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.)

epigenetics

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.

Sure.

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.

Chronic-Fatigue-Syndrome-3

 

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.

snake-oil-bottle-cropped-label

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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.

 

snake-oil-bottle-cropped-label

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.

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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Cancer: Bad luck, bad writing, and maybe a bad paper

 

Few papers have stimulated bloggery like the one on the randomness of cancer  by Bert Vogelstein and Cristian Tomasetti, which Science published January 2 (paywall). That doubtless has something to do with the fact of Vogelstein. It’s hard to overstate his stature in cancer research; he’s known for his work on tumor suppressor genes and much else. When Vogelstein speaks, people listen.

Bloggers bashed journalists, the press release, the paper itself, particular statistical approaches to cancer, and minimizing the role of lifestyle in the disease(s). Turns out, too, that people disagree about the meaning of the word “luck.”

It’s not too much to say, really, that at bottom this was an epistemological debate about the nature of the universe. Before I wade into the heavy stuff, though, the paper itself:

No, it did not say that two out of three cancers are caused by bad luck, as most headline writers and many journalists reported. Whatever “bad luck” means.

To my mind, inheriting faulty DNA-repair genes is bad luck, and so is being a smoker long before smoking’s dangers were known. But the resulting cancers would be classified today as, respectively, genetic and environmental rather than random or sporadic or a matter of chance or bad luck. Among the blogging discussions of this paper the terms usually mean one of two somewhat different things: “bad luck” designates either a cancer due to random (postconception) mutation or a cancer that is not preventable.

What the authors of the paper meant by “bad luck”–the term appeared in the paper’s abstract and the scare quotes are theirs–is “random mutations arising during DNA replication in normal, noncancerous stem cells.” That’s not your everyday definition of bad luck.

Colored scanning electron micrograph of a lung cancer cell during cell division. Credit: NIH.

Colored scanning electron micrograph of a lung cancer cell during cell division. Credit: NIH.

Some tissues are much more prone to cancer than others, and the researchers’ idea is that these cancer differences can be explained by the number of stem cell divisions characteristic of a tissue.  The more cell divisions, the more chance for errors in DNA copying that lead to the untrammeled cell growth that is cancer. The paper’s Editor’s Summary concluded, “Remarkably, this ‘bad luck’ component explains a far greater number of cancers than do hereditary and environmental factors.”

 

Bloggers try to explain what the paper means–and doesn’t mean

Statistician David Spiegelhalter, who blogs at Understanding Uncertainty, said the paper claimed that “around two-thirds of the variation in incidence rates is explained by chance mutations of stem-cells.” The authors, he said, conclude in their abstract that “’only a third of the variation in cancer risk among tissues is attributable to environmental factors or inherited predispositions’, which may be a fairly reasonable statement to make about population rates in different tissues, but of course says nothing about variation in risks between individuals, and certainly does not say that two-thirds of cases are just luck.”

The anonymous blogger at Plumbum (a statistician? an oncologist?) put it somewhat differently: “I emphasize that ‘two thirds of cancer types’ is not at all the same as ‘two thirds of cancer cases’.”

Some bloggers were furious that in emphasizing the random nature of many cancers, the reports seem to suggest that lifestyle didn’t matter. A heartfelt example was Henry Scowcroft’s at Cancer Research UK’s Science Blog. Reports about the paper at places like the BBC “appeared to contradict the message that many organisations have been trying to hammer home (including us): that although there are no guarantees, we can stack the odds of avoiding cancer in our favour if we embrace a healthy lifestyle.” (Emphasis his.)  That’s a huge shame, he said, and to prove it cited this tweet:

“THANKYOU BBC!! Smoking doesn’t cause cancer. It’s just bad luck.”

OK, that’s scary. Unless the twit was just being facetious.

A dividing cell. Credit: Jean Cook and Ted Salmon Labs, University of North Carolina School of Medicine

A dividing cell. Credit: Jean Cook and Ted Salmon Labs, University of North Carolina School of Medicine

In their severe blast at the media in the Guardian, statistician Bob O’Hara and GrrlScientist said the paper’s data “suggest there is a relationship between risk of cancer and number of cell divisions. But it says nothing about the proportion of cancers due to cell division.” Spiegelhalter likewise noted that media treatment of the paper frequently conflated the population rate for particular cancers with individual risks, and that even when the journalist made the distinction, the headlines usually did not. For this Spiegelhalter blamed the Vogelstein-Tomasetti paper itself more than the media.

