Moratorium on virus research, epigenetics and fear, open access to journals

 

A moratorium shuts down research on flu, MERS, and SARS viruses

The debate began quickly over the moratorium that the White House has  declared on certain sorts of virus research, the sort where researchers are deliberately trying to make a disease virus more virulent or infective. These are often called gain-of-function experiments, but that does not mean all gain-of-function work is potentially dangerous.

Deliberately making a disease organism more scary sounds loony at first glance, and lots of people think it’s loony no matter how many glances you give it. See, for example, Steven Salzberg’s post at Genomics, Medicine, and Pseudoscience. Salzberg is one of the scientists involved in the Cambridge Working Group, which has been pressuring the administration to restrict the experiments–pressure that was one factor leading to the moratorium.

Credit: Star5112 via Flickr

Credit: Star5112 via Flickr

The moratorium applies to the viruses that cause flu, SARS, and MERS–influenza, severe acute respiratory syndrome, and Middle East respiratory syndrome. Here’s what the White House blog had to say about the decision, with links to commentary from other US government agencies.  At ScienceInsider, Jocelyn Kaiser reports that about two dozen NIH-funded studies will be affected, plus some at the Department of Agriculture.

There are, arguably, reasons for doing this sort of gain-of-function research. One example is the need to develop small animal models to better study a disease. One researcher is claiming the moratorium will halt her surveillance of circulating flu viruses. Another points out that potential flu drugs must be tested on wild strains, which could produce resistant viruses.

The risk assessment began immediately on Wednesday when the previously moribund National Science Advisory Board for Biosecurity met for the first time since 2012. There’s a story there that hasn’t been told yet. Anyway, the NSABB heard from scientists who believe a moratorium is more of a threat to public health than the research is.

But the dismaying truth is that historically, bioterrorism has been much less of a risk than accidents emanating from well-meant research efforts to protect ourselves, a topic I wrote about here at On Science Blogs in June. Thus the White House has decided to err–and lot of scientists do think it’s an error–on the side of safety.

The moratorium is supposed to be voluntary and temporary, until the risks can be better assessed. But Nell Greenfieldboyce reports at Shots that some researchers who study these viruses say the National Institutes of Health, which holds the purse strings, has already sent them “cease-and-desist” letters.

The White House says the decision was prompted largely by the recent revelations about sloppy and potentially worrisome conditions at several government labs–where, for example, cleanup crews happened upon forgotten stores of the smallpox virus, supposedly banished from the face of the Earth to the safety of repositories in Russia and at the US Centers for Disease Control and Prevention decades ago. (You can read about this revelation at an On Science Blogs post from July.)

I can’t help wondering, though, how much the irrational panic over US cases of Ebola–and the vituperation President Obama’s opponents have loosed upon him as a result–doesn’t have something to do with the moratorium. Details of the Ebola panic, collected by Maryn McKenna at Superbug, will astound you. (HT also to McKenna for bringing us the marvelous “panic button” photo, which I have appropriated herewith. And hearty thanks to Star5112, who shot it. Brilliant.)

 

Inheritance of fear unto the third generation

A paper showing that unconditioned mice could inherit memories of the conditioned fears of their grandfathers , which appeared late last year, made quite a media splash. The work was done by Brian Dias and Kerry Ressler of Emory University, and the paper ran in Nature Neuroscience.

The embrace of its findings–which made the case for transgenerational epigenetics,  transfer of a memory of behavior for three generations–was more than usually rapturous. In the two items I wrote about the paper, here at On Science Blogs and in my weekly column at the Genetic Literacy Project, I noted that other scientists would be racing to replicate the study. Since mouse generation time is short, I hoped we might have confirmation of the startling findings (or failure to replicate) pretty soon.

Attempts at replication of the work haven’t been reported yet, but something else  has. Gregory Francis, a psychologist at Purdue, argues in the journal Genetics that the paper’s statistics are too good to be true. He notes that the researchers reported uniformly positive results for the epigenetic memory experiments. The probability of such a result is only 2.3%, Francis says. And if you add in the other positive neuroanatomical results the paper reports, the probability of the reported numbers drops to 0.4%.

Neuroskeptic doesn’t know what to make of this critique, noting that if the reported probability was one in a million, there would be cause for serious concern. But, using Francis’s analysis, Neuroskeptic says the probability is about one in 300. A one-in-300 event may be unlikely, but it’s by no means impossible.

In a comment on the Neuroskeptic post, Francis says “these odds are estimates of replication success, and it seems that most scientists want odds better than 1 in 2. . . The 1 in 300 odds might be high enough to imply that Dias & Ressler were simply (un)lucky with their experimental findings, but their data still does not provide good support for their theoretical ideas.”

Francis’s critique in Genetics is accompanied by a reply from Dias and Ressler, who say they have been able to replicate the work themselves “multiple times.” Francis told me in an email, “I find the Dias and Ressler reply to be disappointing. In particular, one can hardly dodge a critique of being too successful by reporting more replication success.”

The critique is preceded by comments from Genetics‘s editor Gary Churchill. He seems to be presenting an Argument from Authority in favor of Dias and Ressler’s findings, declaring that an important journal like Nature Neuroscience wouldn’t have published the paper without thorough vetting.

For further discussion (and critiques) of Francis’s critique, see Kate Yandell’s piece at The Scientist. I would be delighted refer you to the paper itself–and the reply by Dias and Ressler, and  Churchill’s comments. But I can’t. The papers are not open access.

I was startled by the fact that the papers and commentary were not easily available, having grown accustomed to even closed-access journals often granting free access to papers of unusual interest. It seemed particularly odd in this case since Genetics is published by a professional association, the Genetics Society of America, among whose members are K-12 teachers and community college instructors.

 

Against the tide of open-access

It seems particularly odd since this week I encountered a delightful statistic: At the Nature News Blog, Richard Van Noorden tells us that more than half the peer-reviewed papers published between 2007 and 2012 are now available free for downloading. Many other interesting details in this post. Which you can read for free because, although Nature is paywalled, Van Noorden’s post about open access–is open-access.

The recent papers, the ones we want to see most, are of course an entirely different story. Compared to olden times, however, even recent papers are often pretty easy to get.

  • Search the paper through PubMed and you’ll be linked to full text or author manuscript if available. An encouraging number are.
  • If not, email the corresponding author. Your copy will quite often arrive within a few hours; that’s how quickly Francis sent me his paper, plus the comments from Churchill and Dias and Ressler.
  • Or email the senior author’s PIO or the journal’s PR department.
  • Sometimes an even quicker solution is to find it on somebody’s site. Google the paper’s exact title in quotes (leaving off the period, if any.)

 

 

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Out in the cold: Freezing feces and human eggs. Also, scientific easter eggs

 

More germ warfare, this time about fecal microbiota transplants

Despite their mind-boggling track record, fecal transplants as  effective treatments for intestinal disorders (and possibly those elsewhere in the body) have encountered PR problems–what Loom blogger Carl Zimmer calls the yuck factor.

That’s doubtless chiefly because of what they are, literal shit. After a century and a half of sanitation inculcation, it’s hard to get the mind around the idea that the microbes they contain are life-giving. At Pacific Standard, Bryn Nelson recounts a tidy theory that once upon a time, in agricultural societies, feces were looked upon with favor as fertilizer. But when we moved to cities, close quarters, the appalling state of the streets, and and disease transmission (cholera in particular) turned friendly fertilizer feces into something dangerous and disgusting.

The implication is that the yuck factor is not an inborn and inevitable human reaction to our own excrement, but a historical development born of demographic changes. Be that as it may, the yuck factor is surely the reason that the adoption of therapeutic fecal transplants–which, Nelson tells us, originated in China more than 1500 years ago and were experimented with successfully in the US in the 1950s but then vanished–has been so slow.

Now comes a development that could help change that: frozen feces in pill form. A smallish experimental study at Massachusetts General Hospital has shown that the frozen feces pills are as effective as the predominant forms of feces administration: enemas and nasogastric feeding tubes. Both are embarrassing and–especially the tube method–painful.

Credit: Hohmann Lab

Credit: Hohmann Lab

Also, as Nancy Shute points out at Shots, with the tube method there’s the possibility of inhaling feces. That’s not just yuck or even gross, it’s potentially dangerous. Excrement makes good fertilizer and is full of microbes that are essential for good health and even life. But there are bad bugs in there too.

The researchers have now tried frozen feces on some 40 patients with infections from Clostridium difficile, the antibiotic-resistant, debilitating, potentially fatal cause of massive diarrhea. It often follows antibiotic treatment for some other infection that kills the target bug but also the normal resident microbes that usually keep C. diff from getting the upper hand.

The cure rate in this treatment was 90%, similar to other C. diff fecal transplant tales. These terrific results were reported at a meeting only last Saturday, but the Journal of the American Medical Association had snapped  up the paper and published it (open access) the same day, to the researchers’ delight. “I’ve been a microbiology researcher for 25 years, and this is the biggest thing we’ve done,” lab head and senior author Elizabeth Hohman told Shute.

The researchers are making the frozen pills available “to qualified patients” without formal clinical trials, according to the New York Times. I don’t know who they regard as a qualified patient, but I’m betting there’s a stampede of desperate people toward Mass General.

