Category Archives: evolution

academia, evolution, religion, science

Looks Like PLOS ONE Screwed Up the “Creator” Retraction, Too

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Okay, that “Creator” paper has officially been retracted by PLOS ONE (previously, and here). Based on what we now know, that looks like the wrong decision — at once unfair to the authors and completely failing to address the actual issue.

When PLOS ONE first announced its intention to retract the article, they stated that “the peer review process did not adequately evaluate several aspects of the work”, which makes it sound like they found problems other than inclusion of the “Creator” language that meant it should not have been published. Now that the formal retraction has happened, here’s the official statement:

Upon receiving these concerns, the PLOS ONE editors have carried out an evaluation of the manuscript and the pre-publication process, and they sought further advice on the work from experts in the editorial board. This evaluation confirmed concerns with the scientific rationale, presentation and language, which were not adequately addressed during peer review.

Consequently, the PLOS ONE editors consider that the work cannot be relied upon and retract this publication.

The editors apologize to readers for the inappropriate language in the article and the errors during the evaluation process.

This is infuriatingly vague, but it makes it sound as if the primary issue was the “Creator” language. The authors have insisted that this was a translation problem. In the context of the rest of the paper, that seems entirely plausible to me. In support of this explanation, check out this comment from over at Complex Roots (spelling corrected):

I am so surprised that so many people assert that there is no way a translation error though they don’t speak any Chinese.

In fact, there is special phrase in Chinese, which is “zao wu zhe”. If we translate it literally and directly into English, it is “the one who creates” or ‘creator’. Ancient Chinese people use it a lot in poems, way long before Christian is introduced in China. The meaning is same as “nature” because they believe that nature ‘creates’ everything, not a special man, or a God. There is a sentence in a poem written in Song Dynasty (more than 1000 years ago) by Su Shi, which saying that ‘we can enjoy the the breeze of the river, the moon between the mountain; this is the inexhaustible treasure that the creator have, and all of us can appreciate them together’. So here ‘creator’ means nature. (poem link: http://www.rthk.org.hk/chiculture/chilit/dy05_1205.htm)

Or you can use google translator to check this page (a Chinese dictionary): https://www.moedict.tw/%E9%80%A0%E7%89%A9%E8%80%85
It will tell you that ‘zao wu zhe’, which means who created all things. It refers to nature.

However, in English, Creator is epithet of God because people firstly say it believe God creates everything. That’s the difference. The author used capitalized ‘Creator’ because he thought that the underling meaning of this idiom in Chinese and English is same.

Unless there were technical issues with the science, the authors should have been given the opportunity to edit the paper to correct the offending language.

As I argued previously, the fact that this error slipped through is troubling, not because it plays into some creationist agenda, but because it reveals a review and editorial process that involved absolutely no care or effort.

Now, it seems that PLOS has responded to the twitter/comment outrage by throwing the authors under the bus, while giving no reason to believe that any other manuscripts, present or future, are going to receive any more care and attention than this one did.

academia, biology, evolution, religion

“Creator” Paper Retracted at PLOS One

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Well, true to their word, the editorial staff at PLOS ONE acted quickly to review that paper from January that interpreted their study of biomechanical characteristics of hand coordination as evidence of “proper design by the Creator”. (Look here for background.) They issued this statement today:

The PLOS ONE editors have followed up on the concerns raised about this publication. We have completed an evaluation of the history of the submission and received advice from two experts in our editorial board. Our internal review and the advice we have received have confirmed the concerns about the article and revealed that the peer review process did not adequately evaluate several aspects of the work.

In light of the concerns identified, the PLOS ONE editors have decided to retract the article, the retraction is being processed and will be posted as soon as possible. We apologize for the errors and oversight leading to the publication of this paper.

The paper’s first author, Ming-Jin Liu, has posted multiple comments asserting that there was no creationist agenda, and that this was simply an issue of non-native English speakers misunderstanding the implications of using “the Creator” when they had meant “natural selection”.

Personally, I’m inclined to believe this explanation, and if this were the only problem with the paper, I would let them make a correction. If, in each of the three places where the Creator is credited, the authors were to cite their findings as “evidence of exquisite adaptation” or some such thing, the meaning would be largely unchanged, and no eyebrows would be raised.

