A fix for GMO battles? Plus sexual harassment during field research


Give us this day a fix for the GMO battles?

Two papers published in the last week were signal events for agricultural genomics. First was the draft of the huge, and hugely complex, genome of bread wheat, the staff of life for 30 percent of humanity. The other, from Chinese scientists reporting advanced gene editing of bread wheat to make it resist the fungal pathogen powdery mildew, claims to have brought us a technical method for reducing the political battles over GMOs–genetically modified organisms.

I’m doubtful, but let’s see.

I wrote about the bread wheat papers in my Tuesday column for the Genetic Literacy Project. I won’t recap much here, except to note that wheat’s promiscuity over the past several hundred thousand years is unusually wanton even in the permissive plant Kingdom. The more-than-usually incestuous result has been bread that tastes heavenly but has made the work lives of genome sequencers hellish.

Unlike corn crops, where it’s nearly impossible to find examples that are not GMOs, almost no wheat is genetically engineered. Agricultural researchers are excited about the wheat genome project because having even a draft version will be a big help to conventional breeding.

There are good reasons to bestow new traits on wheat. Not just disease resistance, as in the Chinese example, but especially resistance to drought. Wheat needs to be better equipped for the hotter, drier planet our descendants will have to live with.

Comment on the powdery mildew paper has centered on the its methodology: CRISPR (clustered regularly interspersed short palindromic repeats), which can be viewed, the commentators say, as a natural process. A sort of mutation. CRISPR, one of Science‘s “Breakthroughs of the Year” in 2013, is a trendy darling just now. At Gene Expression, Razib Khan wrote in March, “This may indeed be a world-turned-upside-down moment, and CRISPR may finally cash out the promise that biological science is going to result in a flowering of engineering analogous to what occurred during physics’ ‘atomic age.’”


And what is CRISPR?

CRISPR is a new genetic engineering method, one of a group often called advanced gene editing. It is based on a kind of adaptive immune system that bacteria invented three billion years ago. Bacteria remember the viruses that have infected them and put together a targeted molecular defense so that the next time the same virus comes around, it is cut up and killed.

The CRISPR enzyme (green and red) binds to a stretch of double-stranded DNA (purple and red), preparing to snip out the faulty part. Credit: Jennifer Doudna/UC Berkeley

The CRISPR enzyme (green and red) binds to a stretch of double-stranded DNA (purple and red), preparing to snip out the faulty part.
Credit: Jennifer Doudna/UC Berkeley

CRISPR makes possible targeted modifications of almost any gene. Specific genes can be turned off, turned on, and/or edited. The potential applications of  the CRISPR system can hardly be overstated. And it is simpler and cheaper than any other current approach to genome modification.

Irresistible. I described what CRISPR is and how it works and what its future holds–a lot of intriguing and possibly scary stuff, including genetic modifications of Homo sap–in a column I wrote for GLP in February. That piece was triggered by a paper reporting on using CRISPR to create monkey infants with genetic changes.

The Chinese work on powdery mildew in wheat was a (relatively) simple use of CRISPR. The researchers used it to disable three wheat genes that make wheat more vulnerable to the fungus. They inserted no foreign genes.

In a Technology Review post about the research, David Talbot quoted Xing-Wang Deng, who heads a joint research center for plant molecular genetics and agricultural biotech at Peking University and Yale. “And this could be considered as a nontransgenic technology, so that can be very significant. I hope the government would not consider this transgenic, because the end result is no different than a natural mutation.”


CRISPR for genetic modification of wild populations and whole ecosystems?

But other potential uses of gene editing go way beyond natural mutation. At a SciAm Guest Blog last week, Kevin Esvelt, George Church and Jeantine Lunshof urged the use of gene editing “to alter not just domesticated species, but entire wild populations and ecosystems.” They want to edit mosquito DNA to make the insects more resistant to infection by malaria parasites–and thus unable to transmit malaria to people. Another proposal is to return herbicide-resistant weeds to their natural vulnerable state.

Carl Zimmer explained and explored this proposal for mosquito modification in his New York Times column, quoting other scientists who worry that the plan is risky. Church and colleagues say that devising regulations before such a project is launched would reduce the risks, and so would coming up with a Plan B for what to do in case something goes wrong.

In my February column about CRISPR, I described its potential applications for gene therapy, for the study of gene functions, for making epigenetic modifications that can turn genes off and on in precise ways, for “smart bombs” that can target disease-causing bacteria without harming benign bugs, and for making genetically modified animals. That includes attempts at improving humans.

Gene editing may not use traditional biotechnology tools for genetic modification, but it could speed up the process of rewriting genomes–our own included. Do these seem to you like projects that GMO opponents will not oppose because the methodology is novel? They strike me as examples of what my former philosopher colleagues would have called a distinction without a difference.

My guess is that anti-GMO activists are likely to see in these techniques the same potential outcomes that have always driven them nuts, outcomes like control of must-have crop varieties by agribusiness conglomerates and unpredictable disastrous ecological consequences. It’s hard to imagine they will be converted to the cause of genetic modification because the methodology is based loosely on a technique bacteria evolved billions of years ago.


Sexual harassment in the field

Biological anthropologist Kate Clancy has been publishing accounts of sexual harassment in science on her SciAm blog Context and Variation since early in 2012. Now she and three of her anthropology colleagues –Robin G. Nelson, Julienne N. Rutherford, and Katie Hinde–have released  their survey accounts of sexual harassment during anthropology and archaeology field work. The paper appeared in PLOS One on July 16, and they blogged about their study at HuffPo.

Knight Science Journalism Tracker Faye Flam has thorough coverage of how the mainstream media handled the news (and how some of them bungled the data.) Her pick for the best story is the one from ClimateWire’s Henry Gass, who related this survey to sexual misbehavior in another discipline with intensive field work, climate science. Is there something about being in the field that encourages gamy conduct?

sexual harassment

The survey covered self-reports from 142 men and 516 women across scientific disciplines. The chief findings: 64% of the respondents said they had experienced sexual harassment–defined as inappropriate sexual remarks, comments about physical beauty, or jokes about cognitive sex differences–in the field. Five of these reports came from high school students. Sexual assault (which included unwanted touching as well as outright rape) was reported by 22% of the sample, 26% of the women respondents and 6% of the men.

Men were hit on mostly by their peers. Most of the victims were women students and postdocs and most of the perpetrators were their superiors, principal investigators and site supervisors. Which suggests that this sort of molestation has a lot to do not just with sex but with power relationships.

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Lab safety, smallpox and more virulent flu, marijuana benefits, plus headless, heedless, and clueless at Science

Lab safety is even worse than you thought

The best single blog source for keeping up with the current smallpox-anthrax-flu-lab safety fiasco is Maryn McKenna’s Superbug, one of the Wired blogs.  Some recent posts:

About the cache of old vials apparently containing infectious agents and found in an FDA lab at the National Institutes of Health: In addition to the ones disclosed last week (the six vials labeled “variola,” which is the virus that causes smallpox, and ten other samples with unclear labeling), there were actually a total of 327 vials. The labels indicated that, besides smallpox, they contained dengue, influenza, Q fever, and rickettsia. Some of these, McKenna says, are “‘select agents,’ infectious pathogens considered serious enough — for the illness they create, or the lack of a vaccine to prevent or drugs to treat them — to be considered potential bioterror agents.”

A vial of smallpox found earlier this month at NIH. Credit: CDC

A vial of smallpox found earlier this month at NIH. Credit: CDC

The Energy and Commerce Committee of the House of Representatives held a hearing Wednesday (July 16, 2014) on the two other of this month’s revelations about infectious-organism mishandling, these in the CDC’s anthrax and influenza labs. The Congresspersons grilled CDC Director Thomas Frieden, staff from the Government Accountability Office and the Animal and Plant Health Inspection Services of USDA, and assorted others, including academics. McKenna posted a video of the entire session, 2 hrs 40+ min, at the bottom of this page.  She described pre-hearing statements from the actors in a different post here.

For another journalist’s account of the hearing, see Jocelyn Kaiser’s post at ScienceInsider. She says Frieden vowed to do better, but outside investigators have seen far-flung scary conditions at the CDC. A new report on CDC from USDA’s Animal and Plant Health Inspection Service (APHIS) describes “expired disinfectant, anthrax stored in unsecure freezers and labs, samples stored in Ziploc bags.”

Lab safety protocols: the Ziploc method

Ziploc bags, huh? Essential equipment for 21st century life to be sure, but how many times have you opened your refrigerator to find leaks from a not-quite-ziplocked bag congealed on shelves or dribbled into your veg bin? Chez Powledge, I can report such an incident, involving syrupy leftover baked beans, just this week. We should probably put the syrupy stuff in bowls, but at least it was a recent-enough leftover so that it was not a deadly pathogen. Yet.

At Life as an Extreme Sport, Kelly Hills also shares thoughts about the Ziploc School of Biohazard Lab Safety. But her post is mostly about the National Science Advisory Board for Biosecurity and why it hasn’t met since 2012 even though its charter specifies that it is supposed to oversee dual-use research. (Simply put, dual-use research is an obfuscatory term for research with applications to both war and peace. Like microbes that could be turned into weapons. Smallpox. Anthrax. Etc. The ones involved in the recent incidents we’re talking about here.)