Regulatory agencies will doubtless have something to say about that. But they’re going to have to move fast. The approaches to fecal transplants are changing all the time, and the demand for this near-miraculous cure is unstoppable. Alexander Gaffney points out at Regulatory Focus that the Food and Drug Administration is already in a quandary over how to deal with fecal transplants. FDA issued something close to a cease-and-desist order in the spring of 2013 and ended up in deep shit.

 

From freezing feces to freezing eggs

Apple and Facebook probably thought they’d be seen as deserving a lot of, um, brownie points when they offered women employees an unlooked-for reproductive benefit: up to $20,000 to freeze their eggs.

Some women probably do like the idea of a company assist with postponing childbearing. They might change their minds if they read up on the risks of egg recovery and the disappointments of in vitro fertilization and other forms of assisted reproduction.

egg n sperm

There are several reasons why offering women a chunk of money as enticement to delay childbearing in order to continue working (because that is what this “benefit” is) is a rotten idea.  Canadian bioethicist Françoise Baylis lists 7 of them at the Impact Ethics blog.

The most potent argument against putting off children is that pregnancy and childbirth become increasingly iffy with time. For one thing, a woman’s eggs are present at her birth, and they age right along with her.  As Ricki Lewis, my colleague here at the PLOS Blog Network, points out at her blog DNA Science, the eggs of a female fetus start developing when a pregnancy is about 5 months along. So a pregnant woman is carrying not only her own potential children, but her grandchildren too.

The most common abnormality among the children of older women is an extra chromosome, as is the case in Down syndrome. Lewis says that the specific reason older women are more likely to generate eggs with extra or missing chromosomes is not known. But the statistical fact is that for a woman in her 20s, the risk of a fetus with an extra chromosome is about 3%. For a woman in her 40s, though, the risk increases tenfold, to more than 30%.

I suppose the companies might argue that’s exactly the reason to undergo egg freezing when you’re younger, and here’s $20,000 to help you do it. But, Lewis argues,”Facebook and Apple are attempting to pay female employees to undergo a very risky procedure with not-well-understood consequences, when we don’t even know the mechanism behind the maternal age effect.”

 

Speaking of eggs, easter eggs in scientific papers.

HT to science writer and sleep expert Lynne Lamberg, who sent along this amusing tale of risqué acronyms in scientific papers. I suspect distribution may be a bit limited, however, since to get the the jokes you not only have to be pretty good at French, you have to be pretty good at idiomatic French expressions of the naughty kind.

But that item triggered my hunting instinct. Recalling that software engineers have named the jokey items they bury in their programs “easter eggs,” and that the term has now migrated to jokes hidden in computer games, on YouTube, and divers elsewhere, I searched “easter eggs in scientific papers”.

Lo and behold. A treasure trove devoted to bringing  public attention to little inside science jokes, and named exactly my search string. I wasn’t really surprised. You can find anything on the Internet. Be warned, though, that many are (like the French one) examples of inside baseball.

Easter Eggs in Scientific Papers is up-to-date with an example from the new chemistry Nobel winner, Stanford’s William Moerner, who has worked on microscopy of single molecules. He writes of a guacamole, which he says is the inverse of a mole.

To get that chemical joke, you have to know that a mole is a quantity of something that contains  6.02×1023  particles, and 6.02×1023  is known as Avogadro’s Number. (A mole, About Education explains, is simply shorthand for A Very Large Number.) According to Moerner, guacamole is, of course, one single molecule [that is, 1/(Avocado's Number) of moles.]

As I said, inside baseball.

But the author of Easter Eggs in Scientific Papers, an anonymous self-described computational biologist, is nothing if not thorough. He has traced the origin of Avocado’s Number back to 1988, to another Nobel Laureate, the beloved molecular biologist Sydney Brenner. Brenner defines it differently. A guacamole does indeed depend on Avocado’s Number, but Avocado’s Number can be anything you want it to be, Brenner says. “So a guacamole is I don’t know how many numbers.”

Here’s another science easter egg, from the same archivist on a different blog. Still inside baseball of a kind, but intelligible at least to anyone familiar with the academic world. From a scientific paper: “Order of authorship was determined by proximity to tenure decisions.”

Credit: Tony Esopi from el

Credit: Tony Esopi from el

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RIP ScienceOnline, cave art in Indonesia is as old as European cave art, how human were Neandertals?

This just in: RIP ScienceOnline (#scioX)

ScienceOnline, which for the past few years has run the small annual meeting in North Carolina that brought together a disparate bunch of scientists and science groupies, most of them bloggers, is no more. Knight Science Journalism Tracker Paul Raeburn has details.

The sexual harassment disgrace of the ScienceOnline co-founder Bora Zivkovic last fall, which I covered (more than once) here at On Science Blogs, was doubtless a big part of the reason the project couldn’t find funding and has been abandoned. But I suspect there were other reasons too, not least that the science blogging world, and science online, has gotten huge and incoherent.

scienceonline logo

The last session I attended, in 2011 I think, seemed to me to take place in separate enclaves: journalists, scientists, educators, multimedia types, etc. There was little talk across those borders. The borders hadn’t mattered, hadn’t even existed, in the early meetings, when science blogging was a small and pioneering world. The fact that they did it, and did it with great seriousness, was enough to give people lots to talk about.

The Bora Affair was a terrible blow, and no doubt made potential funders run away screaming. But #scio’s end may have been in part a natural death too.

Thank you all, especially Karyn, for your midwifery. You played an enormous part in bringing science blogging into the world.

 

Take that, Chauvet

One reason the revelations about Indonesian cave art being 40,000 years old has gotten so much attention is the snarking it encourages. See, for example, Razib Khan at Gene Expression. It’s yet another blow to the idea that Europeans are more advanced culturally than other H. saps.

The cave art long known from the Indonesian island of Sulawesi has been redated and shown to be nearly 40,000 years old, just as old as the oldest cave art in Europe. John Timmer explains at Ars Technica.  A post at Vox by Joseph Stromberg contains especially nice photos and a video. Good photos comparing the Sulawesi and European paintings and a video on cave art at the BBC.

The discovery poses an interesting question about human evolution. Here’s one view, expressed by Annalee Newitz at io9: “Something happened to humans roughly 40 thousand years ago, some evolutionary and cultural development, that allowed us to start expressing ourselves symbolically. It’s extraordinary to imagine it arising in disconnected human communities throughout the world.”

Is the artistic impulse a trait that arose simultaneously in human brains on the opposite ends of the Earth, as Newitz says? Or–much more plausible to me than the orphic pulse of cultural synchronicity that she suggests–does it date from before that?

Did we start getting arty sometime after we evolved in Africa but before we set out for parts unknown some 60,000 years ago? Did people arrive in France and Sulawesi already experienced at putting pigment to stone? There’s a bit of evidence that might be so, early evidence of use of pigment in Africa (although no cave art. Yet. Absence of evidence is not evidence of absence.)

“I think these exciting discoveries allow us to move away from Eurocentric ideas on the development of figurative art to consider the alternative possibility that such artistic expression was a fundamental part of human nature 60,000 years ago, when modern humans not only occupied most of Africa but were beginning to disperse out towards Europe and the Far East,” said Chris Stringer, of London’s Natural History Museum. He was quoted in a post by Hayley Dunning at the Museum’s blog, Nature Plus.

Stringer predicts even older art finds on Sulawesi and mainland Asia and in Africa too. Kate Wong, at the SciAm Editor’s blog Observations, agrees. “I’m betting that archaeologists will eventually find much older examples of such art in humanity’s motherland,” she says.

The oldest hand stencil, Sulawesi. Credit: Kinez Riza

The oldest hand stencil, Sulawesi. Credit: Kinez Riza

On the other hand, ahem, I wonder whether cave art, originally, was an artistic impulse at all. The very earliest artwork on Sulawesi, laid down just under 40,000 years ago, is a stencil of an individual hand, and hands are far more common than animal portraits. The oldest hand there is also a little older than the oldest hand stencil in Europe, where there are also plenty of hands on cave walls.

That hand stencils seem to have happened before the animal cave paintings suggests to me that the aesthetic urge may not have originated as the desire to capture the world our distant forebears found themselves in so much as it was the desire to leave one’s mark. Not unlike what the New York subway system looked like years ago, or what the class of 2014 painted on water towers across the country last spring. Pay attention, I was here. The earliest graffiti.

 

Speaking of cave art, what about the Neandertals?

So glad the Indonesian find came up this week because it gives me a chance to segue to that possible perhaps maybe Neandertal rock art in Gibraltar that surfaced last month and that I didn’t have space to write about then.

It’s not a hand stencil, let alone an animal. And it’s not painted, it’s etched into the rock with a stone. As many have noted, it calls to mind tic-tac-toe or a hashtag. (Which one springs to mind immediately may depend on how old you are.)

The Gibraltar etching. Credit: Stewart Finlayson

The Gibraltar etching. Credit: Stewart Finlayson

The abstract crosshatching was definitely deliberate, not accidental or produced by natural forces. African engravings dated at 60,000 and 77,000 years ago are abstract patterns too.

