Saturday, July 4, 2020

Recent evolution of the British population



Frederick Morgan – Off for the Honeymoon (Wikicommons) Over the past 2,000 years, the British gene pool has shifted toward alleles that favor lighter hair, sunburn, and educational attainment. Was this because high-status men tended to mate with blonder, fairer women?



Have we evolved over the past two thousand years? Until recently, the answer was thought to be 'no.' Cultural evolution took over from genetic evolution around the time farming took over from hunting and gathering, some ten thousand years ago, thus putting our ancestors on a path to increasing social complexity: sedentary living, growth of towns and villages, formation of states, trade and specialization of labor, and so on. It was culture that changed during recorded history, not genes.

Well, things are not that simple. Genes and culture have coevolved with each other. Yes, culture has been changing rapidly over the past ten thousand years. But so have genes. During that time, our genetic evolution has been driven by adaptation not only to natural environments but also to cultural environments. Increasingly so. We live more and more in cultural environments of our making (Chen et al., 2016; Cochran and Harpending 2009; Hawks et al. 2007).

In what ways have we changed genetically during the past ten thousand years? In the ways we digest food. With the shift to dairy farming, and the resulting increase in milk consumption by adults, natural selection favored those who could digest milk sugar, an ability previously confined to infants.

We have also changed in the ways we think and behave. That kind of evolution is not difficult. A few point mutations may alter a behavior by changing its timing, its intensity, or its threshold of stimulation. Other alterations have been much more polygenic. Cognitive ability, for instance, seems to have increased through mutations at many genes, with each mutation causing only a tiny fraction of the increase.

Because recent evolutionary change has so often been polygenic, we need to examine it in relation to many genetic variants spread over the entire genome, i.e., by means of genome-wide association studies. Such studies can take many forms. A recent one, proposed by Stern et al. (2020), may be better than earlier versions, particularly in avoiding biases due to population structure and population stratification.

I nonetheless have a few reservation about this proposed method:

1. Population stratification can be a factor in evolutionary change. Let's take the work of Gregory Clark on the growth of the English middle class. He found it grew steadily from the twelfth century onward, its descendants not only growing in number but also replacing the lower classes through downward mobility. By the 1800s its lineages accounted for most of the English population. Parallel to that demographic growth, English society became more and more middle class in its values. "Thrift, prudence, negotiation, and hard work were becoming values for communities that previously had been spendthrift, impulsive, violent, and leisure loving" (Clark 2007, p. 166). Isn't that evolutionary change through population stratification? Or am I missing something?

2. The new method can reveal only evidence of directional selection. It thus fails to capture other interesting forms of selection, like diversifying selection.


How the British have evolved over the past 2,000 years

Stern et al. (2020) used their method to study how the British population has evolved over the past two thousand years. They found increases in the prevalence of lighter hair, in tanning and sunburn, in age at first birth, in bone mineral density, and in the risk of type 2 diabetes. They also found decreases in the risk of neuroticism and in the risk of high glycated hemoglobin levels.

Some of these changes correlate with each other. In such cases, we should step back and try to identify the common cause.

Lighter hair, more sunburn ... and higher educational attainment

Over the past 2,000 years, the British gene pool has shifted toward alleles that favor lighter hair, sunburn, and educational attainment. These changes in allele frequency correlate with each other, so what, exactly, was driving the overall change?

There is genetic linkage between light hair and pale skin, but it's weak. In fact, pale skin often coexists with dark hair. Moreover, we still have to explain the link to educational attainment. The common cause for all three changes may have been sexual selection mediated by social class. In other words, high-status men tended to mate with blonder, fairer women.

This form of sexual selection was observed in a Japanese study on social class and skin color. Upper-class men were shown to be fairer-skinned than lower-class men, even when the latter were factory workers and not farmers and even though the measurements were taken on unexposed skin. Wealthier men have a wider range of prospective brides and can thus choose the fairest women, for "skin color has long been regarded, by the Japanese, as one of the criteria for evaluating physical attractiveness, especially in young females" (Hulse 1967). Similarly, in India "[w]ealthy landowning families often have a tradition of seeking light-skinned brides among poorer members of their subcaste. It is very common to find a high concentration of lighter-skinned people among established land-owning families" (Béteille 1967).

Darwin discussed this sexual selection with reference to English social classes:

Many persons are convinced, as it appears to me with justice, that our aristocracy, including under this term all wealthy families in which primogeniture has long prevailed, from having chosen during many generations from all classes the more beautiful women as their wives, have become handsomer, according to the European standard, than the middle classes; yet the middle classes are placed under equally favorable conditions of life for the perfect development of the body. (Darwin 1936[1888], p. 892)

Until the 20th century, higher social status meant higher fertility (Clark 2007). Thus, the physical and mental characteristics of the upper and middle classes tended to displace those of the lower class.

