Do AA and other 12-step programs work? Does breastfeeding raise IQ?

Do 12-step programs for addiction treatment work?

Are 12-step programs like Alcoholics Anonymous and Narcotics Anonymous effective treatments for addiction? That long-time dispute has just popped up again, prompted mostly by an Atlantic article with the click-worthy title “The Irrationality of Alcoholics Anonymous.”

Gabrielle Glaser’s central argument is that there are other addiction therapies that work, but the 12-step programs are just not based on science. It’s a reasonable point historically. For one thing, many 12-step studies have tended to ignore a crucial problem in research design: selection bias. It’s reasonable to think that people in AA, NA, etc joined because they were especially motivated to quit. Members are probably not a random sample of addicts.

alcoholics anonymous

But Jesse Singal’s riposte to Glaser at Science of Us argues semi-persuasively that there may be recent data showing that 12-step programs can be effective.

Glaser emphasized the equivocal nature of the science collected in the 2006 meta-analysis in a Cochrane review, which found “no experimental studies unequivocally demonstrated the effectiveness of AA or [12-step] approaches for reducing alcohol dependence or problems.” Singal seems to interpret that as saying the programs were not effective, but of course that isn’t what the Cochrane folks said (or, it appears, what Glaser was saying either.)  They said effectiveness had yet to be demonstrated. The quality of previous studies was often questionable, and it was also hard to compare them.

New evidence that AA works?

Singal quotes doc John Kelly thus: “There’s quite a bit of evidence now, actually, that’s shown that AA works.” Kelly is an addiction specialist at Mass General and Harvard Med and one of the authors of  a new Cochrane review to be published in August.

But the Singal post has problems too. It does not, for instance, take up drug therapies for addiction: methadone, naltrexone, etc. That leaves me in the dark about their effectiveness. I gather that 12-step programs in general don’t approve in principle of substituting one drug for another and so don’t want their participants to be using “therapeutic” drugs.

In talking about the newly revealed success rate, Kelly seems to be emphasizing research not on 12-steps themselves but on 12-step facilitation programs. Acronymed TSF, these programs sound something like prep courses for AA. Kelly claims these (plus a 12-step) have been shown to have up to a 20% advantage over one alternative treatment, cognitive behavioral therapy.

The lead author of the 2006 Cochrane Review, Stanford doc Keith Humphreys, will also be an author on the upcoming revisionist paper. He posted on his updated views about a strengthened scientific basis for AA etc last June at WonkBlog. This post, however, also was about the effectiveness of TSF, not 12-step programs by themselves with no introductory TSF boot camp.

Are 12-step facilitation programs the new AA?

But since TSF programs are not themselves regular 12-step sessions, I find these claims confusing. Is TSF a new, improved AA? Can measuring the effects of TSF plus a 12-step sojurn legitimately serve as what the clinical trials folk call “surrogate endpoints?” Is a TSF required for 12-step success, or does it simply increase the success rate? (Or, of course, neither, but both Kelly and Humphreys appear to rule that out.)

What Humphreys concludes is that TSF followed by 12-step participation is as effective as any other professional therapy. That may be good news, but it is also not an evaluation of the plain old AA, NA, etc. that millions of hopeful recoverers count on.

Also, a not unimportant point: the TSF pre-interventions require a therapist. Classic TSF is a three-month program. Humphreys also praises a mini-TSF, a “brief, structured introduction to AA,” without defining “brief.” A three-month stint run by a therapist will cost at least several hundred dollars, and even a brief one will cost something.

Contrast that with the ubiquitous–nearby and frequent–12-step sessions, which are free. Although you are supposed to contribute for the coffee. You can’t beat that for accessibility.

Glaser points out that the question of what works has taken on new urgency because Obamacare requires insurers and Medicaid to pay for substance abuse treatment. I wonder if that fact might help speed up reliable efficacy research. It would be nice to spend that money on stuff that works. Patients trying to get clean would probably prefer that too. Most of them.

Or, assuming that it turns out there is good evidence that 12-step programs can work, with or without TSF prep sessions, is it possible to do a better job of moving that information into physicians’ offices? Not to mention their brains? Along with the data on other approaches like cognitive behavior therapy and meds?

We are, we are being told, entering the age of Personalized Medicine. Surely time to lay out the smorgasbord of addiction therapies with attached price tags and data on what works.

Does breastfeeding increase adult intelligence and income?

The media loved the idea that breastfeeding improves intelligence. And, even better, that a breastfed baby earns more in adulthood. Who wouldn’t?

There have been other studies saying breastfeeding raises IQ (and some that say not). The New England Journal of Medicine‘s JWatch has made its past comments on these studies available free. But this new study, from Brazil and published in The Lancet, attracted so much attention because it went on for more than 30 years, which made it seem particularly persuasive.

Even venues where one might expect critical consideration reported with little analysis. The New York Times health blog Well, for instance. Vox’s Julia Belluz, an unusually skeptical eye, was pretty accepting of the Brazil study too. (Although a few days later she was writing about why you shouldn’t believe what you hear about exciting new medical studies, a series of cautionary tales for journos if there ever was one.)

There is much to praise in this ambitious long-term study. Spare a thought just for the amount of work involved over decades. At the Guardian’s Brain Flapping blog, Dean Burnett’s critical take begins with praise: “It’s a well-designed study which tries to take into account as many variable and confounding factors that could distort the results as possible.” Burnett’s critique leans heavily on the fact that IQ was measured with the always-controversial Wechsler Adult Intelligence Scale.

He also wonders how this widely-praised study will increase the already heavy pressure on new mothers to breastfeed. This concern he bolstered with personal experience: his wife’s breastfeeding instructor, a health care worker, vilified women who considered formula feeding.

What’s wrong with the Brazil study of breastfeeding and intelligence?

Adrienne LaFrance based her Atlantic criticism largely on details of the study–especially that so many of the study subjects enrolled in 1982–5914 of them–were, as population researchers say, “lost to follow-up.” After 30 years, only 3493 were still available. That’s perhaps understandable in such a long-term study, but it does raise questions about the data’s validity.

She points out other difficulties too. Accounts of breastfeeding practices were collected years after the births, and were based on self-reports by the mothers. Self-reports are intrinsically subject to question.

“And even if breastfed babies really do grow up to have higher IQs and make more money, how do we know it’s because they were breastfed?” LaFrance asks. Although social class differences in breastfeeding practices seem to be less important in Brazil than in many other countries, it still is the case that nursing mothers tend to be better off and more educated than mothers who don’t (or can’t) breastfeed.


There were other reported adult differences between those breastfed as babies and those who were not. The researchers compared babies who were breastfed for a month or less with those who were breastfed for a year or more. The differences were statistically significant, but not enormous. The income difference amounted to a little over $100 per month at today’s exchange rate, and as with IQ can perhaps be explained by other advantages in the breastfed. Breastfed children stayed in school longer, but less than a year longer. Also, IQ differences amounted to less than 4 points on average.

LaFrance concludes, “And though breastfeeding may play a role in how a kid turns out, 30 years of parenting surely has more to do with what kind of adult a baby becomes.”

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Apple Watch ResearchKit ethics, NYT flubs cellphone risks, scientists urge halt to human genome work

An Apple all day keeps the doctors monitoring you 24/7

I wasn’t paying much attention to the miasma emanating from last week’s Apple presentation, which seemed to consist entirely of The Watch and its astonishing pricing. So the news about Apple’s ResearchKit came to me in an uncommon way: in an office visit with my cardiologist, who is quite excited about the app’s clinical research possibilities.

He’s not the only one; there’s real giddiness about extracting Big Clinical Data 24/7 from people whose digital devices are their constant companions, all but surgically implanted. Theral Timpson of Mendelspod summed it up thus, “It’s an all out open source platform for medical research that has open science folks drooling.”


I guess ResearchKit is the logical endpoint of FitBit and other manifestations of the mania for self-monitoring. ResearchKit will pull health data (with permission, Apple hastened to assure us) from people’s iPhones, Apple Watches, and maybe other devices, and deposit it with research projects. It’s open source, so at Wired Marcus Woo says it could be available eventually for non-iThings, but no firm word on that yet.

Woo quotes researchers as saying the fact that there are millions of iPhone users will rule out selection bias in the studies, but also points out that Apple device users are on the whole young, white  and Asian, and affluent. He notes, “Not exactly representative.”

