Smooth Pebbles

Why the Mona Lisa's smile vanishes

Stumbled across this early this morning: Why the Mona Lisa's smile is so strangely alluring, and seems to come and go. From the website of Harvard neuroscientist Margaret LIvingstone:

The elusive quality of the Mona Lisa's smile can be explained by the fact that her smile is almost entirely in low spatial frequencies, and so is seen best by your peripheral vision (Science, 290, 1299). These three images show her face filtered to show selectively lowest (left) low (middle) and high (right) spatial frequencies.

So when you look at her eyes or the background, you see a smile like the one on the left, or in the middle, and you think she is smiling. But when you look directly at her mouth, it looks more like the panel on the right, and her smile seems to vanish. The fact that the degree of her smile varies so much with gaze angle makes her expression dynamic, and the fact that her smile vanishes when you look directly at it, makes it seem elusive.

Livingstone has done some other fascinating work on depth perception in artists; check it out at her web page.

A Debate over Hopeless Monsters (and Sloppy Narratives)

A bit o' squabble has broken out about hopeful monsters. As paleontologist evolutionary geneticist Jerry Coyne notes in a guest post at The Loom, Carl Zimmer's blog, hopeful monsters are the products of ... well, there's the problem: They were either the product of sudden large evolutionary forces, as suggested in a recent NY Times blog by Olivia Judson or, in Coyne's view, the product of overactive imaginations and underactive skepticism and fact-tending among biologists like Judson.

Both Judson's and Coyne's pieces are good fun reads. I find Coyne's more convincing, and there's no buying both here, I think; Coyne says the hopeful monster idea is a pop-up clown that, though horrid science, keeps popping up, basically because there is something cute about it. Clearly he has fun knocking it down, too.

Anyway, as I noted in a comment at Carl's blog, there's a lot going on here, including a perennial tension found in both science and writing about science that I find fascinating: The attraction to the attractive narrative on one hand and a commitment to rigor and what scientists call parsimony (the more simpler, more spare, more cautious explanation) on the other.

I once heard this expressed this way: At a table full of scientists and scientist types (groupies?), someone quoted Ptolemy (perhaps apocryphally; I can't find it anywhere):

"The goal of science is finding the most compelling story consistent with the facts."

Someone else at the table said,

"No! It is finding the simplest story consistent with the facts."

Betwixt lies all sorts of room for disagreement, including, it seems, this one between Judson & Coyne. I'm not saying both Coyne and Judson are consistent with the facts on this one. (I'm no qualified judge, but Coyne convinces me Judson wandered astray.) But you see that tension here -- and elsewhere, constantly. In the pivotal 19th-century argument over evolution, for instance, which pitted two beautiful, compelling narratives each other: Louis Agassiz's creationist yarn, which was a gorgeous narrative spun by an electrifying speaker with a dazzling intellect, and Charles Darwin's story of evolution by natural selection, which also had great narrative drive (if no teleological 'motive') and a compelling aesthetic unity. Darwin's won out, of course (well, mostly ...), because he proved his story more consistent with the facts. The debate shaped not just the scientific consensus on the species question but the defini tion

And right now we're seeing this in the debate over whether the mirror-neuron theory is being wildlly overextended.

But the same tension was at play. We find attractive narrative explanations that are simple -- but not TOO simple. And we like NOVEL things (or apparently novel things). This affects both scientists and scientific journalists. I would say, by the way, that sci journalists, just like others, DO have an obligation to describe a field accurately. Doesn't mean they can't go out on a limb with their own opinion or reading of something, though, as long as they make clear that -- and not reporting -- is what they're doing. This has its dangers, of course, which Judson has encountered in Coyne's post.

Thanks to Coyne for writing this and Carl for putting it up there.

What's Under the Rock: Full Data Shows SSRIs Barely Best Placebo

I've written before, both here in Smooth Pebbles and in print, about how FDA policy and drug company practices have allowed drug makers to publish (and the FDA to base approval on) only the most flattering drug-trial results while keeping less-flattering studies in the drawer. Today a New England Journal of Medicine report shows how things change when you include the results from the drawer: The effectiveness of many SSRIs dives to near placebo-level. This despite that the companies design and conduct most of these trials in a way calculated to produce positive results.

