Neanderthal Genes, New Flu, Obamacare Agonistes

 

Were Neanderthals a Different Species?

It’s no longer news that everybody except (most? some? SEE FOOTNOTE) Africans possesses a bit of Neanderthal DNA. And it really is just a bit; the latest two studies, published just last week and drawn from the 1000 Genomes Project databank, put the average at less than 2 percent.

It turns out, though, that your 2 percent is likely somewhat different from my 2 percent. Adding up the disparate bits means that Neanderthals have contributed at least 20 percent of their genomes to anatomically modern humans. (“Anatomically modern humans,” that’s us, the last Homo standing, and for clarity and convenience, occasionally I will use the shorthand designation some paleontologists use:  AMH.)

The Neanderthal DNA scattered around the billions of modern human genomes could total as much as 40 percent or more of the Neanderthal genome, the researchers say. That means it might not always be necessary to raid precious fossils for their DNA or go through contortions to assemble error-free ancient DNA sequences and prevent contamination by modern DNA. It might be possible to do fossil-free studies of the Neanderthal genome, studies carried out on their DNA carefully preserved for science in billions of today’s human genomes.

We AMHs, it appears, are walking labs for the study of paleogenomics.

 

How Neanderthal DNA helped us

A portion of that legacy DNA seems to have done us good. About 3 in 5 of the AMH genomes from the 1000 Genomes Project that were examined in these two studies possess the Neanderthal versions of some DNA involved in making skin and hair. The researchers believe that may have helped our migrating ancestors adapt to a Northern climate, one that was colder and less sunny than their original home in Africa. It may also have bolstered our defenses against new pathogens.

But there are also big stretches of the AMH genome that contain no Neanderthal DNA at all. “To me, these ‘holes of Neanderthal sequence’ are the most interesting aspect,” Joshua Akey told me in an email. (Akey, who is at the University of Washington, is an author of one of last week’s papers, which appeared in Science. )”[T]hey might provide a roadmap to positions in the genome that endow uniquely human traits.”

Where they are absent, natural selection may have decided that the AMH versions were doing a better job and so eliminated the Neanderthal counterparts. Hence these “deserts” may help define the most important genetic differences between us and them.

 

Credit: Neanderthal Museum (Mettmann, Germany)

Credit: Neanderthal Museum (Mettmann, Germany)

What the DNA “deserts” mean

There are deserts on the X chromosome and in genes involved in the testes. Patterns like these in other species ranging from rabbits to fruit flies are regarded as signs that one species is about to split into two.

Hybrid males descended from both branches tend to be infertile, like mules. That’s because males have only one X chromosome, and if it happens to be one that impairs their fertility, then they may not reproduce. Females have two X chromosomes, so even if one is impaired, if the other one is normal, it can rescue her ability to bear young.

“So this suggests that the male hybrids might not have been fertile, whereas the females might have been fully fertile,” Svante Pääbo told Richard Harris of National Public Radio. Pääbo, the grand old man of ancient DNA based at the Max Planck Institute for Evolutionary Anthropology in Leipzig, was an author of the other paper, which appeared in Nature. We might have inherited most of our Neanderthal genes through hybrid females, he said. Fox News quoted Pääbo as saying Neanderthals must have been disappointed in their sons.

Another author, David Reich of Harvard Medical School, told reporters that we and Neanderthals “were at the edge of biological compatibility.”

“This underlines that modern humans and Neanderthals are indeed different species,” Fred Spoor told New Scientist. Spoor is also at the Leipzig Max Planck but was not a part of the Neanderthal research. Other scientists are more cautious about making so firm a declaration, but it’s clear that many lean toward that same conclusion, that Neanderthals were not Homo sapiens neanderthalensis but, rather, Homo neanderthalensis.

Darren Curnoe, a human evolutionary biologist at the University of New South Wales, blogged, “The latest findings from genome comparisons reinforce the status of Neanderthals and modern humans as distinct species. Those anthropologists who continue to regard Neanderthals as members of Homo sapiens now face a stronger challenge than ever reconciling their position with the DNA.”

 

Speak up

If there is one trait above all others that is responsible for our success, it is fluent language. That’s why a detail almost buried in the Science paper caught my eye, and a few other writers mentioned it in passing. The authors reported that none of the modern genomes they examined contained the Neanderthal version of the chromosome region where the FOXP2 gene is situated. In these 665 people, that region, on the long arm of chromosome 7, was one of those Neanderthal deserts.

All land vertebrates possess a version of this gene. One type of FOXP2 has been shown to be associated with vocal learning in young songbirds. More than a decade ago, researchers linked a mutant version of the human gene with a set of unusual language difficulties in a particular family.

Despite what you may have heard, FOXP2 is not a “language gene” per se. Among other functions, Andrea Andriadis said in a SciAm guest blog, it seems to affect motor neuron control in parts of the brain involved in the ability to vocalize.

In 2011, Pääbo reported that the modern human and Neanderthal FOXP2 genes were identical, according to Carl Zimmer at The Loom. This led to excited speculation that Neanderthals could probably speak as we do. But last year researchers discovered differences in the way the AMH and Neanderthal FOXP2 genes are regulated. The protein-coding sequences may be the same, but they are controlled in different ways.

The fact that none of the contemporary genomes studied seem to possess exactly the same version of FOXP2 as Neanderthals after all, that it looks as if none of the 665 people examined has hung on to the Neanderthal version, suggests that we may have found it wanting and evolution eliminated it entirely from our line. Which suggests, in turn, that Neanderthals might not have had our fluent speaking abilities after all.

(Please note that I’m just running my mouth here in the usual speculative Homo sap fashion, and that we are speaking of data from only 665 people; the Neanderthal capacity for speech has not been established either way.)

But since no evolutionary development has been more important to the rise of anatomically modern humans and our domination of the planet than language, it might perhaps be said that fluent speech by itself is a defining characteristic of our species.

And that hominins that lack it are not us.

 

Here’s the footnote mentioned in the first graf above

Africans may no longer be an exception to the Neanderthal intromission. It appears that Europeans and/or Eurasians went back to Africa a few thousand years ago. As is the human wont, they deposited DNA hither and thither, and some of it could have been tidbits of the Neanderthal DNA they carried.

This news grows out of a new paper showing that the Khoisan people, the click-speaking pastoralists of southern Africa, have some Eurasian DNA (up to 14 percent of the genomes in one population), and they got it between 900-1800 years ago.  This looks to have been the result of matings between Africans and Eurasians in East Africa about 3000 years ago. Another study reports a Neanderthal signal in the Yoruba.

In New Scientist, Catherine Brahic speculates that this means Neanderthal DNA may actually be widespread in Africa, courtesy of European carriers.  She quotes study author David Reich of Harvard thus: “I actually am not sure there’s any population that doesn’t have west Eurasian [DNA].”  He means DNA acquired in olden times, not the many cross-cultural “exchanges” of the last few hundred years.

 

Obamacare Agonistes

Obamacare has been having a very bad week, thanks to a new report from the Congressional Budget Office. The bad week is due partly to misinterpretations of the report’s conclusions, even by some very respectable media.  The misinterpretations have been trumpeted by enemies of this infant remodel of the US health care system, who capered with joy at this gift.  And it can be said that even correct interpretations of the data can be disconcerting in their potential implications.

The misinterpretation was that Obamacare (aka ACA) is going to cost 2 million jobs. But the report didn’t say that. It predicted that the labor force would be reduced by 2 million, quite a different matter.  Specifically, it said the ACA provides incentives for 2 million people to leave full-time employment by 2024. Some people will stop working jobs they have been hanging on to for the medical insurance. Others will abandon low-paying jobs in order to qualify for larger insurance subsidies. Keith Hennessey argues at length that the generous subsidies will trap low-income people and prevent them from climbing into the middle class.

Eric Wemple’s blog at the Washington  Post recounted how a number of publications had to revise their headlines,  including the Wall Street Journal, Politico, Forbes, and the Washington Post itsownself, which declared that Obamacare would result in 2 million fewer jobs.  (The revision said Obamacare would result in 2 million fewer workers.)   The National Review stuck with The CBO Just Nuked Obamacare.  A reasonable choice.  No incorrect specifics to revise, and I suppose it might even turn out to be accurate.  Horrors.

At Wonkblog, Sarah Kliff delves into specifics of the CBO report.  It concludes, she says, that the much-decried “insurance company bailout” will actually save money, but because of the botched rollout and web site nightmares of last fall (not yet entirely eliminated), 2 million fewer people than expected will enroll. In a different post, she sorts out details of research that helped the CBO arrive at its employment projections.

Paul Krugman disagrees with Kliff about insurance enrollment projections, and reproduces a CBO table to prove it.  He says, “Oh noes! The exchanges will cover 6 million people, not the 7 million we expected! The number of uninsured will fall 13 million, not 14 million!

