Category Archives: biology

biology, evolution, science

Best postdoc ever: last call

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So, a few weeks ago I posted about three-year postdoc opportunities at the Santa Fe Institute. This is a reminder, since applications are due on November 1. Go to the original post for a complete explanation of why you should be applying for one of these positions.

Here’s the short version: it’s three years of complete freedom to pursue whatever research you want in an intellectually stimulating transdisciplinary environment with a bunch of cool colleagues.

Read more about the fellowship and access the online application here.

biology, evolution, science

I owe Martin Nowak an apology

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So, if you’re an Evolutionary Biologist, you’re already familiar with the dust-up prompted by a Nature paper published in 2010 by Martin Nowak, Corina Tarnita, and E. O. Wilson.  If not, I wrote about the paper, and the response from the community, here and here.

Briefly, the article attacked one class of approaches to modeling the evolution of traits affecting social interaction: models based on kin selection and inclusive fitness. The authors made strong claims about the effectiveness of such models, claiming that they were useless or even wrong for thinking about eusociality (e.g., in species of bees and ants). The paper prompted a number of written responses, in blogs and in letters to Nature, one co-authored by 137 prominent biologists, refuting many of the claims of the paper.

The paper comes with a weighty appendix, which contains a lot of calculations. Those calculations are not problematic. Rather, it is the main text (the only part most people will read) that triggered the vocal response. The main text made a bunch of unsupported (and wrong) claims, knocking down a straw-man caricature of kin-selection models. It was this straw-man caricature that people found so offensive, along with the failure to cite a huge body of literature (which would have undermined that straw man).

The disconnect between the careful, meticulous appendix and the swaggering, irresponsible main text led most readers to assume that we were looking at a frankenpaper, the imperfectly integrated product of multiple authors. In this sort of circumstance, the impulse is to partition blame among the authors.

My sense was that most people held Tarnita, a postdoc with Nowak at the time, blameless, a talented junior scientist in the wrong place at the wrong time.

The blame, in most people’s eyes, fell primarily on Nowak, for a complex set of reasons that I tried to untangle here.  In particular, Nowak has a reputation for not being generous in attribution of credit to other scientists.

Wilson was not blamed. He is, after all, a living legend among evolutionary biologists. If anything, the discussion about Wilson was along the lines of, “Why is Wilson keeping such bad company?” Some people even speculated that he was perhaps being taken advantage of, that he had been roped into putting his name on the paper.

It now appears that I, along with all the other rumor-mongering evolutionary biologists, owe Nowak an apology.

Over the past year, Wilson has been on the warpath, giving various interviews in which he reiterates the major arguments presented in the paper. The most recent just appeared here in the Atlantic. This article, I think, makes it clear that Wilson was the ideological driving force behind all of the misrepresentation in the original Nature article. It also seems to indicate that the disingenuous argument will be expanded to book length in Wilson’s forthcoming The Social Conquest of Earth.

The richest part of the Atlantic article comes in Wilson’s trashing of Stephen Jay Gould. Trashing Gould is, of course, a popular pastime among evolutionary biologists.

“I believe Gould was a charlatan,” [Wilson] told me. “I believe that he was … seeking reputation and credibility as a scientist and writer, and he did it consistently by distorting what other scientists were saying and devising arguments based upon that distortion.” 

This is a valid enough criticism of Gould. It is also a dead-on description of what was wrong with the Nowak et al. paper. I suspect that the irony is lost on Wilson.

Nowak, M., Tarnita, C., & Wilson, E. (2010). The evolution of eusociality Nature, 466 (7310), 1057-1062 DOI: 10.1038/nature09205

biology, Linkasaurolophus, Occupy Wall Street, Politics, science, sex

Sunday Linkasaurolophus: October 16, 2011

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So, a few items for the Linkasaurolophus this week.

Remember, it’s like Linkaroni, but 100% gluten free.

Let’s start with the good news. If you haven’t seen it, this is a beautiful articulation of what the whole Occupy Wall Street, 99% thing is all about. It was written as an open letter to “the 53% guy,” a critic of the protests, on Daily Kos. If you’ve got relatives who think that the protests are just a bunch of lazy whiners who want someone to blame for their lot in life, send them this. Here’s an excerpt:

So, if you think being a liberal means that I don’t value hard work or a strong work ethic, you’re wrong.  I think everyone appreciates the industry and dedication a person like you displays.  I’m sure you’re a great employee, and if you have entrepreneurial ambitions, I’m sure these qualities will serve you there too.  I’ll wish you the best of luck, even though a guy like you will probably need luck less than most.

I understand your pride in what you’ve accomplished, but I want to ask you something.

