Plato’s reading suggestions, episode 101

Here it is, our regular Friday diet of suggested readings for the weekend:

Half the universe’s missing baryonic matter has just been found.

The difference between good vegans and bad vegans: honesty about science.

When did language evolve, exactly?

Archeologists decipher tablet that helps to unravel the mystery of civilization’s collapse at the end of the Bronze Age.

E.O. Wilson gets it wrong again. Because of scientism, of course.

More fundamental disagreements among fundamental physicists…

Research on the genetics of skin color differences deals yet another blow to the idea that races are real.

A new way to look at emotions, and why Darwin was wrong about them.

_____

Please notice that the duration of the comments window is three days (including publication day), and that comments are moderated for relevance (to the post one is allegedly commenting on), redundancy (not good), and tone (constructive is what we aim for). This applies to both the suggested readings and the regular posts. Thanks!

78 thoughts on “Plato’s reading suggestions, episode 101”

  1. davidlduffy

    Here is a fairly easy to read review article. As usual, “Lewontin’s fallacy” makes an appearance viz differences at any one locus between populations are usually small, but when one combines evidence from multiple loci, it is easy to assess group membership and contribution of different ancestries to admixed individuals. The same point comes up with differences between the sexes – at any single (sex-shared) feature, a woman may overlap the male distribution (eg height) – but in a multivariate space will still be easy to recognize as female.

    https://humgenomics.biomedcentral.com/articles/10.1186/s40246-014-0023-x

    Availability of genetic markers that are ancestry-informative and newly developed statistical methods may overcome concerns regarding race/ethnicity categorization. There is evidence that measures of genetic ancestry can improve clinical care for people of mixed race. For example, physicians assessing lung disease can make more accurate diagnoses when they use a reference standard from the patients’ actual genetic ancestry than self-reported race or ethnicity. A large proportion of Native American ancestry is associated with a greater risk of childhood acute lymphoblastic leukemia. Children with more than 10% Native American ancestry need an additional round of chemotherapy to respond to the treatment. Differences in ancestry proportion in admixed population could introduce variation among individuals of the same race and potentially alter genetic association and the therapeutic efficacy of commonly used asthma therapies…

    Several studies have associated genetic ancestry with numerous clinical endpoints. African ancestry was inversely related to FEV1 (p = 0.007), FVC (p = 0.0003), and FEV1/FVC (p = 0.035) (Table 2, Figure 3) [38,62]. Higher vs. lower proportion of African ancestry, categorized based on median value, has also been shown to be associated with greater decline in the lung function per pack-year of smoking (−5.7 vs. –4.6 ml FEV1 per pack-year) in contrast to the −3.9 ml FEV1 per pack-year smoked observed among European Americans [63]. Additionally, African Americans with higher proportions of African ancestry have a greater risk of losing lung function while smoking. Studies have shown that each percentage increase in African ancestry was associated with an 8.9-ml decrease in FEV1 (p = 0.001) and an 11.8-ml decrease in FVC (p = 0.0001). Higher African ancestry was associated with a greater likelihood for an asthma-related physician visit (p = 0.004) and greater frequency of urgent or ED visits among asthmatics treated with an inhaled glucocorticoid (p = 0.01). In African Americans with more severe asthma, the magnitude of decreased lung function associated with African ancestry was twice that observed in the general population (−8.9 ml vs. −4 ml for FEV1 per percentage African ancestry [38]). These investigators found that adding genetically measured ancestry to the standard lung function prediction equations, rather than relying on self-identified race, reduced misclassification and resulted in the reclassification of asthma severity by 5%.

    As to BunsenBurner’s query about races, genetic clustering analyses always pick out the “continental races” eg
    “…the value K = 5 minimizes cross-validation error (not shown). The solution at K = 5 corresponds to major continental groups (Sub-Saharan Africans, Oceanians, East Asians, Native Americans, and West Eurasians)”

    I think I have previously posted this plot

    http://users.tpg.com.au/davidd02/index.html#20171023

    Liked by 1 person

  2. Massimo Post author

    David,

    No, genetic clustering doesn’t pick up anything. One can set an arbitrary threshold, in which case one can pick up 5, or 20, or 100, or 500 different “races.” That’s because there is no phylogenetic clustering among human populations, at all. There are overlapping geographic distances. It is seriously depressing that this needs to be said over and over and over again.

