Archive for Nature

new trajectories?

Posted in Books, Statistics with tags , , , , , , , , , , , on July 11, 2021 by xi'an

Nature French tidbits

Posted in Books, pictures, University life with tags , , , , , , , , , on July 4, 2021 by xi'an

As I was going over breakfast through a pile of Nature journals I hadn’t time to read, I came across this issue of 27 May with an editorial about the closure of the École Nationale d’Administration (ÉNA) by Emmanuel Macron (who graduated from ÉNA). While I have no opinion about the school or its closure (although it sounds more like a populist move than an in-depth reshuffle of the French high administration), the editorial did not seem particularly relevant or appropriate for a journal like Nature. While complaining about the lack of scientific training for the (higher) civil servants, it also pointed out at the lack of research agenda and  at the absence of a professorial body. Which would seem indeed surprising were it a regular academic body, which it is not as it trains civil servants who already hold one or several graduate degrees, incl. some from Polytechnique… Again, I have no opinion on the reformation of that school but a lack of social diversity and a fetishism of bureaucratic rules would sound like more immediate areas demanding improvement.

A second paper in this same issue was about the highly controversial figure of Didier Raoult, who was turned into a modern saint by social networks for defending hydroxychloroquine as the way to treat COVID-19, who objected in Le Monde to mathematical modelling, and who is now under investigation by the Medical Council. A microbiologist pointing out “many potential problems with the way the data and the peer review process were handled” in one then many of his papers is the recipient of a criminal complaint by Raoult and one of his coauthors, Chabrière, for “moral harassment”. Which sounds absurd, as with more than 3000 publications cosigned by Raoult, one would think that all are open to criticisms and some are statistically bound to contain errors or mistakes!

how many T-Rex can you fit in your backyard?

Posted in Statistics with tags , , , , , on April 30, 2021 by xi'an

A fascinating question examined in this issue of Science [as pointed out by Nature!] in a paper by Marshall et al. on how many T. Rex(es) roamed the Earth at a given time (in the Cretaceous).  The figure is evaluated from Damuth’s Law and relying on estimates of their body mass (8 tons?), the range of its habitat, the longevity of the species (1.2 million years?), its generation time (18 years?), somewhat surprisingly taking the maximum age (28 years) as the age of the oldest observed fossil.

“We assessed the impact of uncertainties in the data used with Monte Carlo simulations, but these simulations do not accommodate uncertainties that might stem from the choices made in the design of our approach.”

The resulting global evaluation is of an abundance of about 20,000 individuals at a given time, albeit with a 95% confidence interval between 1300 and 328,000 animals, with around 127,000 generations, and a total number of T. rex that ever lived amounting to 2.5 billion animals. Fun exercise, but I am rather reserved at the validity of the evaluation, given the uncertainty and poor data about most terms in the equation.

ten computer codes that transformed science

Posted in Books, Linux, R, Statistics, University life with tags , , , , , , , , , , , , , , , , , , , on April 23, 2021 by xi'an

In a “Feature” article of 21 January 2021, Nature goes over a poll on “software tools that have had a big impact on the world of science”. Among those,

the Fortran compiler (1957), which is one of the first symbolic languages, developed by IBM. This is the first computer language I learned (in 1982) and one of the two (with SAS) I ever coded on punch cards for the massive computers of INSEE. I quickly and enthusiastically switched to Pascal (and the Apple IIe) the year after and despite an attempt at moving to C, I alas kept the Pascal programming style in my subsequent C codes (until I gave up in the early 2000’s!). Moving to R full time, even though I had been using Splus since a Unix version was produced. Interestingly, a later survey of Nature readers put R at the top of the list of what should have been included!, incidentally including Monte Carlo algorithms into the list (and I did not vote in that poll!),

the fast Fourier transform (1965), co-introduced by John Tukey, but which I never ever used (or at least knowingly!),

arXiv (1991), which was started as an emailed preprint list by Paul Ginsparg at Los Alamos, getting the current name by 1998, and where I only started publishing (or arXiving) in 2007, perhaps because it then sounded difficult to submit a preprint there, perhaps because having a worldwide preprint server sounded more like bother (esp. since we had then to publish our preprints on the local servers) than revolution, perhaps because of a vague worry of being overtaken by others… Anyway, I now see arXiv as the primary outlet for publishing papers, with the possible added features of arXiv-backed journals and Peer Community validations,

the IPython Notebook (2011), by Fernando Pérez, which started by 259 lines of Python code, and turned into Jupyter in 2014. I know nothing about this, but I can relate to the relevance of the project when thinking about Rmarkdown, which I find more and more to be a great way to work on collaborative projects and to teach. And for producing reproducible research. (I do remember writing once a paper in Sweave, but not which one…!)

Sheer Thursday in Nature

Posted in Books, Kids, University life with tags , , , , on April 2, 2021 by xi'an

As on this (sheer or maundy) Thursday, it happens from time to time a religious tribune worms its way into the scientific journal Nature. This one calls for a collaboration between scientists and “people of faith” towards stalling climate change. Which is obviously well intentioned, as any initiative towards that goal cannot hurt on principle. But against the scientific method as well: the  tribune calls for convincing religious communities of the need to act by relating scientific facts to “sacred” texts, for focussing on communities of the same faith impacted by climate change, and never argue against anti-science religious arguments… And somewhat irrational even without considering the conservatism of most religious groups, as “people of faith” are about as diverse as the whole society.