Steven Pinker’s Style Guide

By Carl Zimmer | November 16, 2012 1:33 pm

Each year I run a workshop for science graduate students at Yale, encouraging them to write clearly, compellingly, and effectively. I’m tempted next year to just cue up this video of Steven Pinker discussing his next book–a psychology-based guide to good writing–and kick back.

[via]

CATEGORIZED UNDER: Meta, Teaching

Creeping Out the Kids: @TEDYouth tomorrow

By Carl Zimmer | November 16, 2012 12:35 pm

TEDYouth is in its second year of putting together an afternoon of short talks for high school students. I’ll be joining in with a quick introduction to my favorite parasite. The event, which takes place in New York City, will be live-streamed–visit this page for more information for viewing. It will run from 1 pm to 6 pm ET. I’m scheduled to talk at 2:45.

CATEGORIZED UNDER: Talks

Fear, Reward, and The Bottle: An Update to My Column on Neurogenetics

By Carl Zimmer | November 15, 2012 12:50 pm

In May I wrote in Discover about a major experiment in neuroscience. Ahmad Hariri, a neuroscientist at Duke, is gathering lots of data from hundreds of college students–everything from genetic markers to psychological profiles to fMRI scans. He hopes that the Duke Neurogenetics Study, as he’s dubbed it, will reveal some of the ways in which the variations in our genes influence our brain circuitry and, ultimately, our personality and behavior.

Hariri plans to collect data from over 1000 people, but he and his colleagues are already starting to analyze the hundreds of students they’ve already examined to look for emerging patterns. In the open-access journal Biology of Mood and Anxiety Disorders, they’ve just published some of their first results. While the results are, of course, preliminary, they do offer an interesting look at the future of neuroscience. Rather than pointing to some particular gene or brain region to explain some feature of human behavior, neuroscientists are learning how to find patterns that emerge from several factors working together.

For their new study, Hariri and his colleagues looked in particular at problem drinking. They hoped to find factors that predicted whether students would start imbibing worrisome amounts of alcohol. Other scientists have previously found evidence that a stressful event–the death of a parent, failing a class, and such–sometimes leads students to hit the bottle. But plenty of students endure these hardships and don’t end up getting drunk so often. Hariri and his colleagues suspected that the difference might have to do with how our brains respond to both stress and alcohol.

When they sifted through their data from 200 students, they found two factors helped predict whether a student was a problem drinker or not. One was how strongly their brains responded to rewards. Hariri and his colleagues tested this reward response by having students play a guessing game while having their brains scanned. They had to guess the value of a number on a card, and then they saw whether they got it right or not. Success brought a surge of blood to a region of the brain called the ventral striatum–a region that responds to many pleasures. Recovering alcoholics who see a picture of a bottle will experience a surge in the ventral striatum, for example. The surge was stronger in some students than others. Students who had a stronger surge in the ventral striatum had higher levels of problem drinking in the wake of stressful events.

But that wasn’t the whole story, Hariri found. There was one more requirement. In another test, he and his colleagues tested how people’s brains responded to fearful images–pictures of scared faces, for example. Such sights usually trigger a surge of activity in a region called the amygdala. And some people have a stronger response there than others to the same picture. Hariri found that people with a strong reward response started drinking after a stressful event if they also had a weak response from the amygdala to fearful images.

The suffering that comes from losing a job or being assaulted can lead people to seek solace through alcohol. Hariri’s research suggests that the stronger a reward a person experiences from a drug like alcohol, the more they’ll drink. But that’s not the case if a high-reward person also has a high fear response in the amygdala. A person with a strong amygdala response may feel anxiety about the dangers of getting too drunk and back away from problem drinking. If people don’t sense the threat so keenly, however, then they may have nothing standing in the way of taking in too much alcohol. The scientists found this three-way interaction between stress, reward, and threat when they looked at students who were problem drinkers at the time of the study, and they also found it when they followed up three months later and discovered some of their students had developed a new drinking problem.

As with any study like this, we’ll have to wait and see if it gets supported by replicated studies. Hariri himself will be able to run that sort of study when he has collected more data from other students. If it holds up, scientists may eventually be able to find gene variants that are associated with the high-reward low-threat brain. Some studies even have suggested that a single variant can produce both changes. Perhaps a report from a DNA-sequencing company might include a list of the variants that make some people more prone to drink in stressful situations. On the other hand, it’s also possible that the problem drinking among the students came first, and led to their experiencing stressful events. Teasing apart all the strands will take some time.

