With the meeting wrapping up today, the celebrated researcher Frans de Waal brought Darwin’s legacy into the modern world at a symposium on the evolution of morality.

Human morality has perplexed scientists and thinkers since Darwin’s time, but De Waal argued that it was not perplexing to Darwin himself, because he saw morality as linked to emotion, and saw reflections of human emotion all around us in other animals. De Waal, of the Yerkes National Primate Center at Emory University in Atlanta, described today the years of evidence that he and other scientists have gathered to support the idea that other animals show emotional and moral behaviors much like those in the human species.

For instance, chimpanzees shown videos of other chimps yawning yawn themselves, exhibiting a phenomenon called “motor contagion.” And mice show “emotional contagion,” responding to pain applied to other mice. Both these mechanisms are ways in which one animal can share the experience of another, which is an essential part of empathy, De Waal said.

Monkeys also show “prosocial behavior” in a task in which they are asked to choose either a block that will elicit a treat for themselves and a partner monkey, or a block that will only elicit a treat for themselves, De Waal said. The monkeys in this experiment more often choose to distribute treats to both themselves and the partner monkey, especially if the partner is related to them, De Waal said: “Monkeys do care about someone else,” he argued.

And finally, De Waal said, monkeys also reject unfair treatment – and here’s where he brought the whole argument back to the human world. His group trained pairs of monkeys to perform a simple task and get a piece of food – either a cucumber or a far tastier grape - as a reward. If both monkeys in the pair are rewarded with cucumbers, they happily perform the task eagerly and often. Yet if one monkey suddenly starts receiving grape rewards, while the other is stuck with cucumbers, the cucumber recipient tosses the inferior food out of his cage. And eventually, he goes to the corner of his cage and refuses to perform the task any more.

To De Waal, this signifies that monkeys, like humans, have a strong sense of fairness – a finding that has been reinforced in other animals, such as dogs. So, De Waal argued, it makes perfect sense in the light of evolution that we become outraged when we hear that Wall Street bankers are receiving extravagant bonuses while the rest of us are struggling to fill our gas tanks and pay our mortgages. “I always think we live in cucumber land and they live in grape land,” De Waal said.

And with that, the meeting ends this afternoon. My brain is overstuffed and I could use a good night’s sleep, but it’s been a fascinating and thought-provoking few days in cucumber land.

Posted by Erika Check Hayden on February 16, 2009
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Whenever I see Elaine Ostrander talk about dogs, I feel sorry for human geneticists. Ostrander, a researcher at the U.S. National Human Genome Research Institute on Bethesda, Maryland, studies the hundreds of dog breeds that exist in the world. And because human breeders have simplified dog genetics enormously, it’s a lot easier to answer questions about the genetic basis of all kinds of traits in dogs than it is in humans.

For instance, a few years ago, Ostrander’s group found that a single gene explains most of the variation in size that exists across dog breeds, from the massive Great Dane to the diminutive Chihuahua pictured below. And today, it almost seemed like Ostrander was showing off, as she revealed new results that shed light on the very same question I heard discussed here last night: how important are genetic parasites, called transposons, in diversity and disease?

Ostrander and her colleagues asked whether one genetic mutation underlies the short-legged, squat dog body type seen in breeds such as the basset hound and the corgi. (The technical term for this short and waddly body type is “chondrodysplasic.”) Her group studied 45,000 genetic markers in 95 dogs from 8 different “short” breeds and compared the same markers to 702 dogs from 64 larger breeds. Sure enough, they found that a single genetic variant appears to account for the squat body type across the eight “short” breeds.

Oddly, this variant consists of an extra copy of a growth gene that has been inserted into dog DNA by – you guessed it – a retrotransposon – one of those pesky genetic parasites that Jef Boeke was talking about last night. Ostrander said this is the first ever example of a retrotransposon causing variation within a single species of mammal. She said that the example shows the power of dog genetics to reveal how new forms of genetic diversity could indeed be important in humans.

