Archives For science

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I haven’t written here about the CDC “whistleblower” issue, because I was in Shanghai when the story broke with both limited internet access and limited desire to take time away from adventures to write. Orac did an excellent job of staying on top of the story, and I refer the interested reader to his series of posts on the subject, as well as this excellent summary by Todd W. at Harpocrates Speaks, and this one by Retraction Watch.

However, as many people who read Violent Metaphors have a specific interest in vaccine/anti-vaccine issues, I thought it would be worth talking about the most recent development in the story; specifically, the retraction of Brian Hooker’s journal article purporting to show an increased risk of autism among African American boys who receive the MMR vaccine.

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I’ve been waiting for this paper for months! The Willerslev group has just published the results of their study on ancient DNA from Paleo-Eskimos in the North American Arctic. Unfortunately, this article is behind a paywall at the journal Science, but I’ll give you a brief summary of the results, and talk a bit about why this paper matters and what it means for our understanding of the peopling of the Americas. Continue Reading…

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In a series of recent posts I and several others have strongly criticized Nicholas Wade’s recent book “A Troublesome History”, which purports to show that human races are biologically meaningful categories, characterized by different behavioral tendencies (which have resulted in different degrees of socio-political success). Now 139 professors with expertise in genetics, human biology, biological anthropology, and evolution have added their voices to this discussion, criticizing Wade’s book in a strongly worded letter that appears in the New York Times today. The full text of their letter can be found here. Organized by Grahm Coop, Michael Eisen, Rasmus Nielsen, Molly Przeworski, and Noah Rosenberg, the signatories include many of the leading researchers in human genomics (a full list of signatories and their affiliations can be found here).

Several of the authors are people whose research Mr. Wade cited approvingly in his book as supporting his thesis, such as Dr. Sarah Tishkoff, Dr. David Reich, and Dr. Noah Rosenberg (lead author of the 2002 paper that Mr. Wade uses as the primary evidence for his conception of genetically distinct races).

According to Michael Balter in an article appearing today in Science:

The letter was spearheaded by five population geneticists who had informally discussed the book at conferences, says co-organizer Rasmus Nielsen of the University of California, Berkeley. “There was a feeling that our research had been hijacked by Wade to promote his ideological agenda,” Nielsen says. “The outrage … was palpable.”

The authors don’t mince words:

Wade juxtaposes an incomplete and inaccurate account of our research on human genetic differences with speculation that recent natural selection has led to worldwide differences in I.Q. test results, political institutions and economic development. We reject Wade’s implication that our findings substantiate his guesswork. They do not.

We are in full agreement that there is no support from the field of population genetics for Wade’s conjectures.

This letter is highly inconvenient for Mr. Wade, making it clear that the senior researchers in the fields from which he’s trying to marshal support categorically reject his storytelling and bad science. Nor can he continue to make the (untrue) argument that critiques of his book are largely politically based, and conducted mainly by social scientists. A strong blow has been dealt to scientific racism today.

 

For further reading, check out the Nature blog on the subject: http://blogs.nature.com/news/2014/08/geneticists-say-popular-book-misrepresents-research-on-human-evolution.html, and Jeremy Yoder’s post: http://nothinginbiology.org/2014/08/08/population-geneticists-to-nicholas-wade-you-know-nothing-of-our-work/

 

UPDATE: Mr. Wade has issued a statement responding to the letter.  He starts out reasserting the position I claimed above that he can’t continue to hold:

“This letter is driven by politics, not science. I am confident that most of the signatories have not read my book and are responding to a slanted summary devised by the organizers.

As no reader of the letter could possibly guess, “A Troublesome Inheritance” argues that opposition to racism should be based on principle, not on the anti-evolutionary myth that there is no biological basis to race.  Unfortunately many social scientists have long denied that there is a biological basis to race. This creed, prominent throughout the academic world, increasingly impedes research. Biologists risk damaging their careers if they write explicitly about race.

 

In yesterday’s post on the subject, Mr. David Dobbs described who several of the authors are:

Those signers include

  • Noah Rosenberg, the lead author of a 2002 paper that Wade leans on especially heavily, ”Genetic Structure of Human Populations,“ as well as at least two other authors of the paper.

  • Yale’s Kenneth Kidd, who is one of the world’s most respected population geneticists, a central figure in establishing the field, and another co-author on the 2002 Rosenberg paper.

