Friday, January 2, 2015

Bullying in the Genome Blogosphere by Academics

Dear Readers,

I normally like to keep personal comments off this blog.  However, out of concern for other members of the public who follow blogs about population genetic prehistory, I will comment directly here about some of my experiences over the last five years in the genome "blogosphere".

As many of you know, this blog is for fun and a way for me to follow developments in the fields of ancient DNA as well as archaeology.  I also enjoy covering topics in ethnography and mythology as they might relate to human prehistory.

This blog got started about five years ago after I stumbled on a blog called Dienekes' Anthropology blog.  As it happens, my husband's parents are from the Pindos Mountains in Northern Greece.  After a number of visits to the Pindos, I became interested in the prehistory and archaeology of this area, and of the Balkans in general.  One day after googling around about Northern Greek history, I noticed that Dienekes's Anthropology blog had many articles that were covering the prehistory of Greece as well as other areas of Europe.  Needless to say, I got wrapped up with making comments on Dienekes' blog for about six months. 

At some point, Dienekes started to post Admixture data on populations of Europe and the Middle East.  Given my electrical engineering and linear systems background, it wasn't very difficult to notice that some of the genetic components adhered to a pattern of algebraically linear variation over geography.  I remember commenting about this on the blog.  Out of the blue, one of the other commenters, "Ponto", in response to my posts, suggested that I was "racist".  I was pretty surprised by this, but now realize it was obviously an attempt to intimidate me from trying to analyze the patterns I was seeing.

It was at this point that I decided I could start my own blog and didn't need to waste my time on Dienekes' blog.  So that's what I did.

About a month later, Paul Givargidze emailed me asking me if I would use some of the linear analysis methods I was using on my blog to look at Eurogenes Admixture data.  Paul was very keen on showing that Jews were related to Assyrians.  After using MATLAB to arrange the data geographically, I told Paul that I didn't think that you could argue that Jews were related specifically to Assyrians.  Paul didn't seem very happy about that, and in the end, went ahead and used my observation about the Gaussian distribution over geography (an effect of absolute density regulation) in order to publish an article with Razib Khan. Needless to say, Paul was happy to use my idea without reference.

Shortly after starting my blog, an article was published in Nature discussing genome blogging.  The article mentioned the Eurogenes blog, Dienekes' Anthropology blog, as well as Joe Pickrell, and David Wesolowski, so clearly, "Dienekes", Joe Pickrell and "David Wesolowski" have known each other since 2010.

Busy with other things, I stopped doing linear analysis with Admixture data about six months after starting this blog. 

Later, as topics of interest passed my way, I would write about them.  I didn't want to do more analysis.  I realized I wasn't well connected enough to promote my work and anything that I published on my blog would probably be stolen.  So I focused on topics that were fun, of interest to me, rather than doing analysis.

Since the mid nineties, I'd been interested in the effort to sequence the Neanderthal Genome.  The IEEE magazine Spectrum, the magazine for electrical engineers, covered this topic over the years, so I often came across articles about it.  Some of the articles on this blog reflect my interest in the algorithms involved in looking at the Neanderthal genome and other archaic genomes.

Another interest related to genetic prehistory was how humans migrated out of Africa and how they might be related to each other.  Growing up in Western Canada, where there are Native Canadian people, I'd wondered how these vibrant cultures were related to me and to each other.

Having lived in West Africa as a child, its been fascinating to see how genetic data can illustrate the prehistory of West Africa and other parts of Africa.

Climate and ice ages, especially as they have impacted human population movements, have been another avenue of investigation.

Other topics, such as mythology or ethnography, are mostly for fun.  They're not really related to population models, but they can be somewhat informative.  For instance, many myths contain stories of floods, which could have recorded the human experience of sea level rise since the last glacial maximum.  Ethnographers in Russia have tried to use the analysis of myths to track population movements across Eurasia into the Americas.

Every once in a while, you run across a blog which is really stunning.  Many of you in my blog roll have delighted me with your extraordinary breadth of blog research and writing.

About two years ago, I ran across a blog called Aggsbach's Paleolithic blog.  I'd always been captivated by geology and rocks.  My father had a passing interest in lithics and rock art, so when I discovered Aggsbach's blog, I was absolutely captivated.  After following it for about a year, I realized it was the blog of Jean-Jacques Hublin, the famous paleoanthropologist. Some of the archaeology articles on this blog come from this blog, and Hublin's other blog,

Since last spring, I hadn't been blogging very much, and had been busy with other things, including a heavy professional workload.  I'm also a wife and mom, so my life is often pretty hectic.