Higher risk of Type 2 diabetes and glycated hemoglobin

Why would natural selection favor type 2 diabetes? Isn't diabetes harmful? It is, in a modern environment that lets you ingest calories almost without limit. That wasn't the case in Britain for most of the past two thousand years. During that time, food was scarce for most people, and natural selection favored the ability to get as many calories as possible out of our food.

Less neuroticism

This evolutionary change may be related to the demographic success of the middle class and associated mental and behavioral traits, particularly lower time preference and higher future orientation. The nascent English middle class valued being “calm, cool, and collected,” as opposed to reacting emotionally to negative outcomes.


References

Béteille, A. (1967). Race and descent as social categories in India. Daedalus 96(2): 444-463.

Chen, C., R.K. Moyzis, X. Lei, C. Chen, and Q. Dong. (2016). The encultured genome: Molecular evidence for recent divergent evolution in human neurotransmitter genes. In: J.Y. Chiao, S.-C. Li, R. Seligman, and R. Turner, Eds, The Oxford handbook of cultural neuroscience. New York, NY: Oxford University Press, 315-336.

Clark, G. (2007). A Farewell to Alms. A Brief Economic History of the World, 1st ed.; Princeton University Press: Princeton.

Cochran, G., and H. Harpending. (2009). The 10,000 Year Explosion: How Civilization Accelerated Human Evolution. Basic Books.

Darwin, C. (1936 [1888]). The Descent of Man and Selection in relation to Sex. reprint of 2nd edition, The Modern Library, New York: Random House.

Hawks, J., E.T. Wang, G.M. Cochran, H.C. Harpending, and R.K. Moyzis. (2007). Recent acceleration of human adaptive evolution. Proceedings of the National Academy of Sciences, 104(52), 20753-20758.

Hulse, F.S. (1967). Selection for skin color among the Japanese. American Journal of Physical Anthropology 27(2): 143-156.

Hysi, P.G., A.M. Valdes, F. Liu, N.A. Furlotte, D.M. Evans, V. Bataille, et al. (2018). Genome-wide association meta-analysis of individuals of European ancestry identifies new loci explaining a substantial fraction of hair color variation and heritability. Nature Genetics 50(5): 652-656.

Morgan, M.D., E. Pairo-Castineira, K. Rawlik, O. Canela-Xandri, J. Rees, D. Sims, A. Tenesa, and I.J. Jackson. (2018). Genome-wide study of hair colour in UK Biobank explains most of the SNP heritability. Nature Communications 9: 5271

Neel, J. V. (1962). Diabetes mellitus: a 'thrifty' genotype rendered detrimental by 'progress'? American Journal of Human Genetics 14: 353-362.

Stern, A.J., L. Speidel, N.A. Zaitlen, and R. Nielsen. (2020). Disentangling selection on genetically correlated polygenic traits using whole-genome genealogies
bioRxiv 2020.05.07.083402

Friday, June 26, 2020

When the mob decides truth



The Film Mercury, 1926 (Wikicommons) – When the mob decides truth.

Until recently, it was almost impossible to remove an article from the published scientific literature. You would have to ask each university library for permission to go to the stacks and tear it out from a bound volume. Your request would almost certainly be denied.

All of that has changed with online publishing. Now, you only need permission from the publishing company, and removal is just a click away. The ease of online removal can lead to abuse, as noted back in 2005:

Before the advent of electronic journals, it was very hard for publishers to purge articles from their journals. At best, they could publish a later retraction. [...]

Now, however, with publishers controlling their own digital archives, and print copies no longer being produced, it has proven to be entirely too easy for some publishers to purge these archives of unwanted articles, much to the dismay of those who, like me, fear for the long-term integrity and trustworthiness of the published record of science and our intellectual heritage. In addition, if such materials can be removed, it often means they can be modified after publication as well.

Elsevier, for example, has removed about 30 articles so far from its ScienceDirect journal article archive, just since the year 2000, for various reasons. [...] The fear that many of us have is that individuals, corporate entities, and even governments, including ours, will begin to use such techniques to control the published record for political purposes or in order to cover up embarrassing information. (Davidson 2005)

That fear has come true with the removal of a paper by J. Phillippe Rushton and Donald Templer from the psychology journal Personality and Individual Differences. Rushton is known for his belief that cognitive ability varies not only between individuals but also between human populations. That was not, however, the subject of the removed paper. The subject was body coloration, specifically the fact that darker animals tend to be larger, more polygynous, and more aggressive. This correlation seems to hold true not only between species but also within species.