The carving was lying under a layer of Neandertal stone tools and has been dated at before 39,000 years ago. Anatomically modern humans–that’s us, the last Homo standing–had not yet come to Gibraltar by then.

Kate Wong discusses the find at Observations and provides links to other posts about Neandertal cognition. Iain Davidson offers some caveats at The Conversation.

Among them, his reservations about the dating: “[T]he radiocarbon dates obtained from the layer above the marks are rather mixed, with younger dates found below older dates, even in an area claimed to have been a hearth. This means that it would be possible to argue that the sediments were redeposited some time after the latest date (about 29,000 years ago).”

 

Are we and Neandertals the same species?

The arguments about this find are, at bottom, about Neandertal cognition. How smart were our vanished close relatives? Did they have language? Are these crosshatch incisions evidence of symbolic behavior that would make them more like us than like the cavemen of the comics?

Davidson, I sense, would like to believe this, but thinks the evidence is just not there yet. He speculates that perhaps the crosshatching could be related to the emerging ability to count.

Anthropologist Rosemary Joyce, who blogs at What Makes Us Human at Psychology Today, says the hashtags provide “a Rorschach Test for our comfort level with the complexity of our human heritage.” She thinks we may be suffering from guilt about our possible (plausible) role in why Neandertals disappeared about 40,000 years ago.

She points out that people don’t seem to be able to get the caveman prototype out of their heads. That’s probably true, but I doubt you need the formal tools of psychology to explain it. As science writers know to their despair, the fact that the caveman image lingers may have more to do with widespread ignorance of science, in this case recent scientific discoveries about Neandertals. For example, the fact that most of today’s humans are, genetically speaking, part Neandertal.

I concede that some may be horrified at the news that most of us are part Neandertal. Not to mention that some of us are also part Denisovan. I am reminded of the apocryphal 19th Century tale about Darwin’s work, which appears to have really originated with Ashley Montagu about 1940: “It is said that when the theory of evolution was first announced it was received by the wife of the Canon of Worcester Cathedral with the remark, ‘Descended from the apes! My dear, we will hope it is not true. But if it is, let us pray that it may not become generally known.’” HT to Laelaps for unearthing the Montagu quote.

Alas, despite the best efforts of some of us, the fact that we possess Neandertal and Denisovan genes has still not become generally known.

 

Language as the defining trait of our species

Joyce writes that “Spoken language and symbolic thought become the central battlefield for maintaining that we are not them.” I wouldn’t characterize it as a battlefield. Whether Neandertals could speak and think as we do seem to me perfectly legitimate questions about how similar we are.  To ask those reasonable questions is not at all the same thing as embracing the caveman caricature.

I won’t tackle “symbolic thought” here because I’m never sure what people mean when they use that term. But spoken language does mark a real dividing line. It is not too much to say that we owe our stunning success–7 billion of us and counting–to our ability to speak to others and to understand what they say to us.

The invention of writing some 5000 years ago, plus widespread literacy (and numeracy) in the last few hundred years, were essential to bringing us where we are today, of course. But they are built on our fluent speech, and on brains that handle language universally and easily almost from birth.

How long ago did spoken language originate? Long enough ago that it was present, at least in nascent form, in the ancestor of us and the Neandertals? There are opinions, but no one knows.

The genetic evidence on whether Neandertals had the capacity for speech is murky. I took up that topic in a piece I wrote a few months ago about whether we and the Neandertals are the same species. I’m happy to call many of our archaic relatives human, and I very much hope they died out of natural causes rather than us. But the ability to speak is, to my mind, the very definition of our species. If Neandertals (or any other archaic humans we interbred with) could do it, then they r us.

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Very old new species, hospice v. hospital, & once more: how many microbes in the human body?

New animal, perhaps from before the Cambrian Explosion

They look sort of like mushrooms, but they are animals. All hail discovery of not just a new species, but possibly a new phylum. Possibly even an animal remnant, thought to be extinct, from before the Cambrian Explosion that began about 542 million years ago and gave rise to most of today’s animal life.

Becky Oskin provides an intro to the PLOS One paper describing the new genus, Dendrogramma, at LiveScience. Get more detail on the circumstances of the find and where it might or might not fit on the Tree of Life from Jennifer Frazer at The Artful Amoeba.

Dendrogramma discoides (starred, at left.) The others are D. enigmatica. Credit: Just et al. 2014

Dendrogramma discoides (starred, at left.) The others are D. enigmatica. Credit: Just et al. 2014

Frazer points out that the Dendrogramma, recovered from the ocean off the coast of Southeastern Australia in 1986, were preserved in formalin and alcohol. So there’s no hope of recovering DNA that might settle the question of when and where they came from and who they’re related to. The paper classifies them as Animalia, Metazoa incertae sedis. That’s Latin for “of uncertain placement,” and according to Wikipedia, a couple dozen lifeforms are in this category.

At Why Evolution is True, Jerry Coyne explains that the question of where the major groups of multicellular animals fit in evolutionary terms is still unsettled, a further complication. He also brings us a guest post by Latha Menon, who studies pre-Cambrian life in a rich assemblage in Newfoundland. She points out something I didn’t realize, which is that none of these early lifeforms is known by its fossils. Everything scientists have learned about pre-Cambrian life comes indirectly, from impressions they left in rocks.

 

End-of-life care: Hospice or hospital?

Congress did something wildly uncharacteristic a few weeks ago: both houses passed a health care bill. The bill provided for somewhat increased oversight of hospice care. Paul Raeburn, the sole remaining Knight Science Journalism Tracker, wondered why this important legislation had been so poorly covered. “Are all the healthcare reporters covering ISIS? Or the National Football League?” he asked.

One of the concerns, Raeburn notes, is that hospices have been taken over by the for-profit health care industry. There’s a suspicion that these for-profit hospices are recruiting patients who don’t really need hospice care yet.

In a comment on Raeburn’s post, Laura Newman, who blogs at Patient POV, says the legislation doesn’t provide much to cheer about, which was perhaps why it was supported by the hospice industry.

The once-every-three-years inspection that the legislation provides (pre-scheduled, not a surprise visit) is not going to achieve much reform, she says. She also argues that long lengths of stay do not necessarily mean that the for-profit hospice industry is gaming the system. Palliative care experts are urging the dying to enroll earlier because they can’t get the kind of care they really need elsewhere.

At Covering Health, the blog of the Association of Health Care Journalists, Paul Kleyman complains that the bigger problem with end-of-life care is “the relegation of dying patients to painful and unwanted high-tech medical interventions.” He cites a significant jump in the number of U.S. patients treated by 10 or more physicians in their last six months of life.

In 2012, the median length of service in US hospices declined to 18.7 days. He agrees with Laura Newman: Rather than overusing hospice services they don’t yet need, Kleyman says, nearly 2 out of 3 hospice patients aren’t getting there soon enough. Almost one-third of Medicare’s budget is spent not on hospice care, but on in-and-out hospital stays in the last two years of life.

 

Once more, germ warfare: How many microbes in the human body?

I’ve written several times here at On Science Blogs on my favorite statistic, which is that only 1 in 10 cells in your body is you; the other 90% is microbes.

It’s just such a dazzling idea, the notion that we lumbering apes, in addition to being DNA’s way of making more DNA, are also microbes’ way of making more microbes. And it gets even more dazzling in light of the increasing evidence that our microbiomes have profound effects on our health and even our brain and behavior. That they are, in fact, essential to our lives.

microbiome

Last time, late last year, I described bioinformatician Neil Saunders’ noble attempt to trace the original source of this statistic, which even major figures in microbiology quote. In “We’re only 10% human. According to…who?”, Saunders ascribed it to an obscure scientist named T.D. Luckey, who calculated this number in a 1972 article in the American Journal of Clinical Nutrition.

Judah Rosner, who heads a lab that studies antibiotic resistance at the National Institute of Diabetes and Digestive and Kidney Diseases, was one of the commenters on the Saunders post, noting that the Luckey paper has to be a low estimate because it counted only bugs that could be grown in the lab, and now we know that many can’t be.  The number, he speculated, could be 10-fold greater.

Rosner attacked the data more systematically in a letter-to-the-editor in Microbe, a magazine from the American Society for Microbiology. He quoted a great range in  the number of human body cells from a recent estimate: as few (!) as 10.5 trillion to as many (!!) as 724 trillion. In 1999, Rosner says, the number of gut microbes was estimated at between 30 and 400 trillion. Which doesn’t count our other microbe communities, on our skin and in our noses and reproductive passages, for example.

In his letter, Rosner also pointed out that microbe numbers are likely to vary in each of us depending on many factors: diet, body size, age, ethnicity, culture, stage of life, state of health, and the environment around us. He says, “there is no a priori reason for thinking that the ratio of microbial to human cells is constant among humans or even for one individual in the course of a lifetime.”

See also the post by Meredith Knight at the Genetic Literacy Project, who called my attention to a piece by journalist by Peter Andrey Smith at the Boston Globe, writing about Rosner’s letter in Microbe. Smith managed to unearth some facts about the eccentric T.D. Luckey, who produced his immortal 1972 estimate of a 10-to-1 ratio by counting microbes in one gram of feces.