He also noted that the idea that most cancers are random and unpreventable is not new. Cancer Research UK late last year announced that 40% of cancers are preventable. Which means that 60% are not. Pretty similar, really, to the Vogelstein-Tomasetti estimate.

At Evolving Economics, Jason Collins blamed much of the journalists’ confusion on the initial press release from the researchers’ institution, Johns Hopkins, and noted that a corrected release issued later didn’t really explain why the first one was misleading. (Gary Schwitzer pointed out at Health News Review that a misleading press release doesn’t excuse misleading journalism. Science and medical journalists are supposed to go way beyond the press release, reading the paper itself carefully and consulting other sources before writing.)

In her ScienceInsider mea culpa for her own reporting on the paper, Jennifer Couzin-Frankel acknowledged that she had a hard time grasping just what the researchers were getting at, which is this: “Some tissues are overtaken by cancer more readily than others, and mutations accumulating in stem cells explained two-thirds of that variability.” Her post has been praised for its forthrightness, for example in another post by Schwitzer.

When I looked back at her original piece, though, it didn’t seem to me she had much to apologize for–except, maybe, for writing that the paper said stem-cell mutations “explained two-thirds of all cancers.” In fact the study didn’t include all cancers. Indeed, it excluded two of the most common, breast and prostate cancer, because the authors couldn’t find good data on stem cell divisions in those cancers.

 

Seeking clarity?

If you’re floundering a little on the statistical blogs, flee to PZ Myers at Pharyngula for clear explanations of what the paper found.  But the most comprehensive post I encountered was cancer specialist David Gorski’s at Science-Based Medicine. It’s long, but covers nearly all the points mentioned by other bloggers.

Gorski explained the theory behind the paper, cited several journalistic misinterpretations (noting that many were probably based on the misleading Hopkins press release), and described what the paper found. He also criticized it, for instance the puzzling inclusion of melanoma in the random group although nearly all cases are due to UV light exposure.

Gorski also noted that, oddly enough, even if the paper is (mis)interpreted as showing that 2 out of 3 cancer cases are due to chance, the conclusions are reasonable. In most cases, the cause of a particular cancer is a mystery.

Does that mean that Tomasetti and Vogelstein are “on to something in concluding that stem cell replication over one’s lifetime primarily determines the ‘stochastic’ component of cancer risk for each organ? That remains to be seen, but their preliminary finding makes sense, both from the perspective of producing a result that’s in the ballpark of what we already know based on epidemiology and being biologically plausible based on basic cancer biology.”

 

Enter epistemology: the meaning of “luck” and “random” and “chance”

Vogelstein and Tomasetti set the stage for misinterpretation and complaints by calling on “bad luck.” They introduced the term in the abstract, guaranteeing that “bad luck” would be part of how the paper was explained to others. The authors defined the term precisely enough, but of course their definition–”random mutations arising during DNA replication in normal, noncancerous stem cells”–isn’t what the rest of the world means by “bad luck.”

Gorski put the problem this way: “[S]ome of the objections to this paper seem to flow from a belief in inflated estimates of just what proportion of cancer is due to ‘environment’ and is therefore potentially preventable. It’s been suggested that cancer biologists might be too fast to blame unknown causes on ‘randomness,’ the assumption being that not knowing something means that we will know it in the future and more prevention will be possible. The problem is that not knowing something doesn’t mean that there’s a realistic way of obtaining that missing knowledge or that even if we obtained that knowledge that we’d be able to do anything with it.”

Myers was not so understanding. In another Pharyngula post, he described eye-opening (for him) Twitter exchanges with people who have “a striking psychological antipathy to the whole idea of random effects.” This came as a surprise to him. His early training was in genetics, he explained, “and there you acquire a strong appreciation for the importance of chance events.”

I can’t help wondering if the fact that Myers is a scientist (an evolutionary biologist) is related to his thinking the belief that everything has a cause is “weird.” Gorski, an oncologist who sees patients, has a different view. Humans, he said, crave explanation.