I believe such a correlation exists, but it’s not a simple one of cause and effect (see my last post). In any case, my opinion doesn’t matter. What matters is the right of all researchers to present their findings and interpretations in the scientific literature. If errors are made, others will point them out. That’s how the system works. 

Unfortunately, that’s not how some people want the system to work. Rushton had enemies, and they now see an opportunity to destroy his legacy, much of it being papers he published in Elsevier journals. I suspect they identified the above paper as the easiest target for removal, a kind of “test case.” It’s not about human cognition and is viewed with skepticism even by Rushton’s defenders, who seem to have fallen back to a defense line around his IQ work. Pauvres naïfs.

Demands for removal began a year ago, but it was really the events of the last month that made the journal give in.


My email exchange

Initially, I wasn't sure who authorized the removal. Was it Elsevier, i.e., the publisher? Or was it the current editor of Personality and Individual Differences? I emailed the latter, Don Saklofske, partly to protest this decision and partly to confirm he had been responsible. The following is my email exchange with him and with Elsevier:


Dear Dr. Saklofske:

I am writing with regard to your decision to remove the 2012 article by J. Philippe Rushton and Donald Templer from your journal.  This is an unusual move and breaks with longstanding practice. Once an article has passed peer review and been published, it remains in the scientific literature even if subsequently proven wrong. There have been a few cases of articles being withdrawn shortly after publication, but there have been no cases, until now, of an article being removed eight years later.

My personal judgment of this article is like that of many articles I read. I agree with parts of it and disagree with others. It is true that darker-colored animals tend to be larger and more aggressive, this being true not only between species but also within species. We can disagree about the causes, but the correlation is real and has been confirmed by other researchers.

I could argue this point at greater length, but I shouldn't have to. None of us has the right to sit in judgment on an article that is already established in the scientific literature. If one disagrees with an article, one is always free to write down one's criticisms and submit them for publication to the journal in question, but no one has the right to "unpublish" an existing article, however much one disagrees with it.

I urge you to reconsider your decision. You have created a dangerous precedent.

Yours sincerely,

Peter Frost

----------------------------------------------------------------------

Hello Peter... thank you for your email.  Indeed this was a difficult and challenging investigation and resulting decision that began last year but for which the controversy had been ongoing even before I became editor of PAID.  I am forwarding your letter to Catriona Fennell, Director of Publishing Services at Elsevier, who would have a much greater knowledge of the timelines on retracted articles following publication.

Sincerely

don

D.H. Saklofske, Ph.D

Editor: PAID

----------------------------------------------------------------------

Don,

Perhaps I am mistaken. Was this your decision or was it Elsevier's? In other words, who actually made the decision and who will take responsibility for it?

Sincerely,

Peter Frost

-----------------------------------------------------------------------

Hello Peter...  decisions related to corrigendums, letters of concern/warning, and retractions 'rests with the editor'!   I along with a panel of PAID Sr. Associate Editors comprised the signatories who reviewed the 'evidence' resulting in the decision to retract the Rushton and Templer article.

This was NOT Elsevier's decision; their office was consulted and advised of our investigation and actions only because they are the owners and publishers of the journal and it was important that I then understand their position on such matters re. legal and ethical guidelines. However I also thought you were also raising the point of 'time between publication to retraction' and this might be better known by the publisher of PAID and many other journals across varying disciplines. Should I have misunderstood, I apologize and withdraw my previous request to Elsevier.

Lastly,  retraction of journal articles  is not so uncommon (e.g. see Brainard and You; www.sciencemag.org › news › 2018/10 ›) and while the time from publication to retraction is usually less than 8 years, we began our examination of this paper last year (2019) following increased concerns from the scientific community, and two years after my appointment as editor.

Thank you for sharing your comments and viewpoint.

don

D.H. Saklofske, Ph.D

Editor: PAID

cc.  Elsevier: Catriona Fennell and Gail Rodney

-----------------------------------------------------------------------

Dear Dr Frost,

Thank you for your comments, we appreciate that there are a variety of views on how the literature should be corrected.

Since 2009, the Committee on Publication Ethics (COPE) guidelines (updated in 2019) have recommended retraction for cases where misconduct has taken place, but also in cases of error:
"Journal editors should consider retracting a publication if:
• they have clear evidence that the findings are unreliable, either as a result of misconduct (e.g. data fabrication) or honest error (e.g. miscalculation or experimental error)"
https://publicationethics.org/files/u661/Retractions_COPE_gline_final_3_Sept_09__2_.pdf

Elsevier journals endorse these guidelines from COPE and put them into practice, as do most major publishing houses.  Analysis by Retraction Watch, who have compiled a database of >18,000 retractions, found that at least 40% of retractions were due to error rather than to fraud:
https://www.sciencemag.org/news/2018/10/what-massive-database-retracted-papers-reveals-about-science-publishing-s-death-penalty
However, it is likely that retractions due to misconduct receive more amount of attention in the media and community.