The irrepressible microbiologist Jonathan Eisen says at his Tree of Life blog that he meant to write about this specious datum in 2007 but got distracted. He confesses that he even found himself quoting it in a TED talk, although he had sworn he wouldn’t.

Here’s the upshot: Despite the fact that this zombie Microbiology Legend of 10 to 1 has even top scientists in its thrall, neither they nor we have a clue what the true ratio of microbes to human cells is.

It’s not known even how many cells we have, let alone the number of single-cell organisms we’re host to. The ten-to-one figure may be arbitrary, but not much more so than 3-to-1 or 40-to-1 or even the remote possibility that human cells outnumber microbes nearly 2-to-1.

I don’t know where that leaves science writers, but I’m hoping that last one, that we have twice as many human as microbe cells, doesn’t turn out to be true. Call me a romantic.

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Jack the Ripper, more poison at NIH, Rosetta & the comet

 

Ripped from the headlines

Scientists have greeted with hoots and catcalls the claim that Jack the Ripper, the near-mythical late-19th Century London serial killer, has been identified from DNA as an immigrant Polish baker named Aaron Kosminski.

The DNA evidence is from a bloodstained shawl that maybe perhaps belonged to one of the victims. Besides the maybe perhaps victim’s blood, the shawl is said to also bear semen stains and an epithelial cell containing mitochondrial DNA that purportedly matches the mtDNA of one of Kosminski’s relatives.

"Nemesis of Neglect": Jack the Ripper as a phantom embodiment of social neglect. Punch cartoon, 1888.

“Nemesis of Neglect”: Jack the Ripper as a phantom embodiment of social neglect. Punch cartoon, 1888.

It might be true that he did the Ripper murders. Kosminski was one of the top suspects at the time, was confined to an asylum three years after the last Ripper murder, and spent the rest of his life in assorted similar institutions. But Naming Jack the Ripper, the book recounting this hypothetical by self-described armchair detective and Ripper tour operator Russell Edwards, is not persuasive.

Any decent TV defense attorney would rip the shawl to shreds. It must  contain dozens of DNA deposits from the many people who have handled it in the past century and a quarter. Svante Pääbo, who believes that as far as DNA analysis is concerned, cleanliness is lots better than godliness, would faint dead away. At Neurologica, Steven Novello is quite dubious about the meaning of the shawl and its contents and calls for independent replication of the results.

The evidence has not been published, and certainly not peer-reviewed.  At the BioMed Central Blog, James Balm calls that omission a pretty important hurdle to ignore. The samples were not blinded. There appear to have been no controls. Etc.

In a Pacific Standard post, Ted Scheinman dryly notes that the provenance of the maybe perhaps victim’s shawl “remains semi-conjectural.” He quotes British geneticist Sir Alec Jeffreys as pointing out that “no actual evidence has yet been provided.”

Novello also notes that there will be a lot of resistance to this idea, if only because the whole reason the Jack the Ripper tale–at least five brutal murders and maybe as many as 11–is so fascinating is that it’s a mystery. If it is truly solved, and solved in such a conventional way–a series of prostitute murders committed by a misogynist madman who was eventually locked up for good, instead of (as I believe one theory holds) the syphilitic Prince of Wales who became, briefly, King of England–well, that’s no fun.

At Comment is Free, historian Julia Laite wonders why Jack in particular commands so much public attention more than a century after the grisly murders. She thinks it has to do partly with how gruesomely savage they were, with parts of sexual organs–a uterus, a vagina–cut out and carried away. Trophies?

And the victims were whores, lost women from another world. It was possible to feel fascination without feeling empathy. She tells us that at least one of them, the lady of the maybe perhaps shawl in fact, was not a sex worker, and calls for more attention to the victims, not Jack.

More toxins galore

I can’t decide whether this makes me feel better about my slapdash housekeeping or not. It’s yet another Ooops! moment for the National Institutes of Health. More bad stuff has been found hither and yon in its labs, some of it said to date back to 1914. Plague, tularemia, botulinum–that’s Botox to you–and, oh yes, the deadly poison ricin.

Castor beans, the source of ricin.  Credit:  HediBougghanmi2014

Castor beans, the source of ricin. Credit: HediBougghanmi2014

These were found in a thorough search undertaken after the various finds of toxics stored higgledy-piggledy–some in Ziploc bags–in labs at the Centers for Disease Control and Prevention and the Food and Drug Administration. I wrote about that here at On Science Blogs in July.

Jocelyn Kaiser’s account of the recent discoveries at Science Insider includes the text of a memo from NIH director Francis Collins. He conceded that the new finds highlighted the need for constant vigilance, but also said that the samples, while not stored properly, were sealed and never endangered anyone. To my mind, NIH gets at least a few points for going in for some serious housecleaning. Probably terrified of what it would find. Maybe relieved that it wasn’t as bad as feared.

At C&EN’s Safety Zone, Jyllian Kemsley predicts that more unsettling toxic finds may lie ahead. A White House memo dated August 18 recommends that government labs and nongovernment labs that get federal money do “an immediate sweep of their facilities that possess, use, or transfer human, animal, or plant infectious agent or toxin holdings to identify Biological Select Agents and Toxins (BSA) and ensure their proper registration, safe stewardship, and secure storage or disposal.”

Kemsley has a theory about how this bad stuff accumulates. “Someone left without clearing their bench or their lab. Someone else took over. Instead of cleaning out, they pushed the samples to the back of the fridge or storage area. Repeat.”

Rosetta and 67P/Churyumov-Gerasimenko

On Monday (September 15), the European Space Agency will announce  the site where the Rosetta spacecraft will land on the comet 67P/Churyumov-Gerasimenko in November.

Josh Witten at The Finch & Pea republished tweets explaining why that’s a big deal: the Rosetta team has identified four potential landing sites, but all are riskier than had been hoped. Pamela L. Gay (@starstryder) explained: Landing site needs Sun 7-8hr/day for power, but want day-night cycle, also onsite gas&dust activity, organics, & not too sloped.

Credit: ESA/Rosetta/MPS for OSIRIS Team MPS/UPD/LAM/IAA/SSO/INTA/UPM/DASP/IDA

Credit: ESA/Rosetta/MPS for OSIRIS Team MPS/UPD/LAM/IAA/SSO/INTA/UPM/DASP/IDA

The multicolor pic came from Deborah Byrd at EarthSky, who explains,
“A preliminary map of morphologically different regions on the surface of Comet 67P/Churyumov-Gerasimenko – as revealed by the Rosetta spacecraft – shows the comet to be a unique, multifaceted world. We now know that comets can have cliffs, depressions, craters, boulders or even parallel grooves.”

I just thought it was cool. Also, that’s the longest (and yet unintelligible) photo credit ever, heading for the territory occupied by authors on a physics paper or organismal genome sequence.

Hiatus, probably

I’m off to family events, including a wedding, and will be on the road until the end of this month. Meaning it’s very likely I will not be posting here at On Science Blogs again until Friday, October 3. Unless I get inspired. Or bored. At a family wedding, though, bored is not likely to happen.

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Low carb v. low fat for losing weight plus Knight Science Journalism Tracker again

 

Those dueling diets

This week we have a replay of the dueling diets thing, low carb vs. low fat. Low carb continues to appear to have a very slight edge, with many caveats.  The sane advice continues to be that the best diet for weight control is the one you’re most likely to stick to.

The paper that made the bigger splash came from the Annals of Internal Medicine (paywall) on Monday.  The splash happened partly because it appeared to be the most careful comparative study yet. And it seemed to show that low carb was better, and that’s what the media said.

That’s also what some bloggers I’d expect to be more careful with the data said. Shocking example: Incidental Economist Aaron Carroll.  His hed read: “Low carb crushes low fat. Screw you guys! I’m going home.”

Bottom line: After a year, the partly-Paleos lost 11.7 pounds on average and the low-fat folks a measly 4. Low carb was also better for cardio risk factors.

But not so fast. The study may have been the most careful yet, but that’s not much of a compliment. Obesity doc Yoni Freedhoff actually read the paper and pointed out at the blog Weighty Matters:

 

  •     Food consumption tallies were based on self-reports. i.e., not reliable.
  •     The low carb group lost 88% of their weight in the first 3 months. They were supposed to be eating no more than 40 grams of carbs/da but self-reported 80g during that time–and by the end said they were eating 112g.
  •     Their self-reported calorie intake was lowest in the first 3 months too. It increased during the year, but by the end they were still taking in 100 cal/da fewer than the low-fat folks.
  •     They did eat somewhat more protein than the low-fatties, and Freedhoff is one who thinks higher protein consumption may have more to do with low-carb diet success than reducing carbohydrates.
  •     Both groups received diet counseling and a replacement meal bar or shake every day. Freedman thinks that controlled meal may have had a significant impact on the weight loss in both groups–which was in any case pretty modest.
  •     He also concludes that the low carb diet was not truly that, nor was the low-fat diet (which specified 30% of calories from fat) truly low.

Kamal Patel makes some of these points and has some additional cautions at Examine.com.  First, and maybe most important, 90% of the subjects were women. I’m not going to complain about including women in medical research. It took too many decades to get to NIH’s current policy of insisting on a more rational sex ratio in clinical studies. But it does introduce the question of whether these results, unscintillating as they may be, apply to both sexes. There were 75 people in the low-carb group, and only 9 were men.