Photo of a Great Dane and a Chihuahua by Deanne Fitzmaurice courtesy of Science magazine

Posted by Erika Check Hayden on February 15, 2009
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With this being the big old Darwin anniversary extravaganza year, one of the issues scientists are talking about at this meeting is how evolution shaped human beings into what they are. What’s fascinating to me is the emerging debate over whether some uniquely human traits may have resulted from what is essentially genetic detritus.

For instance, scientists have discovered in the past few years that the human genome is littered with genetic parasites that have no known mission in life apart from colonizing our DNA. More than half of our genome consists of large tracts that feature these parasites, which are called transposons. A big question of biology today is how much of an impact transposons have had on human evolution.

Jef Boeke of Johns Hopkins University School of Medicine in Baltimore, who spoke today, thinks transposons may be crucial to both normal human diversity and, possibly, to disease. He talked about one particular type of transposon called an L1 element, which has copied itself more than 100,000 times in the human genome. Boeke’s lab has devised a way to count the number of L1 elements in individual people’s genomes, and to figure out where the transposons fall in a person’s DNA.

Boeke’s lab used this method to count L1 elements on the X chromosomes of 117 people. The team found 34 differences in how the element had incorporated itself on just this one chromosome among the different individuals. Extrapolating that finding to the rest of the genome, and performing a rough back-of-the envelope calculation, Boeke estimated that L1 alone contributes to a “staggering” amount of human variation. Therefore, “We can say that everyone in this room - unless there are identical twins in the room - is different,” Boeke said. “There’s no question these elements are a major part of human diversity.”

But so what – what do transposons actually do? Boeke has asked that question by examining L1 elements in 70 men with mental retardation that has no known cause, but that appears to be related to mutations on their X chromosomes. Boeke’s group found seven L1 insertions that don’t appear in 500 normal men. Some of these insertions interrupt genes that are expressed in the brain, indicating they might somehow be involved in contributing to mental impairment. Of course, Boeke’s group still needs to figure out whether or not the insertions really are causing disease. But he is encouraged by these results: “We’re very excited about this as a potential approach to find new disease alleles” he said.

Posted by Erika Check Hayden on February 14, 2009
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Ordinarily, Paul Ekman is to be found doing rigorous, detailed studies of facial expression, body movement, emotion and deception. And his results are not just academic. These days he is an emeritus professor of psychology at the University of California, San Francisco, but he and his associates still give courses on how to recognize concealed emotions via subtle changes in facial expressions, body language and such--with a roster of students that include police and national security officials, corporate negotiators and health professionals. He's also the scientific adviser to the FoxTV series Lie to Me.

Not surprisingly, given his interests, Ekman is very familiar with Charles Darwin's 1872 book, The Expression of the Emotions in Man and Animals. And a few years ago, he found himself discussing Darwin's views on one particular emotion, compassion, with the Dalai Lama.

"Darwin said that!?" Ekman remembers the Dalai Lama exclaiming at one point.

Further discussions--which eventually resulted in a book coauthored by the two men, Emotional Awareness (2008) -- revealed that Darwin's ideas were virtually identical to Buddhist teachings on the subject. For example, Darwin believed that the seeds for compassion lie in the mother-infant bond. ("Focus on the 'other' as 'mother'," says the Dalai Lama.) Darwn likewise believed that compassion is reinforced by the fact that when I see you suffer, it makes me suffer. ("In helping you, I help myself more," says the Dalai Lama.) And Darwin wrote that the highest moral value is to be concerned for the welfare of all sentient beings--a phrasing that matches almost word for word the teachings in Buddhist texts, translations of which were available in England at the time.

Perhaps the convergence of ideas was a coincidence, says Ekman. But in his AAAS talk, he listed eight possible ways that Darwin might have known about Buddhist teachings, and been influenced by them. These include contacts via his wife, various friends, and the aforementioned texts. "It's like a historical detective story," says Ekman.

Posted by Mitch Waldrop on February 14, 2009
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A leader of the the Intergovernmental Panel on Climate Change told the meeting today that the world's climate is likely to change much faster than predicted, leaving the world with two choices: start cutting carbon emissions earlier, or make the cuts deeper.