Something very odd seems to be going on at the NSABB. Half of its 23 members were fired with no warning last Sunday (July 13), McKenna says “mysteriously.” Several of the dispatched have been publicly critical of what they are calling the creation of potential pandemic pathogens (often referred to as “gain-of-function” experiments.) McKenna has details here. Jon Cohen has an account of the firings and interviews with some of the principals at ScienceInsider.

Let us hope that journalists will soon reveal what this particular disconcerting event in the general biosafety hullabaloo is all about.  And the prospect that this semi-defunct watchdog agency will develop some teeth.

Let’s destroy smallpox and not create more virulent flu

In a Monday post, McKenna interviewed D.A. Henderson, the doc who headed the triumphant international campaign to wipe out smallpox–the last case seen was in 1978–and who today co-edits the journal Biosecurity and Bioterrorism. He advocates destroying the remaining known stocks of the smallpox virus, and the interview makes a persuasive case that he’s right.

A number of cogent others agree that variola should begone. Not everybody, though. Epidemiologist-in-training Tania Browne, writing at the Guardian’s Notes&Theories blog, thinks the recent accidents are exactly the reason for keeping smallpox around. To her, the fact that accidents will happen means that we might in future need it to deal with them–although McKenna’s Henderson interview deals explicitly with that point.

smallpox poster rsch

And then there’s flu, the subject of the gain-of-function experiments, which were attempts to increase the infectious talents of flu viruses. At microBEnet, microbiologist Jonathan Eisen praises an OpEd by his colleague Marc Lipsitch. It argued that there are several safe strategies for investigating pandemic flu; no need to create one that could kill millions if it escaped.

At his Virology Blog, Vincent Racaniello disputes Lipsitch, saying that the flu experiments were aimed at explaining aerosol transmission of viruses. “In my opinion aerosol transmission experiments on avian influenza viruses are well worth the risk. We know nothing about what controls aerosol transmission of viruses. The way to obtain this information is to take a virus that does not transmit by aerosol, derive a transmissible version, and determine why the virus has this new property.”

High time for research on marijuana’s benefits

Last Tuesday (July 15) I wrote about the new Cannabis Genome Project and the leisurely pace of research on medical applications of marijuana; the piece ran at the Genetic Literacy Project.

On Wednesday, ScienceInsider ran an interview with Ian Mitchell, a Canadian doc who blogs at Clinical Cannabis in Context. The interview was with Lizzie Wade, and they talked about the political forces arrayed against research on medical marijuana and in favor of looking only at abuse and ill effects.

Despite that, Mitchell says, research on pot is “flowering.” He points to Colorado, where pot is newly legal, and part of the state’s revenue will be going to research on its benefits. Colorado is also the base for the Cannabis Genome Project.

I don’t know how much a single state can accomplish, but I hope he’s right and I wish them well. I drew a crumb of optimism from the the review on marijuana’s dangers that the New England Journal of Medicine ran last month. The first author was Nora Volkow, who heads the National Institute on Drug Abuse. NIDA’s mission is to fund research on the evils of drugs.

Despite that, Volkow and her colleagues devoted the last part of the review to a rundown of what is known (or, mostly, suspected, since little is actually known) about pot’s medical benefits. Given the authors and the venue, both quintessentially a part of the research Establishment, the review seems like a significant step toward official acknowledgement that cannabis is not all bad–and possibly even an oblique endorsement of the need for research on its medical applications.

The research sluggishness is especially alarming now that medical pot is legal in nearly half the states and being actively lobbied in others. This is a vast experiment many thousands of people are conducting on themselves. But I fear that medical marijuana investigations will continue to move slowly. Researchers are up against nearly a century’s worth of anti-pot propaganda–and the very real risks to a small proportion of users, especially young ones.

Off with their heads

Evolutionary biologist Prosanta Chakrabarty tweeted, “When we said we wanted more women in Science this is not what we meant.”

science-transgend cover

Whatever the editors at Science meant to achieve by last week’s cover photo of headless transgender sex workers in Jakarta, they didn’t. In her brief not-quite-apology, Editor-in-Chief Marcia McNutt says the cover selection was made “after much discussion by a large group.” Soon to be enshrined in psychology and econ textbooks as one of those really bad group decisions, I imagine. No wisdom of the crowd on display here.

When it arrived in the mail chez Powledge my first thought was, Oh, dear. Science trying to seem trendy and daring and just not getting it at all. Editors who know better keeping their mouths shut because they didn’t want to seem to be bigots or sexists or homophobes or, worst of all, narrow-minded.

That was bad enough, but Science Careers Editor Jim Austin made it worse with his supercilious responses to Chakrabarty and the other women who tweeted complaints. Concluding with this jarring non sequitur: “Am I the only one who finds moral indignation really boring?”

Read the whole sorry tale in Zoë Schlanger’s Newsweek piece. Here’s Science‘s caption for the cover.  And selected blogging:

It did occur to me that the heedless headlessness may have been a bungled attempt at protecting the subjects from retaliation by Jakarta authorities. In other parts of the world, however, the decision revealed that some science media folk–even powerful ones, or maybe particularly powerful ones–remain inexplicably clueless about science’s much-talked about gender problems.

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Birth control, Hobby Lobby, and the war against women

Anything left to be said about the US Supreme Court’s latest decisions about women?

The US Supreme Court finished out its term with decisions that were terrible for women. This piece concentrates on only one of them, Burwell v. Hobby Lobby, because that case is largely about topics covered here at On Science Blogs. The case was decided nearly two weeks ago, but there’s still a lot to be said about it.

So what is left to be said? Well, we could wring our hands over the court’s declaration that science is irrelevant to legal decisions involving religious beliefs. That it sided 5-4 with Hobby Lobby’s insistence that it shouldn’t have to comply with one provision of the Affordable Care Act (ACA, aka Obamacare) by providing its employees with free access to four specific methods of birth control.

birth control VictorianPostcard

These were two brands of emergency contraception (i.e., “morning after” pills) and two models of intrauterine devices.  The company says it believes all four cause abortions by preventing implantation of a fertilized egg in the uterus. This despite what is widely said to be a scientific consensus that the four do not prevent implantation, although that seems a bit iffy. The scientific consensus is also, mostly, that nothing happening before implantation can be considered abortion because there is no pregnancy until after implantation.

Unfortunately, that declared scientific consensus is seriously undermined by the fact that the FDA-required labels on these birth control methods warn that they may prevent implantation. Ooops. In a post at The Daily Beast, Tiffany Stanley explains why the labels haven’t been updated to take account of the science. She also says the IUDs can inhibit implantation.  At Vox, Julia Belluz lays out details about how the four do their work.

At the Incidental Economist, Nicholas Bagley seems to side with the court. It’s good to honor Hobby Lobby’s religious beliefs because scientists can’t say for certain that the four would never prevent implantation, he argues. In fact, he implies, it’s good to honor them even if it could be proved that these beliefs are dead wrong. Because religious freedom.

Incipient anthropologist Dick Powis seems to approve too, and for a similar reason. At Savage Minds he declares that  the Hobby Lobby decision is a win for what he calls ethnophysiology. Ethnophysiology “is the way in which the human body and its functions are understood in a cultural context.” And, he concludes, “Call David Green [Hobby Lobby's founder], five-ninths of the Supreme Court, and the Christian understanding of human reproduction misogynistic if you want, but to say that they eschew intelligence, logic, and reason because they use the word “abortion” differently is just ethnocentric.”

Oy. Welcome to a mind-bogglingly slippery slope. What about the appalling practices that can be ignored because if you object you’re just being ethnocentric? Human sacrifice. Female genital mutilation. Beheadings. Genocide. Sending non-Aryans to the gas chamber. Etc.

Short-term effects on health care

How will the Hobby Lobby decision affect health care more broadly? That’s what Paul Raeburn wants to know at the Knight Science Journalism Tracker.

In the immediate future, the answer is probably not much. Sara Rosenbaum, Adam Sonfield, and Rachel Benson Gold say at the Health Affairs Blog that, as written, the Hobby Lobby decision does not apply widely.

It does not apply to women whose employers do not impose religious beliefs on their workers, nor to women on Medicaid, nor to women who are covered through insurance purchased privately (including via the federal and state Obamacare health insurance marketplaces.) “All of those women are still guaranteed coverage of contraceptives without out-of-pocket costs,” they say.

It will probably not affect most women with employer-sponsored insurance either–although Rosenberg et al point out that the number of companies and employees affected is impossible to quantify.

I haven’t been able to nail this down for sure, but by implication, even Hobby Lobby itself might happily handle the paperwork for several kinds of no-cost contraception for its employees. This could include the pill and other widely used methods of birth control that were not among the four the company’s legal case was about.

Hobby Lobby’s owners are Protestant Christians, not Roman Catholics, and apparently have in the past not objected to all forms of birth control in principle, as Roman Catholics do (except for the very unreliable periodic abstention from sex called “rhythm.”) Oddly, this is a point nothing I’ve read clarifies, so to me it appears to be an open question whether Hobby Lobby employees will have free access to at least some forms of birth control.

Future effects on health care

In the longer term, the Hobby Lobby decision might have a lot of impact, and not only on health care. In her dissent, Justice Ruth Bader Ginsburg was scathing, arguing that the decision had “startling breadth” and foreseeing that it could lead to restrictions on other medical procedures that some object to on religious grounds.

These could include vaccination, blood transfusion, infertility treatment, some psychiatric treatment, and perhaps even hospice care. She is also worried about whether the ruling can be extended to religious objections on nonmedical matters, for example to anti-discrimination laws protecting gays and forbidding plain old-fashioned gender discrimination.