“In short, CBO thinks that reform has been only mildly set back by the healthcare.gov mess, that at this point it’s going pretty well. And by the way, these are predictions we’ll be able to test in real time, unlike the labor force estimates, which will get lost in statistical noise.”

 

The influence of influenza

The new H10N8 bird flu virus killed an elderly Chinese lady in November, Karen Kaplan tells us at the LA Times’s Science Now. That’s the first death reported from H10N8, and there’s no evidence yet of person-to-person transmission. H10N8 has two mutations that seem to make it particularly virulent in mammals.

H7N9 flu data from last April. Deaths now number 300, a quarter of them fatal.

H7N9 flu data from last April. Deaths now number 300, a quarter of them fatal.

Meanwhile, the H7N9 no-longer-just-bird flu is rocketing along,  although  according to a just-published paper in the New England Journal of Medicine, person-to-person transmission has yet to be established.  Some 300 Chinese cases are now reported, about a quarter of them fatal. That’s a big and worrisome increase.  At ViroBlogy, Ed Rybicki asks, “So THIS is the next one?  Possibly?”

He’s happy a vaccine is in the works. Me too.

Judy Stone brings helpful clarity to her post all about flu at Molecules and Medicine. She sorts out the nomenclature, the history, and the prospects.  Excellent background.

 

Department of Self-Interest

The Neanderthal post above appeared in a somewhat different form last Tuesday at the Genetic Literacy Project, where I am a weekly columnist.  New posts on Tuesdays.  You can see my past posts here.  Along with some original contributions like mine, the Genetic Literacy Project (“Where Science Trumps Ideology”)  is an aggregation of genetics news with an emphasis on human and agricultural applications.  The aggregators are not digital, I am happy to report, but members of our very own species, AMH. They are adept at digging out a wide range of material, a lot of it from specialized nontechnical sources that will be new to you.

 

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Replication. Not.

Top science writer George Johnson has started a new column in the New York Times called Raw Data, and Knight Science Journalism Tracker Faye Flam took his first post apart.

Johnson’s topic was raw data indeed: the fact that so many scientific findings turn out not to be true, or at least turn out not to be reproducible. Flam pointed out that, although Johnson seemed to be excoriating science in general, all his examples were from medical research. She notes, “There’s no physics mentioned in Johnson’s column, nor is there any astronomy, chemistry or evolutionary biology.”

She’s certainly right that, assuming Johnson’s topic was the failings of medical science, he should have said so. If it was science more generally, he should have given non-medical examples. Not many of his readers except those of us professionally interested in science are going to know that different fields of science have very different track records.

No question that both clinical and biomedical research are being viewed with alarm by scientists and journals and, most important, by funding agencies. That alarm is deserved, medical research having presented a string of recent examples ranging from methodologically dubious and outright fraudulent results to many results that may seem all right at first but that others have not been able to replicate.

Proposed remedies for medical research

There are several suggested fixes, some of them mentioned by Retraction Watch’s Ivan Oransky in his post advocating what he calls a Reproducibility Index. Instead of the Citation Index, he says, judge a paper by how well it stands up to scrutiny.

Credit: Harry Collins, Cardiff School of Social Sciences

Credit: Harry Collins, Cardiff School of Social Sciences

Bonnie Swoger, at Information Culture, describes some new programs designed to foster reproducibility investigations, but she emphasizes that funding agencies, by and large, would rather underwrite new (and, preferably, dazzling) investigations rather than spend time and money trying to validate old ones

Mike the Mad Biologist is gobsmacked on reading a recent Nature paper by Francis Collins and Lawrence Tabak describing the National Institutes of Health’s efforts to “enhance reproducibility.” The paper points out that “Funding agencies often uncritically encourage the overvaluation of research published in high-profile journals.” Mike wants to know, since Collins is the head of NIH (which is in fact a concatenation of 27 different funding agencies), isn’t he, of all people, in a position to do something about this overemphasis on results appearing in top journals?

 

The failures of social science, especially psychology

Recent research history has also been particularly egregious in the social sciences, especially psychology, and I have written about that several times here at On Science Blogs.

At Not Exactly Rocket Science, Ed Yong has a long post analyzing the Many Labs Project. This was an impressive effort by psychologists to investigate whether a number of classic findings in psychology can be replicated. Most of them appear to hold up: 10 out of 13. That’s more than you might expect, given all the recent bad news coming out of  psychology.

Psychologist Rolf Zwaan goes into even more detail on the Many Labs project, concluding that the size of this project holds lessons not just for replication studies, but for research methods themselves. He agrees with the Many Labs authors that “a consortium of laboratories could provide mutual support for each other by conducting similar large-scale investigations on original research questions, not just replications.”

Christian Jarrett, at the British Psychological Society’s Research Digest, describes the “replication recipe” devised by a group of psychologists. It includes obvious but frequently ignored steps such as defining methods as precisely as possible and having a big enough sample size to make it likely that the project’s results (probably) reflect the real world. Some of these points, it seems to me, could be instituted if journals insisted, such as a detailed (and replicable) description of methods.

 

Critiquing a critique of the critiques

Derek Lowe, at In the Pipeline, analyzes a critique of the critiques, a post by Jeff Leek at Simply Statistics. Leek wishes to persuade us that the reproducibility problem is nothing like as awful as the alarmists would have us believe.

Leek’s argument is that the critiques shouldn’t count for much because they aren’t truly scientific, meaning that they mostly contain no data. Lowe acknowledges that it’s true enough that the critiques have not gone through statistical vetting. “But the way that they’re all pointing in the same direction is suggestive. And it’s worth keeping in mind that all of these parties have an interest in the answer being the opposite of what they’re finding – we’d all like for the literature reports of great new targets and breakthroughs to be true.”

Lowe notes that Leek thinks highly of the Many Labs project, in part because it showed that nearly all the scientific papers it investigated held up to scrutiny. That bothers Lowe, and–to bring us full circle–it bothers him for the same reason Faye Flam took exception to George Johnson’s column. “The Many Labs people were trying to replicate results in experimental psychology, and while there’s probably some relevance to the replications problems in biology and chemistry, there are big differences, too. I worry that everything is getting lumped together as Science,” Lowe says.

 

The state of science in the State of the Union

At ScienceInsider, David Malakoff noted that President Obama didn’t announce any new science policy initiatives in his State of the Union message Tuesday night. But he did set some priorities. Obama continues to support rolling back last year’s mandatory budget cuts, known as sequestration, which had quite an impact on science funding. He also plans to ignore the recalcitrant Congress and use his executive powers–such as they are, which is limited–to boost research on reducing greenhouse gases and expanding natural gas production. Malakoff’s piece includes transcripts of parts of the speech related to science.

At SciAm’s Observations, Dina Fine Maron took an additive approach to parsing what what Obama’s speech would–or could–mean for science. “[H]e devoted roughly a fifth of his speech to topics including climate change, renewable energy and investing in science and education opportunities. His prepared remarks came in at a word count of 6,778 words.” I couldn’t resist doing the math. Let’s see, that’s 1355.6 words about science. Or we could throw caution to the winds and round up. 1356 words.

 

Correctional Institution

From the New York Times:

Correction: January 23, 2014
An earlier version of this article misstated the plantings on the building’s green roof. They were native flora, not native fauna.

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Scientific Ideas for the Garbage Dump

These scientific ideas will drive you crazy

Much has been made of this year’s question at John Brockman’s Edge, generally described as an online salon. Brockman asked for recommendations about which scientific ideas should be retired, and some 170 salonists replied.  Dennis Overbye plucked up a few proposed discards for consideration at Out There, concluding, “No matter who you are, you are bound to find something that will drive you crazy.”

 

edgemovie171821.1020.A

I guess being driven crazy explains Wesley Smith’s fulminations at National Review. “The attack on human exceptionalism these days is unremitting–and highly ideological. The latest assault on our uniqueness comes from Edge.org, which asked the world’s supposedly most ‘brilliant minds’ to come up with ideas that should be retired in science. Harvard professor (of course!) Irene Pepperberg–oh, so predictably–argues that the time has come to reject human uniqueness.”

Which poses the question: Just who is the ideologue here?  Although I’m inclined to a bit of fulmination myself, driven crazy by the execrable neologism titling Pepperberg’s piece: Humaniqueness. At least Smith didn’t go that far.

But here’s a science Fun Fact that turned into a Tangled Tale. I googled and found that the term “humaniqueness” seems to have surfaced at the 2008 AAAS meeting in a talk by evolutionary biologist Marc Hauser, formerly Pepperberg’s colleague at Harvard. John Hawks, another evolutionary biologist, in his case of the paleo kind, had this to say of “humaniqueness”: “Sounds like a perfume.”

