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Does Your Genetic Information Long to Be Free? You’re fixin’ to find out

Posted on by David Dobbs / 0 Comment

John Hawks ponders the day, very soon to come, when high school students will run their genome sequences in bio lab instead of their blood types. He’s riffing off an article by Ronald Bailey in Reason about Bailey’s experiences with his own genomic knowledge (“I’ll Show You My Genome. Will You Show Me Yours?”)

Some time before the end of this decade [Bailey writes], kids are going to be running gene scans and maybe even whole genome sequencing experiments in their ninth-grade biology classes, just the way some of us did blood typing experiments back in the mid-20th century. Then they are going to share that information with their friends on whatever social media follow Facebook and Twitter, and they’ll do it without parental consent. Nerdy high school sweethearts might swap DNA profiles and run them through computer programs designed to predict what their potential children might look like. In the process, of course, they will also be sharing information about their parents’ genes.

At this point, many writers would sound the alarm. Not Hawks:

I find a twisted appeal in the idea that postdocs now are doing what high school science projects will be about in ten years. …

Consider a time when genotyping can be done for $2 a chip in bulk. Each year, a new chip design is distributed to high schools across a state. One year, it may be dandelions. The kids sample yards across the state, collect plant phenotype data, and submit data to a common pool. Dispersal patterns, flowering time, other phenotypes are all possible targets of study. A structured population enables them to stratify their sample, exploit linkage due to historical events, and study traits linked to biological invasion.

For the price of one R01 grant, kids across a whole state might develop a new model organism, learn the principles of genomics and produce the data equivalent of dozens of research papers.… I think we have to acknowledge that most of what today’s genomics postdocs are doing is exactly the kind of analysis that I’m describing for high school kids in 2020, except with much smaller, poorly-designed samples. What makes this Ph.D.-level work is that our current software is not very good at it — in large part because the current software is mostly written by postdocs with little training in systems design.

Hawks is just taking a quick look at this, and as he notes, he’s just calling it out rather than drawing any Big Conclusion. But what struck me reading it is that the current hand-wringing about letting this data genie out of the bottle — What are we willing to peek at in our own genomes? How much should we share with siblings or children or spouses or potential dates? OMGOMG— could be fast outrun as genomic data becomes easy and cheap to get. To be fair, that speed is exactly why some people are pushing to answer these questions now: a good thing, for example, that we’ve barred health insurers (but not life insurers!) from using the data. As things move forward, I find myself more of the mind of George Church or (somewhat similar) Misha Angrist: This stuff will out faster than we can build a filter, so get used to the idea, and get ready for the Data. Church and Angrist put their money down: They published their entire genomes, everything, on the web.

But I wonder if the rest of us have only so much time to deliberate before the info lands in our laps. When I genotyped just one single polymorphism last year, for instance, I thought hard about whether I should do it and how to explain its meaning to my siblings and, someday, my children. I’m now pondering whether, when entire genotypes get down around $500 or so, I would do the whole thing and what I would share, and how I would explain things like risk genes to my kids. Good, thoughtful David! The way things are moving, however, it’s not hard to imagine being interrupted in my careful deliberations by the news that my oldest son, now in his majority, has run his entire genome: Look Dad! Here’s half your genome! And all the data I was so carefully deliberating whether to share with him.

To me the big question — well, not The Big One, but the one I find particularly intriguing — is whether people will recognize or learn that with very few exceptions, the greater part of a gene’s meaning lies in its interaction with a person’s environment and experience. I’m not sure we’ll get that.

[A note on the vid: Life brings the strangest disappointments. I always liked this ad, which I think I saw maybe three times. It’s more really that I liked remembering the ad, and I liked remembering because in my remembered version, the redneck passenger, when asked if that thing has a hemi, says, “You’re fixin’ to find out.” Fixin’ is one of my favorite southern regionalisms (along with “Shit, I reckon.”). But the guy doesn’t say Fixin’. He says “You’re about to find out.” Damn. I think the writers missed a great chance here.]

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Are We There Yet? Slow travel with Peter Matthiessen

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Wish I could do some really fast travel to get to this:

FRI DEC 17

“Are We There Yet?: A Zen Journey Through Space and Time,” discussion by authors Michel Dobbs and Peter Matthiessen retracing Matthiessen´s Nine-Headed Dragon River journey. 6 p.m. Canio’s Cultural Café, 290 Main Street, Sag Harbor. Free. 725-4926.

Matthiessen fans — or just fans of writing, or of the fine-writing novelist and essayist Howard Norman — will enjoy the Paris Review interview Norman did of Matthiessen a few years back. For example:

INTERVIEWER

And when did you start your first novel?

