Archive for xkcd

Britain re-labeled

Posted in Books, Kids, pictures with tags , , on November 20, 2016 by xi'an

Nature snapshot [Volume 539 Number 7627]

Posted in Books, Statistics, University life with tags , , , , , , , , , , on November 15, 2016 by xi'an

A number of entries of interest [to me] in that Nature issue: from the Capuchin monkeys that break stones in a way that resembles early hominins biface tools, to the persistent association between some sounds and some meanings across numerous languages, to the use of infected mosquitoes in South America to fight Zika, to the call for more maths in psychiatry by the NIMH director, where since prevision is mentioned I presumed stats is included, to the potentially earthshaking green power revolution in Africa, to the reconstruction of the first HIV strains in North America, along with the deconstruction of the “Patient 0” myth, helped by Bayesian phylogenetic analyses, to a cover of the Open Syllabus Project, with Monte Carlo Statistical Methods arriving first [in the Monte Carlo list]….

“Observations should not converge on one model but aim to find anomalies that carry clues about the nature of dark matter, dark energy or initial conditions of the Universe. Further observations should be motivated by testing unconventional interpretations of those anomalies (such as exotic forms of dark matter or modified theories of gravity). Vast data sets may contain evidence for unusual behaviour that was unanticipated when the projects were conceived.” Avi Loeb

One editorial particularly drew my attention, Good data are not enough, by the astronomer Avi Loeb. as illustrated  by the quote above, Loeb objects to data being interpreted and even to data being collected towards the assessment of the standard model. While I agree that this model contains a lot of fudge factors like dark matter and dark energy, which apparently constitutes most of the available matter, the discussion is quite curious, in that interpreting data according to alternative theories sounds impossible and certainly beyond the reach of most PhD students [as Loeb criticises the analysis of some data in a recent thesis he evaluated].

“modern cosmology is augmented by unsubstantiated, mathematically sophisticated ideas — of the multiverse, anthropic reasoning and string theory.

The author argues to always allow for alternative interpretations of the data, which sounds fine at a primary level but again calls for the conception of such alternative models. When discrepancies are found between the standard model and the data, they can be due to errors in the measurement itself, in the measurement model, or in the theoretical model. However, they may be impossible to analyse outside the model, in the neutral way called and wished by Loeb. Designing neutral experiments sounds even less meaningful. Which is why I am fairly taken aback by the call to “a research frontier [that] should maintain at least two ways of interpreting data so that new experiments will aim to select the correct one”! Why two and not more?! And which ones?! I am not aware of fully developed alternative theories and cannot see how experiments designed under one model could produce indications about a new and incomplete model.

“Such simple, off-the-shelf remedies could help us to avoid the scientific fate of the otherwise admirable Mayan civilization.”

Hence I am bemused by the whole exercise, which deepest arguments seem to be a paper written by the author last year and an interdisciplinary centre on black holes also launched recently by the same author.

copy code at your own peril

Posted in Books, Kids, R, Statistics, University life with tags , , , , , on November 14, 2016 by xi'an

I have come several times upon cases of scientists [I mean, real, recognised, publishing, senior scientists!] from other fields blindly copying MCMC code from a paper or website, and expecting the program to operate on their own problem… One illustration is from last week, when I read a X Validated question [from 2013] about an attempt of that kind, on a rather standard Normal posterior, but using an R code where the posterior function was not even defined. (I foolishly replied, despite having no expectation of a reply from the person asking the question.)

ontological argument

Posted in Books, Kids, pictures with tags , , on April 25, 2015 by xi'an

eliminating an important obstacle to creative thinking: statistics…

Posted in Books, Kids, Statistics, University life with tags , , , , , , , , , , , , , on March 12, 2015 by xi'an

“We hope and anticipate that banning the NHSTP will have the effect of increasing the quality of submitted manuscripts by liberating authors from the stultified structure of NHSTP thinking thereby eliminating an important obstacle to creative thinking.”