After writing this blog for five years, and reading broadly across archaeology and population genetics, its not hard to see problems with certain papers.  For instance, when the Lazarides paper was published on December 23, 2013, I was puzzled by a part of their model that stated that "We model these populations' deep relationships and show that EEF had ~44% ancestry from a “Basal Eurasian” lineage that split prior to the diversification of all other non-African lineages."  Mostly, I could not understand how a population event, this "Basal Eurasian" split, which had to have happened more than 50 thousand years ago, could be teased from ancient DNA data, when we still had so much trouble resolving more recent population events.

A few months ago, I stumbled on an article published in the New York Times under the title Science: From Ancient DNA, a clearer picture of Europeans Today.  It was Carl Zimmer again, publishing for the Reich Lab.  So I read the article, and what do you know, I almost fell off my chair when I read this:

"But most living Europeans also carry genes from a third population, which appears to have arrived more recently. Dr. Reich and his colleagues found the closest match in DNA taken from a 24,000-year-old individual in Siberia, suggesting that the third wave of immigrants hailed from north Eurasia. The ancient Europeans that the scientists studied did not share this North Eurasian DNA. They concluded that this third wave must have moved into Europe after 7,000 years ago."

Having followed the Reich lab papers for the last few years, I knew that this third wave they were taking about, the North Eurasian DNA, was at least partly associated with the Late Paleolithic and Mesolithic DNA of countries like Lithuania, Finland, Poland, Belarus, the Ukraine and the Volga. It's true that the particular sample they got the DNA from was from Lake Baikal, but it could hardly be argued that all "North Eurasian DNA" comes "from north Eurasia" "into Europe after 7,000 years ago."

I'd been working on a conference paper over the summer looking at the Late Paleolithic and Mesolithic of Northern Europe using the definitive reference The Oxford Handbook of the Archaeology and Anthropology of Hunter-Gatherers published this year (2014, see, for instance, page 541).  Reich's statement about "North Eurasians" arriving only 7,000 years ago in Northern Europe didn't add up with what archaeologists were saying about the post Ice Age repopulation of Northern Europe.

I next noticed an article in the Harvard Gazette, published on December 3rd, where Patterson, who is associated with the Reich Lab, made the statement "that linguistic evidence has tracked the ancestral language, called “late proto-Indo-European” to about 3,500 years ago in the Caucasus, among a people who had wheeled vehicles at a time when they were just being put into use."

I eventually stumbled on the Eurogenes blog in which a number of bloggers, obviously many of them insiders to the Reich lab, were discussing the soon to be published paper regarding Patterson's "late proto-Indo-European" hypothesis.

Rather than bore you with the details, you can read the kind of discourse these professors engage in yourself.  Here's ryukendo kendow on the Eurogenes blog.  And here he is explaining a fudge in his model for the evolution of Eurasians.

The problem with all of this anonymous blogging by professors is that when they disagree with a member of the public, because they are blogging anonymously, they sometimes feel entitled to bully. I've personally experienced these academics telling me that I'm an idiot, that my blog is junk because it has too much ethnography and artifact information, that it's not quantitative enough, and that I shouldn't be allowed to call it "linear population model". I've been called racist, crazy and stupid. I've been wrongfully associated with the ideas of others, simply because I occasionally have blog interchanges with people these researchers don't like. I've been accused of being an idiot because I don't use D statistics on my blog.

So, I think it is time for some of these anonymous professors to come out of the woodwork.

List of professors that blog on Dienekes' Anthropology blog and the Eurogenes blog under pseudonyms:

Dienekes' Anthropology blog is very likely the blog of Manolis Kellis. It's also likely that Manolis blogs at the Eurogenes blog under the pseudonym "Helgenes50". He is a professor with the MIT Computational Biology Group and the Broad Institute of MIT and Harvard. Kellis is generally polite, but he is a professor and he is participating anonymously on the questionable Eurogenes blog.

"ryukendo kendow" is likely the pseudonym of Joe Pickrell of the New York Genome Center in lower Manhattan, and is affiliated with the Department of Biological Sciences at Columbia University.

Sad to say, "Krefter", "About Time", "eurologist", "DDeden", "ZeGrammarNazi", "carlos lascoutx", "capra internetensis", "Fanty", and "barackobama",  are all Jean-Jacques Hublin, currently a Professor at the Max Planck Institute for Evolutionary Anthropology in Leipzig (Germany), where he serves as the Director of the Department of Human Evolution.  As someone who's research I respect, I'm sad to say that I've found him anonymously bullying me on a number of occasions.

Judging by his posts, "Balaji" is probably the pseudonym of David Reich himself, Professor at Harvard Medical School.

"Davidski" is either Wolfgang Haak or David Wesolowski.  They may be the same person.  See the post, Publications of Wolfgang Haak.

"Chad Rohlfsen" is a person associated with the Genographic Consortium.  The Genographic Consortium has funded some of the research at the David Reich Lab at Harvard.

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