Do you really want the bar set this high?  Do you really want to live in a society where just getting by requires a person to hold down two jobs and work 60 to 70 hours a week?  Is that your idea of the American Dream?

Hat tip to Jon Woodward on that one.

Next up, New York is currently all out of the Plan B (“morning after”) contraceptive. This was covered by the Health Editor at an online magazine called XO Jane. You can read the column here, but I really don’t recommend it, as it is excruciatingly self absorbed, written in a style you might expect from someone so famous, or so rich, that they are accustomed to having to put no effort into their conversations, because everyone laughs at all of their jokes no matter what.

But, more importantly, it contains statements about birth control that are just factually wrong. It has been tackled by scicurous, who details some of the problems, and end with this piece of advice:

Far be it from me to tell XO Jane how to handle their hiring, but I do think it’s generally wise to have a heath editor who’s taken a health course. And who can read. But perhaps I’m too picky.

Finally, there’s an update on the faster-than-light neutron thing. A paper has appeared on the Physics ArXiv that claims that the Italian physicists who wrote the original paper failed to account for certain relativistic effects, and that when those effects are taken into account, the correction of 64 nanoseconds is just enough to bring the neutrino speeds back under the speed limit.

The paper, by Ronald van Elburg, can be found here.

The result has been covered by the Physics ArXiv blog, and at Bad Astronomy. Both writers caution that, while the results seem convincing, we need to wait for the response from the Italian team, and generally let the process play out before concluding that the result has definitively been debunked.

If van Elburg is right, though, it is worth noting that, rather than being a refutation of Einstein’s theory, the neutrino experiment looks more like a dramatic confirmation of it.

Recall that last week, the Wall Street Journal published a moronic editorial as part of their ongoing commitment to propagating lies about climate science. The pinnacle fo moronicity in the moronic editorial was the following moronic claim:

The science is not settled, not by a long shot. Last month, scientists at CERN, the prestigious high-energy physics lab in Switzerland, reported that neutrinos might—repeat, might—travel faster than the speed of light. If serious scientists can question Einstein’s theory of relativity, then there must be room for debate about the workings and complexities of the Earth’s atmosphere.

Do you think that, in light of van Elburg’s calculation, the Journal will now publish a retraction, saying that, well, maybe we should be recognizing the broad consensus among climate scientists?

Yeah, me neither.

Behavior, biology, Books, Genetical Book Review, science

The Genetical Book Review: The Psychopath Test

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So, welcome back to the Genetical Book Review! This episode? The Psychopath Test, by Jon Ronon. Ronson is the author of The Men Who Stare at Goats, which the movie was based on.

Also, his name is what my name would be if I were from Iceland.

The Psychopath Test traces Ronson’s exploration of psychopathy: what a psychopath is, how you identify one, the effect they have on society, and society’s efforts to contain them. The book is written engagingly, and makes for a quick read, even if you’re as slow a reader as I am. Ronson mixes historical and medical information with interviews of both psychopaths and the doctors who have sought to define and/or treat them. Some of the accounts, you can imagine, touch on some fairly gruesome events, but the light manner of the writing should make the material palatable even for those with weaker stomachs for that sort of thing.

One of the most interesting things about the book is the fact that the material is presented chronologically — not in the order that things happened, but in the order that Ronson learned about and understood them (ostensibly, at least). The effect is a really interesting one, which fits well with what seems to be one of the books goals. By the end of the book, Ronson has deconstructed the whole notion of sanity/insanity, as well as the motives of doctors, pharmaceutical companies, police, the entertainment industry, and journalists, including himself.

He achieves the effect by writing in a sort of semi-gonzo, close first person, chronicling his own reactions and beliefs along the journey. First, he learns x, and so he believes X. Then, in the next chapter, he learns y, and starts to doubt his belief in X. And so on throughout the book. The result is a message that is fragmented, but also nuanced and faceted. This mixture of sometimes contradictory conclusions actually seems quite fitting, given the complexity of the phenomenon, and our limited understanding of it.

Even out of that complexity though, there are two big take-home messages that rise above the others.

First is the fact that psychopathy is not really a well-defined, discrete thing. There is a continuum not only of severity, but of type. Two people could both score high on the eponymous psychopath test (constructed by Bob Hare, who features prominently in the book), but actually exhibit quite different suites of behavior.

This, of course, is not news to anyone who has spent time studying psychiatric disorders (or any other sort of complex disease). Labeling is a necessary part of science and of medicine, as it is what allows us to communicate with each other in an efficient way. However, we need to keep reminding ourselves that these labels refer to abstractions, and that the thing we care about is typically a lot more complicated, and a lots less well understood, than a monolithic label implies.

Which is to say, while it might not be news, it is always good to be reminded of it.