MATTHIESSEN

Almost at once. It was situated on an island off the New England coast. I had scarcely begun when I realized that what I had here at the very least was the Great American Novel. I sent off the first 150 pages to Bernice and hung around the post office for the next two weeks. At last an answer came. It read as follows: “Dear Peter, James Fenimore Cooper wrote this 150 years ago, only he wrote it better, Yours, Bernice.”

Peter Matthiessen

It’s an interesting collision, Norman and Matthiessen. I think Matthiessen, despite his grace and immense intelligence, can be fairly accused of a certain arrogance, and it comes across here at times; I say this never having met him, but having heard and read much about him. At one point in the interview, for instance, he claims that no writers have influenced his work, something that’s essentially impossible.

Norman, meanwhile, I do know a bit, as he summers near my home in Vermont, and we’ve visited there some, since we both love many of the same writers and have both written about the culture(s) of the far north (he further north than I); he is quite unassuming and humble and generous and decidedly not arrogant, despite being a highly accomplished and splendid, luminous writer.

Howard Norman. Photo: Emma Norman

His “The Bird Artist has one of the most arresting first paragraphs I’ve ever read and is of the best novels I’ve ever read — a magnificent, luminous piece of work. Somewhere in my brain are Bird-Artist-specific synaptic and myelin structures built in the beautiful couple of days that I read that book; I can remember exactly where I was sitting when I read that first paragraph, and shouting. It’s an enriching, engrossing, and an “easy” read; grab it, you won’t regret it.

This interview is decidedly Matthiessen’s. Yet Norman’s unique combination of strength, subtly, economy, and directness come across in his brief questions. I like his first: “Define yourself.” It’s a nice read.

Culture of Science/Uncategorized

Arsenic and Primordial Ooze: A History Lesson

Posted on by David Dobbs / 0 Comment

In the Guardian’s weekly podcast today, I discuss the Wolfe-Simon Mono Lake bacteria paper with science editor Alok Jha and astrobiologist Zita Martins. Our post-mortem covers the hype before and after the press conference; the questions raised about the study’s methods and findings; NASA’s attempt to ignore (and get everyone else to ignore) those questions; some broader issues of how science should be evaluated; and, briefly, the difference between doing science to prove a point and doing science to test a question.

You can listen to the podcast over yonder. Meantime, I wanted to note here something that struck me repeatedly in the last week, and which came up obliquely a couple times in the podcast: A sense of history can serve one well during a fracas like this. One feels repetitive warning that those who don’t know history are doomed to repeat it — but by golly, it keeps happening!

So what can zooming back a bit teach or remind us about?

First, we should remember that the printed science journal was originally created to expand the discussion of science, allowing it to move beyond face-to-face contact at salons and saloons and meetings and into a medium more widely shared. It’s silly to now cite the printed journal’s traditions as a way to limit discussion.

Second, contrary to statements otherwise, it’s good for the public to see this mess. Scientists have long debated methods and findings in  outside peer-review journals and closed conferences. In the 18th and 19th centuries in particular, they argued vigorously in popular magazines, lectures, and public debates.

This is perfectly natural and perfectly healthy. In fact, it could actually help ease the rampant politicization of science rather than aggravate it. This Lake Mono bug, for instance, is a controversial scientifically but not politically. So it’s good that people see the scientific debate here is messy and spirited and confusing and even sometimes a bit nasty. Because if the general public sees this sort of row in routine findings — if they understand that science routinely sparks arguments over data and method —  they’re less likely to see such messy debate as  sinister when they see it in something like climate science.

Both failure and success offer great opportunities. I’ve been thinking about this a lot. Some 150 years ago, another bold-thinking biologist, Thomas Huxley, aka Darwin’s bulldog, suffered a reversal after he claimed to have discovered a “primoridal ooze” that he dubbed BathybIus. This episode was increasingly on my mind as the problems with the arsenic paper came increasingly to light.

The Bathybius discovery occurred during the long debate over Darwin’s theory or evolution in the mid-1800s. Huxley liked Bathybius — perhaps he saw Bathybius — partly because it seemed the sort of primordial life form from which all other life might arise, which in turn supported Darwin’s idea of constantly evolving life forms. I tell a brief version of this story in my book Reef Madness: Charles Darwin, Alexander Agassiz, and the Meaning of Coral:

Darwin’s just-published theory of evolution … held that evolution proceeded rapidly in fast-changing environments and slowly amid stasis. If this were true, the presumably little-changing [ocean] deep might include unchanged species — “living fossils” — from the evolutionary past. This notion was encouraged when … Thomas Huxley (an able working biologist when not writing or debating) … found in some specimen bottles from [one of his] early deep-sea expeditions a mysterious, protoplasmic goo — a “primordial ooze” or “living slime” — that he proposed might be both the base of the ocean food chain and the bottom rung of the evolutionary ladder. He called it Bathybius haecklii after his Darwinist compatriot Ernst Haeckel.

