Archive for Nature

Nature highlights

Posted in Books, Kids, pictures, Statistics with tags , , , , , , , , , , , , , on October 16, 2016 by xi'an

Among several interesting (general public) entries and the fascinating article reconstituting the death of Lucy by a fall from a tree, I spotted in the current Sept. 22 issue of Nature two short summaries involving statistical significance, one in linguistics about repeated (and significant) links between some sounds and some concepts (like ‘n’ and ‘nose’) shared between independent languages, another about the (significant) discovery of a π meson and a K meson. The first anonymous editorial, entitled “Algorithm and blues“, was rather gloomy about the impact of proprietary algorithms on our daily life and on our democracies (or what is left of them), like the reliance on such algorithms to grant loan or determining the length of a sentence (based on the estimated probability of re-offending). The article called for more accountability of such tools, from going completely open-source to allowing for some form of strong auditing. This reminded me of the current (regional) debate about the algorithm allocating Greater Paris high school students to local universities and colleges based on their grades, wishes, and available positions. The apparent randomness and arbitrariness of those allocations prompted many (parents) to complain about the algorithm and ask for its move to the open. (Besides the pun in the title, the paper also contained a line about “affirmative algorithmic action”!) There was also a perfectly irrelevant tribune from a representative of the Church of England about its desire to give a higher profile to science in the/their church. Whatever. And I also was bemused by a news article on the difficulty to build a genetic map of Australia Aboriginals due to cultural reticence of Aboriginals to the use of body parts from their communities in genetic research. While I understand and agree with the concept of data privacy, so that to restrain to expose personal information, it is much less clear [to me] why data collected a century ago should come under such protections if it does not create a risk of exposing living individuals. It reminded me of this earlier Nature news article about North-America Aboriginals claiming right to a 8,000 year old skeleton. On a more positive side, this news part also mentioned the first catalogue produced by the Gaia European Space Agency project, from the publication of more than a billion star positions to the open access nature of the database, in that the Gaia team had hardly any prior access to such wealth of data. A special issue part of the journal was dedicated to the impact of social inequalities in the production of (future) scientists, but this sounds rather shallow, at least at the level of the few pages produced on the topic and it did not mention a comparison with other areas of society, where they are also most obviously at work!

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.

Darwin’s radio [book review]

Posted in Books, Kids, pictures, University life with tags , , , , , , , , , , , , , , , , on September 10, 2016 by xi'an

When in Sacramento two weeks ago I came across the Beers Books Center bookstore, with a large collection of used and (nearly) new cheap books and among other books I bought Greg Bear’s Darwin Radio. I had (rather) enjoyed another book of his’, Hull Zero Three, not to mention one of his first books, Blood Music, I read in the mid 1980’s, and the premises of this novel sounded promising, not mentioning the Nebula award. The theme is of a major biological threat, apparently due to a new virus, and of the scientific unraveling of what the threat really means. (Spoilers alert!) In that respect it sounds rather similar to the (great) Crichton‘s The Andromeda Strain, which is actually mentioned by some characters in this book. As is Ebola, as a sort of contrapoint (since Ebola is a deadly virus, although the epidemic in Western Africa now seems to have vanished). The biological concept exploited here is dormant DNA in non-coding parts of the genome that periodically get awaken and induce massive steps in the evolution. So massive that carriers of those mutations are killed by locals. Until the day it happens in an all-connected World and the mutation can no longer be stopped. The concept is compelling if not completely convincing of course, while the outcome of a new human race, which is to Homo Sapiens what Homo Sapiens was to Neanderthal, is rather disappointing. (How could it be otherwise?!) But I did appreciate the postulate of a massive and immediate change in the genome, even though the details were disputable and the dismissal of Dawkins‘ perspective poorly defended. From a stylistic perspective, the style is at time heavy, while there are too many chance occurrences, like the main character happening to be in Georgia for a business deal (spoilers, spoilers!) at the times of the opening of collective graves, or the second main character coming upon a couple of Neanderthal mummies with a Sapiens baby, or yet this pair of main characters falling in love and delivering a live mutant baby-girl. But I enjoyed reading it between San Francisco and Melbourne, with a few hours of lost sleep and work. It is a page turner, no doubt! I also like the political undercurrents, from riots to emergency measures, to an effective dictatorship controlling pregnancies and detaining newborns and their mothers.