Here’s the thing, though: at this point, I have no confidence that there is not something else dreadfully wrong with the paper. Including three references to “the Creator” — one in the abstract — raises such an obvious red flags that even a cursory read should have identified this as a problem. The capital C makes the word jump out if you even scan the abstract.

I think I would feel the same way if the paper were littered with errors involving there, their, and they’re: it’s a mistake a non-native speaker could make, and it would not make the science wrong. But the only way those errors make it all the way through to publication is if multiple people fail to do their jobs.

So what this says to me is that none of the people involved in the editorial and review process put in even a modest effort. I don’t know if there are major, even fatal, technical flaws with the paper. However, I am confident that if there are major flaws, the careless review process applied to this paper would never have identified them.

The question, then, is how much of an outlier this was. Can we trust that the rest of the articles at PLOS ONE are actually going through a legitimate review process (as imperfect as that is under the best of circumstances)? Or should we assume it has slid into the predatory open-access model of publishing?

In short, I don’t really care whether or not this particular paper is retracted. I do care whether or not PLOS can do something to shore up its review process.

Or is this another piece of evidence in favor of post-publication peer review? It is certainly true that an advantage of that model is that avoids creating a false sense of authority.

One bright side of the controversy is that it provides an excuse to revisit this piece of awesomeness from the New York Dolls:

biology, cooperation, evolution, science

Is E O Wilson Senile, Narcissistic, or Just an Asshole?

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Last weekend, renowned evolutionary biologist E. O. Wilson was interviewed by BBC Newsnight. In the course of the interview, he continued his public feud with Richard Dawkins. Like most feuds, this one probably can be attributed to multiple causes, but it centers primarily around Wilson’s disavowal of kin selection.

The bit of the interview that has received the most attention is where Wilson calls Dawkins a “journalist”:

There is no dispute between me and Richard Dawkins and there never has been, because he’s a journalist, and journalists are people that report what the scientists have found, and the arguments I’ve had have actually been with scientists doing research.

This is pretty Oh-Snap! in the world of science, which is full of polite trash-talk centered on establishing who is more of a real scientist. Just like how you can insult a physicist by calling them an engineer, or how you can insult an economist by emphasizing “Memorial” in “Nobel Memorial Prize in Economic Sciences”.

The thing that struck me, though, was this bit, quoted in the Guardian’s coverage:

Wilson was asked about his current views on the concept of a selfish gene, to which he replied: “I have abandoned it and I think most serious scientists working on it have abandoned it. Some defenders may be out there, but they have been relatively or almost totally silenced since our major paper came out.”

The paper Wilson is referring to is his 2010 Nature paper co-authored with Martin Nowak and Corina Tarnita. This is a paper that prompted a condemnation signed by 137 prominent population geneticists. (That’s about 130 more than the number of population geneticists who could legitimately be considered “prominent”.)

Now, it’s one thing for Wilson to continue to defend the paper. That would just make him wrong. But to claim that it silenced everyone who disagrees with him comes off as profoundly disingenuous.

Disingenuousness, by the way, is exactly what was wrong with the paper in the first place. The mathematical model it presented (mostly in the Appendix) was fine. However, the main text was filled with misrepresentations of other people’s work. The point of the paper was to show that everyone in the field was wrong, because they had neglected factors X, Y, and Z. Of course, it’s not hard to prove people wrong when you lie about the work they’ve done.

It’s basically like if you reformatted Fox News as a Nature paper.

If you’re interested, I’ve written about this paper and the controversy surrounding it on a number of occasions (here, here, here, and here), and even made a little video dramatizing some of the criticisms of the paper.

But here’s today’s question: What is Wilson thinking? Is he starting to lose it? Or is he so arrogant that he feels comfortable dismissing any criticisms of his ideas, even to the point of denying their existence? Or has he constructed a bubble for himself, where he no longer encounters critical voices?

Or is he is so hell-bent on building a legacy as The Guy Who Proved Everyone Wrong that he does not really care whether or not anything he says is actually true?

I’m honestly puzzled. Wilson is a giant in the field. He’s a smart guy who presumably knows what it means to be a scientist. And he doesn’t (or at least didn’t) have a reputation for being a horrible person — a reputation that is common among people of his stature.

