Author Archives: Ewen Callaway

US to lift ban on blood donations from gay men

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The US Food and Drug Administration has announced plans to end a lifetime ban on blood donation for men who have sex with men that has been in place since 1983. The current ban covered all men who have had sex with men at any time since 1977, and was intended to prevent the spread of the HIV virus but was seen by gay-rights activists as discriminatory.

The new policy, revealed on 23 December, will allow gay and bisexual men who have abstained from sex for a year to donate blood. The move follows the recommendations of a US government advisory panel.

The United Kingdom lifted an analogous ban in 2011, also allowing donations by gay men who have abstained from sex for a year.

In a statement, Adaora Adimora, Chair of the HIV Medicines Association, supported the rule change, but said it fell short of some advocates’ hopes:

“[W]e are concerned that the new policy retains an unnecessary and unique exclusion of men who have sex with men from donating blood for one year. Requiring a one-year abstinence period for men who have sex with men, regardless of risk behavior is not grounded in science regarding transmission risks or supported by current diagnostics for detecting HIV infection and other blood-borne pathogens.”

In 2015, the FDA will issue the detailed draft policy, which will be open for public comment before being finalized.

Brain positioning system wins medicine Nobel

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{credit}Akademie/Alamy{/credit}

The 2014 Nobel Prize in Physiology or Medicine has been awarded to John O’Keefe, May-Britt Moser and Edvard Moser.

The researchers discovered how the brain helps us navigate the world around us. O’Keefe, a neuroscientist at University College London, discovered specialized “place cells” that were activated when a rat explored a room.

In 2005, the Mosers (a married couple who share a laboratory at the Norwegian University of Science and Technology in Trondheim, Norway) together discovered another component of the brain’s positioning system. The “grid cells” they found create a coordinate system by firing at regular spatial intervals as an animal explores a space. They went on to show how grid cells and place cells work together.

Keep watching this blog for reaction.

Update 11:05 a.m.

As coincidence would have it, Nature was planning to publish a feature story on the Mosers in this week’s issue. Here it is.

Update 11:11 a.m.

The Mosers explain how grid cells work in this 2011 video. For more videos from the duo, follow this link.

Update 11:32 a.m.

In their press release (download the PDF here) announcing today’s award, the Nobel Committee recognizes work that O’Keefe did in the 1970s and research in the Mosers’ lab three decades later. But the three all worked together in 1995. The Mosers were fresh out of graduate school, and they did a short stint in O’Keefe’s lab, learning how to take electrical recordings of place cells. “This was probably the most intense learning experience in our lives,” they write, in a nice summary of their work on their lab website.

Update 11:52 a.m.

The Nobel website has a recording of May-Britt Moser’s response to the news. She says her husband is still on a plane and hasn’t yet heard the news. He’s due to land in Munich soon. “That would be fantastic if people were waiting at the airport. He would be in shock,” she says.

Update 12:07 p.m.

John Stein, a physiologist at the University of Oxford, says that O’Keefe’s discovery of place cells initially raised more than a few eyebrows. In a statement sent to reporters by the UK Science Media Centre he says: “I remember how great was the scoffing in the early 1970s when John first described ‘place cells’.  “Bound to be an artifact”, “He clearly underestimates rats’ sense of smell” were typical reactions.  Now, like so many ideas that were at first highly controversial, people say “Well that’s obvious”!”

Updated 1:39 p.m. Corrected affiliation of May-Britt and Edvard Moser

PNAS narrows pathway to publication

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One door to publishing in the Proceedings of the National Academy of Sciences (PNAS) has slammed shut. In an editorial this week, editor-in chief Inder Verma said the prestigious US journal will no longer accept submitted papers that come with a prearranged editor (who is a member of the National Academy of Sciences).

The journal formalized this publication track in 2010, when it eliminated ‘communicated’ papers, which allowed academy members to usher papers from non-member colleagues through to publication. Papers with prearranged editors (known in PNAS-speak as PE) went through peer review, but the process was shepherded by an academy member pre-chosen by the author of the paper, rather than an editor selected by journal. The intention was to encourage papers that were interdisciplinary or ‘ahead of their time’, and deserving of special attention. According to Verma’s letter: “The PE process was intended to be used on rare occasions but, since we formalized the PE process, more than 11,000 papers have been submitted by authors with a PE designation. Although we are certain that some of these papers truly needed special attention, the vast majority likely did not, and therefore we are discontinuing the PE process as of October 1, 2014.” Papers already submitted through that track won’t be affected by the change.