The comments came the morning after former U.S. Vice President Al Gore called on scientists at the meeting to help convey a sense of urgency about climate change to policy makers and the public.

"We are basically looking now at a future climate that is beyond anything we've considered seriously in climate model simulations," said Chris Field, co-chair of the IPCC's second working group and a professor at Stanford University and the Carnegie Institution for Science.

This is because the rate at which carbon is entering the atmosphere is increasing much faster than the IPPC modeled in its last report, issued in 2007. That report estimated that world temperatures could increase by between 1.1 to 6.4 degrees Celsius by 2100. But the surge in the use of coal to generate power in developing countries, combined with climate impacts on natural carbon sinks, such as oceans, forests and tundra, mean that future climate impacts will likely be more severe than the IPPC realized, Field said.

"We have higher emissions, and we have a less friendly natural system to picking up these higher emissions, and they both mean that looking forward, the challenge of stabilizing atmospheric carbon dioxide is getting more complicated than we thought it was before," Field said.

Holly Gibbs, a researcher at Stanford University's Woods Institute for the Environment, also showed data that attempts to help clarify one aspect of the climate debate. Two papers published last year suggested that clearing tropical forests to plant biofuel crops might actually worsen climate change, but that planting biofuels crops on "degraded" land - such as abandoned agricultural land - offers a net benefit to climate. Gibbs analyzed satellite images taken from 1980 to 2000 to try to answer the question of whether tropical crops are largely being planted on deforested or degraded land. She found that the majority of new crops were planted on freshly deforested rather than degraded land.

Gibbs said she could not tell from her data whether the new crops were planted for food or fuel. But she added, "What we know is that biofuell use is definitely fueling deforestation." She said when biofuel prices increase, the amount of deforestation increases as well. She said she would personally estimate that between one-third to two-thirds of deforestation over the past couple of years has been due to the planting of biofuel crops.

"If we run our cars on biofuels produced in the tropics, chances are good that we are effectively burning rainforests in our gas tanks," Gibbs said.

Deforestation is a major issue in international negotiations on a successor agreement to replace the Kyoto Protocol, which is set to expire in 2012. Negotiators will meet formally again this December in Copenhagen. But despite the fact that climate is likely changing more rapidly than expected, and the fact that the next IPCC assessment will not be published until 2014, Field said it is difficult to envision any way to speed up the formal IPCC process.

"The feeling has always been that you can either make an assessment good or fast," Field said. He said the IPPC is adding more special reports, such as one underway on renewable energy and a possible special report on climate extremes and adaptation. "I think we'll see somewhere between two and five of these special reports in the next assessment cycle, but I don't think the IPPC is going to deviate from its emphasis on quality and I don't think we have any ideas on how to keep the quality and accelerate the timelines."

Photo of land clearance for oil palm production in Ecuador provided by World Land Trust, via Science-AAAS.

Posted by Erika Check Hayden on February 14, 2009
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'Science journalism in crisis' was the title of a special press briefing this afternoon, jammed with worried-looking science reporters. And the news, as expected, was bleak--but not entirely so.

The organizer, University of Wisconsin journalism professor (and Pulitzer prize winner) Deborah Blum, explained that the session was precipitated by CNN's decision last December to axe its entire space, science and environment unit--which was only the most dramatic of many other such decisions made by media organizations in recent years. In hard economic times, said Blum, science coverage is being perceived as a luxury, and thus expendable.

Some data to quantify that trend in the US was given by Cristine Russell, a former science reporter for the Washington Post, and now the president of the US Council for the Advancement of Science Writing. Membership in the largest professional organization, the National Association of Science Writers, currently stands at 2222. But of those only 79 are full-time staff reporters on newspapers, a significant drop over previous years, and only 15 work for science magazines. But some 860 are freelancers, a number that appears to be growing over time. The number working for Internet sites is growing, as well. A survey of the smaller Society of Environmental Journalists shows similar trends.

Meanwhile, says Russell, the number of dedicated science pages in US newspapers has fallen from a peak of 95 in 1989 to 34 in 2005, and is still dropping--with a big shift toward consumer and health reporting in those remaining.