Second is the idea that there are a lot of aspects of society that have a vested interest in reducing people to their maddest edges, as Ronson puts it. Reality television and daytime talk shows seek out people who have something going on that is crazy enough to be entertaining, and then edit out all the boring (read “sane”) bits. Journalists do likewise, seeking out the extreme behaviors and personalities that will make for good quotations and compelling stories. Pharmaceutical companies benefit monetarily from the application of clinical labels to any behavior that lies outside the norm.

And so forth.

There are obviously a lot of very ill people out there. But there are also people in the middle, getting overlabeled, becoming nothing more than a big splurge of madness in the minds of the people who benefit from it.

The other thing that struck me was the chapter on the DSM, the big book that defines all mental illnesses. I think I had always assumed that there was some sort of rigorous, evidence-based process by which disorders were included or excluded. It seems that, well, not so much. It seems more like it is a veneer of codification laid on top of a bunch of idiosyncratic opinions, passed through a filter of special interests. Sigh.

Basically, if you work in the field, you may already be familiar with many of the stories, and may already have internalized many of the punchlines. But, for most people, The Psychopath Test provides an entertaining, informative, and often troubling look at medicalization and exploitation of mental health in our society.

Ronson, Jon. The Psychopath Test. New York: Riverhead Books, 2011.

Hare, R. D. (1980). A research scale for the assessment of psychopathy in criminal populations Personality and Individual Differences, 1 (2), 111-120 : 10.1016/0191-8869(80)90028-8

Buy it now!!

What’s that? You say you want to buy this book? And you want to support Lost in Transcription at the same time? Well, for you, sir and/or madam, I present these links.

Buy The Psychopath Test  now through:

Amazon

Barnes and Nobleicon

indiebound

Alibrisicon

biology, science, scientific misconduct

Hauser Plagiarism Case Tabled (for the moment)

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So, a couple of days ago, Gilbert Harman, Philosophy Professor at Princeton, wrote four pages arguing that Marc Hauser’s 2006 book, Moral Minds: How Nature Designed our Universal Sense of Right and Wrong, plagiarized the work of John Mikhail. I mentioned it and linked to it in my Sunday Linkasaurolophus post.

Since then, the paper has been taken down from Harman’s website.

Apparently, Harman did not intend for the argument to be made public. It was more like brainstorming, a first step at putting together “the case for the prosecution,” as Harman puts it. It was a draft that he had meant to be presented only to a small circle, as Harman explained here:

For the record, my discussion was intended as a draft of a case for the prosecution and not a final verdict on this topic. I thought I was making it available for only a few people in order to get comments, but apparently it has had a somewhat wider audience than I intended. In the light of various comments I have received, I need to rethink the “case”, something I cannot do immediately, so I have removed that version from my web site.

Interestingly, my earlier post received an anonymous comment from someone claiming to be a student of Hauser’s. The comment stated that Harman’s piece was retracted, and that Hauser could not possibly have had a culture of fear in his lab, since he has trained so many successful scientists, and has won awards for teaching and mentoring.

I mention that just to point out two things. First, based on Harman’s own comment, the piece has not been retracted so much as it has been shelved until Harman has more time. When and if he puts something together that he is willing to stand behind in a public forum, it might be less critical of Hauser, or it might be more critical. We’ll just have to wait and see. In any event, I don’t think that the removal of the piece should necessarily be viewed as a repudiation of the original claims. Certainly, it seems reasonable to assume that the facts that Harman presented wil not change, even if his interpretation of them does.

Second, yes, Hauser has a reputation as a gifted communicator, teacher, and mentor. Yes, Hauser has trained a lot of successful scientists. And, I have no doubt that there are people out there who think very highly of him, at least highly enough to anonymously defend him in blog comment threads.

However, none of that is inconsistent with the portrayal of Hauser’s lab presented by other lab members, which paints Hauser as, at best, dismissive impatient, and, at worst, a bit of a bully.

That being said, my use of the phrase “culture of fear” to describe Hauser’s lab may have been a bit over the top.

I’ll keep my ear to the ground, and will post anything new that comes up on the Harman piece. In the meantime, if you’re interested in the whole Hauser saga, David Dobbs wrote several nice posts on it, four of which you can find (in chronological order) here, here, here, and here.

biology, culture, Linkasaurolophus, media, philosophy, science, scientific misconduct

Sunday Linkasaurolophus: September 25, 2011

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So, welcome back to Linkasaurolophus.

Remember, it’s like Linkasaurus Rex, but paints me as a knowledgable insider, the kind of person who knows the name of more than one kind of dinosaur. Maybe two. To the other knowledgable insiders, it also implies that these links have a big crest on their head, which they may or may not have been used millions of years ago to play a jaunty tune.

