Category Archives: science

DNA Confirms Tyrolean Iceman Died of Extreme Fashion Violation

In 1991, the five-thousand year-old mummified remains of a man were discovered in the Italian Alps. Numerous DNA analyses have been performed on those remains in the past, providing a lot of information about who he was and what he ate. But now, a team of Italian and Irish researchers have analyzed ancient mitochondrial DNA recovered from his clothing, providing critical insight into his likely cause of death.

The results were published earlier this month  in Scientific Reports, and hoo boy is the ghost of Joan Rivers angry. Shoelaces made from cattle, sheepskin loincloth, and goatskin leggings; a quiver made from roe deer and a bearskin hat. His coat? Goat and sheep! I mean, this guy was basically wearing a Guy Fieri nacho recipe.

Artist’s reconstruction of the iceman’s ensemble. Image via

The results provide information about the ancient phylogeography of these animals, as well as insight into the iceman’s lifestyle. The cattle, goats, and sheep all appear to be closely related to contemporary domesticated populations in Europe, consistent with an agricultural/pastoral existence. The deer and bear point to an important additional role for the use of wild species.

Other analysis has suggested that this iceman died as a result of an arrow wound. Alternative theory: this is evidence of early mirror technology — a technology that, like the nanobots in Wool, developed before the culture was advanced enough to handle it.

Balter Provides Some Background on Why Science Magazine Fired Him

Yesterday we learned that Michael Balter had been fired by Science magazine, and that it had something to do with his article last month on sexual harassment in academia. Today, he has published his promised blog post in which he has provided some additional background.

Based on the additional details he provides, it sounds like it was a combination of a couple of things.

First, a historical pattern of not being sufficiently deferential to the higher-ups. Particularly troubling was this tidbit:

I’ve already talked above about the culture at AAAS that allowed four colleagues to be fired precipitously in 2014, and will not elaborate on that here–except to say that just as I was beginning the Brian Richmond investigation, one of my editors asked me to delete a key blog post about that episode in which I criticized our Editor-in-Chief Marcia McNutt for parroting the party line put out by former AAAS CEO Alan Leshner. I declined to engage in this sanitizing of the historical record, not least because I consider that episode to be one of the proudest moments of my life. It’s not often that one gets to put one’s career on the line for something one believes in, and I have no regrets.

Second, it sounds like the editors, or at least some of them, were never fully on board:

But it is important to note that Science did not jump on the story when we first found out about the allegations concerning Richmond last August. There was discussion about whether we should focus on this one person, about whether Richmond and his alleged actions were important enough to write a story about, and related issues. I don’t think my editors will contest the fact that I pushed the hardest for us to do a story; but even after the Geoff Marcy sexual harassment case broke at Berkeley, and the astronomer was forced to resign, there was still a great deal of ambivalence about whether the Richmond case was newsworthy.

Balter seems to suggest that Science‘s reluctance was motivated primarily by an excess of caution — fear of lawsuits, and I’m sure that was part of the story.

But it is also important to keep in mind that Science is one of the most prominent mouthpieces of the scientific establishment. That’s one of the things that made the original article so powerful and important.

That’s not to say that the scientific establishment is pro-sexual harassment per se. But, the fact is that power, including sexual power, over young people has long been one of the implicit perks of success in academia. Some people exploit that power, and some don’t, but giving away power is rarely a high priority.

I’m not arguing for a conspiracy here. It’s just that the people closely associated with a publication like Science, whether as editors, or publishers, or authors, or journalists, are people who have risen to the top in the current system — often with good cause. But it is natural for them to be wary of things that challenge the status quo.

Natural, just not admirable.

As Balter notes, it will be interesting to hear what, if anything, Science says publicly about this. In the meantime, the good news is that there’s an excellent science journalist out there with some time on his hands. You should hire him.

Update: AAAS has issued this statement:

Michael Balter was provided notice on March 10, 2016 that his contract as a freelance writer for Science magazine was being discontinued. Mr. Balter has written many stories for Science‘s news section, including one published February 9, 2016 on a sexual misconduct case.

Science editors stand by the February 9, 2016 story as published. The goal of editing was to ensure that the story was both powerful and fair.

AAAS remains committed to providing leadership on stopping sexual harassment in science and empowering women in STEM fields.

Which, you know, okay.

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.

