SciAm Blog Network revamp plus List of 2014 “best of” lists, Part I

Big changes at the Scientific American Blog Network

Revamping the Scientific American Blog Network is quite a big deal. As Knight Science Journalism Tracker Paul Raeburn reports, SciAm is eliminating about half the bloggers in the network and instituting a new editorial guidelines policy that foretells much more editorial oversight for bloggers.

Which leads DrugMonkey to observe, “So… maybe don’t pretend to have blogs? Just call them columns like you used to?

Worth pondering. Is this the beginning of the end of blogging as, in Dave Winer’s classic definition, “the unedited voice of a person?” SciAm’s quite reasonable rationale is that it’s a news outlet and so its standards must differ. Does that mean we can expect that blogs (at least blogs associated with Serious Publications) will, inevitably, turn into columns? What about, for example, the New York Times? I don’t know it for a fact, but I strongly suspect that the Times does not edit Andy Revkin or the undeniably controversial Paul Krugman.

New guidelines for SciAm blogging

The new guidelines give SciAm editors what Raeburn calls “significant control” over blog content. As announced, the way this will be done is a little confusing. Staff blogs will be edited in the usual way staff contributions are edited. But posts from nonstaff bloggers, Raeburn reports, will not be edited in advance. OTOH they can be yanked after the fact. Bloggers are instructed to stick to their areas of expertise and to consult with editors if they don’t, especially if the planned post will be controversial.

Which of course raises the question of what’s controversial. This is a point Paige Brown Jarreau makes in her extended analysis at From The Lab Bench. (Highly recommended for reasons discussed below.) Controversy is very much in the eye of the beholder. A comment that seems to a blogger to be both obviously true and innocuous can stimulate a barrage of enraged (and sometimes organized) tweets.

At The Finch & Pea, Josh Witten mourns the loss of friends’ gigs. Of the guidelines he says, “The new “Blog Network Guidelines” are strict, and appear specifically geared to preventing controversies like a blog posting racist and sexist arguments.”

Raeburn quotes the (relatively new) SciAm Blog Czar Curtis Brainard as saying “there will be more internal communication and coordination around upcoming content . . .” One interpretation of that comment is that bloggers will be encouraged to write on particular themes at particular times, and those themes might relate to articles in the magazine(s). Depending on the topic and the approach, that need not necessarily turn blogs into marketing tools. But it’s also a possible slippery slope.

Who’s going and who’s staying?

Jarreau did a detailed analysis of blogs going and staying in an attempt to figure out how SciAm is hoping to shape its reorganized blog network. As she points out, a  substantial number of the eliminated blogs published posts infrequently. That’s as good a reason as any to show a blogger the door. Surely one of the points of blogging is repeat business, trying to build an audience that will return often to see what’s up. That regularity is the lifeblood of a publication that wants advertisers.

But as Jarreau points out, infrequent posting is not characteristic of all the dismissed bloggers. Her comments on the ex-blogs that were updated frequently:

“It’s interesting that of these blogs being cut, several deal with ‘inside science/academia’ topics, science communication and culture of science and journalism. I don’t see such topics represented much in the blogs staying on the network, other than Danielle Lee’s superb blog, which often deals with women in science and diversity in science issues. Perhaps this is a matter of cutting more of the blogs that counted other scientists, graduate students and science writers among their primary audience, as opposed to broader and more explanatory science communication?”

Her other observation about about these blogs: “Most of the blogs being cut for it would seem reasons other than posting frequency, are written by women.”

Black and white. The Cocos fire in San Diego County, May 15, 2014. Credit: DigitalGlobe

Black and white. The Cocos fire in San Diego County, May 15, 2014. Credit: DigitalGlobe

But of the blogs that are staying she says, “[T]here is still a good mixture of both male and female blog authors, career scientists and career writers/communicators. The topic areas represented seem to be quite ‘popular’ for lay readers of science. Interestingly, several bloggers who have recently been irregular in posting frequency are staying on the network.”

Matt Shipman also blogged about the SciAm Blog Network developments at Communication Breakdown. The post includes a brief Q&A with SciAm’s Brainard.

A bit of irony: Both Shipman’s and Jarreau’s blogs are part of the SciLogs Blog Network, and Jarreau is also the Czar of that network–although she says she edits none of the posts. SciLogs is “associated”–not clear quite what that means–with Nature.com, part of Nature Publishing. Which also owns Scientific American.

There are many hundreds of science blogs, perhaps thousands of them. But science blogging is still something of a small world.

List of best of top ten science lists, 2014. Part I

We used to be able to rely on Charlie Petit at the Knight Science Journalism Tracker for an incredible amount of research in putting together his lists of the year-end “Best of lists” relating to science. But, sob, Charlie was retired last summer in the (coming) reorganization at MIT’s Knight Science Journalism program. So I’m all on my own, but be assured that I’m not putting nearly as much work into it as Charlie did.

So, for this last post of 2014, I’ve culled (pretty randomly) a selection of the various science-attuned “best of” lists. This is Part I. There will be more such lists in the coming weeks, and I’ll cover a selection of them in Part II next year.

List of Lists 2014: Top Science Stories

Speaking of Scientific American, first on its Top Ten science stories list was Ebola, of course. So many others were covering–and overcovering–Ebola that I decided not to pursue it here at On Science Blogs. But you could read about some of SciAm’s Top Ten here too:  Rosetta’s comet-hunt and successful (if short-lived) touchdown on a comet, the BICEP2 proof-of-the universe’s inflation-or-maybe-not, the atrocious handling of dangerous microbes at government labs, and the shell our remote ancestor Homo erectus possibly maybe  etched in an abstract crisscross pattern half a million years ago.

Several of those topics were on the Science News top stories list too, but they selected 25.  (These appear to be free to read.) Ebola was #1 here too, but also selected were Rosetta and the comet, an ancient human DNA roundup, and dusty BICEP2.

List of Lists 2014: Physics

Jennifer Ouellette, proprietor of the SciAm blog Cocktail Party Physics, has compiled a couple of physics lists. Best 20 physics papers of 2014 included some that were, she says, just appealingly silly, and I don’t know whether that’s how she characterizes her #3 choice, Schrödinger’s Picture, or not. See her post for an explanation.

Jennifer Ouellette's #3 physics paper was Schrödinger's Picture. Credit: Gabriela Barreto

Jennifer Ouellette’s #3 physics paper was Schrödinger’s Picture. Credit: Gabriela Barreto

The biggest physics story of the year, she says, is still the BICEP2 announcement that it had direct evidence of the universe’s inflation, despite the subsequent assertions that what they had seen was just . . . dust.

