Archive for the 'science experiments' Category

Missed opportunity – not debacle – in bogus schizophrenia genes coverage

July 6, 2009

Journalist Brandon Keim has a smart post about how he approached last week’s over-hyped schizophrenia genetics story, the latest in a long string of them.

Basically, some high-tech efforts to scan the genome for links to schizophrenia turned up thousands of rare gene variants, each of which might account for some tiny fraction of all schizophrenia cases, and together explained only about 30 percent of all cases. (Papers here, here and here.)

Given that researchers had been looking for meatier schizophrenia genes for years and years without finding anything substantial, this was to be expected, especially if you’re the kind of person who questions whether there are very many genes “for” anything.

Brandon notes that a number of web stories uncritically hyped the journal’s spin, namely, that this was a big, juicy, pharmacologically relevant finding, which it wasn’t. He uses NYTimes reporter Nicholas Wade as his stalking horse, following Wade’s transformation from “gene-whiz” kid to genomics realist.

Here’s Brandon’s point of view:

From a journalistic perspective, there are two possible stories here. First, the straight story: schizophrenia is extraordinarily complicated, and genetics can’t now explain it in any useful way. And two, the contextual angle: for years, the public has expected, and scientists have sometimes promised, that genetics would illuminate this disease — and it failed, just as it has for nearly every disease. 

(Useful perspective: search Eurekalert for “schizophrenia” and “gene.”)

When these studies showed up in my pre-embargo pipeline, I made a quick note of them — see above — and moved on. I’m already reporting for a long-form article on the disappointment of genomics, and this didn’t feel like a Wired daily news story. It would require at least a half-dozen interviews, and ultimately produce a narrative preaching caution, tempered expectations and patience. Instead I chose to write about an interesting finding on salamander limb regeneration, and waited for the inevitable onslaught of “Schizophrenia! Unlocked!” stories.

Brandon links to a number of such stories. He wants to portray this as a failure of science journalists — his subject line calls the story a debacle — which I’m inclined to second-guess. As journalists, we tend to critique ourselves from the supply side: we look at the world and see bad things, then look at what our colleagues are doing and see bad things, and then try to link the two, because it reinforces our sense of efficacy. And that’s probably appropriate here.

The other half of the story is the demand side. Can we prevent uncritical science stories from being published? Not by ourselves as journalists. It’s a structural issue that journalists can and should address in the only way they can — by directing skepticism at their own motivations, at least where times allows, and it doesn’t allow much these days for a working journalist. If I was living in a Brooklyn apartment right now instead of my mom’s place in Nashville, you probably wouldn’t be reading these words, although who knows.

I’d argue that Brandon inadvertently makes my point for me.

Knowing that others news outlets would herald the finding uncritically, and assuming that was a bad thing — which calling the coverage a “debacle” implies — what should Brandon have done? By passing on this story in favor of salamander limb regeneration, he passed on an opportunity to confront scientists in real web time about the unmet promise of genomics in understanding complex disease. It could have started something like “Studies appearing in Nature today will be trumpeted as a triumph for the genetics of schizophrenia, and they shouldn’t be,” similar to Nick Wade’s blog post about the coverage, which Brandon says was the only piece to get the story right.

As someone who’s been there, I know what I’m suggesting is easier said than done, although Brandon obviously had the chops to write the tougher story. I’ll forgive him (this time), if for no other reason than because, like he says above, he’s working on a bigger story about the failed promise of genomics, which I can’t wait to read.

So what to make of the schizophrenia coverage? Barring demand-side evidence to the contrary, it was hardly a debacle. The subtext of Brandon’s post is that it’s actually the culmination of a long story arc. It reflects an underlying attitude of scientists and journalists. Attitudes take time to change, and rightly so. I wish I was in a better position to argue about whether the human genome project was oversold, and whether the big daddy gene assumption represents an institutionalized failure of a masculinist theoretical assumption, to paraphrase Evelyn Fox Keller.

