Archive for March, 2024

Paráid Lá Fhéile Pádraig i Maigh Nuad

Posted in Biographical, Maynooth with tags , , on March 17, 2024 by telescoper

Lá Fhéile Pádraig sona daoibh go léir!

Today being 17th March, it is St Patrick’s Day, so I decided to make the most of my last day in Not-Barcelona and go watch the festivities. Here are some snaps I took on Straffan Road as the Parade made its way into town. As you can see it was a bit overcast, and it was also a bit breezy, but it wasn’t cold and everyone seemed to be enjoying themselves!

As usual, the bin wagon was the star of the show.

If you want some live action, you can see this on my Instagram:

Academic Publishing: Never Mind the Quality…

Posted in Open Access with tags , , , , , , , , on March 16, 2024 by telescoper

I was interested to see that the latest issue of Private Eye contains a short item about academic publishing:

I’ve heard many stories of this type, with publishers putting pressure on their Editorial Boards to allow more papers to be published. This is undoubtedly motivated by the Gold Open Access model in which authors or their institutions are forced to pay thousands of dollars upfront to publish papers. Since the publisher makes an eye-watering profit on every article, why not publish as many as possible? The recent decision by the Royal Astronomical Society adopt this model is highly likely to have a similar effect there, as its journals will be able to increase revenue at the expense of quality. Under the older subscription-based system, publishers could sell their product to libraries on the basis of quality but they no longer need to do that to make a profit.

The academic publishing industry is perverse enough without adding this obvious incentive to lower editorial standards. There are far too many low quality papers being published already, a situation driven not only by the profiteering of the publishing industry but also by the absurd policies of academia itself which require researchers to churn out huge numbers of papers to get promotion, win research grants, etc.

This part of the academic system is definitely broken. To fix it, academic publishing must be taken out of the hands of commercial publishers and put into the care of research institutions whose libraries are perfectly capable of publishing and curating articles on a non-profit basis. But that won’t be enough: we need also to overhaul how we do research assessment. The principles outlined in the San Francisco Declaration on Research Assessment would be a start.

Cavete Quod Idibus Martiis

Posted in Film, History with tags , , on March 15, 2024 by telescoper

I almost forgot that today is the Ides of March , but I’ve remembered now and it’s not too late a priceless bit of cultural history relevant to such this fateful day. This is from the First Folio Edition of Carry On Cleo, and stars the sublime Kenneth Williams as Julius Caesar delivering one of the funniest lines in the whole Carry On series. The joke may be nearly as old as me, but it’s still a cracker…

And if one old joke isn’t enough for you, here is a Caesar Salad:

Scopus Update

Posted in Open Access with tags , , on March 15, 2024 by telescoper

A couple of months ago I blogged about how the Open Journal of Astrophysics had been accepted for listing on Scopus. The process has turned out to be much slower than I was led to believe and the “technical team” responsible for the indexing required much more help than I’d imagined, so we’re not fully there yet. However, I can confirm that we are in the process. This is an excerpt from the accepted titles list which you can find here:

The Scopus indexation process seems to involve processing every article manually, so it’s possible that there will be some errors. Here is a verbatim excerpt from a recent email from the Scopus team that perhaps illustrates why I lack confidence in the process:

We have activated your journal for Scopus indexation and you will be able to find the content indexed online shortly. The title, however, will take some time to have a source page and you will not be able to view it on source list. If the articles indexed on Scopus exceeds 15, Source Page for your title will be automatically created during Scopus browser update. Post which the title will be discoverable on Scopus source list as well.

I hope this clarifies the situation.

My First Maynooth PhD!

Posted in Maynooth, The Universe and Stuff with tags , , , , , , on March 14, 2024 by telescoper

Today saw the viva voce examination of the first PhD student at Maynooth to have completed their degree under my supervision, although in this case the student started his postgraduate degree under another supervisor and I only took over responsibility when that person retired, a few years ago.

Anyway, I delayed my return to Barcelona so I could be present today. It’s not normal practice for the supervisor of a PhD to be present at the examination of the candidate. The rules allow for it – usually at the request of the student – but the supervisor must remain silent unless and until invited to comment by the examiners. I think it’s a very bad idea for both student and supervisor, and the one example that I can recall of a supervisor attending the PhD examination of his student was a very uncomfortable experience. My presence today was limited to supplying a couple of anticipatory bottles of champagne and then waiting nervously for the examination to finish.