She also selected 20 videos, ranging from #1, 3-D fractals, mind-blowing even in black and white, to the evolution of the universe (inexplicably at #20.) #12, watching ice melt, reminded me of nothing so much as the light shows of, gulp, 40 years ago. Which you’re probably too young to remember.

List of lists 2014: Neuroscience and mental health

Thomas Insel is director of the National Institute of Mental Health, and his blog is one of the finest around, certainly the finest “official” blog I know of. I assume he doesn’t write it himself, in which case laurels to the science writer(s) who do. Swell job. Useful, informative, clear. If he does do the writing, apologies for my doubts, and I am stunned.

This post sums up the top mental health stories of the year. Examples: the rise of optogenetics as a terrific tool for brain investigations, discovery of rare genetic variants in autism and common genetic variants in schizophrenia, and the deeply distressing problem of failure to replicate some 70% of preclinical studies. The main problem is not misconduct, he says. “Lack of rigor in experimental design or data analysis appears to be a much more important factor, along with the complexity of behavioral and biological research.”

List of lists 2014: Science books

At the Guardian, Grrl Scientist throws herself into Best Books Lists, with separate posts on biology, physical science and math, nature, and even bird books, birds being her area of expertise. A sampling: The Sixth Extinction (the Elizabeth Kolbert book about the present and the future that’s on everybody’s Best list this year, even the non-science lists); Neanderthal Man, Svante Pääbo’s memoir of how he invented the study of ancient DNA, which I reviewed over at the Genetic Literacy Project. Also Christine Kenneally’s The Invisible History of the Human Race, which I also reviewed and didn’t like as much as everybody else did.

As you might expect, Wired‘s best science books list has a tech slant. It starts off, however, with Being Mortal, Atul Gawande’s meditation on how badly we manage the end of life, which I suppose can be viewed as anti-tech. But it also includes Faster, Higher, Stronger, in which Mark McClusky checks out how sports medicine is building better humans, and Geek Sublime, by Vikram Chandra, which my spouse got for our daughter and I am frantically trying to find time to finish before she gets here and takes it away.

You can listen to Science Friday’s best books list, discussed by Deborah Blum (soon to be of the Knight Science Journalism program) and Annalee Newitz (always at io9), along with host Ira Flatow. Or you can read the list at the same site. It includes Being Mortal and Invisible History, but also several books not duplicated on other lists.

Also on the list is The Martian, one of those fairy-tale publishing stories that fill tormented writers with anguish. And hope. First a self-published ebook, then picked up by a trade publisher, and soon to be a Major Motion Picture directed by Ridley Scott and starring Matt Damon. Merry Christmas, author Andy Weir! Also Happy New Year!

List of Lists 2014:Graphics

At Wired, Betsy Mason has pulled together her annual lists of stunning science graphics. Starting off with images of our world from WorldView-3, a satellite with the highest resolution of any commercial satellite, launched early this year by Digital Globe. (Example: the San Diego fire, above.)

A butter daisy (Melampodium divaricatum) magnified 2X. Credit: Oleksandr Holovachov

A butter daisy (Melampodium divaricatum) magnified 2X. Credit: Oleksandr Holovachov

That’s the big picture, but she also assembled the magnificent microscopy winners from the Olympus BioScapes Digital Imaging competition. First prize winner was a video, not a still, reporting development of a fruit fly embryo over 24 hours. In its mobile black-and-whiteness, it reminded me of the fractals video I mentioned above.

And of course, Nature’s list of videos of the 10 cutest animals–although they cheated by including robots: one disguised as a baby penguin and another video of self-assembling robots. A brilliant marketing strategy, capturing media and remarkably benign Twitter attention. No trolls here. Some scathing denigration on science writer listservs, but my hunch is that Nature regarded this experiment in in showing that Science Can Be Cute as a singular success. I can’t wait to see what they come up with next year.

List of Lists 2014: Miscellany

At io9, Robbie Gonzalez departs from the annual tradition of annual-ness and promotes a new National Geographic book about 5 covers in the magazine’s history and the stories behind them.

The eyes of Sharbat Gula, from the cover of the June 1985 issue of National Geographic. Credit: Steve McCurry

The eyes of Sharbat Gula, from the cover of the June 1985 issue of National Geographic. Credit: Steve McCurry

DrugMonkey did his annual year-end summation, selecting a post from each month of the past year and quoting the first sentence.  DrugMonkey is a very satisfying blogger, but I gotta say he does not write a great lede. Still, it’s given me an idea for a post that I may pursue next year. We’ll see.

Speaking of next year, I’m taking off the next couple of weeks and will be back on Friday, January 9, 2015. Happy New Year!

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TORTURE

The science of torture

The Senate Intelligence Committee report on its years-long investigation of the Central Intelligence Agency’s immoral torture-based interrogation methods says the CIA got no information that stopped terror attacks. Which is not surprising. Scientists have been telling us for a long time that torture is a lousy way to get people to tell you the things you want to know.

“The scientific community has never established that coercive interrogation methods are an effective means of obtaining reliable intelligence information.” Martin Robbins leads off his indignant post at The Lay Scientist with this quote from a 2006 report of the Intelligence Science Board, formed to give scientific advice to US intelligence services. The Board was abolished in 2010, ostensibly for the sake of efficiency and the budget. I can’t help wondering if it was dumped because it told intelligence agencies–a misnomer if ever there was one–things they didn’t want to hear. Such as: torture doesn’t work.

In 2005, the Colombian artist Francisco Botero unveiled a series of over 80 paintings and drawings which depicted stylized renditions of the prisoner abuse by American military guards at Abu Ghraib prison in Iraq. Photos had come to light in 2004.

In 2005, the Colombian artist Francisco Botero unveiled a series of over 80 paintings and drawings which depicted stylized renditions of the prisoner abuse by American military guards at Abu Ghraib prison in Iraq. Photos had come to light in 2004.

The idea that torture is effective is deeply ingrained, surely at least in part because pop culture fictions tell us so. Robbins points out that there’s even a TV trope called Torture Always Works, summarized as: torture is an instant source of 100% reliable information. I never watched 24, but I gather it was built around that trope. I am watching Homeland, which takes the moral issues with torture more seriously. Quinn really hates torturing people, just hates it. He suffers almost as much as the torturee. Still, he does it, because it’s the only way to, you know, Prevent Explosion of the Ticking Time Bomb.

