Science Publishes “Arsenic is Life” Critiques. Game On.

Alert readers will remember the scuffle that broke out last summer December over the “arsenic-is-life” paper by Felisa Wolfe-Simon and colleagues that claimed to have found that a bacterium from Mono Lake had been coaxed into substituting arsenic for phosphorous in its DNA. Many, including me, criticized both the paper and its presentation: the paper for making claims that seemed to be beyond the evidence; the presentation — particularly the high-profile press conference followed by a refusal to engage critics and journalists — for hype and a refusal to answer legitimate critiques. I chimed in several times; Carl Zimmer rounded up some withering critiques and then some more; the Guardian ably tracked it, as did the Knight Science Journalism Tracker; and in probably the best single round-up, Ed Yong wrapped up his own and other coverage. And @BoraZ assembled a wonderful rabbit hole of a link list.

Then a long silence ensued, broken by brief skirmishes. Now, it seems the battle is re-engaged. Though the paper was never officially published (it remained online, but was never published in print), Science has now published a number of peer-reviewed responses to the paper, as well as responses to the responses.

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Reef Madness 1: Louis Agassiz, Creationist Magpie

Below is the first in a series of self-standing excerpts from my book Reef Madness: Charles Darwin, Alexander Agassiz, and the Meaning of Coral (Pantheon, 2005), that, in an experimental act of re-publishing, I will run a dozen or so of these over the next several weeks, partially serializing the book. Each post will stand on its own as an intriguing story within a larger context: the struggle of some of history’s smartest and most determined people, including Charles Darwin, to figure out how to do science — to look at the world accurately, generate ideas about how it works, and test those ideas in a way that gives you reliable answers. This was usually (certainly not always, as we’ll see) a polite debate. Yet it was also, always, a high-stakes war about what science is, and that war continues today. In this case it revolved around two of the 19th century’s hottest scientific questions: the origin of species, and the origin of coral reefs.

Today the main argument about coral reefs is how to save them. But in the 1800s, the question of how coral reefs arose, known as the “coral reef problem,” ranked second only to the “the species question” in ferocity. In many ways it reprised the evolutionary debate, engaging many of the same people and ideas. It provided both an overture and a long coda to the fight over Darwinism. The coral reef problem did not concern the origin of species or humankind’s descent. Yet it reiterated the evolutionary debate’s vexing questions about the importance of evidence, the proper construction of theory, and the reliability of powerful abstractions.

And in one of the era’s many oddities and inversions, the coral reef debate found Darwin, who had won the species debate by amassing mounds of evidence, holding the weaker evidentiary hand — even as he faced the son of Louis Agassiz, the renowned creationist he had soundly and humiliatingly deposed, and one of the most brilliant and confounding scientists of his time. If you’re one of the few who know how this story ends — that is, whose coral theory proved correct  — please refrain from spoilers. You wouldn’t want to ruin things for those who read all the way through.

We start with Louis.


1. Magpie

from Reef Madness: Charles Darwin, Alexander Agassiz, and the Meaning of Coral

© David Dobbs, all rights reserved

The name Agassiz, from the southern, Francophone area of what is now Switzerland, means magpie — a bird, of course, but also a person, as Webster puts it, “who chatters noisily.” If this did not hang well on the reserved man that Alexander Agassiz would become, it fit his father snug. Louis Agassiz talked as voluminously and engagingly as anyone ever has about science, or for that matter about almost anything. He could mesmerize a room full of scientists, an auditorium flush with factory workers, or a parlor pack of literati, including his salon companions Oliver Wendell Holmes, Ralph Waldo Emerson, and Henry Wadsworth Longfellow — the sharpest talkers in a smart and garrulous town. He was one of those brilliant, babblative sorts whose immense skill in their main work is nearly eclipsed by their gift for talk.

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Those Who Waited Get Impatient Too: or how new journo tools can get you out of old school

A couple weeks ago, Ed Yong published a talk by RadioLab’s Robert Krulwich that went viral in journalism and  science-writing circles, for good reason. Speaking to graduating journalism students at UC Berkeley, Krulwich, who does some fine blogging of his own, expressed his pleasure and wonder at how blogs, twitter, and other newish tools allow sharp, hardworking young writers to bypass the traditional career-advancement paths* and publish prominently much faster than was generally possible 10 or 20 years ago. As I’ve noted before, I think this is fantastic, even if it sometimes distresses people who did it old school. It gives hope and work and exposed practice to newcomers and makes veterans quicker and more alert. Yong dubbed this the “There are some people who don’t wait,” talk, and it’s a great talk and you should go read it.