Nature noted Verma’s desire to eliminate prearranged editor submissions in a recent feature on PNAS (“The Inside Track”): “One in five direct submissions published in 2013 used a prearranged editor, and the acceptance rate for these papers is higher than for other direct submissions. ‘More and more the playing field will be levelled,’ says Verma.” That story focused on PNAS’s ‘contributed’ path to publication, which lets academy members publish up to four papers per year using peer reviewers they select (whose comments the members can take or leave). As our story noted, many members rarely or never use the ‘contributed’  track, and just a handful make regular use of it. This publication track remains unchanged, so academy members don’t need to make an ‘Indiana Jones’ style dash through a closing door just yet.

hat tip: In the Pipeline

Digital mapping uncovers ‘super henge’ that dwarfed Stonehenge

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{credit}Ludwig Boltzmann Institute{/credit}

Every summer solstice, tens of thousands of people throng to Stonehenge, creating a festival-like atmosphere at the 4,400-year-old stone monument. For the 2015 solstice, they will have a bit more room to spread out. A just-completed four-year project to map the vicinity of Stonehenge reveals a sprawling complex that includes 17 newly discovered monuments and signs of a 1.5-kilometre-around ‘super henge’.

The digital map — made from high-resolution radar and magnetic and laser scans that accumulated several terabytes of data — shatters the picture of Stonehenge as a desolate and exclusive site that was visited by few, says Vincent Gaffney, an archaeologist at the University of Birmingham, UK, who co-led the effort.

Take the cursus, a 3-kilometre-long, 100-metre-wide ditch north of Stonehenge that was thought to act as barrier. The team’s mapping uncovered gaps in the cursus leading to Stonehenge, as well as several large pits, one of which would have been perfectly aligned with the setting solstice Sun. New magnetic and radar surveys of the Durrington Walls (which had been excavated before) uncovered more than 60 now-buried holes in which stones would have sat, and a few stones still buried.

“They look as they may have been pushed over. That’s a big prehistoric monument which we never knew anything about,” says Gaffney, who calls the structure a ‘super henge.’ His team will discuss the work at the British Science Festival this week, and they plan to present it to the institutions that manage the site. “I’m sure it will guide future excavations,” Gaffney says.

Geneticists say popular book misrepresents research on human evolution

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Courtesy of Penguin Press

More than 130 leading population geneticists have condemned a book arguing that genetic variation between human populations could underlie global economic, political and social differences.

A Troublesome Inheritance, by science journalist Nicholas Wade, was published in June by Penguin Press in New York. The 278-page work garnered widespread criticism, much of it from scientists, for suggesting that genetic differences (rather than culture) explain, for instance, why Western governments are more stable than those in African countries. Wade is former staff reporter and editor at the New York Times, Science and Nature.

But the letter — signed by a who’s-who of researchers in population genetics and human evolution — and published in the 10 August issue of the New York Times — represents a rare unified statement from scientists in the field and includes many whose work was cited by Wade. “It’s just a measure of how unified people are in their disdain for what was done with the field,” says Michael Eisen, a geneticist at the University of California, Berkeley, who helped to draft the letter.

“Wade juxtaposes an incomplete and inaccurate explanation of our research on human genetic differences with speculation that recent natural selection has led to worldwide differences in IQ test results, political institutions and economic development. We reject Wade’s implication that our findings substantiate his guesswork. They do not,” write the authors of the letter, which is a response to a critical review of the book published in the New York Times.

“This letter is driven by politics, not science,” Wade said in a statement. “I am confident that most of the signatories have not read my book and are responding to a slanted summary devised by the organizers.”

Wade added that he had asked the letter’s authors — Eisen and Graham Coop, a population geneticist at the University of California, Davis — for a list of errors so that he could correct future editions of the book. According to Wade, Coop did not reply and Eisen promised a response but has yet to deliver one.

The book, Wade said, “argues that opposition to racism should be based on principle, not on the anti-evolutionary myth that there is no biological basis to race”.

Coop says the idea for the letter emerged over discussions at conferences. “There was a strong feeling that we as a community needed to respond,” he says. Like many of the signers, Coop is not pleased about how his research was explained by Wade.

The first portion of the book summarizes recent research in human population genetics, to support the author’s argument that geographically defined ‘races’ are supported by patterns of genetic variation, and that the different environments encountered by these groups led to genetic adaptations after humans left Africa more than 50,000 years ago — such as lighter skin or the ability to digest milk sugar (lactose) into adulthood.