Robbins also notes that the techniques torturers employ, like pain and sleep deprivation, are if anything counterproductive because they are almost guaranteed to interfere with memory. At SciAm’s Observations, Joshua Krisch expands on that point, arguing that, when torture subjects lie, the lie may not even be intentional. It’s a product of torture’s effects on the brain and memory.

Krisch links to links to past SciAm articles on torture. He also links to documents claiming that CIA interrogation techniques were not really torture and that the information gleaned thereby saved countless lives. (Note that this vindication site has a .com domain name, not .gov.)

The Senate report took many years to put together and is said to be 6000 pages long. We’ll probably never know because we’ll probably never see it. What the Intelligence Committee finally released on Tuesday may be the longest Executive Summary on record, 525 pages. A PDF can be had a number of places, for example CNN.

Many of the Botero works were fantasies, not based on things known to have happened at Abu Ghraib. This one wasn't a fantasy. It's waterboarding.

Many of the Botero works were fantasies, not based on things known to have happened at Abu Ghraib. This one wasn’t a fantasy. It’s waterboarding.

Psychological torture

The CIA itself knows torture does not work–or at least it knew that, and said so, before 9/11, according to Robbins. So how and why did this horrid stuff happen?

At Mind Hacks, Vaughan Bell explains, under a hed that says it all in brief: Snake Oil salesmen selling torture. The salesmen were two former Air Force psychologists, James Mitchell and Bruce Jessen, whose previous experience with interrogation techniques consisted of trying to train soldiers to resist them. They secured a generous long-term contract to run the CIA’s interrogations program and even collected $81 million before it was cancelled in 2009.

The Mitchell-Jessen program was based on a misunderstanding (willful?) of the concept of “learned helplessness.” The concept was developed by psychologist Martin Seligman, who found that subjecting dogs to repeated electrical shocks that they can’t escape eventually makes them passive; they hunker down and just take it. (Seligman is distraught over this distortion of his work and has said so emphatically, according to Jesse Singal at Science of Us.)

Mitchell and Jessen theorized that prisoners forced into this passive state would be more cooperative. “This, to be frank, is just bizarre. The theory predicts the opposite would happen and this is, rather grimly, exactly what occurred,” Bell says. He also notes that the report says CIA staff, including staff psychologists, argued repeatedly against the Mitchell-Jessen approach, but were overruled.

So the interesting question is why these two bozos were put in charge and backed up  so strongly even in the face of reasonable criticism. The new report does not appear to have answered that question. And neither, really, does the 2009 NY Times piece that chronicled the rise and fall of Mitchell and Jessen. (The fall came via the newly elected President Obama, who shut the CIA interrogation program down.) The Times piece says the two were persuasive, especially Mitchell. Is that really all it was? That the CIA needed an interrogation program and these two turned up and said, “Yeah, we’ll do it. Scientifically.”

No fantasy in this drawing either. Dogs were used to threaten prisoners at Abu Ghraib.

No fantasy in this drawing either. Dogs were used to threaten prisoners at Abu Ghraib.

What does work?

Establishing rapport.

Psychologist Wray Herbert, at the Huffington Post, describes the work of the High Value Detainee Interrogation Group, which has been conducting field and lab studies on effective interrogation techniques.

It has supported psychologist Laurence Alison of the University of Liverpool, who described what he does at The Conversation. “In our own work, based on hundreds of hours of observation of field interviews, we found that interrogators that used approaches more akin to methods used in therapy were more effective at both decreasing detainee disengagement (including “no comment” interviews) and eliciting useful information and evidence,” he says. Alison notes that these methods are nothing new, are widely used by law enforcement too, and are backed by studies showing that rapport-based methods also work in clinical settings, such as addiction treatment.

Posts at the British Psychological Society’s site describe individual research projects that back up this point. One retrospective study of techniques employed by interrogators from several countries with suspected terrorists found that rapport-based techniques generated far more information than coercive ones.

Even some TV writers have gotten that message. You can now occasionally see a cop show where the interrogator–often a woman, fancy that–brings the prisoner a soda, sympathizes with his problems, lays off the accusatory mode, and gradually draws out useful information. It’s lots less dramatic than torture and threats and doesn’t feed our involuntary desire to see the bad guys tormented for their badness. But maybe it’s the start of a pop culture lesson on how to get people to tell you what you want to know.

Coda

Having excoriated psychologists for participating in this evil and pointless practice, let us turn briefly to the medical profession.The report is searchable, and so bioethicist Craig Klugman searched it for terms like doctor, physician, medical etc. He tells us at the Bioethics.net Blog that physicians agreed to be involved with torture–administering torture, judging whether “detainees” were healthy enough for torture, designing interrogation, and failure to report it–despite the fact that these things are forbidden by medical ethics and explicitly by medical professional associations.

Klugman is dismayed that his fellow bioethicists have not spoken out strongly against torture, which he argues is wrong by the standards of nearly all schools of ethics. Because torture does not yield reliable information, he says, even utilitarians should be outraged.

Finally, I urge you to read Michael Hare’s post “On doing bad things, being a bad person, making a living, and having a voice” at The Reality-Based Community. It is only tangentially about the CIA report and involves science hardly at all except for mention of William Shockley’s racial opinions. But it is exceptionally sane and enjoyable withal, and I got the idea of using the Boteros as illustrations here from him.

Exhibits of these Botero works, some scatological and explicit in other ways, have drawn disapproving comments. See http://goo.gl/wZn9rk, http://goo.gl/E0lFsv, http://goo.gl/ez9jvV

Exhibits of these Botero works, some scatological and explicit in other ways, have drawn disapproving comments. See http://goo.gl/wZn9rk, http://goo.gl/E0lFsv, http://goo.gl/ez9jvV
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Artistic Homo erectus, boozing began 10mya, gay genes, KSJ Tracker & HealthNewsReview

 

Homo erectus, the Jackson Pollock of her/his day?

You may be tempted to regard that find of a shell from the Pacific island of Java–supposedly engraved by our ancestor  Homo erectus half a million years ago–as a scientific blunder or maybe even a hoax. After all, everybody knows that the first artists, the only artists, were us, Homo sapiens sapiens, the anatomically modern humans that only evolved a couple of hundred thousand years ago in Africa.

I advise caution with your skepticism and snark. The paper reporting this analysis has been getting a generally respectful reception along with the usual few doubts. Among those being respectful is John Hawks, the University of Wisconsin paleontologist and pioneer science blogger, who helped make blogging respectable for scientists. “The authors considered many alternative scenarios and convincingly show that the design was created deliberately by early humans,” he says.

