Planet Nature

1. What made you want to be a chemist?

The serious but predictable answer is a couple of really good science teachers, so thanks should go to the inspirational Andrew Munro and Jeremy Bushrod. The fun answer is John Nettles. I guess I should qualify that answer. It was my enthusiasm for a variety of TV cop shows – I use the term broadly to encompass a whole variety of mystery drama that initially made me consider forensic science as a career. Thankfully one or both of the above teachers encouraged me to keep my options open and study something broader – like chemistry. It’s a relief that at university I became more interested in organic chemistry, since I’ve saved myself from needing to be an expert in pathology, ballistics, analytical chemistry and all the other multi-talents exhibited by the average main character in these shows. Don’t get me wrong, I still watch these things, but the truth about the science gets heavily bent by the writer’s artistic licence.

2. If you weren’t a chemist and could do any other job, what would it be - and why?

I’m now too old to dream about becoming a professional sportsman of any sort, but whilst at the University of Sheffield, I took up playing snooker. I’m not good enough to do that professionally either, but I think I could make a decent stab at being a referee. I’d get to travel the world while doing something I love, and everyday would be different. The similarities to being a journal editor are quite frankly astonishing.

3. How can chemists best contribute to the world at large?

Aside from the obvious – solutions to disease, food shortage, energy, etc. – I think it would be great if we could dispel some of the myths about science. I’m forever disappointed that science is presented in schools as a long list of undeniable facts – the result of which is that many people who potentially could be great scientists are turned off at an early age and never return.

4. Which historical figure would you most like to have dinner with - and why?

Francis Bacon, one of the fathers of modern science philosophy. In many ways this relates to my answer to question 3. I’d also like to be able to check and dispel the myth that he was Shakespeare.

5. When was the last time you did an experiment in the lab - and what was it?

In the midst of the sink of entropy that was my fume cupboard – ask any who have shared a lab with me – it was probably a diazo-thioketone coupling reaction that is the cornerstone of making some of the light driven molecular motors of the Feringa group. I was rather pleased as I achieved a >90% yield in a reaction that was often problematic, although I think the particular combination of reactants I was using was the telling factor.

6. If exiled on a desert island, what one book and one CD would you take with you?

Queens’s greatest hits – I’m not sure how this works, but I know from experience that with time all music kept in a car becomes a Queen CD. I thought perhaps taking this with me would mean I would have access to a whole selection of music. As for the book – March’s Organic chemistry! No, seriously I’d have to take a fairly hefty tome though, I rarely read a book twice and I’d need something to keep me going for a long while once I realised that the Queen CD was a bad idea. Perhaps a survival guide might be a good idea as well – particularly if it included instructions on how to build a raft out of coconut shells.

Stephen Davey is an Associate Editor for Nature Chemistry.

This weekly Nautilus column highlights some of the online discussion at Nature Network in the preceding week that is of relevance to scientists as authors.
The Nature Network week column is archived here.

For those interested in consistency of nomenclature, Jennifer Rohn (Mind the Gap) posts about some of the challenges, after discoverinng that a particular "gene’s ‘official’ symbol was ZNF265 according to OMIM, but ZRANB2 according to NCBI Entrez and HGNC." As well as the challenge of researchers agreeing on common nomenclatures for entities such as genes and viruses with many variants (subtypes, polymorphisms and so on) and depositing the information in an appropriate database, the databases themselves sometimes do not update frequently. It does not get better, as Jennifer writes: "Looking up your new gene of interest in PubMed is not an easy way to grasp a coherent idea of what’s been published in the literature. Abstracts are littered with synonyms (and some pairs of different genes have the same synonym), but there is no unique gene identifier, as far as I can see, associated with the abstracts." And, as Euan Adie remarks in the comment thread: "even if you used database identifiers instead of HGNC names you could run into trouble – in the abstract did you mean the gene as we knew it in 2000, or in 2002, after we discovered those extra exons? In the position it was in on the initial genome assembly, or a million basepairs further down in the latest version? The same gene in different contexts needs different identifiers (or at least version numbers), but you still need to be able to pull all that together somehow and pull out the information you need." Further discussion continues, to which you are welcome to contribute. Views from authors (past, present and future) on topics such as this one are invaluable to journals in helping them to shape their policies.

So you use Nature Network, but what do you really think of the impact of Web 2.0 (the 'social' web) on research? The TalkScience team at the British Library has set up a group Scientific researchers and Web 2.0, posing a few questions about why busy scientists should invest in Web 2.0; using the web to share data and preprints; whether concern about confientiality will lead groups to set up "gated communities"; relevance of taxonomies, folksonomies, semantic web and other Web 3.0 concepts; and user-participation, necessary to keep these new web services alive. There are already discussions on scientific method in the era of big data, advertising by stealth, open notebook science, Web 2.0 in neuroscience, and more. Please join the group, which will be providing details of the TalkScience evening at the British Library in London in September, where some of these issues will be debated. Keep an eye out for the notice on this group to attend this free event.

The official programme for Science Blogging 2008 is now up. Whether you are a blogger and regular user of the Internet, or whether you have never written an online comment but are interested to learn more, this meeting is for you, so please head on over to the Nature Network group to find out more about the programme, contribute to the make-up of the sessions, discover where to find cheap accommodation, and sign up for some science-themed outings. As a taster, here is the abstract for one panel: "Mistrust of scientists is common, and misinterpretation of scientific results rampant. Science blogs can serve as a bridge between scientists and the general public. Blogs build a community of scientists in which they can discuss the peculiarities of their jobs, their work, and their results. More than that, science blogs have the power to demystify the scientific process for the public and to reverse deeply held stereotypes of scientists. In this session, we will discuss how science blogs can change the public’s perception of scientists and provide a support framework for scientists themselves."

Previous Nature Network columns.

The California scientists most likely to receive state grants for making new cell lines were those who proposed comparing embryonic stem cell lines and induced pluripotent stem (iPS) cell lines. Overall, thirty-two percent of all grant applications (16 of 50) were funded. Four of the five grants that proposed comparisons got funds. The unfunded grant application crossed into less favored categories, as it also proposed making lines from parthenotes and through nuclear transfer. None of the grant applications that sought to make cell lines using human oocytes were funded. Two proposed cloning through nuclear transfer, one proposed stimulating unfertilized eggs to divide into parthenotes, and one application proposed using both methods.

