Causation, Correlation, And The Perfection Of Science

The Director of STATS.org, a professor of mathematical sciences, wrote in Causation vs Correlation, how journalists and others have the problem of how one establishes causality – and avoid misleading the public.

Though a controlled study?

Say for example you give one set of people Apples and the other group something that seems superficially like apples.

If all the Apples group got Dyspepsia and the control group didn’t, we’d have a jolly good excuse to believe Apples cause Dyspepsia.

But what if Apples cause Burping which causes Collywobbles which then causes Dyspepsia… and yet if you could prevent B or C in the chain, then D didn’t happen? Where exactly has your A “causes” D gone now? Is it now wrong? What if B and C can never be prevented? Would A cause D after all? What if B and C could be prevented but it never happens naturally and no-one knows how to do it and won’t until 2099? Now not even Uzoma’s clever comment that “x causes y if the lagged values of x improve the predictability of the current value of y”, seems totally reliable.

The confused sadness we feel at this point is called philosophy. But the more we ponder it, the more interesting and entertaining it becomes. One cause of philosophy is when concepts we thought were single identical blocks, turn out to come in different kinds. When your concept of X differs from ours, you can have a war. Even if everyone agreed (never happens), you may realise a concept contains moving or separable parts. You can then get a multi-sided war in your own mind, since our knowledge is in the form of networks of nested rules, and some rules want to stay the same and others want to change. It’s mainly conscientious thoughtful people this seriously affects, though it may throw anyone into doubt, some way down the line, if they remember the confusion, and have to make a serious decision.

Sometimes it helps to see exactly what is happening, even if on lifting the lid or getting out and looking underneath, the picture becomes complex. I find it helpful to reveal the view that knowledge is a system of models that enable us to predict the future, and predict our best actions to ensure individual and multi-generational survival, and their proxy: happiness. This makes things easier because it explodes the whole trouble-making concept of “cause”. It’s not about a real “truth”. It’s about strategies that people, animals, plants and other agents can do or should do to choose their best behaviour.

When an atom bomb explodes, the “unavoidability” of the sequence of events it follows is only the one we impose. Every sub-atomic particle is working out its own salvation on its own with no memory of what happened in the past and no sense of individual or group duty. The fact that airborne nuclear explosions always seem to cause a mushroom cloud, is just the way it always turns out, and always comes as a complete surprise to all the particles involved. The rule, and the fact, are concepts created by us. Facts, rules and truths are only psychological entities that nature has allowed us to create and use, to help us survive. They’re not really even engineering or scientific entities. Truth is like the image formed in a camera. It does depend on the outside world but it wouldn’t happen at all without the camera. If so, it wouldn’t be easy for entities like us to tell the difference between the concepts of absolute truth, and a subconscious mental process that gives us the feeling of a real thing out there in the world, like a (potentially erroneous) visual image.

That ridiculous mush now gives us a sound foundation on which we can build our truth/causality/etc processing machine plant, because it has dissolved the concepts of absolute truth/causality/etc. Now we only need to find handy rules by which we can create models or rules to deal with our observations and other aspects of the world. The first gift it delivers is the answer to why no-one has ever been able to nail truth, causality, the best way to establish a fact, etc. A truth is a model of a bit of the world we are prepared to rely on. It doesn’t make sense without the rest of our model of the world, and our bits of model change over time and differ from others’.

So we only have to make up some handy rules on how best to do scientific experiments, given limits on time, expense, and reliability requirements. We don’t have to find and prove strategies that ensure we’re doing the best possible thing. When people give up on finding an absolutely perfect strategy, it’s not a failing. There is no perfect strategy.

Nonetheless the rumour that there are cells in a rat’s brain that fire when it thinks it has learned a causality, are justifiable. It may certainly feel it has established a causality, and that process will no doubt help ratdome survive. We may well have somewhat similar cells. When they fire in our brain or in a rat’s it doesn’t need to mean an absolute truth has been discovered, and that doesn’t matter. It helps us survive, or the process does in the long run. We are prepared to treat it as a truth. It works. It will never be perfect and it doesn’t matter.

This is a disruptive idea worth billions. There is a rumour that facts can only be produced through a somewhat secretive process controlled until recently by publishing companies, and involving subjective unpaid opinions of unelected individuals whose expertise is arbitrarily accepted. Those individuals are/were social contacts of workers in those companies, but it so happens that the proportion of them that are saints is exactly the same as the proportion that are perfect philosophers. If the process is valid that proportion is 100%. It has a lot in common with selecting a pope, and this is because they are both typical power-brokering behaviours of humans. The extent to which the publishing industry has been imposing this process and its justification on the fact creation industry, is not widely known, but if wouldn’t be if it were done well. It has been done well enough for people to believe the necessity for the publishing industry is a fact and always has been, although the deception and its name have only been around since the 1970’s. It has been done so well that this process is believed by some to be the sine qua non of science. It has been done so well that another definition of science, the careful execution of controlled experiments, has repeatedly determined that the publisher-intimate process is perhaps the most corrupted and corrupting currently accepted process science has ever studied, and actively works against the best new scientific theories… and yet, it is either the foundation of science, or an essential pillar of it.

How weird it would be if science violated its own principles! How unusual it would be for people not to think things through for themselves, and not to ask awkward questions. If you could see through all this, and even worse, could tell that you had to satisfy managers whom you knew also knew it but followed it regardless, it would be like living in The Handmaid’s Tale or 1984.

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Hey! A May Hay Holiday! Kiri Bloom Walden and Helen Castor

Perhaps an hour spent laughing at badstockphotosofmyjob late on Monday night prepared me for a bit of frivolity, so when I noticed Helen Castor was talking at the Hay festival the next day, I checked out the programme of speakers. Rose Tremaine offered a catalogue of horrible things that had happened to her so I was glad that was too early the next morning for me to get to. Helen Castor was talking about Queen Elizabeth I, but surely that would be just like a TV programme? However there were two speakers on storytelling-type themes, and these looked like just the kind of thing a Top Notch blogger should be on top of! I decided to sleep on it, and if I woke up early enough…

A thirty-five minute flurry of Hay Fest programme speed-reading, Google Maps and Traveline (shocking how slickly G Maps manages to do public transport now!), washing, dressing, lunch-packing, even managed egg on toast, and I was on the train. Just after I’d bought my ticket I learned with sadness that both Traveline and Google Maps thought there were no buses back from Hay to Hereford after midday. And this is what Hay railway station currently looks like:

Hay-on-Wye railway station nowadays. Looks like we missed the last train. By Ben Brooksbank, CC BY-SA 2.0 via wikipedia.