Of a particularly stinky sort, I would add. Hawks also critiqued Hauser’s talk, bless his heart. And I can’t resist noting that Hauser resigned from Harvard in disgrace in 2012, accused, among other things, of fabricating data.  Or that Smith was critiquing Pepperberg’s humaniqueness piece by arguing that humans are unique because they are moral beings.

You can read the blow-by-blow on Hauser at the indispensable Retraction Watch. Hauser seems to have a predilection for inventing bunglesome words. I don’t suppose that is an offense against science, only an offense against another uniquely human trait, language. Some of us think that’s very nearly as bad.

 

More scientific ideas for the trash heap

Ed Yong particularly praised a couple of the Edge posts at his blog Not Exactly Rocket Science.  One was the post by anthropologist Kate Clancy, whose blog Context and Variation appears at SciAm. Her candidate for the discard pile she called “The Way We Produce and Advance Science.” That might mean a great many things, but what it means to Clancy is, “The lives of scientists need to be prioritized over scientific discovery in the interest of actually doing better science.” She says the data show that “An inclusive, humane workplace is actually the one that will lead to the most rigorous, world-changing scientific discoveries.” To achieve such a productive scientific workplace, trainees need unions and institutional policies to protect them, and senior scientists need to enact cultural change. These sound like good ideas for a lot of workplaces. The partner track at law firms. Medical school. Journalism. Etc.

And here’s an idea we can all get behind: Dump that left-brain/right-brain hogwash. Cognitive neuroscientist Sarah-Jayne Blakemore points out there is no basis for that beloved misapprehension. Despite the fact that some activities originate in certain brain locales, the two brain hemispheres are normally in constant communication. Unfortunately, the left-brain/right-brain thing is firmly embedded in popular culture and even, horrors, education. Rooting it out will certainly take a very long time, if it can be done at all.

 

Science is (not) self-correcting

Another post Yong liked is by psychologist Alex Holcombe, who thinks we need to rid ourselves of the notion that science is self-correcting. “The pace of scientific production has quickened, and self-correction has suffered. Findings that might correct old results are considered less interesting than results from more original research questions. Potential corrections are also more contested.”

It is certainly true that replication studies are few and far between, but I wonder if that’s particularly new. I doubt that much glory (or grant money)has ever attended attempts to confirm findings. What has changed, and much for the better, is the pace of retractions, a phenomenon now documented daily at Retraction Watch, as I noted above. Deo gratias. Or, rather, Adam Marcus and Ivan Oransky gratias.

That may be partly due to  journals feeling pressure to be more open to outside comment and to publishing retractions, and no doubt is much influenced by how easy the Internet has made it to hear opposing voices. There are also efforts to sort out competing or confusing claims; for example the Cochrane Reviews.

Also, new studies, ones that are not particularly aimed at replication, do overturn old scientific ideas. Alfred Wegener looked at a map of the world and noticed how well the South American east coast fitted together with the African west coast, thought up continental drift, and was mocked and reviled for half a century until supporting data began to accumulate. Barbara McClintock developed ideas about how mobile genetic elements (we now call them transposons) hopped around in the genome and regulated genes, but hostility from other scientists led her to stop publishing on them. At least she lived to win a Nobel Prize; Wegener did not. Twenty years ago all of neuroscience knew for sure that the human brain made no new neurons after birth. Wrong. These are among the best-known examples, but there are plenty of others.

In his defense, Holcombe is particularly wrought up over the messy research that plagues his own and other behavioral science fields, and about that he is certainly right. He has some suggestions about how to fix things, and good luck to him.

More on the $1000 human genome: a reality check

Last week I wrote some about the HiSeq X Ten, Illumina’s group of 10 million-dollar sequencers that, the company declares, can finally sequence a human genome for $1000. For reasons that are not entirely clear, the $1000 genome has been a goal of genomics since early in this century and even an official US government project for the past decade. So any claim of success is big news.

I have assembled more detail and more commentary about the $1000 human genome since the post here at On Science Blogs, and I disgorged it earlier this week at the Genetic Literacy Project. Particularly noteworthy is the possibility that fast high-volume sequencing may be slowed down by the immense demands it makes on computing power. Find “The $1000 Human Genome: A Reality Check” here.

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Human microbiome, Vitamin E for Alzheimer’s, Tweets, $1000 Genome

 

More on how much of you is microbes

In my final post of last year, I discussed the origin and reliability of my favorite statistic, which is that nine out of ten of the cells in my body, and yours, and everybody’s, are not really yours. They belong to microbes that are essential to your life and your quality of life.

But it’s a new year. And apparently that means new statistics on your cell ratio of resident microbes. This I gleaned from a new report from the American Society for Microbiology, which I learned about from Jonathan Eisen’s Tree of Life blog.  The report is called FAQ: Human Microbiome, and you can get a (free) copy here.

FAQ etc explains the basics, but also goes into detail. There’s a nice clear explanation, for instance, of Koch’s postulates; see p. 12. The report also emphasizes that, while we have grasped the importance of the human microbiome, we know very little about the specifics of what it does in health and disease or about its individual components, normal and abnormal, which can be quite variable. This is a point Eisen emphasizes at Tree of Life, where he often picks apart the many overblown (and false) claims about microbes and health and complains about marketing hype for probiotics.

Anyway, see p. 6 of the FAQ for what I assume is the latest on my beloved statistic. Authors Ann Reid and Shannon Greene think the claim of a 10 to 1 ratio, microbes vs human, is overblown. They say it’s more like 3 microbes for every human cell.

The new number, however, is not based on microbe recounts. The estimate for the human microbiome remains at 100 trillion microbial cells, mostly bacteria and not including viruses. Rather, the revision is due to new estimates of the number of human cells. The human body is now thought to contain not 10 trillion cells but something more like 37 trillion. Hence the revised cell ratio: microbe 3, human 1.  And they say there are an estimated 10-fold fewer fungal cells on/in us than bacteria, so I guess that means we’re home to about 10 trillion fungal cells.

Reid and Greene also say we harbor an estimated 5 times more viruses than bacterial cells, which would bring our viral load up to 500 trillion. Not clear whether that number is supposed to be only the number of free-living (sort of) viruses moving in and out of our cells at any one time or whether it includes all the viruses that have inserted themselves permanently into the human genome over the aeons.

I have written the authors to ask for references that underly the new data and will let you know. I am a bit mournful about this development. The idea of 10 microbes to every human cell is so much cooler than only 3 to 1. I am wondering if I will have to find a new favorite statistic. Or maybe start citing the viral-to-human-cell ratio: 50 to 1.

 

Tweets don’t measure scientific impact

My pal Beryl Benderly, who writes the Science Careers blog at Science, has posted on a study showing that the number of tweets a scientific paper gets doesn’t seem to be related to its impact as measured by citations.

The authors of the study observe that much-tweeted papers usually either are about some health issue or about funny or surprising findings. That seems accurate to me; tweets are, by and large, not about really serious subjects. There are exceptions, certainly, but the Twitter froth level is very high. Also, it’s my impression that citation records often take time to build, sometimes years. So even if tweets did affect citation numbers, I’m not sure that Twitter has been around long enough for an effect to show up this soon.

 

Vitamin E slows down Alzheimer’s disease?

The paper in JAMA reports that large doses of vitamin E seem to slow functional decline in Alzheimer’s patients. At Science-Based Medicine, Harriet Hall analyzed the study. She points out that the daily functioning of all the study subjects got worse. What was noteworthy was that the patients taking vitamin E alone got worse more slowly.

This is potentially huge news. Anything that makes it easier for Alzheimer’s patients to carry out normal activities of daily living is potentially huge news, not only for its impact on the lives of afflicted patients and their afflicted families but because something–particularly an inexpensive something like vitamin E–that would slow down the rise in financial costs and custodial care of Alzheimer’s disease even a little bit would save a ton of money.

Hall advised caution given the many unaswered questions remaining. And she was, of course, against impulse purchases of carloads of vitamin E. But on the whole she thought the study was carefully done and encouraging. This is very nearly high praise at Science-Based Medicine, generally a bastion of lambasting.

Gary Schwitzer had a different take at HealthNewsReview, arguing that media reception of the paper was sometimes way out of proportion to the actual findings of the study. The study related to possible improvement of Alzheimer’s symptoms, but he noted that the media often seemed to imply that vitamin E was slowing the disease process itself, which the paper did not claim and for which there is no evidence whatever.

Schwitzer also took media to task for glossing over statistics in the paper suggesting that vitamin E effects on patient behavior, if any, were very small. But expecting journalists, even science journalists who have some understanding of statistics, to explain confidence intervals to their readers is . . . not realistic.

A more important point, which Schwitzer said the stories also ignored, is that the safety of high doses of vitamin E has by no means been established. There are data suggesting the opposite, that they may be dangerous.

The $1000 Genome Machine(s)

The $1000 Genome Machine(s)

At last, here’s the $1000 genome?