We need journalists to step up, in part so other journalists will step up. I am Spartacus, right? With than in mind, I take Brandon’s critique of Wade as a positive.

Not long ago, Wade could be relied upon for reductionist coverage of genetic links to disease. (On the subject of genes and schizophrenia, here’s Wade in July 2002: “Researchers hope they are now starting to close in on some of the genes that go awry in schizophrenia.” In December 2002: “The long search for a gene that helps cause schizophrenia may at last be bearing fruit after many false starts and disappointments, scientists are reporting.” In April 2006: “Researchers have made progress in understanding how a variant gene linked to schizophrenia may exert its influence in the brain.”)

But Wade, who arrived at the Times in 1981, seems to have finally lost patience with the “gene-linked-to-(fill in the blank)” narrative that he and so many others told, and were sold, for so long.

That’s called intellectual honesty! And it’s something all science journalists should aspire to, starting… now.

Related: NYTimes | 1) A Dissenting Voice as the Genome Is Sifted to Fight Disease, 2) Gene-Hunters Find Hope and Hurdles in Schizophrenia Studies

Question for somebody: To what extent do genetic studies reflect a desire to treat the disease, as opposed to wishing we could find a gene to make it go away?

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The road to self-lovability

July 6, 2009

*PR science blogging alert*

Psychological Science is quickly becoming my favorite journal.

Allow me to — gasp! — quote the latest press release:

Psychologists Joanne V. Wood and John W. Lee from the University of Waterloo, and W.Q. Elaine Perunovic from the University of New Brunswick, found that individuals with low self-esteem actually felt worse about themselves after repeating positive self-statements.

The researchers asked participants with low self-esteem and high self-esteem to repeat the self-help book phrase “I am a lovable person.” The psychologists then measured the participants’ moods and their momentary feelings about themselves. As it turned out, the individuals with low self-esteem felt worse after repeating the positive self-statement compared to another low self-esteem group who did not repeat the self-statement. The individuals with high self-esteem felt better after repeating the positive self-statement–but only slightly.

In a follow-up study, the psychologists allowed the participants to list negative self-thoughts along with positive self-thoughts. They found that, paradoxically, low self-esteem participants’ moods fared better when they were allowed to have negative thoughts than when they were asked to focus exclusively on affirmative thoughts.

The idea is that for people with low self-esteem (as measured, I’m guessing, by numerical responses to statements such as “I am a capable person”), telling themselves how great they are sets up contradictory thoughts, because, you know, their entire world view depends on how ungreat they are. To admit to greatness would entail drastic changes in their way of being.

Like a psychologist tells the BBC:

“If you’re not close to your parents, don’t have many friends, are unemployed and are unhappy with your appearance, it might be hard to have high self-esteem.”

A good therapist teaches you to find the upside to your down traits, and then to isolate the negative world view that’s twisting the expression of that upside, e.g., “I would communicate my feelings honestly to friends and loved ones, but a) my feelings don’t matter and b) I would be rejected anyway.”

Seeing the upside — a desire for honest communication — gives you a foundation for making (incrementally) better decisions. Then you can seize on any improved outcome as signs of your newfound potency.

Or in other words, it’s like Bill Murray said: “baby steps.” Even with 20 pounds of explosives strapped to your torso.

Update: Did I accidentally kill Robert McNamara? 

If ever there was a guy who needed to calibrate his self-love, it was Robert McNamara, the much-vilified defense secretary who was forever tarnished by his role in the Vietnam War. This weekend I re-watched The Fog of War, the Errol Morris documentary in which McNamara very nearly breaks down with regret for his mistakes. Today I learn that McNamara has died. By Jenny McCarthy’s logic, I am partially responsible for the death. I regret my involvement.

North Korea finally cooperating

July 5, 2009

Pyongyang wants to help us test our missile defense system, says the L.A. Times. Their Jedi training is almost complete!