And he publicized it heavily — trumpeted it in Nature, talked it up, wrote about it often, as did others. But 7 years after Huxley discovered it, Bathybius met an ugly death when a scientist on the famous oceanographic expedition taken by the HMS Challenger found that Huxley  — well, I’ll let me tell it:

One day, when one of the Challenger scientists poured a large quantity of alcohol into a bottle containing deep-sea ooze and the mixture almost instantly produced something remarkably like the mysterious Bathybius, they realized that Huxley’s ancient slime was simply a new goo produced by the reaction between ordinary ooze made up of planktonic skeletons and alcohol. The stuff in Huxley’s tubes had apparently been formed more slowly by the traces of alcohol left after washing. [Chief scientist] Thomson immediately wrote Huxley, breaking the news with remarkable tact, and Huxley promptly sent the letter to be published in Nature along with a graceful and funny letter confessing his error.

Wolfe-Simon and company may well prove out their arsenic theory and show us that GFAJ really does live on arsenic and incorporates the stuff into its DNA. If so, they’ll astonish even more people than they already have. And if they go on to find the sort of shadow biosphere that they talk about, we’ll be truly wowed — and they’ll have rights to be every bit as triumphant as Huxley was contrite.

At this point, however, there remains a frightening (and unnecessary) possibility that the team has spoken a bit too soon. They not only apparently did the equivalent of failing to wash their glassware thoroughly enough, but failed to do a fairly simple mass spectrometry analysis that several scientists say would decisively show whether the bacteria took arsenic into its DNA — their biggest and most consequential claim. Several scientists wondered why they didn’t do this simple test. If it’s as decisive a test as these critics say, the authors’ failure to run it — and Science’s failure to ask for it — is mystifying. As one scientist told Zimmer, “The curious thing is that if getting powerful data is so easy, why was this printed in its current form?”

It was also this failure that led another critic levy perhaps the most damning criticism, which was that “the paper represents something that all graduate students are told to think about – develop experiments that are aimed to reject your hypothesis, not support it. If you cannot reject it, then you must accept it. These experiments [in the Wolfe-Simon paper] in most cases were shown to ’support’, not test the central hypothesis. It’s a newbie mistake and the mentors, reviewers and editors are as much at fault for not catching that as anyone.”

Everyone makes mistakes. Huxley didn’t wash his bottles well enough, and so created a mess he thought was a new life form. If they’re proven wrong, Wolfe-Simon and colleagues can take solace in some good company who’ve also seen what they wanted to see — a common error that scientists call confirmation bias. Huxley did it, and as I explain in my book, Darwin did too, when he made an early but painful mistake about the geology of Glen Roy. That youthful mistake — he downplayed some evidence contrary to his theory and magnified some that supported it —  led to a humiliating reversal at the hands of Louis Agassiz. And Louis would later suffer a much greater reversal, partly because of how Darwin responded to his mistake.

The key thing is that when confronted with contrary evidence, both Huxley and Darwin admitted their mistakes and learned from them. Darwin’s insights from his bumble at Glen Roy helped him forge the brilliant balance of imagination and rigor that were his mark.

If mass spectrometry and other suggested tests are indeed definitive tests of Wolfe-Simon’s arsenic claims,  she and her co-authors will likely soon be proven (or, if they’re really on the ball, prove themselves) either profoundly mistaken or stunningly correct. Either way, they’ll face an important moment. Both grave failure and spectacular success bring their opportunities for growth. Here too history offers models:

Darwin learned both boldness and caution from his [mistake at Glen Roy]. Louis Agassiz, however, took from Glen Roy an opposite lesson: He felt emboldened to push his speculative theories ever further. At Glen Roy, Darwin had stumbled, collected himself, and adjusted his gait. Louis had sprung across a valley and landed safely. He would soon put so much faith in his leaps that even when his support was delusory, he would land and feel solid ground.

This lack of humility did not serve him well.

___

Image: The murky valley that is Glen Roy. Courtesy Wikipedia Commons.

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Maybe the Coolest Lego Gizmo Ever: The Antikythera Mechanism

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One of the prettier things I’ve seen on the ‘net lately: a recreation of an ancient computing device called the Antikythera Mechanism.

The Antikythera Mechanism in Lego from Small Mammal on Vimeo.

The Antikythera Mechanism — just one is known — is an ancient Greek computing device discovered in a shipwreck in 1901. It took a century for scientists to figure out what it was for: The Greeks apparently used it to calculate astronomical positions.

The Wikipedia entry on this gizmo and its history is almost as captivating as this model, which was made with thousands of Lego Technic part and shot in stop-action, which took 40 days. Adam Rutherford, of Nature, had the idea; convinced gizmo-maker Andrew Carol to build it; and enlisted writer and filmmaker John Pavlus, who runs Small Mammal (and is a friendly online acquaintance of mine) to shoot the film. Nature A new website and operation called Digital Science underwrote the project, and bully for them.