Success rates for grants proposing the derivation of only ES or only iPS cells were each 33%, but there were twice as many grants for iPS cells. That’s astounding considering that the grant program was announced in October 2007, a month before the first publications that human cells could be successfully reprogrammed.

Four proposals to make pluripotent lines using cells derived from the placenta, testes, or amniotic fluid were rejected. But a proposal to make spermatagonial stem cells, ES cells, and iPS cells was funded and highly praised, with reviewers particularly keen to see a comparison of iPS and spermatagonial stem cells from the same individual.

Three proposals to derive lines from biopsied or unviable embryos were turned down on the basis that the work was technically difficult and that any lines produced would be at best comparable to lines derived from leftover embryos obtained from IVF clinics.

Of the 50 grant applications received, 12 were from for-profit companies (See CIRM press release in February). However, all 16 grants awarded went to academic institutions.

For some of the rejected grant applications, reviewers objected that the proposed lines were not sufficiently distinct from lines that already exist. Overall, the reviewers seemed particularly concerned that every approved grant would result in a cell line that might have clinical applications. This applied not just to the embryonic stem (ES) cell and somatic cell nuclear transfer (SCNT) grants, which aren’t eligible for federal funding, but also to the iPS grants, which are. For example, reviewers doubted that attempts to reprogram neurons would be successful and thought that even if attempts to reprogram cancer cells did work, such cell lines could not be used clinically; consequently, grants proposing these experiments were not funded. For SCNT applications, reviewers worried that researchers couldn’t get enough oocytes.

No joy for SCNT

Perhaps most vocally disappointed was Kenneth Woolcott of Cascade Therapeutics, a company co-founded by Shoukhrat Mitalipov, who successfully cloned embryonic stem cells from monkeys through nuclear transfer. Though Mitalipov works in Oregon, the company was established in California largely in hopes of capturing CIRM grants. One reason the reviewers cited for rejecting the grant was the difficulty of getting enough eggs for experiments, since the ratio of established stem cell lines to oocytes used was around 0.3%. Woolcott says the grant reviewers got the facts wrong because the reported efficiency is 0.67%. (According to their publication, the team needed 304 eggs to make two stem cell lines (0.67%); however, one was genetically abnormal, so the efficiency would be 0.33% if only the normal line was considered). But Woolcott adds that the current efficiency, based on unpublished work, is over 3%, and he discounts reviewers’ concerns that Mitalipov would have trouble getting to San Diego when human eggs were collected. (See Nature Reports coverage of this breakthrough as well as comments from scientists who reviewed the paper. )

Woolcott accused CIRM of moving the goal posts in the middle of the game. “Dr. Trounson [CIRM’s president] said he was concerned about the access to oocytes, and they weren’t going to do any SCNT funding at this time until they worked out the oocyte issue.” (This is covered extensively in the June 30 blog on the California Stem Cell Report.)

Another rejected grant proposing SCNT is most likely from Stemagen, which previously reported cloning a human blastocyst in the peer-reviewed journal Stem Cells.The reviewers were also worried about the access to oocytes in this case, and had additional concerns about the techniques proposed for creating and growing embryos. (See our free blog post which includes description and link to a Nature News story that requires a subscription.)

Also called therapeutic cloning, SCNT involves inserting the nucleus from one cell into an egg from which the nucleus has been removed. Then the egg is stimulated to grow into a blastocyst, which would be destroyed to collect the innermost cells from which embryonic stem cells can be derived. Though harvesting these inner cells is the typical way of creating embryonic stem cells, it hasn’t worked yet for SCNT in humans, a failure blamed on an insufficient number of eggs for the attempts required to generate healthy blastocysts.

The advantage of SCNT would be that the cells would be compatible with the cell donor, and that stem cell lines from people with specific diseases could be studied. Induced pluripotent stem cells promise similar advantages from a skin biopsy, but it's still unclear what the differences between iPS and ES cells are, or whether those differences matter, and researchers are eager to study cell lines produced from both methods side by side.

Egg hunt
That’s likely to fuel the debate over what incentives CIRM can or should offer to encourage women to give their eggs for research. Compensating egg donors is federally barred in the US and particularly forbidden to CIRM grantees.

This shortage has been sufficiently pronounced to merit a news article in Nature when a woman volunteered to offer her eggs to Harvard researchers so they could try to create embryonic stem cells through nuclear transfer.

The recent Nature news article covered it well. If you don’t have a subscription, you can’t read the entire article, but here are relevant paragraphs. I’ll put some more links at the end.

“The US National Academy of Sciences (NAS) guidelines barring compensation were set in part to protect poor people from being exploited by labs that might offer large sums of money — along the lines of rules barring compensation for organ donation. But Alta Charo, a lawyer and bioethicist at the University of Wisconsin Law School in Madison, who liaised with the NAS committee that set donor-compensation guidelines in 2005, says the move was as much political as ethical. In California, supporters of Proposition 71, which allows funding for stem-cell and cloning research in the absence of federal funding, adopted compensation prohibition in part, Charo claims, “to assuage a fringe group of the women's movement” that was aligned against the assisted-reproduction community.
The NAS guidelines followed the lead taken by California and some countries to ensure that stem cells could easily cross state and international borders. The United Kingdom, however, essentially changed the rules two years ago. In 2006, Alison Murdoch of Newcastle University received approval for a plan to allow couples to defray the costs of fertility treatments if they are willing to share some eggs for research purposes. This could create disparity in the quality of care available to people who don’t have the money to undergo fertility treatments, says Charo, but it could also provide access to such treatments for more people. Murdoch has so far collected more than 100 eggs in this fashion.
Wood says that this egg-sharing workaround presents a problem; the eggs being used for research are from older individuals, presumably with fertility problems. Using eggs donated by women aged 20–24, he has reportedly achieved cloning success rates near 25%.
And there are ethical concerns. Marcy Darnovsky of the Center for Genetics and Society in Oakland, California, says that such schemes split the doctor’s duty of care three ways: between donor, fertility patient and researchers. And the focus on compensation, she says, distracts from concerns about risks from this one research avenue when other avenues seem open.”
The promised links:
An overview in the New England Journal of Medicine.