  • Stanford’s Jonathan Pritchard, another co-author on that paper and the researcher whose lab designed the ”Structure“ genetic analysis software that created the ”clustering“ data Wade says supports his argument.

  • Sarah Tishkoff, lead author of a 2009 paper on ”The Genetic Structure and History of Africans and African-Americans“ that Wade cited extensively as crucial support.

  • Jun Li and Richard Myers, the lead and senior authors of a 2008 paper, ”Worldwide Human Relationships Inferred from Genome-Wide Patterns of Variation,” that, as I noted in my review, Wade misrepresented as supporting his argument.

 

These and the other signatories of the letter are the leaders in the field of human population genetics. They do not shy away from research and writing about human genetic variation. Mr. Wade is wrong to imply that they are being intimidated by cultural anthropologists. The fact that they agree on a single statement (on anything) is extraordinary and should be treated seriously.

Further, I suspect that more people on that list have read his book than he believes, simply because I’ve talked to them. In fact, Jerry Coyne, one of the signers of the letter has read it twice. (I encourage you to read his thoughts on the subject at the link above).

Disturbingly, Mr. Wade appears to be adopting the methodology of his “HBD” followers in claiming that evolution requires acceptance of his view of race. The data do not support that position, and saying so doesn’t make any of us anti-evolution, no matter how loudly he says it.

He goes on:

These attacks have included repeated assertions that the book is scientifically inaccurate, a charge for which I have seen no basis. In the same vein, this letter issues general charges without supporting evidence.

True, the letter doesn’t go into a detailed scientific refutation of his book. But there’s hardly space in the letter section of the NY Times to document his numerous errors, and many of us have done that already (For example “The troublesome ignorance of Nicholas Wade” by Agustin Fuentes, “How A Troublesome Inheritance gets human genetics wrong” by Jeremy Yoder, “The genes made us do it: The new pseudoscience of race” by Jon Marks, “A guide to the science and pseudoscience of ‘A Troublesome Inheritance’” by Chris Smith, “A Troubling Tome” by Greg Laden, “On the origin of white power” by Eric Michael Johnson, and “The fault in our DNA” by David Dobbs). If you take a look at the various reviews of his book, you’ll see that they tend to cover many of the same points. Mr. Wade has consistently ignored all of them. His only responses to critics (myself, Agustin Fuentes, Jon Marks, and later Pete Shanks), has been to dismiss our credentials without seriously engaging with the substance of our points, calling us “incoherent with rage”. He’s ignored many other detailed critiques. Given all of this, I’m fairly certain that there are no terms in which 139 professors could couch a critique that would satisfy Mr. Wade. Who is actually being political here?

 

You might find this American Anthropological Association-sponsored debate between Agustin Fuentes and Nicholas Wade illuminating:

 

 

ETA (8/10/14): I mistakenly listed only Dr. Coop as the organizer of the letter. I’ve edited to add the names of the other professors who organized and wrote it. My sincere apologies for the oversight.

Sign

This week Mike Adams, the self-styled “Health Ranger”, who runs the alternative medicine website Natural News, posted one of the most disturbing tirades against scientists that I’ve ever seen. He’s always been a promoter of pseudoscientific arguments against GMOs, but he has gone much, much further in his latest piece “Biotech genocide, Monsanto collaborators and the Nazi legacy of ‘science’ as justification for murder” (WARNING: Graphic and disturbing imagery of Holocaust victims at the link). Continue Reading…

Excavating a cemetery in Barrow, AK. One of the best crews I've ever been on.

Excavating a cemetery in Barrow, AK. One of the best crews I’ve ever been on.

 

My friend and colleague, Julienne Rutherford, and her co-authors Kathryn Clancy, Robin Nelson, and Katie Hinde have just published a groundbreaking study on fieldwork experiences among women in science. Disturbingly (though unsurprisingly for those of us who have done fieldwork), a majority (72.4%) of respondents to their survey “reported that they had directly observed or been told about the occurrence of other field site researchers and/or colleagues making inappropriate or sexual remarks at their most recent or most notable field site.” Further, a majority (64%) reported that they had personally experienced sexual harassment. (It’s important to note that men also responded to this survey to report experiencing and/or witnessing harassment, although at a lower frequency than women.)

