Fisher’s pipe and Haldane’s moustache return in the new Darwin Eats Cake
As always, to observe this in its native habitat, visit http://darwineatscake.com/comic/en/181
Fisher’s pipe and Haldane’s moustache return in the new Darwin Eats Cake
As always, to observe this in its native habitat, visit http://darwineatscake.com/comic/en/181
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:
Good news this week for the Astronomy community! Unlike the previous three cases, the latest instance of high-profile professorial sexual misconduct to hit the press comes out of molecular biology. So, yay?
Jason Lieb resigned from the University of Chicago after he was found to have violated the University’s sexual misconduct policy. According to the report from the New York Times:
The professor, Jason Lieb, 43, made unwelcome sexual advances to several female graduate students at an off-campus retreat of the molecular biosciences division, according to a university investigation letter obtained by The New York Times, and engaged in sexual activity with a student who was “incapacitated due to alcohol and therefore could not consent.”
Notwithstanding the fact that “sexual misconduct” seems to be a pretty euphemistic description of what sounds like criminal sexual assault, this is actually a pretty heartening story in a lot of ways. The University of Chicago seems to have acted quickly, recommending that Lieb be fired. That’s in sharp contrast with (and perhaps in reaction to) the handling of other cases, where it often seems that universities’ first impulse is to protect the faculty (and their research funding), only doing the right thing if and when the public finds out, and the negative press coverage threatens to become too costly.
However, there are still some questions about Chicago’s decision to hire Lieb in the first place. There were apparently rumors about Lieb, and suggestions that inappropriate sexual behavior was the reason for his having left Princeton and, before that, the University of North Carolina. However, accusers were anonymous, universities “could not comment on personnel matters”, and so . . .
At Chicago, the hiring committee struggled, Dr. Gilad said, to balance a desire to protect students with a desire not to convict someone without evidence. He said Dr. Lieb had not been found guilty of any offense at North Carolina. The department of human genetics voted unanimously to hire him.
But at the same time,
Separately, Dr. Gilad acknowledged, during the interviews of Dr. Lieb, he admitted that he had had a monthslong affair with a graduate student in his laboratory at the University of North Carolina.
So Lieb did something completely inappropriate (relationship with student in his lab), which makes the rumors feel a little less unsubsantiated. But the hiring committee fell back on the old “Well, he wasn’t formally found guilty, so our hands were tied.”
This is what always happens, in faculty meetings and comment sections — invocation of “innocent until proven guilty”. While that’s an important standard to uphold in criminal court, it’s not the standard for hiring decisions. And when hiring someone for a faculty job, it is a dangerous and destructive impulse.
A faculty job is different from (most) other jobs because of the structure of academia. Professors have enormous power over the students and postdocs who come through their labs. And there’s not an easy way to fix that power structure, because it is baked in.
If you’re a student or postdoc, your career is profoundly dependent on the good will of your advisor. You need an advisor who is willing to go to bat for you, in letters of recommendation and in person. And sure, that might be somewhat less true if there were some magical way to reduce the role of cronyism in academia, but just a bit. If you’re actually engaged in cutting-edge research, the number of people in the world who can really evaluate your work is small. And the number of people who will actually spend the time to really evaluate it is smaller still — probably mostly your co-authors.
Combine that with the extreme competition for faculty jobs, and you’ve got a system where crossing your advisor is career suicide, even if you’re in the right. People who have blow-outs with their advisors rarely land academic jobs. (Many wind up with jobs of various sorts, but rarely tenure-track positions at research universities.) In my observation, it’s mostly when the blow-out happens early on, and someone else in the department adopts them. And even then, the disruption may set them back months or years.
That puts a much greater burden on the hiring process — or at least it should. Every time you hire a new professor, especially if you’re bringing them in with tenure, you’re putting them in a position of authority over students. And if they abuse that authority, those students will have to choose between tolerating that abuse and risking their careers, no matter how good your grievance process is.
Hiring faculty should be more like hiring a babysitter. You don’t have a moral obligation to hire the skeevy guy with the windowless van just because the jury found insufficient grounds to convict him after his previous two babysitting gigs.
Now, if you were considering Lieb for a position at a research laboratory where he would be working with peers, it would be reasonable to give him a bit more benefit of the doubt. Or at least it might have been reasonable before the whole sexual assault thing.
But if you’re thinking of handing him the keys to a fiefdom where young people are entirely dependent on him, and you ignore red flags, you are absolutely responsible for the damage he causes when he turns out to be exactly what he seems.
Check out this excellent evolution GIF by animator Nicolás Fong.
You can see more of his stuff at his Tumblr, which it trippy and sometimes borderline NSFW.
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.
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:
Now, 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!
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!
So, over at the Ronin Blog, I have posted my thoughts on the column written by new Nobel Laureate Randy Schekman where he urges all of us to boycott the journals Science, Nature, and Cell.
The basic argument is that the core problem is not these journals, but the use of publication in these journals (and other, equally superficial metrics) as proxies for quality.
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.
* Answer: You want to be your field’s Lon Chaney.
So, if you are a Physicist, or if you know a Physicist and are very patient, you’ve heard all about the arXiv, the preprint server that kicked off the open-access publication movement. If not, here’s what you need to know. The idea is that when you write up a paper, you post it online, where it becomes immediately and freely available to the world. If you revise, you can post the revised paper. And, even if you go on to publish the work traditionally, there will be a version out there that is not behind some journal’s paywall.
Most arXiv users do, in fact, go on to publish their work in traditional, peer-reviewed journals. But by posting to the arXiv first, you get your work out quickly. If you’re a naive idealist, this lubricates the flow and speeds the creation of knowledge. If you’re a paranoid careerist, it allows you to date-stamp your ideas to guard against being scooped.
While the arXiv has a “Quantitative Biology” section, preprint culture has never really taken hold in the Biology community the way it has in Physics. But here’s something that will maybe help to push things in the right direction: bioRxiv, Biology’s very own preprint server! The server features twenty-four sub-fields of Biology, and, as of this writing, Evolutionary Biology is WINNING with eight posted manuscripts.
If you’re worried about whether posting a preprint of your manuscript might interfere with your ability to publish in a traditional journal:
Now get to posting!