Detail of the engraving on fossil mussel shell  from Java. Credit: Wim Lustenhouwer, VU University Amsterdam

Detail of the engraving on fossil mussel shell from Java. Credit: Wim Lustenhouwer, VU University Amsterdam

 

Furthermore, seems it’s definitely not a hoax, mischief worked a century ago by one of discoverer Eugene Dubois’ bored  assistants on his lunch hour. According to Michael Balter at ScienceInsider, the marks are not like the sharp and jaggedy fresh edges carved on shells experimentally by the researchers. The edges of the engravings are softened and weathered, signs of burial in Javanese sediment for hundreds of thousands of years. In fact, the ancient date was derived by analyzing those sediments trapped in the shells.

OTOH, Balter quotes Russell Ciochon, a paleoanthropologist at the University of Iowa, arguing that both the Homo fossils and the shells were washed into the site by a flood, so it’s not at all clear they were associated in real life. Dubois’ famous H. erectus skullcap was found with a thigh bone that some think is H. sap, not erectus. Maybe, Ciochon speculates, one of us passed by hundreds of thousands of years later and marked the shell.

That’s not impossible, I guess, but it doesn’t account for the fact that the engraved shell is one of 166 remnants of a now-extinct freshwater mussel–and one-third of those shells had been punctured at precisely the point that would sever the muscle holding the shells closed. Given the dates of the sediments in the shells, it’s more plausible to think that our forebear H. erectus used a small pointed object, perhaps a shark’s tooth, to get mussels for dinner. A shark’s tooth might have been the engraving tool, too.

Inside of the fossil mussel shell showing that the hole made by Homo erectus is exactly at the spot where the mussel's muscle attaches the upper and lower shells.  Credit: Henk Caspers, Naturalis, Leiden, The Netherlands

Inside of the fossil mussel shell showing that the hole made by Homo erectus is exactly at the spot where the mussel’s muscle attaches the upper and lower shells.
Credit: Henk Caspers, Naturalis, Leiden, The Netherlands

We’ll probably never know what the ancient engraver was up to. The “M” shape on the shell impresses because it’s so precise. But the other markings look far more random. Maybe this early artist was just . . . doodling? The Hawks post discusses this idea and other examples of early possible proto-artwork. Turns out, in fact, that some examples are even older than this one.

The story of how that engraved shell was discovered is almost as enthralling as the idea that artistic inclinations were stirring in early members of the genus Homo half a million years ago. The shells were unearthed by Eugene Dubois 123 years ago as part of the dig in Java where Dubois found the type specimen of H. erectus–a find that has overshadowed everything else about that legendary dig. For more than a century the shells lay unexamined in a Netherlands museum until a grad student named Stephen Munro, who was studying ancient mollusks, found the engraved shell. Munro told Balter, “I almost fell off my chair.”

Munro is probably only the first in a parade of grad students who will now comb through long-neglected museum collections in hopes of finding a dissertation topic and, perhaps, a reputation and a job. Hawks says that the most important thing about this find is that it’s probably not unique. He’s optimistic about the prospects for finding more very early doodles artwork, declaring confidently, “It is not going to be the last Homo erectus intentionally marked artifact.”

 

Alcohol consumption in our primate forebears

Formerly the experts thought the human love affair with alcohol began only 10,000 years ago, with the advent of agriculture. Now it appears that this complicated relationship– associated with so much pleasure and pain and good health and death and friendship and bar fights–actually dates back more than 10 million years. It was a gift, or curse, from the primate ancestors of chimps, gorillas, and us.

One of my favorite science bloggers, Faye Flam (late of the Philadelphia Inquirer and Philly.com, now blogging at Forbes) portrays drinking as the outcome of a war between plants and the creatures that must consume them to live. Plants started making toxic substances like alcohols as a strategy to avoid being eaten. Animals started making chemicals that could detoxify those substances so they could go on eating.

Alcohol dehydrogenases are a group of animal enzymes that break down alcohols in plants. The researchers found that about 10 million years ago our primate ancestors evolved a form of alcohol dehydrogenase, ADH4, that could metabolize ethanol, a common form of alcohol and the one that’s (now) drinkable.

The researchers say this occurred around the time primates began to descend from their treed life to walk the earth as a result of ecosystem changes that had begun transforming forests into grasslands, according to Eliza Barclay at The Salt. Expanding their diets from fresh ripe fruit collected while still on the trees to include fallen fruits added nutrition. But if the fruit had started to ferment, it included a bit of alcohol too.

Credit: Elke Wetzig (Elya)

Credit: Elke Wetzig (Elya)

One theory about alcoholism and other ills related to consuming ethanol is that–like diabetes and chronic cardiovascular disease–it’s one more manifestation of how our evolution hasn’t caught up with our lifestyles. That theory grew out of archaeological evidence that alcohol consumption began with agriculture. Beer and wine are ways of storing surplus fruit and grain, and give pleasure in their consumption. The researchers observe, “any organism with metabolic adaptations that permit the exploitation of ethanolic food would have access to a specialized niche or important fallback foods unavailable to organisms without this metabolic capacity.”

The researchers say that the small amounts of alcohol in fermenting fruit is “a source of ethanol that is remarkably similar in concentration and form (i.e., with food) to the moderate ethanol consumption now recognized to be healthy for many humans.” That suggests that maybe we are adapted to at least the small relaxing amounts found in the new rule of 1 drink a day for women and 2 for men.

The problems began when toolmaking Homo saps developed technology for fermenting larger amounts of fruits and grains into larger amounts of ethanol–and then drank the larger amounts. That problem was much compounded when distillation was invented less than a thousand years ago.

 

Here come those gay genes, maybe

The paper about gay genes from a couple weeks ago was of particular interest  because it confirmed a much-disputed finding from the 1990s that DNA related to at least some kinds of male homosexuality lies on the X chromosome. The paper employed linkage analysis, a methodology now all but abandoned in favor of genome-wide association studies (GWAS). GWAS are much more useful because they can home in on particular genes, not just areas of DNA that can contain hundreds of genes.

The researchers used linkage analysis because they were trying to replicate Dean Hamer’s heavily-disputed findings in the 1993 paper, which used linkage analysis. They are doing another study, using an even bigger sample than the recent paper, and it will be a GWAS.

I did a post about this paper last week for the Genetic Literacy Project, and that’s the place to find details. But a point I want to emphasize here is that, if there are genes influencing male homosexuality, or subsets of male homosexuality, the new GWAS study stands a good chance of finding them. At Gene Expression, blogger Razib Khan is confident, predicting “[A]at some point in the next ten years I’m pretty sure we’ll localize the genes which carry variants which do result in a higher than typical likelihood of an individual exhibiting homosexual orientation.”