Though military officials said a clash between missiles of opposing nations was unlikely, preparations for possible action are at the most advanced stage yet. That is in part because of fears that a North Korean test as early as this weekend could involve a missile directed toward Hawaii.

Pff, “unlikely.” Let’s blow shit up!

Citing a potential threat to Hawaii, the U.S. last month deployed a gigantic sea-based radar system that officials say can guide underground interceptor missiles in Alaska and California toward long-range missiles in flight. The military also has intermediate-range land-based missiles, as well as specially equipped ships from which interceptors could be launched.

Wow, this is like reading Tom Clancy.

The system is known as sea-based X-band radar, a reference to the electromagnetic frequency at which it operates.

Now this is some Death Star looking shit right here:

Developed at a cost of about $900 million, the system looks like a giant white ball mounted atop a modified oil-drilling platform that can be moved around. The X-band system is based in Alaska and has made previous trips to Hawaii.

Ok, already, I want to blow shit up!

Still, many experts and critics of the missile defense system think the confidence is misplaced. “It is completely unwarranted, and it is a wild speculation based on assumptions that are almost certainly untrue,” said Theodore Postol, an MIT professor who has studied the system.

Wait, what?

Despite Pentagon claims of technological advances, for example, Postol argued that the U.S. interceptors would have a difficult time telling a missile warhead from “countermeasures” — decoys or other debris meant to fool the interceptors.

Um.

Critics also consider the North Korean threat overstated, especially given the long-standing inaccuracy of Pyongyang’s missiles and the fact that they are not equipped during test launches with any kind of warhead, nuclear or nonnuclear.

Whatever, L.A. Times writer person. The first part of your article was way cooler.

“Why would you want to shoot at it? It is not armed with a nuclear weapon, and it is going to land in the ocean,” Postol said. “What we are talking about is shooting at a missile that is not a threat with a missile that can’t intercept it.”

Yeah, that’s what I’m talkin’ about! Blow. Shit. UP!!

Why you should think soothing thoughts

July 1, 2009

Here’s Peter Orszag, director of the Office of Management and Budget, on the placebo effect, from a Slate Q&A:

One of the more fascinating studies I’ve come across in this vein was done by two Harvard psychologists who studied hotel cleaning staff and the effect of “perceived” exercise. At the outset, they found that most hotel workers didn’t believe their work was exercise—two-thirds reported that they didn’t exercise regularly, and more than one-third reported not exercising at all. But when the researchers informed a group of these workers that their eight-hour-a-day activity of cleaning rooms counted as “exercise,” the effects were similar to an increase in actual exercise. The workers lost weight and lowered their blood pressure, apparently just by thinking that the same activity they were already doing was exercise! That’s just one example that shows the power of human psychology.

Here’s the study.

Here’s a book the authors cite, about stress and health.

Psst, hey you guys.

June 25, 2009

© CERN

© CERN

There’s a new way… to possibly study THE HIGGS BOSON OMFG!!!!

In 2007, CDF researchers observed hints of exclusive, virtual gluon reactions in the form of high-energy photons radiating from colliding protons and antiprotons. Now the team has sifted through nearly 500 muon-antimuon pairs, identifying 65 that must have come from the decay of the Χc–very close to the rate predicted in 2005 by a team at Durham University in England [1]. Because the Χc has similar particle properties to the much heavier Higgs boson, the same basic reaction should produce the Higgs at the higher collision energies provided by the LHC, says Albrow. “It’s the strongest evidence that the Higgs boson must be produced this way, if it does exist.”

Physical Review Focus | A Higgs Boson without the Mess

Coastal intellectuals were so uptight about human pheromones

June 3, 2009

And by “were,” I mean in 2006.

Remember the story from that year about an interesting link between smell and sexuality? Well, I was working last night on my single-mechanism theory of male sexuality — how’s yours coming? let’s compare notes — and I got to the end of the theorizing — which is the fun part, involving chemicals — and then started looking at the data — which is the equally fun part, involving telecommunications — and the most salient bit of data I knew of was that 2006 study.

