Prostate cancer screening dispute, microbiome hype

Once more, screening for prostate cancer

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

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

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

Looking closely at the European research

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

A sectioned prostate, with cancer. Credit: Netha Hussain

A sectioned prostate, with cancer. Credit: Netha Hussain

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

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

The researchers weren’t convinced either

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

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

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

Geezer screening

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

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

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

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

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

The human microbiome, hyped

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

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

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

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

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

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

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

Microbes as puppet masters

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

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

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

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

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

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

 

RIP Knight Science Journalism Tracker, sort of

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

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

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

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

 Original Post

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

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

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

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

deborah blum

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

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

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

Farewells from Trackers

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

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

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

What is blogging?

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

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

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

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

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

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

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

RIP Robin Williams: Depression, bipolar disorder, and creativity

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

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

Robin-Williams

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

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

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

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

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

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

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

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

Lords of the zings

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

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

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

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

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

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

Blogging, con and pro

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

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

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

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

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

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

Are we there yet?

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

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

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

The most crazy bonkers comet in the solar system

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

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

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

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

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

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

Legalizing cannabis in order to legalize cannabis research?

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

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

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

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

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

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

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

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

Credit: NMA.tv via Mashable

Credit: NMA.tv via Mashable

Google X’s new Baseline Study on health

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

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

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

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

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

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

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

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

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

All hail Retraction Watch

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

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

retractionwatch3-e1406619862289

Let’s regulate gene editing and gene drives!

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

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

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

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

 

Give us this day a fix for the GMO battles?

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

I’m doubtful, but let’s see.

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

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

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

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

 

And what is CRISPR?

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

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

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

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

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

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

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

 

CRISPR for genetic modification of wild populations and whole ecosystems?

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

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

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

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

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

 

Sexual harassment in the field

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

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

sexual harassment

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

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

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

Lab safety is even worse than you thought

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

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

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

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

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

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

Lab safety protocols: the Ziploc method

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

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

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

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

Let’s destroy smallpox and not create more virulent flu

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

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

smallpox poster rsch

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

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

High time for research on marijuana’s benefits

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

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

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

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

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

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

Off with their heads

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

science-transgend cover

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

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

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

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

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

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Birth control, Hobby Lobby, and the war against women

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

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

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

birth control VictorianPostcard

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

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

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

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

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

Short-term effects on health care

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

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

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

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

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

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

Future effects on health care

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

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

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

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

Birth_Control_Review_1919b

Finally, the religious war against women

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

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

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

Accidental anthrax

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

Bacillus anthracis. Credit: Centers for Disease Control and Prevention

Bacillus anthracis. Credit: Centers for Disease Control and Prevention

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

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

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

 

“Most published research findings are false”

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

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

Ouch.

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

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

John Ioannidis. Why is this man smiling?

John Ioannidis. Why is this man smiling?

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

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

 

Loss of function

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

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

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

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

 

Mea maxima culpa

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

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

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

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

Huh?

 

Fourth of July holiday: freedom from mobile phone searches

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

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

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

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

flag 13 stars

 

 

 

 

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Women and science writing

Women in science writing

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

women in science writing logo

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

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

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

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

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

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

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

The state of women

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

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

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

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

Scicurious revealed!

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

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

scicurious psuedonymity-kitteh

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

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

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

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

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

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

Soccer to ‘em

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

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

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

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

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

Meet Tolypeutes tricinctus

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

Fuleco

Fuleco

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

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

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

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

World Cup health

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

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

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

Soccer vs. football

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

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

Still more soccer science–and math, and gambling

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

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

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

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

Ahem.

Touring the Turing Test

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

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

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

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

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

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

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

The scales have fallen from my eyes.

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

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

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