For instance, in making the argument that populations outside of Africa experienced more evolutionary adaptations known as ‘selective sweeps’ than Africans did, Wade quotes a 2002 paper by Coop, in which his team wrote: “A plausible explanation is that humans experienced many novel selective pressures as they spread out of Africa into new habitats and cooler climates … Hence there may have been more sustained selective pressure on non-Africans for novel phenotypes.”

But Coop notes that Wade omitted key caveats, including the statement that African populations may have actually experienced more selective sweeps than non-Africans, but which the researchers missed for technical reasons. “While Wade is obviously welcome to choose his quotes and observations, he consistently seems to ignore the caveats and cautions people lay out in their papers when they do not suit his ends,” Coop says.

Sarah Tishkoff, a population geneticist at the University of Pennsylvania in Philadelphia who studies human variation in Africa, finds the book’s efforts to explain race in genetic terms to be problematic.

Wade cites a study from another team that analysed genome data from 1,056 humans from around the world using a computer program that divides people into clusters on the basis of their genetic similarity. If the researchers instructed the program to put people into five clusters, the assignments corresponded to continental groups — Africa, East Asia, Europe and the Middle East, the Americas and the Pacific Islands. Wade cited that study and others as evidence for the existence of five human races.

But Tishkoff says that the five clusters are somewhat arbitrary. In a 2009 study that included numerous African populations, her team found that 14 clusters (most of them composed of Africans) were a better explanation for global genetic diversity. “You may see that individuals cluster by major geographic regions. The problem is, there are no firm boundaries,” she says.

Tishkoff also acknowledges that natural selection has created biological differences that vary with geography. For example, her team discovered mutations that allows some African populations to digest lactose. But she scoffs at the idea, proposed by Wade, that natural selection has shaped cognitive and behavioural differences between populations around the world. “We don’t have any strong candidates for playing a role in behaviour,” she says.

But she and the other letter signers are most riled by what, they feel, is Wade’s contention that his book is an objective account of their research. “He’s claiming to be a spokesperson for the science and, no, he’s not,” she says.

UK funders get tough on privacy breaches

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Leading UK organizations that fund research have threatened to revoke the funding of scientists who determine the identities of participants in medical and genomic studies who had expressed a wish to remain anonymous.

The warning was issued on 24 March by the Medical Research Council and the Economic and Social Research Council — both government agencies — and by two charities, the Wellcome Trust and Cancer Research UK. It came as a part of recommendations that are aimed at preventing the identification of study participants whose information has supposedly been made anonymous.

“Whilst it is impossible to eliminate entirely the risk of re-identification of individuals, it is possible to minimise this risk with proportionate safeguards,” said Wellcome Trust Director Jeremy Farrar in a statement. “We believe that a deliberate attempt to re-identify individuals should be viewed as malpractice and be met with appropriate sanctions.”

In addition to being subject to sanctions,  studies should also be regularly reviewed to gauge the potential for re-identification in light of new technological developments, the funders said. And participants should be told during the consent process that there is a small risk that their identities will be revealed.

The recommendations (first laid out in an October 2013 report by an expert advisory group and endorsed by those funders today) are a response to growing concerns that private medical details and genomic information of participants in research studies could be determined by analysing freely available information.

A study published in Science last year, for instance, showed that a subset of participants in the 1000 Genomes Project could be identified by cross-referencing publicly available, yet anonymous, genome data with genetic genealogical databases. The study participants had acknowledged the risk of being identified, and none of their identities were ever published (see “Privacy loophole found in genetic databases”).

Yaniv Erlich, a human geneticist at the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts, who led that research, believes that private interests such as health insurers are far more likely than scientists to re-identify researchers participants against their permission. But he welcomes policies that protect the privacy of research participants. “The whole point is to increase the trust that the general public has with the scientific community,” Erlich says. “We need to have better legal methods to fight these breaches of genetic privacy.”

More Nature coverage on re-identification:

Privacy protections: the genome hacker

Balancing privacy with public benefit

Genetic privacy needs a more nuanced approach

Be prepared for the big genome leak

UK moves to legalize controversial IVF technique

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The United Kingdom today inched closer to legalizing a controversial method of reproduction, known as mitochondrial replacement, or ‘three-parent IVF’. The Department of Health announced a public consultation of draft legislation that would allow the procedures, which are intended to prevent children from inheriting diseases caused by faulty mitochondria.

The consultation, which runs until 21 May, is an early step toward amending the Human Fertilisation and Embryology Act, which would allow the mitochondrial replacement procedures. The UK government must then decide whether to put such legislation to Parliament for approval (see “UK sets sights on gene therapy in eggs“).