I want to add something to Krulwich’s huzzah: These new tools don’t empower just the young and hungry. They freshly arm the not-quite-so-young and established hungry: writers who’ve been at it a decade or more, waited their turn and more or less made it trotting the old path — yet still find the old path sometimes so ludicrously inefficient they’re ready cut fresh trail themselves.

Krulwich’s essay struck me at a ripe moment, for the old system has failed me notably a few times lately, as it does most writers, and I’m damned glad to have tools to try to compensate for it. Before I explain how, I should explain that while I’ve enjoyed great luck in the mainstream media over the past decade — making a living doing work I love; publishing some deeply satisfying stories in top magazines; publishing three books and getting a nice contract that supports my work on a fourth — I keenly feel the constraints of the older media ecosystem and feel it too often fails both me and readers. I know I’m not alone in this, for when I talk to other writers selling to top magazines, they share their own infuriating stories of stories mangled and orphaned, deals gone bad, promises broken, and — and this is the heart of it, the thing we really hate — good work that gets eighty-sixed and never sees the light of day.

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The Old is the New New. So Paleoblog, Will You?

A recent twitter exchange between Tim Carmody, Alexis Madrigal, Alison Arieff, and Brendan Koerner drew my attention to this nice Snarkmarket post from Carmody on digging up material from offline, which Carmody calls paleoblogging:

Two weeks ago I praised Harper’s Scott Horton, who in addition to tiptop legal/political commentary regularly serves up poignant and relevant chunks of older texts, and lamented that more bloggers don’t mine the past as well or as often as they do the just-this-minute.

I don’t have to impress upon you the need to embrace the new… You have to continue to challenge yourself as a reader – a serious reader. And as one who learns – a serious student. That you have not calcified. That you do not know what you think you know, least of all who or what or where or especially WHEN is important… Get a library card and wander somewhere dusty. Find something real. And then blog about it — bring it into this world. Scan that creaky wisdom, make it sing.

I wish we saw more of this: the recognition that at this point much of the freshest material is stuff that was created before everything was created online,. or somehow remains outside of it. To digitize the undigital. It’s fresher because it’s a little hard to get at. You can’t just keystroke it. You have to dig it out and contextualize it.

The old is the new new.

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Jonathan Eisen Frees (Almost All) His Father’s Papers

Jonathan Eisen
In a touching post at his blog, The Tree of Life, evo biologist and microbug master Jonathan Eisen reports that he has substantially completed the mission I described last week in my article Free Science, One Paper at a Time: finding and re-publishing his deceased father’s papers.

Yesterday marked a major achievement in my goal to free up the scientific publications of my father Howard J. Eisen, who passed away in 1987 when I was in college. I have been working for the last 3+ years or so.… But [at times] I got caught up in life and the effort to free my dad’s publications slowed down. That was, until David’s blog post came out: Free Science, One Paper at a Time | Wired Science | The piece moved me.  It scared me a bit at first, since there are some really personal details in there, but I realized when reading it why he had focused in on this story. So, with his post out there – for all to read — I realized I had to get my shit together and redouble my efforts to free up my father’s publications.  So over the last week or so I have been scavenging around (with some help from people around the web) trying to dig up PDFs of as many of my father’s papers as possible.  Note – I generally would like to obtain these papers without having to pay for them but I am trying to not break any laws either.

I am writing today because I have nearly completed the task of getting PDFs of all of his papers…  So now on the Howard Eisen Mendeley page almost all of his papers are there for anyone to obtain.

Howard Eisen

As a son and a father, as someone who sometimes struggles to get copies of scientific papers (the ones published last week, much less those published 30 or 40 years ago) I find this a moving and enormous accomplishment — the more so having read his other posts chronicling his necessarily on-and-off quest. It’s good to see him get almost all of these papers up and available at Mendeley.

Science and family are complex, consequential, sometimes maddeningly tangled chains of influence, replication, correction, and confirmation. Jonathan Eisen has done both an immense honor.

What is Mental Illness? A Peek Through the Murk

This guest post — a book review of Richard J. McNally’s What is Mental Illness — is by Jason Goldman, a University of Southern California graduate student in developmental psychology who blogs on behavior and psychology at The Thoughtful Animal. Goldman is also the psychology and neuroscience editor at and edited the science-writing anthology Open Lab 2010.

When most of us think about psychopathology, or abnormal psychology, we think of mental illness. We think of disability. We think of something perhaps maladaptive, at least in the everyday sense of psychosocial functioning, if not in the larger evolutionary sense. We tend to think that something is fundamentally broken. This seems reasonable, but if you dive deeper, the waters get murky.