It is not particularly unusual for older papers to be retracted, please see below some examples of retractions from Elsevier journals several years after publication, in one case a 1985 paper being retracted in 2013. More data is available, also from other publishing houses, from the Retraction Watch database: http://retractiondatabase.org/

Sincerely yours,

Catriona Fennell

Director Publishing Services
STM Journals
Elsevier
Radarweg 29, 1043NX Amsterdam, The Netherlands.

-------------------------------------------------------------------------

Dear Catriona Fennell,

I looked through the examples of retractions you provided. All of them concern papers in engineering or the medical sciences. Most of them were retracted because the same material had been published elsewhere, either by the same author (duplication) or by another author (plagiarism). There were a few other reasons:

- Paper retracted at author's request
- Fabrication or falsification of data
- Inability to confirm authorship of the paper and inability to interrogate the data presented in the paper

None of these examples resembles the retraction of the paper by J. Philippe Rushton and Donald Templer. That paper was in the social sciences, and there was no duplication or plagiarism involved. Nor do any of the other reasons apply. The reason seems to be more ideological. Am I right?

Sincerely,

Peter Frost



Conclusion

There were no further replies from Catriona Fennell or Don Saklofske. Perhaps they consider the case closed. They did prove me wrong on one point: several longstanding articles have already been removed from the scientific literature. The record is a paper published in 1999 and removed in 2019. Removal was justified on the following grounds:

Despite contact with Futase Hospital and Kurume University in place of the co-authors, who could not be located, the Journal was unable to confirm whether ethical approval had been granted for this study and has been unable to confirm the authorship of this paper. The Journal was also unable to interrogate the data presented in this paper as no records have remained of this study. This constitutes a violation of our publishing policies and publishing ethics standards.https://www.sciencedirect.com/science/article/pii/S8756328298001859?via%3Dihub

After twenty years it’s often difficult to locate the authors of a paper, especially if they are grad students. Their academic affiliation has changed or they may have left academia entirely. Even if they can be located, they may no longer have the raw data to support their findings. My PhD data files are on floppy disks. How can I read them today? And would they still be readable?

So if you dislike a scientific paper, and if its authors are no longer available, you can get rid of it by making a plausible accusation. Who is going to prove you wrong? This is another kind of abuse alongside the political and ideological one. "Science" increasingly belongs to established researchers with secure positions and access to legal assistance. Yet, historically, most innovative research has been done by individuals working alone with little institutional support. Charles Darwin was a country squire with no academic affiliation. Albert Einstein published major papers while working at a patent office. Intellectual breakthroughs tend to be made by outsiders.

Outsiders are losing their place in the academic community, especially ideological outsiders. This may be one reason why scientific and technological progress is slowing down. Indeed, such progress may sow the seeds of its destruction by creating better ways to manage information. And people.

But there’s another reason why outsiders are being squeezed out of academia. During the late 20th century, Christianity could no longer control what people said and believed, but it was still strong enough to keep other belief systems from taking over and imposing their controls. That happy interregnum is over. We’re moving into an intellectual environment where insiders are no longer interested in finding truth. They want to decide truth. To that end, they want to decide who gets published and who remains published. If you fall out of favor, they may delete all of your publications, and you will cease to exist as an intellectual entity. You’ll be unpersoned.


A few words to the journal editor

Don Saklofske,

You have created a precedent, and we’ll see more of these “removals.” I suspect you realize the gravity of your decision but feel you had no choice. Such a decision must be especially difficult for you, an evolutionary psychologist who has worked on genetic determination of cognition, impulsiveness, and empathy. Your research interests, however, have to be weighed against the treatment you’ve seen meted out to certain academics, including some at your university. Why share their fate?

So you had no choice. Anyway, someone else would have done the same thing sooner or later.
And, anyway, J. Philippe Rushton was a racist, like those Confederate generals whose statues have been torn down and taken away.

Apparently, Rushton is like a lot of people nowadays, such as Christopher Columbus, George Washington, Thomas Jefferson, and Sir John A. Macdonald. Of course, you’re not like those people either. Your name is further down the list, and it’s not a statue that will disappear when your time comes.

So remember: the more you give in now, the more you’ll have to give in later. At best, you’re buying yourself time, and not as much as you think.