The one explanation that is off the table at this point (as far as I’m concerned) is that he is a gifted scientist trying in good faith to pursue the truth, and that this is some sort of legitimate scientific disagreement.

academia, biology, evolution, genetics, religion, science

Jerry Coyne sees a picture of my poster on twitter, is a dick

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Last week I was in Raleigh, NC for Evolution 2014, this year’s edition of the annual joint meeting of the Society for the Study of Evolution, the Society of Systematic Biology, and the American Society of Naturalists. I brought a poster that presented some work I’ve been doing on how noise (e.g., environmental fluctuation) can select for epistasis (non-linear interactions among different genes). On Monday evening, when I was hanging out by my poster, someone showed me that my Acknowledgements section had made it to twitter:

Screen Shot 2014-06-29 at 7.52.48 PMNow, this is what you might call an underdetermined tweet. Not knowing Alex, I was not sure what the intent was. Was this a sanctimonious evolutionary biologist expressing outrage about the fact that I had funding from the Templeton Foundation, which is viewed skeptically by many biologists because of its interest in religious topics? Or was it someone who thought it was unacceptable to include jokes in your acknowledgement section?

Fortunately, it turns out to be the only answer that won’t make you lose faith in humanity: it was someone being ironic. Alex Stewart is a postdoc working with Josh Plotkin at U Penn. Last year Alex and Josh published a paper in the Proceedings of the National Academy of Sciences, and in their acknowledgements section they thanked a number of funding sources, including the “Foundational Questions in Evolutionary Biology Fund”.

Through some mechanism that appears to be named “Todd”, this paper was brought to the attention of Jerry Coyne, evolutionary biologist at U Chicago and blogger at Why Evolution is True.  Along with people like PZ Myers and Richard Dawkins, Coyne is a prominent and vocal critic of Intelligent Design and of the efforts by religious groups to undermine the teaching and study of evolution.

So why did Coyne care about this paper? Because apparently, if you look into the Foundational Questions in Evolutionary Biology Fund, it is a big pot of money at Harvard Univeristy, which was put there by the John Templeton Foundation. Coyne gets mad whenever anyone has anything to do with Templeton. And, in this case, he professed outrage over the fact that they had “disguised” their funding source.

Now, I’m guessing that when Coyne saw Alex’s picture, he did not notice or recognize the name, as he seems to have read the comment as straight-up, unironic outrage, and he jumped on the bandwagon with his own short post, summed up by his comment, “Unacceptable indeed!” He goes on:

Okay, who are these miscreants?

The good news is that scientists clearly recognize the woo-ish nature of Templeton, as well as its nefarious mission to pollute science with religion. (Note, though that, contra the slide, Templeton has disavowed all forms of creationism, including intelligent design.)

The bad news is that four collaborators on this project took Templeton money anyway.

This is pretty awesome. I don’t think I’ve ever been called a miscreant before.

The rest of this is sort of weird, though. I think it is fair to say that the scientists recognize the fact that Templeton is perceived as “woo-ish” by many in the evolutionary biology community. However, most of their funding these days, including this grant, is pretty much straight-up science. Also, if you read the acknowledgements, which state that the work is not creationist, and then read Coyne’s comment, it makes you wonder if he knows what contra means.

That is, the point here is not to say, “This is not creationism, unlike most of what Templeton funds”. The point is to say, “This is not creationism, despite what you might wrongly assume about what Templeton funds.”

Most of the comments go back and forth on the issues you’d expect, so I’ll limit myself to Coyne’s. His first is this:

Would you take money from the Council of Conservative Citizens (a segregationist organization), or the Tea Party to do pure science? How about the Nazi Party? Is there no organization so nefarious that you wouldn’t take their money?

Really, people take it not to further the science, but to further their careers, because you need funding to get tenure, promotions, and so on.

I do fault those who take Templeton money, for they’re lending their imprimatur to an organization whose aim is the corruption of science. That’s precisely why Templeton funds “pure” science–to give them cover for their investigations of “spirituality and science”–the so-called “Big Questions.”

That’s some classic straw-man bullshit right there, although you have to give him credit for going full Godwin in his first comment, thereby saving his community the embarrassment of being the first to bring up a bogus Nazi analogy. That’s leadership!