For more — and who wouldn’t want more? — see

  • The Science Direct page on the project.
  • A Nature article on the Mechanism.
  • 1080p HD version of the film at the site of Pavlus’s Small Mammal site
  • A fascinating interview with designer/builder Andrew Carol on the device’s history and his own design process, including films of him tweaking it.
  • Behind the scenes post on making the film (40 days of animation).

Friday, February 25, 2011: Corrected to credit Digital Science rather than Nature; added links to reflect same.

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The Wrong Stuff: NASA Dismisses Arsenic Critique Because Critical Priest Not Standing on Altar

Posted on by David Dobbs / 0 Comment
The right stuff: John Glenn after riding a tin can into space and back, 1962

A NASA spokesperson has dismissed a major critique of the Science arsenic bug paper based not on the criticism’s merits, but on its venue — it appeared in a blog rather than a peer-reviewed journal. Apparently ideas are valid (or not) based not on their content, or even the reputation of the author, but on where they’re published.

NASA spokesperson Dwayne Brown expressed these rather anti-empirical notions in a CBC News story about the substantive and detailed reservations about the Science paper raised by University of British Columbia researcher Rosie Redfield in her blog, which I covered here night before last. As I noted then, Redfield’s criticisms were quickly echoed by other  qualified researchers. But Brown sets aside Redfield’s critique without even referring to its substance or merits.

From “NASA’s arsenic microbe science slammed,” at CBC News:

When NASA spokesman Dwayne Brown was asked about public criticisms of the paper in the blogosphere, he noted that the article was peer-reviewed and published in one of the most prestigious scientific journals. He added that Wolfe-Simon will not be responding to individual criticisms, as the agency doesn’t feel it is appropriate to debate the science using the media and bloggers. Instead, it believes that should be done in scientific publications.

This is a call to pre-Enlighentment thinking. Brown is telling us to judge utterances not by their content, not even by the integrity, reputation, and experience of the individuals who deliver them, but by whether they’re delivered from the proper place in the proper building —  in pre-Enlightenment days, the Church of Rome;  in Brown’s post-arsenic days, the Church of the Peer-reviewed Journal.

It’s an extraordinary dismissal. Rosie Redfield is a full-bore member of the academy and a researcher in the field under question. She is — to extend the metaphor — a priest. But though Redfield wears the proper robes, Brown wants to dismiss her because she’s not standing on the proper altar.

Even the best peer-reviewed journals make mistakes. Hype can take over. Groupthink can rule. People screw up. And sometimes journals defend mistakes by refusing to publish sharp critiques of them. All this stuff happens, and not just once in a blue moon. Peer review — and especially so in the sort of artificially and arbitrarily constricted sense that Brown gives it here.

What he fails to see or refuses to acknowledge is that Rosie Redfield is a peer, and her blog is peer review. NASA has bungled its presentation of this paper from start to finish. It makes worse by trying to dismiss critiques this way. This is the wrong stuff.

PS later Tue Dec 7: Grant Jacobs has a similar reaction to NASA’s idea of free and open exchange of ideas, as does Deepak Singh. Texas A&M researcher Jim Hu adds some more peer review, most substantially here. And the Guardian has a good story tracker on the issue where they’re posting updates as well.

____

Image: The right stuff: Astronaut John Glenn relaxes aboard the USS Noa after being recovered from the Atlantic near Grand Turk Island after his historic Mercury flight, 1962. Glenn became the first American to orbit the Earth on February 20 of that year in his “Friendship 7” capsule. The Noa picked him up 21 minutes after impact.

Image and caption courtesy NASA

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Is That Arsenic-Loving Bug — Formerly an Alien — a Dog?

Posted on by David Dobbs / 0 Comment

You know that arsenic-loving bacteria briefly mistaken for an alien? The bug, which roiled the science press earlier this week when it rode an unusually high and steep hype parabola, endured a firey re-entry today when University of British Columbia bacteriologist Rosie Redfield ripped into both the research and the paper — and was quickly backed quickly by several scientists, including heavyweight extremophile-bacteria researcher Jonathan Eisen.

I can’t claim to follow the technicalities of this argument, so can’t pass judgment on the research itself. Fortunately for clarity’s sake, Redfield’s critique, though it gets quite technical, does not leave you wondering what the author really thinks of the paper under the microscope. On Twitter she calls it “shamefully bad science.” She’s just as frank in the analysis on her blog:

Bottom line: Lots of flim-flam, but very little reliable information.… If this data was presented by a PhD student at their committee meeting, I’d send them back to the bench to do more cleanup and controls.