Russell cited the example of the Boston Globe, which has had an outstanding science section with seven health and science reporters plus two editors. Last April, science coverage was moved to the inside of the newspaper's front section. Then in January, it was cut from 3 pages to 2. And recently the Globe announced that it would be eliminated entirely as a separate entity, with science and technology going into the business section.

The good news, said Russell, is that science is central to many front-page issues that aren't 'science' in the conventional sense--some obvious examples being climate change, energy, stem cells, reproductive technology, natural disasters, and nuclear proliferation. So there are things science reporters can do, assuming that the higher-ups will listen. Perhaps most important, they should not shy away from the policy aspects of their stories, but should work to keep a place at the top table, where the decisions are made about how news is covered. The New York Times is conducting an interesting experiment along those lines, in which it will coordinate and integrate all its environmental reporting, whether it comes from the science, business, national or international sections.

Finally, said Russell, it's critical that professional societies work harder to document what is happening, and where people laid off from conventional media jobs are going.

Posted by Mitch Waldrop on February 14, 2009
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Since it's Valentine's Day tomorrow, you know what I'm talking about. That's right, it's love. Valentine's Day always happens some time during this conference, to the eternal consternation (or relief?) of conference-goers forced to spend the holiday apart from their adored ones. But it usually means we get treated to some "science of romance" stories, and this year is no exception, as the conference organizers thoughtfully organized a press conference on the science of kissing.

But I eschewed the kissing thing (no offense, but it always leads to gross visions of spit and slobber and lots of tortured metaphors) in favor of a session at which my favorite rodent was featured. That's right - the indomitable prairie vole (pictured below). They're not just my favorite U.S.-dwelling rodent because I am a proud daughter of Illinois, whose official motto is "The Prairie State." They have also managed to make themselves indispensable to biologists merely by an accident of nature, which is the fact that they behave a lot like ideal humans in their romantic endeavours. They choose one partner, stick with that partner, and share their baby-rearing duties with that partner. For life.

Prairie voles and their relatives have selflessly provided evidence of all sorts of things, such as the fact that male polygamous voles can be turned monogamous by genetic engineering or by the injection of a brain chemical. And the same types of brain chemicals involved in adult bonding are also essential to helping voles raise their babies well, Sue Carter of the University of Illinois, Chicago told the meeting today.

Carter has found that the prairie voles suffer when removed from their partners; their heart rates skyrocket and, if they're confronted with a stressful situation, their heart rates go up even more, and take longer to drop back to normal. But if they're injected with the brain chemical oxytocin, the voles don't succumb to the stress of isolation.

Now, Carter is studying what happens to adult prairie voles who are deprived of social bonding, and the brain chemicals involved with it, as babies. Baby voles who are picked up and held just once as babies are better dads than those who are never held at all, Carter said. But if injected with one dose of oxytocin, the voles who were deprived of touch as babies were just as good at parenting as their coddled counterparts.

Carter's data is powerful evidence of the fact that love - or at least, attachment - is not purely psychological. There's a chemical component to it, too...at least in the voles.

But that doesn't mean that the secret to love can be found in a potion - at least not in the oxytocin potions that are sold routinely on the Internet. No one has ever studied what happens to people who take it for long periods of time. "We have no idea what it's going to be like for people who go around sniffing this stuff," Carter said.

Photo credit: Purdue News Service

Posted by Erika Check Hayden on February 13, 2009
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Stanford University's Drew Endy is still one of the great enthusiasts for synthetic biology: the visionary field that looks forward to the day in which bio-engineers will create new functions for cells by plugging together synthesized-from-scratch 'devices' such as DNA, control structures, and even whole reaction pathways. "Biology is the most impressive platform for manufacturing stuff we've ever encountered," Endydeclared at press conference on Friday. And to fully harness that power, he added, we need to be able to design the inner workings of the cell with as much confidence as electrical engineers now bring to microchip design.