References

Davidson, L.A. (2005). The End of Print: Digitization and Its Consequence-Revolutionary Changes in Scholarly and Social Communication and in Scientific Research. International Journal of Toxicology 24(1): 25-34

Rushton, J. P., and D.I. Templer. (2012). Do pigmentation and the melanocortin system modulate aggression and sexuality in humans as they do in other animals? Personality and Individual Differences 53(1): 4-8

Friday, June 19, 2020

Cleansing the scientific literature ... again



J. Philippe Rushton (Wikicommons). Eight years later, one of his studies is being “removed” from the scientific literature.



Seven years ago I wrote about Danish psychologist Helmuth Nyborg and the attempts to "unpublish" a study he had already published. At first thought, the idea seemed strange to me:

I was initially stumped by the ruling that Dr. Nyborg must withdraw his study from the scientific literature. How can one withdraw an already published study? Then the penny dropped. Most journals are now published online, and cash-strapped university libraries have been phasing out their paper subscriptions. (Frost 2013)

I and many others complained to the Danish minister responsible for that decision, and it was reversed.

Now, the same thing is happening again, in the heart of the Free World:

An article claiming that skin pigmentation is related to aggression and sexuality in humans will be retracted, Elsevier announced today. The study, "Do pigmentation and the melanocortin system modulate aggression and sexuality in humans as they do in other animals?" was published online in Personality and Individual Differences, an Elsevier journal, on March 15, 2012. The study's authors, John Rushton and Donald Templer, both deceased, hypothesized that skin color was related to aggression and sexuality in humans. It has been cited just nine times in eight years, according to Clarivate Analytics' Web of Science. (Retraction Watch 2020)

According to Google Scholar it has been cited fifteen times. Anyway, a study’s worthiness isn't decided by a show of hands, either now or in the future. Opinions change, and fringe science may eventually become mainstream. Or vice versa.

That brings me to another point. For eight years that study was legitimate. Now, it no longer is. Thanks to George Floyd.

Actually, his death was only a pretext. The mob feels no differently today than it did before May 25. What has changed is its ability to get what it wants ... with no pushback. Let’s not kid ourselves. This is a power grab by people who already have much power over the most important aspect of human culture—the flow of information. If you control a few chokepoints, you can get most people to believe almost anything.

“Power” may not be the right word. The aim is not simply to control institutions but rather to control how we perceive and understand reality. These are people who believe that ideas matter, and they want control over ideas, even in the scientific literature (!).

I don't wish to judge whether Rushton and Templer were "right." Once a study has passed peer review and been published, that judgement belongs solely to the reader. Personally, I feel they were right in some respects and wrong in others. They were right to argue that darker-colored animals tend to be larger and more aggressive, this being true not only between species but also within species:

Ducrest et al. (2008) reviewed data on over 40 wild vertebrate species showing that within each species, darker pigmented individuals averaged higher levels of aggression and sexual activity than lighter pigmented individuals, with a larger body mass, more resistance to stress, and greater physical activity when grooming. The relationship between coloring and behavioral dominance was robust across three species of mammal (African lion, soay sheep, and white-tailed deer), four species of fish (mosquito fish, guppy, green swordtail, and Arctic charr), four species of reptile (asp viper, adder, fence lizard, and spiny lizard), one amphibian species (spadefoot toad) and 36 species of bird.

In captive Hermann's tortoises (Eurotestudo boettgeri), another reptile species, Mafli, Wakamatsu, and Roulin (2011) found darker shell coloration predicted greater aggressiveness and boldness. Darker individuals were more aggressive in male-male confrontations and bolder towards humans, independent of body size and ambient temperature. (Melanin based color traits are a criterion in mate choice.)

Validation of the pigmentation system as causal to the naturalistic observations was demonstrated by experimentally manipulating pharmacological dosages and by studies of cross-fostering (Ducrest et al., 2008). Thus, melanocortin hormone levels predicted the amount of testosterone and other sexual steroids along with concomitant increases (or decreases) in aggression and sexual behavior. Placing darker versus lighter pigmented individuals with adoptive parents of the opposite pigmentation did not modify offspring behavior. (Rushton and Templer 2012)

Yes, melanin does correlate with aggressiveness, especially male aggressiveness. Unlike Rushton and Templer, however, I don't believe the correlation is causal, at least not wholly. It probably began as an accidental association: newborns are generally less pigmented, and this has resulted in a mental association of lightness with weakness and immaturity. Conversely, darkness is associated with strength and maturity. The age difference in pigmentation has been amplified by sexual selection in many species, particularly polygynous species where males have to compete against each other for access to females

We humans make the same mental association, particularly darker-skinned humans. Among them, the contrast between infant and adult pigmentation is striking:

There is a rather widespread concept in Black Africa, according to which human beings, before "coming" into this world, dwell in heaven, where they are white. For, heaven itself is white and all the beings dwelling there are also white. Therefore the whiter a child is at birth, the more splendid it is. In other words, at that particular moment in a person's life, special importance is attached to the whiteness of his colour, which is endowed with exceptional qualities.