When I wrote on this a couple years ago, UCSF professor and Journal of the American Medical Association editor Drummond Rennie, told me, "If a company does ten trials on a drug and two show it helps but eight show it works no better than Rice Krispies, I'm not exactly getting a scientific view if they publish only the two positive studies.... How can we practice sophisticated medicine if the drug companies are hiding their results? That's not science. That's marketing."

The problem remains. Depressing. I recommend a good run.

Benedict Carey has a good story on it at the Times. And here's the meat of the abstract from the NEJM:

Among 74 FDA-registered studies, 31%, accounting for 3449 study participants, were not published. Whether and how the studies were published were associated with the study outcome. A total of 37 studies viewed by the FDA as having positive results were published; 1 study viewed as positive was not published. Studies viewed by the FDA as having negative or questionable results were, with 3 exceptions, either not published (22 studies) or published in a way that, in our opinion, conveyed a positive outcome (11 studies). According to the published literature, it appeared that 94% of the trials conducted were positive. By contrast, the FDA analysis showed that 51% were positive. Separate meta-analyses of the FDA and journal data sets showed that the increase in effect size ranged from 11 to 69% for individual drugs and was 32% overall.

You paid for this research, now you get to read it

The public will soon start getting quicker access to research results it sponsors. From BioMed Central Blog : NIH Public Access Policy to become mandatory:

NIH Public Access Policy to become mandatory

Many open access advocates will already have heard that NIH's Public Access Policy, until now voluntary, is set to become mandatory following President Bush's approval on Dec 26th 2007 of the latest NIH appropriations bill, which includes the following wording:

"The Director of the National Institutes of Health shall require that all investigators funded by the NIH submit or have submitted for them to the National Library of Medicine's PubMed Central an electronic version of their final, peer-reviewed manuscripts upon acceptance for publication to be made publicly available no later than 12 months after the official date of publication: Provided, That the NIH shall implement the public access policy in a manner consistent with copyright law."

This is great news both for researchers and for the general public. Peter Suber's January SPARC Open Access Newsletter contains a detailed analysis of what the change means, and identifies some of the key issues that remain to be resolved.

More at BioMed Central Blog : NIH Public Access Policy to become mandatory

Cod, climate, and Nature's new Climate Change journal

A new journal from the Nature Publishing Group (publishers of Nature, Nature Neuroscience, and other favorites of mine) has just started a journal about climate change, and to my delight they feature a story about climate change and Atlantic cod, an old love of mine from my time on the Gulf of Maine.

Atlantic cod, Gadus callarius Linneaus, by Goode, from the magnificent Bigelow and Schroeder, Fishes of the Gulf of Maine, 1953, the best field guide I've ever read, now online.

Cod aren't doing terribly well, because of overfishing and decimation of inshore spawning stocks, though some pockets still produce nice numbers of this lovely fish. The Nature Climate Change story gives a heads-up to a study about how cod fared in previous climate change cycles. This is a hot topic, as many fishermen and scientists wonder whether warming seas have already contributed to the cod's decline so far or might inhibit its recovery. The new study finds that previous large swings in climate have cut cod populations back by as much as a fifth, knocking it down but not out. But the authors don't seem optimistic on how well they'll fare in this one.

Having read a few of these papers, I gather that the jury is still out on how much climate change will complicate the cod's future.

The Natural Environment Research Center actually writes it up more cleanly than the Nature Climate Change story does:

The new findings, published online today (14 November 2007) in Proceedings of the Royal Society B, show that natural climate change has previously reduced the range of cod to around a fifth of present-day values. Despite this, cod continued to populate both sides of the North Atlantic.

The researchers used a computer model and DNA techniques to estimate where cod could be found in the ice age, when colder temperatures and lower sea-levels caused the extinction of some populations and the isolation of others. ....

Professor Bigg [the lead researcher] said "This research shows that cod populations have been able to survive in periods of extreme climatic change, demonstrating a considerable resilience. However this does not necessarily mean that cod will show the same resilience to the effects of future climatic changes due to global warming."