“The New Push for Eggs” by Jesse Reynolds, of the Center for Genetics and Society, which objects to cloning and believes the risks of egg-harvesting procedures are grossly under-reported. He also analyzes results of this round of CIRM grants. See also an earlier article on Egg extraction for stem cell research )

Charis Thompson of the University of California Berkeley says women who provide eggs are providing a service and should get paid. See her article in Regenerative Medicine.

Deborah Spar from Harvard on “The Egg Trade” in the New England Journal of Medicine. , also summarized and analyzed in a post by the bioethics blog that concludes “Spar’s proposals to understand and mitigate the risks of egg donation, insure that all consent to donation is informed, and have a serious debate on whether any women should be allowed to sell eggs are all sensible, but don’t look for any progress anytime soon.”

Some additional statistics
I went through the grant descriptions provided by CIRM to tally these.
For iPS: 24 grant applications, 8 funded.
For ESC: 12 applications, 4 funded. None of the 3 grants proposing SCNT were funded.
For comparing iPS, ES and other lines: 5 applications, 4 funded.
For other sources, including unfertilized eggs: 6 applications, none funded.
For using nonviable embryos or embryo biopsies, 3 applications, none funded.

If anyone wants to see my Excel spreadsheets tallying whether a grant was for ES, iPS, something else, or a combination, let me know and I’ll email it to you. Just let me know if you find a mistake or something interesting.

As the celebrations for Darwin’s 200th birthday begin to gear up, Newsweek has decided to make sure the man doesn’t get posthumously too big for his boots.

Emblazoned across its cover this week: Lincoln VS Darwin.

Charles and Abe were both born on the same day, 12 February 1809, and that’s all the peg needed to ask who was more important. Newsweek doesn’t actually out and out declare Lincoln the winner, it does though say:

It's an apples-and-oranges—or Superman-vs.-Santa—comparison. But if you limit the question to influence, it bears pondering, all the more if you turn the question around and ask, what might have happened if one of these men had not been born? Very quickly the balance tips in Lincoln's favor.

This is argued on the basis of ideas similar to Darwin’s being arrived at by Wallace. Lincoln is “irreplaceable”, Darwin is not.

Unsurprisingly the blog world has had something to say about this...

The eTrilobite.com blog asks the question many are pondering: “What was Newsweek thinking?” It goes on to imagine the article’s creation before pointing out that arguing only Lincoln could have saved the United States is “history at it’s worst (besides outright lies, of course)”.

Over on Laelaps, ecology and evolution student Brian Switek gets in on the party, asking “Who is more important: Me or Michael Bolton?” He also takes issue with the accuracy of Newsweek’s Darwin.

“There is nothing as egregious as saying Darwin converted on his deathbed or anything of that sort but there are many small errors that add up to little more than some rehashed textbook cardboard,” says Switek.

Nate on the slightly expletive-prone Science Gone Mad blog details how he was not allowed to comment on Newsweek’s website. His blocked comment starts thus, “I think that this is simply an asinine comparison.” And ends thus: “Seriously, Newsweek ... epic fail.”

PZ Myers is similarly unimpressed.

Biologist Larry Moran thinks Newsweek is biased towards the American, noting, “In fairness, if you only consider the United States of America, then the answer might be correct. Darwin's ideas do not have much influence there.”

Want more fights? The Skepchic blog has declared Benjamin Franklin better than Tycho Brahe, Marie Curie better than Louis Pasteur and Jane Goodall better than Margaret Mead.

It’s noisy in the world of science this week, we’ve got screaming earths, singing cave men and musical jelly.

Star Scream

Scientists looking at the auroral kilometric radiation have come up with an interesting by-product. This awful noise.

This radio emission is caused in a similar way to the northern lights. When charged particles from the Sun hit Earth’s ionosphere it seems they don’t just make a light show, they make noise. It’s like some kind of demented space disco (press release).

The serious point of this work is to look at how this auroral kilometric radiation spreads out, as Space.com notes:

Theorists had long figured the radio waves, which were not well studied, oozed into space in an ever-widening cone, like light from a torch.

But new data from the European Space Agency's Cluster mission, a group of four high-flying satellites, reveals the bursts of radio waves head off to the cosmos in beam-like fashion, instead.

And looking for this noisy radiation could help us detect planets orbiting other stars, say the researchers.
Here’s the research paper. And you can hear another AKR noise recording here, along with other cool space noises.

Singing Cave Men

Livescience has an interesting, if wildly speculative, musical story. Iegor Reznikoff, of the University of Paris X in Nanterre, says ancient cave men liked a good tune.

He is going to tell a forthcoming conference that the areas of their caves with the most painting also have the best acoustics.

“Why would the Paleolithic tribes choose preferably resonant locations for painting,” asks Reznikoff, “if it were not for making sounds and singing in some kind of ritual celebrations related with the pictures?”

Even better, Live Science says, “Humming into some bends in the wall even produced sounds mimicking the animals painted there.”

Jelly music

Finally, at an architectural banquet later this week the noise of wobbling jellys will be converted into music, according to the Times.

This story is also discussed on this week’s Nature Podcast.

A mathematical glitch means we’ve been massively underestimating how at risk endangered species are, according to a paper in this week’s Nature (paper, press coverage).

By failing to include random variations in individuals within a species, such as size and male-to-female sex ratios, risk estimates have been out by up to 100 times, say Brett Melbourne, of the University of Colorado at Boulder, and Alan Hasting, of the University of California, Davis. Which means animals like the Sumatran tiger could go extinct 100 times faster than we thought.

“This seems subtle and technical, but it turns out to be important,” Melbourne told AFP.

After developing new models that did incorporate some of the missing factors, Melbourne and Hastings confirmed them experimentally using a population of beetles in their lab.

“When we apply our new mathematical model to species extinction rates, it shows that things are worse than we thought,” says Melbourne (press release). “By accounting for random differences between individuals, extinction rates for endangered species can be orders of magnitude higher than conservation biologists have believed.”

This could have big implications for the IUCN, which manages the endangered species ‘red list’.

“We are certainly underestimating the number of species that are in danger of becoming extinct because there are around 1.8m described species and we’ve only been able to assess 41,000 of those,” says Craig Hilton-Taylor, of the IUCN (Guardian). “We are constantly looking at how we evaluate extinction risk, and it may be they have hit on something that can help us.”