ResearchKit is already around in 5 pre-Watch apps available for the iPhone, so if you’re eager to be a research subject, you don’t have to wait until April. At Stanford Medicine, one of Apple’s A-list collaborators in ResearchKit, Becky Bach blogged at Scope that they were pretty darn excited about MyHeart Counts.  Alan Yeung, MD, an app architect and medical director of the Stanford Cardiovascular Health Department, rhapsodized about the potential for a million downloads, for doing much larger population studies than in the past, and also for significant improvement of data accuracy because it’s being gathered automagically.

On March 18, Scope’s Kris Newby reported proudly that nearly 28,000 people had consented already to provide their data to the MyHeart Counts study on cardiovascular health.

Seems to me ResearchKit might also lower the cost of research. Or maybe I mean it will shift the cost, of data collection at least, to research subjects. MyHeart Counts is at least a free app, but to participate in the research people will have to buy expensive devices like iPhones and Apple Watches and also pay carriers to provide service in perpetuity to send the data to researchers. I concede that the purchases will permit them also to make phone calls, text, do Facebook, play Sudoku, set an alarm, check their stocks, etc. But still.

The other four apps already in existence include mPower, a diagnostic tool for Parkinson’s disease that uses the iPhone touch screen to measure hand tremors and the mic to assess voice tremors. Plus apps for research on asthma, diabetes, and breast-cancer treatment recovery.

Bioethics and ResearchKit

The most extensive take on the research ethics issues that ResearchKit poses comes from an unexpected (to me) source: The Verge. Arielle Duhaime-Ross is concerned, for one thing, about participation by minors without parental consent. She reports that she was able to lie about her age to the Asthma Health app. This apparently is also possible with mPower and the breast cancer app Share the Journey.

The post also explores the obvious issues of privacy and confidentiality. Apple proclaims proudly that it will not see your data, but keeping data anonymous will also be a challenge for the research projects that receive it. One of the researchers admits to Duhaime-Ross up front that there’s no guarantee that a research subject couldn’t be outed.

The blog is concerned enough about ResearchKit’s bioethical aspects to have posted a link to a Time piece that suggests ethical issues may arise beyond the obvious privacy and confidentiality concerns. For example, will richer institutions be able to attract patients away from trials that might make sense for them but have less funding and can’t provide an app?

At Ars Technica, Jonathan Gitlin thinks the Food and Drug Administration may have something to say about ResearchKit too, although no such potential barrier was mentioned during the Apple festivities launching it. Not every mobile health app is a candidate for regulation, he says, but FDA does have oversight of diagnostic devices, and apps like mPower are offering diagnosis. (And, it strikes me, mPower and its ilk could be a godsend to hypochondriacal obsessives, who will keep pushing the touch screen in search of tremors.)


The International New York Times wonders whether an Apple all day will bring doctors to stay

Not often you see a New York Times piece on science and medicine so thoroughly trashed as the one whose original (and, thanks to intervention by the NYT science department, short-lived) hed read: “Could Wearable Computers Be as Harmful as Cigarettes?”

The science-and-medicine blogosphere roared “NO!”, including the Times‘s own Public Editor Margaret Sullivan (who may, btw, be the best NYT Public Editor ever. She bravely and consistently cuts her employer not much slack.)

The many problems with the piece may well be traceable to the fact that it appeared in the Disruptions blog/column, which runs in the Style section. These departmental divisions are irrelevant to readers, but my hunch is that they may still prevail, hangovers from the dead-tree days, in the editing process.

Meaning that the column, by technology writer Nick Bilton, simply didn’t get the kind of going-over that would have happened in Science or Health. It appears also that Bilton, who may know all there is to know about Silicon Valley, has little background in the squishy and long-disputed medical subjects he tackled here, chiefly the cellphone-as-potential-health-risk saga.

He added insult to that injury by quoting only the infamous (among health writers) Joseph Mercola. “Why is the New York Times turning to Joseph Mercola as an expert on cancer risk?” thundered Kevin Lomangino at HealthNewsReview, pointing out that Mercola is an alternative medicine doctor who believes cancer is caused by root canals.

At Collide-a-Scape, Keith Kloor characterizes Mercola as “an osteopath who is notorious for his many unsubstantiated medical claims, some of which have drawn a warning from the U.S. Food & Drug Administration.” Orac, at Respectful Ignorance, presents great detail and several links about the colorful health advice career of Joe Mercola.

At Risk Science, Andrew Maynard walks you through the evidence on cellphone risk, concluding that a 2011 report from International Agency for Research on Cancer (a WHO body)  “found tentative evidence that very high use of cell phones might possibly lead to an increase in the relatively rare conditions glioma, and acoustic neuroma.” Not, in short, at all comparable to health risks from cigarettes.

apple watch gold

Maynard then turns to possible danger from the Apple Watch, which was presumably the viral-topic-of-the-moment reason Bilton decided to do his piece. As Maynard points out,  watches are different from phones because they are not held near the brain and they don’t emit high-power radio waves. “In other words, there is exactly nothing about a wrist-based wearable that, from the IARC report, would suggest that it could cause cancer.  Nothing.”


Decision day for designing future humans

Should we tinker with the genes of our descendants? It’s been a debate topic for half a century or more. Always an intriguing question to mull over in the comfortable absence of good ways of doing it.

Now there are good ways. Gene-editing techniques in particular make it possible to modify the next generation’s genomes, and so future generations as well. In any species. Including Homo sap. These techniques, known as germline modification, are (relatively) cheap and simple. In other species they have also been remarkably effective.

So the discussion is, suddenly, theoretical no more. We know that for sure, because lots of scientists are yelling “STOP!” Or at least “Pause!”

The latest shout comes via this week’s Science (March 20). Attention will be paid because the assembled authors are luminaries. Jennifer Doudna, an inventor of CRISPR, one of the gene-editing methodologies that have bumped this formerly hypothetical question to the top of the ToDo list. David Baltimore, Nobel laureate and former president of Cal Tech. George Church, whose Harvard lab is a hotbed of genetic innovation, including germ line gene editing–the editing of genes in sperm, eggs, and early embryos, changes that will be passed on to future generations. Bioethicists R. Alta Charo and Hank Greely.

And several other notables–including, intriguingly, Paul Berg. A Nobel laureate too, Berg was an organizer of the historic 1975 Asilomar conference, which brought together scores of scientists and a few lawyers to draft guidelines for dealing with the (then) brand-new prospect of being able to directly modify genomes. At that point, the potential risks were unknown.

Asilomar is a fine analogy for what scientists are calling for now. Some kind of summit meeting. Some kind of guidelines. Some kind of policy. And, faint hope, some way of making it apply to labs all over the world.

Recalling what Berg said in a 2008 look back at Asilomar reveals what the new paper is about: “[T]here is a lesson in Asilomar for all of science: the best way to respond to concerns created by emerging knowledge or early-stage technologies is for scientists from publicly-funded institutions to find common cause with the wider public about the best way to regulate — as early as possible. Once scientists from corporations begin to dominate the research enterprise, it will simply be too late.”

In this case, though, scientists from private enterprise are also alarmed, writing last week in Nature to urge a research moratorium. I covered that development, and a lot of background on current efforts at human germline genetic engineering, in my weekly post at the Genetic Literacy Project for last Tuesday (March 17). Scientists in China, it is rumored, have already submitted papers reporting success with modifying the germlines of early human embryos.

germ cell gene editing

Gretchen Vogel describes differences between the commentaries in Nature and Science, and names other concerned scientific groups, in what I think is an open-access piece at Science.  She quotes Church on human germ line gene editing, “What is the scenario that we’re actually worried about? That it won’t work well enough? Or that it will work too well?”

Seems pretty obvious to me. Both.


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A century of Einstein’s general #relativity, life on a Saturn moon, sugar industry influences dental research

Everything’s relative

Einstein’s paper on general relativity was published in 1915. The paper didn’t appear until December of that year, but there’s already been some celebratory centennial doings. Science published a special issue last week, and it looks as if the contents are open-access, free to read.