PS: For the data geeks, here’s a figure from the paper. The brain in (A) shows the reward-related activity in the ventral striatum. B shows the amygdala’s response to fear. The graphs show how likely people are to experience problem drinking after a stressful event. The left graph shows the response from people with a low reward response from the ventral striatum, and the graph to the right shows high-responders. In each graph, the scientists break out the high amygdala response (green line) and low (blue). The one line that stands out belongs to the high-reward, low-threat subjects.

[Image: Dominic “Dome” on Flickr via Creative Commons]

CATEGORIZED UNDER: Brains, Writing Elsewhere

Excuse The Hoot!

By Carl Zimmer | November 14, 2012 11:00 am

The American Association for the Advancement of Science has just announced this year’s Kavli Awards for Science Journalism. I’m pleased to report that I won in the category of newspapers with a circulation of 100,000 or more.

The award was for three stories I wrote for The New York Times. They didn’t have much in common, which is how I like it:

A Sharp Rise in Retractions Prompts Calls for Reform (April 17)–The scientific enterprise is getting dysfunctional. The fact that this article received 341 comments suggests to me that it hit a nerve.

Studies of Microbiome Yield New Insights (June 19)–I explore the emerging concept of medical ecology, in which we look at our bodies as wildlife parks to be managed, rather than battlegrounds to be carpet-bombed.

Evolution Right Under Our Noses (July 26)–My editor at the time, James Gorman, came across a cool paper on the rapid evolution of fish in the Hudson River. I said, “It’s nice, but it’s not unique by any means. I mean, evolution’s going on all over New York.” Gorman, with that sharp editorial nose of his, said, “Really? Then write about that.” So off I went to the wilderness of Manhattan parks and median strips.

I am now officially barred from winning this award again, having won it in 2004 for my writing here at The Loom and in 2009 for another batch of stories for the Times. I happily hang up my cleats and thank AAAS for all three honors.

Of course, you can’t win a prize for newspaper writing without a newspaper to write for, so I have to give heaps of thanks to the Times, to which I’ve been contributing stories for the past eight years. Along with Jim Gorman, I’ve worked with many other fine folks at the Science Times (including David Corcoran, Michael Mason, Jill Taylor, Jennifer Kingson, and Barbara Strauch), as well as Jamie Ryerson at the Sunday Review. They are compatriots in curiosity. Over the past eight years we have looked anxiously at the woes faced by our dear Gray Lady, as the entire world of journalism has shuddered with changes. Things are not all lollipops and rainbows in 2012, but there are many reasons for optimism–not least of which, I think, is the mere existence of the Science Times, still dedicating every Tuesday to the world beyond elections and quarterly employment reports after more than 30 years.

I’ll be heading up to Boston in February to pick up the prize at AAAS’s annual meeting. My wife Grace will be accompanying me, which only makes sense, since she makes it possible for me to scurry off after new species of ants living on Broadway without the rest of our life collapsing in on itself. Ultimately, all thanks must go to her–including thanks for going to Boston in February.

[Image: Portrait of Brother David With A Mandolin, Marc Chagall, via Wiki Paintings]

CATEGORIZED UNDER: Meta, Writing Elsewhere

Herman Melville, Science Writer

By Carl Zimmer | November 11, 2012 11:00 am

Over the past few weeks, I’ve been dipping into a project called “Moby Dick Big Read.” Plymouth University in England is posting a reading of Moby Dick, one chapter a day. The readers are a mix of writers, artists, and actors, including Tilda Swinton.  They are also posting the chapters on SoundCloud, which makes them very easy to embed. Here is one of my personal favorites, Chapter 32, “Cetology.”

When I was an English major in college, I read Moby Dick under the guidance of English professors and literary critics. They only paid attention to a fraction of the book–the fraction that followed Ishmael on his adventures with Captain Ahab. This was the part of the book that they could easily compare to other great novels, the part they could use for their vague critiques of imperialism, the part–in other words–that you could read without having to bother much with learning about the particulars of the world beyond people: about ships, about oceans, and, most of all, about whales. How many teachers, assigning Moby Dick to their students, have told them on the sly that they could skip over great slabs of the book? How many students have missed the fine passages of “Cetology”?

I’ve read Moby Dick several times since graduating college and becoming a science writer. I look back now at the way I was taught the book, and I can see it was a disaster, foisted upon me by people who either didn’t understand science or were hostile to it, or both. Of course the historical particulars of the book matter. It’s a book, in part, about globalization–the first worldwide energy network. But the biology of the book is essential to its whole point. Just as Ahab becomes obsessed with Moby Dick, the scientific mind of the nineteenth century became mad with whales.