Note, however, that this work has nothing to say about the potential for genetic influences on lesbians or bisexuals. Researchers have given those topics hardly any attention at all. Wonder why . . .

 

Gary Schwitzer and HealthNewsReview.org are baaaaack!

This great news is what the sole remaining Knight Science Journalism Tracker Paul Raeburn is reporting. Schwitzer has new funding and says he will add staff and resurrect reviews of medical journalism, which historically have been unsparing. All medical journalists take note. You are Being Watched.  %^)

Also this month, a much sadder reminder: the Tracker will disappear. For a history of this wrenching news, see my On Science Blogs posts here and also here. Raeburn tells me in an email that his contract is up December 31, and he expects his last post will appear around then. %^(

But don’t lose hope. No news yet from the Knight Science Journalism folks about their future plans for a Tracker-like project. However, from Raeburn’s email (quoted with permission): “But you might not be rid of me yet. I’m exploring opportunities elsewhere to continue what I’ve been doing at the Tracker. ” %^)

I will, of course, keep you informed.

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Updates: Comet landing, #shirtstorm, virus moratorium, Jonah Lehrer

For today, bringing you up to date on a few past posts.

Adieu, Philae. Or is it au ‘voir?

In our last episode, the plucky little lander Philae was finally on the surface of  Comet 67P/Churyumov–Gerasimenko. But Philae wasn’t getting enough sun, so its solar battery was running out. European Space Agency scientists to the rescue! Could they move Philae into the sunlight in time for its several-week mission to continue?

No.

Philae died.

The End.

Or, long shot, maybe not. There’s a literal ray of hope. It’s possible that the comet’s position as it nears the sun (its closest approach is next August) will move Philae out of the shade and its battery will recharge. Stay tuned.

Philae lander photographed from mother ship Rosetta as it falls toward the comet. Credit: ESA/Rosetta/MPS for OSIRIS Team MPS/UPD/LAM/IAA/SSO/INTA/UPM/DASP/IDA. From the Science slide show.

Philae lander photographed from mother ship Rosetta as it falls toward the comet. Credit: ESA/Rosetta/MPS for OSIRIS Team MPS/UPD/LAM/IAA/SSO/INTA/UPM/DASP/IDA. From the Science slide show.

Clara Moskowitz’s SciAm post is a nice summary of our necessary mixed feelings about Philae’s traumatic landing on Comet 67P/Churyumov–Gerasimenko: sorrow that the little lander ended up in a shady place where its solar battery gave out and put an end to its mission, joy that the Rosetta mission did, in fact, put a lander on a comet. Pretty unlikely, really. A triumph, even.

Bad astronomer Phil Plait rhapsodizes a bit–justifiably–about human successes in space, pretty damn marvelous when you remember that we’ve only been flying for a century or so. “We’ve sent our spacecraft to every major body in the solar system, and quite a few minor ones besides. We’ve continuously occupied space for years, and we’ve launched observatories into orbit that examine the Universe in every wavelength regime of the electromagnetic spectrum. And we’ve done even more: We’ve set down on other worlds.” All this in a few decades, less than a human lifetime.

 

Doing science on a comet

During its brief lifetime, Philae did manage some science. It detected organic molecules. That might be a big deal because one of the theories about the origin of life on Earth is that it was triggered by organics delivered here by comets. But George Dvorsky at io9 says organics are not a big deal, or at least not yet, because the European Space Agency hasn’t released information on just which organics.

Amino acids could be a very big deal. Methane, not so much, even though it can be produced by living creatures. Organics, as it happens, are abundant in the universe.

Scientists gathered lots of other data too, in the couple of days when Philae’s battery was still functioning. Those data will take months to analyze, according to Eric Hand at ScienceInsider, and Rosetta will continue to orbit the comet for another year.  Science also has an open-access slide show of its favorite photos of the landing process.

 

Final Frontier Miscellany

It’s nice that Rhett Allain at Dot Physics has enough time on his hands to figure out how big Comet 67P/Churyumov–Gerasimenko is in relation to other big things. For example, if you laid the six 725 meter-long concourses at the Atlanta airport end to end, they would be about the length of the comet. Looks like quite a bumpy surface too, so a long uncomfortable walk, even with a spinner bag.

A Brit consortium wants to go back to the moon and has launched a Kickstarter campaign to pay for the project.

 

Conspiracy Theory about the comet mission

The conspiracy theorists at the Breitbart site are alleging that Philae could have survived to do its work except for those !@#$%^&*! environmentalists. “[G]reen lobbyists were behind moves to bar rocket scientists from using nuclear energy to power the device forcing scientists to rely on solar power instead.”

It seems possible that this is not just right-wing nutcase babble but that nuclear power for a spacecraft is a question for reasonable debate. See, for example, the brief post by Ethan Siegel at Starts with a Bang and his longer argument at Medium about why the ESA scientists should have used Plutonium-238 to power Philae.

I await some journalist(s) to explain the arguments pro and con.

 

The #shirtstorm

I can’t leave this topic without a brief mention of the #shirtstorm over the garment that ESA project scientist Matt Taylor was wearing, and the comment he made, when he appeared at a press conference to talk about the Philae landing. His inevitable later apology seemed sincere, and I have no reason to think that the episode wasn’t misogyny but rather largely a manifestation of clumsy, clueless geekery. I wish deeply that one of his colleagues had had the wit to say, “Hey, Matt, I’d wear a different shirt if I were you,” and I expect he does too, now. Maybe they are all clueless geeks.

The shirt. Credit: Phil Price

The shirt. Credit: Phil Price

I won’t recap because several others have done so. A selection: Phil Price at Statistical Modeling, Causal Inference, and Social Science, an odd-sounding repository for this screed; Janet Stemwedel at Doing Good Science; the anonymous physicist at Skulls in the Stars.

What these critiques argue is that the shirt and comment are just another small expression of the idea that the point of women is their orfices, and that science is a boys’ club, No Girls Allowed. Isis the Scientist sums it up: “So, the issue isn’t that it’s one shirt. It’s that as a woman scientist, I see the equivalent of that shirt numerous times a day.”

I know that’s true, but it seems to me unnecessarily parochial. Women in other professions–indeed, women of every age and occupation–can tell similar stories. If you’re in science, of course you want to fix the problem in science. But I don’t want us to forget that this is not a problem just for women in science. It is a problem for women (and, worse, for girls.)