Let’s start with Facebook: TNG

You’ve probably by now experienced the panopticon bar that Facebook introduced this week. The winning commentary on the New Facebook comes from Dan Lyons (NB: not the same Dan Lyons I went to high school with, although he, also, is awesome). Excerpt:

I prepared myself. On Wednesday night I ate a light dinner and went to bed early, in order to get extra sleep for Thursday morning. Nevertheless, 24 hours later, my hands are still shaking. I’m unable to focus. No matter where I am, I am thinking about Facebook and the new, deeper connection that I immediately feel to everyone I know. It’s so deep, so rich and personal and dare I say, intimate, that the effect is almost overwhelming. It’s like Stendhal Syndrome, where you get overwhelmed by looking at a work of art. I am shellshocked. No, even that is too small a word. I sit and gaze upon the Facebook home page and my emotions begin to sweep and swirl. One moment I am elated. Then I’m struck by anxiety and panic, and want to hide under my desk. A minute later I’m sobbing, uncontrollably, at the beauty of what they’ve done. Why, Mark Zuckerberg? Why do you do this to me? To the world? You are not a businessman, not a geek, not an engineer — you are an artist, and your canvas is the human race itself, the collective hive-mind of modernity.

If you’ve not already read it (which you probably have, as it’s been making the rounds) do yourself a favor and read the whole thing here.

And, here’s something to keep in mind when you’re griping about the Facebook changes, and your supercilious friend chastises you, reminding you again that you have no right to complain about a service that is provided to you for free:

Hat tip to Chris Smith, who was the secret inspiration for U2s fifth album, The Joshua Tree.

Also, you should get better friends.

In non-Facebook news:

The estimable John S. Wilkins (no recent relation) put up an excellent, and very broadly accessible answer to the question “What is philosophy?” You should read it.

Neuroskeptic posted a discussion of the Nipah virus, which provided the inspiration for the virus in the movie Contagion. (Actually, Nipah provided only part of the inspiration. The rest was provided by the universal desire to watch Gwyneth Paltrow die a horrible, horrible death).

You’ll recall the case of Marc Hauser, erstwhile Harvard Professor, who was accused of scientific misconduct, including possibly falsifying data. Around here, we like to call him “the man who put the a** in a**ertainment bias.” Well, Princeton Philosophy Professor Gilbert Harman makes an interesting case that Hauser’s 2006 book, Moral Minds: How Nature Designed Our Universal Sense of Right and Wrong, may have plagiarized the work of John Mikhail. Or, as Harman puts it, “When the ideas taken from Mikhail are subtracted from Hauser’s book, it is unclear what of value is left.” You can read about it (about three-and-a-half pages) here.

If I’ve missed anything, perhaps Neutrino Superman can fly around the world, so that I have a chance to retroactively add it.

biology, Darwin Eats Cake, evolution, genetics, genomic imprinting, science

Genomic Imprinting at Darwin Eats Cake

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So, I’ve posted the new Darwin Eats Cake, which is about genomic imprinting. I tried to do some explaining in the comic, but I suspect that there is not enough information there for the thing to make sense unless you already have at least a passing familiarity with the phenomenon.

If you’re actually interested, I’ve got a set of primers on imprinting that I’ve been working on here. You can find links to them here.

Or you can just forge ahead:

Best URL for sharing: http://www.darwineatscake.com/?id=51
Permanent image URL for hotlinking or embedding: http://www.darwineatscake.com/img/comic/51.jpg

biology, evolution, Ronin Institute, science

On ronin and the future

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So, for the past six years, I have been on the resident faculty at the Santa Fe Institute. As I am writing this, I am sitting at a laundromat in Santa Fe, preparing for a cross-country road trip to Montclair, New Jersey, where I am going to be founding my own research institute.

What does that mean? Well, technically speaking, I will be forming a non-profit dedicated to research. At least to start with, the non-profit will consist of me, so, practically speaking, it’s like I’m becoming a freelance scholar.

My new outfit will be called the Ronin Institute. Ronin refers to a masterless samurai. It may be familiar to you from this:

or maybe from this:

Since this is a career path that is a bit different from the one that most academics follow, I thought it might be interesting to write about it here. I’ll share some of the details of what is involved in establishing a non-profit, and the process of becoming an independent scholar. This is a new venture for me, one that is going to involve some trial and error. As I go along, I’ll let you know what’s working and what isn’t. Most of you are probably not going to start your own institutes (although I hope a few of you will), but many of you may be interested in thinking about alternatives to the archetypal academic career trajectory. I’m hoping that my experience will be helpful in thinking about your own plans.

Or maybe it will at least be comforting and entertaining to you in a schadenfreude kind of way.