At Last Word on Nothing, Richard Panek wonders whether the fact that one of the more important side effects of general relativity, the idea that gravity distorts space and time, has appeared in two mass-market movies (Interstellar and A Brief History of Time) means that this formerly mind-blowing idea is today widely accepted. Is it a ho-hum factlet now part of mainstream human thought? Or do many of us still need an introduction to space curvature and time dilation?

Einstein's theory of general relativity predicts that massive objects warp the space-time around them. NASA's Gravity Probe B found that the space-time around Earth is indeed curved by our planet, and twisted by its rotation. Credit: NASA

Einstein’s theory of general relativity predicts that massive objects warp the space-time around them. NASA’s Gravity Probe B found that the space-time around Earth is indeed curved by our planet, and twisted by its rotation. Credit: NASA

Speaking strictly for myself (an English lit major who, bizarrely, managed to sneak into grad school to study genetics because it seemed, well, kinda interesting), a physics brush-up never hurts.

Fortunately, one is available from Mike Wall at, who points out that General Relativity was a radical idea that has held up remarkably well under a century of intense scrutiny. Wall notes that scientists are using it today to study black holes, neutron stars and other celestial phenomena. Also “researchers will keep trying to unify general relativity with quantum mechanics, to marry the world of the very large with that of the very small.”

If successful, Wall says, this would produce the “grand and longed-for ‘theory of everything.'” In her centennial take at LiveScience, which describes attempts to get general relativity to break down, Tanya Lewis looks forward to a ToE too.

Life on Enceladus, a giant of a tiny moon?

Now this is cool. Or, rather, warm. Enceladus, one of Saturn’s many moons, is a ball of ice maybe 30 miles thick, but underneath the ice is liquid water. And, a new paper asserts, at the bottom of this ice-encased ocean are hydrothermal vents. And you know what hydrothermal vents could mean. Which is why, of a sudden, Enceladus has become a place to look for life.

The evidence is indirect and even a little weird, inferred from nanoparticles of silica adrift in the space around the moon and detected in Cassini spacecraft images. The particles form one of Saturn’s rings (the E ring), but it appears their source is Enceladus.

The blue "stripes" on Enceladus spew ice particles and minerals that are incorporated into Saturn's E-ring. Credit: Cassini Imaging Team, SSI, JPL, ESA, NASA

The blue “stripes” on Enceladus spew ice particles and minerals that are incorporated into Saturn’s E-ring. Credit: Cassini Imaging Team, SSI, JPL, ESA, NASA

One of the few ways minuscule silica particles just like this can exist is if minerals dissolved in hot water come suddenly into contact with cold water. This causes them to precipitate. Icy geysers shoot up 200 km from Enceladus, and they can blast the particles out into space to eventually encircle the giant gas planet.

The geysers are cold, but the silica nanoparticles couldn’t exist if they weren’t created first in hot water. So, the scientists reason, there must be hot water (at least 90 degrees C.) on icy Enceladus.

Such hydrothermal vents would be colder than most vents on Earth. But there is an Earthly precedent, the cooler Lost City vents in the mid-Atlantic. Lots of life there anyway. Scott Johnson explains the chemistry and geology at Ars Technica.

How can tiny Enceladus, only ~ 250km around, have hot springs? One standard explanation is tidal friction from mighty Saturn, which heaves and squeezes all its dozens of moons, and keeps Enceladus’s ocean liquid. But the researchers told Susanne Dambeck at the SciLogs Lindau blog that they think Saturn’s kneading action isn’t enough to explain the degree of heat that must be present on Enceladus. At Vox, Joseph Stromberg suggests maybe the additional heat comes from radioactive decay of isotopes.

If you want to know more about those plumes of ice and water vapor shooting up from Enceladus, Deepak Dhingra reports on several recent geyser papers at the Planetary Society guest blog.

Sugar, sugar

In 1998, the attorneys general of 46 states settled their lawsuit for recovery of tobacco-related health care costs against the four largest US tobacco companies. The companies agreed to pay more than $200 billion in just the first 25 years, and more in perpetuity.

States handled this windfall stupidly in many cases, mortgaging their shares of future payments to investors for pennies on the dollar and in some cases sticking themselves with billions in future debt, according to ProPublica.

Maybe they’ll have a chance to be smarter next time, with the sugar industry. That’s if dentist Christin Kearns has her way. Kearns is the first author of a paper PLOS Medicine published this week. Drawing on a recently unearthed trove of official documents and memos, the paper shows that, beginning late in the 1960s, the sugar industry influenced the National Institutes of Health’s National Institute of Dental Research to largely ignore the role of sugar in tooth decay.

“The documents reveal a virtual capture of the NIDR by an affected industry,” said Michael F. Jacobson, executive director of the Center for Science in the Public Interest, in a guest post at PLOS’s Speaking of Medicine blog. “The sugar industry convinced the U.S. National Institutes of Health (NIH) that studies that might persuade people to cut back on sugary foods should not be part of a national plan to fight childhood tooth decay,” Jocelyn Kaiser said at ScienceInsider.

This paper, Kearns told Lisa Aliferis at Shots, is only the beginning. There are lots more documents to be discovered, lots more sugar industry tactics to be disclosed. Litigation is “certainly a possibility.” A good possibility, it looks like, since one of her co-authors is Stanton Glantz, the American Legacy Foundation Distinguished Professor of Tobacco Control and head of the Center for Tobacco Control Research and Education at UCSF.

Meantime, the World Health Organization has just officially released its recommendation to eat less sugar, less than 10% of daily calories. Said Marion Nestle at Food Politics, “The last time WHO tried to issue the 10% of calories advice in 2003, it got clobbered by lobbyists. This time, lobbyists didn’t succeed.  This is progress.”

Credit: Rodale News

Credit: Rodale News

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Imperfect science of #TheDress, RIP Leonard Nimoy and Mr. Spock

Devil in a blue dress

See, this is part of the reason why people don’t trust science.  People crave complete explanations for the phenomena of life. Science is frustrating because mostly it can generate only partial explanations for now and offer cautious and ill-defined promissory notes for full illumination in future. No use explaining that accumulating information layer by layer, and discarding some layers as we go, is just the way science works. Not satisfying.

A current example is what Nature called the “Hues and cry” over the true color of that hideous dress. You could hardly avoid hearing the clamor that made its way late last week from Tumbler to Twitter to the MSM at a speed and volume that puzzled even those who study how things become viral.

In a BuzzFeed poll that so far involves well over 3 million people, about one-third of the respondents say the dress is blue with black lace, and two-thirds say white with gold lace.  (BuzzFeed sees things in black and white, asking for no input from the small number of us who say blue with gold lace, or maybe brown lace, and those of us who can, with conscious effort, switch back and forth between blue and white.)

blue white blue dress

The actual dress is a vivid royal blue, both darker and brighter than the paler blue of the original photo, with lots of black lace that makes it darker still. (Also comes in red, pinkish, and, yes, white, although the sales copy calls that one “ivory.” Lace on all of them is black.)

An optical illusion?

The main “scientific” explanation for why people see the color of #TheDress differently is that it’s an optical illusion.

The illusion is said by some blogging authorities to be due to lighting and a cellphone photo that gives no hint of that lighting or other context. The brilliant Randall Munroe, perpetrator of the xkcd webcomic, shows how background color can govern the dress’s apparent color.

At Neurologica, Steven Novello says the illusion is an example of color constancy at work. Our brains evolved to favor consistency over accuracy, in both memory and perception. So the brain uses color and shading correction algorithms to ensure that we “see” an object as the same color no matter the lighting. But the dress photo is also an ambiguous optical illusion, one where the brain is given conflicting information, or there are different ways to resolve the image that are equally valid.

“The photo of the dress just happens to hit the sweet spot of ambiguity in terms of lighting and shading. Different people’s brains will therefore make different assumptions and correct for either apparent overexposure or underexposure,” he says. “This is how our brains work all the time. What we perceive is a constructed illusion, based upon algorithms that make reasonable assumptions about distance, shading, size, movement, and color – but they are assumptions, none-the-less, and sometimes they can be wrong or misleading.”

But how to explain the dramatic lack of agreement about color?

At Mind Hacks, Vaughan Bell doesn’t buy the color constancy theory because it doesn’t really explain why people see different dress colors. “In fact, all of the ‘science explanations’ have simply recounted how perceived colours can change but not the most important thing which is why people are having two stable but contradictory experiences.”