The thousand-dollar genome is here at last. At last, that is, it’s here for those who can afford to purchase 10 of Illumina’s sequencers for a million dollars each. Illumina is calling this gang of sequencers that work together the HiSeqX Ten. The company made the announcement the other day, and John Timmer was quick to publish a reality check at Ars Technica.

I don’t know exactly when the $1000 genome became the goal of sequencing technology, but it was well before 2005, when I wrote about how the $1000 genome had just become an official US government project. That was the year NIH committed to spending $32 million to develop technology aimed explicitly at sequencing genomes of individual patients for $1000.

Note that the HiSeqX Ten is not that, not at all. I have no idea whether any of that $32 million, or any taxpayer money at all, went to helping Illumina toward faster sequencing. As Matthew Herper makes clear at Forbes, HiSeqX Ten does not mean consumers can get their genomes sequenced for $1000 any time soon. “There are other costs, like analysis, that matter, and this does not include commercial markup for the providers of genetic tests.”

The government, by the way, is still plugging away at a true $1000 genome.  The latest NIH request for applications closed last fall, a request “to develop novel technologies that will enable extremely low-cost, high quality DNA sequencing.  The goal of this initiative is to reduce the cost of sequencing a mammalian-sized genome to approximately $1000.”  The call urges applicants to explore methods other than those currently in use, especially “high-risk/high-payoff applications.”

Why does this cheer me up, since I suppose this project could well turn out to be a dead-end use of taxpayer money? It would be useful to know how the government-sponsored $1000 Genome Project has fared since 2005. Has it contributed ideas and technology and gotten us closer to the goal in the last almost-decade? I hope so, but whether it has or not, there’s something wonderful about a government that still employs officials who encourage people to go for it. No HiSeqX Ten-type solutions need apply.

I suppose the NIH fantasy is a desktop machine suitable for a doc’s office. Or, who knows, maybe a kitchen table. Which is a very long way from the HiSeqX Ten.

 

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2013 in Science and Medicine: List of Lists of Lists

Happy New Year. Looking for something to read?  This should keep you busy through much of 2014: A roundup of Top Ten and Best of lists related to science and medicine in 2013. In 2012 the Higgs bosun topped everybody’s lists. 2013 was more of a miscellany.

Pavlof volcano in the Aleutian arc erupts in this image captured by astronauts on the International Space Station on May 18, 2013. Credit: NASA

Pavlof volcano in the Aleutian arc erupts in this image captured by astronauts on the International Space Station on May 18, 2013. Credit: NASA

Tracking the lists

Let’s begin with our friends at the Knight Science Journalism Tracker. They have kindly assembled several such lists, so I don’t have to. Many thanks.

First up, Tracker Charlie Petit, who not only presents us with his annual compilation of top ten and best of lists, but this year mines them to come up with a consensus list of 2013′s most important science stories.

In his List of Lists, he covers Discover‘s top 100 stories of 2013, Real Clear Science’s Top Ten, and also its list of Worst of the Worst, the biggest junk science stories in 2013. Plus the Australian Media Center’s Top Ten Best and also Top Ten Weirdest, Time magazine’s many Top Ten lists (only some of which pertain to science and medicine), and the Times (UK) list of most-read stories.

Topping Scientific American‘s Top Ten news stories was the sequester because of its impact on US science funding. That’s an odd self-seeking choice because the sequester affected government support of many things in addition to science. But never mind. There is also Wired Science’s list of top discoveries, Longform’s best stories, and Live Science’s list.

Science chose to promote what it called Top Ten Breakthroughs. Arrrrgh! For shame, doesn’t Science, of all places, know that “breakthrough” is a banished term if you’re serious about science?

Then Charlie consulted all his lists and drew from them a consensus on the biggest science stories of 2013. There turned out to be four that were  widely agreed upon by list-assemblers:

  • Atmospheric CO2 reaching 400 parts per million for the first time in modern history.
  • Cloning human stem cells and getting them to differentiate.
  • The Chelyabinsk meteor explosion over Russia.
  • Voyager 1 entering interstellar space, which–as Charlie is at pains to point out several times–is not the same thing as leaving the solar system.

More tracking from the Trackers

Tracker Faye Flam presented 2013 science stories “in which reporters repeated a conclusion that was not supported by the evidence they presented.”  One example was the claim that reading fiction makes you more empathetic. She also cited an Economist piece on how science gets it wrong. The piece focuses on mistakes and fraud in clinical and behavioral research and extrapolates to argue that all science is riddled with error. That reminded me of one of Jonah Lehrer’s New Yorker pieces, one from 2010, before his public disgrace, in which he argued that it’s OK to choose what to believe about scientific conclusions. The piece generated a lot of perfectly justified indignation, which I wrote about at the time.

She also presents discouraging examples of a continuing issue in science writing: the mistaken conflation of correlation and cause. This ought to be a simple problem to fix.  But it keeps happening, so apparently not. I suppose it’s partly due to non-science writers writing about research who don’t understand that just because two events occur together doesn’t mean that one causes the other. But some of  these misleading conclusions seem to be asserted by science writers who should know better. Perhaps they can’t resist the lure of potential headlines for what seems to be an off-the-wall finding.

Faye Flam’s example is a New York Times story claiming that women should avoid short-term relationships because they result in bad sex. She notes that the writer never considered another plausible explanation of the data, which is that bad sex causes women to cut relationships short. She’s quite right, of course. If I had time I’d deconstruct those two possible conclusions. I’d  point out that the first one is a product of reflexive woman-as-victim-and/or-slut thinking, while the second assumes women are in charge of their relationships. If I had time.

Head Tracker Paul Raeburn alerted us to 2013′s longer features related to science that you may have missed. Another of Paul’s year-end summations calls attention to a post about 2013′s worst health-related press releases, this from the estimable Gary Schwitzer of HealthNewsReview. Paul quotes Schwitzer thus: “I don’t think all public relations messages about health care are crap,” he writes. “But most of what I see is. And I can’t stand seeing public relations that may end up hurting the public.”

Paul also wrote ruefully about the publications that trumpeted “cures” that were nothing of the kind: cures for AIDS and HIV infection, several different cures for cancer (these from, among others, Time magazine and the New York Times), cures for type 1 diabetes and high cholesterol. And, my favorite, junk food as a cure for obesity. Looking forward to 2014, Paul says, “I predict, with great confidence, that we will see many more ‘cures.’ Modern medicine is a wonderful thing. Not to mention modern reporting.”

Mars dry ice.  Mars is so cold that frozen carbon dioxide, or dry ice, remains from season to season at its south pole. White areas are this residual dry ice cap; the darker parts are water ice with dust and particles trapped in it. From a Wired Science Gallery. Credit:  NASA/JPL/University of Arizona

Mars dry ice. Mars is so cold that frozen carbon dioxide, or dry ice, remains from season to season at its south pole. White areas are this residual dry ice cap; the darker parts are water ice with dust and particles trapped in it. From a Wired Science Gallery. Credit: NASA/JPL/University of Arizona

Some other 2013 Top Ten and Best-of lists

Betsy Mason of Wired Science has put together several galleries of 2013′s best images. They range from striking landforms to microscopic structures to many gorgeous spiders (and some that eat bats.) There’s also a gallery of best photos of Earth from space. Feast your eyes, terrific stuff. I am including a couple of them here, both NASA images because they’re in the public domain and I won’t get sued for copyright infringement.

Technology Review provides several “Best of” lists. They are all about their own articles, but that shouldn’t put you off.  Check out pieces on the origin of life and also best communications stories (topped by the controversy over NSA spying, which if anything seems to be getting bigger rather than fading away.   See also best computing stories, best biomedicine stories, best energy stories, and best long reads.

And now, the top medical news of 2013.

The New England Journal of Medicine‘s Journal Watch is a pay publication aimed at medical professionals, mainly docs, who are presumably too busy to actually read journals in their specialties. Quite helpful to science writers too. Journal Watch does offer some of its posts free. These include year-in-review summaries for several medical specialties with links to their top articles on each.

There’s also a list of NEJM Journal Watch General Medicine’s most important medical topics overall, but those links are behind the pay wall.  Odd. The list all by itself, though, is useful for a glimpse into what topics the medical profession believes matters.

Looking forward to 2014

From space.com, new space missions.

All this month Medpage Today is running a video series on hot topics for medicine in 2014. They cover cardiology and heart surgery, infectious disease, breast cancer, Alzheimer’s disease, autism, diabetes, prostate cancer, diet, Crohn’s disease, asthma and allergy, AIDS, dermatology, rheumatology, emergency medicine, women’s health, stroke, health policy, and lung cancer. Some topics command more than one video, and several haven’t been posted yet.

