Archive for evolution

bats [and viruses]

Posted in Statistics with tags , , , , , , , , , , , on February 9, 2020 by xi'an

Children of Time [book review]

Posted in Books, pictures, Travel with tags , , , , , , , , , , on October 8, 2017 by xi'an

I came by this book in the common room of the mathematics department of the University of Warwick, which I visit regularly during my stays there, for it enjoys a book sharing box where I leave the books I’ve read (and do not want to carry back to Paris) and where I check for potential catches… One of these books was Tchaikovsky’s children of time, a great space-opera novel à la Arthur C Clarke, which got the 2016 Arthur C Clarke award, deservedly so (even though I very much enjoyed the long way to a small angry planet, Tchaikosky’s book is much more of an epic cliffhanger where the survival of an entire race is at stake). The children of time are indeed the last remnants of the human race, surviving in an artificial sleep aboard an ancient spaceship that irremediably deteriorates. Until there is no solution but landing on a terraformed planet created eons ago. And defended by an AI spanned (or spammed) by the scientist in charge of the terra-formation, who created a virus that speeds up evolution, with unintended consequences. Given that the strength of the book relies on these consequences, I cannot get into much details about the alternative pathway to technology (incl. artificial intelligence) followed by the inhabitants of this new world, and even less about the conclusive chapters that make up for a rather slow progression towards this final confrontation. An admirable and deep book I will most likely bring back to the common room on my next trip to Warwick! (As an aside I wonder if the title was chosen in connection with Goya’s picture of Chronus [Time] devouring his children…)

snapshots from Nature

Posted in Books, Kids, pictures, University life with tags , , , , , , , , , , on September 19, 2016 by xi'an

Among many interesting things I read from the pile of Nature issues that had accumulated over a month of travelling, with a warning these are mostly “old” news by now!:

  • the very special and untouched case of Cuba in terms of the Zika epidemics, thanks to a long term policy fighting mosquitoes at all levels of the society;
  • an impressive map of the human cortex, which statistical analysis would be fascinating;
  • an excerpt from Nature 13 August 1966 where the Poisson distribution was said to describe the distribution of scores during the 1966 World Cup;
  • an analysis of a genetic experiment on evolution involving 50,000 generations (!) of Escherichia coli;
  • a look back at the great novel Flowers for Algernon, novel I read eons ago;
  • a Nature paper on the first soft robot, or octobot, along with some easier introduction, which did not tell which kind of operations could be accomplished by such a robot;
  • a vignette on a Science paper about the interaction between honey hunters and hunting birds, which I also heard depicted on the French National Radio, with an experiment comparing the actual hunting (human) song, a basic sentence in the local language, and the imitation of the song of another bird. I could not understand why the experiment did not include hunting songs from other hunting groups, as they are highly different but just as effective. It would have helped in understanding how innate the reaction of the bird is;
  • another literary entry at the science behind Mary Shelley’s Frankenstein;
  • a study of the Mathematical Genealogy Project in terms of the few mathematicians who started most genealogies of mathematicians, including d’Alembert, advisor to Laplace of whom I am one of the many descendants, although the finding is not that astounding when considering usual genealogies where most branches die off and the highly hierarchical structure of power in universities of old.

reversible chain[saw] massacre

Posted in Books, pictures, R, Statistics, University life with tags , , , , , , , , on May 16, 2016 by xi'an

A paper in Nature this week that uses reversible-jump MCMC, phylogenetic trees, and Bayes factors. And that looks at institutionalised or ritual murders in Austronesian cultures. How better can it get?!

“by applying Bayesian phylogenetic methods (…) we find strong support for models in which human sacrifice stabilizes social stratification once stratification has arisen, and promotes a shift to strictly inherited class systems.” Joseph Watts et al.

The aim of the paper is to establish that societies with human sacrifices are more likely to have become stratified and stable than societies without such niceties. The hypothesis to be tested is then about the evolution towards more stratified societies rather the existence of a high level of stratification.

“The social control hypothesis predicts that human sacrifice (i) co-evolves with social stratification, (ii) increases the chance of a culture gaining social stratification, and (iii) reduces the chance of a culture losing social stratification once stratification has arisen.” Joseph Watts et al.

The methodological question is then how can this be tested when considering those are extinct societies about which little is known. Grouping together moderate and high stratification societies against egalitarian societies, the authors tested independence of both traits versus dependence, with a resulting Bayes factor of 3.78 in favour of the latest. Other hypotheses of a similar flavour led to Bayes factors in the same range. Which is thus not overwhelming. Actually, given that the models are quite simplistic, I do not agree that those Bayes factors prove anything of the magnitude of such anthropological conjectures. Even if the presence/absence of human sacrifices is confirmed in all of the 93 societies, and if the stratification of the cultures is free from uncertainties, the evolutionary part is rather involved, from my neophyte point of view: the evolutionary structure (reproduced above) is based on a sample of 4,200 trees based on Bayesian analysis of Austronesian basic vocabulary items, followed by a call to the BayesTrait software to infer about evolution patterns between stratification levels, concluding (with p-values!) at a phylogenetic structure of the data. BayesTrait was also instrumental in deriving MLEs for the various transition rates, “in order to inform our choice of priors” (!). BayesTrait has an MCMC function used by the authors “to test for correlated evolution between traits” and derive the above Bayes factors. Using a stepping-stone method I am unaware of. And 10⁹ iterations (repeated 3 times for checking consistency)… Reversible jump is apparently used to move between constrained and unconstrained models, leading to the pie charts at the inner nodes of the above picture. Again a by-product of BayesTrait. The trees on the left and the right are completely identical, the difference being in the inference about stratification evolution (right) and sacrifice evolution (left). While the overall hypothesis makes sense at my layman level (as a culture has to be stratified enough to impose sacrifices from its members), I am not convinced that this involved statistical analysis brings that strong a support. (But it would make a fantastic topic for an undergraduate or a Master thesis!)

latest interviews on the philosophy of religion(s)

Posted in Books, Kids with tags , , , , , , , , , , on November 1, 2014 by xi'an

“But is the existence of God just a philosophical question, like, say, the definition of knowledge or the existence of Plato’s forms?” Gary Gutting, NYT

Although I stopped following The Stone‘s interviews of philosophers about their views on religion, six more took place and Gary Gutting has now closed the series he started a while ago with a self-interview. On this occasion, I went quickly through the last interviews, which had the same variability in depth and appeal as the earlier ones. A lot of them were somewhat misplaced in trying to understand or justify the reasons for believing in a god (a.k.a., God), which sounds more appropriate for a psychology or sociology perspective. I presume that what I was expecting from the series was more a “science vs. religion” debate, rather than entries into the metaphysics of various religions… Continue reading