I always feel nervous when a student of mine is having their viva voce examination, probably because I’m a bit protective and such an occasion always brings back painful memories of the similar ordeal I went through thirty-odd years ago. However, this is something a PhD candidate has to go through on their own, a sort of rite of passage during which the supervisor has to stand aside and let them stand up for their own work.

The examination turned out to be quite a long one – about three and a half hours – but ended happily. Unfortunately, I had to leave the celebrations early in order to do yet another Euclid-related Zoom call but when that was over I was able to find the pub to which everyone had adjourned and had a pint there with them. I have a feeling the celebrants might make a night of it tonight, but I’m a bit too tired after recent exertions to join them.

The student’s name, by the way, is Aonghus Hunter-McCabe and the title of the thesis is Differential geometric and general relativistic techniques in non-relativistic laboratory systems. If you’re looking for a postdoc to work in related areas then Aonghus might just be the person you want!

P.S. About a decade ago I did a post on the occasion of the PhD examination of another student of mine, Ian Harrison. I found out recently that Ian now has a permanent position at Cardiff University. Congratulations to him!

Desktop – John J. Ronan

Posted in Poetry with tags , , on March 14, 2024 by telescoper

I’m a bit jetlagged and have a busy day ahead, but fortunately I found this interesting and vaguely relevant poem in an old copy of the TLS last night, so will share it in lieu of a proper post.

Travel Travails

Posted in Barcelona, Biographical with tags , , , on March 13, 2024 by telescoper

I’m sitting in Heathrow Airport Terminal 2 waiting for a flight to Dublin to complete the return home from Phoenix. The transatlantic part of this journey went pretty well despite an unpromising start. The terminal at Phoenix was incredibly crowded, and the gate area far too small to accommodate the number of passengers on the flight. The Club World lounge was completely full and operating a wait list just to get in. I waited for 30 minutes to enter and then gave up without succeeding. Had I actually paid a business class fare I would have been very angry about that. The general overcrowding led to my flight taking off about 30 minutes late, but at least that didn’t get significantly worse and I got to Heathrow with plenty of time to make my connection.

I have to admit that the fatigue and disorientation resulting from the excessive travel I’ve been doing over the past few weeks is getting to me a bit. I don’t think I’m cut out for the jet set! It’s not quite over yet, either. After flying back to Dublin I will spend a few days in Maynooth to recover and celebrate the (predicted) success of a PhD student whose examination is tomorrow, then fly back to Barcelona. Fortunately that’s just a short-haul flight and then I’ll be able to settle there until at least July.

Update: I got back to a very rainy Maynooth safely and ahead of time: I managed to get a Hopper bus I should have missed, but which was 10 minutes late!

New Publication at the Open Journal of Astrophysics

Posted in OJAp Papers, Open Access, The Universe and Stuff with tags , , , , , on March 12, 2024 by telescoper

It’s my last morning in Phoenix and since I was too busy at the weekend to post the usual update from the Open Journal of Astrophysics I will do so now, before I go to the Airport for my flight home.

Looking at the workflow I see that there is a considerable backlog of papers that have been accepted but are waiting for the authors to put the final version on arXiv.  As a result there is only one paper to report for last week, being the 17th paper in Volume 7 (2024)  and the 132nd altogether; it was published on March 6 2024. I expect more soon!

The title of the latest paper is “Bayesian analysis of a Unified Dark Matter model with transition: can it alleviate the H0tension?” and it  is in the folder marked Cosmology and NonGalactic Astrophysics.  The article presents an investigation using Bayesian techniques of a specific cosmological model, in which dark matter and dark energy are aspects of a single component, with particular emphasis on the Hubble tension.

The authors are seven in number: Emmanuel Frion (University of Helsinki, Finland, and Western University, Canada); David Camarena (University of New Mexico, USA); Leonardo Giani (University of Queensland, Australia); Tays Miranda (University of Helsinki and University of Jyväskylä, both in Finland); Daniele Bertacca (Università degli Studi di Padova, Italy); Valerio Marra (Universidade Federal do Espírito Santo, Brazil and Osservatorio Astronomico di Trieste, Italy);
and Oliver F. Piattella (Università degli Studi dell’Insubria, Como, Italy).