Nancy Tcheou, who is acknowledged in the paper, says (of her acknowledgement), “I guess working in the beetle lab for more than a year kinda pays off… in addition to the fact that I’ve counted to 50 more times than countable. Just beetles. Yep.”

Nature Geoscience publishes a regular feature called BackStory, at the back of the journal or on the journal's website, in which the authors of a paper in the current issue of the journal answer questions about their field work -- providing an unusual perspective on the region of the world that contributed to the paper. The Backstory in the July issue (Nature Geoscience 1, 482; 2008), Sailing for a stretched lithosphere, describes how Jenny Collier and colleagues, having managed to get themselves and all their instruments on board a ship not too far away from an imminent war zone, enjoyed the serenity of life at sea as they investigated the rifted continental margin of India.

How long did it take to plan the fieldwork?

Two years elapsed between getting the project approved and setting sail. We wanted to use a particular vessel, the RRS Charles Darwin, which was already in the Indian Ocean and had the scientific capability that we needed. Unfortunately, we had to join a rather long waiting list. Coordination was a nightmare — our scientific instruments were all in different parts of the world, taking part in experiments that were also subject to scheduling changes. When we finally had our chance, the build-up to the Iraq invasion resulted in several changes to our port of embarkation. It was a huge relief when we finally set sail with all the equipment onboard!

See Nature Geoscience's website for the rest of the Backstory.
The paper featured is: The relationship between rifting and magmatism in the northeastern Arabian Sea, by Timothy A. Minshull, Christine I. Lane, Jenny S. Collier & Robert B. Whitmarsh (Nature Geoscience 1, 463-467; 2008).

Here is another brilliant example for our occasional periodic table series. This beast is currently residing outside the American Chemical Society building in Washington.

More Great Beyond elements
Elementary mistakes
Periodic Table Printmaking Project

Image: courtesy of Emily Unell

Next week, here on Climate Feedback, I'll be reporting directly from Hokkaido, Japan's nothernmost island, where leaders from rich nations and emerging economies will be meeting to discuss some of the world’s most pressing problems.

Gathering from July 7-9 will be the Group of Eight (G8) - an exclusive but informal bloc of nations, comprising the world's seven leading economies Canada, France, Germany, Italy, Japan, the United Kingdom, and the United States, plus Russia. This year's summit will extend to an additional eight industrialised nations on the final day to facilitate US President George Bush’s Major Economies Meeting.

Climate Change is expected to top the agenda of both meetings. Pressure is on G8 delegates to go above and beyond the political breakthrough of the 2007 Summit in Heilegendamm, Germany, where leaders agreed to seriously consider slashing emissions by half of 1990 levels by 2050. And George Bush seems keen to leave some sort of a legacy on tackling climate change through this meeting of major economies (or just any sort of a legacy other than Iraq actually).

But are binding emissions a realistic expectation of the G8? Will oil prices and global food shortages bump global warming down the agenda? And what progress on climate change is likely under the current US administration? I've written a preview in this week's Nature on what's being hoped for, and expected, from what should be a very interesting round of talks.

Tune in here from next Monday to follow the events as they take place.

Olive Heffernan

A watchdop group has called on the US Food and Drug Administration to shed some light on sunscreens. The government agency has failed to finalize standards for testing and labeling sunscreens, says a report by the Washington, DC-based nonprofit Environmental Working Group. The report also concludes that 85% of sunscreens on the market either contain potentially toxic ingredients or fail to provide enough protection from both UVB and UVA radiation. Most products shield the skin from UVB rays, which cause sunburn as well as DNA damage associated with skin cancer.

A study published yesterday in the journal of the Federation of American Societies for Experimental Biology (FASEB), provides details to support the idea that UVB rays are more likely to cause cancer. However, research published in May suggests that the deeper-penetrating UVA rays that cause skin aging also suppress the immune system, compromising the body’s ability to protect itself against the development and spread of skin cancer.

The FDA is currently considering sunscreen labeling changes to help consumers make better choices, but in the meantime, the American Academy of Dermatology offers this advice: Use broad spectrum sunscreen products of SPF 15 that protect against UVA and UVB rays. Lather it on everyday and wear protective clothing.

Image by Daquella manera

They say that knowledge is power, and some 15 US states are poised to apply that philosophy in tackling the obesity epidemic. These states are considering legislation that would require fast food chains and certain restaurants to provide consumers with nutritional information such as calorie, fat and sodium content of food items. New York and California may be the first to pass laws mandating statewide menu labeling, which could set the trend for other states to follow. The public seems to be embracing the idea, particularly in New York, where a recent poll found that 80 percent of people want nutritional tables posted in fast food eateries. The point of these laws is to encourage consumers to make informed – and thus presumably healthier – decisions about what they are eating. Ultimately, the new laws aim to curb America’s obesity epidemic – which is at an all-time high (34% of adults are obese, and 32% of school-aged children are overweight or obese) – and lower the rate of diseases associated with obesity, such as diabetes, hypertension, and certain types of cancer.

But will people actually use the information to modify their eating habits? Perhaps the best place to inquire is New York City, where a menu-labeling rule is already in place (ahead of the possible statewide regulations). In January, the city’s Board of Health voted in favor of a regulation requiring restaurant chains (businesses with more than 15 units nationally) to prominently list calories on menus and menu boards. The industry group New York State Restaurant Association has challenged the regulation, and the 2nd US Circuit Court of Appeals will probably deliberate the case for another few weeks, according to a Restaurant Association representative. Meanwhile, the FDA has sided with New York City.

I conducted an informal survey in lower Manhattan and found that, although people seem to be noticing these calorie counts, they way it drives their behavior is variable.

“For me personally, it doesn’t change what I do,” said a man I met in a fast food chain, noting that he is not concerned about his weight. “But I think with other people it does.”

“I don’t pay attention to it,” said a woman sitting nearby. “I don’t believe that a plain bagel has 300 calories,” she added, referring to the posted calorie content.

But according to the employee working behind the register, the nutritional tables are deterring customers from buying high-calorie foods—to the detriment of business. "The people, when they ask about the muffins’ calories, they don’t buy them,” said the employee, pointing at the 400-calorie ‘reduced fat’ item. “It’s affecting my sales.”