One important thread in the book deals with anthropology digs getting against Native claims to corpses and general opposition to such digs. This reminded me of a very recent article in Nature where a local Indian tribe had claimed rights to several thousand year old skeletons, whose DNA was then showed to be more related with far away groups than the claimants. But where the tribe was still granted the last word, in a rather worrying jurisprudence.

a discovery that mean can be impacted by extreme values

Posted in University life with tags , , , , , , on August 6, 2016 by xi'an

A surprising editorial in Nature about the misleading uses of impact factors, since as means they are heavily impacted by extreme values. With the realisation that the mean is not the median for skewed distributions…

To be fair(er), Nature published a subsequent paper this week about publishing additional metrics like the two-year median.

no thesis no more?!

Posted in Kids, University life with tags , , , on August 5, 2016 by xi'an

thez“The traditional goal is to demonstrate the candidate’s ability to conduct independent research on a novel concept and to communicate the results in an accessible way. Where the academics differ is on how best to achieve that goal.”

Nature had an editorial and more on the changing nature of the PhD thesis and the possible abandonment of the thing. This is an interesting if radical proposal. There are many cases of highly successful research careers that bypassed the PhD station. Take for instance Julian Besag. On the one hand, what matters most for granting a PhD is the ability to produce independent research that is innovative enough. For this purpose, publication in a serious scientific journal is the right filter. (Serious as opposed to predatory.) Asking referees to review a thesis when the chapters have been published and hence refereed sounds like a waste of time. Nature also mentions the issue of the oral defence, which varies a lot across countries and institutions from inexistent to highly formal. If the relevance of the oral defence is to assess the ability of the candidate to present one’s work in an understandable manner, conferences should do. Except that talks are never assessed. If a speaker is poor, he or she may not get invited again by those who attended the talk. May. But this is somewhat secondary in that examples abound of geniuses who were or are unable to deliver good lectures, with no consequence on the quality of their research and collaborations. Collaborations is actually a sensitive aspect, as more and more papers that make the PhD thesis are written jointly. Evaluations of the contribution of the PhD candidate then get delicate, especially when several PhDs are involved. (I used to refrain from co-signing publications with my students during their thesis, but I have loosened this rule in the past years as I find myself more involved in some projects and hence more eager or impatient to see the outcome completed!)

On the other hand, a PhD thesis may help in getting students to focus on broader issues, when compared with published short papers on marginal improvements in quick succession. But this may not be enough of an incentive. The status of the PhD student is also somewhat unique and provides a buffer between studies and research position, where the student gradually morphs into a researcher (or gives up). If we were to abandon the PhD thesis, there would need to be some equivalent structure to give them status and financial support. However, most places accommodate graduate researchers and the ability to support them for variable periods. It would just mean adjusting for longer durations and some degree of protection…

[The above picture is copied from the site that compiles theses published in France and produces some basic statistics, which are all wrong in my case!]

difficult times for postdocs

Posted in Kids, Travel, University life with tags , , , , , on July 16, 2016 by xi'an

Flight to Montpellier, Dec. 06, 2011In the plane to Warwick on Monday, I was reading my latest issue of Nature and found an interesting editorial on the financial plight of many graduates and post-docs in both the US and the UK (and certainly elsewhere). Who, despite having a fellowship, cannot make ends meet. This is particularly true in expensive cities like London, Oxford or even Paris, where rents force those new researchers to face long commuting hours. The editorial suggests taking extra-jobs to make up for financial difficulties, but this does not sound to me like a particularly pertinent recommendation if it means taking time off one’s research, at the period in a researcher’s career where one’s energy should be mostly directed at the production of papers towards securing a (more) permanent job. Even teaching can prove too time consuming for finishing PhD students. An adequation between the needs of those young researchers and the institutional support they receive would sound like a natural requirement, while graduates looking for fellowship should truly assess the adequation in detail before accepting an offer.Which of course is not always easy. In countries where post-doctoral contracts are not negotiable and are set at a national level (like, e.g., France), checking with earlier fellows is a must. (As it happens or happened, I was quite lucky to spend my post-doctoral years in cheap places with decent support from the local universities, but this is not relevant in today’s environment!)

Sunday morning reading

Posted in Books, Kids, University life with tags , , , , , on June 30, 2016 by xi'an

A very interesting issue of Nature I read this morning while having breakfast. A post-brexit read of a pre-brexit issue. Apart from the several articles arguing against Brexit and its dire consequences on British science [but preaching to the converted for which percentage of the Brexit voters does read Nature?!], a short vignette on the differences between fields for the average time spent for refereeing a paper (maths takes twice as long as social sciences and academics older than 65 half the time of researchers under 36!). A letter calling for action against predatory publishers. And the first maths paper published since I started reading Nature on an almost-regular basis: it studies mean first-passage time for non-Markov random walks. Which are specified as time-homogeneous increments. It is sort of a weird maths paper in that I do not see where the maths novelty stands and why the paper only contains half a dozen formulas… Maybe not a maths paper after all.