On Heers’ inclined plane work on evolution of birds and their flight, and further comments

Audobon posted on Heers’ work rationalising the Inclined Plane theory of the evolution of bird flight – a version of the “Ground up” theory, which is physically impossible and not surprisingly shows no signs of being recapitulated to any extent by extant animals (unlike the alternative, “Trees down”, which is).

I had to make a comment:

I feel sorry for Ashley; having been taught science research by Dial was a tragedy. Science is not the kind of thing you can wander into unprepared and start producing something of value; you need to be genuinely plugged in to the work of genuinely worthwhile science workers of the past, and also to bring real skills with you. Understanding evolution is not just a process of saying “this might have happened” or “this happened by mistake”. Anyone who has, for example, studied simulations of evolution, as I have, will know apparent randomness does not mean just anything can happen. Some direct evolutionary leaps just cannot be made, no matter how much time you give evolution. A leap from climbing using hand claws, to ascending slopes by flapping wings of any design SIMPLY CANNOT HAPPEN except indirectly by a significant sequence of diversions… which will end up not following the inclined plane theory. The gap between using hand claws to using wings of any effectiveness could never happen directly, as you would find if you tried to simulate it: the gap between not using the claws and employing hard-to-evolve thrust generating wings cannot simply be stepped across.

Of course no dinobird palaeontologist understands this because none have ever done enough evolutionary simulation to understand evolution – or indeed ANY simulation of anything to understand the value of simulations. I have never been able to find anyone working as a dinobird palaeontologist who has ever compiled a computer program, OR is able to manage research level statistics well enough to do more than simply follow directions, OR has any experience with devising any experiment of a sophistication that undergraduates in psychology or a host of other disciplines could manage… or most importantly, who have ever opened a philosophy of science book and gained anything useful from it. That’s why you can poll any number of such palaeontologists and they will keep giving the same stupid answers generation after generation. That’s what you get when you insist that all students entering the field have only irrelevant qualifications.

It’s hard to know where to start. Brusatte’s supposedly “groundbreaking doctoral work on dinosaur and bird family trees” mentioned in the Audobon piece is pseudo science. Neither Brusatte, nor, as far as I can tell, any of his teachers, have a professional level qualification in any information science. Someone who has, myself for example, can see multiple errors in every sentence he utters on the subject. When they mention “evidence shows”, they show they don’t understand the nature of scientific evidence. For example: “In 2003 Dial had published evidence that living birds engage in what he called “wing-assisted incline running…”; that work is most definitely NOT evidence that bird flight evolved in this way. An observation is only evidence FOR a theory if competing theories cannot explain the evidence as well as yours. Competing theories actually explain flight evolution in ways that do not violate principles of evolutionary processes, nor issues of physics, as all ground-up theories, which include inclined-plane, do.

It doesn’t matter that Heers might have done meaningful work on the developmental processes in chicks; the conclusion: “In her doctoral thesis, Heers demonstrated that feathered dinosaurs had gone through similar stages during their evolution into birds capable of fully powered flight…” is most certainly was NOT any kind of demonstration that inclined-plane was an essential stage. The competing theories would have had to have been completely refuted, and to put it mildly, they weren’t.

You could write a book on the rubbish peddled here by this lot – and I did. Suffice it to say that the culture of pseudo-scientific palaeontology it represents could only survive if the qualified and knowledgeable were strenuousy kept out – as they have been and continue to be. The Peer Review system they rely on, proved yet again in December, through genuine science [Siler et al, PNAS Dec 2014], to be little more than a pseudo-scientific scam, is a godsend for pseudo-scientifc greasy-pole climbers. I remember Brusatte greasing his career path many years ago by describing Tom Holtz as a genius. At what was that, pray? Now: As for Heers, he says, “She’s brilliant. She’s not a traditional paleontologist but a real ornithologist.” None of this work was brilliant, and much was incompetent. And if Padian says it’s good – place a bet that it isn’t. Padian’s achievements have been to use computer programs wrongly, to teach others to use them wrongly, and to claim pterosaurs habitually ran bipedally, which they didn’t.