Writing for the majority, Justice Kennedy said, essentially, “No it won’t.” It remains to be seen how reliable the Justice’s prophecy skills are. At the New Yorker, Jeffrey Toobin describes how this court has historically employed seemingly limited decisions as an opening wedge to get to subsequent broader rulings, as in its serial decisions that have gradually constricted voting rights.

Already dozens of companies have gone to court to fight Obamacare provisions, although Rosenbaum et al think it’s doubtful that large number of companies will seize on the religious exception. For one thing, they say, the immediate economics favor birth control. When employees avoid pregnancy, companies save money.


Finally, the religious war against women

After all the jibber-jabber about how this court was in surprising agreement so much of the time, a point I messed up on a couple weeks ago, these cases turned out to be quite the other thing.

Supreme Court decisions about women’s wombs this term were pretty nakedly made by the men justices against the women justices. And they were not just men, they were all the Roman Catholic men on the Court. Stephen Breyer, the lone man who sided with the court’s three women justices in the Hobby Lobby case, is a Jew. As are Ruth Bader Ginsburg, who wrote the stinging Hobby Lobby dissent, and Elena Kagan. Sonia Sotomayor is a Catholic, but she didn’t let that stop her.

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Anthrax, false research, triglycerides, mea culpa, cellphone freedom

Accidental anthrax

Which is the more likely threat to public safety?  A single big release of deadly organisms by terrorists, the nightmare that fuels much bioweapons research and a string of lookalike novels that are nearly a genre in themselves? Or a series of much smaller accidental releases “from the high-level biodefense labs that have proliferated in the wake of the anthrax attacks of 2001″? Christine Gorman asks this at Observations, the SciAm editors blog.

Bacillus anthracis. Credit: Centers for Disease Control and Prevention

Bacillus anthracis. Credit: Centers for Disease Control and Prevention

The data argue that we are in far more danger from accidents emanating from well-meant research efforts to protect ourselves. To date there have been no bioterrorists. The 2001 attack killed 5 and was probably carried out using a research anthrax strain from a US lab. Several incidents occurred in the 1970s. In 1978, smallpox escaped from an English lab killed a photographer. A similar 1971 release from a Soviet lab killed at least three; it’s not known whether that was an accident or deliberate. The accidental 1979 release of anthrax at Sverdlovsk may have killed as many as 100.

Gorman’s brief history of lethal microbial escapees from research labs was prompted, of course, by last week’s news from the Centers for Disease Control and Prevention that at least 75 of its staff members may have been exposed accidentally to live anthrax as it was transferred from one lab to another. This because safety procedures that were supposed to be followed were not, and why they were flouted is not known.

Nobody has turned up sick yet, but the incubation period has not quite expired, according to Susannah Locke’s updated report at Vox. David Malakoff’s June 19 report at ScienceInsider has a lot of details.


“Most published research findings are false”

John Ioannidis’s 2005 PLOS Medicine article, the one with the forthright but startling title, “Why Most Published Research Findings Are False,” reached a milestone earlier this year: a million page views, the first PLOS article to attract that much traffic. To celebrate, the PLOS Blog Network published a brief interview with Ioannidis carried out by PLOS’s Erica Kritsberg.

Ioannidis, who is Professor of Medicine, of Health Research and Policy, and of Statistics at Stanford, says he sent the paper to PLOS Medicine because the journal was new and seeking to be adventurous. “Given the breadth and importance of the topic, specialty journals would certainly find it uninteresting.”


He emphasizes that his results apply mostly to what he calls “silo” research, where a single principal investigator “is trying to outpace the others, finding significance in his/her own results without sharing and combining information. The opposite holds true when scientists join forces to examine the cumulative evidence. Sadly, in most fields the siloed investigator writing grants where he promises that he/she alone will discover something worthy of the Nobel Prize is still the dominant paradigm. This sort of principal investigator culture is a problem, especially for popular fields where the literature is flooded with tens of thousands of irreproducible papers.”

Last year Ioannidis joined with Daniele Fanelli, of the University of Edinburgh, in a PNAS paper arguing that studies involving behavior were more likely to claim extreme effects, to exaggerate their results, especially if the authors were based in the US. Why? “Our preferred hypothesis is derived from the fact that researchers in the United States have been exposed for a longer time than those in other countries to an unfortunate combination of pressures to publish and winner-takes-all system of rewards” They also forecast that researchers outside the US would likely soon catch up in the bad behavior department. Ivan Oransky analyzed the paper at Retraction Watch.

John Ioannidis. Why is this man smiling?

John Ioannidis. Why is this man smiling?

For more on Ioannidis and his dispiriting contention that scientific results are, for the most part, untrustworthy, see a post by Julia Belluz, who blogs at Science-ish for Maclean’s magazine in Canada. She reports on a session Ioannidis gave early this year at the Harvard School of Public Health, educating a roomful of doctors on the bad news about the state of science.

It does make one wonder what we’re all doing here.


Loss of function

I wonder what John Ioannidis would make of the New England Journal of Medicine papers reporting on mutations that silence the APOC3 gene and prevent formation of fats called triglycerides. This, they say, reduces the risks of heart attacks and strokes by 40 percent.  There are two of them, conducted independently but reporting similar results. The fact that the two studies from two different research groups come to similar conclusions does suggest they may be on to something.

At Forbes, the very reliable Larry Husten doesn’t challenge the papers, but he is doubtful about their interpretation by some researchers and science writers. These sources have promoted the idea that the heretofore ambiguous role of triglycerides has now been clarified and reveals that they are important in development of cardiovascular disease. The papers have also been interpreted as downgrading the importance of high-density lipoprotein, HDL, the “good” cholesterol, which has been thought to protect the cardiovascular system.

Husten argues that the papers suggest “that it may be very difficult to link the effect of APOC3 to its specific impact on triglycerides.” The loss-of-function mutations that shut down APOC3 do accompany a reduction in triglycerides, he notes. But low-density lipoprotein, LDL, the “bad” cholesterol, is also reduced–and HDL goes up. “So it may be hard to figure out exactly what APOC3 is doing, and it’s probably too soon to dethrone HDL and elevate triglycerides. We just don’t know enough at this point.”

Husten quotes leading cardiologist Harlan Krumholz as saying the research, “has absolutely no implications for clinical practice. It might one day be seen as a pivotal study that led to the development of remarkable drugs, but that is far away.”


Mea maxima culpa

That emphasis might please Knight Science Journalism Tracker Paul Raeburn, who uses Gina Kolata’s New York Times piece on the two papers as a jumping-off point for a mea culpa. Raeburn is distressed that Kolata’s emphasis (as is the case in nearly all journalism about medical research developments) is on the potential for therapy, especially drug therapy. The stories usually caution (as this one does) that the potential therapies might not pan out. (As, indeed, they rarely do.)

Raeburn acknowledges that he has often said the same sort of thing, and he is not alone. I certainly have, and so has everyone who writes about this stuff. Mea maxima culpa.

So we should all take to heart his suggested revised approach to getting rid of this promise-of-therapy reflex. “I think we need to step away from the boilerplate promise-and-unpromise paragraph that we’ve written so often, and query researchers more carefully about exactly how and when their research might lead to new treatments. What problems remain to be solved? What are the potential side effects? How much might it cost? Would the FDA be likely to approve it? Does it raise ethical questions?”

While I’m up, I feel compelled to draw attention to an unrelated but really odd blog comment on the triglyceride papers. Recall that the gene alterations under study are loss-of-function mutations that shut down APOC3 activity. From Uncommon Descent, an “intelligent” design blog:  “Is this Darwinian evolution in action? No, because loss of function is the opposite of gain in function, which is what Darwin’s theory (natural selection acting on random mutation) proposes to explain. Loss of function is a form of evolution, but is[sic, I expect they mean "its"] resources are very limited.”



Fourth of July holiday: freedom from mobile phone searches

Next Friday, July 4, is Independence Day, our most important national holiday here in the US. So I will not be bringing you On Science Blogs because I will be celebrating the birth of our freedom. You, too, I hope.

Our freedom was epitomized this week by the US Supreme Court’s unanimous ruling–especially astonishing because this is not a Court that does much of anything unanimously– [more mea culpa, see comments below] that police can’t search people’s cellphones without a warrant.

While you are lazing away the long weekend, or even sooner, you will want to read the incomparable Linda Greenhouse on the cellphone ruling. Her analysis: The justices came together in this case because they all own mobile phones.

Yay, freedom. Back in two weeks, Friday, July 11.

flag 13 stars





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Women and science writing

Women in science writing

The Women in Science Writing: Solutions Summit last weekend at MIT was aimed at seeking ways of rooting out bias against and sexual harassment of women science writers. Here’s the conference Web site, with a link to Maryn McKenna’s assiduous tweeting and Storifys of #SciWriSum14, plus another Storify by attendee Alberto Roca.

women in science writing logo

I expected considerable blogging about the meeting because there were 90 attendees, nearly all writers. But I haven’t been able to find much yet; still early days, I guess. Ed Bertschinger has a brief post at Women in Astronomy. Cris Russell has a more detailed report at CJR’s Observatory blog on science writing.

Russell notes an increase in women going into science writing in bad economic times, a time also when the upending of the publishing industry means fewer and fewer staff jobs. Among the suggested remedies for bias and sexual harassment: A science writers’ bill of rights, an online clearinghouse on sexual harassment, mentoring networks, updated codes of conduct, and efforts to reduce tokenism.