    Liked by 2 people

  4. SocraticGadfly

    Robin, from The Book of Many Universes, Chapter 2: First shalt thou take out the Holy Inflation, then shalt thou count to three, no more, no less. Three shall be the number thou shalt count, and the number of the counting shall be three. Four shalt thou not count, neither count thou two, excepting that thou then proceed to three. Five is right out. Once the number three, being the third number, that shall be the number of universes thou shalt have.

    ==

    Or, per CERN, you can ask why is there even one? https://cosmosmagazine.com/physics/universe-shouldn-t-exist-cern-physicists-conclude

    Liked by 1 person

  5. davidlduffy

    Dear Massimo.

    Given we see Neanderthal introgression cum hybridization mainly in Europeans and Denisovan contributions mainly in Asians, I don’t think “no phylogenetic clustering” is quite correct. As a general comment about statistical clustering, sure, one can pull out more and more “statistically significant” clusters as one’s sample size increases (in a likelihood based mixtures framework), but this does not mean the lumpiness is not there. It simply means you can see finer and finer gradations with increasing statistical power. So if I look at someone’s features and skin colour and decide they are African, it is a very reasonable assumption that I will see certain (and a wider variety of) haplotypes than in a European on average. Ditto the medical examples cited above. So I will continue to use “race specific” infant birth weight distribution curves, growth trajectories and lung function prediction equations because they are still simpler than plugging in genotypes at a 1000 or 10000 SNPs, and which I don’t have for most people anyway.

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  6. synred

    David,

    Just because an effect or clustering is statistically significant does not mean it is significant. Lots of data and lots of variables let us pull out lots of noise.

    E.g., saccharin causes cancer in rats breed to get cancer.

    Like

  7. Massimo Post author

    David,

    It doesn’t work that way. First off, most of the genetic variation in humans is within, not between populations. This is a reflection of no phylogenetic subdivision in H. sapiens sapiens. Neanderthals were a different sub-species, definitely phylogenetically distinct, which is precisely why you can see introgression of their genes. None of the above, again, means that genetics gives you no clues to geographical origin, of course it does. But there are no meaningfully distinct clusters, just continuous variation.

    Liked by 2 people

  8. Coel

    Massimo,

    I don’t bother anymore. It’s simply not worth it. Nothing, ever, I wrote here changed your mind. About anything. Not even a tiny bit.

    Arguments work better than dismissive comments in changing people’s minds. (And I’ve not seen you give a list of all the times that I’ve changed your mind.)

    Anyhow, we are not really disagreeing much about the biology (despite you claiming I’m “getting the biology so utterly wrong”) since I’m pretty much in-line with the Pigliucci and Kaplan paper** (and with Coyne and plenty of other biologists).

    We’re really disagreeing on what the common understanding of “race” is. You’re suggesting that people have a single-marker conception of “race” in terms of skin shade alone. I’m suggesting that by “race” most people mean a concept primarily in terms of shared-ancestry clusterings, with secondary features such as skin shade being one aspect of a wider package.

    Neither of us has presented evidence as to how people in general think about this, but I’d be surprised if your version were the case.

    **Note that the Pigliucci and Kaplan paper states that part of the reason for arguing that races don’t exist is political/ideological: “Biological research on race has often been seen as motivated by or lending credence to underlying racist attitudes; in part for this reason, recently philosophers and biologists have gone through great pains to essentially deny the existence of biological human races.”

    The paper then starts: “It has become commonplace to claim that, insofar as “race” is a biological concept, there are no human races. This claim, while widely defended, is misguided.”

    What the paper does do is reject the idea of discrete, sharp-edged “essentialist” notions of race (surely everyone agrees, unless one were a creationist arguing for polygenism and the separate creation of different races; this has been argued by some in the past but is surely not at all prevalent today). It also rejects single-marker folk categories such as “black” as biologically meaningful (again, agreed).

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  9. Bunsen Burner

    Robin:

    Wallace considers the number of worlds indeterminate since decoherence is taking place on multiple levels, and at the lower levels discrete structure is lost because of interference. The larger the system the more decoherence. If you fix the scale I would argue that the number of decoherent histories is finite.

    ‘ is it true of EQM that if X is physically possible then the probability that there is at least one universe in which X happens is exactly 1’

    At best you can probably say that it has a non zero probability of occurring.

