👓 Mathematics matters | Bits of DNA

Read Mathematics matters by Lior PachterLior Pachter (Bits of DNA)
Six years ago I received an email from a colleague in the mathematics department at UC Berkeley asking me whether he should participate in a study that involved “collecting DNA from the brigh…

Not sure how I had missed this in the brouhaha a few weeks back, but it’s one of the more sober accounts from someone who’s actually got some math background and some reasonable idea about the evolutionary theory involved. It had struck me quite significantly that both Gowers and Tao weighed in as they did given their areas of expertise (or not). Perhaps it was worthwhile simply for the attention they brought? Gowers did specifically at least call out his lack of experience and asked for corrections, though I didn’t have the fortitude to wade through his hundreds of comments–perhaps this stands in part because there was little, if any indication of the background and direct identity of any of the respondents within the thread. As an simple example, while reading the comments on Dr. Pachter’s site, I’m surprised there is very little indication of Nicholas Bray’s standing there as he’s one of Pachter’s students. It would be much nicer if, in fact, Bray had a more fully formed and fleshed out identity there or on his linked Gravatar page which has no detail at all, much less an actual avatar!

This post, Gowers’, and Tao’s are all excellent reasons for a more IndieWeb philosophical approach in academic blogging (and other scientific communication). Many of the respondents/commenters have little, if any, indication of their identities or backgrounds which makes it imminently harder to judge or trust their bonafides within the discussion. Some even chose to remain anonymous and throw bombs. If each of the respondents were commenting (preferably using their real names) on their own websites and using the Webmention protocol, I suspect the discussion would have been richer and more worthwhile by an order of magnitude. Rivin at least had a linked Twitter account with an avatar, though I find it less than useful that his Twitter account is protected, a fact that makes me wonder if he’s only done so recently as a result of fallout from this incident? I do note that it at least appears his Twitter account links to his university website and vice-versa, so there’s a high likelihood that they’re at least the same person.

I’ll also note that a commenter noted that they felt that their reply had been moderated out of existence, something which Lior Pachter certainly has the ability and right to do on his own website, but which could have been mitigated had the commenter posted their reply on their own website and syndicated it to Pachter’s.

Hiding in the comments, which are generally civil and even-tempered, there’s an interesting discussion about academic publishing that could have been its own standalone post. Beyond the science involved (or not) in this entire saga, a lot of the background for the real story is one of process, so this comment was one of my favorite parts.

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🔖 A New Factor in Evolution by James Mark Baldwin | The American Naturalist: Vol 30, No 354

Bookmarked A New Factor in Evolution by James Mark Baldwin (The American Naturalist: Vol 30, No 354 )

In several recent publications I have developed, from different points of view, some considerations which tend to bring out a certain influence at work in organic evolution which I venture to call "a new factor". I give below the list of references [1] to these publications and shall refer to them by number as this paper proceeds. The object of the present paper is to gather into one sketch an outline of the view of the process of development which these different publications have hinged upon.

The problems involved in a theory of organic development may be gathered up under three great heads: Ontogeny, Phylogeny, Heredity. The general consideration, the " factor " which I propose to bring out, is operative in the first instance, in the field of Ontogeny; I shall consequently speak first of the problem of Ontogeny, then of that of Phylogeny, in so far as the topic dealt with makes it necessary, then of that of Heredity, under the same limitation, and finally, give some definitions and conclusions.

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👓 Baldwin effect | Wikipedia

Read Baldwin effect (Wikipedia)
In evolutionary biology, the Baldwin effect describes the effect of learned behavior on evolution. In brief, James Mark Baldwin and others suggested during the eclipse of Darwinism in the late 19th century that an organism's ability to learn new behaviors (e.g. to acclimatise to a new stressor) will affect its reproductive success and will therefore have an effect on the genetic makeup of its species through natural selection. Though this process appears similar to Lamarckian evolution, Lamarck proposed that living things inherited their parents' acquired characteristics. The Baldwin effect has been independently proposed several times, and today it is generally recognized as part of the modern synthesis.

Reminded about this by the lizard article I saw the other day. Worth digging back into again…

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🔖 [1703.04184v2] A Theory for Gender Differences in Variability by Theodore P. Hill and Sergei Tabachnikov

Bookmarked [1703.04184v2] A Theory for Gender Differences in Variability by Theodore P. Hill, Sergei Tabachnikov (arxiv.org)
A selectivity theory is proposed to help explain how one gender of a species might tend to evolve with greater variability than the other gender. Briefly, the theory says that if one sex is relatively selective, then more variable subpopulations of the opposite sex will tend to prevail over those with lesser variability; and conversely, if one sex is relatively non-selective, then less variable subpopulations of the opposite sex will tend to prevail over those with greater variability. This theory makes no assumptions about differences in means between the sexes, nor does it presume that one sex is selective and the other non-selective. Two mathematical models are presented: a statistical analysis using normally distributed fitness values, and a deterministic analysis using a standard system of coupled ordinary differential equations with exponentially distributed fitness levels. The theory is applied to the classical greater male variability hypothesis.
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👓 Hill Statement | Ted Hill