She also describes results from a survey of science writers in which respondents were self-selected. One of them surprised me quite a bit. Fifty-four perecent of the women respondents felt that overt or unconscious gender bias exists in science writing and journalism. That seems low to me. It’s true that overt bias is less than in olden times, but there’s still plenty around. Unconsious bias is pervasive, and because it’s unconscious it will be quite a challenge to eliminate.

Pervasive bias is, well, pervasive. It affects science writers and many others, and it certainly applies in science generally. Just last month I noted the increased inclusion of women in research but  the dearth of research on female lab animals. Earlier this year, Drug Monkey noted that while the sex ratio of NIH grantees had improved dramatically, it was still the case that there are always, always, more men on the list of successful applicants. Microbiologist Jonathan Eisen regularly rails against conference agendas top-heavy with male organizers and presenters at his blog Tree of Life.

At the MIT meeting, reports of sexual harassment were, not unexpectedly, more common than bias reports. More than 80 percent of the women respondents said they had been subjected to sexual comments, unwanted touching, and the like; fewer than 20 percent of the men did. One in three women encountered this bad behavior in professional contexts. That seems low to me too. Perhaps it means that these days potential harassers are laying off because they know they are inviting trouble–which not so long ago was not the case.

Russell also reported on statistics gathered from elsewhere. In a survey of major news organizations, women produced only 35 percent of tech and 38 percent of science stories, and–this surprised me–health stories were produced about equally by men and women. Great news if health writing is no longer a female ghetto; that really is progress.

In anthologies of science writing, about 80 percent of contributions are by men and 70 percent of guest editors are men. Far more men than women are quoted as sources in stories. A lot of these findings are likely to involve that hard-to-get-rid of unconscious bias. But identifying the problem is the first step in getting rid of it. Consciously.

The state of women

Bias and sexual harassment are plenty burdensome for nearly all women, and in many parts of the world they suffer lots worse than distasteful dirty talk. They are sequestered and swathed head to foot. They are barred from education. They are beaten and tortured. They are slaughtered at birth, and raped and murdered as children and adults.

Here in the privileged West, we are living in the best time and place for women in the 200,000 years of our species’ existence. The best so far, if still imperfect.

Good to keep in mind, our great good fortune in being here and now and having the tools to do even better. But it does give us a different set of barriers to beat. Also, it’s not clear that losing desirable assignments and promotions and undergoing sexual harassment are bigger problems for women science writers than for women in other lines of work.

Obviously consciousness-raising within a group is key to fixing the problem, although maybe the second order of business is to get beyond preaching to the converted. How to reach the folks who need to have their heads banged together because they can make the bias-changing decisions? It might make sense to collaborate with other professional groups to brainstorm solutions.

Scicurious revealed!

I have several times cited posts by Scicurious here at On Science Blogs. I especially admire her deconstructions of neuroscience research. Nobody does a better job of science blogging, and that’s not just my opinion. She’s won lots of awards.

But last year Scicurious moved out of the shadows of pseudonymousness and stood revealed as: Bethany Brookshire. I was going to say that she switched careers, but what she really did was let go of one of her careers–bench scientist–in order to give full time to the one that made her a famous blogger: science writing.

scicurious psuedonymity-kitteh

She landed a terrific–paying!–job at Science News, where she writes for the magazine and still blogs as Scicurious once weekly.  She told me in an email: “the rest of the time I run the Eureka! Lab blog.  A blog that is devoted to getting more students interested and inspired in STEM (watch out for a post coming out early next week, it’s on squirrels and I’m so excited about it!). The Eureka! Lab blog has posts up to 5 times a week and is written at a 7th grade level.”

She also has a several-year perspective on science blogging and “tribes” in science writing: “[I]t’s funny how the science blogsphere has changed over time. Much ‘official’ science blogging is now just like science reporting, with outside comment, etc, and makes me wonder why on Earth bloggers still get paid less (though it should be noted, as a staff writer, I get what staff writers get. PHEW!).

“I’ve also noticed recently, as I’ve moved into the field, that science writing has its own ‘tribes,’ just like academic science. Who went to what journalism program, who’s written for what publication, etc. I realized that I’m part of the ‘blogging’ tribe that’s been around since 2006 or so.”

Early this year, at her blog Neurotic Physiology, Brookshire posted on her decision to leave academia. A noteworthy post on the nature of failure, one that drew many comments–including some from Ed Yong relaying his experience with failure.

Comforting to realize that it’s possible to fail upward. Is that really failure?

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World Cup! Soccer or football! Turing Test & artificial intelligence!

Soccer to ‘em

World Cup soccer/football blah blah blah, world’s most popular game blah blah blah, but Brazil deserves a World Cup for its performance in saving its Amazon rainforest and preventing carbon dioxide emissions, according to a paper Science is publishing today. Bouncing up and down with little glad cries, Andrew Revkin gives details at Dot Earth.

Credit: Roman.b   Read all about the Brazuca at http://goo.gl/IEG9Pc

Credit: Roman.b
Read all about the Brazuca at http://goo.gl/IEG9Pc

It’s a stunning achievement. The forecast is that clearcutting the Amazon rainforest will have stopped by 2020. In 2005, nearly 20,000 square kilometers were being cleared every year. Last year, Amazon clearcutting was down 70%, to well under 6000 square kilometers. That’s a world record for cutting greenhouse gas emissions, down more than a billion metric tons. At the same time, Brazil is producing more soybeans and beef on the same amount of land. The gains, researchers say, are fragile, but real.

A post at New Scientist celebrates this and also  other Brazilian science: research on a vaccine for schistosomiasis, building a dark matter detector under the Andes, and a plan to use genetically modified mosquitoes as a control for dengue fever. Brazil is also getting into the space business and has a program to encourage entrepreneurs. And you don’t have to be Brazilian to qualify.

Meet Tolypeutes tricinctus

The three-banded armadillo, Tolypeutes tricinctus–or, rather, a peppy Disneyesque version called Fuleco that bears little resemblance to the very homely real animal–is the World Cup mascot. T. tricinctus was picked, I guess, because in situations when it feels that armor isn’t enough, it rolls itself into a spherical shape that to some looks a bit like a soccer ball.



Fuleco is everywhere, but T. tricinctus, which is easy to catch and barbecue, lives only in a Northeast corner of Brazil and has been classified as “vulnerable” to extinction. FIFA, the Fédération Internationale de Football Association, has attempted to wrest some benefit for its universally despised position as soccer’s governing body by saying its choice of the armadillo is an attempt to help save it. The International Union for Conservation of Nature says whether the beast’s mascot status will help remains to be seen.

The real three-banded armadillo, Tolypeutes tricinctus.  Credit: Chatsam

The real three-banded armadillo, Tolypeutes tricinctus. Credit: Chatsam

Henry Nicholls, blogging at the Guardian’s AnimalMagic, is quite a bit more emphatic. In fact, he’s seriously annoyed because FIFA stands to make a great deal of money from Fuleco but, despite its vows, has yet to pledge any of it to saving T. tricinctus. Nicholls has started a Change.org petition to FIFA’s head of Corporate Social Responsibility–is it possible to hold that job with a straight face?–asking for a serious committment to saving the armadillo and its ecosystem. Find the petition (and sign it) here.

World Cup health

The British Medical Journal blogs are using the World Cup to promote healthful behaviors–or at least to decry unhealthful ones. Tiago Villanueva claims research shows physical inactivity of the sort encouraged by hours of soccer/football of both kinds on television is responsible for over 5 million deaths a year, more than smoking. One in three adults and four out of five of kids between 13-15 don’t get the recommended amount of physical activity, 150 minutes per week for adults and an hour a day for adolescents.

Villanueva is also alarmed about the health effects of increases in alcohol consumption during the World Cup. Emergency room visits associated with assaults went up 37% in the UK during the 2010 World Cup.  The Brazilian government has long banned booze in the country’s stadiums, but FIFA persuaded the government to lift the ban. You will be astonished to learn that one of the World Cup sponsors is Budweiser.

Also at BMJ, Gareth Iacobucci reports that in China people are buying fake sick notes purportedly from hospitals in order to stay home from work and watch the games without using up vacation time.

Soccer vs. football

And why do we (and a number of other English-speaking countries) call it soccer when much of the soccer-mad world calls it football? Turns out it’s the Brits’ fault. A prof at the University of Michigan School of Kinesiology–an entire school devoted to human movement?–says “soccer” was invented in Britain late in the 19th century, and it was even an upper-class term. An official US Embassy source gives details, saying “soccer” was fabricated because priggish Victorian Oxonians were disinclined to make a nickname out of the first syllable of “Association Football,” which is what the game was called originally.

“Soccer” was used interchangeably with “football” in Britain  until about 1980, but the Brits then dropped it because it had come to be regarded as an American word. Victoria McNally explains at Geekosystem. Doesn’t seem likely that we’ll ever accept “football,” at least as long as football, which only occasionally involves kicking, remains the favorite American game.

Still more soccer science–and math, and gambling

This post would be even longer were it not for the fact that the Guardian has rounded up several sciencey World Cup blog postsSciAm has done the same. Several seem to be items from yesteryear. But there’s also an interview with neuroengineer Miguel Nicolelis, the driving force behind that mind-controlled robotic suit that paraplegic Juliano Pinto wore to kick off the games. I’m happy to report that the robotic kickoff happened on schedule.