As the year began, things were looking up for the Affordable Care Act, aka Obamacare, aka ACA. The federal web site was doing better, people were enrolling in new insurance plans, and the giant attempt at a capitalist version of health care reform was looking as if it would survive after all last fall’s attempts to bring it down (although perhaps in modified form, depending on Congress.) On January 2 Phil Galewitz took stock at Kaiser Health News, outlining six developments that may alter public perception of Obamacare for the better.   Kaiser is, of course, following Obamacare closely; find its (very long) story list here.

Also on January 2, the CDC warned that the H1N1 pandemic flu strain that first surfaced in 2009 appears to be this winter’s predominant flu type. The elderly are usually the chief victims of flu, but this strain hits mostly the young and middle-aged. Find the CDC weekly flu surveillance report here.

China's 2013 trip to the moon--the first lunar landing in 4 decades-- unaccountably didn't get many headlines. This photo of the moon rover Yutu was shot by the Chang'e-3 lander. Credit: CNSA/CCTV via Universe Today

China’s 2013 trip to the moon–the first lunar landing in 4 decades– unaccountably didn’t get many headlines. This photo of the moon rover Yutu was shot by the Chang’e-3 lander. Credit: CNSA/CCTV via Universe Today

Inside BGI, the world’s largest genomics institution

China’s visibility in science continues to grow, and maybe we ought to be paying more attention. In 2013, China went to the moon.  We begin 2014 with Michael Specter’s long piece about the Chinese genomics giant BGI, which generates a startling 25% of the world’s genome data.   The piece appeared in the January 6 New Yorker. It’s behind a paywall, but I wrote about it Tuesday for the Genetic Literacy Project, which is not behind a paywall.

Specter’s piece is stuffed with information about the little-known BGI, a Chinese institution–I keep wanting to call it a company–with outposts all over the world. It’s also quite a nice example of science writing.   My take: “It’s a case study in how to place an enormous amount of scientific information before a largely non-technical audience with no pedagogical seams showing. While telling the BGI story, Specter has achieved a compact and uncomplicated primer on genetic basics, genes and their molecules. He even explains, very simply to be sure, how a sequencing machine works.”

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Microbe Counts and Transgenerational Epigenetics

 

Friday the 13th

 

90 per cent of you is not you. True?

My favorite statistic, as I have said here more than once, is this one: 9 out of 10 of your body cells are not “you” at all. They are microbes. Bacteria mostly, but the occasional odd member of other Kingdoms–notably fungi and archaea–as well. (We’re not counting viruses here, which would drive up those “not you” numbers enormously.)

That 9/10 figure is embedded in a lot of papers and textbooks, but even when there is a reference, the source is secondary. I concede that I have used it profligately without trying to nail it down precisely, hoping that all those papers and textbooks are enough to back me up.  It’s a statistic that belongs in the journalistic category of Too Good to Check.

Bioinformatician Neil Saunders is considerably more conscientious than I. He bravely went after the origin of the 9/10 data at his blog What You’re Doing is Rather Desperate.  (For an amusing–and profound–explanation of the blog title, see here.)

Saunders tracks the 9/10 statistic down to a 1971 article in the American Journal of Clinical Nutrition by one T.D. Luckey. A cool name. Saunders quoted from the paper: “Adult man carries 1012 microbes associated with his epidermis and 1014 microbes in his alimentary tract. . . The latter number is based upon 1011 microbes/g contents of an alimentary tract with a capacity of approximately 1 liter. The 1013 cells in his body are a distinct numerical minority of the total being that we call man. If we abandon anthropomorphism for the microbic view, we must admire the efficiency of these microbes in using man as a vehicle to further their own cause.”

Exactly. I am reminded of E.O. Wilson’s remark in Sociobiology: “the organism is only DNA’s way of making more DNA.”  Something similar might be said of our commensals: We lumbering apes are only the microbes’ way of making more microbes.

However, the comments to the Saunders post make a case that the 9/10 figure may not be accurate. One comment notes that the real number might be much higher because 9/10 is an extrapolation from bacteria that can be cultivated in the lab. A great many cannot be.

Another commenter argues that the true count might be lower because population sampling was from the gut and the skin, where microbes are most numerous. “The bacterial diversity and sheer numbers there are not even close to being representative of the rest of the body. What about the brain, or even the bladder?” “Liz” asked.

So, in the full knowledge that an accurate count of our resident microbes might be either considerably fewer than 9/10 or considerably more, I intend to go right on using that standard ratio. If it’s good enough for countless scientists, it’s good enough for me. The idea that 9 out of 10 of the cells I’m dragging around and nourishing in fact belong to other organisms is too astonishing give up.

 

Jean-Baptiste de Monet Chevalier de Lamarck (1744-1829)in about 1802, oil portrait by Charles Thévenin via Wikimedia Commons

Jean-Baptiste de Monet Chevalier de Lamarck (1744-1829) in about 1802, oil portrait by Charles Thévenin via Wikimedia Commons

Here comes Jean-Baptiste Lamarck?

This is about the research showing that male mice trained to fear a particular harmless smell–the cherry-smelling scent of acetophenone–before they sire offspring can pass the memory of that specific fear on to their children and grandchildren.

The research, published early this month, appears to be an example of transgenerational epigenetics.  Epigenetics is not a concept with a consensus definition, which is to say that just what it includes is a matter of scientific dispute. For our purposes, it’s enough to say that epigenetics encompasses a heterogeneous set of biochemical mechanisms that change the behavior of genetic material without changing any DNA sequences. Epigenetics seeks to explain how the environment turns genes off and on in particular cells at particular times. It’s about how nurture shapes nature.

Transgenerational epigenetics is, literally, epigenetics at a whole other level.  The idea is that epigenetic alterations acquired in one generation can be passed on to future generations. Transgenerational epigenetics is a pretty well-established phenomenon in plants. There is evidence that transgenerational epigenetics happens in animals, but it’s often controversial, especially when it is about our own species.

I blogged about the blogging about this paper earlier this week at the Genetic Literacy Project. (This post is based partly on that one.) A barrier to taking transgenerational epigenetics seriously is thinking up a mechanism to explain how such a crazy thing could happen. In the post I explore a couple of possibilities.

The day after that post I got the good news that BioScience, the journal of the American Institute of Biological Sciences, which is now in the sheltering arms of Oxford University Press, has gone open access. Yay for open access! Yay in particular for open-access BioScience, because it means you can now get easily to my two-part series on epigenetics. Marvelous timing. Part 1, covering the basics of epigenetics, appeared in 2009, but the basics haven’t changed much since then.  Part 2, published in 2011, focused on the epigenetics of behavior. It included a section on transgenerational epigenetics and the difficulties of studying it. 

 

A revolution in evolution?

Yesterday I ran across a post by Gregg Henriques, a psychologist blogging at Psychology Today. He greeted the new fear-of-smell paper with a hed calling it “A Revolution in Evolution.” He rhapsodizes: “From a psychological perspective, this is a HUGE finding. For starters, the idea of inter-generational trauma becomes much more complicated with an almost infinite number of possible causal pathways. At a more abstract level, the possibilities become truly remarkable—things like generational psychological legacies and notions such as Carl Jung’s collective unconscious archetypes, which might have seemed farfetched in the past, become more scientifically plausible.”

Whoa. Jung? Yikes.

An editorial in New Scientist wonders whether the smell of fear research means new respectability for a dirty word. The dirty word is “Lamarck.” That would be Jean-Baptiste Lamarck, the biologist whose work was mocked and rejected even in his own 18th century times. Henriques trots Lamarck out too.

Poor Lamarck, usually mocked and rejected today even though some of his work was praised by such illustrious figures as Stephen Jay Gould and Charles Darwin himself. Lamarck is most often associated with the supposedly discredited notion of inheritance of acquired characteristics. That’s the idea that traits taken on during life can be passed on to descendants. The oft-cited example, trotted out by both Henriques and New Scientist: “if giraffes stretch their necks to reach high leaves, their offspring have longer necks.”  The New Scientist editorialist says the fear memory work “seems consistent with Lamarckian inheritance . . . It fits with natural selection—and may yet give Lamarck’s name a sheen of respectability.”

 

No. Not natural selection. Not Lamarck either

About this, New Scientist and Henriques are mistaken. The smell of fear research really doesn’t fit with natural selection, at least not yet. Lamarckian inheritance of acquired characteristics has been controversial because the characteristics are supposed to be permanent. They shape evolution. All giraffes have long necks, and so do their descendants, even when they are snacking on greenery of moderate height.

The new paper describes the fear memory persisting in the grandchildren of the research subjects. There’s no claim that this process is affecting evolution. In fact, as far as I can tell, the length of this study contradicts none of the previous work on transgenerational epigenetics. When biological responses in one generation have been passed on to descendants, the changes characteristically don’t persist beyond three or four generations. They peter out.