According to the same concept, it is also claimed that a newborn baby is not only white but also a soft being during the time between his birth and his acceptance into the society. Furthermore, during this entire period, he is not considered a real person, and this may go so far that parents and society may do away with him at will for reasons that are peculiar to each social group. Having been done away with, these beings are considered to return automatically to the place where they came from, that is, to heaven. (Zahan 1974, pp. 385-387)

This mental association may have become a factor in the struggle by men for mates. In highly polygynous societies, such as those of sub-Saharan Africa, darker-skinned men would be seen as more masculine, and threatening, by other men ... and by women.  Among human populations, darkness of skin correlates significantly with the polygyny rate, even after adjusting for latitudinal variation in skin color (Manning et al. 2004). It looks like selection has favored a darker color in adult males, particularly in a context of intra-male rivalry for mates, and this selection has probably occurred in many species.

I may be wrong. Perhaps Rushton and Templer were wrong. Perhaps nobody knows the truth on this point. That's why we don't unpublish scientific studies. No one has the last word in intellectual debate, and that's how things should be.

Elsevier is aware of the taboo it's treading on:

It is a general principle of scholarly communication that the editor of a learned journal is solely and independently responsible for deciding which articles submitted to the journal shall be published. In making this decision the editor is guided by policies of the journal's editorial board and constrained by such legal requirements in force regarding libel, copyright infringement and plagiarism.  An outcome of this principle is the importance of the scholarly archive as a permanent, historic record of the transactions of scholarship. Articles that have been published shall remain extant, exact and unaltered as far as is possible. However, very occasionally circumstances may arise where an article is published that must later be retracted or even removed. (Elsevier 2020)

Until now, unpublishing wasn’t even “very occasional.” I know of a few cases where a paper was retracted shortly after publication. But eight years after? That just wasn’t done. Now it’s been done. The taboo has been broken, and we're going to see more and more "removals."


References

Elsevier (2020). Article withdrawal. https://www.elsevier.com/about/policies/article-withdrawal

Frost, P. (2012). Dark coloration and male aggressiveness: Is there a link? Evo and Proud, March 31
https://evoandproud.blogspot.com/2012/03/dark-coloration-and-male-aggressiveness.html

Frost, P. (2013). Cleansing the scientific literature. Evo and Proud, November 23
http://evoandproud.blogspot.com/2013/11/cleansing-scientific-literature.html

Manning, J.T., P.E. Bundred, and F.M. Mather. (2004). Second to fourth digit ratio, sexual selection, and skin colour. Evolution and Human Behavior 25(1): 38-50.
https://doi.org/10.1016/s1090-5138(03)00082-5

Retraction Watch. (2020). Elsevier journal to retract 2012 paper widely derided as racist. June 17 https://retractionwatch.com/2020/06/17/elsevier-journal-to-retract-2012-paper-widely-derided-as-racist/

Rushton, J. P., and D.I. Templer. (2012). Do pigmentation and the melanocortin system modulate aggression and sexuality in humans as they do in other animals? Personality and Individual Differences 53(1): 4-8
https://www.sciencedirect.com/science/article/pii/S0191886912000840 

Zahan, D. (1974). White, Red and Black: Colour Symbolism in Black Africa. In A. Portmann and R. Ritsema (Eds.) The Realms of Colour, Eranos 41 (1972): 365-395, Leiden: Eranos.
https://doi.org/10.2307/1573594

Friday, May 22, 2020

This is where the virus is least deadly


Patterson Town Hall, (Wikicommons - Anthony22). Putnam County NY has the lowest IFR for COVID-19 in the United States.



SARS-CoV-2 is more virulent in southern Europe than in northern Europe. The reason, I’ve argued, is that the Mediterranean Basin is one of several regions where humans have coevolved for a longer time with crowded social environments. By "crowded" I mean not only proximity to other people but also proximity to domesticated animals. In such environments, which are prone to deadly pulmonary diseases like tuberculosis and pneumonia, natural selection may have favored susceptibility to infection by coronaviruses, which are normally mild in their effects, as a means to maintain a strong immune response to respiratory infections (Frost 2020). 

If we look at case fatality rates, Italy and Spain have been hit much worse than Germany, Switzerland, Austria, and Iceland. The United Kingdom falls between the two extremes, although a confounding factor is its large population of non-native origin (Singh 2020).

This pattern also shows up in a meta-study of infection fatality rates. Meyerowitz-Katz and Merone (2020) examined thirteen estimates of IFR from a wide range of countries. They came to two main conclusions:

- Mean IFR is 0.75% but varies considerably between countries;

- IFR has increased over time, being lower in February and March than in April and May.