Patel concludes, “it would be disingenuous to state that ‘low carb is superior to low fat for long term weight loss’. . . A more accurate headline would have been: ‘If you are obese, decreasing carbs and upping protein may lead to greater weight loss, but sticking to any diet that has you eat less will lead to weight loss.’”

The meta analysis

The week’s second diet study appeared in JAMA on Wednesday behind a paywall. It was a meta analysis of several named diets, for example the canonical low-carb Atkins and the equally canonical low-fat Ornish. The results showed low carb slightly ahead at 6 months but the two approaches were pretty much a wash at 12 months. Low fat and low carb, the paper said, turn out to be equally good.

Or, actually, bad. Average weight loss on either was between about 12 and 20 pounds. After a year.

These equivocal findings could explain why the JAMA paper hasn’t yet gotten anything like the reception of the earlier study, which was interpreted as proclaiming that low carb was superior.

Doc Howard LeWine examines both studies at the Harvard Health Blog and concludes that the Mediterranean Diet combines the virtues of both approaches, although it doesn’t seem low carb to me. He’s part of the any-diet-that-you-can-stay-on-is-a-good-diet school.

It’s easy to understand the craving for a conclusive answer. This rigamarole has gone on too long. There is certainly enough information now to at least make it clear that insisting on low fat as the only way to go is just plain wrong. Not only inaccurate, but maybe verging on morally wrong too. That includes various professional associations. Also the government.

Speaking of which, the Centers for Disease Control and Prevention has seized the moment and just published its depressing 2013 map of self-reported obesity state by state.

obesity map cdc

 

Fin del Tracker?

The sole remaining Knight Science Journalism Tracker, Paul Raeburn, said goodbye to his (former) Tracker colleagues Wednesday, thanking Charlie Petit, Faye Flam, and Pere Estupinya, who finished their tours of duty last week. Raeburn traced the Tracker history briefly from its founding by Charlie Petit and Boyce Rensberger in 2006 to now, its last few months.

Or are they the last few months? I suspect we have just been given a taste of the kind of thing the new Tracker, assuming there is one, could contain.

Yesterday (Thursday) a most intriguing guest post went up on the old Tracker. It’s a fine piece by freelance science journalist Nadia Drake, a polite, almost decorous, well-researched savaging of the cover story in the September-October issue of the Columbia Journalism Review.

Columbia J Rev cover

The CJR story is a profile (apparently a fawning profile; I haven’t read it) of Elise Andrew, proprietor of the Facebook page I Fucking Love Science, which has acquired more than 18 million Likes and is turning into a mini-media empire featuring a news site, a YouTube channel, live events, and a TV show in the pipeline.

Among the problems with IFLS that the CJR profile skates over, Drake says, is a past history of copyright violations/plagiarism on images and a consistent inability to get the science right. Fucking loving science appears not to always require understanding it or being capable of explaining it.

The profile was written by Alexis Sobel Fitts, now editor of CJR’s sciency column The Observatory, formerly run by Curtis Brainard, now blog editor at SciAm. The response to the profile, Drake says, has not been friendly, partly because it “appeared in a journalistic publication, written in an unjournalistic way, about a person whose work is not journalism.” She concludes, “Having a large, loyal audience does not make you immune to the rules – if anything, it makes you even more beholden to them. And I don’t think either IFLS or CJR should get a pass on this one.”

This unusual post got into the Tracker via Deb Blum, who is not officially in charge of the Knight Science Journalism Program until next summer but who is clearly a big part of its current affairs. Blum told me in an email that Drake proposed the piece to her. “I think she did a great job of analyzing both the CJR story and about issues at IFLS and of backing up her points. I’m really glad we could host it and I hope it reminds people that we’re very open to these kind of posts at KSJ.”

If that’s not an invitation, guys, I don’t know what is.

A somewhat broader audience?

Among the dozen mostly mournful comments on the Raeburn post was one by Wade Roush, who is temporarily heading the Knight Science Journalism Program until Blum arrives. Roush said:

     I wanted to explain once again, however, that we are *not at all* discontinuing our support for the idea of publishing a regular, expertly curated collection of reviews and commentaries on science and technology reporting.
The real situation is that the Tracker is going on hiatus while we rework the concept. We have some big plans for introducing a renewed daily publishing operation that will serve a somewhat broader audience and, we hope, have an even deeper impact. For a number of practical reasons, we need to stop publishing the existing Tracker (effective January 2015) while we do that.

That’s a slight clarification of future plans that have seemed murky to many. But it’s also a bit confusing. Big plans for a daily publishing operation of reviews and commentaries on science and technology reporting sounds just the ticket. Hurray! But what is this “somewhat broader audience?”

Re: the broader audience, Deb Blum told me, “[W]e’d like to make it higher profile and draw an even larger audience. At least that’s definitely what I would like.”

In an email Roush told me they want to widen the subject matter to include technology. (Hmmm. The Knight Program is based at MIT, also the home of Technology Review.)

Also, they want to include more types of media. (Hmmm. I hope this doesn’t include the completely useless and mischief-making television news, a field HealthNewsReview’s Gary Schwitzer abandoned in despair a while back. But wouldn’t it be intriguing if they took on, say, YouTube and other video? Hands off blogs, please!)

In addition to the core science writing audience, Roush said, they plan on “serving up material that’s useful to the larger circle of people involved in engaging the public around technology and science.” (Hmmm. Policy-makers? PIOs? The producers at NOVA?)

The Tracker as practicum

The Tracker has been a valuable resource for science writers because its judgements about science journalism have set professional standards for a broad science-writing audience when nobody else was doing that. You can catch up on background about this decision to cease publication, cause of universal science writer kvetching, in my On Science Blogs post of a few weeks ago here.

Just an example of the Tracker’s practical value to science writers, something that happened to me this very week. In my column for the Genetic Literacy Project Tuesday I wrote about the two arresting studies on modification of memory published last week. Both were technically complex, the one on changing an unpleasant mouse memory to a good one in particular.

My real subject was the long-term impacts–policy, ethical, and whatnot–of being able to modify memory, not the science itself, which I didn’t have space to explain in detail. Fortunately, Faye Flam had evaluated several news stories about the mouse study. It was her final Tracker post in fact. She had found most of them lacking, but I was able to refer readers interested in technical details to her post and her recommendation, which was to Emily Underwood’s open-access piece at Science.

Charlie Petit’s last post was about the fastest-moving science story of the moment, Ebola. First, genetic sequencing of strains of the virus, replete with the throbbing detail that five of the paper’s authors had died of Ebola. Also, details on a hurried test of an experimental vaccine. Many links, which is what we’ve always gotten from Tracker posts. If you’re writing about Ebola, and who isn’t, save this URL.

Pere Estupinya, who Tracked Spanish-language media in the Spanish language, said farewell with a collection of his favorite posts–and a reminder of what a big world this is. He hopes, he said, that Tracker v.2 “considers the science, health, environment and innovation journalism published in Spanish. Latin America is a vibrant region full of challenges and opportunities for science journalism. Honestly, it really is.”

I believe him.

Pere Estupinya waves goodbye

Pere Estupinya waves goodbye

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Prostate cancer screening dispute, microbiome hype

Once more, screening for prostate cancer

It’s pretty much conventional wisdom among the experts that routine prostate cancer screening for the prostate-specific antigen can cause more harm than good. The recent results of the European study of routine PSA screening after 13 years of follow-up, which The Lancet published early this month, also viewed population PSA screening with a jaundiced eye–even though its data showed that screening reduced the death rate from prostate cancer by about 20%.

How can your average aging man cope with that kind of seeming contradiction–and from the so-called experts too? Can we blame him for taking a chance on the considerable risks of PSA screening, including unnecessary surgery, for the sake of being among those whose lives are saved? For some, even the risk of urinary tract damage and impotence could seem like a reasonable trade-off.

A man might make a different decision, though, if he was told that a 20% reduction in the death rate means that the average middle-aged man’s risk would drop from about 3% to about 2.4%, which is what Tara Parker-Pope says at Well. The absolute figure quoted in The Conversation post about the study was just one man’s life saved out of 780.

Looking closely at the European research

At her blog Patient POV, Laura Newman delves into the research presented in that paper, consults other experts, and comes to conclusions that call into question even the finding about the 20% death rate reduction.

A sectioned prostate, with cancer. Credit: Netha Hussain

A sectioned prostate, with cancer. Credit: Netha Hussain

The study covered eight countries in Europe, but screening benefits were seen in only two: Sweden and Holland–and the results in Holland were on the cusp of not being statistically significant. Newman quotes Anthony Zietman, a prominent radiation oncologist at Harvard Medical School, as saying “Explain that if you can! I know I can’t.”

Finland, which has a prostate cancer rate comparable to Sweden’s, which is as high as the rate among African-Americans, contributed the largest number of patients to the study. Still, there were no benefits to PSA screening in Finland. Peter Albertsen, surgeon at the University of Connecticut Health Center, told Newman that in the other five countries, sample sizes were too small to have sufficient statistical power.