Here is the overlay of the paper containing the abstract:

 

You can click on the image of the overlay to make it larger should you wish to do so. You can also find the officially accepted version of the paper on the arXiv here.

 

Irrationalism and Deductivism in Science

Posted in Bad Statistics, The Universe and Stuff with tags , , , , , , , , , , , , , , on March 11, 2024 by telescoper

I thought I would use today’s post to share the above reading list which was posted on the wall at the meeting I was at this weekend; it was only two days long and has now finished. Seeing the first book on the list, however, it seems a good idea to follow this up with a brief discussion -largely inspired by David Stove’s book – of some of the philosophical issues raised at the workshop.

It is ironic that the pioneers of probability theory, principally Laplace, unquestionably adopted a Bayesian rather than frequentist interpretation for his probabilities. Frequentism arose during the nineteenth century and held sway until recently. I recall giving a conference talk about Bayesian reasoning only to be heckled by the audience with comments about “new-fangled, trendy Bayesian methods”. Nothing could have been less apt. Probability theory pre-dates the rise of sampling theory and all the frequentist-inspired techniques that modern-day statisticians like to employ.

Most disturbing of all is the influence that frequentist and other non-Bayesian views of probability have had upon the development of a philosophy of science, which I believe has a strong element of inverse reasoning or inductivism in it. The argument about whether there is a role for this type of thought in science goes back at least as far as Roger Bacon who lived in the 13th Century. Much later the brilliant Scottish empiricist philosopher and enlightenment figure David Hume argued strongly against induction. Most modern anti-inductivists can be traced back to this source. Pierre Duhem has argued that theory and experiment never meet face-to-face because in reality there are hosts of auxiliary assumptions involved in making this comparison. This is nowadays called the Quine-Duhem thesis.

Actually, for a Bayesian this doesn’t pose a logical difficulty at all. All one has to do is set up prior probability distributions for the required parameters, calculate their posterior probabilities and then integrate over those that aren’t related to measurements. This is just an expanded version of the idea of marginalization, explained here.

Rudolf Carnap, a logical positivist, attempted to construct a complete theory of inductive reasoning which bears some relationship to Bayesian thought, but he failed to apply Bayes’ theorem in the correct way. Carnap distinguished between two types or probabilities – logical and factual. Bayesians don’t – and I don’t – think this is necessary. The Bayesian definition seems to me to be quite coherent on its own.

Other philosophers of science reject the notion that inductive reasoning has any epistemological value at all. This anti-inductivist stance, often somewhat misleadingly called deductivist (irrationalist would be a better description) is evident in the thinking of three of the most influential philosophers of science of the last century: Karl PopperThomas Kuhn and, most recently, Paul Feyerabend. Regardless of the ferocity of their arguments with each other, these have in common that at the core of their systems of thought likes the rejection of all forms of inductive reasoning. The line of thought that ended in this intellectual cul-de-sac began, as I stated above, with the work of the Scottish empiricist philosopher David Hume. For a thorough analysis of the anti-inductivists mentioned above and their obvious debt to Hume, see David Stove’s book Popper and After: Four Modern Irrationalists. I will just make a few inflammatory remarks here.

Karl Popper really began the modern era of science philosophy with his Logik der Forschung, which was published in 1934. There isn’t really much about (Bayesian) probability theory in this book, which is strange for a work which claims to be about the logic of science. Popper also managed to, on the one hand, accept probability theory (in its frequentist form), but on the other, to reject induction. I find it therefore very hard to make sense of his work at all. It is also clear that, at least outside Britain, Popper is not really taken seriously by many people as a philosopher. Inside Britain it is very different,and I’m not at all sure I understand why. Nevertheless, in my experience, most working physicists seem to subscribe to some version of Popper’s basic philosophy.

Among the things Popper has claimed is that all observations are “theory-laden” and that “sense-data, untheoretical items of observation, simply do not exist”. I don’t think it is possible to defend this view, unless one asserts that numbers do not exist. Data are numbers. They can be incorporated in the form of propositions about parameters in any theoretical framework we like. It is of course true that the possibility space is theory-laden. It is a space of theories, after all. Theory does suggest what kinds of experiment should be done and what data is likely to be useful. But data can be used to update probabilities of anything.