In short, they do not become an example of evolution. The idea that a fear can be passed on to grandchildren through some so-far-unidentified biological mechanism is startling. But it is not really Lamarckian.

Not so far, anyway. Perhaps eventually there will be papers telling us what happens in the grandchildren of the affected grandchildren in this study. It would be pretty intriguing to learn that sixth-generation mice are also afraid of acetophenone. That news would certainly suggest an innate fear might be on the way to becoming a fixed evolutionary event.  The history of research on mammalian transgenerational epigenetics to date argues against it, but we’ll see.

There will almost certainly be papers attempting to replicate this work. Will they confirm it? Or contradict it? Mice have a relatively short generation time, so we might find out quite quickly whether the smell-of-fear results hold up.

 

Happy New Year

Time for the season of total family immersion. Have swell holidays.  See you next year, on January 10.

 

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Ancient DNA Gets Older and Multiple Births Get Bigger

 

Ancient human DNA gets older and older

Big stories involving ancient DNA are popping up nearly every week.  This week’s ancient DNA news is recovery of the oldest human DNA yet, from a Spanish cave chamber called Sima de los Huesos, the Pit of Bones. The aptly named pit provides excellent storage conditions and contains bones from many animals and about 30 humans.

A fossil human skeleton from Spain's Pit of Bones. Credit: Javier Trueba, Madrid Scientific Films

A fossil human skeleton from Spain’s Pit of Bones. Credit: Javier Trueba, Madrid Scientific Films

A thigh bone from the Sima has yielded–not without a struggle–human DNA estimated to be about 400,000 years old. Or call it hominin DNA if you insist on applying the term “human” only to the most recent incarnation and sole surviving member of the genus Homo. Which is to say, us. Although so narrow (and narrow-minded) a definition strikes me and others as a phylogenetic classification error as well as a philsophical and psychological one.

Be that as it may, DNA from 400,000 years ago is undeniably a big deal. But we might get back as far as a million years before too long, as I note in a post I did Tuesday for the Genetic Literacy Project. That’s because technological developments are making it possible to recover and analyze tiny bits of DNA.

DNA is much like the living beings that house it: The older it gets, the more likely it is to fall apart. Fragments are all that remain. Which means that getting complete nuclear genomes from very old material, plant or animal, is a long shot.

The Pit of Bones human DNA is mitochondrial DNA, the small genome–containing only 37 genes–powering the structures that supply a cell’s energy. There’s only one nuclear genome per cell, but there can be thousands of mitochondria. So the chance of finding mtDNA in a fossil is much greater than the chance of finding DNA from a cell nucleus–although it’s nuclear DNA, which contains about 22,300 genes, that we generally mean when we’re talking about “the genome.”

You can find details and speculations about the Spanish discoveries at Carl Zimmer’s always-informative blog The Loom. He answers reader questions too.  The equally informative Ed Yong, writing at The Scientist, is very good here on the technical wizardry that achieved this–I shudder to use such a shoddy and verboten term–”breakthrough.” In Ed’s defense, he didn’t say breakthrough, the top-level ancient DNA expert David Reich did.

But still.

 

Surprising and mysterious? Not if you’ve been paying attention

There’s a tendency for the media to treat scientific discoveries as surprising and/or mysterious. That’s partly due to an unfortunate truth about journalism, which is that your editor may not be interested unless you can make the case that your piece will startle readers.

Ancient DNA work is often a fine example. From the Pit of Bones we get heds like these: ‘Oldest’ Human DNA Reveals Mystery (Voice of America), Baffling 400000-Year-Old Clue to Human Origins (New York Times), Oldest Human DNA Discovered, Muddles Picture of Our Origin (Time).

This week’s ancient DNA strikes some people as mysterious for the same reason that other recent finds do, for example the 24,000 year-old Siberian boy with what appears to be European ancestry that I wrote about at GLP last week. These discoveries seem surprising in part because many of us are still in the grip of a now-untenable idea: That human evolution (or, actually, evolution of many organisms) is lineal, a straight line of descent.

It is now clear, however, that our ancestors were enthusiastic networkers, driven by wanderlust and the other kind of lust. Just, in fact, like us–although that seems to have come as a shock in some quarters.

John Hawks, everybody’s favorite paleoanthropologist-blogger, uses the Pit of Bones paper to explain why straight-line descent is utterly inadequate to explain what ancient human DNA is telling us. Although he also discusses nuclear DNA, in the quote below Hawks invites you to look at the evidence just on mtDNA. And note that because it’s mtDNA, which is inherited only from mothers, the subtext is a commentary on how women, not men, moved around and mated:

“Humans today descend in part from Neandertals, even though Neandertal mtDNA is gone. Europeans today are largely different from the Europeans of 10,000 years ago, with a massive mtDNA replacement along with the introduction of Neolithic culture, and at least a second later large-scale replacement of genetic diversity. Earlier Neandertals in Europe have different mtDNA diversity than later Neandertals in Europe. Denisova cave [in Russia] was home to an earlier population of hominins with different mtDNA than the later Neandertals who lived there. Mitochondrial DNA has never been a straight line linking earlier and later populations within a single location. Whenever we look at ancient DNA in hominins, the earlier populations have different mtDNA diversity than the later ones.”

I could go on and on, but Hawks is the oracle on this topic.  A must-read if you care about human evolution, and who among us does not?

 

How to control multiple births

Speaking of human reproduction, a study from the Centers for Disease Control and Prevention, just published in the New England Journal of Medicine, is reporting that fertility drugs are now the most important cause of multiple births.

In the US the proportion of multiple births doubled, from 1.8 percent to 3.5 percent, between 1971 and 2011. Nearly all of the increase was due to fertility treatments, Nancy Shute reports at Shots.

Credit: Dustin M. Ramsey via Wikimedia Commons

Credit: Dustin M. Ramsey via Wikimedia Commons

Used to be that in vitro fertilization was the culprit. (I say culprit because, despite the public oohs and aahs and media gushes over twins, triplets, and especially beyond, the human uterus is designed to hold a single fetus. Non-singleton pregnancies are riskier–sometimes much riskier–for both mother and babes.) Back in the last century, docs often transferred three or more lab-created embryos into a waiting uterus in order to increase the chances that at least one would survive.

The practice of transferring multiple embryos was discouraged in 1998 as a result of new guidelines for ART–one of my favorite acronyms, standing for “assisted reproductive technology.”  Now increases in multiples are being driven by fertility drugs, which stimulate ovulation and often release more than one egg at a time.  But super-ovulation can be better controlled, according to Rachael Rettner at LiveScience, for example by lowering fertility drug doses.

Now that semi-alarming data on lab-created multiple births are backed by the authority of the CDC, the health-watchdog government agency, plus NEJM, the top medical journal, it is pretty safe to predict that ARTists will shortly feel pressure to practice safety measures like these.

 

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Post Removed: Yet More On Sexual Harassment

PLOS BLOGS has determined that the “On Science Blogs” post that had occupied this page  violated one of the key principles we hold for our blog network, specifically, the following language which is included in our independent blogger contract:  PLOS is interested in hosting civilized commentary and debate on matters of scientific interest. Blogger will refrain from name calling and engaging in inflammatory rhetoric. 

Because, after careful review, we’ve determined that this post crossed the line delineated in this tenet, we’re taking the post down. We’ve left the comments intact.

We’re sorry for any distress that the content of this post caused to the target, Emily Willingham, and hope that discussion and debate can continue on the original and vitally important topic of sexual harassment  without resorting to this level of exchange.

Comments and questions can be sent to blogs@plos.org

—Victoria Costello, PLOS BLOGS Community Manager

 

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More on Sexual Harassment. Also, Billions of Earth-like Planets

Sexual Harassment and Science Writing

The recent events involving sexual harassment and former SciAm uber-blogger Bora Zivkovic are no longer dominating science blogs. But they have not vanished from science blogging’s consciousness. The National Association of Science Writers met last week and devoted a session to thinking about what can be done to banish sexual harassment from our professional lives.  I’ve written about the recent controversy  a lot here  and also here. For follow-up, I asked the veteran science journalist Beryl Benderly, an NASW officer and a friend of long standing, to write an account of the NASW session, titled The XX Question,  to share here. Thank you, Beryl, for this illuminating contribution to getting the word out. UPDATE: I can’t imagine that any of you think On Science Blogs is something other than a personal take on things. But I have been asked officially to add this official disclaimer. I am delighted to do so. –TMP.   This post reflects the personal opinions and reporting of the individual authors. While both Tabitha Powledge and Beryl Benderly are board members of the National Association of Science Writers, the post was not written in that capacity and does not reflect an official position, interpretation or commentary of the NASW.

The XX Question

By Beryl Benderly

The National Association of Science Writers met as a community at its annual meeting on November 2 to confront what had come to be known as “recent events”—the revelations of prominent editor Bora Zivkovic’s serial sexual harassment of several women bloggers. About two hundred members of both genders attended a session originally intended to examine the issues facing women in the science writing business but now broadened in focus and moved to a larger room and a time slot with no other competing session.