Mitochondrial replacement involves transferring the nuclear material from an egg cell with defective mitochondria to a healthy donor egg cell in which these power-generating organelles function normally, but which has had its nucleus removed. The techniques have been tested in monkeys, yielding healthy offspring, as well as in human egg cells (see “DNA swap could avoid inherited diseases” and “DNA swap technology almost ready for fertility clinic”).

If the procedures are eventually legalized, doctors would not necessarily be given a green light to begin offering them to parents. The draft regulation would require any clinic seeking to conduct mitochondrial replacements to be licensed by the Human Fertilisation and Embryology Authority, a statutory body that regulates reproductive techniques such as in vitro fertilisation.

Although the UK is leading the way in considering mitochondrial replacement in humans, others are testing the waters. On 25 and 26 February, a US Food and Drug Administration advisory panel examined the science behind the technologies, as well as their potential safety if tested in humans (see “Regulators weigh benefits of three parent fertilization“).

Even after prodding, animal researchers omit key details

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Lab_mouse_mg_3140Preclinical animal studies often lack important details needed for other researchers to assess and replicate the work, and they use statistical calculations that are not fit for purpose.

Those conclusions come from a new analysis of recent papers that use a popular animal model for multiple sclerosis. Published today in PLoS Biology, the analysis concludes that voluntary reporting guidelines for animal studies, which have been endorsed by hundreds of research journals, are largely being ignored.

David Baker, a neuroimmonologist at Queen Mary University of London who led the study, says journals ought to compel animal researchers to disclose experimental details that could lead to bias, such as whether animals were randomly assigned to different treatment groups or not. “Unless there is enforcement there is no change,” he says.

In 2010, the UK National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3R) laid out best practices in the Animal Research: Reporting of In Vivo Experiments (ARRIVE) guidelines. Modeled after clinical-trial guidelines, ARRIVE is a 20-item checklist that addresses study design, experimental procedures and animal care. More than 300 research journals, including Nature Publishing Group (NPG) and PLoS journals, have since endorsed the guidelines.

To see if researchers and journals were following those suggestions, Baker and his team analysed papers published in NPG journals and PLoS journals that used a multiple sclerosis model called experimental autoimmune encephalomyelitis (EAE). The team compared papers published in the two years before ARRIVE was released with papers published in the following two years.

The ARRIVE guidelines did not have much impact on which details were included in papers, Baker’s team found. For instance, less than 21% of the NPG or PLoS journal articles reported whether animals were randomly assigned to experimental groups or not, both before and after the ARRIVE guidelines were issued. Similarly, before and after 2010, less than 7% of studies reported whether or not they conducted sample size analyses, which can indicate whether enough animals were used in the experiment to tell if it worked or not. Baker’s team noticed some uptick in the reporting of the sex, age and number of animals used, particularly in Nature journals.

In a separate analysis, Baker’s team found problems with how statistics were reported in papers using EAE data. The researchers analysed 180 papers using the model between 1 December 2011 and 21 May 2012 and calculated how many used so called “non-parametric” statistical tests. Baker says non-parametric tests are most appropriate for EAE data because they make no assumptions about the relationship between data points or the overall distribution of data. (Not all researchers agree with his argument.)

The team found that only 39% reported the use of non-parametric statistical calculations for the data. In the case of Nature, Science and Cell, just 4% of papers indicated that they used such tests. Baker says these studies are more likely to report false positives, indicating, for instance, that an experimental treatment for multiple sclerosis is effective.

“There’s this very vocal minority of clinicians who say ‘animal data is rubbish, it never translates into human benefit,’” Baker says. “By doing bad science which is of poor quality and experimental design, we just pander to that problem.”

Baker says journals should compel researchers to report key details from animal experiments, which would allow other scientists to assess and replicate the work. Because of such requirements, statements about ethical approval for research are more likely to appear in manuscripts than in the 1970s or 1980s, Baker says.

According to an editorial published alongside Baker’s article, PLoS ONE is likely to require all researchers conducting animal experiments to fill out a checklist including the ARRIVE guidelines, and PLoS Medicine already has this requirement (though it publishes few animal studies). PLoS Biology is mulling its options, according to the editorial.

“Voluntary guidelines are very important, but journals need to take tangible steps to implement them with standards flexible enough to work for a broad range of studies,” says Nature’s Editor-in-Chief, Philip Campbell. In May 2013, NPG journals began asking researchers to fill out a checklist addressing statistical calculations and some details of animal experiments. (See “Reducing our Irreproducibility“) “These guidelines were established in consultation with the community to address the most common problems in transparency and potential bias in research papers. We will be reviewing their implementation and impact later this year,” Campbell adds.