“Mystery of the Creator’s Invention” at PLOS One


PLOS One published a paper in January with the title “Biomechanical Characteristics of Hand Coordination in Grasping Activities of Daily Living“. And the abstract contains this line:

The explicit functional link indicates that the biomechanical characteristic of tendinous connective architecture between muscles and articulations is the proper design by the Creator to perform a multitude of daily tasks in a comfortable way.

The main text contains two more references to “the Creator”. The Introduction notes that

Hand coordination should indicate the mystery of the Creator’s invention.

And the end of the Discussion:

In conclusion, our study can improve the understanding of the human hand and confirm that the mechanical architecture is the proper design by the Creator for dexterous performance of numerous functions following the evolutionary remodeling of the ancestral hand for millions of years.

Today, someone seems to have noticed this “Creator” stuff and brought it to the attention of the journal, which issued a statement that they’re looking into it.

So what happened?

This does not read to me like it is part of some sort of conspiracy to infiltrate the biology literature with intelligent design propaganda. However, it is a good illustration of the issue with the PLOS One model as it is implemented in practice.

Screen Shot 2016-03-02 at 3.52.50 PM

PLOS One is based on an interesting idea. The papers are peer-reviewed, but evaluation is explicitly supposed to focus on technical accuracy, ignoring “impact”. This was a brilliant idea. Historically limited space (in print) and a pathological pursuit of citation metrics means that lots of good science has a hard time getting published, either because it is not flashy enough, or because journals are reluctant to publish things that do not fit squarely in the domain of what they imagine their readers’ interests to be.

In a sense, PLOS One aims to split the difference between traditional publishing and the preprint / post-pub-peer-review model. It is someplace where you can publish interdisciplinary work, weird little fun studies, negative results, etc. But in principle you get the benefit of knowing that the work itself has been vetted.

Or at least as vetted as you ever get with peer review, which is to say, imperfectly and highly variably.

As a result, PLOS One publishes lots of cool stuff, and it provides a valuable service to the community. But when something like this happens, it makes it seem like the editorial policy in practice is something more along the lines of “just make sure the check clears”.

Decuplet of Bushes at Darwin Eats Cake

Man, it seems like there are so many Bushes in the world! How can we possibly keep them all straight? How are they organized?

Fortunately, frutexophysicists have developed a theory that uses Lie groups to organize the previously unmanageable zoo of Bushes into simple representations. The latest Darwin Eats Cake presents one of these representations: the decuplet for Bushes with spin –3/2. Note that this theory predicts the existence of an as-yet-unobserved Bush (Omega Bush) with maximum charm and minimum strangeness. The Omega Bush is thought to be stable only at extremely high energies not seen since shortly after the Big Bang.


Here’s What’s Up with the Color of that Dress

After the continuation of net neutrality and the onset of the llama revolution, the most exciting thing to hit the internet yesterday was this dress, which some people claim is white and gold, while others claim it is blue and black.

guys please help me - is this dress white and gold, or blue and black? Me and my friends can’t agree and we are freaking the fuck out

Buzzfeed has been running a poll. As of right now, the results are running 71% white and gold versus 29% blue and black. Gawker media is also on the case, concluding that everyone is an idiot, while Slate says you’re looking at the dress wrong.

Here’s what I think is going on. First off, here are the two colors, extracted from the image and presented out of context:


To me, that’s a sort-of steely blue-gray on the left and brown with maybe a hint of gold on the right. According to Adobe Illustrator, the RGB values are: R: 140, G: 146, B: 185 on the left and R: 137, G: 115, B:81 on the right. Depending on where, exactly you sample from, the values vary a bit, obviously, but are always pretty close to these.

In each case, these values are on a scale that runs from 0 to 255. So that means the Red and Green channels are running at about 50% in both cases. If all three were 50%, we would have something that looked like a middle-of-the-road gray. Relative to that, we have some extra blue on the left, and we have some blue taken away on the right. So we can think of the blue-gray as a bluish gray. The brown we can think of as a yellowish gray, or maybe an orangish gray.


So, those are the actual colors in the picture, but the color of the dress is a different question. Why is it that some people look at the top photo and see a white dress with gold trim, while others see a blue dress with black trim?