About a month ago, David Trafimow and Michael Marks, the current editors of the journal Basic and Applied Social Psychology published an editorial banning all null hypothesis significance testing procedures (acronym-ed into the ugly NHSTP which sounds like a particularly nasty venereal disease!) from papers published by the journal. My first reaction was “Great! This will bring more substance to the papers by preventing significance fishing and undisclosed multiple testing! Power to the statisticians!” However, after reading the said editorial, I realised it was inspired by a nihilistic anti-statistical stance, backed by an apparent lack of understanding of the nature of statistical inference, rather than a call for saner and safer statistical practice. The editors most clearly state that inferential statistical procedures are no longer needed to publish in the journal, only “strong descriptive statistics”. Maybe to keep in tune with the “Basic” in the name of the journal!

“In the NHSTP, the problem is in traversing the distance from the probability of the finding, given the null hypothesis, to the probability of the null hypothesis, given the finding. Regarding confidence intervals, the problem is that, for example, a 95% confidence interval does not indicate that the parameter of interest has a 95% probability of being within the interval.”

The above quote could be a motivation for a Bayesian approach to the testing problem, a revolutionary stance for journal editors!, but it only illustrate that the editors wish for a procedure that would eliminate the uncertainty inherent to statistical inference, i.e., to decision making under… erm, uncertainty: “The state of the art remains uncertain.” To fail to separate significance from certainty is fairly appalling from an epistemological perspective and should be a case for impeachment, were any such thing to exist for a journal board. This means the editors cannot distinguish data from parameter and model from reality! Even more fundamentally, to bar statistical procedures from being used in a scientific study is nothing short of reactionary. While encouraging the inclusion of data is a step forward, restricting the validation or in-validation of hypotheses to gazing at descriptive statistics is many steps backward and does completely jeopardize the academic reputation of the journal, which editorial may end up being the last quoted paper. Is deconstruction now reaching psychology journals?! To quote from a critic of this approach, “Thus, the general weaknesses of the deconstructive enterprise become self-justifying. With such an approach I am indeed not sympathetic.” (Searle, 1983).

“The usual problem with Bayesian procedures is that they depend on some sort of Laplacian assumption to generate numbers where none exist (…) With respect to Bayesian procedures, we reserve the right to make case-by-case judgments, and thus Bayesian procedures are neither required nor banned from BASP.”

The section of Bayesian approaches is trying to be sympathetic to the Bayesian paradigm but again reflects upon the poor understanding of the authors. By “Laplacian assumption”, they mean Laplace´s Principle of Indifference, i.e., the use of uniform priors, which is not seriously considered as a sound principle since the mid-1930’s. Except maybe in recent papers of Trafimow. I also love the notion of “generat[ing] numbers when none exist”, as if the prior distribution had to be grounded in some physical reality! Although it is meaningless, it has some poetic value… (Plus, bringing Popper and Fisher to the rescue sounds like shooting Bayes himself in the foot.)  At least, the fact that the editors will consider Bayesian papers in a case-by-case basis indicate they may engage in a subjective Bayesian analysis of each paper rather than using an automated p-value against the 100% rejection bound!

[Note: this entry was suggested by Alexandra Schmidt, current ISBA President, towards an incoming column on this decision of Basic and Applied Social Psychology for the ISBA Bulletin.]

 

xkcd [interview & book]

Posted in Books, Kids, Statistics with tags , , , , , , , on September 14, 2014 by xi'an

Of interest for xkcd fans: What If?: Serious Scientific Answers to Absurd Hypothetical Questions is out! Actually, it is currently the #1 bestseller on amazon! (A physics book makes it to the top of the bestseller list, a few weeks after a theoretical economics book got there. Nice! Actually, a statistics book also made it to the top: Nate Silver’s The SIgnal and the Noise….) I did not read the book, but it is made of some of the questions answered by Randall Munroe (the father of xkcd) on his what if blog. In connection with this publication, Randall Munroe is interviewed on FiveThirtyEight (Nate Silver’s website), as kindly pointed out to me by Bill Jefferys. The main message is trying to give people a feeling about numbers, a rough sense of numeracy. Which was also the purpose of the guesstimation books.

editor’s nightmare

Posted in Books, Kids, pictures, University life with tags , , , , , on June 24, 2014 by xi'an