There’s a difference between controls done to genuinely test your hypothesis and those done when you just want to show that your hypothesis is true. The authors have done some of the latter, but not the former.…

I don’t know whether the authors are just bad scientists or whether they’re unscrupulously pushing NASA’s ‘There’s life in outer space!’ agenda. I hesitate to blame the reviewers, as their objections are likely to have been overruled by Science’s editors in their eagerness to score such a high-impact publication.

I don’t know Redfield, so didn’t know exactly what to make of her critique. But her opinion was quickly seconded in the blog’s comments and on Twitter by many sharp scientists. UC Davis’s Jonathan Eisen, who knows his extremophile bacteria and and his evo-sci quite well, tweeted that he “was gonna write about bad science & arsenic but no need – Rosie Redfield has all you need.” Evolutionary biologist John Hawks thought the Science paper clearly lacked the necessary controls to draw its conclusions. And Alex Bradley concluded that “this study lacks any real evidence for arsenate-based DNA; unfortunately these exciting claims are very very shaky.”

If the paper is as weak as these critiques hold, NASA appears to have been not just overzealous but reckless — and Science not only went along for the ride, cheering wildly, but put all the gas in the car.

I imagine — and certainly hope — that we’ll get a better picture of whether that’s the case as the technicalities get batted about. Meanwhile, what does this say about the state of science journalism? I think the answer there depends on what happens from here on out. The overhyped stories that appeared before and just after the embargo lifted were obviously a problem. But much of the press — both outlets-formerly-known-as-mainstream such as Nature News and the New York Times and high-quality-science-writers-formerly-known-as-just-bloggers, such as Ed Yong, did a good job correcting these. These same outlets tended to extend a benefit of the doubt to the paper, as seems reasonable enough if they hadn’t run into sharp doubts. True, most of these measured accounts tended to fall into a tone of “damned interesting, and I mean damned interesting … with caveats,” and you might want to complain that they hadn’t caught the slop. But as a version of my old favorite “Interesting if true,” I can accept that — especially given the constrictions imposed by the short-turn embargo system, which lets journalists have exclusive access to papers a few days, but only a few days, before they are published, in exchange for promising they won’t publish on them till a certain date and time. (I’d feel differently if I knew a reporter heard but dismissed truly sharp criticism such as that that Redfield has leveled, if it came from someone as reputable as Redfield appears to be.)

Here’s the problem: When a paper is still under embargo and we journalists call an outside expert to get comment on it, the expert has often not actually seen the paper yet, since, well, it’s under embargo. If time allows (often not, since one usually has only a few days and everyone is busy) then you can send the expert(s) the paper, and they can read the paper and get back. But as the experts usually lack time to compare impressions with peers, few will go out on a limb and really lay into a paper under those circumstances. You usually get either “This looks interesting, with a few caveats I’d like to note” or “I’d rather not comment.” You’ll rarely get an outright dismissal. They lack the time and probably the taste for the trouble it’ll make.

So we get what we got: some measured check on the hype from the best journalists, but mainly, since the claimed findings are ambitious, an esepcially fascinated version of “This looks damned interesting, and is truly interesting if true, and [this next part usually doesn’t get actually written] I sort of hope it is true, ‘cuz it’s cool.” I don’t think there’s much wrong with that if you follow through and cover objections that rise down the road.

What to make of this? First, this is one of those reminders — every science writer gets one now and then — that any of us can get excited enough to overlook some slop, especially if the slop is technical in nature. The test is in how you react afterwards.

It also attests to the immense value of having scientists that blog, despite that they get little credit (and often some flak) for doing so. No matter how this sugars out, Redfield’s use of her blog to call BS when she sees it has put science’s self-correcting feature — far too often asleep these days — into high gear.

Finally, as Ivan Oransky and many others have pointed out, this episode illustrates how utterly ridiculous and toxic the embargo system can be, especially when it is systematically and intentionally exploited to drum up hype. The NASA press release shamelessly used words like “astrobiology” and “extraterrestrial life” to tease the biggest response they could get. True, NASA never said they’d discovered extraterrestrial life. But if you think that you can throw language like that around in a press release that announces a high-profile news conference with five scientists, including the director of the astrobiology program, and not seriously risk generating speculative stories about aliens, then you’re not thinking empirically.

It was entirely predictable that they’d get stories about alien life. You could repeat this experiment 40 times and you’d get the same result. To complain that, Well dammit, the press release didn’t say “We found aliens!”, and then argue that the real problem was that some of the more impatient quarters of the press, Can you believe it?, jumped to that conclusion and overhyped the story anyway, is to indulge in fantasy. It’s like laying out chocolate cupcakes in front of a table of hungry two-year-olds, leaving the room saying, “I’m just fetching the broccoli for you little darlings, so hold on now, you know what’s good for you, save those cupcakes for later” — and then professing surprise and disappointment when you return to find that … “Why, the cupcakes are just GONE!” Please to give me a break.