One new SciAm post is Michael Moyer’s, on the math behind World Cup predictions. But my favorite World Cup gambling post is Daniel Altman’s sly take at Big Think’s Econ201. The secret of successful World Cup prediction, Altman says, is to exploit public ignorance about probability and mathematical models. Here’s how to do it:

Brazil is the strong favorite among bookies, so assign that team a 45%-49% chance of winning. Altman says, “If Brazil comes through, the statistically naive among the public will say, ‘The model was right!’ If Brazil doesn’t win, you’ll say, ‘Well, the chance of Brazil losing was greater than 50 percent,’ and the public will nod in agreement. Either way, the model looks like it was correct.”

Altman suggests gleefully that his is a “win-win strategy that the most visible predictors may in fact be using.” Altman names no names, but  Moyer points out that Goldman Sachs’ Macroeconomics Insights gives Brazil a 48.5 percent chance of winning, and Nate Silver’s FiveThirtyEight puts the odds at 45%.


Touring the Turing Test

Why did so many writers fall for the claim that the artificial intelligence apotheosis had been achieved? That a computer program–a chatbot–had passed the Turing Test and was able to fool judges into thinking a five-minute text-based dialog with a computer was actually a conversation with a 13 year-old Ukrainian boy named Eugene Goostman?

The Turing Test is called that because a version of it was suggested by mathematician Alan Turing, OBE, FRS. The Alan Turing who helped win World War II by cracking German ciphers. The Alan Turing who is a venerated founder of theoretical computer science and the study of artificial intelligence. The Alan Turing who was prosecuted for homosexuality and chemically castrated. The Alan Turing who took cyanide and died in 1954. Yes, that Alan Turing.

Turing in slate at Bletchley Park, site of WWII cryptography triumphs. Credit: Jon Callas

Turing in slate at Bletchley Park, site of WWII cryptography triumphs. Credit: Jon Callas

Knight Science Journalism Tracker Paul Raeburn links to a number of sources that simply regurgitated what they were fed in a press release, the claim that Eugene had fooled judges (among them an actor who played the robot Kryten in the 1980s television series Red Dwarf.) Raeburn also cites others, notably bloggers, who had more sense.

Raeburn speculates that reporters can’t resist a good story, and the idea of computers deceiving people is a good story. That’s a slightly more respectable theory than mine, which is that (some) reporters can’t resist the idea of doing a quick-and-dirty piece based on a press release. Digging around to find qualified comment and interviewing outside sources takes time.

This applies, to my dismay, even to sources I have believed are trustworthy–and that certainly know better. At Ars Technica, shockingly, Staff Editor Nathan Matisse, with an entirely straight face, posted the Eugene tale based solely on the news release and other secondary sources. More shockingly, the site doesn’t seem to have taken it back or corrected it or acknowledged in any way that Eugene’s victory was in dispute. At Ars Technica! A Staff Editor! In the Information Technology section! At Ars Technica! Ars Technica!

The scales have fallen from my eyes.

At Neurologica, Steven Novella says that the competition was gamed by pretending that the responses were from a 13 year-old Ukrainian boy, which would help excuse and account for weird responses. In any case, Novella argues, Turing’s test is not “a true test of AI self-awareness, or true AI. It really is just a test of how well a computer can simulate human conversation.”

There is an online version of Eugene available to play with, although the program’s developers say it’s not the same as the competition version. A couple bloggers have chatted with the online version, Tom Bartlett at Pecolator and Scott Aaronson at Shtetl-Optimized. Not only are the dialogues unpersuasive, the two  are remarkably alike,  with Eugene reiterating a few canned responses and questions. This is the best that chatbot programmers can muster?

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Goodbye coal? Female hurricanes are more deadly?


Coal black

At Bad Astronomy, Phil Plait says President Obama’s proposed new plan for slowing down atmospheric carbon dioxide by reducing coal use for generating electricity is huge.

Credit: J.C. Leyendecker, 1918. HT to Melissa Lott at SciAm's Plugged In  http://goo.gl/rLV5SN

Credit: J.C. Leyendecker, 1918. HT to Melissa Lott at SciAm’s Plugged In http://goo.gl/rLV5SN

But is it huge? As a mind set, a psychological Rubicon, an opening wedge for more government action on greenhouse gases and climate change, maybe. But in terms of practical impact on greenhouse gases, not so much. Here’s why.

The aim is to cut carbon-dioxide emissions from the nation’s power plants as much as 30 percent below 2005 levels by 2030. Brad Plumer summarizes and explains the proposals at Vox–and he points out that the goal is not really as ambitious as you might think.

That’s because natural gas has gotten so cheap, and the Great Recession has reduced power use so much, that power-plant emissions plunged by 15 percent between 2005 and 2013. So they are already halfway to the 2030 goal. They achieved the first half of emissions reduction in well under ten years, and now they have more than 15 years to get the rest of the way. Dot Earth’s Andrew Revkin parsed the proposed rules and assembled several comments on why they aren’t enough.

Plumer followed up his first Vox post with a summary of how the EPA’s new rules would work. A central feature is that there are different emissions goals for each of the 49 states that have coal-fired power plants. That’s going to be fun.

At Watts Up With That, Anthony Watts has turned his skeptical platform over to Patrick Michaels, the high-profile climatologist/climate-change skeptic. Michaels points out, correctly, that there is no chance this new policy will have any detectable effect on global temperature. Thus he agrees with climate-change activists that the policy does not go nearly far enough. He also says the only way the 30 percent reduction can be achieved is by “upgrading almost all combustion units, and the ultimate cost of the upgrades will make coal noncompetitive with much-less-expensive natural gas–fired facilities.”

Um, I think that’s the whole point.


The death of Big Coal is greatly exaggerated

In his two-part roundup of media coverage of the announcement, Knight Science Journalism Tracker Charlie Petit forecasts that “Big Coal in the US may be looking death in the face. It is unleashing its armies.”  In a second post, Petit praises Paul Barrett’s BloombergBusinessweek analysis of what Barrett calls the phony war on the Obama plan and also partly takes back his forecast of Big Coal’s demise. Turns out that when we reach that coal reduction apotheosis in 2030, coal will still be generating 30% of US electricity. Last year it was 39%.

David Wogan, in a post last fall at SciAm’s Plugged In, argued that EPA rules are not really a War on Coal. Structural and market forces have been attacking coal’s position for some time, so it’s likely that coal will bite the dust eventually anyway, even if the process takes several decades. Natural gas is beating it to death, and nearly all coal-fired power plants are elderly and near-moribund anyway.


Follow the money

Chris Mooney explains at Grist why Republican claims that the new climate rules will wreck the economy are wrong. The US Chamber of Commerce has also issued a report inveighing against what it claims are the enormous costs of the new EPA coal regulations.

Anti-coal protesters at  Australia's Maules Creek mine.  Credit: Greenpeace Australia/AAP

Anti-coal protesters at Australia’s Maules Creek mine. Credit: Greenpeace Australia/AAP

But at his blog Conscience of a Liberal, economist Paul Krugman took a look at their data and found–somewhat to his own surprise, it sounds like–that even the Chamber’s own estimate of $50 billion would amount to only 0.2 percent of GDP. The Nobel Prize-winning economist’s academic technical analysis:”That’s cheap!”

If there is a War on Coal, Jonathan Weisman says at the New York Times, it’s going to be like the War on Tobacco in the 1990s. It will feature buyouts and compensation for the most-affected states. But Weisman quotes Republican economist Doug Holtz-Eakin arguing that the analogy is less than perfect. “In the end, smoking became unacceptable. That was not a legal statement. It was a social statement, and consensus was broad and has held for a long time,” Mr. Holtz-Eakin said. “Maybe you get there on carbon emissions, but right now, this is an issue for the elites.”

Those compensation programs can be extraordinarily effective. I was living in southern Maryland, at that point a tobacco-growing region, when in the 1990s Maryland launched a program to compensate farmers into giving up tobacco and moving to other crops. The huge leafy plants disappeared from my neighbors’ fields almost overnight, and the ubiquitous tobacco barns fell into picturesque decay with startling suddenness.

A collapsed former tobacco barn in Southern Maryland, once the home of extensive tobacco farming. Credit: © 2010 Fred Powledge

A collapsed former tobacco barn in Southern Maryland, once the home of extensive tobacco farming. Credit: © 2010 Fred Powledge

Where the campaign to reduce coal is analogous to the tobacco buyout is that, like tobacco, coal has serious health effects. And EPA is exploiting that fact in arguing for its program. In his post, Revkin pointed out that the EPA’s new rhetorical approach–talking about carbon pollution rather than carbon dioxide or greenhouse gas emissions–signals that the agency plans to emphasize the immediate health benefits of using less coal.

At the Washington Post‘s new To Your Health blog, Lenny Bernstein describes some of these benefits. The American Lung Association says the plan would  ”prevent up to 4,000 premature deaths and 100,000 asthma attacks” just in its first year. This because power plant emissions contain sulfur dioxide, nitrogen oxide and mercury. All contribute to lung disease, heart attacks and asthma. There will also be lung benefits from a reduction in tiny particles of soot, which clog lungs.


