by glucose generated by their host could power medical devices in humans or environmental sensors in animals.

Evgeny Katz and his colleagues made the electrodes of their fuel cell out of densely packed carbon nanotubes, and attached glucose-oxidizing and oxygen-reducing enzymes to them. The authors then implanted the electrodes into a snail (Neohelix albolabris). After decreasing the rate of current extraction to match the snail’s slow glucose transport and metabolism, they got continuous electrical output for an hour. The amount of electricity produced was far below that of just one AAA battery, but the group of scientists aim to increase it in future experiments. The fuel cell remained functional in the snail for several months during which the animal was allowed to roam freely and live an almost normal life.

The aim of this research is creating insect cyborgs, an idea that has been funded by the U.S. Department of Defense.

 

Reference

Lenka Halámková, Jan Halámek, Vera Bocharova, Alon Szczupak, Lital Alfonta, Evgeny Katz. Implanted Biofuel Cell Operating in a Living Snail. Journal of the American Chemical Society, 2012; : 120308155036002 DOI:10.1021/ja211714w

You can find the article here:  http://pubs.acs.org/doi/abs/10.1021/ja211714w 

 

 

Greedy Black Holes Eat Two Meals at a Time

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By Stephen Sadler

Researchers at the University of Leicester may have solved a long-standing mystery in astrophysics, namely: how do black holes grow so massive? In a recent paper in the journal Notes of the Royal Astronomical Society, Christopher Nixon and Andrew King from the University of Leicester, along with their collaborator Daniel Price from Monash University in Australia, put forward a new theory of black hole growth in which the gluttonous space-time singularities are able to put on weight more than 100 times faster than their conventional diet allows.

Black holes are ubiquitous in the universe, but the real heavyweights reside at the centre of galaxies like our own Milky Way, and can weigh in anywhere up to 10 billion times the mass of the Sun. They grow by a process called accretion, gobbling up gas from a disc around their equator as it gradually loses angular momentum and spirals inwards, like water down a plug hole.

Except that this can’t possibly be correct, as Professor King explains: “These hugely massive black holes were already full-grown when the universe was very young, less than a tenth of its present age.”

“We needed a faster mechanism,” says Chris Nixon, also at Leicester, “so we wondered what would happen if gas came in from different directions.”

The team made a computer simulation of a black hole orbited by two accretion discs at different angles. At the points where the discs collide, the angular momentum keeping the gas in orbit cancels out, and the gas quickly falls into the central regions, either becoming the black hole’s next meal, or recircularising into a smaller disc, depending on how much angular momentum it managed to hold onto (see picture below).

Simulation of a black hole orbited by two accretion discs, after evolving for approximately 10 orbits. The structure of the two original discs can be seen in blue, whereas the white disc near the centre is formed of gas that has collided and fallen in, before restabilising at a smaller radius.

“If two guys ride motorbikes on a Wall of Death and they collide, they lose the centrifugal force holding them to the walls and fall,” says King. The same thing happens to the gas in these discs, and it falls in towards the hole.

The regions at the centre of young galaxies provide the chaotic conditions thought to give rise to such double-disc accretion systems, providing the greedy young black holes with all the gaseous sustainence they need to grow into the giants we observe today.

 

The group’s paper can be found at: http://www.astro.le.ac.uk/~cjn12/papers/twist.pdf