We thought we were getting cupcakes. Some of us wanted cupcakes. Who doesn’t want cupcakes? Now everybody’s got humble pie in front of them, quite a bit to eat yet, and no dessert on the menu.

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The Real Scoop on Aliens Oops Arsenic in Old Lakes

Posted on by David Dobbs / 0 Comment

Been a lot of hype over some strange life forms found in Lake Mono, encouraged, unfortunately, by some breathless, teasing press releases from NASA. But amid the muddle you can find some nuanced clarity in two stories in particular, from Nature News and Not Exactly Rocket Science.

First, Alla Katsnelson brings some good balanced coverage at Nature News:

A bacterium found in the arsenic-filled waters of a Californian lake is poised to overturn scientists’ understanding of the biochemistry of living organisms. The microbe seems to be able to replace phosphorus with arsenic in some of its basic cellular processes — suggesting the possibility of a biochemistry very different from the one we know, which could be used by organisms in past or present extreme environments on Earth, or even on other planets.

You could stop right there and know what this is and what it isn’t (aliens). But it’s a great treatment, so get the whole thing.

If you want more and/or want some needed swipes at the hype machine, check out Ed Yong’s treatment at Not Exactly Rocket Science:

The discovery is amazing, but it’s easy to go overboard with it. For example, this breathlessly hyperbolic piece, published last year, suggests that finding such bacteria would be “one of the most significant scientific discoveries of all time”. It would imply that “Mono Lake was home to a form of life biologically distinct from all other known life on Earth” and “strongly suggest that life got started on our planet not once, but at least twice”.

The results do nothing of the sort. For a start, the bacteria – a strain known as GFAJ-1 – don’t depend on arsenic. They still contain detectable levels of phosphorus in their molecules and they actually grow better on phosphorus if given the chance. It’s just that they might be able to do without this typically essential element – an extreme and impressive ability in itself.

Nor do the bacteria belong to a second branch of life on Earth – the so-called “shadow biosphere” that Wolfe-Simon talked about a year ago. When she studied the genes of these arsenic-lovers, she found that they belong to a group called the Oceanospirillales. They are no stranger to difficult diets. Bacteria from the same order are munching away at the oil that was spilled into the Gulf of Mexico earlier this year. The arsenic-based bacteria aren’t a parallel branch of life; they’re very much part of the same tree that the rest of us belong too.

That doesn’t, however, make them any less extraordinary.

At which point Yong goes long, laying out what is awesome about this finding while reigning in the excess. UniverseToday gets kudos too for sounding the alarm early.

Finally, fun and useful too, especially to media and meta geeks, is Ivan Oransky’s dissection of how the hype machine and the embargo fed each other.

So this wrong call on holding the embargo until just now was Science‘s. And what better way to fuel even more speculation, and build suspense, than to not officially allow the very press that you supposedly hope will get things right to, um, get things right and tamp down that speculation? See, if Science won’t allow anyone to say what exactly the paper says, and meanwhile says the reports you’ve read — which by then included stories saying this wasn’t ET — were erroneous, there’s still a chance that NASA has discovered life on Mars after all!

But that frenzy goes away once you do the right thing lift the embargo. I should know. I’m deflating as I write this, knowing that the suspense of not knowing what I’ll tell my legions of fans will dissipate as soon as it posts. (But building suspense isn’t why I didn’t post. I didn’t post because I work at a big news organization and caution dictates that I don’t give embargoing institutions any reason to yank my access or that of my colleagues.)

It’s Wag the Dog. Or maybe the scene in Casablanca in which Captain Renault is “shocked, shocked” to find out that gambling is going on at Rick’s, only to be handed his winnings by a croupier.

Media. Got to mediate it. Don’t believe everything you read in the paper. Or here.

Image: Scientist searching for aliens arsenic in Mono Lake, California.

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Aglitter in the Net

Posted on by David Dobbs / 0 Comment

Recent favorites, notables, and retweets:

Down on the Body Farm: Inside the Dirty World of Forensic Science A good read from the Atlantic.

History of Female Madness in the APA Monitor A bit unsettling, which is probably why it’s an important reminder. .

The dark side of oxytocin, much more than just a “love hormone” Ed Yong continues his well-advised check against oversimplification of matters genetic, hormonal, and neurotransmittical.

Trust and Temperature Jonah Lehrer ‘splains what he’d do if he were a con-man. I feel better that when we had lunch, he suggested I get the (cold) salad. Was damned good. He paid for it. Not sure what all that means.