Hay-on-Wye railway station nowadays. Looks like we missed the last train. By Ben Brooksbank, CC BY-SA 2.0 via wikipedia.

I seemed to be heading for Serious Adventure land.

Couldn’t get in to the “HD39. Jen Lunn Read for Good: Secrets of the Storytelling Universe”, so I went to HC’s QEI talk instead. Unlike the other two talks that were in rooms big enough for about 20, Helen Castor’s hall had room for about 2,000 , and I must have got one of the last places. It were Grand. She revealed to us that Elizabeth was not only very canny, but that it was only through her unusual intelligence and self-control that she managed to avoid being killed (as Helen usually referred to it, as in the case of Elizabeth’s mother Anne Boleyn, instead of “executed”). Elizabeth would take up a carefully considered and prepared position and defend it faultlessly to the death, or in her case, to the avoidance of death. More than once The Authorities very strongly suspected her of being involved in conspiracies but just couldn’t quite pin anything on her. She also seems never to have spoken of her mother, only praised her father.

Elizabeth I's locket ring with minature of mum Anne Boleyn.  Click pic for original from theanneboleynfiles

Elizabeth I’s locket ring with minature of mum Anne Boleyn. Click pic for original from theanneboleynfiles

And yet… she had the most delightful signet ring which opened to display a tiny portrait of her mother and someone else – not dad. That ring is kept very carefully under wraps somewhere and not even HC has been able to see it, although it was once loaned to an exhibition. Afterwards, one of the questions was about that ring. An Absolutely Gorgeous Jewel, as that bloke on the Antiques Roadshow might say. The Guardian’s view on it.

HC has recently started showing us unfailingly entertaining extracts from the Ladybird historical books, on Twitter, and her talk here started with the Ladybird Elizabeth I. Page one shows Anne Boleyn holding the newly born Elizabeth I wrapped in swaddling clothes I think they’re called, with Henry VIII looking on. Anne is doting, but although Helen described Henry as being portrayed not too badly in the book, he is glaring nastily at Anne and the baby, and as the text reports, he wasn’t pleased it wasn’t a son. Elizabeth’s older sister Mary was described as a different sort of person (yup, catholic), and, to much mirth, Helen read out that “Henry had been married before”. Yup, many of the audience seemed to have heard about that, by the sound of it 🙂 . I think they must have enjoyed writing those Ladybird books.

But I was wrong about it being like TV programme. It wasn’t, but it was clear that HC is an accomplished lecturer, expertly taking slow half steps back from the lectern from time to time help the legs with the standing, and speaking very easily. Into this hour she packed well over two hours-worth of TV time, but no-one was ever anything less than wrapt. She does “lady” very well in her TV appearances, but it’s clear from her footballing tweets she’s some way towards being a tomboy. It was a hot day and we discovered she has a tomboy’s knees 🙂 . I like that in a celebrity historian. Judging by the audience response at the end, we were all very pleased with her. She’s very able but seems to have no nastiness. I think she was slightly surprised by the extended applause at the end; she said it was the first time she’d been at Hay (as a speaker I presume). I’m sure they’d be happy to have her back. As usual, the unfair treatment of women was a recurring theme, and one of her comments that will bear repeating was: “No-one ever seems to accuse Henry VIII of being bossy and emotional”. Helen Castor has written the Elizabeth I book, in the 25,000 word Penguin Monarch series. See if you agree with The Guardian’s view on it.

I filled the two hours to the next talk with fried squid and chips, and a £4 ice-cream, but as people I was chatting to agreed, it was a holiday after all. They also agreed it was full of almost exclusively Radio 4 listeners-type people. Remembering Mickey Flanagan’s joke about places “with atmosphere” having no “working-class” people, I always feel rather guilty at Hay – but it doesn’t stop me enjoying it – even basking in it. While I was wandering about, expertly licking my ice-cream, a few people started giving me funny looks. Only later did I realise that despite my care and attention, I’d dropped four trails of melted ice-cream down my dark shirt :-S . However I was able to discover some of the fascinating stands there: Jackie Morris had a crowd round her desk full of otters.

Jackie Morris' Otters of the aphabet.

Jackie Morris’ Otters of the aphabet. Hay 2018.


Jackie Morris' names of the otter.  Hay 2018.

Jackie Morris’ names of the otter. Hay 2018.


I think I may just have missed her drawing a new full-sized one with an ink-soaked piece of sponge. Fablus. Check out her Otters of the alphabet http://www.jackiemorris.co.uk/blog/more-on-the-language-of-liquid/

She illustrates with gold-leaf too.

Some of Jackie Morris' stuff at Hay 2018.

Some of Jackie Morris’ stuff at Hay 2018.


Jackie Morris illustrated books Hay 2018.

Jackie Morris illustrated books Hay 2018.

There was Mari Thomas there, and what most caught my eye was a sort of parchment effect made of gold or silver, with the words disappearing through a threadbare gold or silver fabric.

Mari Thomas bookmark showing her eroded gold or silver parchment design

Mari Thomas bookmark showing her eroded gold or silver parchment design

In the second talk I attended, Kiri Bloom Walden took us through the four-minute Scene d’Amour clip from Hitchcock’s “Vertigo” where James Stewart meets a woman who is supposed to be imitating a lost love of his. There was such a lot of film culture crammed into this. First she explained that westerners automatically become expert in standard film technique, so that when it’s violated, as it often is in horror films, it has quite a powerful effect. There’s a thing called film language, and also just langue. Didn’t quite fully understand that, but for example during a conversation, you get the view from behind one person’s shoulder at the other person’s face and then vice versa: “shot reverse shot”. Not doing that in the scene added disquiet. Also you expect to have a quick glimpse round a room upon entering it, but Hitchcock denies us that in the Vertigo scene. He spent time with the German film makers as his careeer was starting, and was influenced by Fritz Lange. Apparently a director who likes to control everything is called an auteur, though interestingly, once Hitchcock had had full control over the casting, he tended to give the actors surprisingly free reign. KBW showed the use of shadow and colour in the form of a green mist, harking back to a graveyard scene earlier in the film. Also, there were three doors in the bedroom in the later part of the scene, which was supposed to be ominous. One of them seemed to have a window in it, a bit like some kind of hospital or something.