Read Hill Statement by Ted Hill (tphill.net)
Comments on Wilkinson's and Farb's Official Statements About Hill's 9/7/18 Quillette Article: https://math.uchicago.edu/~wilkinso/Statement.html (accessed 9/13/18) https://www.math.uchicago.edu/~farb/statement (accessed 9/13/18) Allegations that Wilkinson does not deny in her statement: 1. Wilkinson asked her father to write to the Intelligencer criticizing the paper. 2. Wilkinson falsely blamed divulgence of her name on the Intelligencer. 3. Hill wrote a polite email (copied below) to Wilkinson that she never answered even though she claims she had "scientific criticisms" of the article. 4. Hill wrote a longer rebuttal to Wilkinson's father asking for more discussion. He also did not reply to Hill. 5. Even after the Intelligencer article was rescinded, Wilkinson "continued to trash both the journal and the editor-in-chief on social media". 6. Wilkinson falsely announced on Facebook that a substantially different paper had been accepted.. 7. Even after the NYJM article was deleted, Wilkinson "was threatening Facebook friends with 'unfriending' unless they severed social media ties with" [Igor Rivin, the editor who had solicited the paper].
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👓 Echo Chamber Incites Online Mob to Attack Math Profs | Statistical Modeling, Causal Inference, and Social Science | Andrew Gelman

Read Echo Chamber Incites Online Mob to Attack Math Profs by Andrew Gelman (Statistical Modeling, Causal Inference, and Social Science)
Trying to make sense of the story With this in mind, there were a few aspects of Hill’s blog entry that didn’t completely make sense to me. First, the research article did not seem politically objectionable to me. I could see how people with strong views on the topic of sex differences would find things to criticize in his paper, and he could well be missing some important points of the biology, and if you really tried to apply his model to data I don’t think it would work at all, so, sure, the paper’s not perfect. But as a math paper that touches on an interesting topic, it is what it is, and I was surprised there’d be a campaign to suppress it.

Not as influential in the debate as one of the referring articles led me to have believed.

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👓 Additional thoughts on the Ted Hill paper | Timothy Gowers

Read Additional thoughts on the Ted Hill paper by Timothy Gowers (Gowers's Weblog)
First, I’d like to thank the large number of commenters on my previous post for keeping the discussion surprisingly calm and respectful given the topic discussed. In that spirit, and to try t…

The analysis here makes me think there might be some useful tidbits hiding in the 300+ comments of his prior article. I wish I had the time to dig back into it.

Highlights, Quotes, Annotations, & Marginalia

Our prehistoric ancestors were not doing higher mathematics, so we would need to think of some way that being on the spectrum could have caused a man at that time to become highly attractive to women.  

One needs to remember that it isn’t always the men that themselves need to propagate the genes directly (ie, they don’t mate with someone to hand their genes down to their progeny directly). Perhaps a man on the autism spectrum, while not necessarily attractive himself, has traits which improve the lives and fitness of the offspring of his sister’s children? Then it’s not his specific genes which are passed on as a result, but those of his sister’s which have a proportion of his genes since they both share their parent’s genes in common.
September 19, 2018 at 03:35PM

variability amongst males  

Does it need to be a mate-related thing? Why not an environmental one. I seem to recall that external temperature had a marked effect on the sexual selection within alligator populations such that a several degree change during gestation would swing the sex proportion one way or another. Could these effects of environment have caused a greater variability?

Further, what other factors may be at play? What about in sea horse populations where males carry the young? Does this make a difference?
September 19, 2018 at 03:41PM

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👓 Has an uncomfortable truth been suppressed? | Timothy Gowers

Read Has an uncomfortable truth been suppressed? by Timothy Gowers (Gowers's Weblog)
Update to post, added 11th September. As expected, there is another side to the story discussed below. See this statement about the decision by the Mathematical Intelligencer and this one about the…

I agree in large part with his assessment, and do so in part based on Ted Hill’s Quillette article and not having read the actual paper yet.

I will say that far more people have now either heard about or read Hill’s paper than would have ever otherwise been aware of it had it actually gone ahead and actually been published and kept up. This is definitely an academic case of the Barbara Streisand effect, though done somewhat in reverse.

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👓 Statement by Benson Farb in response to Ted Hill’s unfounded allegations. | Benson Farb

Read Statement by Benson Farb in response to Ted Hill's unfounded allegations. by Benson Farb (math.uchicago.edu)

This statement is meant to set the record straight on the unfounded accusations of Ted Hill regarding his submission to the New York Journal of Mathematics (NYJM), where I was one of 24 editors serving under an editor-in-chief. Hill's paper raised several red flags to me and other editors, giving concern not just about the quality of the paper, but also the question of whether it underwent the usual rigorous review process. Hill's paper also looked totally inappropriate for this theoretical math journal: in addition to the paucity of math in the paper, its subject classification (given by the authors themselves) appeared in no other paper in NYJM's 24 year history, and did not fall into any of the areas of expertise of the editors of NYJM, as listed on the NYJM website.