This is one of those rare cases where I don’t need to recap the findings of the article, because the authors have published it in an open-access journal (PLOS ONE), and so I encourage you to go read the study itself here, and the Science news report about it by Ann Gibbons here.

Fieldwork is an occasional, but very important part of my job, and from my experiences I can attest that junior people in the field, particularly students, are extremely vulnerable. I applaud these researchers for calling attention to this problem, and I hope that it will be the beginning of a very important conversation about how to make fieldwork safer for everyone.

*** UPDATE: This piece, by Andrew David Thaler, is a must-read. I’d been debating about whether to write about the Richard Feynman controversy going on in the last few days, but instead I’ll just recommend that you check out the links in the first paragraph, particularly to Matthew Francis’ post on the subject.

impediment

In recent weeks, Nicholas Wade’s book A Troublesome Inheritance has been soundly criticized on the basis of his misunderstanding (or misrepresentation) of the statistical methods used to study human genetic variation (see Jeremy Yoder’s critique here, Chris Smith’s here, Joseph Graves’ here, and mine here ), his misunderstanding of evolution (see Michael Eisen’s critique here, and Eric Michael Johnson’s here ), and his misunderstanding of human biological variation (see Greg Laden’s critique here,  Agustin Fuentes’ critique here, and Jon Marks’ here ). These criticisms–all from biologists and biological anthropologists– can be boiled down into a single statement: Mr. Wade’s book is scientifically unsound.

His responses thus far (to those of us who published in the Huffington Post) have failed to engage any of the substantive issues that have been raised. Instead, he dismissed our standing for discussing this issue, calling me a “postdoctoral student” (A science journalist should be aware that postdocs aren’t students), and dismissing Dr. Fuentes’ and Dr. Marks’ research background and credentials (as if biological anthropologists were not scientists). I have not seen any response yet to the numerous other critiques from biologists that have appeared elsewhere (many listed in the previous paragraph), which raise many of the same concerns.

Mr. Wade may feel that he can ignore the substantive critiques of his book by scientists. But can he do the same for fellow science journalists? David Dobbs’ review of Mr. Wade’s book appeared in the New York Times Book Review this past Sunday (the online version can be read here). It is not favorable.  Mr. Dobbs calls the book “deeply flawed, deceptive, and dangerous.”

In discussing the study (critiqued by most of us above) that Mr. Wade claims supports the genetic basis for three (or is it five?) “continental races”, Mr. Dobbs notes that the paper itself

“directly contradicts Wade’s argument. Yet he baldly claims the study as support.  And he does this sort of thing repeatedly: He constantly gathers up long shots, speculations and spurious claims, then declares they add up to substantiate his case. The result is a deeply flawed, deceptive and dangerous book.”

Mr. Dobbs elaborates on this in the companion piece on his blog:

“Wade demonstrates how a lucid, well-written, selective presentation of evidence — eloquent, elegant cherry-picking — can convince smart people of pernicious ideas that seem scientific, but which science does not support. Much of the sleight of hand in this book will not be evident to people who don’t know the field. In some cases one has to read a specific paper cited by Wade to recognize that he thoroughly misrepresents its findings.”

I encourage you to go read both of Mr. Dobbs’ critiques. It will be interesting to see how Mr. Wade responds.

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Update: Here are a few other critiques worth mentioning:

A Troublesome Ghost by Dr. John Edward Terrell

In addition to the post I cited above, Dr. Chris Smith also takes on Wade’s mischaracterization of
the genetic basis for violent behavior in different populations.

He also discusses in detail Wade’s repeated assertion that human evolution has been “recent, copious and regional”.

And if you’d like to listen to an interesting discussion on race, genetics, ancestry testing, and human biology, here’s an appearance by Agustin Fuentes on the Center for Environmental Health podcast.

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Things have been pretty quiet around here while I finish up a couple of manuscripts for publication. However, I did want to take a moment to express my sincere gratitude to the people who have translated my article (“Dear parents, you are being lied to”) into many different languages (including German, Spanish, Italian, Slovakian, Portuguese, and Croatian) over the last few months. I’m overwhelmed by the response it has gotten, and grateful to have heard from so many of you that you found it useful.