Popper has also insisted that science is deductive rather than inductive. Part of this claim is just a semantic confusion. It is necessary at some point to deduce what the measurable consequences of a theory might be before one does any experiments, but that doesn’t mean the whole process of science is deductive. He does, however, reject the basic application of inductive reasoning in updating probabilities in the light of measured data; he asserts that no theory ever becomes more probable when evidence is found in its favour. Every scientific theory begins infinitely improbable, and is doomed to remain so.

Now there is a grain of truth in this, or can be if the space of possibilities is infinite. Standard methods for assigning priors often spread the unit total probability over an infinite space, leading to a prior probability which is formally zero. This is the problem of improper priors. But this is not a killer blow to Bayesianism. Even if the prior is not strictly normalizable, the posterior probability can be. In any case, given sufficient relevant data the cycle of experiment-measurement-update of probability assignment usually soon leaves the prior far behind. Data usually count in the end.

The idea by which Popper is best known is the dogma of falsification. According to this doctrine, a hypothesis is only said to be scientific if it is capable of being proved false. In real science certain “falsehood” and certain “truth” are almost never achieved. Theories are simply more probable or less probable than the alternatives on the market. The idea that experimental scientists struggle through their entire life simply to prove theorists wrong is a very strange one, although I definitely know some experimentalists who chase theories like lions chase gazelles. To a Bayesian, the right criterion is not falsifiability but testability, the ability of the theory to be rendered more or less probable using further data. Nevertheless, scientific theories generally do have untestable components. Any theory has its interpretation, which is the untestable baggage that we need to supply to make it comprehensible to us. But whatever can be tested can be scientific.

Popper’s work on the philosophical ideas that ultimately led to falsificationism began in Vienna, but the approach subsequently gained enormous popularity in western Europe. The American Thomas Kuhn later took up the anti-inductivist baton in his book The Structure of Scientific Revolutions. Kuhn is undoubtedly a first-rate historian of science and this book contains many perceptive analyses of episodes in the development of physics. His view of scientific progress is cyclic. It begins with a mass of confused observations and controversial theories, moves into a quiescent phase when one theory has triumphed over the others, and lapses into chaos again when the further testing exposes anomalies in the favoured theory. Kuhn adopted the word paradigm to describe the model that rules during the middle stage,

The history of science is littered with examples of this process, which is why so many scientists find Kuhn’s account in good accord with their experience. But there is a problem when attempts are made to fuse this historical observation into a philosophy based on anti-inductivism. Kuhn claims that we “have to relinquish the notion that changes of paradigm carry scientists ..closer and closer to the truth.” Einstein’s theory of relativity provides a closer fit to a wider range of observations than Newtonian mechanics, but in Kuhn’s view this success counts for nothing.

Paul Feyerabend has extended this anti-inductivist streak to its logical (though irrational) extreme. His approach has been dubbed “epistemological anarchism”, and it is clear that he believed that all theories are equally wrong. He is on record as stating that normal science is a fairytale, and that equal time and resources should be spent on “astrology, acupuncture and witchcraft”. He also categorised science alongside “religion, prostitution, and so on”. His thesis is basically that science is just one of many possible internally consistent views of the world, and that the choice between which of these views to adopt can only be made on socio-political grounds.

Feyerabend’s views could only have flourished in a society deeply disillusioned with science. Of course, many bad things have been done in science’s name, and many social institutions are deeply flawed. But one can’t expect anything operated by people to run perfectly. It’s also quite reasonable to argue on ethical grounds which bits of science should be funded and which should not. But the bottom line is that science does have a firm methodological basis which distinguishes it from pseudo-science, the occult and new age silliness. Science is distinguished from other belief-systems by its rigorous application of inductive reasoning and its willingness to subject itself to experimental test. Not all science is done properly, of course, and bad science is as bad as anything.

The Bayesian interpretation of probability leads to a philosophy of science which is essentially epistemological rather than ontological. Probabilities are not “out there” in external reality, but in our minds, representing our imperfect knowledge and understanding. Scientific theories are not absolute truths. Our knowledge of reality is never certain, but we are able to reason consistently about which of our theories provides the best available description of what is known at any given time. If that description fails when more data are gathered, we move on, introducing new elements or abandoning the theory for an alternative. This process could go on forever. There may never be a final theory. But although the game might have no end, at least we know the rules….