Michael Nielsen » The mismeasurement of science The issue of what scientists get credit for — publication, being famous, reviewing papers, whatnot — has a huge influence on what scientists do. They react to incentives just as everyone else does. And right now, almost all the incentives favor flashy publications in certain journals, even as they discourage data-sharing and the evaluation of others’ work and fail to necessarily reward the biggest ideas. (As he notes, one of the biggest ideas in 20th-century physics was in a footnote.) Nielsen here offers one of the most readable and constructive proposals of how to rejigger academia’s credit/incentive/reward/reputational system.

Simple rubber device mimics complex bird songs What it says

and from the twittersphere:

imascientist: On why humanities are vital too RT @alokjha Such a gorgeous article. Angry, but well-contained. Exactly what’s needed. http://bit.ly/aN3Aff

edyong209: RT @Dirk57: RT @jonahlehrer: The long history of “information overload” anxiety: http://tinyurl.com/236rkct

Brains and Behavior/Uncategorized

If You’re Gonna Touch My Junk, At Least Grab the Data

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“Do I have the right to refuse this search?”

This is a question I heard many times during my law enforcement career. Often my answer was no. But occasionally it would be “yes,” followed by an admonition to have a good day.

For the last half of my career, I would have documented each interaction, whether or not it involved an arrest. I would have written down the nature and length of the interaction, the gender, race, and age of the person, and the outcome of the contact (arrest, citation, etc.).

I carry the baggage of this history with me as I’ve traveled over the last eight years, mindlessly placing my luggage on the conveyer belt and removing my shoes for TSA inspection.

Recently, something changed.

Diedre Walker, a retired assistant chief of police, sounds as if she was a pretty good cop, and she writes well here, at Homeland Security Watch, of her growing dismay with the Transportation Safety Administration’s practices. What grabs me most is her point about the TSA’s apparent failure to collect any data about the patterns of their ‘random’ searches: Why do they choose the people they choose for the more thorough searches? What, in other words, is their version of “random”? And do they keep track of what they find when they do wand versus body versus scanner searches, or how well personnel at different locales or in different crews follow procedures? Do they compare and contrast? Do they even know whether their “random” searches are truly random?

Walker thinks not.

Within the last few months, I have been singled out for “additional screening” roughly half the time I step into an airport security line. On Friday, October 9, as I stepped out of the full-body scanning device at BWI, I decided I needed more information to identify why it is that I have become such an appealing candidate for secondary screening.

Little did I know this would be only the first of many questions I now have regarding my airport experiences.

This alone perked me up. I’m 6’4″, weigh 195 pounds, and am fairly fit, so you’d think I’d be one of the last people you’d want to get on a plane with a weapon and bad intentions. Yet in scores of flights since 9/11, I’ve been asked to step aside only once — and that was before the recent revisions toward more thorough screening, and the pat-down was so ludicrously polite that it would have revealed only something in a shoulder holster or a pocket. True, the searches are supposed to be random, so I shouldn’t be getting singled out just because I’m big. But Walker suggests the TSA is actually more likely to search her than me — precisely because she seems less threatening:

As I watched the screening officers, I wondered what information drives their decisions. Left only to my observations, I concluded that their decisions were entirely random, and likely based upon three criteria: passenger load, staffing, and whim.

I was left to conclude that I am not screened because I look like a terrorist. I am routinely screened because I look like someone who will readily comply. I decided then that my next invitation to enjoy additional screening would be met with more inquiry.

I did not have wait very long. On my return through Albany to BWI — Surprise! – I got “randomly selected” for additional screening.

If Walker is right — TSA personnel are unconsciously and understandably inclined to single out less threatening or more apparently compliant people to put through the fine filter — then they may actually be practicing a sort of reverse profiling that misses the very people who pose the greatest threats.

More seriously, if Walker is right that the TSA is not recording stats on its searches — and I’ve seen nothing in the typical search-line chaos and lassitude that suggests they are collecting data — then we have an even bigger problem: The TSA is taking a lot of effort and spending a ton of money and causing a lot of disruption and creating the trappings, psychology, and a main apparatus (search at will) of a police state — and we no way of knowing a) how consistent they are being or b) what sorts of searches, procedures, or practices are most effective.

This bears a disturbing resemblance to the US’s failure to track the effectiveness of its medical and educational practices. We throw tons of money at these problems — but because we don’t keep track of what works and what doesn’t, or even what everyone is doing, we have no idea what works.

This is too bad, because as every frequent flyer knows, the procedures and skill of the screeners varies widely, and many seem, well, not from the A-team. So Walker found when she refused a “puffer machine” meant to detect explosives so was subjected to a body search. What followed sounds like a checkpoint being run by uncertain high-schoolers:

I shrugged and waited while the screeners figured out what to do next. One of the screeners said “Who is the supervisor? Notify a supervisor.” I waited two to three minutes with two female screeners. I was then approached by a uniformed screener and the following exchange took place.