The goal, said session moderator Deborah Blum, was to have a frank—and Twitter-free—in-person conversation that would move the discussion forward. As a starting point, she noted how men very disproportionately dominate the mastheads and tables of contents of the major publications and also the lists of winners of major prizes (except, as it happens, NASW’s own Science In Society awards.)  She also presented a manifesto that she and the session’s panelists had developed:

  • Equal pay for equal work
  • More gender equality in bylines and mastheads
  • Equal recognition of award-worthy work
  • A recognized code of conduct that includes freelances
  • A safe and clear process for reporting sexual harassment
  • Encouragement to speak frankly and directly.

She then introduced a panel of women science writers who each gave their impressions of women’s current situation.

Credit: Neurocritic

Credit: Neurocritic

 

 Hearing from Women

Among the panelists’ comments, Emily Willingham explained the concept of social privilege, which is advantage derived from a feature of a person that he or she did not create.  This reality, she said, imposes responsibilities on those who possess such features—responsibilities that the privileged often ignore.  Christie Aschwanden noted that the scandal had surprised men and not women and also described her feelings of marginalization in the world of science writing.  Maryn McKenna noted that science journalism will soon be a majority female occupation, but that won’t in itself end the marginalization of women. And Kathleen Raven, one of those who came forward to accuse Zivkovic, told of doing all she could, to no avail, to stop the harassment, including repeated warnings.  She will, she said, be much more clear about ground rules of interactions in the future.

When Blum opened the floor to comments from the audience, women came forward to tell their own experiences of harassment and marginalization.  The special vulnerability of freelances—who generally depend on personal relationships to get assignments and rarely know publications’ anti-harassment policies or reporting procedures—was a common theme.  In addition,  Ginger Campbell, a practicing physician as well as a podcaster, brought word from the world outside science writing.  Numbers alone will not end these problems; on that point she agreed with McKenna.  The medical profession is now also heavily female, she said, but there, too, invisibility is everywhere

 

Hearing from Men

But some of the most powerful and significant statements came from men.  Mike Lemonick described his astonishment at the different reactions of men and women to the revelations.  Men, he said, were amazed that harassment appeared to be common.  Women were not.  He, like many men, had simply been unaware, a situation that needs to end.  Unless men’s consciousness is raised, he said, men will continue to be unconscious.

Mitch Waldrop recalled that when he rose to a position of editorial power, he didn’t feel powerful or get any training on how to think about  or deal with power differentials that can cause innocently intended behavior to be misinterpreted.  Editors, he said, need such training.  Waldrop, an NASW board member, also mentioned that the board is taking the issue very seriously and is working on several approaches to help.

But Rob Irion, who directs the science writing program at University of California, Santa Cruz,  went to the crux of the matter.  In an emotional statement, he confessed that, having learned of the scandal and heard the testimony in the room, he deeply regrets that in the past, when he heard of incidents, he listened sympathetically but took no action to protect the victim.  That, he said, will not happen again because he now recognizes his personal responsibility to speak.  He will, he says, go to perpetrators and say the behavior must stop immediately, and if it does not, he will have no compunctions about going to the person’s boss.  He will also spread this message at his own institution and in his own interactions.

The conversation seemed to end with a consensus that the solution lies not only in official statements and codes of conduct but in a shift of cultural values that make harassment unacceptable, much as smoking indoors—which was once prevalent in all social occasions—is now considered beyond the pale.  For this to happen, individuals must take responsibility to spread the change. The conversation indeed appears to have moved forward.  Whether it results in improvement, however, remains to be seen.

Many thanks, Beryl. We Now Return You to Our Regularly Scheduled Program


Watching Other Worlds: WOW

The biggest science story of the week, the month, perhaps the decade is the Kepler spacecraft‘s estimation that there may be at least 4 billion, maybe tens of billions, Earth-like planets in our galaxy, the Milky Way.  Earth-like in this case means planets of a similar size and with similar temperatures as the Earth, and yes, that’s billion-with-a-b. And because there are billions of galaxies, there could be billion trillion Earth-like planets in the entire Universe. Wow indeed.

Bad Astronomer Phil Plait walks us through the data, the math, and the caveats.  Going by statistics alone, he says, the nearest Earth-like planet might be only 12 light years away.  That, I realized, makes it a near neighbor that could be visited easily in a human lifetime–just as soon as we invent turbo spacecraft that can travel close to 186,000 miles per second, the speed of light.

Knight Science Journalism Tracker Faye Flam took off from Giordano Bruno’s intuition, in 1584, of “numberless earths circling around their suns, no worse and no less than this globe of ours.” (For this and other heresies, Bruno was burned at the stake.) Flam’s point is that, while there is nothing new in the idea of numberless Earths circling around their suns, that’s no reason not to respond to the Kepler data with: Wow. She cites several news stories that do so.

Find another Wow by Seth Shostak, from the SETI Institute, blogging at HuffPo.  The Kepler data paper, published Monday in the Proceedings of the National Academy of Sciences, is open access. Get to the full-text PDF from the Abstract here.

This image of the Milky Way Galaxy from NASA has been overlaid with the "Star Trek" method of viewing the galaxy. Yellow notes the major (fictional) political forces in the Star Trek world. Additional information from the The Canadian Galactic Plane Survey and StarTrek.com. Derivative work by Codehydro based on a galaxy photo from NASA/JPL-Caltech/R. Hurt

This image of the Milky Way Galaxy from NASA has been overlaid with the “Star Trek” method of viewing the galaxy. Yellow notes the major (fictional) political forces in the Star Trek world. Additional information from the The Canadian Galactic Plane Survey and StarTrek.com. Derivative work by Codehydro based on a galaxy photo from NASA/JPL-Caltech/R. Hurt

Why Didn’t NASA say Wow too?

A Wow also from Keith Cowling at NASA Watch. It’s “stunning news,” he says, quoting Shostak (approvingly). Cowling illustrates his post with maps from the Star Wars and Star Trek Universes. The maps are, he says, now usable as illustrations of Kepler data, which make those fictional Universes, now embedded in the culture, seem plausible.

Cowling is baffled, though, by what he sees as NASA’s incomprehensibly low-key release of the data. “NASA itself seems to be sound asleep when it comes to the profound ramifications of this news. Indeed, it looks like NASA really doesn’t care.”

I am wondering if, rather, NASA does care, care deeply about the thrashings it has received over some notable recent PR bungles. The space agency may be overcompensating.

First there was the notorious arsenic bacteria case of 2010-2011. As pre-publication bait, NASA implied the discovery of an alien life form. The alien turned out to be a bacterium from California. Not alien, not even an illegal. Furthermore, the bug didn’t in the end possess the weird metabolism claimed for it.  And then a year ago there was the hoo-hah over whether the Curiosity rover had found evidence of life on Mars. In that case, NASA didn’t move fast enough to “clarify”–i.e., quash–an ambiguous comment from one of the researchers.

I suppose it’s possible that NASA is now erring in the opposite direction, failing to get journalists to properly appreciate a pretty spectacular finding: the Galaxy is teeming with Earth-like planets.

 

Billions and Billions of Earth-like worlds

A dip into the anti-evolution/Intelligent Design chatter on this topic has its amusements. Take, for example, Evolution News and Views (which is heavy on Views, not News.) There Denyse O’Leary argues that those who believe in billions of Earth-like planets are lacking evidence. Their beliefs are, she says, based entirely on faith. And she says this with no whiff of irony about the faith-based underpinnings of Intelligent Design.

But she’s wrong. I don’t deny that faith has been involved in the long-held belief in other worlds, from Giordano Bruno on. But now we do have evidence. Actual data.

The biggest caveat, I suppose, is that these numbers, while not guesses, are just estimates, extrapolations based on surveys of a small patch of sky. And even if the numbers approximate reality, these Earth-like planets are not all, or maybe even mostly, habitable planets. Habitable at least by carbon-based life forms like Earth’s.

 

The field of view of NASA's Kepler space telescope, which stared at a single region of stars--the cross-hatched area--in the constellation Cygnus, just above the plane of the Milky Way Galaxy. Credit: Erik A. Petigura & NASA

The field of view of NASA’s Kepler space telescope, which stared at a single region of stars–the cross-hatched area–in the constellation Cygnus, just above the plane of the Milky Way Galaxy.
Credit: Erik A. Petigura & NASA

 

Is Anybody Out There?

And that, of course, is what we really want to know. Billions and billions of Earth-like planets is great, but the truly interesting question is this one: Is there anybody out there on any of those planets? Carbon-based or not? (Assuming we could even recognize life that was not.)