So I reread the NYTimes‘s coverage and was shocked by the unreasonable amount of hedging that in any other beat would be like saying, “This is study is pointless and possibly bogus.” 

The big data point:

Lesbians react to the smell of certain bodily odors in ways similar to heterosexual men and different from heterosexual women, new research suggests.

Interesting. Go on.

The substances involved are a progesterone derivative produced in male sweat and an estrogenlike steroid that has been detected in female urine. The two smells are processed in the brain differently from ordinary odors.

Ok.

In the experiment, 12 lesbians [small study, I grant you] smelled the two substances while researchers observed blood flow in their brains with PET scans. The scents activated parts of the brain that ordinarily process odors, but the estrogenlike compound also activated a part of the hypothalamus, as it does in heterosexual men.

Animal studies suggest that the hypothalamus is important in sexual behavior. So when that part of the brain lights up under the stimulus of an odor, a sexual response, rather than simply an olfactory one, is implied.

The prior finding:

Heterosexual women responded to the male sweat odor in the hypothalamus rather than in the olfactory portions of the brain, and heterosexual men responded to female estrogen in the hypothalamus. Homosexual men processed the smells in the same way as heterosexual women.

Huh? I can barely follow that. He’s kludging it up so nobody will get what he really wants to say: Here’s another consistency check on whether these chemicals are pheromones, a puzzle we’ll only solve for sure if we knock out a few key control experiments, such as tracking the natural history of these patterns from a young age.

Despite the similarities, lesbians do not respond to these two odors in exactly the same way as heterosexual men, so the analogy with gay men and heterosexual women is imperfect. “This observation could favor the view that male and female homosexuality are different,” said Dr. Savic, an associate professor of neurology at the Karolinska Institute in Stockholm.

The doubletalk:

The researchers also emphasize that their findings have no clinical application. “It is very important to make clear that the study has no implications for possible dynamics in sexual orientation,” Dr. Savic said.

What?? Seriously? Please show me other kinds of research that would have implications for “dynamics in sexual orientation” without using methods like these! It’s a scent that permits heterosexual members of one sex to recognize those of the other sex! Geeeyaaaaad.

Ok, look, I know it’s all correlation equals causation. Maybe we’re witnessing neural correlates of learned patterns of sexuality. And she did say “dynamics,” which every lay reader knows means change over time. And no, I haven’t Googled any single other thing on the subject. And yes, maybe NIcholas Bakalar had a long day that day.

I want nevertheless to record my first reactions upon revisiting that small bit of history.

The mere way the information was framed indicated a high (if only perceived) level of defensiveness on everybody’s part. From reading and talking to everybody, I feel says saying the evolutionary psychologists refuse to understand the subtleties of sexism, so they won’t acknowledge smart arguments by post-structuralists. And the post-it crowd sure as shit is not going to be having the mass media perpetuating the idea, foisted on us by undersexed nerds, of pheromones — human pheromones, for God’s sake! — when Times readers? women the world over are being treated like this and this.

In microcosm, the above is the bottom line message of Fistful of Science: Masculine and feminine; objective and subjective; scientific authorities and critically oriented academics — neither one knows how to talk to the other in this culture. It’s like a stereotypically bad marriage. One side is empowered but whines whenever he has to do anything; the other side is marginalized and forced to lash out to get fair treatment. Both sides have way, way more in common than they want to admit.

Now, regarding the specific issue of human pheromones, the authoritarian in me says, Yes, some people will misuse the likely fact (does anyone have a better, non-ridiculous explanation?) that human sexual orientation has a strong inborn biological component (to say “genetic” would imply single-gene causation; “hereditary” makes it sound like a disease that strikes both sexes).

The libertarian in me says people have nothing to fear but their chains.

And the empiricist in me says, I need more data. Seen any studies?