“Cetology” reminds the reader that Melville came before Darwin. Ishmael tries to make sense of the diversity of whales, and he can only rely on the work of naturalists who lacked a theory of evolution to make sense of the mammalian features on what looked like fish. You couldn’t ask for a better subject for a writer looking for some absurd feature of the natural world that could serve as a wall against which Western science could bang its head.

The people I know who don’t like the “whale stuff” in Moby Dick probably hate this chapter. It seems to do nothing but grind the Ahab-centered story line to a halt. (No movie version of Moby Dick has put “Cetology” on film.) But do you really think that a writer like Melville would just randomly wedge a chapter like “Cetology” into a novel for no reason–not to mention the dozens of other chapters just like it? Or perhaps it would be worth trying to find out what Melville had in mind, even if you might have to do a bit of outside reading about Carl Linnaeus or Richard Owen? It would be quite something if students could be co-taught Moby Dick by English professors and biologists.

“Cetology” is organized, explicitly, as a catalog, but don’t let the systematic divisions of its catalog put you off. This is science writing of the highest order, before there was science writing. Listen to the words he uses to describe each species. If you go whale watching some day and are lucky enough to spot a fin whale raising its sundial-like dorsal fin above the water, chances are you will utter to yourself, “gnomon.” 

On the Occasion of My Belly Button Entering the Scientific Literature

By Carl Zimmer | November 7, 2012 9:25 pm

Our skin is encased in a snug microbial suit, from our scalps to the tips of our toes. Bacteria begin to colonize our skin from the moment we are born, and they continue to coat us throughout life. They do us many favors. They moisturize our skin to keep it supple; they unleash anti-microbial toxins to ward off pathogens that might make us ill. Scientists know that our skin is home to many species, but they can’t yet say exactly how many–or why some species are found more often on the elbow than on the chin.

Two years ago at a conference in North Carolina, I ran into Rob Dunn, a biologist who was conducting a survey of this menagerie. He was interested in the life found in one particular spot on the human body: the belly button. At the conference, he was handing out Q-tips people could use to swab their navels, which he and his colleagues could then study to tally up the species dwelling there.

Five months later, Dunn sent me a preliminary report: “You, my friend, are a wonderland.” I was the proud host of 53 different types of bacteria, including some decidedly weird creatures, such as a microbe only known from the ocean, and another from the soils of Japan.

I was only one of many human hosts to offer up our navel’s residents to Dunn’s scrutiny. Today, Dunn and his colleagues published a scientific paper on the biological diversity found in 60 bellybuttons in the journal PLOS One. They show that the diversity of my navel was not freakish. Even in a tiny divot of human flesh, dozens or even hundreds of species of bacteria can coexist. All told, Dunn and his colleagues identified 2368 different species living in our 60 belly buttons. The average person had 67 species, with the number ranging from a low of 29 species to a swarming high of 107.

Out of those 2368 species, the majority–1458–are new to science. A few of them are very common, while most are exquisitely rare. Dunn and his colleagues found that eight types of bacteria made up nearly half the microbes the scientists detected. Each of them was present on over seventy percent of us. But the vast majority of the species–2188 all told–lived on six or fewer people. Most were found only on a single individual.

It’s possible that the rare microbes are only visitors, dropping by for a short stay in our navels before dying out or traveling on. The most common species the scientists found may have long-term leases, having evolved adaptation that help them thrive in the bellybutton’s distinctive habitat. Dunn and his colleagues found that these abundant species were also closely related to each other compared to the rarer ones. It’s a pattern similar to the one found in rain forests, were only a few lineages of trees dominate, with many species only contributing a few trees. Your belly button, in other words, really is a jungle.

For more information, read Dunn’s account of the study.

P.S. I refer to these bacteria as belonging to “species.” It’s a convenient term but, when it comes to bacteria, not a precise one. Feel free to mentally substitute “operational taxonomic unit” or “phylotype.”

CATEGORIZED UNDER: Microcosm: The Book, Top posts

Evolution Textbook: The App Grows!

By Carl Zimmer | October 31, 2012 3:51 pm

Evolution: Making Sense of Life, the textbook Doug Emlen and I have just published, is now evolving into a full-blown app for the iPad. Once you get the free app, you can download some of the book’s chapters. We’ve now got the first eight chapters in the iTunes store. Chapters 1 (the introduction) and Chapter 8 (natural selection in the wild) are available for free. Chapters 2-7 can be purchased individually for between $4.99 and $9.99. The full book will be available December 1st, 2012; all 18 chapters will be priced at $80.

