Category Archives: religion

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

Okay, that “Creator” paper has officially been retracted by PLOS ONE (previously, and here).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:

Or you can use google translator to check this page (a Chinese dictionary):
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.

“Creator” Paper Retracted at PLOS One

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:

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

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!

Steve Lonegan on Syrian “Others”

So, as some of you may know, we’ve got a special election happening tomorrow here in New Jersey, pitting Democrat Cory Booker, the current Mayor of Newark, against Republican Steve Lonegan, the former Mayor of Bogota. The race got a lot of headlines in the past few days after Rick Shafan, a (since fired) senior staffer with the Lonegan campaign, said that Booker’s communications with a Portland stripper sounded like “what a gay guy would say.” He went on to explain in stomach-churning detail what he (as a representative of straight guys everywhere) would have said to the same stripper. If you haven’t read about it, check it out.

But back in September, we got a recorded phone call from Lonegan, urging us to come to a rally in Montclair against military intervention in Syria. Now, while I doubt that I agree with Lonegan on just about any other issue, I am glad that we found a way not to get involved in another war (even if it was going to be “just” airstrikes).

The American’s-bombing-people-in-Syria issue, is settled, at least for the moment, but there was something telling in the phrasing of the phone message. Here’s my transcript:

America is on the verge of another war, a war we can not afford. A war where we do not belong. I’m Steve Lonegan, I’m the Republican candidate for the United States Senate. Please join me this evening in Montclair at 12 Church Street for our anti-war rally.
We should not be putting our money, our troops, and our nation in harm’s way in a war in Syria that will result in the death of thousands of Syrian Christians, Jews, and Others.
We simply do not belong there. There is no excuse for this war. None. Please send our message to our elected representatives across this state and across this country: “No . . .”

That’s where our answering machine cut off. I assume the message was something along the lines of “No war!”

The interesting part of the message was “Syrian Christians, Jews, and Others.” Hmmm . . .

Here’s my read on this. I have no evidence to suggest that Steve Lonegan himself has anything against Muslims. He might, but I’m happy to give him the benefit of the doubt here.

However, it does seem clear that he is unwilling to say that he is against killing Muslims.

Here’s how I picture the strategy meeting:

STAFFER 1: Okay, it looks like Obama is going to war against Syria. We’re tying Booker to Obama, so we need to come out against the war.

STAFFER 2: But we have to be careful. Killing Muslims is still polling very strong with our base.

STAFFER 1: I’ve got it! We refer to Syrian Muslims as “Others”.  That way we avoid appearing sympathetic to them, and in fact, contributes literally to the “Othering” of Muslims, sensu De Beauvior.

STAFFER 2: We’ve got a mole!

Sadly, STAFFER 1’s body was never found.

Free Tips for ex-Westboro Baptists Apologizing

So, nobody asked me for this advice, but if I only gave out advice when people asked for it, I would probably burst from all the advice building up inside me.

Today, Anderson Cooper apparently interviewed Libby Phelps Alvarez, granddaughter of Westboro Baptist founder Fred Phelps (via Gawker — I did not watch this). She was raised in the church, but fled / escaped / defected in 2009, and has recently started speaking publicly about her experience. Let me just say that she deserves a lot of respect for that. I mean, she had to reject her whole upbringing and family, which must be hard, even if your family is full of Phelpses.

Here’s the thing that pissed me off though. Her interview included the following statement of regret:

I do regret if I hurt people, because that was never my intention.

This is such the standard, cliche pseudo-apology that it is easy at first glance to overlook what an offensive pile of garbage this is. First of all, “if”? Really? Again, this is super common in these circumstances, but if you’ve spent most of your live holding up “God Hates Fags” signs at the funerals of soldiers and children, you know damn well that you hurt people.

Even worse, though, is the second bit. When some politician or celebrity pseudo-apologizes, saying it was never their intention to hurt anyone, it is often at least plausible that they were being careless, and not intentionally hurtful.

In this case though, hurting people is precisely the intention of every public appearance the Westboro Baptist Church makes. Now, maybe you could make the case that you thought you were practicing tough love, hurting people in a way that would lead them back to the path of righteousness, or some such nonsense. This would be bullshit, of course, but it would at least be plausible according to some sort of twisted logic.

The fact is, you did intend to hurt people. I believe that you wish now that you had not hurt people in the past, and that’s great. I believe that you were a kid, did not know better, and are not fully responsible for your actions, at least up to a point. I believe that you think of yourself as a good person, and I am eager to believe that you have become one. But when I see this sort of pseudo-apology, it makes me a little bit skeptical.