The Skulls post recounts the usual particularly appalling eruptions on Twitter, directed at a (female) friend of the blogger who tweeted an objection to the shirt. “Since being targeted, my Female Friend has received thousands of insulting tweets and emails.  Her personal information was released online — a process known as doxxing — and the messages included death threats.  Don’t believe me?  As of today — nearly a week after the landing — people are still attacking her.” If you want proof, he provides it, quoting tweet after noxious tweet. “Trigger warning: lots of nastiness here, a true snapshot of depravity.”

 

Update on the virus research moratorium

Late last month, I posted here at On Science Blogs about the White House’s moratorium on disease virus research involving making the virus more virulent or infective.

On Monday Jocelyn Kaiser reported at ScienceInsider that the moratorium is affecting virus research at 14 institutions. Lots of detail.  At Shots, Nell Greenfieldboyce has a post recounting the particular problems of a MERS researcher.

Screenshot of NIAID stop work order, via Science.

Screenshot of NIAID stop work order, via Science.

The re-Return of Jonah Lehrer

Are you surprised? I’m not. Disgraced science writer Jonah Lehrer has yet another book deal, this one a collaboration with UCLA behavioral economist Shlomo Benartzi. At New York Magazine, Katie Zavadski tells us that it is to be “a Lehrer-esque pop science self-help book focusing on increasing productivity online — at least according to its product description on Amazon.”

Lehrer’s doings and undoings have been recounted in several posts here at On Science Blogs. Most of them appeared when the blog was still on the site of the National Association of Science Writers, before PLOS invited me to become part of the PLOS Blog Network. You can find a list here. It’s a long, juicy story. To science writers, at least. Possibly inside baseball for the rest of you.

When last heard from, Lehrer was supposed to be writing a book about, gasp, Love. Zavadski reports that Simon & Schuster says it has a draft of the love book but no pub date yet.

There’s been next to no blogging about this more recent book development, and that is a bit of a surprise. Razib Khan has a rambling post at Gene Expression urging Lehrer to take up a different line of work and let some other science writer have a chance. Dream on.

 

Thank-you note

Next week I will be taking Friday off to continue giving thanks, and among the things I’m thankful for is readers of On Science Blogs. Much obliged to you all. Next post, Friday December 4. Good grief, December already.

 

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The good news, maybe: Landing on a comet. The bad news, maybe: Supremes vs. Obamacare

 

START HERE for the quite wonderful story of landing on a comet..  And when you get there, click PREV to continue (in reverse chronological order) seeing xkcd’s live comicking of the Philae lander’s arrival on Comet 67P/Churyumov-Gerasimenko (67P/C-P for short).

The first image of the lander on the comet's surface, a  two-image panorama taken by the Philae lander. Credit: European Space Agency

The first image of the lander on the comet’s surface, a two-image panorama taken by the Philae lander. Credit: European Space Agency

For background on the European Space Agency’s 20-year Rosetta mission to land on a comet, see previous posts at On Science Blogs here and also here. Several bloggers have been regularly updating this week’s actual landing, although as I write things have gotten a bit sticky. First, the horse’s mouth: ESA’s Rosetta blog.

John Timmer at Ars Technica on Philae’s post-landing state–exact locale uncertain, and in shadow, with perhaps not enough solar power to keep its battery going beyond 60 hours. Here’s the Ars Technica home page, which will have the latest.

At io9, George Dvorsky has details about how the uncertain landing spot will complicate Philae’s mission. It’s still sending good data to Rosetta from its onboard instruments, but it’s not clear if it will be able to do chemical analyses of the surface as planned.

At ScienceInsider, Eric Hand is updating and live blogging from Rosetta mission control in Germany. Jacob Aron has been doing that too, and Creativist is carrying his New Scientist posts and stories, open access. Of course Phil Plait is writing updates at Bad Astronomy.

VOX is selecting photos for magnificent display, nothing like the tiny snippets posted here. Here’s Day 1. And here’s Day 2.  Caleb Scharf at Life, Unbounded explains why the Rosetta mission is time travel back 4.57 billion years.

Dan Satterfield, who blogs at the American Geophysical Union, loved Rachel Maddow’s MSNBC explanation of why Philae’s landing was so scary.  EarthSky is one of the places where you can hear Comet 67P/Churyumov-Gerasimenko’s “song.”

The snafus are a bit of a downer, to be sure. Still, what with the Middle East, and Ukraine, and the economic picture, and the election, and glaciers melting, and the future of health insurance (see below) etc., etc., etc., it’s cheering to be reminded, as Josh Witten observed at The Finch and the Pea, “No matter what else we might be, we are a species that landed a robot on a comet about 500 million kilometers away for the purpose of scientific exploration. Not too shabby.”

 

The fate of Obamacare

Also at Vox, Joseph Sternberg notes that the Rosetta mission has cost 1.4 billion euros ($1.74 billion). He finds that cost, spread over a couple of decades, compares favorably with a number of other expensive recent projects. For example, it’s about 47 percent of what was spent on the 2014 US midterm elections ($3.67 billion).

Which brings us to the terrifyingly uncertain topic of Obamacare (aka ACA).

First, the guesses about what the new Republican majorities in both houses of Congress will do, or try to do.  At Covering Health, the blog at the Association of Health Care Journalists, Joanne Kenen says there will be attempts at repeal, but they will fail. The House will vote overwhelmingly for repeal, but even with the new Republican majority in the Senate, there won’t be enough votes there–60 are needed–to overcome a filibuster. And in any case, Obama would veto a repeal.

But certain features of Obamacare might be voted away.  For example, the medical device tax, which helps fund patient subsidies. The Republicans might also try to repeal the employer mandate requiring that businesses with more than 50 full-time employees offer affordable health insurance coverage. Kenen mentions other possibilities too, and includes links explaining the possible consequences.

She points out that at this stage no one knows whether the Republicans will be merely confrontational or whether some changes to the law that Obama might accept could be negotiated.

 

Enter the Supreme Court

Another possibility is that Congress will wait to see what the Supreme Court does, a ruling that is expected in June.

And the Supreme Court is where the real terror lies. A week ago, at least four of the Justices unexpectedly agreed to hear a weird challenge to the ACA. If they rule in favor of the challengers, the decision would possibly, or maybe probably, destroy  Obamacare. That’s because it would kill off most of the federal subsidies that make it possible for poorer people to buy health insurance.

A Rosetta mission poster showing the deployment of the Philae lander to comet 67P/Churyumov–Gerasimenko. The image of the comet was taken with the navigation camera on Rosetta. Credit: ESA/Rosetta/NavCam

A Rosetta mission poster showing the deployment of the Philae lander to comet 67P/Churyumov–Gerasimenko. The image of the comet was taken with the navigation camera on Rosetta. Credit: ESA/Rosetta/NavCam

The argument in the case, usually called King v. Burwell but sometimes referred to as Halbig, is a bit technical and intricate. It’s based on sloppy wording in the ACA law that makes it possible to say–although not with an entirely straight face–that only people who buy insurance through the few state insurance exchanges, not the numerous federal insurance exchanges, are entitled to apply for those subsidies.