Central to his vision is BioBricks , a catalog of standard molecular parts with well-characterized behavors that designers can mix and match to achieve the cellular functions they want. Dozens of labs have contributed thousands of parts to the registry over the past few years, says Endy--1500 last year alone. And therein lies the problem: who owns all these parts? And what sort of intellectual property protection do you give them? People do need to get credit for their work, after all. But patenting is out of the question: winning a biological patent typically takes several years and costs roughly $25,000. "The legal framework just doesn't scale," he says.

What you want is something more in the spirit of open source software, in which mechanisms like the Creative Commons license allows people to reused the software freely in non-commercial applications, so long as they give credit to the creator. But the Creative Commons license is grounded in copyright law, which is very differnt from patent law, and which does not apply to genes or other biological systems in any case.

So Endy has been working with the Boston Law firm of Fish and Richardson to devise a public agreement for BioBricks that would have much the same effect as a Creative Commons license, but that would be grounded instead in patent law. He believes that the agreement is the first such mechanism of its kind, and is breaking new legal ground. But in any case, it is now being circulated for legal comment. He and his partners are hoping to go public withit in early March.

Posted by Mitch Waldrop on February 13, 2009
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Posted on behalf of Karen Kaplan

A terrific session about global partnerships that's part of the American Association for the Advancement of Science's annual meeting this week fell a bit afoul of US visa regulations this morning. The panel presentation, "New Partnerships for Science in the Cradle of Humanity," aimed to address and discuss existing and developing industrial, governmental and academic partnerships throughout Africa and with other nations. Great topic, great content. The problem? One of the session's co-organizers, Thomas Egwang, executive director of the African Academy of Sciences in Nairobi, Kenya, couldn't be here for it -- because he couldn't get a US visa.

Sarah Banas, AAAS program organizer, says Egwang's Ugandan passport tripped him up -- he wasn't able to update it in enough time to get the visa. Banas points out that Margaret Kigozi of the Uganda Investment Authority was able to step in to moderate the session, which ran smoothly despite Egwang's absence. But the fact he was shut out from the very presentation he co-organized adds weight to a rising chorus of voices calling for a major overhaul of existing US visa laws.

Posted by Alex Witze on February 13, 2009
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Global warming stories are a mainstream media mainstay now, and the Obama-for-Bush swap in Washington means the climate change beat is heating up. But the media world is going through radical changes of its own. With science and environment reporters often the first cut from dying news organizations, what's in store for climate change coverage?

Among other things, more room for "the dark side"—dishonest climate change deniers—to dupe the general assignment reporters now replacing specialists, according to a panel discussion on climate change in the media. "Specialists are a dying breed," Pallab Ghosh of BBC News and the World Federation of Science Journalists told a conference room packed, largely, with exactly those specialists. "Science and environment reporters are seen as a luxury."

Scientists are already feeling the consequences. Journalists often ask whether "global warming science [is] settled," Stanford University climate scientist Stephen Schneider told the group, suggesting with a look that there are indeed plenty of stupid questions, and he's been asked most of them. Science is an ongoing enterprise of course, not an endpoint, and with climate change risk assessments the focus has to be on the preponderance of evidence, not uncertainties and apparent exceptions. "The denialists take the valid scientific disagreement and say, 'we found an exception!' as if it nullifies the mainstream consensus," Schneider said, comparing this method of falsification to "19th century chemistry." (That's not a compliment.)

So how to keep journos new to the science and environment beat from falling for the denialists' tricks? For the panelists, it comes down to mentoring. "This field does not do well if it stays ghettoized as the science and environment beat," said Peter Spotts of the Christian Science Monitor. With more science stories going to general assignment reporters, "We need to act as mentors on these issues for our colleagues." One example: Spotts suggests a handy pre-interview checklist to help climate cubs do a little risk assessment of their own:

__Is the source a scientist?

__Is the scientist active in the field in question?

__In the particular subdiscipline under dispute?

__If it's a skeptic, is he or she proposing testable alternative hypotheses, as opposed to just throwing brickbats from the sideline?

Answer all four of those in the affirmative and you've probably got a decent source, Spotts says. The more "nos" you get, the more likely it is you're being taken for a ride.