Maybe try something like this: “I know that I hurt a lot of people, and I am sorry. I understand now how hurtful my words and actions were in a way that I did not understand then.”

I feel bad about this. I mean, given where she started from, she has progressed further in the past few years than most people do in their lifetimes. But if you’re going to make amends publicly, a good way to start is by being honest.

God has 4095 parameters

So, over at Nothing in Biology Makes Sense, there is an explicit phylogenetic test of Evolution versus Creationism. With the help of the Akaike Information Criterion, Evolution wins!

Note, however, that this argument works in this specific form only for the Judeo-Islamo-Christian concept of God. Buddha is a Bayesian.

Read about it here.

Greek Pastafarian Arrested for Blasphemy

So, a reader conveyed this news item to Boing Boing:

On September 24, Greece’s Cyber Crimes division arrested a 27 year old man on charges of blasphemy, for his website that mocks a well-known Greek monk Elder Paisios, using the name Elder Pastitsios (the even better-known Greek pasta dish).

First of all, if your country still has blasphemy laws, your country is run by assholes.

It’s being widely reported that the arrest was instigated not by the Greek Orthodox church, but by the neo-Nazi group Golden Dawn, who currently hold seats in Parliament.

That pretty much says it all, doesn’t it?

There is also a link to this blog post, which describes (in Greek) a Pastafarian protest of the arrest. A video of the procession is at the bottom of the post. According to Google Translate, the proceedings involved this prayer:

Lord, the devil abolish the death fucked, cautions us from triskataratou Memorandum and any other demon, multiply Pastitsio this circumstance, as the loaves and fish, bless the social struggle and taxikin Again, amen

and this song:

Rich went into liquidation and epeinasan

And the ekzitountes the Lord

All were reduced CDK pasticcio.

As the hungry liberator,

and defender of the poor,

sick doctor,

progastoron advocate Kimadofore,

Besalomartys Pastitsio,

Christ believed in God,

be saved Tash ventricular us.

Iran and Israel, Love and Peace

So, here’s a pretty cool thing. Yesterday someone started a Facebook page where Israeli and Iranian citizens are sharing messages of mutual respect, love, and peace, in contrast to the rhetoric coming from the two governments. Check it out here.

It’s a small thing, but still cool, and has already built up a pretty good head of steam. And, you know, it is always worth pointing out the fact that it is usually governments that hate each other, not people (except to the extent that they are whipped into a frenzy by misinformation from their war-mongering governments).

Now, I’m neither Israeli nor Iranian, but I am American, and, of course, we have a similar set of issues. On that point, let me just put this up. You’ve already seen it, because it’s all over the internet, but, again, there are some things that can’t be said too many times.

Toxoplasmosis Extravaganza: Ride Complete!

So, this week at Darwin Eats Cake, we celebrated our one-year anniversary with a series of nine strips on the zooparasite Toxoplasma gondii. This parasite, which causes Toxoplasmosis, is the reason why pregnant women are encouraged to avoid cat litter.

Here’s the full series, presented for your one-stop-shopping viewing pleasure. The strips do not, I think, assume any expert biological knowledge, so you don’t need to be a parasitologist to enjoy them. However, a dorky and juvenile sense of humor will help a lot. Alternatively, you can read them on the Darwin Eats Cake website, where they look a little better, I think. The series starts at

At this point, Darwin Eats Cake will return to its regular programming schedule, with twice-a-week updates, usually on Mondays and Thursdays, except for those days that have been recognized as official holidays by the Darwin Eats Cake Council of Freeholders and its chairwoman, the duly elected Queen of Naboo.

So, stop by on Monday for a new strip, or any time to trawl the archive:

It’s Toxoplasmosis week at Darwin Eats Cake

So, tomorrow (March 13) marks the one-year anniversary of the launch of my webcomic Darwin Eats Cake on its very own website (here). Normally, Darwin Eats Cake updates approximately twice a week (hemicircaseptanally), on approximately Monday and Thursday (circa-Mondarily and circa-Thursdarily, I assume). However, to mark this special anniversary occasion, we are rolling out a daily series of strips on Toxoplasma gondii, the parasite responsible for Toxoplasmosis. This bug was recently in the news thanks to a profile of Jaroslav Flegr published recently in the Atlantic (here).

Here are the first two of this week’s six strips:

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