Archive for Nature

chain of lynx and drove of hares

Posted in Books, Kids, pictures, R, Statistics with tags , , , , , , , , , on February 27, 2020 by xi'an

A paper (and an introduction to the paper) in Nature this week seems to have made progress on the existence of indefinite predator-prey cyles. As in the lynx/hare dataset available on R. The paper is focusing on another pair, an invertebrate and its prey, an algae. For which the authors managed a 50 cycle sequence. What I do not get about this experiment is how the cycle can be tested via a rigorous statistical experiment.

“…the predator–prey system showed a strong tendency to return to the dominant dynamical regime with a defined phase relationship. A mathematical model suggests that stochasticity is probably responsible for the reversible shift from coherent to non-coherent oscillations, a notion that was supported by experiments with external forcing by pulsed nutrient supply.”

As I had not renewed my subscription to Nature in time, I could not check the additional material for details, but the modelling seems to involve a wavelet decomposition of the bivariate time series, with correlations between the two series…

sustainable workshops and conferences

Posted in Kids, pictures, Statistics, Travel, University life with tags , , , , , , , , on February 17, 2020 by xi'an

The current uncertainty about whether or not ISBA 2020 will take place (and where it will take place), along with a recent Nature article and a discussion in the common room of the Department of Statistics at Warwick, lead me to renew the call for a more sustainable form of conferencing. By creating a network of local havens or a garland of local magnets (competition open for a catchy “x of local y” denomination) attracting people in the area to gather together, attend some of the video-ed talks in the other knots, and add their own local activities, from talks to collaborative brainstorming. Obviously, this requires additional planning and some technical details, but it should become a habit rather than the exception. ABC in Grenoble is thinking about it, let me know if you are interesting in creating a local image of the workshop.

Rooibos tax for aboriginal communities

Posted in Books, pictures, Travel, Wines with tags , , , , , , , , , , on January 25, 2020 by xi'an

Just read in the 150th anniversary issue of Nature that the South African Government had agreed to a share of the rooibos tea profits be reversed to the aboriginal San and Khoi communities. Following a lengthy debate on whether or not rooibos tea was in use before European settlers invaded the area. I cannot remember when I started drinking rooibos but it may have been connected with reading my first book of the delicious Mma Ramotswe and the №1 Ladies Detective Agency series…! Which author, Alexander McCall Smith is a self-declared tea addict. (Since the story is located in Botswana, I have no idea whether or not tea is exported from this country and if the benefits reach the local communities.)

Nature on predatory journals

Posted in Books, University life with tags , , , , on January 24, 2020 by xi'an

A (long) comment published in Nature this week studies the impact of predatory journals, with a definition (made by the 32 authors of the comment and 9 others at a special meeting in Ottawa) of what constitutes a predatory journal.

Predatory journals and publishers are entities that prioritize self-interest at the expense of scholarship and are characterized by false or misleading information, deviation from best editorial and publication practices, a lack of transparency, and/or the use of aggressive and indiscriminate solicitation practices.”

The article discusses each term in the definition, terms that remain vague (like what’s a “deviation from best”? A terrible website? May be due to English not being the first language of the journal editors…). In my opinion, the main criterion is the “aggressive and indiscriminate solicitation”  and a lack of actual peer review, which can be easily detected when the paper is accepted within a very short time period. (Which is not to state that journals with a very quick rejection time should be a priori considered as predatory!) High publishing fees are certainly part of the predatory landscape but difficult to detect from established journals, even those backed by national or international societies. My only experience with predatory “publishers”, beyond the constant flow of proposals to send a paper, to edit a special edition and so forth, is a paper sent to a journal with the same title as a regular (Elsevier) journal, modulo a permutation!, and a threat of legal action from another source, which I described as “predatory” for proposing to write a general public paper in their glossy magazine. For the first occurrence, the paper was accepted within a day, we never signed any copyright form, and despite requests to withdraw the paper, it almost immediately got published. Even though we never paid the requested fees.