People looking at the XKCD cartoon, he says, don’t markedly disagree about what the perceived colors are. The color effect of each image is very reliable between individuals. That’s not the case with the dress. Also, if the effect was due to context, changing the surroundings of the dress should change the colors. Bell says, “It doesn’t.”

So are we talking about individual differences in color perception, perhaps due to differences in the cones, the eye structures that handle color?  At Vox, Brad Plumer talked to David Williams, director of the Center for Visual Science at the University of Rochester, who doubts it. Except for the color blind, Williams said, “people have remarkably similar visual systems.” His research has shown that, although people vary greatly in numbers of cones, they still tend to see color in the same way.

Williams speculates that the dichotomy in the apparent dress color is due to people making different unconscious assumptions about the illumination of the dress. That’s a vote for the color constancy explanation.

But like Vaughan, Plumer wants to know why people are making these different assumptions. Color constancy doesn’t explain those differences. He speculates that maybe the eye falls randomly on a particular part of the photo, the brain makes a guess at a color, and that decision locks in the perception.

At BuzzFeed, Virginia Hughes talked to John Borghi, a cognitive neuroscientist at Rockefeller University, who told her that people’s perceptions are influenced by their experiences. Maybe people are primed to see a certain color, for example, because of what they looked at just before they looked at the photo. “It could also be that you’ve seen dresses (or fabric) with the same texture or shape before, which could also affect your perception,” he said.

This strikes me as an example of hand-waving, a “then-a-miracle-occurs” moment, as in the old Sidney Harris cartoon. But maybe this vague hypothesizing stage is where we’re at, and why the many versions of the optical illusion explanations don’t really illuminate the central question here.

Which is why (assuming BuzzFeed’s Big Data reflect the true state of affairs) two out of three of us see a (plainly!) blue and black dress as white and gold. To that question, it appears, there is no answer. Yet.

But what I really want to know is this. I have now read dozens of posts, tweets, etc about this topic, and am astonished that nobody, absolutely nobody, has so far seemed to notice this: Whatever its color, this is a truly ugly, tacky, frightful dress.

RIP, Leonard Nimoy

Kind of surprising, the outpouring of affection from geeks and scientists at Leonard Nimoy’s death last week. I hadn’t realized that fondness for the half-human Mr. Spock was more than a pop culture phenomenon. The actor’s portrayal of the logical, dispassionate science officer on Star Trek’s Enterprise was, apparently, an inspiration for many budding scientists (and science writers.)

There’s a string of remembrances from Scientific American and Nature editors here. ScienceInsider wants your comments here. Keith Cowling quotes from NASA tributes and President Obama at NASA Watch. Kendrick Frazier recalls Nimoy and quotes from the actor’s “conversation” with Spock at the American Geophysical Union Blogosphere.

Hank Campbell, at Science 2.0, says he made science cool. At 538’s Data Lab, Ben Casselman notes that, although the original Star Trek’s sexism and racial tokenism was not particularly progressive, its belief in science was. “Unlike the fundamentally anti-technology “Star Wars,” “Star Trek” was driven by a utopian belief in the power of science and technology to eliminate poverty, end war, cure disease and overcome prejudice. Spock, the Enterprise’s tricorder-toting science officer, was the embodiment of that spirit.”

I must say it, of course. Live long and prosper.

nimoy live long

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Cholesterol and coffee ok, plus head transplants soon?


Dietary committee not sweet on sugar

So, what’s most noteworthy about the big fat report just issued by the 2015 Dietary Guidelines Advisory Committee (DGAC)?  The declaration that dietary cholesterol is next to irrelevant? DGAC’s casual endorsement of coffee? Its recommendation to eat much more plant life, much less meat, and hardly any sugar-added food and drink? Its advocacy of a sugar tax?

The DGAC is a non-governmental committee of experts that reviews the scientific literature on nutrition every five years and makes nutrition recommendations to the government. The recommendations may–or may not–be the basis for national food guidelines that are expected from the US Departments of Agriculture and Health and Human Services about a year from now. A lot of background in this Vox post by Julia Belluz.

The scientific literature, the report said, offers little support for the idea that dietary cholesterol is a significant influence on blood cholesterol, the cholesterol important in heart disease. At Forbes, Larry Husten points out that this is a huge about-face, reversing more than half a century’s worth of official preaching that eating eggs and shrimp is bad bad bad.

Fried Egg

DGAC also advised that no more than 10% of daily calories should come from added sugar, and another 10% from saturated fat. Those recommendations got a good deal of press, but just why is a little puzzling. They are actually somewhat more forgiving of the marketing efforts of the meat and sugar-laden industries than past recommendations, which advised no more than 15% of calories from sugar and saturated fat combined.

Still, DGAC was quite tough on sweets in other ways, calling for a tax on sugary food and drink. At the Verge, Jacob Kastrenakes noted that the DGAC even thought a tax alone didn’t go far enough. Also needed are policy “efforts to lower added sugars in beverages and foods and to limit availability of sugar-sweetened beverages and snacks.”

I will be astonished if those ideas are enshrined in the official document next year. Meanwhile, Amanda MacMillan offers 13 ways to give up soda for good at Fox News. Fox News! Her suggestions include tapering off and watering down your Coke®.

What’s wrong with nutrition science

The committee may have done its homework in the literature, but there have been serious questions about the quality of nutrition science for a long time. A central problem is that nearly all of it is based on what people tell researchers about what they eat. At Eat + Run, doc and diet expert Yoni Freedhoff argues, “sometimes something is worse than nothing, in that despite the fact that science knows we can’t trust self-reported dietary recall, the media and public health still latch on to outcomes from flawed self-reported dietary recall studies as if they’re valuable. As a consequence, they draw conclusions and publish guidelines based on faulty data.”

Before you switch to low carbs, he cautions, note that the current recommendations suffer from the same shortcomings. “Trading one set of assumptions built off weak data for another set of assumptions built off weak data doesn’t strike me as all that wise.”

Incidental Economist Aaron Carroll is not so down on nutrition science in general as he is on the dietary guidelines’ past history of ignoring what he regards as good science about the health effects of specific foods. That would be science coming out of randomized clinical trials. For some time, he says, results from those trials have run counter to the conventional wisdom that viewed dietary cholesterol and fats and sodium with alarm and endorsed replacing fats with carbs.

“I understand people’s frustration at the continuing shifts in nutrition recommendations. For decades, they’ve been told what to eat because ‘science says so.’ Unfortunately, that doesn’t appear to be true,” Carroll says. That bad advice not only reduces people’s faith in science, it may have cost some of them their lives.

The so-called American Council on Science and Health, the advocacy organization that cemented its reputation decades ago when it shilled for the tobacco industry, chose not to attack the nutrition recommendations on scientific grounds at this time. Instead it got very huffy about DGAC’s inclusion of sustainability as a criterion for food choices, especially red meat. Not relevant for food recommendations, apparently.

dietary guidelines salad

What are the prospects that the DGAC recommendations will become THE government food recommendations a year from now? David Katz at Eat + Run is hopeful but not optimistic. The meat industry, for one, is sharpening its knives. But Katz isn’t so alarmed about the open protests by self-interested groups as he is about behind-the-scenes lobbying and politicization that will occur over the next year. He concludes, “Sharpened knives on open display may be the least of our worries.”


Off with his head

Reading about the Italian neuroscientist’s nutsy plan to transplant a human head onto a donor body, my first thought was, “He’s off his head.” Bioethicist Art Caplan’s response at Forbes was something similar: “He’s out of his mind.” The plan, Caplan says, is scientifically rotten and ethically lousy.

Helen Thomson, who broke the severed head story at New Scientist, covers the technical details of what would be involved in transplanting a head onto a donor body and Sergio Canavero’s explanations about how he would approach the job.  But despite Canavero’s assurances, Caplan points out, surgeons don’t really know how to rewire the spinal cord. If they did, there would be far fewer paralyzed people.

head transplant

Canavero acknowledges that the project presents ethical problems, and he doesn’t yet know where in the world he might be able to get permission to try his experiment. For Caplan, the major ethical problem stems from the fact that the brain integrates with the body’s chemistry and nervous system. “Would a brain integrate new signals, perceptions, information from a body different from the one it was familiar with? I think the most likely result is insanity or severe mental disability.”