The music was compsed by Bernard Hermann, who also scored Psycho and Taxi Driver, and as KBW said, the music made a huge contribution to Hithcock’s films – for example the stabbing music in the stabbing scene in Psycho. Bernard Hermann was a topic in Radio 4’s The Film Programme this week, discussed by composer Neil Brand, with Francine Stock. I was surprised to hear Hermann described as “minimalist”; even I noticed the huge triumphant Wagnerian crescendo in the central point of the scene.

I have to say the full effect of the scene was never going to work for me because though I could see the woman was affecting Stewart’s character, the style in which Hitchcock likes to portray his central women characters usually drains them of all sex-appeal for me, for example in this clip. Should say though that Anna Massey in Frenzy was an exception. I was also pleased to hear that though Martin Scorsese (or was it the other one?) had this as one of his favourite films, he often felt quite confused by it – as I often am with some Hitchcock films. Probably was Scorsese since he’d used the same composer …who died the day after finishing recording the Taxi Driver music.

Anyway, Fan TASTIC Day out, and not a single Y chromosome between any of the main people who made it for me what it was. And what made it perfect was that there actually is a frequent bus service back to Hereford during the festival 🙂 .

Hay bus timetable.  Click to enlarge.

Hay bus timetable. Click to enlarge.

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Sabine hasn’t killed Popper

Sabine Hossenfelder – the phenomenology of quantum gravity – has I’m glad to say an interest in philosophy of science… and a popular blog called Backreaction.

In her areas of interest, as in mine, there are problems, but in hers it seems it’s always philosophy’s fault, whereas in mine, I tend to blame the practitioners. I don’t think Popper is The Pooper.

First let’s comment on one of her recent postings (I’ll look at earlier ones in later posts).

“Popper is dead.” “…his philosophy, that a scientific idea needs to be falsifiable, is dead….”

Working steadily towards “falsifiable”… no, “Popper” isn’t dead because there is still nothing to beat hypothetico-deductionism, for which “Popper/Popperism” is often used as a handy label. (I do so shamelessly.) Already in 1908, when Popper was only 6, Student’s t test was judging two theories by comparing what each predicted, against the evidence. If you take the one that best predicts the evidence (‘the treatment had an effect’ vs. ‘the treatment didn’t’) , that’s elementary hypothetico-deduction.

Popperism isn’t exactly the same thing as hypothetico-deductivism, and he didn’t have the last word on it any more than he had the first word. But his philosophy is still basically that of H-D:

Science is the search for theories that best explain or predict the observations.

It’s centered on predicting, and sometimes explaining. It’s not actually centered on testing and falsifying. And testing is a subtle issue, though most people think it’s a cube of concrete. He realised the necessity of rooting out “cheating theories” which can never be disproved; but these aren’t good theories because they tend to be bad at PREDICTING what won’t happen.

Why is the heart of the matter prediction? Lifeforms need to work out what to do, and when to do it. That’s why we remember, feel and think: they help us predict the best things to do at each moment. This process soon starts to involve predicting not just our best choice of actions but also simply “what will happen”. That way we can can base our action on what we think will happen, not only on what has just happened. (Theories that always say “anything can happen now”, are as unhelpful as those saying “anything we do now will be just as good for our survival as anything else”. It would be much clearer if the word “predict” meant that predicting one thing implied other things were predicted not to happen. Perhaps there is a better word, meaning “exclusively predicts”.)

Sabine says that according to Popper a good scientific theory has to be testable. But that’s two things: ‘Good’, and ‘Scientific’.

Before going on to her comments about what it means for a theory to be scientific, it’s vital to realise that testing a theory may only become possible with technology (or statistical or philosophical skills) developed in a thousand years’ time. I’m sure some current archaeological theories, mooted or latent, can only be tested by trawling through DNA held in the soil surrounding specimens. It was NOT unscientific to posit such theories prior to 1953, even though few could envisage such a test before then. Much more damage is done to science through unjustified “testing-related” criticism, than by people proffering “untestable” theories. That’s why I considered it essential to cover Testing thoroughly in my guidelines:

11) An untestable theory is one which is intrinsically logically untestable, not one for which no technique for testing it is yet known to some person, or indeed anyone. Deducing the scope of implications, effects, or influences of a hypothesis (via which it might be tested) can be slow and unending. ‘Untestable’ is a rare category, not to be routinely flung at everyone else’s new theory.

12) Tests a new theory can uniquely pass are best offered, and may be needed for superiority, but not for pseudo-criteria like theory status, false ‘testability’, or truth. Insisting on a mechanism for a theory is a classic error. A theory often inspires the discovery of its mechanisms and special tests.

In other words, you Do Not need to worry about testing until Later. And you shouldn’t need to worry about anyone yelling Can You Test That???!? before you’ve even finished working out what your theory is.

Sabine’s blog post:

“In practice, scientists can’t falsify theories. That’s because any theory can be amended in hindsight so that it fits new data. Don’t roll your eyes – updating your knowledge in response to new information is scientifically entirely sound procedure.”

Indeed, refutation is technically impossible in theory. But the other thing – proof positive – is so much worse. That’s why Popper stressed the importance of judging based on evidence against theories. But although you can’t criticise Popper for preferring “evidence against”, you can criticise him for stressing black-and-white, yes/no refutation judgements. In most sciences, even physics, we have to judge our favourite from a number of possible theories, sometimes none absolutely refutable, and each better at some things than their competitors:

2) The worth of a theory depends on such aspects as accuracy, generality, simplicity, and the degree to which its implications are genuine predictions (and the more surprising the better).

Indeed, a theory as originally stated, might make a wrong prediction, but by twiddling the parameters, it can be made to predict any required observations. Popper hated parameter-twiddling, but having seen how animals learn vital skills from their mistakes, I felt it necessary to offer the reminder:

6) A theory is refuted only when all its reasonable instantiations are refuted, not just one. Fixing faults in a theory can mar its other qualities, yet repair is still basic to knowledge development.