And while I can be (and have been) accused of many things, compromising my principles to get tenure may be the least valid.

As for my imprimatur, I can’t lend it to Templeton, because back when I was in Santa Fe, I loaned it to Jeremy Van Cleve, and he never returned it!

And how do you take money from an organization like that without compromising “all principles”? The same way you take money from The Council of Conservative Citizens without compromising all principles?

The fact is that you’ve compromised principles simply by taking the money.

First off, again, the analogy with segregationist or racist organizations (which, to the best of my knowledge, are not major sources of science funding anyway), is ridiculous and seems disingenuous. Or maybe Jerry Coyne honestly believes that Templeton is a force for evil on the level of The Council of Conservative Citizens or the Nazi Party, but I think that’s a position that would be hard to find much support for, even among evolutionary biologists.

So we’re left with what, a slippery slope argument, maybe? Or a one-drop argument?  There’s two problems with that. First, whether or not you let your scientific conclusions be influenced by your funder’s (perceived) agenda is up to you. If you’re an honest scientist, you do your work and say what you believe to be true. If some agency or foundation won’t fund you in the future because they don’t like what you said, so be it.

Second, the same argument applies to all sources of funding. For example, the funding structure at NIH strongly rewards confirmation bias and the overinterpretation of marginally significant statistics. As a consequence, the biomedical literature is riddled with unreproducible results. The funding, hiring, and promotion structures in academia have done far more to corrupt science than even the bogeyman version of Templeton that inhabits Jerry Coyne’s mind.

Maybe the intent [of the acknowledgement] is a bit nebulous, but it’s factually incorrect (Templeton doesn’t fund crea[ti]onism or ID any longer), and unprofessional as well. If you’re going to take money from someone, you don’t diss them in public. I bet if Templeton found out about this (I won’t tell them!) they wouldn’t give any more $$.

I love this last one, as it concisely captures the angry incoherence of the argument. First, it accuses me (inaccurately) of claiming that Templeton funds creationism. Second, it accuses me (inaccurately) of dissing them. Third, it suggests that if Templeton found out they had been dissed (which they weren’t), they would spitefully refuse funding in the future (which they probably wouldn’t).

Note that the overarching theme here is that I am bad and foolish, but for contradictory reasons:

I’m bad for taking money from an organization with an alleged religious agenda. But look! I’m foolish, because they have actually renounced that agenda! Gotcha!

I’m bad for taking money from an organization with an agenda, because I will constrain what I say, for fear of losing future funding. But look! I’m foolish, because I did not constrain what I said! Gotcha!

So, if I may build on Coyne’s Nazi analogy, the morality being proposed seems to be something like this: Jerry Coyne would never take money from the Nazi Party, but if he did, he would never publicly criticize the Nazis!

But, to be fair, these comments were probably never meant to support such a close reading. A more accurate characterization might be that Coyne starts from the ideological position that no one should ever take money from Templeton. As someone who has received funding from Templeton, I am therefore someone who is bad and foolish. Starting from this “bad and foolish” conclusion, Coyne works backwards, using whatever evidence and arguments will get him from my poster to that conclusion. This includes misinterpreting my statement (through disingenuousness, carelessness, or a combination of the two) as well as employing arguments that seem logically inconsistent.

Or maybe this is a Colbert-like performance piece, where he takes on the persona of “Jerry Coyne” to illustrate how dogmatically espousing an ideology corrupts the reasoning process. If that’s the case, my hat is off to you, Professor Coyne! Well played!

biology, evolution, genetics, population genetics, race, science

12,000-Year-Old Underwater Skeleton and the Peopling of the Americas

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So, a paper published in Science yesterday describes the analysis of the skull and mitochondrial DNA of a skeleton discovered in Hoyo Negro, a water-filled cave beneath the surface of the Yucatán Peninsula.  In addition to the human skeleton (whom the scientists named “Naia” before removing her head for further study), the cave contains the remains of 26 other large mammals, including a saber-tooth tiger and some sort of a mammoth-type thing.

Check out the story over at National Geographic for some cool underwater pictures.

There are a couple of things that make this an interesting story. First of all, it’s a freaking underwater cave with a 12,000-year-old human skeleton and a saber-tooth tiger. Second, it adds an interesting piece of data to our understanding of how people first came to America. (Spoiler: the answer is not “Jesus brought them on the Ark”.)