Finding happiness in the saddest thing

May 18, 2009

I’d be annoyed at myself if I didn’t mention a lovely piece in The Atlantic, “What Makes Us Happy?” in which we learn about the Grant Study, an ongoing 60-year+ longitudinal investigation of 268 Harvard dudes, overseen by one George Vaillant.

Extreme comb-overs notwithstanding, I admire any scientist willing to treat psychoanalytic concepts seriously. From Vaillant’s taxonomy of defense mechanisms, also called adaptations:

The healthiest, or “mature,” adaptations include altruism, humor, anticipation (looking ahead and planning for future discomfort), suppression (a conscious decision to postpone attention to an impulse or conflict, to be addressed in good time), and sublimation (finding outlets for feelings, like putting aggression into sport, or lust into courtship).

Note that blogging intellectualization — “mutating the primal stuff of life into objects of formal thought” — ranks as a “neurotic” or third-tier adaptation, which will come back around when I post my thoughts on Daniel Pinchbeck.

“Much of what is labeled mental illness,” Vaillant writes, “simply reflects our ‘unwise’ deployment of defense mechanisms. If we use defenses well, we are deemed mentally healthy, conscientious, funny, creative, and altruistic. If we use them badly, the psychiatrist diagnoses us ill, our neighbors label us unpleasant, and society brands us immoral.”

Oh, the nuance of it all!

So what makes us happy? According to Vaillant’s interpretation of the study data, happiness comes from deploying defense mechanisms in a way that facilitates warm social bonds.

Will Wilkinson among others likes this bit about the downside of happiness:

[P]ositive emotions make us more vulnerable than negative ones. One reason is that they’re future-oriented. Fear and sadness have immediate payoffs—protecting us from attack or attracting resources at times of distress. Gratitude and joy, over time, will yield better health and deeper connections—but in the short term actually put us at risk. That’s because, while negative emotions tend to be insulating, positive emotions expose us to the common elements of rejection and heartbreak.

I can’t help but think of my father, who died last October. It was one of the best things that’s happened to me in, I don’t even know, years? decades? I don’t feel so trapped in myself or in my life anymore. I left New York. I’m finally developing a healthy relationship with my mom and am slowly getting there with my younger brother. Intellectualization flirts with sublimation. I could credit other influences in bringing me to this point, but Pops Minkel’s mortal uncoiling was the catalyst for a lot of very positive change.

Here’s to the upside of sadness. Thanks, Bill.

What’s awesome this week: Let them eat dog food

May 15, 2009

1. How Torture Helped the Allies in WWII

Whatever role the bombings played in hastening Japan’s unconditional surrender, it was probably enhanced by the testimony of captured Air Force First Lieutenant Marcus McDilda. Though he initially professed to know nothing about the Manhattan Project or the atomic bomb that had been dropped on Hiroshima—because he didn’t—under torture he “confessed” that, contrary to Japanese hopes that the Americans could not possibly have produced more than a few, the United States had hundreds ready for deployment, with Tokyo and Kyoto next on the list of targets.

 

A distant Shaftoe relative, no doubt.

 

2. Can People Distinguish Pâté from Dog Food?

 

As seen on Colbert:

To prevent bias, Newman’s Own dog food was prepared with a food processor to have the texture and appearance of a liver mousse. In a double-blind test, subjects were presented with five unlabeled blended meat products, one of which was the prepared dog food. After ranking the samples on the basis of taste, subjects were challenged to identify which of the five was dog food.

 

One of the researchers keeps a blog, Blind Taste.

 

3. Rules for Time Travelers: #5 — Black holes are not time machines.

Sadly, if you fell into a black hole, it would not spit you out at some other time. It wouldn’t spit you out at all — it would gobble you up and grow slightly more corpulent in the process. If the black hole were big enough, you might not even notice when you crossed the point of no return defined by the event horizon. But once you got close to the center of the hole, tidal forces would tug at you — gently at first, but eventually tearing you apart. The technical term is spaghettification. Not a recommended strategy for would-be time adventurers.