Frederick Sanger, father of DNA sequencing, dead at 95

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Fred Sanger

Fred Sanger{credit}Wikimedia Commons{/credit}

Frederick Sanger, who won two Nobel Prizes for his work on DNA and protein sequencing, died yesterday, according to a spokesperson at the Laboratory for Molecular Biology at the University of Cambridge, UK. He was 95.

The chemist won the 1958 Nobel Prize for Chemistry for developing a method to determine the complete amino acid sequence of insulin. Twenty-two years later, the Nobel Committee awarded him the 1980 prize in Chemistry for discovering a way to determine the ordered sequence of DNA molecules. An adaptation of this method — known as Sanger sequencing — was used to sequence the human genome. He is only scientist to have won two Chemistry Nobels. Just two other scientists have been awarded two Nobel Prizes in the sciences: Marie Curie (Physics in 1903 and Chemistry in 1911) and John Bardeen (Physics in 1956 and 1972).

After the announcement of a draft human genome sequence in 2001, Sanger penned an essay for Nature Medicine on the history of DNA sequencing. “When we started working on DNA I don’t believe we were thinking about sequencing the entire human genome — perhaps in our wildest dreams but certainly not within the next 30 years,” Sanger wrote.

His archived lab notes were recently made available by the Wellcome Collection.

Update 12:53 p.m

The Medical Research Council (MRC) Laboratory for Molecular Biology (LMB), where Sanger spent much of his career, has posted an obituary encapsulating his professional life. It also notes that Sanger turned down a knighthood because he did not want to be called “Sir”.

Jeremy Farrar, the new director of the Wellcome Trust (which named its Sanger Institute after him), has issued a statement: “I am deeply saddened to learn of the death of Fred Sanger, one of the greatest scientists of any generation and the only Briton to have been honoured with two Nobel Prizes. Fred can fairly be called the father of the genomic era: his work laid the foundations of humanity’s ability to read and understand the genetic code, which has revolutionised biology and is today contributing to transformative improvements in healthcare.”

Update 1:40 p.m.

J. Craig Venter — whose privately funded effort to sequence the human genome was criticized by Sanger for limiting access — has chimed in via Twitter.

Update 2:00 p.m.

Science journalist and regular Nature contributer Ed Yong has a rather cryptic tribute on his blog: “CGCATTCCGTTTCGCGAAGATAGCGCGAACGGCGAACGC.” This tool will help translate.

Update 2:30 p.m.

University of Oxford neuroscientist and former MRC chief Colin Blakemore had this to say: “[H]e was a disarmingly modest man, who once said: ‘I was just a chap who messed about in his lab’. The journal Science rightly described him as ‘the most self-effacing person you could hope to meet’. Fred Sanger was a real hero of twentieth-century British science.”

Richard Henderson, former director of the LMB, said: “He was a superb hands-on scientist with outstanding judgement and skill, and an extremely modest yet encouraging way of interacting with his younger colleagues. I particularly remember one young scientist who had asked Fred for advice being told ‘I think you should try harder’. The example he set will continue to motivate young scientists even now he has gone.”

Updates to follow as tributes to Sanger, no doubt, pour in.

Leeches’ blood meals could give more clues on saola, world’s rarest mammal

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The saola seen on the right in this camera-trap picture was the first one seen in 15 years.
{credit}WWF{/credit}

The saola, a species so rare it has been called the Asian unicorn, has been photographed for the first time in 15 years.

A camera trap set up by World Wildlife Fund (WWF) in Vietnam captured images of the antelope-like animal in September, according to an announcement today from the conservation group. Saola are critically endangered and probably number in the low hundreds.

The animals are only known to live in the Annamite Mountains on the border between Vietnam and Laos. In 2011 Vietnam established a small saola reserve, but conservation is hindered by the paucity of data on their habitat.

Conservationists had become so desperate to pin down the animal’s habitat that they began surveying DNA from leech blood meals in hopes of finding saola sequences (see “A bloody boon for conservation”).

Nicholas Wilkinson, a Vietnam-based wildlife ecologist at the University of Cambridge, UK, who is leading those efforts, tells Nature that his team is waiting to hear back from lab testing of a very large number of leeches. The researchers also plan to collect large numbers of leeches from the area where the camera trap was located. “I have high hopes we’ll get encouraging results and 2014 will be the year of a proper leech-based survey for the species,” Wilkinson says.