Biologist by Monte Alto

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I, VIRUS: WHY YOU'RE ONLY HALF HUMAN

29 January 2010 by Frank Ryan

WHEN, in 2001, the human genome was sequenced for the first time, we were confronted by several surprises. One was the sheer lack of genes: where we had anticipated perhaps 100,000 there were actually as few as 20,000. A bigger surprise came from analysis of the genetic sequences, which revealed that these genes made up a mere 1.5 per cent of the genome. This is dwarfed by DNA deriving from viruses, which amounts to roughly 9 per cent.

On top of that, huge chunks of the genome are made up of mysterious virus-like entities called retrotransposons, pieces of selfish DNA that appear to serve no function other than to make copies of themselves. These account for no less than 34 per cent of our genome.

All in all, the virus-like components of the human genome amount to almost half of our DNA. This would once have been dismissed as mere "junk DNA", but we now know that some of it plays a critical role in our biology. As to the origins and function of the rest, we simply do not know.

The human genome therefore presents us with a paradox. How does this viral DNA come to be there? What role has it played in our evolution, and what is it doing to our physiology? To answer these questions we need to deconstruct the origins of the human genome - a story more fantastic than anything we previously imagined, with viruses playing a bigger part than you might care to believe.

Around 15 years ago, when I was researching my book Virus X, I came to the conclusion there was more to viruses than meets the eye. Viruses are often associated with plagues - epidemics accompanied by great mortality, such as smallpox, flu and AIDS. I proposed that plague viruses also interact with their hosts in a more subtle way, through symbiosis, with important implications for the evolution of their hosts. Today we have growing evidence that this is true (New Scientist, 30 August 2008, p 38), and overwhelming evidence that viruses have significantly changed human evolution.

Symbiosis was defined by botanist Anton de Bary in 1878 as the living together of dissimilar organisms. The partners are known as symbionts and the sum of the partnership as the holobiont. Types of symbiotic relationships include parasitism, where one partner benefits at the expense of the other, commensalism, where one partner profits without harming the other, and mutualism, in which both partners benefit.

Symbiotic relationships have evolutionary implications for the holobiont. Although selection still operates on the symbionts at an individual level since they reproduce independently, it also operates at partnership level. This is most clearly seen in the pollination mutualisms involving hummingbirds and flowers, where the structure of flower and bill have co-evolved to accommodate each other and make a perfect fit. When symbiosis results in such evolutionary change it is known as symbiogenesis.

Viruses as partners

Symbiosis works at many different levels of biological organisation. At one end of the spectrum is the simple exchange of metabolites. Mycorrhizal partnerships between plant roots and fungi, which supply the plant with minerals and the fungus with sugars, are a good example. At the other end are behavioural symbioses typified by cleaning stations where marine predators line up to have their mouths cleared of parasites and debris by fish and shrimps.

Symbiosis can also operate at the genetic level, with partners sharing genes. A good example is the solar-powered sea slug Elysia chlorotica, which extracts chloroplasts from the alga it eats and transfers them to cells in its gut where they supply the slug with nutrients. The slug's genome also contains genes transferred from the alga, without which the chloroplasts could not function. The slug genome can therefore be seen as a holobiont of slug genes and algal genes.

This concept of genetic symbiosis is crucial to answering our question about the origin of the human genome, because it also applies to viruses and their hosts. Viruses are obligate parasites. They can only reproduce within the cells of their host, so their life cycle involves forming an intimate partnership. Thus, according to de Bary's definition, virus-host interactions are symbiotic.

Source: http://www.newscientist.com/

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Let the sunlight in on climate change

27 January 2010

LET'S hear it for the Intergovernmental Panel on Climate Change. A big round of applause, please. Really. It has done amazing, Herculean work.

The IPCC was tasked by the governments of the world to deliver an encyclopedic consensus on the state of knowledge about one of the most far-reaching yet divisive questions of our time. And this grouping of thousands of scientists, taking time out from their regular jobs has, for more than two decades, delivered. Thanks to the IPCC's work, the world's nations have come together to decide that we must prevent our planet warming by more than 2 °C - even if achieving that goal is proving difficult, to say the least.

The serious error, reported here two weeks ago, that led to the inclusion in an IPCC report of mistaken claims about how fast Himalayan glaciers are melting is undoubtedly damaging to the panel's reputation. But it does not in any way undermine the conclusion that human-induced climate change is happening, is dangerous and requires urgent action.

However, the IPCC's heroic days are probably over. The case for anthropogenic climate change has been established; the Nobel prize is won. So it is time for a rethink of where the IPCC is going, and what its future role should be. Two years ago, in the aftermath of the last major assessment report, many scientists argued that the task should have begun then. It is no less urgent now.

We still need the IPCC to serve as a seeker of truth whose deliberations are open to scrutiny. There is plenty of new science to assess. But it makes little sense to have to wait six years between assessments: though reflection, and time for the replication of findings, are essential, why not have an annual report?