The standard story of the colonization of the Americas goes something like this. Back during the last ice age(s), maybe 15,000 to 25,000 years ago, the sea levels were lower, and there was a land bridge connecting Siberia to Alaska. During that period, people from Northeastern Asia crossed over and spread throughout North and South America. Thousands of years later, their descendants had the misfortune of being discovered by the Europeans.

The dates of archaeological sites throughout the hemisphere generally fit with this story, as do genetic data collected from contemporary Native Americans and from skeletal remains. Native Americans, both past and present, are genetically most closely related to the peoples of Siberia, and the genetic divergence between the two groups is consistent with the populations having separated around the time when the land bridge existed.

The problem is that when you look at skull shapes (“cranio-facial morphology”), they seem to tell a different story.  Contemporary Native Americans have facial features similar to those found in Northeastern Asia. But “Paleoamericans” (dating from more than about 9,000 years ago) have features more closely resembling those found in African and Southeast Asian populations.

Those features suggest a different story, one where humans arrived in America in two waves. In this scenario, the humans who crossed the Bering land bridge would be the second wave, perhaps displacing the original, first-wave settlers. This is a story that entered the public consciousness more than fifteen years ago, following the discovery of “Kennewick Man”, who was described as possessing “caucasoid” features by James Chatters, who is also the first author on this paper. A certain strain of “thinker” took this to mean that the White people who came to America were not colonizers, but liberators, having been the continent’s original inhabitants.

The single-wave model suggests the possibility that the difference in skull morphology observed between earlier and later Paleoamericans represents evolutionary change that occurred after the migration across the land bridge. At first blush, this seems a bit questionable, since it would have the American population evolving to more closely resemble their genetic relatives in Asia, but only after having become geographically separated from those relatives.

The persistence of this controversy is due, in part, to the fact that the genetic data has generally come from different sources than the morphological data. This is where Naia comes in. Naia has the longer, more slender, Africa-esque cranium found in other early sites, but her mitochondrial DNA haplotype is a typical Native American one. This seems to support the idea that the people who left these narrow skulls all over America and the people who left their descendants all over America were the same people.

The biggest caveat, of course, is that this is a single skeleton. It is exciting and informative, since very few samples of this age have been discovered, and none of them have been of this quality. But those small numbers also mean that anything we discover about this skeleton is bound to be consistent with multiple stories, and things are unlikely to be resolved without a lot more data.

The other caveat is that the mitochondrial DNA is only one piece of the genetic history. It is possible that these really were two separate populations, and that Naia just happened to have some second-wave ancestors on her mother’s side. If we were to examine the rest of her genome, we might find some or all of it to be more similar to some other population (like the lost thirteenth tribe, who immigrated to America from Israel and/or Kobol).

Will we get the rest of Naia’s genome? I hope so, but we’ll see. It is relatively easy to collect mitochondrial DNA from archaeological samples, since there are hundreds of copies of the small, circular mitochondrial chromosome in each cell. There are only two copies per cell of the rest of the genes, which reside in the cell’s nucleus. So, it is possible that the sample was sufficiently well preserved that mitochondrial DNA could be extracted, but degraded enough that the nuclear DNA is not recoverable.

Whatever the eventual conclusion, the story will be interesting. Either the peopling of America involved a mixture of multiple populations that will be fun to unravel, or it involved some interesting, almost convergent, morphological evolution. Stay tuned!

academia, biology, evolution, genetics, science, Uncategorized

Five Reasons Biologists Should Use Preprint Servers

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So, following my previous post, I got some interesting feedback from a couple of biologists who were not completely sold on the idea of posting preprints of your work to the arXiv (or, now, the bioRxiv). Or, rather, they were not convinced that the cost-benefit calculus worked out in favor of posting. After all, as one person pointed out, there are already a bunch of hoops to jump through on the way to publication, what with formatting, revising, angrily cursing reviewer number 2, reformatting, resubmitting, and whatnot. What does posting to a preprint server do for you, beyond adding another step?

Well, it occurs to me that this is probably a question shared by a lot of biologists out there, so I thought I would share the reasons I’ve come up with.