Yet another story, this one from the Telegraph and titled "Climate change joins fishing as cod threat," notes that cod don't do so well in their northernmost ranges:

[The] study by Prof Bigg and colleagues shows that cod "are good at surviving habitat reduction, except in the northern half of their range. With regard to future climate change, it is clear that the acceptable habitat will retreat poleward significantly as temperatures warm," [Bigg] says.

"It is not unlikely that acceptable conditions for spawning will disappear from much of the North Atlantic to become restricted to the Arctic."

Cod is currently not found there, apart from the Barents Sea, and so there is the question of whether the currently depleted species is able to colonise new areas faster than its old habitat is lost, says Prof Bigg.

Yet another paper, meanwhile, by Mieszkowska, Sim, and Hawkins [pdf download], concluded that climate change might already be adding pressure to North Sea cod. The jury will doubtless be out on this one a while. But it raises more worries both about what climate change may do to cod -- and about the difficulty of predicting how different species will fare as things warm up.

Left-Hand-Turn Elimination - New York Times

There were a mess of interesting items in the New York Times Magazine annual "Ideas" issue last December 9, but I keep thinking of this one every time a) I wait to make a left-hand turn or b) see a UPS truck. Short v: Avoid left turns and save ...

Here's the whole thing:

Left-Hand-Turn Elimination

By JOEL LOVELL

Published: December 9, 2007

It seems that sitting in the left lane, engine idling, waiting for oncoming traffic to clear so you can make a left-hand turn, is minutely wasteful — of time and peace of mind, for sure, but also of gas and therefore money. Not a ton of gas and money if we’re talking about just you and your Windstar, say, but immensely wasteful if we’re talking about more than 95,000 big square brown trucks delivering packages every day. And this realization — that when you operate a gigantic fleet of vehicles, tiny improvements in the efficiency of each one will translate to huge savings overall — is what led U.P.S. to limit further the number of left-hand turns its drivers make.

The company employs what it calls a “package flow” software program, which among other hyperefficient practices involving the packing and sorting of its cargo, maps out routes for every one of its drivers, drastically reducing the number of left-hand turns they make (taking into consideration, of course, those instances where not to make the left-hand turn would result in a ridiculously circuitous route).

Last year, according to Heather Robinson, a U.P.S. spokeswoman, the software helped the company shave 28.5 million miles off its delivery routes, which has resulted in savings of roughly three million gallons of gas and has reduced CO2 emissions by 31,000 metric tons. So what can Brown do for you? We can’t speak to how good or bad they are in the parcel-delivery world, but they won’t be clogging up the left-hand lane while they do their business.

[From Left-Hand-Turn Elimination - New York Times]

The Garden Waits

You're supposed to bring Adirondack chairs in for the winter, to make them last longer. But I like to leave them in the garden, sitting in their comfortable circle. They look tough, as mountain chairs should. And they remind me the garden, and spring and summer, await.

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Gay Men and Women Navigate Differently ..

Spatial cognition research is a major interest of mine. This one's a doozy. From ScienceDaily, Jan 3, 2008:

Gay Men Navigate In A Similar Way To Women, Virtual Reality Researchers Find
ScienceDaily (Jan. 3, 2008)

Gay men navigate in a similar way to women, according to a new study from researchers at Queen Mary, University of London.

Dr Qazi Rahman, from Queen Mary’s School of Biological and Chemical Sciences used virtual reality scenarios to investigate if spatial learning and memory in humans can be linked to sexual orientation.

Differences in spatial learning and memory (our ability to record and recall information about our environment) are common between men and women. It has been shown that men consistently outperform women on tasks requiring navigation and discovering hidden objects; whereas women are more successful at tests which require them to remember where those objects lie in a particular space.

This is the first study to investigate if those differences are also true for gay, lesbian and straight individuals.

Dr Rahman used virtual reality stimulations of two common tests of spatial learning and memory, designed by researchers at Yale University. In the Morris Water Maze test (MWM), participants found themselves in a virtual pool and had to escape as quickly as possible using spatial clues in the virtual room to find a hidden platform. In the Radial Arm Maze test (RAM), participants had to traverse eight ‘arms’ from a circular junction to find hidden rewards. Four of the arms contained a reward, four did not.