Hericanes and Himicanes

Kind of fascinating, how much statistician ire has been provoked by that PNAS paper claiming that female-named hurricanes have killed more people than male-named ones. The supposed reason being that people in their paths have taken male hurricanes more seriously and gotten out of the way

This false-color image from NASA’s Cassini mission shows the  no-name hurricane  at Saturn’s north pole. Credit: NASA/JPL-Caltech/SSI

This false-color image from NASA’s Cassini mission shows the no-name hurricane at Saturn’s north pole. Credit: NASA/JPL-Caltech/SSI

The statisticians are not objecting to the premise that people respond unconsciously to the relative power implied by male and female names. That seems to strike most of the bloggers as not implausible. But the data and the methodology have statistics-minded commentators jumping up and down with rage. I haven’t seen a single defense, so I conclude that the paper is at best problematic.

For example, the researchers studied hurricane aftermaths from 1950 on, despite the fact that hurricanes all had female names until 1979. You don’t have to be a statistician to find that . . . odd. At The Monkey Cage, statistician Andrew Gelman agrees that including pre-1979 data makes no sense.

The hypothesis might be true, he says, but he doesn’t think the male/female thing is the most important feature of hurricane names. He wonders if it would be more sensible to compare the power implied by some names over others, Omar vs. Irving, for instance. Or whether it’s a good idea to name hurricanes at all, since perhaps names make them seem more cuddly.

A post at the Guardian by evolutionary biologist Grrlscientist and biostatistician Bob O’Hara concludes, “When we compare the data to the model itself, the ‘femininity effect’ of hurricane names completely disappears.” (This post raised a side question for me. Sandy, the megastorm of recent memory that was officially a hurricane for only a part of the time it spent slapping New York and New Jersey around, is classified as female. But Sandy is also a man’s name. Surely the single-sex classification can’t be kosher?)

Gelman refers us to an analysis by the mathematically minded sociologist Jeremy Freese at Scatterplot. Freese has problems with the model too, calling the effect sizes it implies “astonishing.” The paper’s own example claims “that if a hurricane named Eloise killed 42 people, the same hurricane named Charley would be predicted to only kill 15.” In other words, most of the deaths could be prevented if only the hurricane had a masculine name.

Freese considers the actual hurricane Andrew, which was severe in terms of damage but killed only 62 people. The paper’s model fits Andrew well, predicting 59 deaths. But, says Freese, “if the hurricane had been named Diana instead, the model predicts over 25,000 people would have died.” This implies “that tens of thousands of Floridians owe their lives to the fact that Andrew was not preceded by another storm that season, because then what we know as Hurricane Andrew would have been called Hurricane Bonnie.” The dramatically different fatality estimate for Diana (or Bonnie) doesn’t seem likely, does it?


What we have here is another failure of science communication

Freese is also trenchant on the topic of how scientific studies are relayed to the public. I will quote him at length because he is identifying an increasing problem: hype for a piece of research where the hype emanates not originally from journalists (although they are usually blamed for it), but from the authors of a paper and their research institutions.

A different choice of false color for this  image of a Saturnian hurricane from NASA’s Cassini mission. Credit: NASA/JPL-Caltech/SSI

A different choice of false color for this image of a Saturnian hurricane from NASA’s Cassini mission. Credit: NASA/JPL-Caltech/SSI

Just last week I described such a case here, involving a paper on the microbial inhabitants of the human placenta. The first author gave  interviews in which she implied that the paper showed a connection between gum disease and unhealthy pregnancy, especially premature delivery. The paper did not show that, but top-flight science journalists nonetheless relayed her declarations. I discussed this paper and the media clamor surrounding it in a column last week at the Genetic Literacy Project.

In the case of the gendered hurricane naming, Freese points out (and the emphases are his): “The authors’ university issued a press release with a dramatic presentation of results. The release includes quotes from authors and a photo, as well as a quote from a prominent social psychologist calling the study ‘proof positive.’  So this isn’t something that the media just stumbled across and made viral.”

Freese goes on: “I have become especially impatient by the two-step in which a breathless set of claims about findings is provided in a press release, but then the authors backtrack when talking to other scientists about how of course this is just one study and of course more work needs to be done. In particular, I have lost patience with the idea the media are to blame for extreme presentations of scientists’ work, when extreme presentations of the scientists’ work are distributed to the media by the scientists’ employers.”

I rest my case.

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California quaking, swearing off showers for science, overselling the microbiome, MERS update, tropical diseases, cats vs. dogs

Uplift and quaking

When will the next big earthquake hit California, something approximating the one south of the San Andreas fault in 1857 (7.9) or San Francisco in 1906 (7.8)? The forecasts say sometime in the next few decades. Michael Lemonick explains at the New Yorker blog Elements why the current California drought may hasten the day.

Lemonick is writing about a Nature paper arguing that the massive drawdown of California’s water to irrigate California’s farmlands may be causing microquakes, and that big earthquakes are often preceded by lots of little ones. Microquakes will not cause a major quake that would not otherwise have happened, Lemonick says.”But it might bring on the Big One a little bit sooner.”

San Francisco, 1906. Credit: Pillsbury Picture Co.

San Francisco, 1906. Credit: Pillsbury Picture Co.

No soap

It’s been a time of what evolutionary microbiologist Jonathan Eisen, blogging at Tree of Life, calls “overselling the microbiome.” The highest profile item was the New York Times piece by the reporter who went a month without showers, shampoo, or deodorant in order to test a new product, a spray containing an ammonia-oxidizing bug, Nitrosomonas eutropha, that was supposed to keep the bad smells away.

It seems to have mostly worked, although she hated her greasy hair, and who can blame her? I wrote about microbiome matters Tuesday at GLP, and most fascinating to me was Julia Scott’s report that her skin improved remarkably–softer, smoother, zits gone, smaller pores. Can’t help wondering if it might be possible to spray the face and get those benefits while still washing the hair, at least occasionally.

Paul Raeburn blogged about Scott’s piece Wednesday at the Knight Science Journalism Tracker and found the idea somewhat icky. He may be right. I have a hunch we’ll find out before long whether microbes can make it as consumer products.



I won’t compare pimples to the horrifying Clostridium difficile, but they can make life pretty ghastly for adolescents. Now that receiving a transplant of another person’s bowel movement–uh, gut microbiome–is an acceptable and reportedly quite effective therapy for the very unpleasant, tough-to-eradicate, and potentially fatal C. diff infection, spraying a bit of bacteria-laden mist on the face a couple of times a day sounds not so bad.

Overselling the microbiome

As I pointed out Tuesday, Eisen has for years been bestowing awards for overselling the microbiome–complaining about hype and misleading news stories. Last week he posted an exceptional rant.

The topic was a paper describing the microbiome of the human placenta. The placenta seems to be populated not by microbes such as you might expect, for example ones similar to those in the vagina or the gut. No, several of the bugs that turned up are also to be found in the mouth. Note, though, that the paper explicitly said the placental organisms were not pathogens.

Nevertheless, nearly all the articles emphasized a point the lead researcher Kjersti Aagaard made in interviews: that the paper showed a connection between gum disease and unhealthy pregnancy, especially premature delivery. Which it did not.

Aagaard also emphasized the importance of dental hygiene. An excellent recommendation for many reasons, not least because replacing lost teeth is a painful surgical procedure, takes a long time, is often not entirely successful, and is stunningly expensive. Whether flossing can prevent premature birth, however, has yet to be demonstrated.

A tweet from science journalist Ed Yong saying “the oral hygiene msg seems hugely premature to me” prompted the Eisen post. Eisen was especially critical of news stories in Science and the New York Times, although several others (and their headlines) took a beating too.

Update on MERS: Never Mind

A couple weeks ago, on May 16, I did a blogging roundup on MERS, the new coronavirus disease centered in the Middle East. At that point there were two MERS cases in the US, both imported by health care providers who had worked in the Middle East.

On May 17, a third case was announced. This one was particularly scary because it looked as if the third patient, who had not traveled, had caught it from one of the others–even though MERS doesn’t seem to be hugely contagious.

Well, good news. The third so-called MERS case was a false alarm. To  date, no one has become infected in the US, the two imported cases have recovered, and there are now no American cases of MERS. Nothing to see here, move along. Details from Karen Kaplan at the LA Times’s blog Science Now.

If you want to catch up on MERS, though, my post here from May 16 has a lot of links. And if you’d like to know more about viruses, Vincent Racaniello has a post of interest at his Virology Blog. His Columbia virology course is going MOOC in August, and videos of each session are already posted on the course site, YouTube, and iTunes University. Seems like a terrific chance for a deep dive into virology for free and on your own schedule.

But we should mind the tropical diseases invading the US

At the Mermaid’s Tale, Anne Buchanan and Dan Parker call attention to a PLOS paper describing the “New American Underbelly of Tropical Diseases” among the Gulf Coast poor. Also chikungunya, a mosquito-borne infection expected to enter the US soon.

Chikungunya, whose main vector is the Aedes aegypti mosquito, is spreading fast in the Caribbean. Credit: Science.

Chikungunya, whose main vector is the Aedes aegypti mosquito, is spreading fast in the Caribbean. Credit: Science.

The post is a screed against neglect of certain diseases–the World Health Organization says there are 17 neglected tropical diseases–because they are diseases of the poor. Big Pharma, Buchanan and Parker say, is unlikely to invest in developing vaccines. Which is probably true. They also complain “the big research dollars go to sequencing viruses and parasites, generally neglecting the social aspects (like poverty) that lead to these conditions.”