  1. Open Access. You want your work to be available to the widest possible audience, right? When some enthusiastic young researcher is searching the literature, and they stumble across your seminal work on tribble parthenogenesis, you don’t want them getting Spock-blocked by some crappy paywall. Sure, maybe their University has an overpriced subscription to the obscure journal you published in, but maybe it doesn’t. Or maybe it’s a pain for them to access it via the proxy server when they’re off campus. Or maybe this young researcher doesn’t have access because he and/or she is an independent scholar, because they’re actually too smart and creative to work for The Man. Maybe they’ll just scroll down the search results page until they find another paper by your grad-school nemesis — the one who never chipped in his fair share for pizza — and you’ve lost another citation. Don’t let this happen to you! Make sure that your work is freely, and easily, accessible to everyone everywhere.
  2. Speed. You’ve finished your research, you’ve blindly written down the p-value that the software you downloaded from the internet spit out — er, I mean, “double-checked the statistics”, and you’ve written a beautiful discussion section that skillfully implies that your results are going to revolutionize not only your own field, but any field whose scientists have sufficient foresight to follow in your footsteps. But now you have to wait for six months or a year, or maybe longer, before your paper appears in print, and, of course, by that time, even you will have moved on to more interesting problems. If you post to a preprint server, though, your work is available immediately. And, if you make revisions in response to reviewer comments, you can post the revised version there, too. Some journals (e.g., Evolution) will even let you post the final, published, journal-formatted PDF to the preprint server after some time (12 months following publication for Evolution). So, the fact that you’re getting your work out there early does not mean that you’re committing to something less than the final version.
  3. Normalization. At this point, most biology journals are okay with authors posting their manuscripts to preprint servers, but some still are not. Not to name names (*cough* Elsevier *cough*), but some publishers would still like to hold on to an outdated publishing model where they can earn obscene profits through ownership of a product to which they contribute little to no value. The more biologists publish preprints — and commit to publishing only in journals that permit prepublication — the more pressure it places on publishers to stop rent-seeking. Basically, it is a really easy way to nudge the world of academic publishing in the direction of justice. Or, you know, if you prefer, you can keep feeding those paywall parasites like the rest of your Vichy scientist colleagues. No judgment here.
  4. Feedback. When you’re desperately worried about getting out publications so that you can get your degree, or get tenure, or whatever, it is easy to forget the real purpose of peer review. In an ideal world, peer review means that experts in your field look closely at your work and help you to make it better. By posting a preprint, you are able to get comments from the entire community — at an early enough stage that those comments might actually help you to improve the paper before it fossilizes.
  5. The Left Side of History. Look, the fact is, this is the direction that everything is moving. And you need to ask yourself, years from now, do you want to be the stodgy, old, out-of-touch professor who doesn’t post preprints, and who has to get their grad students to help set their powerpoint presentation to full-screen mode? Or do you want to be the super-cool hipster prof, who could say things like, “I’ve been posting on bioRxiv since you were in diapers”, but who would never actually say that, because it would make you sound like a total dickhead? At future Thanksgiving dinners, do you want to be your field’s Liz Cheney, or its Mary Cheney?*

* Answer: You want to be your field’s Lon Chaney.

academia, Darwin Eats Cake, evolution, evolutionary psychology, psychology, science

Basketball, Fraud, and the Broken University Incentive System

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So, in 2005, Nature published a study by a group of researchers at Rutgers University showing that Jamaican teenagers who exhibited a high degree of body symmetry were judged (by other teenagers) to be better dancers than those with less symmetrical bodies. The study was an exploration of the idea that physical symmetry might be a trait subject to sexual selection — with “good dancers” serving as a proxy for “attractive mates.”

In 2013, Rutgers basketball coach Mike Rice received a $475,000 severance after video footage surfaced showing Rice pelting his players with basketballs, grabbing and shoving them, and shouting obscenities at them.

What do these two stories have in common? The stories reveal how Universities are not motivated by their stated missions (truth, education, etc.), so much as by a drive for money and prestige. As a friend of mine recently put it, “Pursuing truth is great, just don’t let it get in the way of your careerism.”