Thomson says Chinese scientist Xiao-Ping Ren, who has already done a head transplant in mice, plans to try Canavero’s protocol in mice and monkeys shortly.

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Epigenome Project, robot ethics, one-way trip to Mars


Here’s the Epigenome Project

The headline on Rachel Feltman’s post at Speaking of Science said the epigenome project was awesome, which is as good an introduction as any. That slew of two dozen papers in Nature and its associated journals described where we are with human epigenomics/epigenetics. (These papers seem to be open access, hosanna.) They were only published Wednesday, so while there are many many many news stories, heavy blogging hasn’t quite kicked in yet.

Explaining the relationship of the genome and the epigenome at a press conference, study coauthor Manolis Kellis of MIT said “All our cells have a copy of the same book [the genome], but they’re all reading different chapters, bookmarking different pages, and highlighting different paragraphs and words.”

The study of epigenetics is about how nurture shapes nature. It seeks to explain how the environment turns genes off and on in particular cells at particular times. The bookmarks Kellis spoke of are biochemical mechanisms that change the behavior of genetic material without changing any DNA sequences.

The two best known and most studied of these mechanisms are DNA methylation and histone modification. In methylation, methyl groups (CH3) stick to DNA and make genes easier or harder to turn on. Histones are the proteins DNA is wrapped tightly around. Their modifications usually involve attachment of an acetyl group (CH3CO.)


For the National Institutes of Health’s Roadmap Epigenomics Program, hundreds of scientists around the world studied epigenetic events in more than 100 types of body tissues, assembling reference epigenomes. These are the epigenetic patterns characteristic of each tissue, information that can be compared to other samples in future.

As Merlin Crossley observed at The Conversation, scientists are finding that mutations don’t usually disrupt genes, they influence how strongly (and when) those genes are expressed. Epigenetics operates as a sort of volume control on genes, but how those controls work is still largely unknown. That’s what the epigenome project is about. The working hypothesis is that variation in disease susceptibility–or any other trait–depends mostly on subtle differences in the expression of genes, which is under epigenetic control.

Here’s robot ethics

“There’s nothing frivolous about it — robot ethics is the most important philosophical issue of our time.” That opinion, from Graham Templeton at ExtremeTech, had me amused but anguished too. The most important issue? Didn’t Graham see a headline now and then? Or even The Daily Show? But I looked into the topic of robot ethics and found that I was seriously behind the times. People have been thinking about the need for robot ethics in its contemporary manifestations for the past few years.

Robot morality discussions have circled mainly around two topics: self-driving cars and automated warfare. Self-driving cars are, of course, supposed to greatly increase road safety. But even if they reduce death and dismemberment dramatically, there will be screwups and–most important from the standpoint of ethics–dilemmas. If an accident is inevitable, should a robocar kill its passengers or a schoolbus full of kids? For a thorough discussion of auto-auto morality, see this post at Wired by Patrick Lin.

Automated warfare, in the form of drones carrying out those “surgical strikes” in the Middle East, has been under the gun for some years now, with no resolution that I’m aware of. On the horizon are many more mechanical horrors of war. See this post (also by Patrick Lin) at the Atlantic.

RI-MAN, designed for human care. Credit: RIKEN, Bio-Mimetic Control Research Center

RI-MAN, designed for human care. Credit: RIKEN, Bio-Mimetic Control Research Center

Asimov’s Three Laws of Robotics (plus another that he added for protecting all of humanity) come inevitably to mind. Are they a good place to start on robot morality? An ArXiv paper from last year discussed at Tech Review argues that our fears of robots are overblown and we don’t even need the Laws. As for automated warfare, that’s not the robots’ doing, it’s the people in charge, and they are already subject to international law.


At io9, George Dvorsky interviews robot and AI experts and concludes that Asimov’s inventiveness can’t protect us from our inventions. For one thing, the Laws are operational forms of rule-based ethics, aka deontology, and rule-based ethical systems just don’t work, according to Louie Helm of the Machine Intelligence Research Institute.

Ben Goertzel, AI theorist, points out to Dvorsky that Asimov devised the Laws and then wrote stories about how they failed. Goertzel concludes, “So the Three Laws were instructive in terms of teaching us how any attempt to legislate ethics in terms of specific rules is bound to fall apart and have various loopholes.”

Here’s Mars One

Mars One, the privately financed project whose announced purpose is to send 4 people on a one-way journey to Mars in the next decade, has winnowed its 200,000-plus applicants down to an even 100, with a couple of dozen the eventual goal. After arriving safely on Mars, the lucky four first colonists are supposed to build a Martian habitat in preparation for more colonists.

Credit: Mars One / Bryan Versteeg

Credit: Mars One / Bryan Versteeg

That’s considerably more ambitious than NASA’s plan, which calls for a human landing on Mars sometime in the 2030s. Well, maybe not really more ambitious, since NASA envisions bringing its voyagers back to Earth.

Why go to Mars? Well, once we’re really ready for the new age of exploration, Mars is a reasonable choice. “Because it’s there,” is good enough for me. Although Dan Van Winkle at the Mary Sue cites a NASA study showing that building cloud cities far above super-hot Venus might in some ways be a more practical goal. Venus is closer than Mars, and temperatures in the upper atmosphere could be manageable.

The cities would consist of solar-powered airships. Oh, the humanity.

Other commentators produce their own justifications for the Mars trip. Aerospace engineer Ashley Dove-Jay’s reason is straight out of Disney’s futurism in WALL-E: we’ve messed up the Earth irretrievably and need to stage a getaway. “If this is where humankind is destined to remain, then we shall find ourselves fighting over whatever is left of it,” he says at The Conversation. Also, space projects are good for global politics, they bring nations together.

Writing at 13.7 Cosmos & Culture, anthropologist Barbara King thinks Mars One may be a chance for humanity’s do-over. She wonders how the colonists will avoid replicating our inequities here on Earth, and draws on the fiction of Kim Stanley Robinson for illumination.

You will not be surprised to learn that there are naysayers like the MIT engineers who say the Mars One project is technically wacko (my interpretation of their courteous conclusions.) The Martians’ locally sourced crops would produce suffocating levels of oxygen, they say, and technologies for wringing water out of that very dry planet don’t yet exist. Also, there’s the problem of getting spare parts.

Furthermore, last year one of the many authorities on Islam, this one based in the United Arab Emirates, issued a fatwa against going to live on Mars. The grounds: Islam forbids suicide.

In his long explainer about what’s required for going to Mars at Starts with a Bang, Ethan Siegel ends up condemning the Mars One project. “I just don’t think hoodwinking and exploiting a bunch of naive explorers, killing them horrifically in short order because you sold them a false promise of what they could’ve achieved, is the way to do it.”

But if Ars Technica’s Sam Machkovech is right, horrific killing may not be outcome at all. In fact, maybe getting to Mars isn’t really the point. The project is endorsed by one of the founders of the reality series Big Brother. The Mars One project, and the leadups to it, are to be financed by a worldwide multiyear TV reality show. To that end, Machkovech points out, the newly winnowed candidate group of 100 “contains some curious choices who seem better suited for reality TV than grueling outer-space missions.”

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Climate modification is insane, chronic fatigue is not insane, those supplement tests might be wrong


Hacking Planet Earth

Blogger responses to the National Academy of Sciences’ two voluminous new reports on geoengineering–the reports want to change that name to “climate intervention,” but what it means is hacking the Earth in hopes of beating back global warming–fall generally into two camps. Some reject geoengineering after thoughtful consideration, and others reject it for being, as one of the report authors said at Slate, “wildly, utterly, howlingly barking mad.”

Department of Thoughtful Consideration Rejection

Tim McDonnell has a temperate overview at Grist. He explains the two main geoengineering proposals, each discussed in a single report: carbon sequestration (pulling carbon from the atmosphere and burying it) and albedo modification (seeding the atmosphere with particles that would reflect sunlight.) Both reports are available as free PDFs.

McDonnell’s summary: “The reports offered a fairly damning critique of geoengineering and found that while there could be value in continuing to research the technology, it will never be a panacea for climate change, and we’re definitely not ready to start using it yet.”

Since I’m fair and balanced, I will quote Eric Worrall, guest posting at the climate “skeptic” site Watts Up With That? He analyzed the reports’ conventional call for more research thus: “The National Academy of Science [sic] has demanded that scientists from disciplines other than climate modelling get a fair turn at the grant trough.”