“Efforts to counter predatory publishing need to be constant and adaptable. The threat is unlikely to disappear as long as universities use how many publications a scholar has produced as a criterion for graduation or career advancement. The publish-or-perish culture, a lack of awareness of predatory publishing and difficulty in discerning legitimate from illegitimate publications fosters an environment for predatory publications to exist. Predatory journals are also quick to adapt to policies and measures designed to foil them.”

It certainly feels impossible to completely counter predatory actions, especially when some researchers seek such publications, but detecting some could be achieved by sending decoys to them, in the form of low-content pseudo-articles that could not pass any serious assessment by a genuine referee. Because no publication is intended, the same decoy could be used over and over by the society initiating the action…

Panch at the helm!

Posted in pictures, Travel, University life with tags , , , , , , , , , , , , on January 8, 2020 by xi'an

Reading somewhat by chance a Nature article on the new Director of the National Science Foundation (NSF) nominated by Trump (and yet to be confirmed by the Senate), I found that his name Sethuraman Panchanathan was the name of a friend of my wife 30⁺ years ago when they were both graduate students in image processing at the University of Ottawa, Department of Electrical Engineering… And looking further into the matter, I realised that this was indeed the very friend we knew from that time, with whom w shared laughs, dinners, and a few day trips together around Ottawa! While this is not the ultimate surprise, given that science administration is usually run by scientists, taken from a population pool that is not that large, as exemplified by earlier cases at the national or European level where I had some acquaintance with a then senior officer, it is nonetheless striking (and fun) to hear of a friend moving to a high visibility position after such a long gap. (When comparing NSF and ERC, the European Research Council, with French mathematician Jean-Pierre Bourguignon as current director also appearing in a recent Nature article, I was surprised to see that the ERC budget was more than twice the NSF budget.) Well, good luck to him for sailing these highly political waters!

Nature science images of the year

Posted in Books, pictures, Travel with tags , , , , , , , on December 19, 2019 by xi'an

limited shelf validity

Posted in Books, pictures, Statistics, University life with tags , , , , , , , , , , , on December 11, 2019 by xi'an

A great article from Steve Stigler in the new, multi-scaled, and so exciting Harvard Data Science Review magisterially operated by Xiao-Li Meng, on the limitations of old datasets. Illustrated by three famous datasets used by three equally famous statisticians, Quetelet, Bortkiewicz, and Gosset. None of whom were fundamentally interested in the data for their own sake. First, Quetelet’s data was (wrongly) reconstructed and missed the opportunity to beat Galton at discovering correlation. Second, Bortkiewicz went looking (or even cherry-picking!) for these rare events in yearly tables of mortality minutely divided between causes such as military horse kicks. The third dataset is not Guinness‘, but a test between two sleeping pills, operated rather crudely over inmates from a psychiatric institution in Kalamazoo, with further mishandling by Gosset himself. Manipulations that turn the data into dead data, as Steve put it. (And illustrates with the above skull collection picture. As well as warning against attempts at resuscitating dead data into what could be called “zombie data”.)

“Successful resurrection is only slightly more common than in Christian theology.”

His global perspective on dead data is that they should stop being used before extending their (shelf) life, rather than turning into benchmarks recycled over and over as a proof of concept. If only (my two cents) because it leads to calibrate (and choose) methods doing well over these benchmarks. Another example that could have been added to the skulls above is the Galaxy Velocity Dataset that makes frequent appearances in works estimating Gaussian mixtures. Which Radford Neal signaled at the 2001 ICMS workshop on mixture estimation as an inappropriate use of the dataset since astrophysical arguments weighted against a mixture modelling.

“…the role of context in shaping data selection and form—context in temporal, political, and social as well as scientific terms—has been shown to be a powerful and interesting phenomenon.”

The potential for “dead-er” data (my neologism!) increases with the epoch in that the careful sleuth work Steve (and others) conducted about these historical datasets is absolutely impossible with the current massive data sets. Massive and proprietary. And presumably discarded once the associated neural net is designed and sold. Letting the burden of unmasking the potential (or highly probable?) biases to others. Most interestingly, this recoups a “comment” in Nature of 17 October by Sabina Leonelli on the transformation of data from a national treasure to a commodity which “ownership can confer and signal power”. But her call for openness and governance of research data seems as illusory as other attempts to sever the GAFAs from their extra-territorial privileges…