Now, you may be wondering how you can get a job at a University where you get to abuse students, and if you get caught and fired, you still walk away with nearly half a million dollars. I mean, you probably thought you could only get a job like that in an S & M dungeon, or maybe the CIA.

Here’s what pisses me off about the whole thing. Rice did not lose his job for abusing his players. He lost his job for embarrassing the University. When the video first surfaced, everything was handled in house. Rice was given a three-game suspension and a $50,000 fine — secretly. Then, when the video showed up on line, he was fired, along with an assistant coach and the athletic director (who received a $1.25 million severance package). (Here‘s one version)

Some players have argued that Rice’s behavior was not as bad as it appears on the video, and David Plotz argued in Slate that this type of behavior from his own high-school coach made him “a better player and a better man.” Maybe they’re right. Maybe we would all be better off if we were berated regularly for our shortcomings. There’s a balance in there somewhere between “preventing bullying” and raising a generation of hothouse flowers, and I’m not always convinced that we, as a society don’t veer too far in the direction of kid gloves.

The point is, you can imagine defending having a coach like Mike Rice. Likewise, you can imagine arguing that behavior like Rice’s is absolutely unacceptable in a University setting. What is bullshit is internally saying, yes, Mike Rice is great, he just needs to tone it down a notch, and then, when the public finds out, being all, “Oh my god! I can’t believe this was happening!” Basically, the sense you get is that no one was interested in figuring out what the right thing to do was. Everyone was motivated by protecting their own careers, and deflecting embarrassment away from the University.

So how does this relate to dancing teenagers in Jamaica?

The 2005 paper had seven co-authors, but the three key players are Robert Trivers and Lee Cronk, both from the Rutgers Anthropology Department, and William Brown (a postdoc at the time, now in the Psych department at University of Bedfordshire).

A couple of years after the paper came out, Trivers started to suspect that Brown had manipulated the data to make the results more compelling than they actually were. He went on to detail his analysis in a book published in 2009.

So what happens when one of the authors of a high profile paper comes out and claims that the results presented in the paper were not just wrong, but fraudulent? A news piece just out at Nature notes that Trivers approached Nature in 2008 about retracting the paper, but they were not interested. After all, why would they be? Nature’s business plan hinges on publishing studies that are exciting — studies that will be cited by a lot of other papers, and that will attract a lot of attention from the popular press.

This means that Nature (and other high-impact journals like Science) are particularly prone to a few types of bad papers. One is the shocking result that would lead to a major paradigm shift if it were true — but it is not true. One is the paper that seems to represent a huge advance, but is a modest advance that seems bigger than it is because it fails to cite much of the relevant literature. And one is the type we’re potentially talking about here, where a paper presents some really beautiful results, which are beautiful because the data has been manipulated in some way.

The problem is that this business model works great. The upsides of citations and press coverage apparently far outweigh the downsides of publishing incorrect, or incorrectly presented results. In general, there is not that much effort that goes into replicating results in science (arguably, a lot less than there should be). And even if a study fails to be replicated, and is shown to have been wrong, this typically happens years later, when no one is paying attention to the original study anymore.

That means that Nature and Science tend to have this funny status. In biology, anyway, everyone dismisses them as “magazines” or “tabloids.” At the same time, everyone is desperate to publish there.

DarwinEatsCake0085

 

So what do you do if you’re one of these journals? Well, if you are driven by a moral principle of promoting truth and spreading the best information possible, you put more effort into vetting papers up front, and when a paper is shown to be wrong, you actively try to correct the misperceptions stemming from the fact that people are saying, “Well, this was published in Nature, so it must be right.” On the other hand, if you are driven by the financial health of your corporation, you continue to publish things that will attract attention, and you retract or correct only when you absolutely have to, and you do it as quietly as possible, so as not to harm your brand.

Similarly, what do you do if you are a University associated with publishing a fraudulent paper? Again, if your guiding principles are truth and honest scholarship . . . oh, who am I kidding, those have not been the guiding principles of Universities for decades. As a University, your guiding principle is to maximize your money and prestige (to the extent that prestige begets money). That means that you will promote truth to the extent that you are required to do so, in order to maintain your brand as an important “research” and “education” institution. But what you really want is to keep the accusations of fraud as quiet as possible.