From the NAS geoengineering rrports

From the NAS geoengineering reports

Geoengineering/climate intervention: the issues

Says John Timmer at Ars Technica: “If carbon removal is expensive but relatively low-risk, albedo modification is its evil twin: cheap but with tremendous risks.”

And both are strategies for dealing with warming after the fact. Neither one addresses the root cause of warming–the buildup of greenhouse gases due to energy-intensive human activity–nor acts to prevent it.

Most viewing with alarm focuses on cheap and relatively easy albedo modification. That might encourage individual actions that the rest of us would be powerless to stop. The fear is that (as David Biello puts it at SciAm’s Observations) “some random billionaire” could underwrite modified jets spewing reflective sulfuric acid that could haze the skies over the Arctic–perhaps as soon as 2020.

Gulp. Brad Plumer does an in-depth job of explaining all this at Vox, although he’s fairly horror-stricken too.


A new label for chronic fatigue syndrome, and perhaps new respectability too

Another controversial report this week, and from the same venue: an arm of the National Academy of Sciences, or maybe a leg: the Institute of Medicine. The 235-page report on what may no longer be called chronic fatigue syndrome is a free PDF too.

IOM wants everybody to acknowledge that chronic fatigue syndrome is a real disease. Chronic fatigue’s sufferers have long languished under the suspicion that it was all in their heads, which meant a dearth of legitimate treatment options. Research into its mysteries and possible causes and cures has languished too, according to Jon Cohen at ScienceInsider.

To that end, IOM wants to change chronic fatigue’s simple, familiar, descriptive name to what seems to me an awkward and obfuscatory and hard-to-remember one: systemic exertion intolerance disease. This relabeling has nothing at all to recommend it, including its uncatchy and unpronounceable acronym. I guess the committee thought a new label would help chronic fatigue to be taken more seriously by the medical profession, especially since the report outlined defining symptoms.

Wrangles over the name, described by David Tuller at Well and Miriam Tucker at Shots, are of long standing. Some patients are said to prefer “myalgic encephalomyelitis” because it anchors CF in bodily manifestations, labeling it as physical and therefore real. But, in addition to being a mouthful, myalgic encephalomyelitis is also an incomplete description of what sufferers suffer.

The report also offered a list of defining symptoms, described by Kris Newby at Scope and elsewhere. They are topped, of course, by “deep fatigue” and much-reduced ability to engage in activities that used to be normal, along with unrefreshing sleep. Symptoms must also get worse after any kind of exertion, including mental stress, and must have persisted for at least 6 months. And the patient must also experience either cognitive impairment or orthostatic intolerance, which you will want to know means the inability to remain upright.



Once more, those herbal supplements with missing herbs

In last week’s post here at On Science Blogs (Feb. 6) I examined the New York State Attorney General’s finding that various store-brand herbal supplements from major retailers–Walmart, Target, GNC, and Walgreen’s–usually lacked the herbs on their labels.

I also mentioned a possible snag: the project used DNA barcoding to look for the herbs, and some critics were saying that DNA barcoding was not the right test to use.

I pursued that point in my regular column for the Genetic Literacy Project, which appeared on Tuesday (Feb 10.) And I regret to report that it’s possible, maybe even likely, that the critics were right.

As a follow-up I consulted Pieter Cohen, a prof at Harvard Medical School and a doc at the Cambridge Health Alliance, who is an outspoken critic of the supplement industry; see his blast on dangerous supplements last year in the New England Journal of Medicine.

Cohen told me in an email that DNA barcoding would probably not find DNA even in perfectly kosher herbal supplements if they involved herbal extracts rather than the herb itself. Making an herbal extract involves heavy processing, and any DNA would likely be destroyed.

DNA barcoding could also explain why the New York project found an array of seemingly extraneous plant matter in the supplements, ranging from rice and wheat to houseplant DNA. Barcoding is super-sensitive, grabbing even small fragments of DNA when they’re present, as they might be in fillers and contaminants. Small amounts of such foreign plant matter are legally permissible in supplements and don’t even have to be listed on the labels, Cohen told me.

What the AG’s office should have done before issuing cease-and-desist orders to the retailers, he said, was to follow up the DNA barcoding with traditional testing methods that detect plant compounds, such as chromatography. That didn’t happen, but you can be damn sure that the supplement industry is doing it.

This news has filled me with dread. If the retailers and supplement makers have right on their side in this case, that will be a huge setback for the forces of supplement virtue, and a huge win for supplement peddlers.

It will also pretty much guarantee that the $13-billion-a-year supplement industry will be able to continue to easily resist any pressure to show that their products are not only safe, but that they actually do what they claim to do.


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Inflationary universe data bites dust, herbs are absent, plus a measles vaccine tale


Nearly fourteen billion years ago expansion started. Wait!

Last March’s claim that the BICEP2 telescope in Antarctica had uncovered proof that the universe had indeed expanded explosively 10-35 seconds after the Big Bang has bitten the dust–the dust that the observations were apparently detecting. The European Space Agency has just made the error official, although word that a new debunking analysis was on the way have been rumored almost since the beginning, as I reported here in May.

Odd, really, that the BICEP2 claims were accepted so immediately and incautiously by other scientists, not to mention the media, as I said at the time. (“Extraordinary claims require extraordinary evidence.” –C. Sagan, 1980.) Bad Astronomer Phil Plait has just apologized for his uncritical reception, which apology I discuss below.

This curlicue pattern in the polarization of the cosmic microwave background radiation from the Big Bang was at first interpreted as confirmation of instant inflation. The dotted lines indicate the region of the southern sky where the BICEP2 observations were made. Credit: ESA/Planck Collab. M.-A. Miville-Deschênes, CNRS, Univ. Paris-XI

This curlicue pattern in the polarization of the cosmic microwave background radiation from the Big Bang was at first interpreted as confirmation of instant inflation. The dotted lines indicate the region of the southern sky where the BICEP2 observations were made. Credit: ESA/Planck Collab. M.-A. Miville-Deschênes, CNRS, Univ. Paris-XI

OTOH, it is crucial, essential, mandatory to understand that the new analysis does NOT show that the inflation idea is wrong, despite some headlines to that effect.   Only that the BICEP2 data didn’t prove it. Inflation theory is still alive and well. At Résonaances, a particle physics blog, Jester describes what’s next.

Mandeep Gill is sympathetic to the BICEP2 team at Quantum Diaries, pointing out that in the paper they published last June, the scientists had already walked back their original claims. “But the B2 observation was totally consistent with all physics we understand currently, and there was no fundamental reason they could not have been right.  Just turns out that interstellar dust apparently can exist with very different properties than we’re accustomed to.” He then added, “At the same time — I will say: if you’re going to go out there and make claims like that, you do have to be prepared for the fallout.”

An embarrassment? Or is this how the best science works?

In a way, the BICEP2 results are yet another cautionary tale about how easy it is to distribute distortions when it’s science by press conference. There are all too many examples. One of my favorites remains how NASA’s invitation to a press conference implied the discovery of extraterrestrials in that Science paper on the arsenic bug (later shown to be, uh, erroneous.)

At 13.7 Cosmos & Culture, physicist Marcelo Gleiser reiterated his belief that public discussion of results should happen only after a paper has been peer-reviewed. That’s what Bad Astronomer Plait seems to think too. When the BICEP2 results were announced last year, he explains, he assumed they had been peer-reviewed. (Why he assumed that I don’t know, but never mind.) “[I]t’s up to the scientists making the claim to make that clear, and to be more circumspect in their announcement … just as it’s up to those of us reporting on big news to be skeptical and make sure that the process of peer review has been fully respected. That’s on me, and I blew it.”

But is conventional peer review a must? At the Crux, Shannon Hall quotes physicist Adam Frank as worrying that the public arguments and revisions about the BICEP2 observations fuel skepticism about science. “If we didn’t live in an age when one of the most important branches of science is being wholly denied by a group in society, then maybe this wouldn’t matter so much,” he said.

However, cosmologists Alan Duffy and Krzysztof Bolejko argue at The Conversation that the publicity enabled many physicists around the world to check BICEP2’s findings, not just the few peer-reviewers selected by a journal. I would add that the publicity may have made the need for confirmation seem more urgent and sped up that analytical process, too.


