Archive for evolution

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

the intelligent-life lottery

Posted in Books, Kids with tags , , , , , , , on August 24, 2014 by xi'an

monkey at Amber FortIn a theme connected with one argument in Dawkins’ The God Delusion, The New York Time just published a piece on the 20th anniversary of the debate between Carl Sagan and Ernst Mayr about the likelihood of the apparition of intelligent life. While 20 years ago, there was very little evidence if any of the existence of Earth-like planets, the current estimate is about 40 billions… The argument against the high likelihood of other inhabited planets is that the appearance of life on Earth is an accumulation of unlikely events. This is where the paper goes off-road and into the ditch, in my opinion, as it makes the comparison of the emergence of intelligent (at the level of human) life to be “as likely as if a Powerball winner kept buying tickets and — round after round — hit a bigger jackpot each time”. The later having a very clearly defined probability of occurring. Since “the chance of winning the grand prize is about one in 175 million”. The paper does not tell where the assessment of this probability can be found for the emergence of human life and I very much doubt it can be justified. Given the myriad of different species found throughout the history of evolution on Earth, some of which evolved and many more which vanished, I indeed find it hard to believe that evolution towards higher intelligence is the result of a basically zero probability event. As to conceive that similar levels of intelligence do exist on other planets, it also seems more likely than not that life took on average the same span to appear and to evolve and thus that other inhabited planets are equally missing means to communicate across galaxies. Or that the signals they managed to send earlier than us have yet to reach us. Or Earth a long time after the last form of intelligent life will have vanished…

on intelligent design…

Posted in Books, Kids, Travel with tags , , , , , , , on August 19, 2014 by xi'an

chicken In connection with Dawkins’ The God delusion, which review is soon to appear on the ‘Og, a poster at an exhibit on evolution in the Harvard Museum of Natural History, which illustrates one of Dawkins’ points on scientific agosticism. Namely, that refusing to take a stand on the logical and philosophical opposition between science and religion(s) is not a scientific position. The last sentence in the poster is thus worse than unnecessary…

les sciences face aux créationnismes [book review]

Posted in Books with tags , , , , , , on March 9, 2014 by xi'an

I spotted this small book during my last visit to CBGP in Montpellier, and borrowed it from the local librarian. It is written (in French) by Guillaume Lecointre, who is professor of Biology at the Muséum National d’Histoire Naturelle in Paris, specialised in population evolution and philogenies. The book is published by Editions Quae, a scientific editor supported by four founding French institutes (CIRAD, IFREMER, INRA and IRSTEA), hence no wonder I would spot it in an INRA lab. The theme of the book is not to argue against creationism and intelligent design theories, but rather to analyse how the debates between scientists—interestingly this term scientist sounds much more like a cult in English than the French noun scientifique— and creationists are conducted and to suggest how they should be conducted. While there are redundancies in the text, I found the overall argumentation quite convincing, with the driving lines that creationists are bypassing the rules of scientific investigation and exchange to bring the debate at a philosophical or ideological level foreign to science definition. Lecointre deconstructs the elements put forward in such debates, from replacing the incompleteness of the scientific knowledge and the temporary nature of scientific theories with a total relativism, to engaging scientific supporters from scientific fields not directly related with the theory of evolution, to confusing methodological materialism with philosophical materialism and more fundamentally to imply that science and scientific theories must have a moral or ideological content, and to posturing as anti-establishment and anti-dogmatic free minds… I also liked the points that (a) what really drives the proponents of intelligent design is a refusal of randomness in the evolution, without any global or cosmic purpose; (b) scientists are very ill-prepared to debate with creationists, because the later do not follow a scientific reasoning; (c) journalists are most often contributing to the confusion by picking out-of-their-field “experts” and encouraging the relativity argument. Hence a reasonable recommendation to abstain from oral debates and to stick to pointing out the complete absence of scientific methodology in creationists’ arguments. (Obviously, readers of Alan Sokal’s Beyond the Hoax will be familiar most of the arguments produced in les sciences face aux créationnismes.)