According to Trivers’s account of events, his going public with his book detailing the case for fraud, Rutgers was forced to undertake an investigation, since the work was supported in part by a grant from the NSF. Had they failed to do so, they might have become ineligible for NSF funds. When they completed their investigation in 2012, the University refused to make the results public. Trivers has posted the report on his own site (here). In brief, the report says that, yes, there is evidence for fraud in the paper (although the Nature news piece notes that Brown still denies having manipulated the data).

There’s another part of the story, though, that is much more disturbing. Trivers tells of an incident where he went to confront co-author Lee Cronk in his office about the situation. Trivers felt that Cronk had backed Brown’s version of events, and that the Rutgers report had vindicated his position over theirs, and he called Cronk a “punk.” Cronk then reported the incident to the campus police, and Trivers wound up getting banned from campus for alleged violation of the University’s anti-violence policy.

Now, clearly, I was not there, and so I have no independent source of knowledge about what happened that day. However, the version of event related by Trivers (read the whole thing here), sounds completely consistent with my own interactions with him. His version of the story suggests motivations and actions on the part of others:

It suggests that Cronk overreacted / acted punitively when Trivers confronted him. Maybe he was embarrassed and angry, and pretended to have felt physically threatened by Trivers in order to get back at him. Maybe he really did feel physically threatened, because, maybe, like most academics, he’s sort of a wuss. Maybe he overreacted in the heat of the moment, later wishing that he had not gotten the police involved. I don’t know. I’ve never met him, but this does pass the sniff test as the type of thing I can imagine a lot of Professor types doing.

It suggests that Rutgers sided against Trivers in the incident, perhaps out of retaliation for his original whistleblowing about the paper and the embarrassment and financial cost his actions imposed on the University. After all, if he had kept his mouth shut, they would not have had to undertake the whole fraud investigation, which I’m sure cost a bundle, and they would not have had the embarrassment of national press coverage. Again, clearly, I have no privileged details here, but this sounds like something you would do if you were a University that

I don’t want to pick on Rutgers in particular here. I think that this is the course of action that would have been taken by any University. That does not make it right, though.

I also don’t want to pick on Brown and Cronk, both of whom I suspect are perfectly bright and competent researchers. Even if Brown did actively manipulate the data, I see that as a pathology of the system, where getting a Nature paper can mean the difference between getting a job and not getting a job. If we didn’t hand out jobs and funding and promotions based on numbers of publications and citations — but rather on the quality and rigor of people’s research — there would not be incentives to manipulate or fabricate data. Even if Cronk maliciously got the Rutgers police to ban Trivers from campus, he did so in the context of a system that almost never rewards standing up and saying, “You know what, I was wrong.”

I know a lot of great scientists, people who are their own harshest critics, who are reluctant to publish results until they are 100% certain, who view even critical reviews of their manuscripts as good opportunities to make their work better. I also know a lot of scientists who are happy to cut corners, exaggerate the significance and importance of their results, and promote themselves, even, sometimes, at the expense of the truth.

Unfortunately, the way the current incentive system works, the latter group tend to have much better jobs than the former.

Until we can fix that, everything is going to conspire to encourage researchers to exaggerate, manipulate, and even fabricate their data. And everything is going to conspire to discourage Universities and journals from addressing and correcting fraudulent and erroneous results.

We have to reward honest, serious work that is not necessarily flashy. And we have to reward people who are willing to admit and correct mistakes.

Most of all, we have to reassert the principle of “truth” as our highest value in academia, and fight against its erosion by the secondary values of fame, prestige, and, most importantly, funding.

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Disclosure statements.

Since 2011, I have had an unpaid adjunct / visiting scholar position at Rutgers in the Genetics Department. During that time, I have gotten to know Trivers a bit, and we, in fact, have plans to work on a project together. In my experience, he is brilliant, boisterous, foul-mouthed, politically incorrect, and honest to a fault — exactly the sort of person all academics should aspire to be. Unfortunately, in their current incarnation, Universities much favor mediocre minds and personalities who will toe the corporate line, and who will bring funding to the University without inconvenient things like “truth” get in the way.

In elementary school, I was once on the losing side of a full-length, YMCA-league basketball game that ended 6 to 5. In junior high, I once attended a week-long basketball camp at the end of which I received the Orwellian “Most Improved Player” award.