I agree in principle that getting rid of disease by getting rid of poverty is a noble goal, but is it a more pragmatic one than genetic investigations of disease organisms? Or, to take a really practical example available right now, distribution of bed nets to keep out vectors? Were it even possible to redirect what’s spent on these things and put the money toward eliminating poverty, how much difference would these relatively small amounts make to the poor? Whereas research on disease organisms themselves is a proven strategy for dealing with disease.

Cat people vs. dog people

It’s irresistible, so I’m concluding with the report claiming that cat people are more intelligent than dog people. I openly acknowledge that this is not an actual paper, one that’s gone through peer review and been published in a respected journal. No, it’s just a poster by Denise Guastello, from Carroll University in Waukesha, Wisconsin, who presented it at the annual Association for Psychological Science meeting just concluded in San Francisco. Between 2:30 and 3:30 last Saturday afternoon. Pacific Daylight Time.

The poster caught the eye of Live Science’s Rachael Rettner, which makes it legitimate fodder here. Rettner reported not only the “more intelligent” datum, but also that “People who said they were dog lovers in the study tended to be more lively — meaning they were more energetic and outgoing — and also tended to follow rules closely. Cat lovers, on the other hand, were more introverted, more open-minded and more sensitive than dog lovers. Cat people also tended to be non-conformists, preferring to be expedient rather than follow the rules.”

Guastello seems to think her findings grow out of the differing sanitation requirements of dogs and cats. “It makes sense that a dog person is going to be more lively, because they’re going to want to be out there, outside, talking to people, bringing their dog,” Guastello said. “Whereas, if you’re more introverted, and sensitive, maybe you’re more at home reading a book, and your cat doesn’t need to go outside for a walk.” Or, I dunno, maybe she’s just talking about exercise.

I expect you’re curious about the study subjects. This was psychology research, so the demographic is easy enough to guess: the psych-obligatory college students. I wonder if they got extra credit.

cats in ur blog

It’s possible Guastello is familiar with a 2010 paper in the journal Anthrozoös reporting on personality differences between cat and dog people. “Results suggest that dog people are higher on Extraversion, Agreeableness, and Conscientiousness, but lower on Neuroticism and Openness than are cat people.” A full-text PDF can be had through a Guardian post on cat people that mentions this paper.

The study was much larger than last Saturday’s, involving more than 4500 people. But, and this is a very big but, a huge but, they volunteered themselves through a web site.

I never get over being flabbergasted at investigators–psychology is rife with them–who seem to be able to get away with flagrant flouting of basic principles of research design.

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Inflationary Universe data in question, but cheer up, there are cures for aging

Has BICEP2 lost its muscle?

Data claiming support for the inflationary theory of the Universe’s beginnings were released at a much ballyhooed press conference in March. (Cosmic inflation is the idea that the Universe expanded spectacularly right after the infinitesimal point that was the Big Bang.)

When I wrote about the announcement here at the time, I said I was surprised at the wholehearted embrace of a report that was so clearly contingent, tentative, preliminary. With few exceptions, physicists and physics groupies were dancing in the streets, paying at best parenthetical lip service to the way science has to work if it is to be truly scientific: results are supposed to be confirmed before they are accepted as Revealed Truth. Especially results as world-shaking as these.

The claims were based on observations of cosmic microwave background radiation left over from the Big Bang, observations made by the BICEP2 telescope at the South Pole. (BICEP is the muscular acronym for the Background Imaging of Cosmic Extragalactic Polarization experiment.)  Well over 300 papers exploring the implications have appeared already, in just a couple of months, rushed into the arXiv e-print database.

We should know fairly soon, within the next year or two, whether what BICEP2 saw was the real thing. The first installment is expected in October, with release of data from Planck. Planck is the space observatory designed to study cosmic background radiation and operated by the European Space Agency. Last fall ESA declared “Mission accomplished!” and deactivated Planck, but analysis of its data goes on and on. Some teaser data were released May 12, which Kathryn Jepsen described at Symmetry.


The Dustup

Beginning last week, however, what physicist Sean Carroll called “Arrrgh Rumors” have been asking whether the BICEP2 results would come to literal dust. At his physics blog Résonaances on May 12, Adam Falkowski asked “Is BICEP wrong?” Noting that in March he had given the BICEP2 results only a 50-50 chance of being right, Falkowski reported that BICEP had wrongly interpreted data from Planck. “Once you correct for that and rescale the Planck results appropriately, some experts claim that the polarized galactic dust emission can account for most of the BICEP signal. The rumor is that the BICEP team has now admitted to the mistake.”

That rumor turned out to be wrong, or at least was roundly denied, according to Lisa Grossman in a May 13 piece at New Scientist.

On May 15, Carroll tweeted “Could the BICEP2 signal be dust, not CMB? Slides from Raphael Flauger suggesting yes” and linked to a public seminar by Princeton physicist Raphael Flauger (slides and video here.) Falkowski reported on the Flauger seminar on May 16. He acknowledged that the BICEP results might still turn out to be valid, but it was now up to the BICEP team to prove it.

The BICEP2 team used a map of the entire sky (left) to estimate the effect of galactic dust on their measurements. Princeton’s Raphael Flauger reconstructed the map from other sources and found the effects from dust may be much stronger (right) than the team had thought. The colors show the degree to which light from different parts of sky is polarized; red is stronger, blue is weaker.  Sky maps from Science News, May 21, 2014.   https://www.sciencenews.org/article/dustup-emerges-over-gravitational-waves-discovery

The BICEP2 team used a map of the entire sky (left) to estimate the effect of galactic dust on their measurements. Princeton’s Raphael Flauger reconstructed the map from other sources and found the effects from dust may be much stronger (right) than the team had thought. The colors show the degree to which light from different parts of sky is polarized; red is stronger, blue is weaker. Sky maps from Science News, May 21, 2014.

Christopher Crockett also described the Flauger analysis May 21 in a fine open-access piece at Science News that explains the rumor story so far. It’s also a clear summary of what the issues are. “This is not so much a squabble, but the discovery process in action,” he concludes.

An early skeptic was cosmologist Peter Coles, who blogs at In the Dark. He, too, analyzed the rumor and its aftermath, and observed, “I’m not particularly keen on the rumour-mongering that has gone on, but then I’m not very keen either on the way the BICEP2 result has been presented in some quarters as being beyond reasonable doubt when it clearly doesn’t have that status. Yet. Rational scepticism is a very good thing. It’s one of the things that makes science what it is. But it all too easily turns into mudslinging.”

Cosmologist Sesh Nadathurm, who blogs at Blank On The Map, dismissed this week’s events as “a minor kerfuffle.” Which it is not, as I explain below. While I think Nadathurm is wrong about the importance of the flap, the post is a clear explanation of the technical issues.


Why the BICEP2 rumor-mongering is not a minor kerfuffle

Here’s why this tale is neither minor nor kerfuffle. As Joel Achenbach declared at Achenblog, “Cosmic inflation had been discussed for more than three decades, but this would be the first strong evidence for it.” Michael Lemonick points out in a May 21 SciAm post, “the BICEP2 results are crucial to verifying inflation, a cornerstone of modern cosmology.”

The rumor about BICEP2 results may have been denied, but it has prompted several physicists to go public with objections they say they have harbored since the findings were released in March. Lemonick rounds up some of these objections and says several physicists have not been able to replicate the BICEP2 calculations. (A BICEP2 paper was posted publicly in March but has not yet been published in a peer-reviewed journal, nor have the original data been released.)

Flauger told Ron Cowen at Nature News that he still hopes a signal will be confirmed. “I’m not trying to pick a fight; this is how science works, that someone presents a result and someone else checks that. But it doesn’t usually happen in public like this.


Young blood reverses aging

How the Universe began is arguably the most important story ever, but for nearly everyone except people who work in astrophysics and those of us who write about it, probably some religious folks too, it’s a topic with no impact on daily life.

This week, however, came science news of interest to pretty much everyone: experiments showing that there’s something in our blood that can reverse aging. Well, not our blood. Mouse blood. But the assumption is that if mice have it, we probably do too. And you can bet the pharmas are trying to concoct a patentable version of whatever it is as we speak.

Credit: National Institutes of Health

Credit: National Institutes of Health


Looks to me as if we need to take seriously these three new papers. These studies are not quack science, and they don’t seem to have been seriously misinterpreted by journalists who failed to understand the work or are trying to grab headlines. Nor is their reception a case of BICEP-like premature enthusiasm for preliminary results. The three are in peer-reviewed journals and are reporting on the latest results from long-term projects.


GDF11: the magic bullet against aging?

Two papers in Science report on recent findings from long-running investigations of what happens when the circulatory systems of young mice and old mice are joined in a somewhat creepy process called parabiosis. Old mice seem to benefit from substances in the young blood, one of which is a protein, GDF11. Doses of the protein alone rejuvenate heart and skeletal muscle and improve brain function: in this case olfaction, a huge part of mouse life.

At Ars Technica, John Timmer says the work implies that brain aging is not intrinsic to neurons but rather is a product of interaction with the environment and therefore might be modified. I expect the line of human volunteers eager to ingest just about anything has formed already.

At In the Pipeline, Derek Lowe says, “You might need a lot of protein, though, and there’s no telling how often you’d need infusions of it, but to roll back aging people would presumably put up with quite a bit of inconvenience.” Lowe thinks it’s likely there might be molecular targets in the GDF11 pathways, which is where the pharmas come in. The speculation is that rejuvenation is due to increased proliferation of stem cells. Lowe notes that up to now GDF11 has been believed to prevent formation of new brain cells, which shows how little is known about it.