A cell preparing to divide. Two copies of each chromosome (blue) are lined up next to each other in the center of the cell. Next, protein strands (red) will pull apart these paired chromosomes and drag them to opposite sides of the cell. The cell will then split to form two daughter cells, each with a single complete set of chromosomes. Credit: Jane Stout, Indiana University

A cell preparing to divide. Two copies of each chromosome (blue) are lined up next to each other in the center of the cell. Next, protein strands (red) will pull apart these paired chromosomes and drag them to opposite sides of the cell. The cell will then split to form two daughter cells, each with a single complete set of chromosomes. Credit: Jane Stout, Indiana University

Gorski described his many uncomfortable moments with patients who want to know why they have cancer. Usually he must tell them he just doesn’t know and there’s nothing they could have done to prevent it. Patients don’t find that answer satisfying. “People—including oncologists—really don’t like the concept of ‘sporadic’ cancer, mainly because humans crave explanation. The default assumption is that everything must happen for a reason and there must be a cause for every disease or cancer.”

That’s exactly what one of Myers’s tweet adversaries said: By definition, “luck” has no cause and is therefore unscientific. Everything has a cause, and therefore in principle the cause ought to be discoverable eventually.

The Myers response: “No matter how hard we work, we will never have a sufficiently detailed explanation of every feature of the universe to negate the importance of chance. . . [physics is saying otherwise] but even if it were found that the universe is completely deterministic, the complexity of the phenomena and the number of parameters means that those kinds of causes are unknowable, and randomness is a good higher-level description of what is going on. So get used to it.”

That may be a rational view of the universe. But I wonder if people who want to believe that events have causes, who need to feel in control of their lives, will find it persuasive.

 

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List of lists Part 2, Tracker, Health News Review

 

The list of lists, continued

Happy New Year, and here’s Part 2 of the On Science Blogs List of Lists–the annual end-of-last-year-beginning-of-this-year retrospective on the best of, top ten etc. (For Part 1, the final On Science Blogs post of 2014, see here.)

Delighted to report that my job has been simplified by the reappearance late in December of Charlie Petit’s annual Best-of lists focusing on science journalism at the Knight Science Journalism Tracker. He noted, as have nearly all other commentators, that the big science stories of 2014 were the Ebola virus, which authorities thought was dying down in the spring, but which resurrected and continues to ravage Africa, and the European Space Agency’s Rosetta mission that successfully planted a lander on Comet 67P/Churyumov-Gerasimenko.

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

Charlie’s list covers Best/Top science stories by Science News, Science, the Guardian, the CBC’s Quirks and Quarks, Discover magazine (top 100!), RealClearScience, the Australian Science Media Centre, top environmental stories, Wired, space science. . .

Also Grist’s top anti-science stories of the year.

 

You’d think that would leave me little to do, but you would be wrong.

The writerly and editorial desire to retrospect is irresistible. Theirs and also mine.

First, my annual clobbering of Science for its annual enshrinement of the dreadful term Breakthrough for its list of the year’s most important science developments. Aaaaargh. The list can’t be ignored despite the forbidden label, alas, because it’s, you know, Science. Top b__________h was the Rosetta mission. Runners up to Rosetta include using young blood to stem aging, the birth of birds, memory manipulation, and the world’s oldest cave art (which, despite what you’ve been told for decades, is not in Europe).

Science has also inaugurated a list of Breakdowns of the Year. At the top is Ebola. In 2014, for the first time since the virus’s identification in 1976, attempts at containment failed and the disease spread widely in Africa–although it was largely ignored elsewhere in the world until it killed two American health workers  in July.

Also on the Breakdowns list are some science claims that have become science fiascos. Turns out that it is not easy to turn adult cells into stem cells after all. Nor is it likely that observations by the BICEP2 telescope in Antarctica established that the early universe grew by inflation.  Not quite settled yet, but it looks as if this can be said of the data: dust thou art and unto dust shalt thou return.

In its January 1 issue, Nature chose to look forward rather than back, forecasting what science might do in 2015.  The Large Hadron Collider at CERN will get up and doing in March, resuming its search for exotic new particles.  Atmospheric carbon dioxide might climb to more than 400 parts per million for the first time in millions of years. The Ebola epidemic will end, if everything goes right.  Paleogenetics may set a new record, sequencing the entire genome of a 400,000 year old human. And much more.