Posted on behalf of Thomas Hayden, lecturer in environmental sustainability at Stanford University and coauthor of "Sex and War: How Biology Explains Warfare and Terrorism and Offers a Path to a Safer World."

Posted by Erika Check Hayden on February 13, 2009
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With the meeting wrapping up today, the celebrated researcher Frans de Waal brought Darwin’s legacy into the modern world at a symposium on the evolution of morality.

Human morality has perplexed scientists and thinkers since Darwin’s time, but De Waal argued that it was not perplexing to Darwin himself, because he saw morality as linked to emotion, and saw reflections of human emotion all around us in other animals. De Waal, of the Yerkes National Primate Center at Emory University in Atlanta, described today the years of evidence that he and other scientists have gathered to support the idea that other animals show emotional and moral behaviors much like those in the human species.

For instance, chimpanzees shown videos of other chimps yawning yawn themselves, exhibiting a phenomenon called “motor contagion.” And mice show “emotional contagion,” responding to pain applied to other mice. Both these mechanisms are ways in which one animal can share the experience of another, which is an essential part of empathy, De Waal said.

Monkeys also show “prosocial behavior” in a task in which they are asked to choose either a block that will elicit a treat for themselves and a partner monkey, or a block that will only elicit a treat for themselves, De Waal said. The monkeys in this experiment more often choose to distribute treats to both themselves and the partner monkey, especially if the partner is related to them, De Waal said: “Monkeys do care about someone else,” he argued.

And finally, De Waal said, monkeys also reject unfair treatment – and here’s where he brought the whole argument back to the human world. His group trained pairs of monkeys to perform a simple task and get a piece of food – either a cucumber or a far tastier grape - as a reward. If both monkeys in the pair are rewarded with cucumbers, they happily perform the task eagerly and often. Yet if one monkey suddenly starts receiving grape rewards, while the other is stuck with cucumbers, the cucumber recipient tosses the inferior food out of his cage. And eventually, he goes to the corner of his cage and refuses to perform the task any more.

To De Waal, this signifies that monkeys, like humans, have a strong sense of fairness – a finding that has been reinforced in other animals, such as dogs. So according to De Waal, it makes perfect sense in the light of evolution that we become outraged when we hear that Wall Street bankers are receiving extravagant bonuses while the rest of us are struggling to fill our gas tanks and pay our mortgages. “I always think we live in cucumber land and they live in grape land,” De Waal said.

And with that, the meeting ends this afternoon. My brain is overstuffed and I could use a good night’s sleep, but it’s been a fascinating and thought-provoking few days in cucumber land.

Posted by Erika Check Hayden on February 13, 2009
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Synthetic biology is edging ever closer to curing disease, scientists told the meeting today.

University of California, Berkeley synthetic biologist Jay Keasling said that he and the company he founded, Amyris Biotechnologies of Emeryville, California, have hit a major milestone in the quest to make affordable malaria drugs.

Keasling and his company have been trying to use synthetic biology, a field that seeks to use engineering principles to improve biological systems, to make a cheaper source of the antimalarial drug artemisinin. The drug costs $3 to $20 per dose - too expensive for most of the millions of patients who need it in poor countries - because it comes from a plant, sweet wormwood, and has been difficult to synthesize.

Keasling and his company have been trying to rewire yeast so that they become factories churning out buckets of the precursor chemical to artemisinin - artemisinic acid. Three years ago, they could only make 100 micrograms per liter of the drug precursor in yeast. Now, Keasling says, they can make 25 grams of the drug per liter – a milestone that should bring the cost of synthetic production down enough so that he and his partners can meet the goal they set last year: to begin selling synthetic biology-derived artemesinin by 2012 for $1 per patient. Amyris and the non-profit drug maker The Institute for OneWorld Health, in San Francisco, signed a deal last March with Paris-based pharmaceutical company sanofi-aventis toward that goal.

“We are now in the scale-up stage and within one to two years, we hope this drug will be out on the shelves in places like Africa at much cheaper cost,” said Keasling. Today, Keasling said one of the synthetic biology tricks used to boost the drug yield involved building biological “scaffolds” into yeast to more efficiently guide enzymes through the drug synthesis pathway. This avoids some of the pitfalls – for instance, the buildup of toxic intermediates – that kept early versions of the system from making large amounts of artemisinic acid. Keasling said more details of the synthetic process he and Amyris used to boost the yield of the drug will be published within a week or two.