4. Neuroeconomics has failed Americans in 5 key ways

The type of punditry I aspire to.

What is their promise? Very simple: Neuroeconomists promise that if investors, taxpayers and voters simply follow the advice of neuroeconomists, they’ll get rich. Your 401(k) and your retirement portfolios will prosper because neuroeconomics promises to make you “less irrational,” in control of your brain, and therefore, a successful investor.

 

Sorry, but that’ll never happen. Never. The human brain is, and always will be, irrational.

5. Free radicals after exercise are good, okay?

Forty men took part in a four-week training program. Half the group also received daily doses of Vitamins C and E. The researchers discovered that exercise on its own improves insulin sensitivity, which keeps diabetes at bay. But taking the vitamins erased that gain—findings that appear in the May 12th issue of the Proceedings of the National Academy of Sciences. 

 

6. The challenge of proving a negative: woman struck by meteorite

 

SylacaugaHulittHodgesW

[T]he Hodges Meteorite […] blasted through the roof of a home in Sylacauga, Ala., in 1954. It bounced off a radio and hit Ann Elizabeth Hodges, badly bruising her hand and hip.

Scientific post-colonialism: randomized trials vs. global poverty

April 24, 2009

Back in ’05 I ganked a story from Marginal Revolution about randomized trials of NGO programs in poor countries. Examples from MIT’s Poverty Action Lab:

Colonialist? You decide. My story:

By randomly splitting people into two groups, one of which receives an experimental intervention, researchers can set up potentially simple, unbiased comparisons between two approaches.

The emergence of cheap, skilled labor in India and other countries during the 1990s changed that, Banerjee says, because these workers could collect the data inexpensively. At the same time, nongovernmental organizations (NGOs) were proliferating and started looking for ways to evaluate their antipoverty programs.

Fast forward to yesterday, when Tyler Cowen tells me two of the economists who co-founded the MIT lab are on somebody’s short-list for an economics prize considered a prelude to the Nobel.

[T]he clear favorite is Esther Duflo, 36, who leads the Massachusetts Institute of Technology’s Jameel Poverty Action Lab with MIT colleague Abhijit Banerjee.

Re: the other co-founder, Sendhil Mullainathan:

One insight: The behavioral weaknesses of the very poor are no different than the weaknesses of people in all walks of life, but because the poor have less margin for error, their behavioral weaknesses can be much more costly.

Ahem. Indeed.

So anyway, where to pitch a story? If only the idea of incremental good works had cultural caché.

Update: the winner was Emmanuel Saez, who studies income inequality.

The LHC ended the String Wars, if not the Trouble with Physics

April 21, 2009

Peter Woit is one of the two lead critics of string theory who touched off the String Wars. Today I was going through his blog scanning for leads and found this, in a post about a Pop Sci story that listed “theoretical physicist” as one of the worst jobs in science:

As mentioned here repeatedly, claims that hiring in particle theory is dominated by string theory are behind the times. String theorists are now yesterday’s fad, with terrible job prospects if they don’t have a permanent position. Today’s fads are LHC phenomenology and cosmology…

LHC of course = that Large Hadron Collider thingy.

String theory is on its way out in American universities it seems, but the long-standing pattern of fad-driven hiring isn’t. Which is one thing that makes the idea of trying for a career in theoretical physics these days about as appealing to many smart young people as the idea of going into the vermin handling business…

Which of course makes perfect sense. The particle theory community has an opportunistic, aphilosophical, arguably hierarchical style because it “evolved” to get a bunch of of people to quickly solve problems coming out of accelerator data. Or so claims Lee Smolin, anyway – the other lead string theory critic – whose book (The Trouble with Physics) I was flipping through last night. So of course when New Scientist caught up with the Horgan-bashing Ed Witten, he was at CERN waiting for the LHC to come back online.

In a word: fascinating!