Archive for Nature

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 theses.fr 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.

a bone of contention

Posted in pictures with tags , , , , , , on May 28, 2016 by xi'an

“In an age in which ancient genomes can reveal startling links between historical populations, we should ask not just whether remains should be reburied, but who decides and on what grounds.”

An article in Nature described the story of fairly old remains (of the Kennewick Man) in North America that were claimed for reburial by several Native American groups and that were found to be closer [in a genetic sense] to groups that were geographically farther (from South America and even Australian aboriginal Australians). What I find difficult to understand (while it stands at the centre of the legal dispute) is how any group of individuals can advance a claim on bones that are 8,000 year old. With such a time gap (and assuming the DNA analysis is trustworthy) the number of individuals who share the owner of the bones as one ancestor is presumably very large and it is hard to imagine all those descendants coming to an agreement about the management of the said bones. Or even that any descendant has any right on the said bones after so many generations which may have seen major changes in the way deceased members of the community are treated. I am thus surprised that a judiciary court or the US government could even consider such requests.

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!)

measuring honesty, with p=.006…

Posted in Books, Kids, pictures, Statistics with tags , , , , , on April 19, 2016 by xi'an


Simon Gächter and Jonathan Schulz recently published a paper in Nature attempting to link intrinsic (individual) honesty with a measure of corruption in the subject home country. Out of more than 2,500 subjects in 23 countries. [I am now reading Nature on a regular basis, thanks to our lab subscribing a coffee room subscription!] Now I may sound naïvely surprised at the methodological contents of the paper and at a publication in Nature but I never read psychology papers, only Andrew’s rants at’em!!!

“The results are consistent with theories of the cultural co-evolution of institutions and values, and show that weak institutions and cultural legacies that generate rule violations not only have direct adverse economic consequences, but might also impair individual intrinsic honesty that is crucial for the smooth functioning of society.”

The experiment behind this article and its rather deep claims is however quite modest: the authors asked people to throw a dice twice without monitoring and rewarded them according to the reported result of the first throw. Being dishonest here means reporting a false result towards a larger monetary gain. This sounds rather artificial and difficult to relate to dishonest behaviours in realistic situations, as I do not see much appeal in cheating for 50 cents or so. Especially since the experiment accounted for a difference in wealth backgrounds, by adapting to the hourly wage in the country (“from $0.7 dollar in Vietnam to $4.2 in the Netherlands“). Furthermore, the subjects of this experiment were undergraduate students in economics departments: depending on the country, this may create a huge bias in terms of social background, as I do not think access to universities is the same in Germany and in Guatemala, say.

“Our expanded scope of societies therefore provides important support and qualifications for the generalizability of these theories—people benchmark their justifiable dishonesty with the extent of dishonesty they see in their societal environment.”

The statistical analysis behind this “important support” is not earth-shattering either. The main argument is based on the empirical cdfs of the gain repartitions per country (in the above graph), with tests that the overall empirical cdf for low corruption countries is higher than the corresponding one for high corruption countries. The comparison of the cumulated or pooled cdf across countries from each group is disputable, in that there is no reason the different countries have the same “honesty” cdf. The groups themselves are built on a rough measure of “prevalence of rule violations”. It is also rather surprising that for both groups the percentage of zero gain answers is “significantly” larger than the expected value of 2.8% if the assumption of “justified dishonesty” holds. In any case, there is no compelling argument as to why students not reporting the value of the first dice would naturally opt for the maximum of the two dices. Hence a certain bemusement at this paper appearing in Nature and even deserving an introductory coverage in the first part of the journal…

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