Remember from 2), that a more complex, and less general theory, even though twiddled to be more accurate (as yet), might well lose out. But our rules for theorising must allow theory development: theory development isn’t a once-and-for-all vote, it’s a marathon.

SH herself rightly claims that in practice, theories can be judged to be inferior, rather than absolutely refuted:

“That’s because repeatedly fixed theories become hideously difficult, not to mention hideous, period. What happens instead of falsification is that scientists transition to simpler explanations.”

We judge by use of subtle qualities, and sometimes, indeed usually, using probabilities. Refutation and even falsification are not words I would have chosen. The words I use are:

1) Science is the generation, judging and honing of theories which model (i.e. explain or predict) the best.

Perhaps “refute” has a slightly different, less absolute, meaning in Popper’s native language. SH would be able to answer that better than me.

“But many physicists not only still believe in Popper, they also opportunistically misinterpret the original Popper.”

Yes. The latter is a big problem.

“Even in his worst moments Popper never said a theory is scientific just because it’s falsifiable.”

I think he did. But it was not “in bad moments” because he was trying to address the “demarcation problem”: “What is a scientific theory?” (I think this is to do with the Wittgenstein business of saying you have no right to speak of subjects about which you know nothing/little or whatever; also there were claims that you could deal only with “facts”, which makes as much sense in advanced cognitive technology as dealing with good and evil in biology. That was the context, and as we might now see it, out-of-date detritus, to be polite, that had to be dealt with at the time.)

That question – what is a scientific theory – is COMPLETELY DIFFERENT from What is a GOOD theory. I think SH confuses those two:

“It’s not hard to come up with theories that are falsifiable but not scientific. By scientific I mean the theory has a reasonable chance of accurately describing nature.”

Yup – she does confuse them. It’s a two-stage process: Check first that the theory does not embody some kind of logical barrier to its evalutation (i.e. that it’s testable – but don’t get obsessed with this for reasons I gave above; it’s all right – we don’t have Wittgenstein or the Vienna Circle or Freddy Ayer to worry about now)… and Second: see if it predicts/explains well (works as a good model – see above also).

“If the only argument that speaks for your idea is that it’s compatible with present data and makes a testable prediction, that’s not enough.”

Oh but it is, so long as its qualities like those mentioned in 2) above are met, compared with other theories.

“My idea that Trump will get shot is totally compatible with all we presently know. And it does make a testable prediction. But it will not enter the annals of science, and why is that? Because you can effortlessly produce some million similar prophecies.”

It’s a perfectly good model of the future, assigning a probability to a future event. Doesn’t deal much with scientific issues, but S H has only introduced it as a red herring, and as far as that goes, it works for her. Also, there ARE indeed infinitely many theories that explain the observations we’ve made – amongst them the theories that will one day take physics forwards beyond the current ones.

“In the foundations of physics, compatibility with existing data is a high bar to jump, or so they want you to believe. That’s because if you cook up a new theory you first have to reproduce all achievements of the already established theories.”

That goes without saying. That’s what it means to model as well as competing theories.

“This bar you will not jump unless you actually understand the present theories, which is why it’s safe to ignore the all-caps insights on my timeline.”

Just because you will probably have to understand existing theories to know what observations they already explain, it doesn’t follow that anyone trying hard to get you to learn the basics of practical philosophy of science, is wrong.

S H draws a picture of her science becoming contaminated by crap theories. I can sympathise – two of my sciences have: three areas of palaeontology have been completely destroyed by it, and social psychology has been seriously contaminated. But she’s not helping much, as her use of “predictions” in the following, shows:

“This overproduction of worthless predictions is the theoreticians’ version of p-value hacking.”

She criticises the easy proliferation of theories that in practice can never be tested… because nature’s deeper secrets are harder to get at. That just shows how far her science has got, not that searching for better theories is bad science.

“The point is that the easier it is to come up with predictions the lower their predictive value.”

Never mind about all that or however many theories it may be theoretically possible to come up with, the theories she hates to see proliferating haven’t done the business: they have NOT explained/predicted better than other theories, and that’s all you need to say to disparage them adequately. No need to confuse theorisation with prediction, or to confuse passing the demarcation test with scientific quality, nor even to confuse the likelihood of evidence given a theory with ‘likelihood of a theory being right’:

“In this argument you don’t want to show that the probability for one particular theory is large, but that the probability for any particular theory is small.”

And no need to throw mud at hypothetico-deductivism. H-D is the process of building the best models of the universe we can, and that’s all we can ever do.

It seems she’s written a book on all this. I make the easy prediction that it will damage the widespread understanding of the philosophy of science. But I can sympathise with what she said on her earlier blog post on the book:

“The current situation in the foundation of physics is a vivid example for how science fails to self-correct. The reasons for this failure, as I lay out in this book, are unaddressed social and cognitive biases.”

I can sympathise with that, to put it mildly. As I laid out in my book.

“But this isn’t a problem specific to the foundations of physics. It’s a problem that befalls all disciplines, just that in my area the prevalence of not-so-scientific thinking is particularly obvious due to the lack of data.”

What physics needs is some huge machine built to produce terragigions of new data per second. That should fix it.

“This isn’t a nice book and sadly it’s foreseeable most of my colleagues will hate it.”

Yup, they will.

“By writing it I waived my hopes of ever getting tenure.”

Do you know, I’ve just realised that my chances of ever getting a top place in palaeo at say Berkeley, AMHN or the NHM in London, may have been seriously compromised by saying everyone there were idiots.

“…But I have waited two decades for things to change and they didn’t change and I came to conclude at the very least I can point to the problems I see.”

Seriously now, you tried to do The Right Thing. But another thing you could do is find the people who know some good practical philosophy of science, and listen to them before writing a book on the subject.