He also said that sanofi, Amyris and OneWorldHealth may be able to undercut other suppliers of the drug that engage in practices that are fueling the spread of resistance to artemisinin. “There are rogue manufacturers getting suboptimal drugs, or selling it as monotherapy,” Keasling said. “If we produce it cheaply in tanks, we can control who gets it, and that will prevent resistance in the future.”

Keasling's artemisinin project is widely seen as at test case for whether synthetic biology will fulfill its promise. But other test cases could be on the way, said Christina Smolke of Stanford University in Palo Alto, California.

Smolke and her colleagues published a paper last October showing how they could combine RNA components into systems that sensed and responded to levels of a drug called theophylline. Now, Smolke says, she and her team have engineered mouse immune cells, called T cells, to grow or stop growing in response to theophylline in mice.

Smolke’s team is now working to modify the same system to work in human T cells. That could aid doctors who are trying to treat cancer by injecting patients with supercharged T cells that destroy tumors. Smolke said if these T cells could be modified so that their growth is tightly controlled by a particular drug, they will be more powerful and safer weapons against cancer.

Posted by Erika Check Hayden on February 13, 2009
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Climate change is causing such dire problems for marine species that scientists are considering trying radical, previously 'sacrilege' methods to save them, they said today.

"From the poles to the equator, the effects of climate change are truly among us," Emily Pidgeon of Conservation International told the meeting. "These ecosystems we cherish now will be fundamanetally different in the coming decades, independent of any action we may take."

As an example, University of Washington, Seattle biologist Dee Boersma talked about Magellanic penguins, which she has studied at one site in Argentina for 26 years. The male penguins travel an average of 25 miles farther to find food, and the females lay their eggs an average of three days later than they did a decade ago, because the anchovies they love to eat are moving north. The penguins are also moving their nests, Boersma said - away from their reserve and onto unprotected private land.

It's scary stories like these that are prompting conservation scientists to revisit the once-taboo idea of "assisted migration" - moving animals to places where they stand a better chance of surviving the impact of climate change.

The idea was once considered 'sacrilege,' Pidgeon said. But, she added, "More and more I've been in discussions where we're deciding that we have to put all the options on the table," even though, as she admitted, assisted migration "still has a certain bad smell to it."

Photo by Graham Harris/Wildlife Conservation Society

Posted by Erika Check Hayden on February 12, 2009
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Scientists have sequenced the genome of modern humans' closest relatives, the Neanderthals. And so far they have found....

...well, not much, actually. At least not much that Svante Paabo, leader of the Neanderthal sequencing project, was willing to share with us this morning. The highlights, briefly: there's very little or no evidence of interbreeding between modern humans and Neanderthals. Neanderthals weren't able to digest milk as adults. They have similar mutations to modern humans in a gene involved in language, FOXP2. And they do not appear to have the version of a gene involved in brain size, microcephalin, that is commonly found in Europeans.

And Paabo does not think it will be possible to clone a Neanderthal from fossil DNA: "I would say [cloning a Neanderthal] starting from the DNA extracted from a fossil is and will remain impossible as far as I can see into the future," he said. But he left open the possibility that some new technology may one day change that state of affairs.

Paabo spoke to a room full of journalists by video conference from Leipzig, Germany, where he directs a center at the Max Planck Institute for Evolutionary Anthropology. But his presentation raised a lot more questions than it answered for me.

Paabo said that scientists assembled DNA from Neanderthal fossils in Croatia, Spain, Russia, and the Neander Valley in Germany into a rough genome draft. This draft is roughly 63 percent complete; for comparison, the reference human genome sequence is more than 90 percent complete. Each base in the Neanderthal draft was sequenced an average of 1.2 times. Again, for comparison, each base in the genome of Nobel laureate James Watson was sequenced an average of 7.4 times using the same technology as is being used in the Neanderthal project. "We still have a lot of gaps, but we have an overview" of what the Neanderthal genome contains, Paabo said.