Earlier estimates were based on the assumption that the average time lag between infection and death is two weeks on average. Actually, it's probably longer, perhaps a month. Later deaths may have thus been missed by estimates made in February and March.

If we look only at IFRs from April and May, the meta-study shows a north-south cline in the virulence of SARS-CoV-2:

Germany - 0.36%
France - 0.70%, 0.80%
Italy - 0.95%, 1.29%, 1.60%

For the same time period, the meta-study also presented three estimates from the United States:

New York City - 0.93%
California - 0.20%
United States - 1.30%

The last study provides estimates ranging from a low of 0.5% in Putnam County NY to a high of 3.6% in King County WA (Basu 2020). These numbers are so high because IFR is calculated only in relation to symptomatic cases. In my opinion, this study is not comparable to the others and should not have been included in the metastudy. It is nonetheless useful for charting the virulence of SARS-CoV-2 within the United States.

So why would the virus be less virulent in Putnam County NY than in King County WA? Let's consider the demographics in each case. The first county is 80% non-Hispanic White, 14% Hispanic, 3% Black, and 2% Asian. The second county is 65% non-Hispanic White, 15% Asian, 9% Hispanic, and 6% Black. Putnam County is whiter and probably less cosmopolitan than King County, which encompasses the Seattle area. This impression is strengthened by the voting pattern in Putnam County, which trends much more Republican than Democrat (Wikipedia 2020). The virus thus seems to be least virulent among "old stock" Euro Americans. I would also predict low virulence in Amerindian communities.

Virulence may also differ between west coast Hispanics and east coast Hispanics, as suggested by the difference between California and New York City. East Coast Hispanics are less often Mexican and more often Puerto Rican. They may thus be more vulnerable because they are more Mediterranean and less Amerindian by ancestry.


References

Basu, A. (2020). Estimating The Infection Fatality Rate Among Symptomatic COVID-19 Cases In The United States. Health affairs (Project Hope). 2020:101377hlthaff202000455.
https://www.healthaffairs.org/doi/full/10.1377/hlthaff.2020.00455

Frost, P. (2020). Does a commensal relationship exist between coronaviruses and some human populations? Journal of Molecular Genetics 3(2): 1-2.
https://researchopenworld.com/does-a-commensal-relationship-exist-between-coronaviruses-and-some-human-populations/

Meyerowitz-Katz, G. and L. Merone. (2020).  A systematic review and meta-analysis of published research data on COVID-19 infection-fatality rates.  medRxiv, May 18, 2020
https://www.medrxiv.org/content/10.1101/2020.05.03.20089854v2 

Singh, S. (2020). BCG vaccines may not reduce COVID-19 mortality rates. medRxiv April 11, 2020 
https://www.medrxiv.org/content/10.1101/2020.04.11.20062232v1

Wikipedia (2020). Putnam County, New York.
https://en.wikipedia.org/wiki/Putnam_County,_New_York 

Friday, May 15, 2020

Does a commensal relationship exist between coronaviruses and some human populations?


Nanjing Road, Shanghai (Wikicommons - Stephen Codrington). Populations with a long history of social crowding may have become more susceptible to coronavirus infection.


I've published a paper on coevolution between coronaviruses and "crowded" social environments. Comments are welcome. Here is the abstract:


Coronaviruses enter lung tissue via the ACE2 receptor, which varies structurally among human populations. In particular, the Chinese population has fewer variants that bind weakly to the coronavirus S-protein. This global variation suggests that the ACE2 receptor has coevolved with different environments, some of which have favored susceptibility to infection of lung tissue by coronaviruses. 

It has been argued that respiratory viruses boost the immune response of lung tissue and thereby prevent more serious pulmonary diseases, like tuberculosis, pneumonia, and pneumonic plague. This preventive effect has been shown with other viral pathogens, notably γherpesvirus 68 and cytomegalovirus. Some human populations may have therefore gained protection from severe respiratory infections by becoming more susceptible to mild respiratory infections, such as those normally caused by coronaviruses. 

This commensal virus-host relationship would have been especially adaptive wherever respiratory pathogens could easily propagate, i.e., in crowded environments, where many people live in proximity not only to each other but also to animal sources of infection. In regions that have long had crowded environments, natural selection may have favored susceptibility to infection by coronaviruses, which are normally mild in their effects, as a means to maintain a strong immune response to deadly pulmonary diseases.