A few blocks away at a fast-food restaurant where king-sized chocolate milkshakes pack over 840 calories, patrons stopped to scan the nutrition table on the wall before approaching the register. One young woman studied the information but claimed that it would not influence her decision; she would have that bacon-double-cheeseburger no matter what. But a traffic policeman said he would chosse menu items based on caloric and fat content. “It’s very important to know the nutritional value of the food,” he told me. A couple from Argentina agreed; they used the nutritional tables to avoid the excessive amount of carbohydrates that characterizes the North American diet.

I could not help but notice that the people who said they used nutritional tables to make decisions appeared lean and fit. All this made me wonder whether menu-labeling will simply reinforce good eating habits in those who already have healthy lifestyles, rather than reform those who most need it. Critics of menu labeling have pointed out that Americans have continued to get more obese despite two decades of nutritional labeling on packaged food. Perhaps better calorie labeling will not change things. What do you think?

Image by ebruli

We at Nature Network are putting on a science blogging conference in London on 30 August 2008. More than 100 bloggers, scientists and science communicators will gather at the Royal Institution to discuss topics such as how science blogging can change (improve?) the public’s perception of science, how blogging can boost your creativity and be used as a teaching tool, how scientists can be more open with their primary research data, and what the future holds for online scientific communication.

Click here for the programme. A few sessions have been set aside to be ‘unconference’ sessions, meaning that the topic and the speakers will be proposed and decided on the day of the event.

Click here for more details about the conference. There’s already been quite a bit of discussion about the event in the conference’s forum on Nature Network.

Registration is free. Just email us (network at nature.com) with your name, affiliation, and a link to your blog if you have one.

Coal needs to hire some better PR people, because it’s taking an awful kicking today.

In America a judge in Georgia has cancelled a permit for a new coal power station citing carbon dioxide emissions concerns. “We think this is the beginning of the end of conventional coal-fired power plants, because of the enormity of their emissions,” says Bruce Nilles, head of the Sierra Club’s anti-coal campaign (Atlanta Journal-Constitution).

In the UK a think tank is recommending a minimum two-year block on coal-power investment. The Institute for Public Policy Research says this is needed to hit Europe’s 21% reduction in heavy industry greenhouse emissions by 2020 (Daily Telegraph).

In Australia eco-campaigners have decried a new AU$750 million coal power plant as “complete madness” (Sidney Morning Herald).

More on all of this below the fold...

America

While cancelling a permit related to air pollution might not instantly appear a big deal, the knock on impact could be sizeable.

The NY Times point out that this is the first time a court decision has linked carbon dioxide to a pollution permit. It shows “that builders of coal plants would face continued difficulties in the court system as well as with elected officials in many states”, says the paper.

A Reuters Analysis piece agrees, quoting Hill & Associates energy analyst Matt Preston. “This adds to the uncertainty as if that was needed,” say Preston. “Until there is a more clear path for coal projects with regard to climate change, it will be more difficult to raise money for coal projects.”

UK

The UK report recommending an investment freeze isn’t official policy, but the Guardian points out its source, the Institute for Public Policy Research, is the ruling Labour party’s “most trusted thinktank”.

The report says if only a proportion of the 75 currently proposed coal plants in Europe are approved the EU’s 21% emission reduction plan will only be achievable through carbon capture and sequestration (report pdf, press release).

Luckily a trial run of sequestration has also kicked off in Europe this week.

Australia

Despite the protests from environmentalists, the Australian government is insisting the new power plant proposed for Latrobe Valley is ‘clean coal’.

“The project uses a process called integrated drying gasification combined cycle which can reduce emissions of CO2 from brown coal-fired power generation by 30% and reduce water consumption by 50%, compared to current best practice for brown coal power generation in the Latrobe Valley,” says energy minister, Peter Batchelor (Sidney Morning Herald).

The valley is also a “dream location” for geothermal power, according to the Latrobe Valley Express.

Image: Getty

Everyone loves penguins, so every journalist loves stories about penguins. Today’s is about Dee Boersma.

For 30 years she’s been working with the critters and she’s just written a new article in the journal BioScience warning that penguins are “sentinels”, and these “canaries in the mine” are telling danger is present. As ever, the danger is sourced to us (press release, paper pdf).

Climate change, fishing and pollutions are all in the frame.

“Penguins are among those species that show us that we are making fundamental changes to our world,” says Boersma, a biologist at the University of Washington (UW press release). “The fate of all species is to go extinct, but there are some species that go extinct before their time and we are facing that possibility with some penguins.”

Her paper notes that penguin numbers at Punta Tombo in Argentina have halved since the late 60s and Galapagos penguins have fallen to a quarter of their 70s numbers.

“What happens to penguins, a few years down the road can happen to a lot of other species and possibly humans,” penguin expert Susie Ellis, who is now a director of the International Rhino Foundation, told AP.

Boersma’s article concludes with a question:

We are changing the world, the course of evolution, and the species with which we share the planet. Can people change to allow other species to persist and coexist? That is the real question: can we, and will we, manage ourselves?

Of course after 30 years there are some great stories to tell. The Seattle PI reports that one particular penguin Boersma studied took a particular fancy to her. “He would come knock on our door with his bill. He would follow us when we went to work, and we'd say, ‘Go home, save your fat!’”

Image: NOAA

A huge warship deemed too-toxic to be broken up in India is to be dismantled in the UK.

The Clemenceau is a 238 metre long, 32,700 ton aircraft carrier, formerly the pride of the French Navy. She will be taken to Teesside and dismantled alongside the controversial US ‘ghost fleet’ by Able UK Limited (press release).

Given the furore around the asbestos-ridden US ships arrival off the coast of England a few years ago, it seems likely that some people are going to be up in arms about the already-controversial Clemenceau.

The vessel was taken initially to be scrapped in India, before furious French politicians forced then-President Jacques Chirac to call it back. It was, they said, outrageous to be “lecturing the world on the environment while having other countries deal with our toxic ships” (Times).

The historical antipathy between ‘The Frogs’ and ‘Les Rosbifs’ means they are unlikely to be so bothered this time. Also, given environmental standards will probably be tighter in the UK than in India, this is being portrayed as a better option ecologically.