 

Moving on to medical science

Journal Watch, the group of daily clinical bulletins from the New England Journal of Medicine, put together “best of 2014″ lists in several medical specialties. The lists themselves are open access,and so are many of the briefs about the items on them, although some are paywalled. The editors chose Top Ten items in, among others, general medicine, cardiology, neurology, and psychiatry.

I’ll bet you can guess what Journal Watch’s top infectious disease item was. The stories about the ten topics on this infectious disease list appear to be free to read.

Credit: Mikael Häggström

Credit: Mikael Häggström

One Journal Watch compendium listed the stories  most clicked on by Physician’s First Watch readers, most of whom are presumably medical professionals. These are all open-access. Most popular was the FDA’s declaration that there is no evidence that aspirin is effective for primary prevention of heart attack or stroke, despite Bayer’s decade-long plea for permission to say so. In his short post, Larry Husten reminds us, however, “that for secondary prevention, aspirin’s benefits outweigh the risks, and it should be used to prevent a second heart attack or stroke after an earlier cardiovascular event.”

Like the aspirin story, several items popular with readers involved debunkery. At #5 is the still-controversial declaration that, for women under 60, annual mammograms result in overdiagnosis and no decrease in deaths.

The #9 item rounded up the evidence on Vitamin D as a cure-all. It concluded that Vitamin D3 (but not D2) lengthens life, but said there was no “highly convincing” evidence that the vitamin mitigated more than 100 different disorders it has been connected to, such as hypertension and colorectal cancer.

#10 concluded that milk does not do a body good. People who drink 3 or more glasses a day die sooner than people who drink less than 1 glass. And despite milk’s reputation for bone-building, women who drink a lot have an elevated risk for fractures, including the potentially deadly fracture of the hip.

PFW also listed its 10 most viral items, the label I guess an example of infectious humor, a medical way of describing highly shared stories. The FDA’s jaundiced view of aspirin was #1 there too, but the rest of the list is different from the most-clicked-on list.

 

Knight Science Journalism Tracker, RIP

As forecast at On Science Blogs here and also here, the Knight Science Journalism Tracker concluded its 8-year run at the end of 2014. In his farewell post, Paul Raeburn, the sole Tracker since late summer, reiterated his previous declarations that science writing is thriving. This despite the consistent criticism at the Tracker, which was, after all, supposed to evaluate science journalism.

Raeburn explains that emphasis on what he calls journalistic malpractice is helpful for teaching what not to do. Journalists’ allegiance should be exclusively to their readers, he says. And points out that they won’t have readers if they aren’t credible.

The Tracker is supposed to return in some form this year. I have asked Deb Blum, who will be running the Knight Science Journalism Program come summer, to describe those plans. No reply yet, but I will update you when/if there is news.

 

The resurrection of HealthNewsReview.org

Raeburn got a nice send-off from Gary Schwitzer, who restarted his new and improved Health News Review as 2015 began. Schwitzer’s first post of the year described plans for an expanded site and linked to an impressively long list of reviewers.

Which post was quickly followed by stern critiques of a couple of 800-pound health news gorillas: a Washington Post story hailing a new obesity drug that has been tested only in mice and a New York Times story purporting to be about how exercise staves off aging that was a fine example of the classic correlation-vs.-cause confusion. Were these healthy older bicyclists healthy because they were biking or biking because they were healthy?

And here’s a new wrinkle: Schwitzer says Health News Review will also be moving on from journalism to add reviews of press releases. Not a moment too soon, given the increasingly sorry record of bad science and medical journalism that is bad because based on bad (i.e., misleading and obfuscating) news releases–releases that the journos, so-called, appear to have swallowed whole.

Which I guess also makes it relevant that (for the first time, I believe) Eurekalert, the press release source from the American Association for the Advancement of Science, has released its top ten list.  People zeroed in most on a release that wasn’t all that science-y, a report on the unintended consequences of revealing wage information about public officials.

I don’t quite know what to make of the fact that the most-visited science press release of 2014 was not about Ebola or landing on comets nor indeed anything from the hard or biomedical sciences. To the extent that it was scientific at all, it emanated from the Dismal Science.

Perhaps appropriate, since 2014 was certainly a Dismal Year. Will things look up in 2015? Beginning the year with the savage slaughter of a dozen cartoonists is not a hopeful sign.

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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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