I’m sorry to be mean but she’ll never listen to my advice, but if she did say anything it would be cheeky. However there were lots of comments to her post, many interesting. It would be cheap to say that not everyone agrees with her, since she said they wouldn’t at the start. But these are some I’m glad I read, starting with one by a certain ‘gowers’ – a Timothy I’d guess, by the classiness. Soon, another talks of mathematicism , and I think he has a point. It was that that nearly killed neural nets. Panda-girl mentions the demarcation problem, and Jayarava Attwood makes my point about the logical positivists. In between them, SH says she isn’t criticising Popper (only burying him, no doubt). Finally someone says Sean Carroll says don’t worry too much about falsifiability. I don’t like Sean Carroll but he’s right that the testability/urgent falsifiablity idea has gone way past its station. And that poster’s comment about Kuhn, has a point. For example, Kuhn saying what people tend to do (demand you provide an alternative theory once you’ve disproved another’s, for example) has too often been taken as advice on what scientists ought to do.

gowers said…

This discussion reminds me of the question of what makes a good mathematical conjecture. It’s not hard at all to come up with a statement that nobody has any idea how to prove or disprove, and therefore that is (i) consistent with the evidence we have so far and (ii) testable (in the sense that somebody might one day come up with a proof or disproof). But that doesn’t make it a good conjecture. A good conjecture is one that makes surprising and testable predictions.

6:55 PM, November 06, 2017
PhDstudent said…

Nice post. I am reminded of the people who post every possible prediction on Twitter for, e.g., the outcome of the 2020 presidential election, then delete all but the one that turned out to be correct after the event and try to convince people that they were psychic.

7:18 PM, November 06, 2017
bud rap said…

“That’s because repeatedly fixed theories become hideously difficult, not to mention hideous, period.”

Well, that succinctly describes particle physics and cosmology alright. Both disciplines are an unscientific compendium of mathematical fantasias that, in the aggregate, bear only a glancing resemblance to physical reality. And it is that lack of resemblance that makes them both so horrible in scientific terms. Observed reality does not contain the features that are prominent in the standard models.

Of course, to a mathematicist (like Max Tegmark for instance), this does not present a problem because the mathematics is thought to underlie and be determinate of reality. If their mathematical models require fractionally charged particles and dark matter, then such must exist. The absence of evidence is not evidence of absence, as the popular sophistry has it. Reality is deficient, not the models which are, by definition, always correct or at least always correctable.

While Tegmark may be an extreme example, it could be argued that mathematicism is the dominant paradigm in the scientific academy and has been for the better part of the past century. Empirical science no longer constitutes an open ended investigation into the nature of physical reality but is now a mere adjunct of theory, dispatched to remote realms in search of confirmation, no matter how threadbare, for the preferred standard models. For evidence of this look no further than the LHC and LIGO, where grandiose claims, of models triumphant, are spun from minuscule evidence that has been lovingly massaged from enormous piles of carefully pawed over data. Science has become a lab assistant in the department that bears its name.

Sabine, you and Lee Smolin are right to be uneasy with the current situation and it is undoubtedly brave of you to speak up, especially since it has rendered your employment situation difficult. Many Worlds, Parallel Universes and similar vapid theoretical concepts are the direct offspring of mathematicism. But mathematicism is essentially just a kind of modern day secular mysticism. Its objects of concern lie in the supernatural realm of the human imagination, far beyond the reach of proper scientific inquiry.

May I suggest that to defeat mathematicism, if that is your purpose, you need only rise to the defense of empiricism and logic as the foundational elements of science. Math will consequently reacquire its proper relevance as a branch of logic, and an essential modeling tool alongside qualitative analysis. Mathematicism will then be free to slink off to the philosophy department, if they’ll have it.

Best of luck. Your blog is a pleasure to read.

8:25 PM, November 06, 2017
panda-girl said…

I agree with richard the naivetheorist. Falsifiability alone cannot make a theory (or hypothesis) scientific. But if a theory is not falsifiable, using your example, one cannot even amend that theory after a test that is not consistent with its prediction. An unfalsifiable theory cannot not contribute to scientific progress. I am sure you would agree with this.

I believe, if you abandoned the falsifiability criteria, you probably would need to replace it with something else to address the demarcation problem. Do you agree, Sabine?

12:52 AM, November 07, 2017
Sabine Hossenfelder said…

Brian,

I am not criticizing Popper. I’m saying Popper alone isn’t enough.

2:36 AM, November 07, 2017
Jayarava Attwood said…

I read this post yesterday and was too boggled by it to comment. I’m still confused today, but allowing it to sink in.

I think to be fair to Popper one must situate him historically. The falsifiability criteria was a response to the Logical Positivists. They argued that a proposition can only be true if it is verified. And Popper countered with the now famous black swan argument. Philosophical truth cannot be sought by verification; we can only show that something is not true by finding counterexamples. There may always be a black swan waiting to come along and falsify something believed to be true.

Of course Popper did not allow for retrospectively changing one’s prediction to fit new data. And maybe in retrospect, that was a mistake. And science doesn’t really seek the truth, IMO it seeks accuracy of explanation and prediction (some scientists believe that this amounts to truth, but naive realism is another story).

I think I knew that Popper was at least incomplete because of Higgs. The LHC was not made to falsify the predictions of Peter Higgs. It was made to “search for the Higgs boson”. To verify the prediction. A lot of scientists are apparently still logical positivists.

Thanks for making me *think*!

BTW the field in which this process has the largest impact is not physics, but economics. The standard economic models constantly fail to predict the real world, but are tweaked to fit the data retrospectively. Economists believe that if they can do this then they understand what is going on. They fail to predict events like the deepest and longest recession in living memory, but keep their jobs anyway. Because their models can be endlessly tweaked.

5:24 AM, November 07, 2017
Phillip Helbig said…

Sean Carroll and others have argued that we should give up falsifiability as an important criterion in science. I disagree. Any scientific theory has to be falsifiable in principle, pretty much by definition. Some things might not be falsifiable in the short term, but that is no reason not to work on them. But one shouldn’t equate these with things which are not falsifiable, even in principle.

I think Kuhn has done much more harm than Popper. 😐

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Steve Jones Says Low Human Diversity Due To Cultural Evolution

Aaaarghgh!!!!!

But let’s keep calm and start from the beginning…

Your DNA is much more like mine than it should be. There should be variation within a species – there should be because it helps any species survive under challenging evolutionary times, but anyway we should expect a lot of variation in a species with our huge population. Obviously in a bigger population you’d expect more diversity, especially if it had been big a long time. But there’s only as much variation in our 7 billion people as you’d expect in a standard/ideal species with a population of 50,000. Our “Effective Population Size”, as the geneticists say, is about 50,000. That’s smaller than the actual population of chimpanzees. It’s even smaller than their effective population size which is almost always quite a bit smaller than the actual population, for any species.