Broken Science Initiative

Posted in Bad Statistics with tags , , , , , , on March 10, 2024 by telescoper

This weekend I find myself at an invitation-only event in Phoenix, Arizona, organized by the Broken Science Initiative and called  The Broken Science Epistemology Camp. I flew here on Thursday and will be returning on Tuesday, so it’s a flying visit to the USA.  I thank the organizers Greg Glassman and Emily Kaplan for inviting me. I wasn’t sure what to expect when I accepted the invitation to come but I welcomed the chance to attend an event that’s a bit different from the usual academic conference. There are some suggestions here for background reading which you may find interesting.

Yesterday we had a series of wide-ranging talks about subjects such as probability and statistics, the philosophy of science, the problems besetting academic research, and so on. One of the speakers was eminent psychologist  Gerd Gigerenzer, the theme of whose talk was the use of p-values in statistic and the effects of bad statistical reasoning in reporting research results and wider issues generated by this. You can find a paper covering many of the points raised by Gigerenzer here (PDF).

I’ve written about this before on this blog – see here for example – and I thought it might be useful to re-iterate some of the points here.

The p-value is a frequentist concept that corresponds to the probability of obtaining a value at least as large as that obtained for a test statistic under a “null hypothesis”. To give an example, the null hypothesis might be that two variates are uncorrelated; the test statistic might be the sample correlation coefficient r obtained from a set of bivariate data. If the data were uncorrelated then r would have a known probability distribution, and if the value measured from the sample were such that its numerical value would be exceeded with a probability of 0.05 then the p-value (or significance level) is 0.05.

Whatever the null hypothesis happens to be, the way a frequentist would proceed would be to calculate what the distribution of measurements would be if it were true. If the actual measurement is deemed to be unlikely (say that it is so high that only 1% of measurements would turn out that big under the null hypothesis) then you reject the null, in this case with a “level of significance” of 1%. If you don’t reject it then you tacitly accept it unless and until another experiment does persuade you to shift your allegiance.

But the p-value merely specifies the probability that you would reject the null-hypothesis if it were correct. This is what you would call making a Type I error. It says nothing at all about the probability that the null hypothesis is actually a correct description of the data or that some other hypothesis is needed. To make that sort of statement you would need to specify an alternative hypothesis, calculate the distribution based on it, and determine the statistical power of the test, i.e. the probability that you would actually reject the null hypothesis when the alternative hypothesis, rather than the null, is correct. To fail to reject the null hypothesis when it’s actually incorrect is to make a Type II error.

If all this stuff about p-values, significance, power and Type I and Type II errors seems a bit bizarre, I think that’s because it is. It’s so bizarre, in fact, that I think most people who quote p-values have absolutely no idea what they really mean. Gerd Gigerenzer gave plenty of examples of this in his talk.

A Nature piece published some time ago argues that in fact that results quoted with a p-value of 0.05 turn out to be wrong about 25% of the time. There are a number of reasons why this could be the case, including that the p-value is being calculated incorrectly, perhaps because some assumption or other turns out not to be true.  For instance, a widespread example is assuming that the variates concerned are normally distributed. Unquestioning application of off-the-shelf statistical methods in inappropriate situations is a serious problem in many disciplines, but is particularly prevalent in the social sciences when samples are also typically rather small.

The suggestion that this issue can be resolved  by simply choosing stricter criteria, i.e. a p-value of 0.005 rather than 0.05, does not help because the p-value is an answer to a question about what the hypothesis says about the probability of the data, which is quite different from that which a scientist would really want to ask, namely what the data have to say about a given hypothesis. Frequentist hypothesis testing is intrinsically confusing compared to the logically clearer Bayesian approach, which does focus on the probability of a hypothesis being right given the data, rather than on properties that the data might have given the hypothesis. If I had my way I’d ban p-values altogether.

The p-value is just one example of a statistical device that is too often applied mechanically without real understanding, as a black box, and which can be manipulated through data dredging (or “p-hacking”). Gerd Gigerenzer went on to bemoan the general use of “mindless statistics”, the prevalence of “statistical rituals” and referred to much statistical reasoning as “a meaningless ordeal of pedantic computations”. It

Bad statistics isn’t the only thing wrong with academic research, but it is a significant factor.