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When Science Meets a Great Writer: Silberman Speaks

Steve Silberman

If you care about how science writers collide with science to produce science writing — and if you’re reading anything at Wired Science, you do care, whether you realize it or not — then you’ll probably love this interview with Steve Silberman at the Open Notebook, where Steve relates how he wrote “The Placebo Problem,” a superb Wired feature that went on to win multiple prizes, including the coveted AAAS Kavli Science Journalism Award.

I should disclose that Silberman is a friend of mine, dearer all the time, in fact — but I consider this not just a disclosure but a recommendation, for Steve became a friend,  and has grown dear to me, because of the same combination of intelligence, humor, and enormous humanity that he brings to his writing. All of that shows in the Placebo Problem and, in a  different way, in this “the making of” interview as well. The interview is full of good stories, insight into craft, and the sort of ferocious, stubborn determination to get the story right — to do the long, deeply (overly) researched stories that I also love to do.

A couple pearls. First, something Steve left on the cutting-room floor. He’s describing here some of the researchers he met and the sorts of things he learned from them:

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Free Science, One Paper at a Time

Howard Eisen, 1942-1987

On Father’s Day three years ago, biologist Jonathan Eisen decided he’d like to republish all his father’s papers. His father, Howard Eisen, a biologist and a researcher at the National Institutes of Health, had published 40-some-odd papers by the time that he died by suicide at age 45. That had been in Febuary 1987, while Jonathan, a sophomore at college, was on the verge of discovering his own love of biology. At the time, virtually all scientific papers were just on paper. Now, of course, everything happens online, and Jonathan, who in addition to researching and teaching also serves as an editor for the open-access, online-only journal PLoS Biology, knows this well. So three years ago, Jonathan decided to reclaim his father’s papers from print limbo and make them freely available online. He wanted to make them part of the scientific record. He also wanted, he says, “to leave a more positive presence” — to ensure his father had a public legacy first and foremost as a scientist.

I researched and wrote this article last summer and fall (2010) under assignment from a magazine that accepted and paid for it but, in the way these things sometimes work, decided not to run it and gave me its blessing to publish it elsewhere. I’m publishing it here at Neuron Culture and also in an identical post at my website, It is based on extensive reporting. I’d like to thank in particular Jonathan Eisen,, for reasons that the article will make obvious; Cameron Neylon, Peter Murray-Rust, Richard Grant, Michael Nielsen, Martin Fenner, Leslie Carr, and Lord Rees, whose ideas are fundamental to the story and its subject; Mark Patterson and Brian Mossop of PLoS; Victor Henning, Jason Hoyt, Ian Mulvany, William Gunn, and Jan Riechelt, all of Mendeley; and Melody Dye, Kristi Holmes, John Timmer, and Sara Wood, who along with Reichelt participated in a session on open science I organized at ScienceOnline 2011. I also had several conversations off-record; you know who you are — thanks.

How hard could it be? Howard Eisen had been a federal employee, so his work rightly lay in some sense in the public domain. And Jonathan, as an heir, presumably owned copyright anyway, along with his brother Michael (also a biologist, and one of the founders of the Public Library of Science, the innovative journal group that publishes PLoS Biology). Yet to the brothers’ continuing chagrin, Jonathan has found securing and publishing his father’s papers to be far harder than he expected.

For instance, even though Jonathan has access to the enormous University of California library system, which subscribes to a particularly high number of journals, he often can’t even find some his father’s papers. And when he finds a paper in a journal the university doesn’t subscribe to, he is asked to pay as much as $50 to read the paper — even though his father did the work with public funds. He’s not alone; one recent study found that even most university researchers have access to only about half the papers they need to cite for a given bit of research. Just yesterday, in fact, Jonathan asked on Twitter if anyone could send him a copy of one of his father’s paper and confronted a paywall asking for his credit card number. “I ain’t payin’,” he replied.

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Fast Birds in Slow Motion – Beautiful

I don’t do many “Would you look at that!” YouTube posts, but this slo-mo film of red kites snatching bits of bacon, made by the Slow-Mo Guys and subject of a lovely blog post by GrrlScientist, is so utterly beautiful I had to call it out.

GrrlScientist notes

If you watch this film in full-screen mode, you will see the air turbulence on the birds’ backs, causing the feathers to ruffle. You can also see how the pupils of the birds’ eyes change upon grabbing the piece of bacon and soaring away.

and adds a lot of other context too, well worth reading. GrrlScientist also curates the Mystery Bird quiz, which is great fun, especially on those rare occasions when I ace it. When you finish watching this vid (DO watch it full screen) and pick your jaw off the floor, go have a look round at GrrlScientist’s Punctuated Equilibrium.