The old reason was that the Toba volcano in Sumatra erupted 75,000 years ago. Its eruption is undisputed, but the effect on the human genome is not universally accepted (just googled it – Oh! That person started it 🙂 . I might have done at that time if I’d thought of it.) If the eruption almost wiped out the human species, we’d obviously only have a small population at that time, and you can’t hold much genetic diversity in a small population. But we’ll come back to all this and other juicy tangents later. First though…

I can honestly say that since I started using eZvol regularly, my life has changed. Or at least I’ve got much more into genetics. It’s taught me a bit, confirmed a bit, and disproved a bit, but I’ve also started reading a lot of stuff. Anyway I can now say with certainty (as I hope I always could) that evolution stops only when it’s working hard, and then only sometimes. It’s pretty obvious really, that if most of your DNA needs to be exactly as it is for you to survive, then almost any mutations will be “ironed out” of your descendants by evolution, within a very few generations. Evolution will be working hard to keep things the same.

On the other hand, if you have a lot of “junk DNA” (glance over your shoulder before you use that term!), then any old change can happen in it, and stay. The DNA we still have in unused decayed form, that helped us twitch our ears like a cat, can change all it likes and it won’t harm our survival chances or those of our offspring. (A little function remains though – nerve impulses are sent towards our ears but not much happens. They use that to see if people are deaf.) So even if the non-junk DNA – the DNA that actually does something – has its brakes firmly on because you’re already the Best A Man Can Get (your gender and age may vary), your junk DNA will still change randomly and freely. In fact if the mutation rate of your junk DNA is one per generation, then after 1,000 generations, you will have about 1,000 new mutations in it (unless your genome is so small that new mutations start going in on top of old ones.) This even applies to the whole gene pool, even if every individual in the population gets just one mutation. The overall clock for the whole population is still one per year. It occured to me while reading King J L & Jukes I W 1969 “Non-Darwinian evolution”, Science 164:788-98, over the weekend that this isn’t actually as obvious as it sounds when it comes to fixation, but it is true. I trust eZvol more than any geneticist now, but the computer says yes, so it’s yes.

What though, when even your non-junk DNA starts behaving like junk because in the mopdern world no matter how unhealthy you are (or allow yourself to become), you can still raise children? One of my favourite examples is traction. Before 1917 when the Thomas procedure was invented, most died if they broke their femur, but now few do. But importantly, in the modern world this also applies to genetic mutations. Because mutations don’t get swept out now, even those that destroyed our ability to chase down a mammoth and bring it home to our freezing kids so we could make a fire from its bones and use its hide and tusks for a house, Mutations Just Stay. And Build Up. Which means our genetic clock and our genetic variation build up faster when the pressure’s off.

Steve Jones said in “Word of Mouth — Language and Our Genes with Dr Steve Jones Michael Rosen talks to Steve Jones about language and our genes, 23rd Oct. 2017, BBC Radio 4”, that since we adapt more using cultural evolution now, genetic evolution does less, which is why we have low genetic diversity. I just shouted “Oh, GOD!!”. I don’t know what the neighbours thought. It was nearly midnight. Behind his statement is the implication that he knows less about genetics than me. And that’s not good news because he was a professor of genetics at a top university. And of course it means that the BBC’s second favourite genetics expert/pundit knows less about genetics than a well-trained third-year genetics undergraduate, since such a person should know more than me.

Interestingly… most genetics professionals would find Jones’ opinion more shocking than I do since they don’t realise as I do that under some circumstances, this time when evolution is working very hard to adapt to changing environments, the genetic algorithm can actually drive the genetic clock faster than the background mutation rate. John Hawks doesn’t think that it can, and he’s already declared himself against the Jones view that human evolution has slowed (or even stopped; of course JH is actually an anthropologist but it’s true for most geneticists too). I think Jones must be taking the view that when a species needs to change, mutations can be selected for and multiplied throughout the population, driven hard by the forces of evolution… and that without evolutionary force, everything slows down. He’s wrong about the last bit but slightly right about the first bit: under strong evolutionary pressure and relatively low mutation rates, things can speed up – faster than the background mutation rate. It’s complicated by the fact that since most of our genome is junk, genetic drift in the junk often or usually overpowers the rate of change in the non-junk – and the genetic clock in the non-junk isn’t always much faster than in the junk. Also, surprisingly, genetic drift in the NON-junk has quite a considerable effect. I’ve never been keen on the idea of genetic drift, but the more you read, the more you realise its importance… and yet non-drift “evolution-driven” genetic change is still more significant than the average modern geneticist realises. But that’s another story.

What then did cause the low genetic diversity in humans? The story now told is that when modern non-Africans did their Moses thing about 65-70 thousand years ago and crossed the Red Sea into Arabia and beyond (by ‘boat’, though the southern end was narrow since much of the sea’s water was locked up in ice), it was a relatively small group. Perhaps very small. That’s why they didn’t bring much diversity with them. But even though they interbred with the Neanderthals they met in Arabia, and some interbred with the Neanderthals’ near relatives the Denisovans before wiping them out, and some interbred with another group in East Asia where people there still have bucket-seat-shaped incisors they probably got in the process, they still had much less variation than exists in Africa to this day. But of course that doesn’t explain why Africa itself has very low diversity.

The reason is this. The Out Of Africa story is only largely true. Most of our evolution did occur in Africa. It’s now accepted that waves of people long before the final eruption, repeatedly left Africa for the rest of the world, and then got impacted by later waves. But humans didn’t necessarily make the final leap to Homo in Africa. There is every reason to believe the mix of early Homo and pre-Homo fossils Lordkipanidze and others found in Dmanisi in Georgia are better evidence for a transition than anything known from Africa – or perhaps will ever be known, if the transition was indeed outside Africa. Incidentally, the physical variation in the Georgia fossils was large, suggesting to me that Georgia was just a place where physically diverse groups met – not necessarily the centre of anything.