Ingvild Jenssen of environmental group Platform on Shipbuilding told AFP, “Overall we're happy to see the ship going to the UK rather than India. ...[A]s far as we know now, Able does have all its environmental permits and planning permits.”

The Clemenceau’s sister ship, meanwhile, got a far better deal and rather than Teeside is enjoying an extended stay in Brasil.

French coverage
Le ‘Clemenceau’ sera démantelé par des Anglais – Le Figaro
L'ex porte-avions français Clemenceau sera démantelé en Angleterre - AFP

In your face Phoenix! While the lately-landed lander is busying itself scraping for ice, old-timer rover Opportunity has been taking some amazing photos; which so far have only had limited press coverage, but really merit a bigger splash.

The ever-anthropomorphised rover has sidled up to a cliff face in Victoria Crater and is tilting its camera skywards. Is this just an attention-seeking ploy now that kid-brother (sister?) Phoenix is showing off finding signs of water ice, and testing the soil, blah blah blah?

I don’t doubt that NASA will be shouting loudly about these images, which as yet have only made it into the raw data files on the Phoenix mission’s web pages. Perhaps they’re going to wait until the rover has nosed closer to the bottom of the cliff and got a better view. The plan seems to be to take some close-up shots of the rocks and see what kind of structure they have, geologically. Coupled with the data that Phoenix is digging up, further north, it looks like Mars is going to be spewing up data for us to devour for a while yet.

(Another great picture below the fold.)

Steven Inchcoombe, who became Managing Director of Nature Publishing Group (NPG) last October, is interviewed in the June/July issue of Research Information. He answers questions about the main information needs of researchers, the role of peer-review, NPG's position on open access, and provides some predictions for the future.

Open access means that authors or their funders may have to pay to publish papers and I think this will make them demand a higher level of service from publishers. They will want more visibility about what is happening in the publishing process. And once papers are published, authors will want to know who has accessed them as they might want to approach them about possible collaborations. In addition, self-archiving mandates require authors to do more work. If publishers are clever they will offer authors more help to do this. Also, as more authors are not native English speakers, publishers may have to help them more in how they express themselves in their papers. There are more and more versions of content available to readers. To justify their versions, publishers must offer serious value such as in forward and backwards citation linking. Another big challenge will be bringing in rich media such as audio and video.

See the Research Information website for the full article.

In its July Editorial Wouldn't you like to know?, Nature Physics (4, 505; 2008) asks how much of the mass of information available online in encyclopaedic form can be trusted. The Editorial discusses various sources: Wikipedia, of course; Citizendium (with its associated Eduzendium); Scholarpedia ; and a brief mention of Encyclopaedia Britannica, which has just begun experimenting with user-generated input (although not noted in the Editorial).
Scholarpedia is the most recent of these resources, and says of itself that it "feels and looks like Wikipedia - the free encyclopedia that anyone can edit. Indeed, both are powered by the same program - MediaWiki. Both allow visitors to review and modify articles simply by clicking on the edit this article link." Scholarpedia is said to differ from Wikipedia in that each article is written by an expert (invited or elected by the public); anonymously peer reviewed to ensure accurate and reliable information; and has a curator - typically its author -- who is responsible for its content and who has to approve any proposed modifications. The website claims that, by this method, "while the initial authorship and review processes are similar to a print journal so that Scholarpedia articles could be cited, they are not frozen and outdated, but dynamic, subject to an ongoing process of improvement moderated by their curators. This allows Scholarpedia to be up-to-date, yet maintain the highest quality of content."
The Nature Physics verdict? "Expert authorship and curatorship of free online information are indeed welcome. If scientists embrace Scholarpedia, then perhaps the opportunity to make sure that their own favourite area is well represented in its pages — as well as the possibility of citations — will prove sufficient incentive to the hard-pressed experts. The potential is huge, and so is the challenge."

The International Mathematical Union has released a report on the use of citations in assessing research quality. The report, Citation Statistics, is written from a mathematical perspective and strongly cautions against the over-reliance on citation statistics such as impact factor and h-index. The belief that these parameters are accurate, objective and simple, is unfounded.
It states that the objectivity of citations is illusory because the meaning of citations is not well-understood. Its meaning can be very far from ‘impact’. Although having a single number to judge quality is indeed simple, it can lead to a shallow understanding of something as complicated as research. Numbers are not inherently superior to sound judgments.
The report, written by mathematicians, promotes the sensible use of citation statistics in evaluating research and points out several common misuses of this widespread application of mathematics. The authors of the report recognize that assessment must be practical and that easily-derived citation statistics will be part of the process, but caution that citations provide only a limited and incomplete view of research quality. Research is too important, they say, for its value to be measured with only a single coarse tool.
(This is a precis of the press release accompanying publication of the report, see links above.)
Further discussion of the report, together with other matters related to citation and quality metrics, is taking place online at the Nature Network Citation in Science group, which all are welcome to join.

An edited version will appear on the site on later this month.
Differentiated cells can be reset to an embryonic-stem-cell-like state, but doing so requires using retroviruses to insert a suite of genes into a culture of cells. Because the viruses insert their cargo at random into the genome, infected cell populations from the same individual are genetically different, and it’s hard to know whether differences between the resulting stem cell lines are due to this genetic variation, the epigenetic state of the original cells, or chance events. Worse, the current use of retroviruses renders the cells unusable for clinical applications.

Now researchers led by Rudolf Jaenisch at the Whitehead Institute in Cambridge Massachusetts show a convenient way to generate genetically identical cell populations that can be converted to induced pluripotent stem (iPS) cells by adding a drug . What’s more, they show that cells from multiple organs can be successfully reprogrammed.

In previous work, Jaenisch and other laboratories had reprogrammed cells using genes that turn on in the presence of a drug called doxycycline. This allowed them to study how long transgenes need to stay active for reprogramming to occur. To prove that the cells with drug-inducible reprogramming genes were pluripotent, researchers mixed the cells with mouse embryos to create chimeric mice.