A decrement of herbs in herbal supplements

It’s bad enough that herbal supplements, exempted from serious Food and Drug Administration oversight since 1994, don’t–can’t–act as advertised to cure your aching joints, your failing heart, your unsatisfactory sex life.

No, it gets worse: The New York State Attorney General’s office has found that, in 4 out of 5 instances, herbal supplements add injury to insult by failing even to contain the useless herbs featured on their labels. The herbs notable for their absence: echinacea, garlic, gingko biloba, ginseng, valerian, St. John’s Wort, and saw palmetto.

Worse still, or maybe better: Deliciously, this revelation makes it impossible for the supplement industry to claim, as usual, that herb chicanery is confined to a few fly-by-night operators. The herb-free herbal supplements were purchased for testing from 4 retail giants: Walgreen’s, Target, WalMart, and GNC. And not just any supplements. No, the stores’ own brands.



Details can be found at Anahad O’Connor’s post at the New York Times health blog Well. It notes that the state investigation was prompted by a 2013 Times article, modestly omitting to mention that the earlier piece was written by O’Connor too.

The one fly in this new! improved! miraculous! ointment is that the testing was done with DNA barcoding. That method looks for specific snippets of DNA known to be present in the genome of a particular species. Some of the tested supplements claimed to be herbal extracts rather than the herb itself. It is possible for an extract to be perfectly kosher and still contain no DNA at all from an extracted plant.

At In the Pipeline, drug researcher Derek Lowe concedes this possibility, but points out that the DNA barcoding did detect DNA from plants used as fillers and contaminants. These should have been, but were not, listed on the supplement labels, even though some of them might cause serious allergic reactions. Contaminants identified included rice, bean, wild carrot, asparagus, wheat, palm tree, radish, citrus, daisy, even the houseplant dracena.

“Tablets or capsules of plant extracts should, by that argument, have no DNA in them at all. They especially should not show evidence of rice, beans, weeds, and houseplants,” Lowe says. He argues that the contaminants are also evidence of sloppy manufacturing, noting the presence of contaminating echinacea and saw palmetto in other tested supplements.

One could hope that these revelations will lead to serious regulation of supplements, akin to the system (itself imperfect) that governs pharmaceuticals. At the very best, however, what might ensue is more ways of ensuring that at least the supplement bottle contains the plant people believe they are buying. Even that is unlikely, though. The $13 billion-per-year supplement industry has an unbroken record of effective lobbying.

What we can be sure will not happen is some way of forcing the supplement industry to show that its extensive varieties of snake oil have anything like the health benefits they claim.


A rash of measles

The rest of the world really discovered measles and the vaccine controversy this week. But I did that topic last week, and what with my short attention span and all just didn’t feel like tackling measles and the anti-vaccine campaign again so soon.

However, Laura Newman’s post at Patient POV is too good to ignore.

gangrene pinky amputation

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SynBio B***********: Genetic recoding. Also, measles goes to Disneyland


An early triumph for the infant synthetic biology?

Do you suppose Science‘s Breakthrough (Arrrrgh!) of the Year for 2015 has already arrived? In January, no less? Via two papers in Nature? Which venue, I suppose, might take it out of the running for being a Science B***********.

These are reports on genetically recoded organisms, GROs, rather than genetically modified organisms, GMOs. In the organisms’  genomes, all instances of a particular codon have been replaced by another.  The amino acid the new codon calls for during protein synthesis is lab-created and does not exist in nature.

The scientists have altered the genetic code of that favorite experimental bacterium, Escherichia coli. These are not just organisms that have never existed before. “We do consider this a new class of organism,” the redoubtable George Church, senior author of one of the papers, told reporters. “It’s not just a new species. In a way it’s a new kingdom.”

“We now have the first example of genome-scale engineering rather than gene editing or genome copying,” Church told Stephanie Dutchen at Phys.Org. “This is the most radically altered genome to date in terms of genome function. We have not only a new code, but also a new amino acid, and the organism is totally dependent on it.”

Genetic recoding is quite a big deal for a number of reasons

First, and this is what media accounts mostly emphasized, it’s the most intriguing, and apparently effective, idea so far for building an escape-proof firewall between genetically modified organisms and the environment. The technique’s virtues have been demonstrated so far only in the lab. But there are giddy speculations about the potential for oil-spill cleanup microbes that could be dismissed from the planet the moment their work was done and, eventually, genetically engineered crops whose foreign genes could not transfer successfully to other plants in the wild.

Credit: Spencer Katz

Credit: Spencer Katz

Also, the bugs can resist infection by viruses. Viruses survive by commandeering a host’s genetic machinery to make their own proteins. But they are stymied by the never-before-encountered genome of the recoded E. coli. This trait might be applied fairly soon to fermentation and other industrial microbiological processes like manufacturing drugs via bacteria, where contaminating viruses can be a serious problem.

At D-brief,  Kari Lydersen said the technique could also provide biotechnologists with built-in intellectual property protection. They could make their own organisms dependent on specific synthetic amino acids. Other companies would have trouble replicating those recoded organisms.

Frankenbug Failsafe Promises Synbio Safety

The technical details of how these miracles are to be accomplished are pretty intricate, which is why most accounts (including this one) leave them out. Take advantage of the explanatory labor of others. See, for example, this post at DNA Science by Ricki Lewis, my colleague here at the PLOS Blog Network. See also this nicely written but unbylined piece from Genetic Engineering News. I stole its alliterative hed for this section. Also consult the ever-reliable John Timmer at Ars Technica and Ian Sample at Guardian Genetics.

The initial stages of recoding experiments were published starting in 2013, and Lewis points out that the approach was considered (and rejected) for Science‘s B*********** of the Year last year. She thinks the idea that GMOs can be made safer will make no difference at all to anti-GMO activists. She’s almost certainly right about that. They talk safety when it suits them, but by and large they aim their vitriol at other targets, like industrial agriculture and global megaconglomerates.

The future of genetic recoding, and of life-as-we-know-it

The researchers’ ideas about the future implications of genetic recoding were not received with universal huzzahs. The Verge quoted Cambridge University plant scientist Alison Smith, who pointed out that complex organisms like plants have a lot more genes than E. coli, and will be much harder to recode. The optimistic speculations about where this work could go, she said, “might be an extrapolation too far.”

There was also skepticism about how much of a failsafe recoding will turn out to be. These cautionary moments were frequently coupled with reference to Jeff Goldblum’s prediction in Jurassic Park: Life finds a way.

Toward the end of Carl Zimmer’s long post at The Loom, he muses briefly about how genetic recoding affects the definition of life. Scientists, he says, have wondered if life-as-we-know-it takes up only a tiny portion of the space of all possible forms of life. Recoded E. coli tell us those speculations are likely true. In just a few years humans have created organisms never before seen–never before possible–on Planet Earth. Yet, he says, within their constricted Universe of artificial amino acids, these inventions are as alive as we are.


It’s a small world when the measles virus is around

A measles epidemic that erupted at Disneyland and is spreading from the Happiest Place on Earth eastward across the US. How irresistible a story is that? The number of confirmed US cases is now creeping toward 100 people, already more than the median annual number for the first decade of this century. Most cases have been linked to Disneyland.


The vaccination status of only a minority of the cases is known. Of those, most of those who caught the disease had never been vaccinated. Some are proclaiming that this is the beginning of the end for the anti-vaccine movement.

Perhaps that will turn out to be true. But, Steven Novella says at Neurologica,  the anti-vaxxers are fighting back, crowing that a number of people infected had been vaccinated. That’s not at all weird. The vaccines don’t seem to work in a small percentage of people.

At Wired, Katie Palmer explains. Take a bunch of people and crowd them together in a confined space with someone who has contracted measles elsewhere. (For example, Disneyland in mid-December.) Statistically, about 90% of them will have been vaccinated, but, also statistically, about 3% of the vaccinated will become infected anyway. Of the 10% who weren’t vaccinated, about 90% will come down with the disease. And of the few who were vaccinated but got infected anyway, many will have quite mild cases.

Steven Novella concludes, “The numbers are very clear. This outbreak would not have occurred at all, or would have been much smaller, were it not for the large numbers of unvaccinated people in the population.”