The researchers weren’t convinced either

There were other methodological issues with the research as well. It’s easy to see why the authors of a study reporting a 20% reduction  in the death rate from prostate cancer associated with PSA screening still ended up unenthusiastic about it. Sounds as if they weren’t convinced either.

Albertsen told Newman, “So screening works for some cancers, but not for others. Now the problem is how to tell these two groups apart.” Newman concludes, “There’s plenty more that has to be done if doctors and patients are going to get on the same page.”

The Conversation post takes off from The Lancet paper but is really an explainer about PSA testing, written by Alexandra Miller and Reema Rattan. It quotes Dragan Illic, an epidemiologist at Monash University, thus: “The problem with the PSA test is that, although it’s prostate specific, it’s not prostate cancer specific.”

Geezer screening

You can almost hear Incidental Economist Aaron Carroll sigh as he writes “The overscreening never seems to end.” He’s talking about a new study from JAMA Internal Medicine showing that routine screening for assorted medical conditions persists pretty much to the end of life–far beyond the point when even a useful test, like the one for cervical cancer, can do a patient any good.

The study zeroed in on patients who were highly likely to die within 9 years and found, for instance, that 55% of the men were being screened for prostate cancer (and the rate was even quite high in the group likely to die within 5 years.) My favorite datum is the PAP smear screening rate–from 34% to 56% among women who had no uterus.

Of course, the fact that the testing does people other than the patients good–the prescribing doc, the testing labs, the test manufacturers–may not be irrelevant. But Carroll declines to engage in this sort of rough stuff. He concludes merely, “Bottom line is that we’re screening a huge number of people who are incredibly unlikely to receive a benefit. Why? It costs a ton of money, and it can lead to harm.”

Howard LeWine, writing at the Harvard Health Blog, points out that the group footing a large part of these unnecessary bills is made up of taxpayers, since the screening tests are covered by Medicare. LeWine is kind about the motives of physicians, assuming that they don’t want to be in the position of making decisions for their patients. I’m sure that’s true of many.

Barak Gaster, a doc, is also kind to his peers at the Well blog, in a post wrestling with the PSA testing dilemma. His patients often ask him what he would do. His answer strikes me as a cop-out. He says he tells patients desperate for advice that it’s an individual decision. Sure it is, but I hope he at least lays out for his patients some of the questions they have to answer for themselves. Such as, could they (and their partners) live with impotence?

The human microbiome, hyped

I am already feeling nostalgic about the blog version of the Knight Science Journalism Tracker, which I wrote about here at On Science Blogs last week because it is going out of business next week. So here’s a farewell comment on a Tracker blog post on a topic dear to my heart, the human microbiome.

The specific subject is the hype surrounding our resident microbes, which I wrote about here at On Science Blogs in May. That post described microbiologist Jonathan Eisen’s continuing campaign against overselling the microbiome.

The new Tracker post is from Paul Raeburn, and he speaks of a Nature commentary about microbiome hype. The author, William P. Hanage, argues that those interpreting research on the body’s microscopic communities, science journalists for example, should ask five questions to guard against hype.

Raeburn discusses one of Hanage’s questions, and another is one that I want to keep harping on because it’s a continuing error in reporting on science: whether a study shows that the factor under study causes a condition or only correlates with it.

Researchers in the Human Microbiome Project are sampling and analyzing genomes of microbes from five sites: nasal passages, mouth, skin, GI tract, and urogenital tract.

Researchers in the Human Microbiome Project are sampling and analyzing genomes of microbes from five sites: nasal passages, mouth, skin, GI tract, and urogenital tract.

Skeptical OB Amy Tuteur is even more emphatic in a post called “Why you shouldn’t believe anything you read about the microbiome.” That’s a high level of skepticism indeed, and I doubt even Eisen would go that far. She does, however, make an intriguing point that is not much discussed, noting that the human microbiome has its own microbiome, which she calls the virome. “[I]t is the interaction between the bacteria and the viruses that prey on them and on human beings, that determines health and disease.”

Microbes as puppet masters

Still, microbial science marches on and so does reporting on it. Not to mention speculation.

Meredith Knight, at the Genetic Literacy Project (disclosure: which I also write for), discussed the new study showing that “giving mice antibiotics early in life shifted the bacterial balance of their guts enough to make them twice as likely to have obesity as adults.” One of the potential links here is to the near-universal practice of feeding livestock antibiotics to make them grow bigger faster. Another is the possibility that normal treatment of an infection in infancy might result in a fat adult.

And then there is Carl Zimmer’s speculation about whether our microbes are manipulating our behavior to suit their own ends. Here’s his brief post on his blog The Loom, which links to his New York Times column on microbes as puppet masters. An exasperated commenter takes him to task for anthropomorphizing our microbes.

Regular Zimmer readers will recall that he also views our parasites, for example Toxoplasma gondii, as puppet masters. Here’s an intriguing question that I hope Zimmer will tackle next: are our parasites and our microbes battling it out for control of our behavior? Does that internal war dispose of our last claim to having free will?

Nevertheless I will assert what remains of my free will and take next Friday (August 29) off. It’s the beginning of Labor Day weekend, and so I shall do no labor. Back here September 5.

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UPDATED: RIP: The Knight Science Journalism Tracker & Robin Williams

 

RIP Knight Science Journalism Tracker, sort of

UPDATE: The comments are piling up on the post announcing the Tracker’s end, 42 as I write, and they are 100% horrified.  I have asked Deb Blum and Wade Roush for comment, and whether there’s any chance they will rethink the decision. Stay tuned.

UPDATE 2: Deb Blum has just emailed me that “we are continuing with the decision to put the Tracker on hold while we figure out the ways we want to improve it.”  They are not surprised at the negative response: “There are so very loyal Tracker followers and we didn’t expect them to embrace this.” She has written a new Tracker post explaining why they made the decision. Here’s the meat:

I’ve thought since that we could have done a better job of providing a sense of the complicated set of circumstances that went into the decision. My colleague, Wade Roush and I wanted to focus on all the positive reasons behind the move. But in the interests of accuracy – a Tracker standard – I’ll tell you also that there were other issues at play: some budget related (especially in the short term) and some personality related, and some purely logistical. Combined with our strong belief that we needed to move quickly on some of our plans to expand on the existing program, that led us to make the announcement now.

And the one thing I regret about the timing is that we ended up pausing the Tracker before we had the new version fully developed. It leaves us in the position of asking you to accept, on faith, that the new version will also be smart, challenging, useful, important.  And I know accepting things on faith is something that journalists don’t do easily.

 Original Post

The big news in science writing this week is that the Knight Science Journalism Tracker, the MIT-based blog that has evaluated science journalism (and not infrequently found it wanting) for >10,000 posts, is winding down.

Most of the current bloggers–Charlie Petit, Faye Flam, Pere Estupinyà–will be gone by the end of August. The Tracker will continue until the end of the year with posts by the current head tracker, Paul Raeburn. But they won’t really be blog posts any more. They’ll be journalism, because they’ll be assigned and edited.

Doing the assigning and editing will be the new regime at the Knight Science Journalism Program at MIT, home of the notable science journalism fellowship program. Director Phil Hilts retired earlier this year, and the new director is quite a catch for MIT and Knight: Pulitzer-prizewinner Deborah Blum, author of (among other books) The Poisoner’s Handbook, who also writes Poison Pen, part of the Well aggregation of columns at the New York Times. She wrote the Elements blog at Wired, too, until taking a book leave in May.

Deb Blum is also, I am delighted to point out, the first woman to head the Knight program. Hurray! About time, and her accomplishments make her a very smart choice indeed.

deborah blum

“What we’re hoping for is more depth analysis, some deeper tracking of trends,” she told me in an email describing plans for the last quarter of the year at the Tracker. There are “a lot of important issues in science journalism that we’d like to see explored here, for instance, the use of crowdsource funding at places like Beacon. Does it work and what does it portend. That’s just an example off the top of my head but I think there are some very interesting stories to be told.”

She will not be formally leaving her teaching job as the Helen Firstbrook Franklin Professor of Journalism at the University of Wisconsin’s School of Journalism and Mass Communication until mid-2015. So Wade Roush is Acting Director of the Knight program in the interim. Roush spent 7 years as an editor at Xconomy, which specializes in news about high-tech entrepreneurship and innovation, and before that was an editor at Technology Review, also based at MIT.

We are told that the Tracker might be resurrected in some form once plans for new ventures at the Knight program get invented. The Fellowship program will continue, but augmented by planning for “a new MIT initiative designed to boost public engagement in technology and science through new forms of storytelling,” according to the Tracker post announcing the changes. Details TBA.

Farewells from Trackers

Current Trackers wrote valedictory posts and received commiserative comments. Charlie Petit, in a post that is also a candid window into the uneasy life of a freelance writer, described how Boyce Rensberger, then directing the Knight program, came up with the idea of the Tracker blog about science journalism and invited Charlie to write it. That’s what he’s been doing since April 2006; 7815 of those 10,000 posts are his, and he promises more before month’s end.

Faye Flam’s farewell was about how being a Tracker gave her a direct connection with readers. I’ve admired Flam’s writing for number of years, particularly impressed with her blog Planet of the Apes for the Philadelphia Inquirer, where she was a reporter for several years. Planet of the Apes was about evolution, and I can’t even imagine her mail and phone calls. Brave, very brave.