At Mindblog, Deric Bownds cautions against profligate shooting up with GDF11. He warns, “waking up too many stem cells to start multiplying might increase the incidence of cancer.”


Young blood serum infusions help the aging brain

The third paper, in Nature, ís in some ways even more intriguing because it shows beneficial brain effects on elderly mice from injections of blood serum from young mice. This, too, is likely to be put into practice with humans immediately. Indeed, the researchers have set up a company to begin clinical trials.

Lowe points out that blood plasma is infused thousands of times daily in every medical center in the country. He wonders what effect this work will have on “the current model of blood donation and banking, if it turns out that plasma from an 18-year-old is worth a great deal more than plasma from a fifty-year-old. I hope that the folks at the Red Cross are keeping up with the literature.”

National Institutes of Health Director Francis Collins proudly blogs a detailed account of all three papers. All this work, it turns out, has been funded by we ourselves, the US taxpayers. Do you suppose small-government commentators and Congresspersons will have the nerve to argue that it’s a waste of public money? Can opposing a cure for aging possibly be good politics?

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Female vs. male research, vaginas, elderly sperm, Nate Silver’s 538, MERS, racial genetics

Sex roundup: Affirmative action in animal research

My list of potential topics is heavy with sex this week. First–and possibly most far-reaching–the National Institutes of Health is coming to grips with the fact that males and females are . . . different. They react differently to drugs, for instance. And that means that research results from one are not necessarily trustworthy for both.

To be fair, let us note that NIH changed the rules to even up the sex ratio in human research some years ago. Today the agency brags that more than half of research participants in human studies are female.

Until now, though, that affirmative action has not applied to studies with lab animals.  It’s possible that decades worth of animal research has been skewed by the fact that female lab animals have been routinely eliminated from research. One reason given: their raging hormones make interpreting results messy. See Susannah Locke’s post at Vox explaining the kinds of problems the present system has created.

Credit: Rob Young

Credit: Rob Young

The agency is writing new animal research guidelines for NIH-funded researchers; they will be released in phases beginning late this year. Researchers will be required to include both sexes in their animal experiments, and to include them in large enough numbers to detect sex differences in the results. Grant reviewers will be instructed to take lab animal sex balance into consideration when considering a proposal. Those who work with cells will be encouraged to use both kinds too, but the rules for cells seem a little more, um, flexible.

Even some researchers who thoroughly approve of organizing a piece of research so that it’s possible to sort out any effects that differ by sex have been made gloomy by this announcement. As Drug Monkey explains, it will increase research costs, and by more than just doubling the costs.

“Let me be clear, I want to do sex-differences studies. I am delighted that this will be a new prescription. I agree with the motivating sentiments. . . What it takes is additional grant funding. Or tolerance on the part of P&T committees, hiring committees and grant review panels for apparently reduced progress on a scientific topic of interest.”

Sex roundup: Researchers have been ignoring vaginas, too

Turns out that female reproductive machinery has been excluded from research along with female lab animals and female cells. Researchers from Europe and Australia report in PLOS Biology that they looked at 25 years’ worth of studies on the evolution of genitals–an increasingly hot topic–and found that just under half, 49%, report on male genitalia only. (44% studied genitalia of both sexes and 8% females only.)

Like the objection to disproportional attention to males in lab animal research, this is a complaint that has nothing at all to do with sexual politics. It’s about how to design studies that don’t skew results and lead to false conclusions.

Some of this may be, if not exactly sexual politics, a hangover from previous centuries: the idea that females are passive recipients of male sexual attention, with few genital features to excite research interest. But a big part of this neglect is because female genitalia are a lot more difficult to study. Male apparatus is usually out there for all to see; female genitalia are more often internal. Elizabeth Gibney reports at the Nature Newsblog that the data support this idea. Female creatures with external genitalia–spiders, for example–are not nearly as neglected by researchers.

At Not Exactly Rocket Science, Ed Yong agrees. A tube, he says, is easier to study than a cavity. But he also thinks old-fashioned (and erroneous) ideas about female passivity during sex linger and divert research attention. He’s got lots of fascinating details from animals to show that females often control, for instance, the ease of mating (in ducks) and the choice of male sperm (in earwigs.)

Sex roundup: Risky older fathers, another flub from Nate Silver’s 538

Knight Science Journalism Tracker Paul Raeburn takes issue with a piece at Nate Silver’s fivethirtyeight.com asserting that tales of birth defects, autism, and other psychiatric and behavior disorders associated with older fathers are overblown. He argues that the piece entirely ignores a crucial paper, a 2012 study from deCODE Genetics showing that the older they get, the more likely men are to pass mutations on to their children.

The 538 piece is by Emily Oster, who at the moment is looking like the only member of the 3-person 538 science staff who’s writing regularly. Most of the work so far posted in the 538 science section is from outsiders, not all of them writers.

Oster is an economist at the University of Chicago, but has been producing a weekly piece of science writing in debunkery mode. I wrote about Nate Silver’s new 538 in March, and my post was partly about another Oster piece. This was a contrarian take on whether acetominophen during pregnancy has long-term consequences for children. I liked some of what she said, especially her emphasis on how science writers so routinely give readers misleading impressions of a study by reporting relative risk figures instead of absolute numbers. But, given the small amount of data she analyzed, I thought the piece was waaaay too long.

The paternal age piece is also quite long, but at least Oster does additional analysis of the data she considers. Which is good, because data is supposed to be what 538 is about. OTOH, not good if she’s leaving out essential data such as the deCODE paper Raeburn describes.

Emerging MERS

As I write, there are now two confirmed US cases of MERS, the new Middle East Respiratory Syndrome coronavirus, which has been fatal in somewhere between a quarter and a third of cases. Both US cases are imports, unrelated to each other, one diagnosed in Indiana and the other in Florida. Both occurred in healthcare workers traveling here from Saudi Arabia, which has been the chief locale of MERS cases.

The disease is not hugely contagious; it appears to require sustained close contact, as with hospital workers or family members caring for a sick relative. The World Health Organization has issued official reassurance: this is not a global public health emergency. Or at least not yet. Find this news in several places, including Physician’s First Watch (from the New England Journal of Medicine). First Watch is also making its archive of MERS articles, a couple of dozen at this point, available free here.

Find exhaustive detail as of last Tuesday at the Centers for Disease Control’s Morbidity and Mortality Weekly Report. Health authorities expect more imported cases of MERS. Jason Beaubien reports at Shots that American hospitals are taking steps to recognize MERS early and keep it from spreading.

Where the virus comes from and how it infects people are uncertain. Its primary source is thought to be the Egyptian tomb bat, an appropriately sepulchral name. I haven’t been able to find out why this animal’s common name is tomb bat. But reportedly it likes to nest in stone structures, so maybe that’s it. It’s a fruit bat, like the bat reservoir for another scary coronavirus, SARS.

The Egyptian tomb bat. Credit: Jakob Fahr, some rights reserved (CC BY-NC)

The Egyptian tomb bat. Credit: Jakob Fahr, some rights reserved (CC BY-NC)

The virus has spread to camels, now suspected of being its intermediate host. A Lancet paper from last fall found antibodies to the virus in some camel populations but not others. The virus itself has been recovered from the noses of Saudi Arabian dromedary camels. (That’s the one-hump kind.)

Laurie Garrett, a long-time and highly decorated science writer who specializes in infectious disease, tells us at Foreign Policy that the geographic range of infected camels “perfectly overlaps the North African terrain of Egyptian tomb bats.” This could mean, she speculates, that sporadic human MERS disease may have occurred in the Middle East, unrecognized, for centuries.

Some MERS patients had contact with camel meat or milk before they fell ill, but camels appear to be involved in only a small number of MERS cases. Which means, Garrett says, “the vast majority of MERS cases seem to have been acquired by other means.”

For a thorough overview of the MERS story so far, see Judy Stone’s post at her SciAm blog Molecules to Medicine. She and Laurie Garrett both delve into the politics of MERS. The Saudi Arabian authorities in particular are tight-fisted with information. A  scientist there was fired for sending a saliva sample to the Netherlands for analysis.

The genetics of race

Science writer Nicholas Wade, late of the New York Times, has a new book out about the genetics of racial classification. Race, it argues, is not a social construct; races are genetically real and it’s time we learned to live with that fact. I reviewed the book this week at the Genetic Literacy Project. A Troublesome Inheritance: Genes, Race and Human History is impressively researched and will tell you things you didn’t know even if you know a lot.

race Wade bk

My chief complaint is that, although Wade pays lip service to the reality that nongenetic factors loom large in human evolution and human development and human life, sometimes he doesn’t seem to believe it. That’s particularly evident in Chapter 7, where he endorses the work of economic historian Gregory Clark.

Clark argues that Brits underwent something of a personality change between 1200 and 1800 because the rich reproduced more than the poor. This resulted in reduced interpersonal aggression and national embrace of virtues like thrift and the work ethic.

Wade believes this was due to the genes of the rich. He produces no evidence for these behavioral genetics influences, however. He simply asserts them, a bad move for a science writer. Given what we know at the moment about these virtuous genes, which is nothing, it’s just as plausible that these changes were shaped by parental habits and cultural inculcation. More detail, and more argument (about this and other evolutionary topics), in my review.

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