CATEGORIZED UNDER: Evolution

In praise of the big old mess

By Carl Zimmer | October 29, 2012 2:22 pm

In June, a writer named Jonah Lehrer got busted for recycling material on a blog at the New Yorker. Lehrer, who specialized in writing about the brain, had been writing a blog called The Frontal Cortex for six years at that point; having just been appointed a staff writer at the New Yorker, he moved it to their web site, where he promptly cut and pasted material from old posts, as well as from magazine and newspaper pieces.

At the time, I just thought he was squandering a marvelous opportunity. When I was asked to comment on the situation, I wrote that some of the things Lehrer had done were uncool, while some were fairly harmless. But Lehrer himself acknowledged that what he was done was stupid, lazy, and wrong. So I figured he’d gotten the sort of school detention that wakes you up and keeps you from getting expelled.

Four months later, I’m struck by how wrong I was.

I’m quoted in the latest of a long string of articles about Lehrer’s misdeeds, a feature in this week’s issue of New York by Boris Kachka. Kachka talked to me for a long while, and it’s clear that he talked to a lot of other people–journalists and scientists alike. He’s ended up with the best account I’ve read of this sad, strange story.

A lot of the other stories and commentaries have been twisted to showcase people’s assorted bugaboos. I’ve lost count of how many times people fussed over Lehrer’s fancy jackets and haircut, as if they were tied up in his moral standing. If Lehrer had a mullet instead, it would not diminish his misdeeds. There was a fierce passion driving people to draw lessons from Lehrer’s story–lessons, I suspect, that they had already drawn and for which they were now just looking for evidence to confirm. In a rare misstep, for example, Reuters blogger Felix Salmon declared Lehrer the exemplar of all that is wrong with TED talks: “TED is a hugely successful franchise; its stars, like Jonah Lehrer, are going to continue to percolate into the world of journalism.” In fact, Lehrer has never given a TED talk. When you’re condemning a culture that promotes the distortion of facts to fit an easy story, it’s best not to distort the facts for an easy story.

In his densely reported piece, Kachka rightly sees two major aspects to this story: Lehrer’s own misdeeds and the culture that fostered and rewarded it.

I was willing to cut Lehrer some slack at first, but as the additional evidence came in, I wondered if I was making excuses for him. The breaking point came when I read about how he had warped a story about a memory prodigy, claiming that he had memorized all of Dante’s Inferno instead of just the first few lines. When someone noted the error, Lehrer blamed it on his editor, but kept on using the enhanced version of the story in his own blog and on Radiolab (which later had to correct their podcast). It’s easy to slip up with facts, but we have an obligation to admit when we’re wrong and not make the same mistake again. It would have been bad enough that Lehrer distorted the facts and continued to do so after having the facts pointed out to him. But he was also willing to damage other people’s reputations along the way. That’s when I signed off.

As for the other side of the story–the culture that fostered Lehrer–I appreciate that Kachka avoided silly sweeping generalizations–that all popular writing about neuroscience has become the worst form of self-help, that speaking about science in public is the intellectual equivalent of pole-dancing. Kachka instead reflects on the trouble that arises when a science writer reduces complex science to a glib lesson. He’s right to zero in on Lehrer’s 2010 New Yorker article “The Decline Effect and the Scientific Method” as an example of this error. For years, a lot of scientists and science writers alike have grown concerned that flashy studies often turn out to be wrong. But Lehrer leaped to a flashy conclusion that science itself is hopelessly flawed.

That makes for great copy (29,000 people liked the story on Facebook), for which I’m sure his editors were grateful. But Lehrer himself didn’t believe what he was writing. If scientific studies were fundamentally unreliable, then why did he continue to publish articles and a book full of emphatic claims about how the brain works–all based on those same supposedly unreliable studies?

The reality is more complicated. After Lehrer’s piece came out, the Columbia statistician Andrew Gelman was asked what he thought of it. “My answer is Yes, there is something wrong with the scientific method,” he wrote–adding (and this is crucial)–“if this method is defined as running experiments and doing data analysis in a patternless way and then reporting, as true, results that pass a statistical significance threshold.”

In other words, this is not a matter about which we should simply issue Milan-Kundera-like utterances, like Lehrer does in his article: “Just because an idea is true doesn’t mean it can be proved. And just because an idea can be proved doesn’t mean it’s true. When the experiments are done, we still have to choose what to believe.” In fact, this is a matter of statistical power, experimental design, posterior Bayesian distributions, and other decidely unsexy issues (Gelman explains the gory details in this American Scientist article [pdf]).