“She refused the puffer. We are supposed to notify a supervisor. You’re a supervisor, right?”

Apparently reminded of his role, the subordinate screener then said “We’re notifying you.” She said nothing further.   The supervisor then informed me that if I did not step into the “puffer” I would be subjected to a full body-pat-down, that I would be “wanded” and that all of my belongings would be fully searched by hand.

By this time, my belongings had already passed through the x-ray and sat oddly unattended on the belt. They had aroused no suspicion, either as they passed through the x-ray or as they sat completely unattended. I thought it odd that my initial refusal to be subjected to the ‘puffer’ now rendered the x-ray examination effectively flawed. I was being cajoled and was then offered the opportunity to change my mind, which, again, I thought rather odd. If I posed such a risk by refusing the secondary screening, why would that risk be now mitigated, if only I were to change my mind?

I did not change my mind. So, I stepped between two glass walls and was subjected to what my police training would allow me to conclude was a procedural vacuum.

I had been told repeatedly I would be subjected to a “pat-down.” I correctly suspected otherwise. During the course of my police career, I have conducted many pat-downs on the street. The Supreme Court has described pat downs as a cursory check of the outer clothing of a person by a police officer, upon articulable suspicion that the officer’s safety is at risk of being compromised. My department’s procedure indicated that this pat-down was to be conducted with an open hand, gently patting the outer clothing of an individual, for purposes of officer safety only, with the goal of detecting weapons. In other words, it is not a search.

What happened to me in Albany was not the promised “pat-down.” It was a full search conducted in full public view. It was also one of the most flawed searches I have ever witnessed.

From the outset, it was very clear that the screener would have preferred to be anywhere else. She acted as if she was afraid of me, though given that I had set myself apart as apparently crazy, perhaps I cannot blame her. With rubber-gloved hands she checked my head, my arms, my legs, my buttocks (and discovered a pen that had fallen into one of my pockets) and even the bottom of my feet. Perhaps in a nod to decorum, she did not check my crotch, my armpits or either breast area.

Here was a big problem: an effective search cannot nod to decorum.

These three areas on a woman, and the crotch area of men, offer the greatest opportunity to seclude weapons and contraband.   Bad guys and girls rely on the type of reluctance displayed by this screener to get weapons and drugs past the authorities. We train cops to realize that their life depends upon the ability to compartmentalize any apprehension about the need to lift and separate. Fatal consequences can and do result when officers fail to detect a secreted weapon which is later used against them.

At the Albany airport, I was left to wonder what kind of training the screener received. I was forced to conclude the answer might be “none.”

My experience has been similar; the screeners vary widely in competence (and courtesy). Some units seem focused and consistent; most are not. My electronics-dense bag draws extra scrutiny (an open-bag check) at one unit and hardly a glance at the next. Some places wand me if I set off the metal detector just once (that damned belt buckle), others let me walk through two or three times, removing belt, watch, and forgotten headset in sequence. And no one ever asks to open my rollerbag to see what’s in those liquids that I now always leave in the bag; I NEVER remove my Dopp kit with my toothpaste, roll-on, contact lens cleaner, and shaving gel because I forgot it once, nothing happened, so I started just leaving it in. And though they make a big deal of asking us to take it out, they never notice that I leave it in.

Meanwhile, of course, the agents who should be trying to do good security seem to increasingly feel compelled to screen people punitively.

You can’t readily correct such lapses, inconsistencies, or abuses if you don’t track what your own people are doing. Neither can you spot bigger inconsistencies that suggest discrimination or abuse.

Currently, there is no way to know whether a certain male screener routinely identifies predominantly women for additional screening. There is no way to identify whether a Latino screener routinely isolates African-Americans, or vice versa. To assert that the screeners are highly trained and do not engaged in this type of discrimination, whether passive or active, is unsupportable because there is no data. You simply cannot solve problems that you do not want to identify.

This is only one of a mess of problems with the TSA, of course. Yet it’s stunning that an effort that claims to be going to great lengths to ensure our security doesn’t take the basic step — a hassle, yes, but basic in the sense of Things You Must Do To Get It Right — of charting its own performance.

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Data Visgasm: Watch the World Get Richer and Healthier

Posted on by David Dobbs / 0 Comment

Talk about bringing the data alive. This clip of Hans Rosling’s work shows the great power of dynamic data visualization. Here we see the entire world get both healthier and wealthier (or or at least less poor), all afloat in some very cool architectural space. Wonderful, riveting stuff. I can’t wait to see the entire show, “The Joy of Stats,” next Tuesday on BBC Four. Our host will be this same Hans Rosling, who says “Statistics is the sexiest thing on the planet.” He may well convince me.

H/t Adam Rutherford