That would mean only people who bought insurance in the 15 states that established their own exchanges could qualify for subsidies. Such a ruling would immediately snatch away the subsidies that have made it possible for 5 million previously uninsured people to buy health insurance.

Even though it’s completely clear that Congress always intended subsidies to be available to everybody everywhere.

Even though the Internal Revenue Service has issued a regulation declaring that anyone who bought insurance through either state or federal exchanges is eligible.

 

The politics of destroying Obamacare

In a series of tweets amounting to a Twitter Essay, Grist’s David Roberts observes: “The Halbig argument, in my mind, marks the point at which the right finally & completely embraced postmodernism. . . It’s like pointing to an apple and saying, “this is an orange.” It takes practice to train your mind to be able to do it. . . Halbig is endpoint of that process: arguing that a law says something that literally everyone involved knows it doesn’t.. . . In this way every dispute, even over matters of fact, becomes a contest of power — loudest, best funded, most persistent voices win.”

Grist has reprinted the entire essay. A stunning political analysis, highly recommended.

Under the headline Obamacare Is Doomed! Everybody Panic!, at Slate Barry Friedman and Dahlia Lithwick consider the Court’s decision to take case and conclude that it is not inevitable that the justices will rule against the ACA. At a Stanford Law School blog, Hank Greely agrees that panic is not the correct response. He recommends “concern and righteous anger.” But he’s not hopeful about the outcome for the ACA.

I gotta say that it’s hard to cling to any shred of hope that Obamacare will survive after Linda Greenhouse’s demoralizing take at the New York Times. I’ve been reading Greenhouse on the Supremes for decades, and I’ve never known her to say things like this:

“This is a naked power grab by conservative justices who two years ago just missed killing the Affordable Care Act in its cradle, before it fully took effect.”

And this, “There is simply no way to describe what the court did last Friday as a neutral act.”

And this, “It bears repeating that what’s at stake is whether the Affordable Care Act can continue on its successful trajectory or whether it will collapse into the “death spiral” it was structured to avoid.”

And, finally, “[The case's] arrival on the Supreme Court’s docket is also profoundly depressing. In decades of court-watching, I have struggled — sometimes it has seemed against all odds — to maintain the belief that the Supreme Court really is a court and not just a collection of politicians in robes. This past week, I’ve found myself struggling against the impulse to say two words: I surrender.”

Oy.

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Election: marijuana, climate change, abortion, Obamacare, soda tax, GMOs

 

Still going to pot

The Republicans won big last Tuesday. But so did marijuana.  Here’s a summary, from Conor Friedersdorf at The Atlantic:

“Oregon and Alaska just became the third and fourth states to legalize the drug. Washington, D.C., voted for legalization, as did the city of South Portland, Maine. The island territory of Guam chose to allow medicinal marijuana. And while Florida voters defeated a constitutional amendment legalizing medicinal weed, it required 60 percent support to pass and received roughly 58 percent of the vote. A healthy majority in the state want medical cannabis to be legal.”

Credit: MarkBuckawicki

Credit: MarkBuckawicki

I have said here before that the push to legalize is one of the most consequential social developments around–especially in light of how little is known about marijuana’s effects, therapeutic and otherwise. This should be a very big research priority, but I’ve seen few signs of that happening.

The National Institutes of Health is in a tough position here. It can’t easily launch a lot more pot research when federal laws are agin it. As a result of new state laws around the country, the pot industry will get richer and mount even more serious lobbying efforts. The federal government will grow even less enthusiastic about enforcing the laws against marijuana, as a practical matter ceding decisions about law enforcement (if any) to the states. And if the federal laws are not enforced, there won’t be much pressure to get rid of them.

It looks to me as if it will be many years before we have a handle on what marijuana is good for and where its bodily dangers lie. Meanwhile, a vast experiment has been launched by the citizenry on the citizenry. Life being what it is, some bad things are going to happen that might have been prevented if we knew more.

 

The environment, climate change, and money

Environmental issues figured big in this election and enormous amounts of money were invested in attempts to influence the outcomes. Advocates of doing something about climate change spent, at a minimum, an estimated $85 million, according to John Light at Grist. Most of that ($50 million plus) came from Tom Steyer. Light doesn’t think green groups got much for their money. That’s partly because, although voters in general care about the environment, it’s not at the top of their priorities as a pocketbook issue. Yet.

Dot Earth’s Andy Revkin argues that to compare the efforts of one side against the other is to set up a false equivalence. “The Koch brothers and their allies want to maintain the status quo, while Steyer and others seeking a political path to a post-carbon economy have an epic challenge in trying to prod Americans out of a fossil-fueled comfort zone that took a century to form.”

More bad news for the environment is likely to come from Congress. The Keystone Pipeline has lots of friends there. At Observations, the SciAm editors’ blog, Joshua A. Krisch notes that the new chairman of the Senate Environment and Public Works Committee, which oversees the Environmental Protection Agency’s budget, will be the notable climate-change denier James Inhofe.

Because the Republicans gained a majority in the US Senate in the election, come January they will occupy the chairs of each Senate committee. ScienceInsider has a complete list of likely incoming chairs of committees that affect science.

Also at ScienceInsider, David Shultz summarized the results from other science-related initiatives on state ballots. In Michigan, for example, they voted down permission to hunt wolves.

 

Health matters in the 2014 mid-term elections

At Kaiser Health News, Phil Galewitz says that wins for Republican governors in Florida, Georgia, Wisconsin, Maine and Kansas is bad news for Medicaid expansion in those states.

Here’s the Kaiser summary (with links to other pieces) of what might possibly perhaps maybe happen to Obamacare (aka ACA). The calls for repeal have grown fainter, but changes (so far not firmly delineated) seem likely. And here’s the Kaiser summary (with links to other pieces) on other health-related election results.

Also at Kaiser, Julie Rovner summarized results on an assortment of health matters in various states. Voters in North Dakota and Colorado “rejected so-called ‘personhood’ amendments that would have recognized rights for unborn fetuses.” In Tennessee, however, voters essentially overturned a state court decision loosening restrictions on abortion.