I have no idea at this point how many people have read it, but I am trying to keep a running list of the different places it’s been published.  If anyone finds more examples, I’d appreciate it if you’d post them in the comments so I can add them to the list below!

 

http://www.danilopianini.org/cari-genitori-vi-stanno-mentendo

http://www.stern.de/gesundheit/impfmythen-liebe-eltern-sie-werden-angelogen-2115041.html

http://www.aftenposten.no/meninger/debatt/Kjare-foreldre-Dere-blir-loyet-til-7589252.html

http://www.dfens-cz.com/view.php?cisloclanku=2014061901

http://www.pianetamamma.it/il-bambino/malattie/vaccini-perche-farli.html

http://www.butac.it/vi-stanno-mentendo/

http://www.detinjarije.com/dragi-roditelji-vama-se-govore-lazi/

“…for he has no right to give names to objects which he cannot define.” –Charles Darwin

Do “races” exist as meaningful biological categories? Physical anthropologists and human biologists have been studying race (i.e., blacks vs. whites, or Europeans vs. Asians) for centuries. For most of that time, they subscribed to the perspective that race was a taxonomic category, and they sought to identify the biological characteristics (such as cranial shape or skin color) that characterized and defined these different groups. This perspective assumed that each individual was a member of a single racial category, that the differences between racial categories were biological, and that these categories were predictive of other traits (such as ancestry, temperament, intelligence, or health).

But it gradually became clear that this understanding was not scientifically sound. Groupings of people by skin color did not produce the same result as groupings of people by skull shape, nor of blood type. Furthermore, as scientists began to study human variation with the tools of genetics (in the process creating my fields, anthropological genetics and human population genetics), it became apparent that human genetic variation does not divide humans into a few discrete groups. There are virtually no sharp boundaries, either with physical features or with patterns of genetic diversity, that show where one population “ends” and the next “begins”. Continue Reading…

 

 

More than 12,000 years ago, a young teenage girl walking through a deep cave (known today as Hoyo Negro) fell down a massive pit. The fall fractured her pelvis, and she died among the remains of giant ground sloths and saber-toothed cats who had met a similar fate. Over the next few millennia, the pit filled with water and their bones were covered with cave formations. They were left undisturbed until discovered in 2007 by cave divers, who named the girl “Naia” in a reference to Greek mythology.

Today, a team of archaeologists and geneticists announced the results from sequencing her mitochondrial genome. She possessed a haplogroup (D1) that evolved in Beringia and is seen in modern Native Americans.

So why is this result so important? The Hoyo Negro girl, like other Paleoindians (the oldest inhabitants of the Americas), had a skull shape that was distinctive from later (younger than 9,000 years before present) ancient Americans, who more closely resembled modern Native Americans. Continue Reading…

Hard at work

Hard at work

 

I am currently working on both a fellowship and a manuscript, so instead of writing a longer piece here, I’m issuing everyone a challenge. I have seen it repeated multiple times throughout the comments here that there seems to be evidence “on both sides” of the vaccines issue, and therefore people should just “go with their gut.” I reject that approach as lazy (at best). Whether or not vaccines are safe and effective is an empirical question, and therefore it should be answerable with data.

If there is any theme to this blog, it would be:  Not all evidence is equivalent, and it takes training and a willingness to admit to ignorance in order to be able to identify good evidence from bad evidence. So how can the average person begin to sort out which information is good, and which is bad? There are many approaches to this question, which I will be exploring further in the coming weeks. But the first one is to honestly take inventory of one’s own knowledge: do you actually understand this issue? Do you, for example understand how the immune system works? No? Then you’d better read more and learn more on the subject before wading into the debate.

A second important step is assessing other people’s knowledge on the subject. This can can be difficult as it’s awfully easy to sound “smart” on the internet. I want to simplify this step here by asking everyone (anti-vaccine, pro-vaccine, or “undecided”) a single question: What kind of evidence would change your mind on this issue? This question has come up several times in our discussions (most recently, I believe, in the comments of gewisn), and I think the answers are so revealing that I want to devote an entire post to it.

Please be as specific and honest as possible. Please define any jargon. If you are talking about specific studies, please cite them so everyone can read them. This comments section will be more heavily moderated than usual in order to keep the discussion on track. Comments that do not answer the question, or go off on tangents will be deleted (although I won’t ban you from discussions unless you violate my general commenting policy).