In that case, there will have been a restricted population having left Africa as pre-Homo about 2 million years ago, restricting the diversity, and then a re-invasion back into Africa, maybe as Homo ergaster, shortly afterwards, restricting it again.

It’s also possible that modern humans didn’t exterminate all the non-moderns in Africa as efficiently as we seem to have done elsewhere – the Denisovans may be an example. We didn’t even exterminate or dilute the Neanderthals as quickly as we might for perhaps two reasons: first, the Neanderthals weren’t a push-over. They were much like us, but perhaps a little less keen on tolerating or trying to meet people they didn’t know. That’s in shorthand but it can be defended rigorously. Also, it’s been suggested that they weren’t very interfertile with us, in much the same way that dogs and wolves don’t interbreed anything like as efficiently as they do amongst their own types, as you would know if you’d tried. There was interbreeding but less than there might have been. But the survival of Homo naledi in the heart(-ish) of Africa, and according to rumour, of other types in West Africa who donated genes to moderns, suggests that for say half a million years at a time, at least, we co-existed somewhere in Africa with others, whereas it only took 40,000 years to remove Neanderthals from Europe. Maybe there were types of locations in Africa we prefered to leave to others.

http://garfield.library.upenn.edu/classics1983/A1983RC02000002.pdf

https://cdn.preterhuman.net/texts/science_and_technology/nature_and_biology/Genetics/Evolutionary%20Genetics%202d%20ed%20-%20MAYNARD%20SMITH.pdf

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Isn’t Nature Wonderful!? #001 Praying Mantis and Hummingbird

Put together from the New York Times online article about Tom Vaughan’s pictures:

Praying maintis catching hummingbird

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Ornithoscelida. Note to Matt Baron on Baron et al.

Hi Matt Baron,

Nice to see your work, because it shows what happens in a divergence investigation when you exclude types that lived too long afterwards, which had accumulated numerous interfering irrelevant characters. This is something I’d advocated on forums widely read (in palaeontological terms) since about 2000. It deserved to have been explained more explicitly than you did, as the size of the consequence, and its response, indicate. As this is something that I and very few others had been advocating for years, it would have been nice if you’d cited us:

The Secret Dinobird Story 3.3:

…[I]n careless hands, cladograms can be published where these two types [allosaurs and tyrannosaurs] are brought closer together than they should. In fact, they should never be included in the same cladogram. By following the principle that lines generally agreed to be separate (like the tyrannosaur and allosaur lineages) should never be analysed together, we would help prevent types probably convergent and perhaps even 80 million years apart from flocking unrealistically together and distorting the picture. Each lineage composing an obvious module of its own (e.g. “the tyrannosaurs”) should occupy its own mini-cladogram. Large confused groupings should be split into these mini-cladograms, and from each a very few early representatives should be selected. These fewer representatives, ideally close in time, should then all be analysed together in the overall cladogram without their later forms (Wagner 1998*). This would help deal with for example top predator convergence. Simulations could easily be devised to confirm the need for and effectiveness of this approach.

*Wagner, P.J. (1998) Saturation of cladistic character space – debunking the myth of the infinite. Geol. Soc. Am. Abstracts with program 30, A-326.

But thanks for observing this principle, and not inviting allosaurs and tyrannosaurs. They’ve spoiled so many parties.

I also liked the result simply because it showed there is no such thing as ‘The Cladistic Approach’. That is where you chuck everything in without thinking. There is clearly a multiplicity of ways to run and ruin a cladogram. Already this has caught Padian out – the bloke who always gets invited to write the overview for Nature’s important dinobird papers. You won’t remember but it was he who poured scorn on the possibility of finding feathered dinosaurs, and before that, guessed wrong about pterosaur bipedality. The latter was acceptable at the time, but the former showed he refused to start to consider possibilities unless they were already blatantly undeniable. This time he said that your study was justifyable because you did it the way it’s usually done – done by people like him of course – but thereby denying the nature of scientific research, where novelty is essential. Again he ignores the principle of finding theories that explain the best (and substrategies thereby implied), as the definition of science, and again he implies that it’s what his group does, not what it does, that counts.

But anyway, you didn’t do it the way it’s always been done! But more important is the indication that qualifying in palaeontology is not learning a science but learning a club. Top statistician and scientific standards crusader Andrew Gelman said recently in a blog post about a psychology clique he’s identified as pseudo-scientific: “It’s a guild, man, nuthin but an ivy-covered Chamber of Commerce. Which is fine—restraint of trade is as American as baseball, hot dogs, apple pie, and Chevrolet…. [but] Psychology is not just a club of academics, and “psychological science” is not just the name of their treehouse”, to which commenter Kane replied: “Sure about that? The evidence here is that this is precisely what psychology and psychological science, in fact, are. You (and I!) just wish that weren’t so . . .”. Padian too is clearly as groupist as he is non-scientific, and even if he’d made huge positive contributions to science instead of an overall negative, selecting one summariser time after time after time as Gee does in selecting Padian, insults moral and scientific principles.

That’s why I don’t do the subculture the honour of asking their permission to publish, and I continue to make plans for alternative channels to the Nature/Berkeley abomination. The internet is free, and sometimes free from Padian/Gee-type bias. But to ignore work just because it hasn’t kow-towed to establishment morons is Not science! That’s why you’ve no excuse for not citing me/Wagner. Remember that peer review (as opposed to simply seeking advice) is an invented irrelevance by people who don’t know what science is. Consider also that most prominent dinobird workers in USA/UK/Canada know who I am and are only pretending I don’t exist. (The publication of my book did something a bit weird, sudden and long-lasting to the posting frequencies of the dml. That couldn’t have happened if it hadn’t been noticed by the group as a whole.)