What I think we have here is a case where there are two different effects, both relating to the fact that our perception of colors is affected by context. What is special in this case is that the two effects are pushing our perception in opposite directions. Plus, they are balanced in magnitude, so which of the two dominates varies from person to person, and can be influenced by little details, like the angle at which you view your computer screen, background lighting, etc. In fact, some people see the colors spontaneously flipping from white-gold to blue-black or vice versa. It’s basically this thing from the New Yorker:

The first effect is we perceive colors in a way that enhances their contrast with nearby colors. Look at these boxes. If you’re like most people, the small square on the left looks like it is a lighter color of gray than the small square on the right:


But in fact, those two center squares are exactly the same shade of gray. The one on the left looks lighter because it is surrounded by a darker gray. The one on the right looks lighter because it is surrounded by a lighter gray. Here are the same two squares with the context removed:


This is a perfectly reasonable thing for your eyes to do, because, in the real world, the intensity of light in the environment varies. If you’re looking for berries to eat, you want to perceive a strawberry in a shady spot as the same type of thing as a strawberry in a sunny spot. So, when everything is dark and shady, you correct your perception, saying essentially that this strawberry must actually be brighter than it looks. Similarly under bright sunlight, you would (correctly) infer that the berry is actually darker than it appears.

The color surrounding much of the dress in the photo is a very bright white. In this context, we perceive the colors as being darker and more saturated than they are, yielding a rich blue and a very dark brown verging on black.

But there’s another way that this correction can play out. Look at this picture:

Figure 0.1. Thechessboard illusion: areas A and B on the board have ...

The punchline here is that the squares labeled A and B are actually exactly the same color (as illustrated in the lower-left corner of the photo. Here, part of the effect is due to the fact that square A is surrounded by lighter squares, and therefore appears darker than it is, while square B is surrounded by darker squares, and appears lighter. But another part of the effect is due to the fact that we perceive a light source off to the right, and we see that the green cylinder is casting a shadow. Since we know that square B is in this shadow, we correct for this, perceiving it not as a gray square, but as a white square that is in the shadows.

In the dress picture, the light is coming from behind the dress, so the entire side of the dress that we can see is in its own shadow. We correct for this by perceiving not a blue-gray dress, but a white dress that has been photographed with horrible backlighting. We implicitly assume that the darkness is an artifact of the photograph.

We can recreate these two effects by taking our original two colors and either shifting them away from white (recreating the effect of perceiving something against a white background), or shifting them towards white (recreating the effect of perceiving something photographed with a light source behind it).

Here, I’ve corrected the saturation and blackness values 1/3 of the way from the original (left) towards pure white (center) or pure black (right):


And here, I’ve corrected all three RGB values 1/3 of the way from the original (left) towards pure white (center) or pure black (right).


So, when you look at the dress, part of your visual system is saying, “Wow, everything is so bright! This dress must actually be really dark in order to look like this!” But another part of your visual system is saying, “Wow, what a horrible shadow! This dress must actually be really bright in order to look like this!”

What is so cool about the picture is that it seems to trigger both of these corrections in roughly equal measure. But just as our perception of a duck-rabbit picture snaps back and forth between duck and rabbit (but it is hard to see both at the same time), our brain chooses one of the two interpretations of the dress photo, and jumps in with both feet. Small differences in our visual systems — or the specific details of the context in which we view the photo — determine which way it jumps. For instance, I find it easier to see the white and gold dress when I look at the top part of the photo (where the backlighting is strongest), and can see the blue and black dress best at the bottom.

Hey look! Mississippi and West Virginia lead the Nation in Something Good!

You know, most of the time when you hear “Mississippi leads the nation in . . .”, it is the lead-in either to a joke or a really depressing statistic. But check out this map from the Washington Post:

All 50 states require vaccination, and all 50 provide for medical exemptions, which is good. But 48 of the 50 also provide religious or “personal belief” exemptions.

Personally, I am most bothered by states that have one or the other of these, and not both. Because saying that you can opt out on the basis of a religious belief, but not a personal one puts the state implicitly in the position of deciding what does and does not qualify as a religion. Doing it the other way around just seems weird, since religious beliefs are personal beliefs held for religious reasons, right?

But only two states have the right law: straight-up requirements for vaccination with only medical exemptions. So, if your children’s health is being threatened by sanctimonious morons spouting discredited pseudo-science about autism, or mercury, or argle blargle pharmaceuticals something something, just remember, if you lived in a less retrograde state, like Mississippi or West Virginia, you wouldn’t have to put up with this bullshit.

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

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.