Kachka understands there’s no easy way out of this dilemma, quoting Daniel Kahneman, the Nobel-prize-winning, best-selling Princeton behavioral economist: “There’s no way to write a science book well. If you write it for a general audience and you are successful, your academic colleagues will hate you, and if you write it for academics, nobody would want to read it.”

I put it to Kachka in a similar way, referring to writers like Lehrer: “They find some research that seems to tell a compelling story and want to make that the lesson. But the fact is that science is usually a big old mess.”

And the very way we choose to read about science makes it hard to convey that messiness. I will use my own work as an example of that failure.

In the current issue of Discover, I examine electroconvulsive therapy. I had about 1500 words to write about it, and so I only focused on a single study recently published in the Proceedings of the National Academy of Sciences. I think it’s an important piece of research, because it uses fMRI for the first time to look at what happens to the brain when ECT pulls people out of major depression.

But it’s also true that the study was necessarily small, that the particular method of fMRI they used is very new, that for now the study remains unreplicated, and that there’s a lot of debate in scientific circles (not to mention beyond) about some of the impacts of the treatment.

In the end, I probably oversimplified, leaving people with too much of a feeling that ECT is a perfect cure (it’s not) and an impression that we know exactly how it works (we don’t). But, to paraphrase Kahneman, there’s no way to write a science article well.

Still, the article I wrote was, I believe, the best of my options for discussing the subject. I didn’t have ten thousand words to use to explore its full complexity. I certainly wasn’t going to get many readers if I wrote a scientific journal paper. And waiting for fifty years to see if this research holds up seems like a worse option as well. So I had to fall short. Again. And I will take the criticism that my article triggers and try to do a better job the next time around.

I don’t mean to sound hopelessly fatalistic. Writers can either tackle this dilemma with eyes wide open, or they can look for a way to cut corners and pretend that the dilemma doesn’t exist. And readers can improve things too. When you find yourself captivated by someone talking to you about science in a way that makes you feel like everything’s wonderfully clear and simple (and conforms to your own way of looking at the world), turn away and go look for the big old mess.

CATEGORIZED UNDER: Meta

Our Viral Future: Video of My Recent Talk

By Carl Zimmer | October 27, 2012 9:17 am

I recently gave a talk in San Francisco about the future of viruses, based in part on my book, A Planet of Viruses. I talk about how deadly new outbreaks may emerge, how we may harness viruses for technology and medicine, and just how many viruses there are out there (hint: 10000000000000000000000000000000).

Author Carl Zimmer: Our Viral Future from Singularity Institute on FORA.tv

CATEGORIZED UNDER: A Planet of Viruses, Talks

Flea-Ridden Page Turners, The Forensics of Vengeance, and More: Catching Up with Download the Universe

By Carl Zimmer | October 22, 2012 12:08 pm

Download the Universe, the science ebook review I started up with some colleagues nine months ago, continues to grow. Here’s the latest batch of reviews:

The Most Ingenious Book: How to Rediscover Micrographia My survey of the digital experiences of Robert Hooke’s 1665 masterpiece.

NASA’s 30 years of Shuttle Missions Is Both Dull and Compelling John Timmer explores NASA’s online history

The Long Quest to Catch a Poisoner Deborah Blum finds the science in a true-crime thriller.

A Medieval Bestiary: When a Book Breaks Your Heart Maggie Koerth-Baker has great hopes for an ebook from the British Library. Hopes are dashed.

Did You Like My Ebook? Don’t Lie! Maia Szalavitz reviews Sam Harris’s ebook on lying.

The Beautiful Planet Meets The Immortal Cassini I take a look at an elegant collection of NASA’s images of Saturn.

Death and Other Options: How To Think (Hopefully!) About Global Health Tom Levenson reviews a TED book on the medical future of our species

Deep Water: A Pretty Good TED Ebook (Really!) About Climate Change John Dupuis considers the strengths and weaknesses of an ebook on climate change.

Interplanetary Cuisine What do people eat in space? Veronique Greenwood tucks in.

The Science of Sports: An eBook Goes for the Gold, Gets A Bronze Jaime Green reviews an ebook from Scientific American on the Olympics. (Remember the Olympics? That creepy giant baby on opening night? Remember?)

CATEGORIZED UNDER: Download the Universe
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The Loom

A blog about life, past and future. Written by DISCOVER contributing editor and columnist Carl Zimmer.
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