Reference

Frost, P. (2020c). Does a commensal relationship exist between coronaviruses and some human populations? Journal of Molecular Genetics 3(2): 1-2.
https://researchopenworld.com/does-a-commensal-relationship-exist-between-coronaviruses-and-some-human-populations/   

Wednesday, April 22, 2020

British hipsters


Why have British women become broader-hipped over the past three thousand years? (Wikicommons: Niek Sprakel)



British women have become broader-hipped over the past three thousand years or so. That's the conclusion of a recent study of alleles that influence female hip circumference, using data from the UKBiobank. 

Audrey Arner and her colleagues at Penn State identified 148 SNPs associated with female hip circumference and 49 SNPs associated with first child birth weight. Nine of them influence both women's hip circumference and first child birth weight. The SNPs associated with female hip circumference seemed to influence first child birth weight but not vice versa. There also seems to have been selection over approximately the last three thousand years for women with broader hips.

The baby's head is the biggest challenge during childbirth:

Human birthing is difficult owing to a tradeoff between large neonatal brain size and maternal pelvic dimensions, which are constrained by aspects of bipedal biomechanics. The net effect is that human neonatal head size closely matches maternal pelvic dimensions, unlike in our closest living relatives, the great apes, whose pelvic dimensions are larger than neonatal head sizes. (Franciscus 2009)

Have female hips become broader over the past three thousand years because the birth canal has had to accommodate babies with larger brains? That hypothesis would be consistent with an analysis of ancient DNA by Michael Woodley of Menie and others, who showed that alleles for educational attainment gradually increased in frequency between 4,560 and 1,210 years ago in Europeans and Central Asians. That increase may have been due to gene-culture coevolution: as societies grew larger and more complex, the average person had to perform mental tasks that likewise became larger in number and more complex. Such an environment would have favored the survival and reproduction of individuals with higher cognitive ability. Mean IQ thus rose over time, as did cranial capacity.

On the other hand, Henneberg (1988) showed that cranial capacity steadily shrank from the Mesolithic to modern times, becoming 9.9% smaller in men and 17.4% smaller in women. His conclusion was based on a large sample: 9,500 male skulls and 3,300 female skulls.

So we have a contradiction. Perhaps cranial capacity didn't really shrink from the Mesolithic to modern times. Perhaps smaller skulls are more likely to decompose faster. The skulls we unearth would therefore be a biased sample, and this bias toward preservation of larger skulls would gradually increase for skulls that have been in the ground longer.

The problem of "preservation bias" has already been noted with respect to female and infant remains:

There are nearly always more males than females in skeletal collections from archeological sites [...]. This has been explained in part by the comparatively rapid disintegration of lightly built female skeletons.

[...] The burial records show that most of the people buried in the Purisima cemetery were either infants, children, or elderly adults. The skeletal remains excavated from the cemetery, in contrast, are predominately those of young adults. The underrepresentation of young children in the skeletal collection is most likely a result of the comparatively rapid disintegration of their incompletely calcified bones.

[...] If, on the other hand, infants or elderly people are more common in a skeletal collection from a recent cemetery than they are in an ancient one, much less can be inferred about differences in the original age structure of the two burial populations. Such a difference would be expected due to differential preservation, even if the age structures of the two burial populations were identical. (Walker et al. 1988)

The same preservation bias might cause an overrepresentation of larger skulls among older remains.


References

Arner, A., H. Reyes-Centeno, G. Perry, and M. Grabowski. (2020). Pleiotropic effects on the recent evolution of human hip circumference and infant body size. The 89th Annual Meeting of the American Association of Physical Anthropologists (2020), April 17
https://meeting.physanth.org/program/2020/session26/arner-2020-pleiotropic-effects-on-the-recent-evolution-of-human-hip-circumference-and-infant-body-size.html  

Franciscus, R.G. (2009). When did the modern human pattern of childbirth arise? New insights from an old Neandertal pelvis. Proceedings of the National Academy of Sciences 106(23): 9125-9126.
https://www.pnas.org/content/106/23/9125.short  

Henneberg, M. (1988). Decrease of human skull size in the Holocene. Human Biology 60: 395-405.
https://www.jstor.org/stable/41464021  

Walker, P.L., J.R. Johnson, and P.M. Lambert. (1988). Age and sex biases in the preservation of human skeletal remains. American Journal of Physical Anthropology 76: 183-188.
https://onlinelibrary.wiley.com/doi/abs/10.1002/ajpa.1330760206

Woodley of Menie, M.A., S. Younuskunju, B. Balan, and D. Piffer. (2017). Holocene selection for variants associated with general cognitive ability: Comparing ancient and modern genomes. Twin Research and Human Genetics 20: 271-280.
https://www.cambridge.org/core/journals/twin-research-and-human-genetics/article/holocene-selection-for-variants-associated-with-general-cognitive-ability-comparing-ancient-and-modern-genomes/BF2A35F0D4F565757875287E59A1F534