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  11. Bunsen Burner

    Coel:

    Then I don’t understand the disagreement. If you are happy with ecotypes, demes and so on, why make a fuss over human races? To 99% of people such genetic distinctions are meaningless and race refers to the complex historical entity with all of its socio-cultural baggage. The community of geneticists has decided there is better terminology to use, one that helps clarify rather than obfuscate. This is no different to the situation with Pluto. Why cling to an antiquated notion of planet when the community of experts has decided there is a better way of organizing planetary bodies?

    Liked by 3 people

  12. brodix

    Bunsen,

    As this is the end of the thread, I will just add I see problems with information as platonic, which is what it would be, if it lacked a dynamic substrate and not subject to change.

    I’m assuming the block time aspect of spacetime can be used to explain away transmission as not being an explicit form of change and thus creation/destruction, but the notion of time as somehow static hasn’t been given the skeptical consideration it deserves.

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  13. davidlduffy

    Hi Arthur/Synred.

    In this case, we have a pretty good idea why particular clusters appear – because of the historical patterns of human migration into different geographical regions starting from Africa. For example, Australian Aborigines travelled to Australia ~50K years ago and stayed here.

    Hi Massimo.

    “Neanderthals were a different sub-species, definitely phylogenetically distinct, which is precisely why you can see introgression of their genes”. This is not a good example. As you know, it is easy to detect introgression of European into African-ancestry genomes, in the US for example. Whenever we use the term population structure, we are talking about phenomena that overlap with the older anthropological concepts of race. Genomes do not uniformly fill the space represented by the first few genetic principal components, even though we do see individuals at every position along the lines between the modes that represent the main continental populations.

    So is self-identified ancestry useful to geneticists? Definitely in the data I analyse.

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  15. Massimo Post author

    Coel,

    “Arguments work better than dismissive comments in changing people’s minds”

    Please do not patronize me. I have given you plenty of arguments over the years, on a variety of subjects. Never made a dent. And now you perversely insist in using my own paper to make an argument that is either irrelevant or entirely at odds with what Kaplan and I wrote. Enjoy yourself, I will not take part.

    Liked by 2 people

  16. Massimo Post author

    David,

    Thanks for the genetics lesson, but, again, you are incorrect. There is no mapping between so-called folk races (i.e., what non specialists think races are, how many, etc.) and genetic diversity and introgression. Sorry, the biology simply does not support the concept. As for Neanderthals, you brought them up, I simply explained why they really were a “race” (or sub-species) of Homo sapiens, which ironically should make the distinction with modern “races” of H. sapiens sapiens even more sharp. If only people would look at the science and drop their ideological glasses.

    Liked by 2 people

  17. synred

    Coel,

    sickle cell trait is common anywhere malaria is endemic. The ‘Cohen’ marker is an accident of history and does not make Jews a separate race (even though it’s presences makes it likely you have a Jewish ancestors d and even a ‘priestly’ heritage). Sell your Lederhosen and buy a yarmulke) [|;-_).

    The point is that the variation within so called races is bigger than that between them. That makes such variations insignificant even though they are statistically significant.

    You can call such clusters ‘race’, but the scientist don’t find that usefully and as it fuel racism it is socially detrimental as well.

    I have nostalgia for Pluto, but not for ‘race’…

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  18. synred

    10/23/2017 7:10 PM

    Book: Indeed, my central argument is that no single prime mover is responsible for the evolution of the human mind. Instead, I highlight the significance of accelerating cycles of evolutionary feedback, whereby an interwoven complex of cultural processes to reinforce each other in an irresistible runaway dynamic that engineered the mind’s breathtaking computational power.

    Laland, Kevin N.. Darwin’s Unfinished Symphony: How Culture Made the Human Mind (p. 3). Princeton University Press. Kindle Edition.

    ==>Other than the word ‘engineered’ there’s nothing radical about that. I take ‘engineered’ to be a loose metaphor of the intentional stance variety.

    ==>Maybe the word ‘irresistible” is a little strong. There was plenty of resistance, e.g., head sizes and birth canals. It’s a lesson not to put in useless adjectives (as my senior (PEP rally) year English teacher told us [a]I

    ==>Strong resistance seems to me to indicate that big brains we strongly adaptive. The odds of getting that the complex, seemingly coordinated changes could well explain why it only happened once and if we ‘reran the tape’ it might not happen at all.

    [a] Though I have found in the internet age that a smattering of weasel words helps avoid flame war.

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