Flam spoke “of writing directly for readers rather than writing to please an editor.” For me, that’s the very definition of blogging. It illustrates the difference between the Tracker today and plans for the Tracker in the last three months of this year (and possibly its future revival?)

What is blogging?

I haven’t thought much about the difference between blogging and journalism since I began this blog in 2009. And for my purposes here at On Science Blogs, I’m not rigorous about about the definition. Thomas Insel’s blog, for instance, which I discuss below re: Robin Williams, is almost certainly written by someone else and vetted before posting. That would make it not truly a blog.

I have done journalism and I have done blogging, both for many years, and the differences between them are huge. With blogging, there’s nobody backstopping you, nobody catching your errors, nobody urging caution and double-checking–but also nobody wrecking your carefully wrought structure and POV and beautifully honed phraseology. It can be a form of high-wire work without a net. Exhilarating but also risky.

That is not to say that very fine science writing can’t be done on blogs; it is, every day. But the absence of infrastructure and oversight makes blogging very different from journalism. Here at On Science Blogs I write about what I feel like writing about. It’s the complete freedom that’s different (and delightful) about blogging–even though it means that sometimes I fall off a cliff.

Wade Roush told me in an email he thinks the difference between blogging and journalism is a semantic one. I strongly disagree.  Deb Blum emailed me: “I think part of the issue is the evolving nature of blogs. The NYT calls my Poison Pen a blog and it’s both assigned and edited. [The situation was d]ifferent at Wired but I don’t think it’s one size fits all.”

Nope. Blogs aren’t evolving. Marketing departments have seized on the term, I guess because they believe the label can make a piece seem fresh and plugged in. A publication can call its content anything it wants, of course. But Poison Pen is what we formerly called a column. Calling it a blog doesn’t make it so. If it’s edited by somebody else, it’s not a blog. If the writer has to confer with an editor on the subject of a piece, it’s not a blog.

Paul Raeburn is a talented journalist, and his editors will be pros. I’m looking forward to his posts post-August and expect to learn from them. I may even quote the pieces, as I have in the past. But come September, what we will be seeing at the Tracker will no longer be blogging. It will be journalism.

This is not a complaint, by the way. Editors have saved my bacon more than once. But journalism is a collaborative product. A blog is naked writer, going it alone, gulp. That’s the whole point.

RIP Robin Williams: Depression, bipolar disorder, and creativity

Nassir Ghaemi, a doc and blogger at Mood Swings, one of the many Psychology Today blogs, complains that much of the writing about Robin Williams’s suicide attributed it to depression. Williams, he says, actually suffered from bipolar disorder, a different disease.

To say “suffered from,” is true enough, but bipolar disorder was also at the heart of–was perhaps even responsible for?–Williams’s  comic genius. Depression is hideous, soul-wrecking, nothing remotely redeeming about it. But bipolar disorder, formerly called manic-depression, is uniquely fascinating because it seems to have an upside–an upside that can be very up indeed. Ghaemi says “‘Depression’” is somewhat acceptable; manic-depression is still mostly taboo. Even mental health clinicians, including many on the PT [Psychology Today] site, downplay or denigrate it. But it exists; it provides great gifts; and it kills.”

Robin-Williams

At Beautiful Minds, Scott Barry Kaufman denies that Williams’s mental affliction had anything to do with his unique talents, although it was responsible for his suicide. “This romanticism of mental illness needs to stop,” he says, denying that there’s any support in the medical literature for “cutesy connections to genius.”

About that, it appears he’s wrong, or at least wrong about no connection between bipolar disorder and creativity. The most recent review, an open-access paper from 2012, concludes that research “provides strong support for links of bipolar disorder of varying levels of expression with lifetime creative accomplishments and creative pursuits.” Needless to say, this being human biology, it’s not a simple one-to-one relationship. The review suggests a number of avenues for clarifying research.

See also reviews by two major figures in the field, Nancy Andreasen from 2008 (open-access), and a 1995 SciAm review by Kay Redfield Jamison, who practically invented the contemporary study of bipolar disorder and creativity. Not open-access, alas.

Naysayer Kaufman wants more funding for mental health, and no wonder. The bioblurb says he is “Scientific Director of The Imagination Institute and a researcher in the Positive Psychology Center at the University of Pennsylvania, where he investigates the measurement and development of imagination.” This is a SciAm blog.

Vaughn Bell, at Mind Hacks, is dismayed by press treatment of Williams’s suicide because it is now an established fact that well-publicized suicides drive up the suicide rate among the vulnerable. Bell says, “sensationalist and simplistic coverage of suicides, particularly celebrity suicides, regularly leads to more deaths.” At The Conversation, Mike Jempson is upset about the reporting too, and so is suicide researcher Sharon Mallon.

Thomas Insel, who directs the National Institute of Mental Health, doesn’t mention bipolar disorder in his blog post about Williams. Insel’s is one of the better blogs from public officials, which I always assume are written by minions. But this post was limp, simply using Williams’s suicide as an opportunity to urge greater attention to mental health issues.

That’s Insel’s job, so I suppose I should cut him some slack. But the post could have said something illuminating about the relationship, or not, of mental afflictions to addiction and creativity. A missed opportunity.

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H. floresiensis or H. sapiens with Down syndrome? Plus landing on a comet

Lords of the zings

I don’t know why the new papers about the “hobbit,” the 2003 find of tiny ancient bones from the Indonesian island of Flores, have made such a splash. No, I take that back. I do know. But it’s still depressing.

The researchers posit that the tiny hominin, designated LB1, suffered from developmental abnormalities, probably Down syndrome specifically. But from almost the first moment of the fossil’s discovery, a vocal contingent of paleoanthropologists, more than a few and not fringe scientists, declared that the hobbit was probably not the new human species its discoverers claimed, Homo floresiensis. Instead, they argued, LB1  was H. sapiens with some kind of developmental disorder.

LB1 in three different views to illustrate facial asymmetry. A is the actual specimen, B is the right side doubled at the midline and mirrored, and C is the left side doubled and mirrored. Differences in left and right facial architectures are apparent, and are meant to illustrate growth abnormalities of LB1. Credit: A, E. Indriati; B & C, D.W. Frayer. Those who argue that the find is a new human species say the deformities result from deep burial for thousands of years.

LB1 in three different views to illustrate facial asymmetry. A is the actual specimen, B is the right side doubled at the midline and mirrored, and C is the left side doubled and mirrored. Differences in left and right facial architectures are apparent, and are meant to illustrate growth abnormalities of LB1. Credit: A, E. Indriati; B & C, D.W. Frayer. Those who argue that the find is a new human species say the deformities result from deep burial for thousands of years.

By and large, the journalism I’ve read about the new papers, which appeared in the Proceedings of the National Academy of Sciences August 4, includes none of that background. One exception is the piece by John Noble Wilford, at the New York Times, who has covered this story from the outset. Another is by Bianca Nogrady, writing at ABC Science. (This is the Australian ABC; see below for why Australia has a special interest in this story.)

Most news stories treated the new studies as an entirely novel and startling bolt from the blue. I know I should probably cut today’s journalists a bit of slack because they are operating under frantic constraints of time and space. But it’s distressing that hardly any bothered with the dead-simple step of googling LB1′s history. Or even Wikipedia. The Wikipedia entry seems to have been written by partisans of the new species hypothesis who are declaring the question settled, which it isn’t. But at least the entry describes the dispute.

Blogging, con and pro

Not a lot of blogging yet, but I guess it’s early days. Two of the researchers, Maciej Henneberg and Robert B. Eckhardt, crowed about their new PNAS papers at The Conversation. They do acknowledge that there were doubters from the beginning, but their chief purpose is to taunt the opposition. Example: “Analogies with characters in works of literary fiction are marketing devices.”

Chris Stringer, star paleoanthropologist at the Natural History Museum, London, rose to the defense of H. floresiensis at the Museum’s blog, NaturePlus. “In my view this paper does not provide a sound basis to challenge the basic conclusion that a primitive human-like species persisted on the island of Flores within the last 100,000 years.”

Paleoanthropologist Alphacaeli posted a brief riposte at The Memory Palace, arguing that LB1 couldn’t have had Down syndrome because “it’s phenomenally improbable that it would have lived to adulthood.” (From tooth wear, LB1 is believed to have been about 30.) I agree that it would be unusual, but by no means impossible. Like most disabilities, Down syndrome is quite variable. Many people with Down syndrome hold simple jobs, live fairly long lives, and fit into their communities just fine.

Alphacaeli also says, “Don’t even get me started on the discussion of humeral morphology. . .” I very much wish she had gotten started. She specializes in shoulder biomechanics, and could presumably provide expert commentary on the paper’s analysis of LB1′s arm bone.

I should add a geographical footnote here. Alphacaeli is Australian, as is Henneberg. LB1 was discovered in an expedition led by other Australians. Some of what we’re seeing here is an internecine feud among Australian paleoanthropologists.

