Archive for Nature

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.

the Ramanujan machine

Posted in Books, Kids, pictures, University life with tags , , , , , , , , , , , on February 18, 2021 by xi'an

Nature of 4 Feb. 2021 offers a rather long (Nature-like) paper on creating Ramanujan-like expressions using an automated process. Associated with a cover in the first pages. The purpose of the AI is to generate conjectures of Ramanujan-like formulas linking famous constants like π or e and algebraic formulas like the novel polynomial continued fraction of 8/π²:

\frac{8}{{{\rm{\pi }}}^{2}}=1-\frac{2\times {1}^{4}-{1}^{3}}{7-\frac{2\times {2}^{4}-{2}^{3}}{19-\frac{2\times {3}^{4}-{3}^{3}}{37-\frac{2\times {4}^{4}-{4}^{3}}{\ldots }}}}

which currently remains unproven. The authors of the “machine” provide Python code that one can run to try uncover new conjectures, possibly named after the discoverer! The article is spending a large proportion of its contents to justify the appeal of generating such conjectures, with several unsuspected formulas later proven for real, but I remain unconvinced of the deeper appeal of the machine (as well as unhappy about the association of Ramanujan and machine, since S. Ramanujan had a mystical and unexplained relation to numbers, defeating Hardy’s logic,  “a mathematician of the highest quality, a man of altogether exceptional originality and power”). The difficulty is in separating worthwhile from anecdotal (true) conjectures, not to mention wrng conjectures. This is certainly of much deeper interest than separating chihuahua faces from blueberry muffins, but does it really “help to create mathematical knowledge”?

love thy command line [Bourne again]

Posted in Books, Kids, Linux, R, University life with tags , , , , , , , , on February 15, 2021 by xi'an

“Prebuilt into macOS and Unix systems (…) the command line (also called the shell) is a powerful text-based interface in which users issue terse instructions to create, find, sort and manipulate files, all without using the mouse. There are actually several distinct (…) shell systems, among the most popular of which [sic?] is Bash, an acronym for the ‘Bourne again shell’ (a reference to the Bourne shell, which it replaced in 1989).”

An hilarious rediscovery of the joys of shell (line) commands in Nature! Which I use by default for most operations on my computer, albeit far from expertly (despite the use of a cheat tee, from time to time!). One of the arguments in the article, “The mouse doesn’t scale,” is definitely mine as well. Among other marketing lines, wrangling files with no software interference (check), handling huge files (very rarely), manipulating spreadsheets (I don’t), parallelising work on remote servers (check), automate via cron (not anymore)…. Unsurprisingly, most of our students are never using terminals of command lines.