The virtual 'water maze' the participants faced.

Dr Rahman and his research assistant, Johanna Koerting, found that during the MWM test gay men and straight women took longer to find the hidden platform than did straight men. However, both gay and straight men spent more of their “dwelling time” in the area where the hidden platform actually was, compared to straight and lesbian women.

Dr Rahman explains: “Not only did straight men get started on the MWM test more quickly than gay men and the two female groups, they also maintained that advantage throughout the test. This might mean that sexual orientation affects the speed at which you acquire spatial information, but not necessarily your eventual memory for that spatial information.

More at ScienceDaily. Same site also has a story on earlier research showing sexual differences in navigation skills and how well they lasted as we age.

Simple checklist saves 1500 lives; feds axe it

A New York Times piece by Atul Gawande gives some good news and bad news about a life-saving checklist developed to prevent fatal infections in intensive care units.




The good news:

A year ago, researchers at Johns Hopkins University published the results of a program that instituted in nearly every intensive care unit in Michigan a simple five-step checklist designed to prevent certain hospital infections. It reminds doctors to make sure, for example, that before putting large intravenous lines into patients, they actually wash their hands and don a sterile gown and gloves.

The results were stunning. Within three months, the rate of bloodstream infections from these I.V. lines fell by two-thirds. The average I.C.U. cut its infection rate from 4 percent to zero. Over 18 months, the program saved more than 1,500 lives and nearly $200 million.

The bad news:

Yet this past month, the Office for Human Research Protections shut the program down. The agency issued notice to the researchers and the Michigan Health and Hospital Association that, by introducing a checklist and tracking the results without written, informed consent from each patient and health-care provider, they had violated scientific ethics regulations. Johns Hopkins had to halt not only the program in Michigan but also its plans to extend it to hospitals in New Jersey and Rhode Island.

The government’s decision was bizarre and dangerous. But there was a certain blinkered logic to it, which went like this: A checklist is an alteration in medical care no less than an experimental drug is. Studying an experimental drug in people without federal monitoring and explicit written permission from each patient is unethical and illegal. Therefore it is no less unethical and illegal to do the same with a checklist. Indeed, a checklist may require even more stringent oversight, the administration ruled, because the data gathered in testing it could put not only the patients but also the doctors at risk — by exposing how poorly some of them follow basic infection-prevention procedures.

Truly stunning. The Times article is not long and is well worth reading, as is the New Yorker article from 12/10/2007 article from 12/10/2007 in which Gawande described the genesis of the checklist program. (That was before the Office for Human Research heard about it and gave it the shaft.)

Mirror Neuron Backlash

A backlash is brewing against the mirror neuron theory, or at least its overextension. (Fair disclosure: I was part of the alleged problem.) I picked this up distinctly at the Society of Neuroscience meeting last November. I've seen it in the literature since. Last week, I convinced Greg Hickok, a cogsci/language researcher at UC Irvine, to make his case in Scientific American's Mind Matters for checking mirror-neuron-theory overreach. An excerpt is below, and you can check out the whole thing at Mirror Neurons -- Rock Stars or Backup Singers?

Sorry, couldn't resist the photo.

Hickok, I should note, keeps a blog called Talking Brain on the neural organization of language with his colleague David Poeppel. Well worth checking out. Meantime his Mind Matters entry on mirror neurons is below:

Mirror neurons are the rock stars of cognitive neuroscience. Discovered in the mid-1990s by Giacomo Rizzolattiand his colleagues at the University of Parma, these brain cells have been claimed to be the neural basis for a host of complex human behaviors including imitation, action understanding, language, empathy, and mind-reading – not psychic mind-reading, but our capacity to "get inside someone else's head" and imagine how they feel or what they might do. Meanwhile, dysfunction of the mirror neuron system has been linked to developmental disorders, such as autism. With that kind of explanatory range, it's no surprise that mirror neurons have headlined in all forms of news media. But is this rock star status deserved? Will mirror neurons have the star power longevity of Mick Jagger? Or are they just back up singers?

[From Mirror Neurons -- Rock Stars or Backup Singers?