I am privy to no details, but as you may know, there’s no more combative scientific discipline than paleoanthropology. The rest of us can only look on in awe and delight. I am myself most grateful for the controversy because it has contributed several deposits to my checking account over the years. Here’s one of my pieces, a 2006 feature from open-access PLOS Biology. It’s a roundup of the many theories about LB1. As you will see, the dispute has not advanced a whole lot in the last 8 years.

Are we there yet?

Yes, we’re there. Well, nearly. After a 10-year 4 billion-mile journey, the European Space Agency’s Rosetta probe got near enough to comet 67P/Churyumov-Gerasimenko early this year to wake up and start shooting pics. Rosetta is now about 100 km from its target and will send a lander to the comet’s surface in November.

The lander, called Philae, is supposed to tether itself to 67P/Churyumov-Gerasimenko in order to keep from flying back into space due to the comet’s low gravity. Philae is scheduled to examine the comet’s surface composition and structure, and even take samples to study up close.

Meanwhile, in other comet news, NASA has decided that its Mars orbiters are probably not in danger from comet Siding Spring after all. That comet is due to fly near Mars in October. Karl Battams explains at a Planetary Society Guest Blog. There’s said to have been some worry about a close call. But given its recent public relations history–remember the arsenic bug?–I can’t help wondering if NASA is engaging in headline-concocting to compete with the ESA plan to actually land on a comet.

The most crazy bonkers comet in the solar system

Rosetta is in orbit around the comet, although it’s not really an orbit, Phil Plait tells us at Bad Astronomy. At present the two are somewhere between Jupiter and Mars. It’s been a roundabout journey for Rosetta, taking so long because it involved slingshot maneuvers around the Earth and Mars to save fuel, John Timmer explains at Ars Technica.

Knight Science Journalism Tracker Charlie Petit says, “The mission is clever, difficult, complex, and inherently appealing.” Yup. He’s got links to several stories and other resources. The photos taken a few days ago are spectacularly sharp, and we are told they will be even higher-res soon. Marc Boucher has posted several at On Orbit.

Image of the Comet 67P/Churyumov-Gerasimenko taken by the Rosetta probe on August 4, 2014. Credit: ESA/Rosetta/MPS for OSIRIS Team

Image of the Comet 67P/Churyumov-Gerasimenko taken by the Rosetta probe on August 4, 2014. Credit: ESA/Rosetta/MPS for OSIRIS Team

Photos also, plus a video, at io9. Observers keep likening 67P/Churyumov-Gerasimenko’s shape to a rubber ducky. I don’t see it myself, but the shape is certainly odd. Robbie Gonzalez quotes ESA senior scientist Mark McCaughrean as calling it “the most crazy bonkers comet in the solar system.”

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Legal marijuana and cannabis research, Google X health project, Retraction Watch, regulating genetic research

Legalizing cannabis in order to legalize cannabis research?

The New York Times has been running a series of editorials and commentaries and blog posts backing legal marijuana.  Even although it’s been clear for some time that’s where we’re headed, the Times‘s endorsement is a landmark event, especially viewed in conjunction with the New England Journal of Medicine review of cannabis’s effects that I wrote about here a couple weeks ago.

Congress will of course be slow to change the anti-pot federal laws, but legalization activity in the states has been so rapid and dramatic that federal laws are fading into irrelevance, at least with respect to penalizing users–especially since the Justice Department has foresworn enforcement. Nearly half the states have made medical marijuana legal, and New York has just joined that bunch. And Colorado and Washington are now wrestling with the introduction of legal recreational pot

This is good news for a number of reasons, especially criminal justice, but as I have observed here before, the US is now launched remarkably casually on a vast experiment with several scary scientific unknowns. We are likely to learn a lot about cannabis in the next several years, much of it the hard way through unpleasant experience.

That’s because there are severe constraints on serious cannabis research, in particular research into its medical applications. Vikas Bajaj described the many barriers the government puts in the way of marijuana research at the Times‘s Taking Note blog. There’s no reason to think that those roadblocks will be removed any time soon. Will a substantial increase in research have to wait on federal legalization or even after? Yikes. That is likely to be several years at least.

One of the best posts I’ve seen on medical marijuana is a roundup by David Gorski at Science-Based Medicine. (Gorski also blogs as Orac at Respectful Insolence, and sometimes crossposts there.) The Science-Based Medicine post calls medical marijuana the new herbalism, with many of the same failings as other herbal medicine. The post has drawn well over 200 comments so far. It is Part 1 of a promised 3; he plans additional posts on marijuana therapy for autism and cancer.

In Part 1 he examines the evidence for efficacy against chronic pain, appetite and nausea, and IBD, plus–as is the case with other herbal meds–the difficulty of getting standardized doses or even being sure that the pot being sold as a particular strain really is.  Gorski also notes that the small amount of medical research on pot has not used the delivery system employed by most users: smoking. “If one were to come up with a delivery method for an effective herb, one would be hard pressed to come up with a worse method than burning it and inhaling it.”

In its current state, he argues, medical marijuana is just another form of herbal medicine. “I believe that marijuana should be legalized, regulated, and taxed, just like alcohol and tobacco. If marijuana is going to be approved for use as medicine rather than for recreational use, however, the standards of evidence it must meet should be no different than any other drug, and for the vast majority of indications for which it’s touted medical cannabis doesn’t even come close to meeting that standard.”

Amen to that. But getting to acceptable standards of evidence on cannabis effects, medical and otherwise, is going to be a long, hard slog. Especially if the work must wait upon federal legislation.

Credit: NMA.tv via Mashable

Credit: NMA.tv via Mashable

Google X’s new Baseline Study on health

Google X, often said to be Google’s top secret innovation lab, announced its big new longitudinal health study exclusively in an open-access piece in the Wall Street Journal. The WSJ trumpeted the Baseline Study as a “moonshot”, a term often applied to other Google X projects too, and called it the “most ambitious and difficult science project ever.”

It appears that’s hyperbole at best. Baseline has left a lot of technology commentators underwhelmed.

The Baseline Study plans to follow thousands of people, investigating their genomes, their body chemistry, and miscellaneous other measurements. The aim is to try to define good health, according to Jocelyn Kaiser at Science Insider. She also notes, though, that the project is not really so radical. “Many groups are amassing DNA and biological samples from large groups of people, both healthy and diseased, and tracking their outcomes. It is also routine in such longitudinal health studies to gather detailed medical data from volunteers and keep their information anonymous, as Google X says it will do.”

Genomic entrepreneur Craig Venter sniffed that Baseline was “a baby step, a much smaller version of what we are doing.” By “we” he means the new company he announced last year, Human Longevity, which plans to sequence a million genomes by 2020 while also collecting “just about everything that can be measured about a person, without cutting them open,” he told Antonio Regalado at TechReview.

Regalado was also dismissive in a separate piece, quoting derogatory tweets and pointing out that the résumé of the guy hired to run Baseline includes a role as co-founder of an expensive health spa near Malibu. (He also served as chief scientific officer at a giant clinical testing lab, which Regalado does not point out.) Regalado regards Google X and its various recently announced glam projects as chiefly a Google publicity tool.

If so, a successful one, even if you only count the WSJ’s glowing review. At Ars Technica, Ron Amadeo described the WSJ piece and offered speculations on the other Google X projects (which include, for example, Google Glass and self-driving cars.) The Google X brand stirs in nerd journos a powerful Need to Know.

Not on the Google X project list is Calico, to be devoted to studying aging and related diseases, which Google formed last year as a separate company. Amadeo’s conclusion about Calico: “Google basically wants to stop you from dying.”

Blaine Price, who studies the relation between mobile tracking apps and privacy, says at the Conversation that the Baseline plan to track healthy people could be medically valuable. But he is concerned about privacy and warns against “data-collection-creep.”

At Re/code, staffer James Temple declares that he’d be happy to volunteer for Baseline. But in what I guess you could call a Re/tort, Dan Munro says, among other objections, that he doesn’t trust Google with his data.

All hail Retraction Watch

There are lots of good science blogs, but I wonder how many of them make a difference. One that unquestionably does is Retraction Watch, run by Adam Marcus and Ivan Oransky, which daily brings us astonishing (and depressing) news, to be found nowhere else, of malfeasance in science.

This week Knight Science Journalism Tracker Paul Raeburn spotted a piece in the Washington Post‘s Morning Mix; here’s the link, but I’m not sure this post is open-access. It recounts the duo’s adventures with disclosing scientific bad behavior. Raeburn points out that there’s plenty of material there for follow-up by other science journalists.

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Let’s regulate gene editing and gene drives!

Last week I wrote here about the likely prodigious impact that the new gene-editing techniques, notably the one called CRISPR, are likely to have on how scientists will be able to revise and remodel any old genome more easily and cheaply than ever before. Not to mention entire species and ecosystems, using procedures known as gene drives.

In my Tuesday column for the Genetic Literacy Project, I expanded on those possibilities and gave myself the great pleasure of calling for regulation of gene editing and gene drive applications. I’d like to pretend that was brave of me, espousing increased regulation of science. But the truth is that oversight of what they’re up to was first proposed by the scientists doing the work, in an open-access paper in Science.

My take is that if the people closest to this research announce in a major journal that they think it needs supervision, the rest of us ought to pay attention and make that happen. ASAP.

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