The big hope of Paabo and other scientists sequencing the Neanderthal genome is that they will be able to compare it to the human and chimp genomes to find evidence of "positive selection" in regions of modern human DNA that have changed since we diverged from Neanderthals at least 500,000 years ago. These selected sites might underlie modern human traits such as symbolic language and social learning. "Studying the Neanderthal genome will tell us what makes modern humans and why we are really humans," said Paabo's colleague at Leipzig, Jean-Jacques Hublin.

Paabo said that his team has found regions of the modern human genome that seem to have been selected since the divergence with Neanderthals - for instance, on chromosome 7. But he couldn't say more about what genes might be in those regions, because, he says, he does not want to compromise his ability to publish the results of his work in a peer-reviewed journal, which he hopes will happen later this year.

He also moved rather quickly through his explanation of how the team has tried to analyze potential contamination from human DNA, which has been a problem for this team in the past. Scientists have now collected at least six different samples of Neanderthal mitochondrial DNA, an independent type of DNA passed down from mother to child. As a result, Paabo said the group has now grown confident that it is sequencing authentic Neanderthal DNA with no more than 0.3 percent contamination.

Paabo's team also used a separate method to estimate contamination: since the group assembled the genome of a female individual, it could estimate the degree of human contamination within it by tallying the places where male-specific DNA was erroneously found. Using this method, the team estimated it had no more than 0.5 percent contamination.

But I don't know how to interpret these contamination rates. Does this mean that each spot in the genome has a 0.3 to 0.5 percent chance of representing modern human rather than ancient Neanderthal DNA? That seems like a really small number, but if you're looking for tiny changes that could signal major differences between species, it seems like it could be a real major problem.

I'm hoping that the published version of the Neanderthal genome, when it appears, will shed a lot more light on that question - and reveal all the juicy details that Paabo seemed reluctant to delve into today!

Illustration credit: Knut Finstermeier

Posted by Erika Check Hayden on February 12, 2009
Categories: American Association for the Advancement of Science | Permalink | Comments (0) | TrackBacks (0)

As the annual meeting of the world's largest general scientific society kicks off in Chicago, Illinois, this morning, there's an atmosphere of celebration despite the chilly temperatures outside. It's not just the double anniversary of both Darwin's and Lincoln's birth. For scientists, the election of U.S. President Barack Obama is a real thawing of the cold shoulder they have felt from Washington, D.C. for the past eight years, said James Mc Carthy, president of the American Association for the Advancement of Science.

Obama recognizes that science is "not just ... a way of keeping these strange members of our society employed who want to go and do quirky things," McCarthy said, and believes that "[scientists] do play an important role in society."

As proof, McCarthy pointed both to Obama's list of all-star scientists appointed to key positions in his administration, and his support for the inclusion of science funding in the massive economic stimulus package now working its way through the U.S. Congress. "This is going to be a very, very important time to recenter our international thinking and contribute to international leadership" on issues such as climate change," McCarthy said. "I am optimistic."

The major themes of the meeting will be climate change and evolution, and McCarthy spoke to the connections between the two. He pointed out that while Darwin was penning his revolutionary book, "On the Origin of Species," published in 1859, inventors were developing the technologies that would spur the Industrial Revolution and result in massive alterations to our world - such as climate change. But McCarthy argued against those who have said that scientists should cede the climate issue to policymakers now that climate change has been proven to exist.

"Some people would say the science is clear and now scientists should get out of the way and let economists and decision makers proceed," McCarthy said. "But the choices to be made are not simple ones. The efficacy of technologies and the potential risks that will come with some of those technologies needs a very critical eye, and scientists need to be involved in all of these discussions about what we might do."

*This entry previously stated that the American Association for the Advancement of Science is the largest scientific society in the world, but has now been corrected to state that it is the largest general scientific society in the world.

Posted by Erika Check Hayden on February 12, 2009
Categories: American Association for the Advancement of Science | Permalink | Comments (0) | TrackBacks (0)