You mention the internet’s reaction. Mickey Mortimer picked holes in your coding of characters etc. but then he picks holes in everyone’s. I do hope he recodes it and produces his own cladogram. Even if he does, it won’t mean your tree is right. I remember reading Mickey’s last posting before his first on your paper. In the comments, his discussion with Marjanovic made me think: “There’s a couple of dodgy characters for you. Have either of them ever even heard of calibration?” You can’t claim scientific status if you haven’t properly compared the tool you rely on (here, cladogenesis) against known and challenging inputs, and noted its response characteristics. Mickey says bootstrapping isn’t as important as people think. In fact bootstrapping seems to be very optimistic – high bootstrapping doesn’t guarantee any validity but low boostrapping warns of likely meaninglessness. But they wouldn’t know this because they can’t think outside their social box and of course they’ve never calibrated bootstrapping or anything else involving cladograms (or anything). Mickey might have started learning about such things if he’d read my book but he hasn’t. If he had, he’d have known which birds other than penguins have no air in their bones (and why). He might even have learned that programmers start counting from 0. When Mike Keesey mentioned this on Mickey’s blog, he received no comment from anyone, not even a cheery hello. The zero issue with TNT seems to be a bit more than that, but zeroing TMK is filthy style by the other commenters. THAT’S why he never criticises their technical blunders from his IT expertise background – because he wants to avoid Being “Othered”.

The internet is set to generate opposition it seems, but they’re not expert tree-surgeons. However your tree might actually be wrong for several reasons: because you’ve wrongly excluded certain types; the root might be wrongly positioned so parts of it might flow in the wrong direction, and of course the topology could be wrong due to e.g. convergence etc.

I expect all those will apply; one piece of evidence is particularly compelling: those waisted slightly hooked pointed teeth of Eoraptor and Laquintasaura shown in your fig 2 c. And where else have we seen them oh yes Archaeopteryx. Which hypercarnivore bequeathed those? It never had a Mesozoic hypercarnivore ancestor with unwaisted teeth and neither did any ornithiscian. So you’re right to suggest the ancestors concerned weren’t specialist carnivores, but omnivory at the root is wrong too. They ate invertebrates (and miniverts) and were almost but not quite invisible to us (as if everything Triassic isn’t!). And the reason they were invisible is that they were very small… and thin boned… and fell into acid soils…

And don’t say there’s no evidence for this: the observation is that the ancestors are mysteriously absent, “Ж10.1: Evidence is those observations not well explained by a theory, or not as well explained by one theory as by another“, and this is so far the only theory that explains the absence. The absence is therefore evidence for this theory.

…Which leads us to primitive pre-feathers and fibres. The first feathers probably weren’t fibrous, fibrous structures might well have evolved more than once from their non-fibrous progenitors, sauropodomorphs might or might not have had fibrous feathers in their ancestry, and all of these are still fully consistent with the observations, as is primitive non-insulatory feathering for all archosaurs.

Such a long way still to go palaeontologically. But there’s plenty of social science of palaeontology to hack through too. The No Reply to Keesey’s comment, and Naish’s instruction in his Tetzoo blog to ignore Dave Peters (even though Peters was at least correct in rejecting the standard basal dinosaur tree, and Naish had implied disapproval of groupism in his Brexit comments)… and Mickey Mortimer doing whatever he did recently to get blocked from Dave Peters’ blog… and Padian’s claim that only what he does is science… and Gee’s refusal to allow Nature to print summaries on dinobird tree papers by anyone with IT expertise… all show that the main name of the game is still groupism (accompanied as usual by incompetence). And if you don’t believe me that groupism combined with IT/stats incompetence is a common problem, ask Gillian Tett.

But I LOVED your use of the word MINDSET!!!! 🙂

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Brussatte’s Pseudoscience in Science 2017

Brussatte continues to occupy a position supposed to be used by a scientist, and has been allowed to write yet another piece of rubbish in Science. He’s commented further on it in Phys.org.

What a mess.

To understand the evolution of a group of animals you need a good family tree, and good trees can be made from analysing DNA in fossils that preserve it. But because evolutionary convergence and reversal appear more in bone shapes than in DNA, Brussatte’s reliance on bone shapes gives wrong family trees. We KNOW this happens: we saw it in the different mammal trees that DNA and bone shapes gave. Brussatte ignores this, having no qualifications or background of any work in the computer science of generating these trees, and being a superb follower of whatever he thinks will go down well with “the group”. What he does fail to follow is any sound hypothetico-deductivism in his work: he never shows any appreciation that backtracking is necessary in theorisation and seems to think that science hops from one fact to another. Even if perfect facts were real they’d be created out of hypotheses; treating every idea as a fact from the start is pseudo science, and could never survive if errors in palaeontology were lethal.

He understands that palaeontology is run as a social game where any CHANGE in an old view is wrong (as it would be if it we had facts instead of having to rely on theories), and because it would annoy those who fear change.

So when he says bird evolution appears to depart from the normal idea of evolution (which he has got right): “a species develops a feature that allows it to do something better; its offspring also express that feature…” and so on till an early minor ability fully develops, and he claims bird flight didn’t do this, he is working from the wrong family trees, and he cannot change his mind.

However a much better real family tree would be distorted by parallelisms and reversals so it would actually resemble the computer-generated trees Brussatte trusts! But he hasn’t the brains to see thus subtlety nor the integrity to respond to it if he did.

In fact the sensible family tree DOES progress nicely from early gliding forms to later flapping ones, many of which lost the power of flight just like ostriches did – so his comment on one site that the ostrich mimic dinosaurs couldn’t have evolved wings for flight as they couldn’t have flown with them is ridiculous. His claim that “anatomical analysis suggests such a development likely had nothing to do with flying” comes from analyses of creatures living long after the first fliers and so had nothing to do with the earliest fight, and the study he emphasises most (Dececchi et al. 2016) refused even to CONSIDER the possibility that flight evolved from gliding! (as well as using wrong trees).

And yet, despite hating the idea of gliding as a precursor to powered flight, gliding is the only possibility the studies consider in the case of Microraptor! They never consider the obvious likelihood that it could even flap its front wings never mind its rear ones!! Yet they both have all they need to flap! The flight-perfect primaries on the rear feet even get in the way of walking! Why does Brussatte think those feathers survived there?!

They’re actually asking us to believe flight evolved by running along the ground flapping, and then decayed into just gliding in several forms perfectly adapted to flapping. He uses the evidence for colour in fossil feathers as evidence against their evolution for flight. Do modern birds with coloured feathers not use them for flight? Lunacy.

Brussatte’s work is the kind of scientific fraud that comes from a field – palaeontology – which recruits only those who have no expertise in any skills useful in it, and science administrators who know nothing about the philosophy of science. The inventor of a fake bomb detector got jailed, you may recall. Brussatte and so many others would be jailed if bad palaeontology cost lives.

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