Novella also notes that the anti-vaxxers dismiss measles as a disease of no consequence. But it certainly can be. Pediatrician Claire McCarthy, blogging at MD Mama, points out that 1 in 10 people with measles will get an ear infection or diarrhea, 1 in 20 will get pneumonia, 1 in 1000 will get encephalitis, which can lead to seizures, deafness, or mental retardation, and 1 or 2 in 1000 will die.

There can be side effects of the vaccine, she acknowledges. One in 6 will get a fever, 1 in 14 will get some temporary pain or stiffness in the joints, 1 in 20 will get a rash, 1 in 75 will get swollen glands. These are all temporary conditions, but there are also more serious, although rare, side effects: 1 in 3000 will get a seizure from a fever, and 1 in 30,000 will have a drop in platelet count, possibly leading to bleeding. Still, McCarthy concludes, “The risks of all of these serious side effects are smaller than the risk of dying of measles.”

Maybe the anti-vaxxers aren’t to blame, exactly?

2014, it turns out, was our worst year for measles in this century so far: 644 cases. Hardly any can be blamed on Disneyland, which didn’t begin until December, and it’s not clear how influential the anti-vaxxers have been. Nearly 60% of last year’s cases were in Ohio, triggered by an Amish farmer who had contracted measles on a visit to the Philippines.

This convoluted tale from Julia Belluz at Vox, who says that only 2% of the population refuses vaccinations outright. The government claims the measles vaccination rate has held steady for a decade at about 92%. She quotes an official of the Centers for Disease Control and Prevention thus, “The people getting measles are those that travel abroad, come back, and live in a community among people who weren’t vaccinated.”

So the reappearance of an exceptionally contagious disease that had all but disappeared from the US is due to a toxic combination of increased foreign travel and the existence of isolated unvaccinated populations.

You don’t need to be part of a religious community to live in one of those isolated populations. A study published last week in Pediatrics showed that geographic clusters of unvaccinated children existed all over the state of California, for instance “a 1.8-mile area in Vallejo, where 22.7 percent of kids were under-vaccinated,” says Liza Gross, who blogged about the study at Shots. You can see how misinformed gossip about vaccines causing autism and suchlike can be passed easily around to parents of kids in neighborhood play groups and nursery schools.

The Ohio Amish do not refuse vaccination as a matter of religious principle. Members of this community have avoided getting vaccinated because, in the 1990s, two Ohio kids got sick, allegedly after the measles vaccine.

Now, Belluz reports, as a result of the 2014 outbreak the Amish seem to be changing their minds. After watching serious measles cases among their friends and relatives, they are getting vaccinated once again.

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State of the Union: precision medicine, the space program, climate change


The state of science and medicine in the State of the Union

As David Malakoff observed at ScienceInsider, science is never the centerpiece of the President’s annual State of the Union speech.  On Tuesday evening, however, science and medicine were sprinkled all through it. At SciAm’s Observations, Dina Fine Maron described in detail the speech’s science-related moments. President Obama strongly defended his climate change policies, and he announced something called the Precision Medicine Initiative.


What is “precision medicine”?

I was mystified about what, precisely, he meant by precision medicine. It wasn’t clear to others either. Maybe he was talking about what is usually called personalized medicine, with diagnosis and treatment based on a patient’s genetic makeup?

That’s what Lenny Bernstein assumed at the Washington Post’s To Your Health. He said it means analyzing the DNA in tumors to figure out what particular drug might work best, or–an example Obama mentioned–using a very specialized drug to treat a tiny genetic subset of people with cystic fibrosis. (Obama didn’t mention just how tiny that subset is: about 4% of CF cases, at most about 1200 patients in the US.)

Personalized medicine is what Julia Belluz assumed at Vox, too. She noted that achieving personalized medicine is much harder than it sounds. That’s an odd way to put it, since scientists know all too well that realizing this medical perfection has been, and will continue to be, very hard indeed.

She’s certainly right that it’s been one of the unmet promises of health care for ages. Jeremy Gruber pointed out at Genetic Watchdog that Bill Clinton said something similar in his 1998 SOTU speech. To be fair, though, Clinton’s aim was funding increases for the National Institutes of Health and the National Science Foundation. He said nothing about personalized medicine.

Under the confident headline “How Obama’s Precision Medicine Initiative Will Revolutionize Healthcare,” io9’s George Dvorsky declared that precision medicine was much more than personalized medicine, which he defined as therapy for a single individual. He said precision medicine uses biological factors to target therapies at specific subgroups. This strikes me as hair-splitting over small semantic differences, since therapies aimed at subgroups are really aimed at individuals in those subgroups. But never mind.

It does appear that Obama’s use of “precision” rather than “personalized” signals a decision by somebody somewhere that “precision medicine” is now the official label. It also appears that I am behind the times. The National Library of Medicine tells me that the term “precision medicine” was first used in 2009 and picked up speed in 2012. Since then more than 250 papers have employed the term in the title or abstract. However, as long as I’m doing medical etymology here, please note that “personalized medicine” first surfaced in a paper title in 1971 and has appeared in a title or abstract more than 4300 times since then. But never mind that, either.

There are challenges for precision medicine, Dvorsky acknowledged: funding, acquiring and analyzing enough data to define subpopulations, and ensuring the confidentiality of sensitive information. “Given the tremendous benefits to be had, it’s a safe bet that we’ll overcome many of these hurdles,” Dvorsky says cheerfully, optimistic as they always are at io9.

From his lips to the Goddess’s ear. But I would be deceiving you if I didn’t add that achieving personalized/precision medicine has been a slow slog so far. A recent piece of mine on how hard it is to identify disease genes in individuals will give you an idea of just how high those hurdles are. It’s good that Obama is fully on board, but there’s no reason to believe his  SOTU nod will speed our long-promised approach to this promised land significantly.


Space, another final frontier

Obama also nodded to our plodding attempts to get into space, with a mention of the recent launch of the Orion capsule, which eventually is supposed to carry astronauts to an asteroid and then to Mars. He also cheered astronaut Scott Kelly, who in a couple of months will try living on the Space Station for a year. Be sure to Instagram it, the President told Kelly, who was seated in a place of honor near Michelle Obama.

NASA astronaut Scott Kelly stands as he is recognized by President  Obama during the State of the Union speech Tuesday. Michelle Obama, front left. Credit: NASA/Bill Ingalls

NASA astronaut Scott Kelly stands as he is recognized by President Obama during the State of the Union speech Tuesday. Michelle Obama, front left. Credit: NASA/Bill Ingalls

Clara Moskowitz, writing at Observations, said the bipartisan applause indicated bipartisan support for NASA even in this determinedly partisan Congress, a cause also high on the Obama agenda. The selection of Kelly, she said, will permit metabolic comparisons with his identical twin, the former astronaut Mark Kelly, who will remain Earthbound.


The state of climate change

The President declared that “no challenge—no challenge—poses a greater threat to future generations than climate change.”  But more widely noted was his heavy kidding of politicians’ “I’m-not-a-scientist” meme of the moment, reflexively and routinely produced for evading rational discussion of climate change.

Some well-known climate bloggers had bones to pick, however. ClimateProgress’s Joe Romm complained that, while Obama bragged about his administration’s record on climate and energy issues, he also bragged about our resurgent oil and gas production. It’s quite right, of course, that boasting simultaneously that the US is doing a lot to mitigate climate change while also boosting production of domestic oil and gas is a fine example of cognitive dissonance. But can you expect a politician not to grab for the credit when gas costs under $2 a gallon? Can you really expect him to tell the truth, which is that what would be good for the climate, if not the climate of opinion, would be very expensive gas, heavily taxed?

Climate scientist Judith Curry, always an outlier at her blog Climate Etc., quoted from several grievances expressed by others, and and added her own list. For example, she said, the claim that humans are causing extreme weather events is not supported by the Intergovernmental Panel on Climate Change. And when the Pentagon warns about climate’s threats to national security, it is confusing weather events with climate change. And the idea that 97% of climate scientists agree that people are causing the climate to change is based on “an erroneous and discredited paper,” which she has critiqued a number of times.

The Curry conclusion: “The apparent ‘contract’ between Obama and his administrators to play politics with climate science seems to be a recipe for anti science and premature policies with negative economic consequences that have little to no impact on the climate.”

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