 

Department of somewhat fuzzy extended election metaphors

At Out There, Corey Powell takes off from Stephen Hawking’s ideas about the eventual collapse of the universe to conclude that the biggest challenge of American politics is not, as so many would have it, entrenched ideology. Instead, he says, the problem is the opposite of ideology. It is “excessive volatility, as voters change their minds too quickly in response to shifting circumstances, and in response to inputs that are too small or inconclusive. Great insights do not emerge that way.”

Greg Laden has a long, peculiar post-election analysis using one of the Harry Potter books as an extended metaphor for describing US political parties. It wasn’t worth my time to figure out what he was getting at, but if you have nothing else on today, you may want to pursue it.

 

Food matters in the 2014 mid-term elections

Some of those election results were about food, and optimist Marion Nestle tells us at Food Politics that there was plenty of good news for the food movement. (Food movement? Given what happens to food after it’s eaten, that’s a curious and somewhat off-putting name choice for diverse political aims. But never mind.)

Credit: pic_p_ter

Credit: pic_p_ter

In Berkeley, 75% of voters agreed to tax soda. In San Francisco a soda tax was not passed even though a majority of voters approved it; passage required two-thirds of them. Initiatives to require foods containing genetically modified ingredients to be labeled as such were voted down in Oregon and Colorado. Nestle says industry spent $60 million in these campaigns.

Grist’s Nathanael Johnson also analyzed election results related to food and farming and promises more detailed analyses in the weeks to come. He has followed up with a meditation on why the GMO labeling efforts keep failing. There are a number of reasons, definitely including the amount of money industry spent fighting labeling. But “The main problem with the anti-GMO crusade is that it picks one very limited issue out of the whole constellation of agricultural practices. And when clear-eyed people see the big picture, they often conclude that there are much more important issues to address.”

Johnson says a big change could come with mandatory labeling, which he thinks may happen in Vermont. People will see the labeling so much that they’ll just ignore it. I agree, and wrote a SciAm blog post last year urging the industry to embrace labeling voluntarily for exactly that reason.

Here’s my plan: Get people used to the idea of GM ingredients by first labeling a beloved and ubiquitous food. A perfect choice is corn chips, which is pretty much 100% GM. And don’t be shy. Make a virtue of necessity. We’re turning a lemon into lemonade here. Slap a great big proud label on the chips. Make the label convey something like this message, maybe in red letters: GM [BRAND NAME HERE] CORN CHIPS—MADE WITH DELICIOUS NUTRITIOUS GENETICALLY MODIFIED CORN!!!

A prospective boutique corn chip maker who sees this as an opportunity to get rich selling non-GM corn chips will likely be frustrated. First, finding corn that hasn’t been genetically modified is going to be really really hard. Nearly all of today’s corn is a GMO. Also, non-GM chips will inevitably cost more.

Meantime, millions of corn chip devotees are not going to deprive themselves, and they’re not going to want to pay a lot more either. Before long, I foresee, they will sink happily back into their couches with their family-size bags of crunchy, salty, tasty, less expensive GM-labeled corn chips. Yum.
Credit: Glane23

Credit: Glane23
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Population Explosion 2.0, perfect writing software, model organism sex, tardiness

 

Son of The Population Explosion?

It matters hardly at all what is done to control population growth. If Homo sap‘s birth and death rates remain more or less as they are, we will grow from 7 billion plus today to number 12 billion people by the end of this century, according to a semi-terrifying new model of population growth just published in the Proceedings of the National Academy of Sciences.

Writing at Science Insider, Jennie Dusheck reports that the Australian researchers who developed the model ran 10 different population-growth scenarios–fiddling with changes in mortality, life span, family size, and a mother’s age at first birth, and the results were much the same. Even collision with an asteroid or other catastrophes that kill as many as half a billion people would reduce 2100 population size only to about 10 billion instead of 12, Dusheck says.

At io9, George Dvorsky says that even two billion deaths in mid-century would leave the planet with 1.5 billion more people in 2100 than we have now. Another way of keeping the population at 7 or 8 billion, Dusheck notes, would be to eliminate all unwanted pregnancies, accounting today for about 16% of live births, or instituting the drastic one-child policy. Good luck with that.

I know, I know, it’s only a model. But still.

 

For writing readers

When I encounter them, I usually read (and am illuminated by) pieces by Edward Mendelson, an authority–indeed, the authority–on W.H. Auden. Mendelson writes not only for the New York Review of Books but also PC Magazine, and is an acquaintance from the early days of personal computers. We were part of  a User Group in New York City that met to provide mutual tech support (or in my case to receive same) for the much-beloved long-gone writing software XyWrite.

Mendelson has a recent post on NYRBlog about another piece of cult writing software, the DOS version of WordPerfect, which dates to before the turn of the century. Mendelson contrasts WP with the program we all love to hate but must use because our editors do, Microsoft Word.

Word, he says, is “almost always wrong as an instrument for writing prose.” This we all know, but he also calls it a work of genius, the embodiment of the Platonic idea of writing form. I won’t spoil the delightful analogy for you by paraphrase; go read it. The point for writers, though, is that DOS WordPerfect, not a work of genius, is far more accommodating to how writing is done.

It’s possible to run DOS WordPerfect in Windows, even the 64-bit kind. As essentially a public service, Mendelson maintains a site telling you, among other things, how to do it. I toyed with this temptation briefly but soon abandoned the fantasy that I might–at last–connect with the perfect writing program. I lost heart and got more realistic about software perfection after two days spent wrestling (to no purpose) with two Windows programs.

You may be made of sterner stuff.

 

Sex in model organisms

Last May the National Institutes of Health announced a new policy requiring researchers to even up the sex ratio in experiments with model animals, nearly always done on males only. I wrote about the new rules here at On Science Blogs at the time. Now Scicurious has explored the problems in more detail.

She emphasizes a pretty crucial clarification of the rules. They do not mean, as some have apparently thought, that researchers must investigate sex differences they turn up the the course of the research. “Instead, they just have to establish whether the sexes respond differently to a particular experiment,” she says. Some researchers, though, say that’s not good science.

minnie mouse n mickey

A big concern is the additional costs the new policy will impose. NIH has said it will provide a $10 million supplement to cover the new expenses, but some believe that’s nowhere near enough.

One commenter to GenomeWeb’s summary of the Scicurious post argued that the new rules would give results much greater clinical utility. “Reminds me of the whining people did when Title IX passed. Embrace the complexity!

 

I’m late, I’m late.

Apologies for this tardy brief post. Exigency. I believe that–except for the occasional holiday–this is the first Friday morning I’ve missed since I began On Science Blogs in 2009. I’ll have to look up the exact date, but I think the 5 year anniversary is near upon us.

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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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