In this paper, the researchers show that cells from multiple organs within these chimeric mice can be efficiently reprogrammed with the addition of doxycycline: reprogrammed cells include neural progenitors, mesenchymal stem cells, and keratinocytes as well as cells taken from muscle, intestinal epithelium, the adrenal gland, and the hematopoietic lineage.

iPS cells generated from different tissues taken from the same mouse are genetically identical, allowing researchers to examine the effects of cell types and retroviral insertion sites. For example, the researchers were able to reprogram intestinal epithelium derived from one iPS cell line, but not another, suggesting that reprogramming requirements vary between cell types. In particular, the expression of transgenes seemed to vary with both cell type and site of insertion in the genome.

The reprogramming rate for `secondary iPS cells’ was 4 to 8 fold higher than for the production of primary iPS cells, presumably because cells in the mice already had the favorable number of proviruses inserted at appropriate sites of the genomes. Still the overall reprogramming rate is low, only between 2% and 4%.

The researchers believe this could be because the drug-inducible transgenes may be more or less responsive to doxycycline even within genetically identical cells and also because reprogramming depends on stochastic events, several of which are required for complete reprogramming.

A source of genetically identical cells will help researchers home in on these and other variables and greatly simplify the search for methods to create clinically acceptable reprogrammed cells.

Wernig, M. et al. A drug-inducible transgenic system for direct reprogramming of multiple somatic cell types. Nat. Biotechnol. doi:10.1038/nbt1483 (Advance online publication July 1, 2008)

Our June editorial discusses the relationship between web traffic and citations. Specifically, can one predict how well any particular paper is cited years after publication, based solely on the number of downloads it receives immediately following its appearance online? Our preliminary analysis suggests that this relationship not only exists, but is surprisingly strong.

I’ll leave you to read the editorial for more of the background as to why we examined this relationship, but I will repeat a few keys things here. The main purpose of this post is to provide more of the details behind the data and analysis, and to initiate a good discussion.

Everyone has their own pet problem with impact factors, whether it be with the calculation method, the non-reproducibility of the actual values, or the disagreement over what IFs really represent, just to name a few. Despite all of these concerns (and more), these numbers are typically used to rate the importance or prominence of a particular journal, and thus by proxy, the importance of the individual papers published within. This is a seriously flawed use of association (see a previous Nature Neuroscience editorial discussing this concept), leading scientists to often equate the total number of citations with scientific impact, which can be fraught with problems. Searching for an alternative measure of impact that is perhaps free of the “bias of authority” (citing a paper because it is from a famous lab) or the “lemming bias” (citing a paper just because everyone else seems to do so whenever broaching a particular subject) led us to explore readership.

The readership of a particular article should roughly reflect the outside interest in the topic and the perceived value of the experiments within. Readership can potentially be quantified through the examination of download statistics from the website where a manuscript is published. These download statistics can be viewed in the same way as the NY Times bestseller list in the sense that the data are indirect; these numbers don’t actually measure readership as much as they measure access and potential readership. In other words, in our case, we are assuming that everyone who downloads a paper (especially the PDF version) actually reads it. Definitely a leap of faith, but nonetheless, we took this caveat in hand and pressed forward.

The papers in our initial dataset were published online between January 2005 and November 2005 (N = 215 papers). Only research articles and reviews were considered. Our download statistics are COUNTER-compliant, an initiative that provides libraries and publishers with more consistent and credible usage data. For the purposes of the editorial and here, the actual numbers are transformed. Our citation data come from Scopus, although we could have probably used Google Scholar or Thomson products just as easily (several studies have found an equivalence in the citation listings between Thomson’s Web of Science and Google Scholar, and there is no reason to believe that Scopus would be any different [Belew, 2005; Pauly & Stergiou, 2005]). Both sets of data were accurate as of the end of March. For web traffic data, total downloads within a particular time frame were calculated starting from the published Advanced Online Publication (AOP) date.

We initially noticed that immediate PDF downloads correlated better with eventual citation counts than did HTML downloads (R = 0.60 vs. 0.65 for HTML and PDF downloads, respectively). Therefore, we focused on PDF web downloads for the remainder of the analysis. It is important to note that this measurement is independent of citation or web traffic differences between fields or different types of papers. The lowest cited, least downloaded paper contributes equally to the weakness or robustness of the correlation as does the most highly cited, heavily downloaded papers.

As the download time frame was extended, the correlation progressively increased up until 180 days post-AOP, but fast-forwarding to 1 year, the correlation dropped significantly (Fig. 1). This makes sense in retrospect, since web traffic typically declines with time (as a paper becomes “old news”), while citation rates increase with time. The divergence in these two measurements dramatically affects the correlation. This peak correlation between downloads and citations at 6 months was also observed in a previous study that examined the relationship between web traffic and citations for papers deposited in the arXiv pre-print server (Brody et al, 2006).

Figure 1 The correlation between downloads and citation counts increases up until 6 months, and then dramatically decreases at 1 year. Correlation coefficients are graphed as a function of time.

We next decided to see how well web download data could predict eventual citations. For this analysis, we calculated a linear best-fit equation for the data graphed in the editorial. We then took all papers published in Nature Neuroscience within the first 3 months of 2006 (N = 55 papers), and used their 90 day PDF download numbers as the ‘X’ input into the equation. This yielded a series of citation values that would produce a predicted linear best-fit line for the 2006 data. Comparing this line to the actual best-fit line for the data, we see that although they are different, the slopes are nearly identical, suggesting that there is an offset in our predicted values, biased towards higher citation rates in a systematic fashion (Fig. 2). This offset could arise because the citation data is not mature enough for papers published so recently, with actual citations lagging behind those predicted by the model, in general.

Figure 2 PDF downloads vs. citations counts for 2006 papers. Predicted line derived from calculations using 2005 best-fit equation.

Finally, we decided to test how this relationship would hold up across another discipline. Previous studies examining downloads vs. citations found that physics and math preprints (Brody et al, 2006) and a subset of the medical literature (Perneger, 2004) revealed a similar positive correlation between downloads and citation counts for individual papers. We extended our own study to papers published in Nature Genetics (N = 168) for 2005. Again, we found a strong correlation between immediate PDF downloads and eventual citation counts (R = 0.71) (Fig. 3). Thus, this relationship is likely to hold up across various disciplines, across journals with different impact factors, and includes pre-prints as well as published articles. With studies suggesting that open-access articles receive more citations than those published behind firewalls (Eysenbach, 2006), it would be interesting to determine how open-access articles (with a presumed higher readership, or at least potential readership) fare in this type of analysis.