Which makes the intriguing blog post by Sean Carroll (the physics one) particularly relevant. He points out that we are prone to assume that if the number of Earth-like planets is really big, as it appears to be, then there must be a lot of intelligent civilizations. (He doesn’t cite it, but Shostak’s post is a lovely example of this faith: “Unless you’re convinced that our watery planet, one of hundreds of billions floating in a non-descript galaxy similar to a hundred billion other galaxies, is somehow more worthy than all the rest, you should expect not merely an occasional Chewbacca or Klingon hanging out in space. The universe is far more likely to be a teeming shore of life, and biology as much a part of nature as rocks and rain.”)

Not so fast, Carroll says. The fraction of Earth-like planets might be as small as 10-100, “in which case there could be billions of Earth-like planets for every particle in the observable universe and still it would be unlikely that any of the others contained intelligent life.”

I don’t know where Carroll gets that number, but who am I to doubt him? And he goes on to say something we can all agree on: “Our knowledge of how easy it is for life to start, and what happens once it does, is pretty pitifully bad right now.”

One reason for doubt is the Fermi paradox: if They are out there, why haven’t we heard? Carroll lists a couple of the standard answers. Intelligent life may be very rare even if life itself is common. Or the anthropomorphic explanation: Intelligent life may, oxymoronically, tend to blow itself up or come to another sort of bad end. Global warming, anyone?

Carroll proposes a third possibility, also disturbing: the Enlightenment/Boredom Hypothesis (EBH). What if a civilization, when sufficiently advanced, gives up all that striving to survive. “Maybe they perfect life, figure out everything worth figuring out, and simply stop. I’m not saying the EBH is likely, but I think it’s on the table as a respectable possibility.”

He notes that humans adopted modern behavior–spoken language, symbolic thought, special skills, culture–only tens of thousands of years ago, and came to science only in the past few hundred years. To which I would add that the ability to read and write–essential for accessing and storing humanity’s accumulated knowledge and making it useful over and over again–became common only recently and is still by no means universal. In short, the creatures we are today are pretty new at being the creatures we are today. There’s no way to tell where (or even if) our evolution will proceed.

The moral of this story, according to Carroll: “Maybe the swashbuckling, galaxy-conquering impulse is something that intelligent species rapidly outgrow or grow tired of. It’s an empirical question — we should keep looking, not be discouraged by speculative musings for which there’s little evidence. While we’re still in swashbuckling mode, there’s no reason we shouldn’t enjoy it a little.”

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Peer review at PubMed Commons. Also, more on marijuana

 

If there is a single basic irreplaceable tool for research in the life sciences, it is surely PubMed, the literature database of the US National Library of Medicine. PubMed is irreplaceable not just for scientists but for anyone with a professional (or even personal) interest in life science research.

That very much includes science writers, for whom PubMed is essential. And deeply beloved. I speak as one who did it the hard way before there was PubMed, spending hours and days in the stacks of difficult-to-access medical libraries, taking notes on 3 x 5 index cards. Looking back, I don’t know how I had time to get anything written at all. PubMed changed my world, very much for the better.

The heart of PubMed is its collection of bibliographic information and abstracts from nearly every journal in the world that touches on the life sciences, which means not just Science and Nature and JAMA and NEJM, but also journals in related fields like anthropology and paleontology and computers and economics and even astronomy and physics. Find the journal list here.

How to get full texts of journal articles

Many years ago I took a science writers tour of NLM and asked the then-director if there was any hope of full texts of journal articles online. He put on a long face and said he didn’t see how it could happen, what with copyright and journals being money-making operations.

That was then. It’s a new world. Some funders now require grantees to deposit their journal articles in PubMed, and even commercial publishers make articles open access on occasion. Full text is increasingly available, and when that’s the case, the PubMed reference includes a link to the complete paper. Here’s PubMed’s tips on how to get full texts.

PubMed goes way beyond journals

Journals are the heart of PubMed, but there are other riches to be had there too.  Here are just a couple of examples; there are many more.

Some PubMed services are of use chiefly to scientists, like access to the human and mouse genome sequences. But writers find treasure there too, such as the directory of human genes and disorders known as OMIM, Online Mendelian Inheritance in Man. Find the many genome resources here.

For some reason it is not widely known that PubMed also provides full-text access to hundreds of textbooks and reports. Start here.

And there is, of course, a mobile site.

And PubMed is all free, a matchless gift from the American taxpayer.

PubMed Commons: Changing peer review forever, and improving science while it’s at it?

I am telling you all this in case you don’t already know about PubMed. And even if you do, you may not know that PubMed has just launched PubMed Commons, a system for commenting on journal abstracts. It’s an experiment that “could change the process of peer assessment of scientific articles forever.”  So says James Coyne at Mind the Brain.

Coyne takes an entirely rosy view of PubMed Commons. It might, he says, be “truly revolutionary. PubMed Commons is effectively taking post-publication peer review out of the hands of editors and putting control firmly in the hands of the consumers of the scientific literature—where it belongs.” His is a long explanatory post, with plenty of criticism of letters-to-the-editor as a vehicle for what evolutionary biologist Michael Eisen calls post-publication peer review.

Eisen, a co-founder of the open-access Public Library of Science, where you’re at right now, has long advocated for post-publication peer review. But the efforts so far, he explains at It is NOT Junk, are either awkward to use or haven’t caught on. Eisen describes himself as excited and cautiously optimistic about PubMed Commons. “The obvious place to build such a commenting/post publication review system has always been directly in PubMed – it has everything and everyone already uses it.” He urges scientists to join up and join in, helping to make the new system work by committing to comment on a paper at least once a week.

Drug Monkey thinks PubMed is just the right place for post-publication review too, and also urges scientists to sign up and contribute to PubMed Commons. He says, “I will be eager to see if there is any adoption of commenting, to see the type of comments that are offered and to assess whether certain kinds of papers get more commentary than do others. All and all this is going to be a neat little experiment for the conduct-of-science geeks to observe.”

I guess I’m one of those conduct-of-science geeks (although I think of myself as more of a nerd than a geek.) And, as it turns out, I can probably qualify to check out the commenting action. And comment myself.

That’s because, although PubMed Commons is a private system for now, many science writers are probably eligible to join. You only have to be an author on any publication in PubMed (even letters-to-the-editor) and then get a registered participant to sign off on you.

It was my impression these membership restrictions apply only to this initial test period, but Ivan Oransky seems to think not. He has a post at Retraction Watch complaining about confining participation to scientists only. The PubMed net is actually wider than he implies; it includes more than just certified scientists. I’d never thought to do a PubMed vanity search before now, but it turns out–to my surprise–that dozens of my publications are listed. Ivan is in there too. So we both qualify–and so, I bet, do a lot of our peers.

Ivan is also unhappy about the exclusion of anonymous comments from PubMed Commons. His post includes ruminations from several of those involved in setting up the new system. They describe internal arguments over whose critiques should be allowed. Dozens of comments follow his post (and a good many, of course, are anonymous.)

Ivan’s quotes from National Library of Medicine director David Lipman suggest to me that the PubMed Commons membership restrictions are not engraved in tablets of stone. PubMed Commons is, after all, in the very earliest experimental stage, which means it will evolve.

At the British Medical Journal Group Blogs, BMJ deputy editor Trish Groves is worried that PubMed Commons will worsen what she thinks is PubMed’s already strong (negative) impact on the future of journals. She points out that the BMJ Rapid Response system has published nearly 100,000 comments about its papers, and they’ve been doing it since 1998. PubMed Commons, she suggests, can discourage journals from doing the right thing in providing for critiques on their own sites.

Maybe she’s right. It’s not good to damage the journal ecosystem unnecessarily, especially excellent journals that are open-access, such as BMJ. Still, the excellent open-access PLOS journals (where On Science Blogs now lives) don’t seem worried. As PLOS co-founder Michael Eisen notes, it’s undeniably efficient and convenient and simple to consolidate post-publication peer review in a single place, one that, like PubMed, people visit all the time anyway.

The first priority needs to be to encourage post-publication peer review and to raise its profile, as PubMed Commons will try to do. Post-pub review is not just navel-gazing or a way to provide disgruntled researchers with a place to vent. It’s one crucial long-term step toward combing the crap out of the scientific literature and making it more trustworthy.

We need more marijuana genome projects

It’s part of blogging culture to self-promote. And since I’ve written about marijuana twice so far here at On Science Blogs, it seems only right to direct you to my most recent disquisition on pot. This one is a blog post about the Cannabis genome, which appeared over at the Genetic Literacy Project.

A tidbit I discovered in researching this piece: while there are a zillion genetically different strains of cannabis, they are all the product of conventional breeding techniques, some of which have been around for thousands of years. Attempts at genetic modification–21st century laboratory techniques for manipulation of single genes–have so far failed. So no worries that what you’re smoking (for medical reasons, of course) is GM pot.

 

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