The organisation also needs to be more focused on providing the science that will address emerging policy challenges. Its best recent work is in its special reports on topics such as aircraft emissions. A special report on geoengineering would be invaluable, as would a dispassionate assessment of how to measure and verify national greenhouse gas emissions, and carbon sinks such as soils and forests.

Should the IPCC remain as an intergovernmental body - in other words, answerable to national governments from around the world? Yes, it probably should. It was the US, during the Reagan presidency back in the 1980s, that insisted on this. At the time, many scientists were dismayed, fearing political interference in the panel's published reports. But these fears largely failed to materialise, and the fact that national governments all sign off each report has reinforced the IPCC's authority. But public attitudes to science are changing. The IPCC was established before the internet revolution. Like it or not, its closed world of peer review is no longer possible, let alone desirable.

The job of scientists is to test theories to destruction, which inevitably makes science adversarial at times. Dispute is good; consensus stultifies. It is neither surprising nor disturbing that disputes about the science break out, within the IPCC and outside it, and such disagreements need to be out in the open.

Many scientists were unhappy about what they saw as excessive caution in the last assessment - reflected, for instance, in under-reporting of emerging science on how disintegrating polar ice sheets might accelerate sea level rise beyond anything yet revealed in climate models. Such argument should be open to public view. A wider discussion of the uncertainties here would have been more honest and avoided giving a false reassurance.

So let the IPCC embrace such debates, rather than retreat from them in the name of spurious consensus. Climate scientists have felt under siege from critics, as leaked emails last year amply demonstrated. But that is no reason to dismiss all criticism as necessarily unwarranted, uninformed or politically motivated.

Some argue that the views of an untutored blogger, or even a scientist from another discipline, should never carry the same weight as those of someone with a lifetime's expertise in a relevant field. But if occasionally the emperors of the lab have no clothes, someone has to say so. The wider review of science made possible by the blogosphere can improve science and foster public confidence in its methods. Scientists should welcome the outside world in to check them out. Their science is useless if no one trusts it.

Source: http://www.newscientist.com/

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Algal power not so green after all, yet

28 January 2010

ALGAE have been touted as a solution to environmental worries over biofuels, but they may be a long way from providing a truly green option.
Unlike maize, soya beans and oilseed rape (canola), algal farms don't take up valuable farmland, so algae-based biofuels don't threaten food supplies. However, Andres Clarens at the University of Virginia in Charlottesville has modelled the environmental impacts of algal farms and concludes that they require six times as much energy as growing land plants - and emit significantly more greenhouse gases (Environmental Science and Technology, DOI: 10.1021/es902838n).
"You have to add a whole lot more fertilisers, and the environmental cost of producing these is the primary drawback," Clarens says.
Using waste water instead of fertilisers helps, but not enough, he says. The only trick that tipped the balance in favour of algae in his models was to use nutrient-rich household waste like concentrated urine to fertilise the algae, but this would require new infrastructure and so is no short-term fix.
Others say recent advances are overcoming these challenges. For instance, bioreactors are being developed as more efficient alternatives to open-pond algae farms. To date, they have been prohibitively expensive, but a group at Jacobs University in Bremen, Germany, is developing affordable reactors that could slash the environmental impact of algal farms.

Source: http://www.newscientist.com/
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Why older brains stand to lose more

22:00 26 January 2010 by Ewen Callaway

Ageing may cloud your financial judgement, thanks to "noise" in an area of the brain critical for predicting pay-offs, suggests a study of people who played an investment game in a brain scanner.

Gregory Samanez-Larkin and Brian Knutson of Stanford University in California, scanned the brains of 110 men and women aged 19 to 85 with functional MRI as they played 100 rounds of a game in which they had to choose one of three possible investments.

One was in a safe bond that always delivers $1, another was a stock twice as likely to pay off $10 than to lose $10. The third was a highly risky stock with those odds flipped. "What we're doing is trying to get closer and closer to real investing," Samanez-Larkin says.

Shrewd investors will keep picking bonds until they figure out which is the profitable stock. The researchers found that volunteers between 67 and 85 took longer to figure this out than their younger counterparts. "When older adults are choosing risky assets they make more errors," says Samanez-Larkin.

Reward sensor
What's more activity in the striatum, a region critical to sensing reward, was more sporadic in these older volunteers – this area only lit up strongly in some rounds, whereas in younger volunteers activation was consistent.

Samanez-Larkin suggests the fluctuating activity could act like noise, clouding someone's ability to work out the best investment.

"This part of the brain seem to be very important for learning from past history about whether something that happens is good or bad," says Scott Huettel, a neuroscientist at Duke University in Durham, North Carolina.

When Samanez-Larkin repeated the game but this time told elderly volunteers what the stakes were, this prompted them to invest just like younger players.

Journal Reference: The Journal of Neuroscience,
DOI: 10.1523/jneurosci.4902-09-2010

Source: http://www.newscientist.com/

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