At the request of several editors, the editor-in-chief pulled the paper temporarily on 11/9/17 so that the entire editorial board could discuss these concerns. A crucial component of such a discussion are the reports by experts judging the novelty and quality of the mathematics in Hill's paper. The editor who handled the paper was asked to share these reports with the entire board. My doubts about the paper - and the process - grew when repeated requests for the reports went unanswered. Nearly 3 months passed until the two reports were finally shared with the entire board on 2/7/18. The reports themselves were not from experts on the topic of the paper. They did not address our concerns about the substantive merit of the paper.

After these reports were shared, the entire board discussed what do. For many of us, there was no compelling evidence that Hill's paper was appropriate for NYJM. Further, the evidence that the paper had undergone rigorous scrutiny before being accepted was scant. In light of this, the board voted (by a 2-to-1 ratio) to rescind the paper. I believe that the editor-in-chief should have added a statement about why this was done, but he did not. Amie Wilkinson played no role in any deliberation of Hill's or any paper at NYJM.

I appreciate those who have taken the time to examine the record, including the University of Chicago.

Benson Farb Professor of Mathematics University of Chicago

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👓 What really happened when two mathematicians tried to publish a paper on gender differences? The tale of the emails | Retraction Watch

Read What really happened when two mathematicians tried to publish a paper on gender differences? The tale of the emails (Retraction Watch)
Retraction Watch readers may be familiar with the story of a paper about gender differences by two mathematicians. Last month, in Weekend Reads, we highlighted an account of that story, which appea…

This article and the related links cover a lot of the questions I had when I read the original in Quillette the other day and only wish I’d had the time to follow up on as a result. Now to go on and read all the associated links and emails….

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👓 Using Medieval DNA to track the barbarian spread into Italy | Ars Technica

Read Using Medieval DNA to track the barbarian spread into Italy (Ars Technica)
Cemeteries from the Longobard spread into Italy tell tales of migration and mixing.
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👓 Adaptable lizards illustrate key evolutionary process proposed a century ago | Science Daily

Read Adaptable lizards illustrate key evolutionary process proposed a century ago (ScienceDaily)
The 'Baldwin effect' has now been demonstrated at the genetic level in a population of dark-colored lizards adapted to live on a lava flow in the desert.

Highlights, Quotes, Annotations, & Marginalia

One explanation has been that many of an animal’s traits are not fixed, but can change during its lifetime. This “phenotypic plasticity” enables individual animals to alter their appearance or behavior enough to survive in a new environment. Eventually, new adaptations promoting survival arise in the population through genetic changes and natural selection, which acts on the population over generations. This is known as the “Baldwin effect” after the psychologist James Mark Baldwin, who presented the idea in a landmark paper published in 1896.  

September 11, 2018 at 08:57AM

Journal article available at: https://www.cell.com/current-biology/pdfExtended/S0960-9822(18)30899-6

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👓 Academic Activists Send a Published Paper Down the Memory Hole | Quillette

Read Academic Activists Send a Published Paper Down the Memory Hole by Theodore P. Hill (Quillette)
In the highly controversial area of human intelligence, the ‘Greater Male Variability Hypothesis’ (GMVH) asserts that there are more idiots and more geniuses among men than among women. Darwin’s research on evolution in the nineteenth century found that, although there are many exceptions for ...

I understand the potential political implications of such research, but blocking publication like this seems a tad underhanded. I’ve not yet read the paper, but want to take a look at it at least from an evolutionary theoretic standpoint. Admittedly on its face it sounds a bit more like pure theory rather than anything supported by actual evidence and underlying research in reality, but there’s no reason to stop the idea if it could potentially be a fruitful area.

If a formally refereed and published paper can later be erased from the scientific record and replaced by a completely different article, without any discussion with the author or any announcement in the journal, what will this mean for the future of electronic journals?

This is a very concerning issue and a good reason why people should also practice samizdat and place multiple copies online in various repositories.

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👓 Caught mid-flow: the “Baldwin effect” | The Economist

Read Caught mid-flow: the “Baldwin effect” (Economist Espresso)
While most side-blotched lizards living in the Mojave desert match the colour of its sand, those
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👓 Mutating DNA caught on film | Science | AAAS

Read Mutating DNA caught on film by Elizabeth Pennisi (Science | AAAS)
Study in bacteria shows how regularly DNA changes and how few of those changes are deadly

This is a rather cool little experiment.

h/t to @moorejh via Twitter:

Bookmarked on March 16, 2018 at 12:15PM

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