Figure 3 PDF downloads vs. citation counts for 2005 articles published in Nature Genetics.

We realize that this analysis is enticing at best, potentially providing a piece of an alternative solution for deciphering the impact of an individual paper. In this current scientific climate where tenure and grant funding decisions are influenced by flawed metrics like impact factor, it is important to make good use of all available technology in an attempt to realize a better system of measuring the scientific impact of any particular paper. This analysis is obviously preliminary and flawed in its own ways, but perhaps metrics such as paper downloads can find a place in a compilation of aggregated stats, painting a more accurate and informative picture of manuscript influence.

This analysis was conducted jointly with Hilary Spencer of Nature Precedings. We would like to thank Jamie Sampson for assistance in acquiring the download statistics.

What do you get if you cross a cow and moose? A bit of an embarrassment it seems.

The French government has quietly killed off a rather unsuccessfully hybrid animal created in February, the half cow / half caribou Vachibou (vache being French for cow).

“The Vachibou is a hybrid animal with a very short lifespan,” a spokesman for the French consulate in Quebec says AFP. The paper refers to the short lived beast as a “chimeric hybrid”.

If this were a real animal it would have an even shorter lifespan that the incredibly short lived chameleon featured on the Great Beyond. Luckily it’s not a real animal, but an example of what happens when designers don’t check their biology facts...

It is, in fact, a logo produced by the French for their sponsored events celebrating Quebec City’s 400th anniversary. The Canadian National Post explains: “Named the Vachibou (Cowibou), the distinctive creature was intended as a hybrid of the dairy cattle of Normandy, homeland of Quebec's original settlers, and the wild caribou that roam the Quebec tundra.”

However when it was unveiled it was noted that the antlers on the design were of a moose, not a caribou. And it was a female cow with male antlers, which seemed odd to some people.

Initial plans to redraft a more “anatomically correct” version of the animal have been shelved and the animal has quietly been put out to pasture.

See a picture of the beast here.

On Monday researchers at the small town of Ketzin near Berlin began pumping carbon dioxide into the ground, the first time this has been done in mainland Europe.

In two years the German Research Centre for Geosciences plans to store 60,000 tons of the greenhouse gas over 600 metres below ground in saltwater-saturated porous rocks (press release). Scientists will then see what happens, aiming to “fill the gap between the numerous conceptual engineering and scientific studies on geological storage and a fully-fledged onshore storage demonstration” (project website).

“The main goal of the project is to develop and test ways of monitoring the stored CO2,” says Hilke Wuerdemann, of the centre (Deutsche Welle)

Spiegel says if the sequestration project is successful it could be used with the nearby Vattenfall coal power plant. There have been concerns, notably from Greenpeace about the facility, especially the potential for the carbon dioxide to leak out of the rock (AFP),

The CO2SINK project is being support by the European Union and features in the 2006 Nature feature Putting the carbon back: The hundred billion tonne challenge.

More on carbon sequestration from Nature
Carbon burial buried article from 2008
A handful of carbon commentary from 2007
Capturing carbon editorial from 2006

If this cute critter looks a bit miserable it’s probably because he doesn’t have much to look forward to.

As detailed in PNAS the newly discovered chameleon, Furcifer labordi, spends most of its year-long life inside an egg and lives just four or five months after hatching (research paper, press coverage).

“Our review of tetrapod longevity (>1,700 species) finds no others with such a short life span,” write Kristopher Karsten, of Oklahoma State University, and colleagues.

Karsten says the animal’s life cycle is more reminiscent of an insect than a traditional terrestrial vertebrate.

It could be a survival tactic says fellow author Christopher Raxworthy, of the American Museum of Natural History. “The best payoff may be to produce larger clutches and more offspring, rather than to conserve reserves and try to make it through the dry season as an adult,” he says (NY Times).

“It is amazing to think that for most of the year, this chameleon species is represented only by developing eggs buried in the ground,” adds Raxworthy (press release). “This species really illustrates just how much there is still to discover about the natural history of Madagascar.”

Given they have such a short time on this Earth it would be nice to think that once they do emerge from their eggs the poor things can experience some fleeting pleasures. Not so, says Karsten, who tells New Scientist it may be their “rather violent” courtship that actually kills them.

The only silver lining here is that this discovery could be good news for pet owners worried about the standard of their chameleon care: “These findings suggest that the notorious rapid death of chameleons in captivity may, for some species, actually represent the natural adult life span,” says Karsten.

Image: Christopher Raxworthy

Good grades in sciences are harder to obtain than the same grades in arts subjects, according to prejudice-confirming research in the UK.

The Guardian sums it up thus:

It’s what scientists have always known: the sciences are harder than the arts and the humanities. Now researchers at Durham University have proved it.

Durham University researchers think that physics, chemistry and biology are a grade harder than drama and media studies and three-quarters of a grade harder than English at ‘A-level’, roughly equivalent to high school diplomas (report pdf).

In the UK press there’s much hand wringing about the fact that “hard” science qualifications may put people off taking these subjects (eg FT). Some teachers may even push their pupils towards easier subjects to boost their school’s league table position, some warn (eg The Daily Telegraph).

“This research shows that science and technology subjects are much more severely graded than subjects like media studies and art,” says Robert Coe, author of the new report on the subject that’s stirred things up (press release).

To reach this conclusion Coe reviewed a host of previous attempts to determine the relative ‘difficulty’ of subjects and conducted his own analysis on examination data from 2006. His work found similar results from five different statistical methods, all of which are rather complicated (maths is hard remember).

These methods either compare the performance of the same candidate in different exams or compare exam grades between people of similar ability, as determined by a reference test of some kind. Science and maths subjects were all at the top of the difficulty range.

Just to stoke the fires a bit, Coe notes, “A student with a grade C in Biology will generally be more able than one with a B in Sociology, for example.”

I’m just going to note now the fact that Coe used to teach maths and the report was commissioned by the Institute of Physics and the Royal Society.

This report, as the press release notes, contradicts an official report from the Qualifications and Curriculum Authority said all the subjects were much of a muchness. A new regulatory body, Ofqual, told the BBC “There is currently no expert consensus as to what statistical outcomes like these mean in terms of grading standards between different subjects.”