I’d like top stop now, but further down, Norell presents yet another target that’s just too easy to shoot down: he tries to argue that the brains of birds’ ancestors were becoming more birdlike. As usual, he forgets that science is about SELECTING the theories that explain the best, so he ignores alternative theories, assumes his own cannot ever be questioned, and insists on implying that Greg Paul’s straightforward theory, that types such as Gallimimus wer actually flightless birds ALREADY, was wrong – and without ever mentioning it.

It’s easy to forget, now, the clever way Norell, Padian et al. have hidden the telling truth that Paul was also one of the first to predict dinosaurs had feathers, when Padian and his fellow pseudoscientists very rudely scoffed. If Paul was right all that time ago, why not consider that possibility he is right now?

For the full account of this scandal, check out The Secret Dinobird Story (US/UK).

Subsequently, an anonymous poster “Sarepedon” trotted out the old uneducated drivel, to which I replied:

This has become an excellent exemplification of the fate of dinobird palaeontology. I’ll take the opportunity to highlight the major points because characterising the people causing the problems in the field will help defeat the problem.

This Sarepedon is not the subject of the original Audubon peice – he is a World of Warcraft enthusiast and an amateur scientist. He is therefore ideal Naish fodder. Darren Naish, whom Sarepedon quotes, collects material discovered or invented by others (as indeed I do – I don’t find fossils either), and spins wonderfully fascinating accounts of the material, but weaves a spell from it which glorifies himself while hardly scratching the surface of science. It can’t do because he has no science skills other than observation, memory and presentation, and just putting two and two together reasonably well like any bloke in a pub could do. But people like Sarepedon don’t notice this because they too find science skills irritating distractions. What they do have in spades, they learned in their earliest school years: groupism. Naish gives them a hero as well as consolidating their group, and the likes of Sarepedon become hopelessly caught up in the excitement. You will notice absolutely no scientific content in Sarepedon’s comments; there is no room, and he has no science to offer. It is however rich in unsupported insults that are both ad hominem and groupist:

“The above diatribe by John Jackson is merely a litany of slurs against respected professional scientists.”

He insults my comments before explaining why they should be insulted; he then tries to suggest I am not a professional scientist, and presumably am not respected – unlike the group he follows. This is argument by unnamed authority, and besides, ignores my years of study, research and teaching – in REAL sciences. He then goes on to ignore the fact that I actually went through the stage of being a knowledge engineer (and therefore “are one” 😉 ) – I qualified for it, and have done research into the nature of knowledge.

“For starters, it might be useful for JJ to return to basics and understand the difference between a “theory” and a “hypothesis”. No, the terms are not interchangeable.”

When someone who has investigated and researched deeply the nature of knowledge, cognition etc, says theory and hypothesis are effectively interchangeable, devotes thousands of words in their book to justifying it, and includes it in a definition of the whole scientific process, then just churlishly contradicting it simply establishes that you are a churl. The essence of historical (and inductive) science is finding good theories which explain evidence well. There isn’t anything else, though that contains a lot. Therefore it doesn’t matter whether you call a theory a hypothesis, a speculation, a hunch, a bet or a conjecture, the only thing that counts is whether it explains the observations. Why did Sarepedon mention this? Because it is part of rule 1 of my sciencepolice-14 rules, which he must have quickly scanned, while checking out my website. But of course he learned nothing since he refuses to learn from those outside his group.

What is the heart of the problem?

I used to think it was…

Not understanding the computer programs that generate the family tree – cladograms – of the dinobirds.

What happens is this:
1: The palaeontologist tips the data describing bones etc into the program and out comes a family tree. Unfortunately this will be the wrong tree if there is too much evolutionary parallelism and convergence. Not only is this a fact but it is also a fact that dinobirds DO show too much convergence etc. for the cladograms to be trusted. But the palaeontologists DO trust them, they get all their theories about the evolution of the creatures from this source ignoring anything else, they DO block from publication or funding anyone who disagrees with these trees or anything deduced from them, and they also DENY that they are doing any of that. From the Naish quote:

“— The constant complaint that palaeontologists as a whole do not understand the mechanics/algorithms of cladistic methodology, and hence cannot and should not use it, is nonsense. Firstly, minor point: cladistics is not unique to palaeontology; it’s widely applied throughout the biological sciences and was invented by an entomologist. You should read the literature on extant organisms some time. “

Not only by treating the cladograms as gospel, do they show they don’t understand any of the fields of mathematics that such tree construction belongs to, but their comments ALWAYS CONTAIN NO RELEVANT JARGON THAT ANYONE COMPETENT IN SUCH FIELDS WOULD HAVE TO EMPLOY. Read Felsenstein 2004 – the bible for cladogenesis, though he is not a cladist since he understands trees may be wrong – for the terms an expert should refer to. Also, dinobird palaeontologists seem to have done no useful work in any relevant info. science field, nor do they have any respectable qualification in them. I’ve only dabbled in cladogenesis but the work I reported in my book vastly exceeds the entire technical research ever done in cladogenesis by all those who have ever been employed as a dinobird palaeontologist (DBP). I’ve even pointed out one or two important flaws in the slightly more advanced areas that DBPs don’t venture near – for example bootstrapping, invented by Felsenstein, is usually misused and gives little assurance of validity in the face of convergence, and unfortunately some of Huelsenbeck’s work can’t be used at all. Naish however is completely mathematically naive and will never be able to make any useful contribution to information science as long as he lives. You’ll have noticed he talks a good game, but I wonder if he can still remember how to do long division. I doubt if he ever got much beyond that.

He makes the Drunk Driver fallacy:

“cladistics […] [is] widely applied throughout the biological sciences “

A drunk driver might justify his drunk driving because lots of other people drive. You then explain that some of the other people who drive do it carefully, unlike the drunk driver. Also, others that also drive carelessly do not justify the drunk copying them.

“Secondly, I don’t actually see why you think you need to understand the statistical algorithms and so on to be a perfectly good user of parsimony software. Please explain why you think this necessary. As someone who actually uses PAUP (also NONA, sometimes) and has generated cladograms, I think it’s far more important that you sort out character polarity, accurate coding etc. “

OK, let me explain why we generate family trees. Because we want to know the family relationships, and using the wrong family trees doesn’t do this for us. He should explain why insisting on telling the world the wrong trees are the right ones is a good idea. If you don’t understand enough about how the statistical algorithms work, you may be stupid enough to trust them when they shuldn’t be trusted. And if you NEVER GET ANY FEEDBACK ON HOW TRUE THE TREES ARE, FIDDLING AROUND WITH CHARACTER POLARITY ETC. IS PRETENTIOUS PSEUDOSCIENCE. How can you know whether it’s important or not if you don’t know if any of it works? As we will see below, we do actually get feedback, but Naish and the gang never pay any attention.

“Thirdly, you are blissfully naive if you really, honestly think that biologists/palaeontologists truly don’t understand this stuff. Maybe you don’t know that some cladists actually write their own software, or that some have spent the better part of their careers writing about the data handling and computation involved in parsimony software.”

The ones that do understand it don’t agree with Naish’s views on cladograms. This is the Drunk Driver fallacy again. And those employed as DBPs DON’T write their own software… though writing the software is different from knowing when you can trust it. I’ve been to some conferences where people who really understand this stuff meet to discuss their work, and they all had total disdain for the cladists, very few cladists were even there, and no DBPs such as Naish at all. NOT ONE. I do remember meeting the cladist who hired Chris Brochu after he left the Field, and that bloke was completely bemused and felt very left out. And the advanced software genuine phylogenetic scientists develop is NEVER used by DBPs.

“Another of your complaints – that the parsimony software we so doggedly adhere to will one day tumble like a house of cards and that, ho ho ho, won’t we all look oh so silly when that day comes – is also rubbish.”

It came the day the family tree of modern mammals generated using DNA, which is less affected by convergence problems, was more believable than the tree generated from the shapes of bones – which I think was before Naish said the above. But Naish’s science looked silly long before then.

“It is universally understood that the cladograms generated by PAUP etc. are hypotheses liable to further testing. Are you seriously saying that we shouldn’t be proposing hypotheses using whatever means we have available?”

It is widely understood that cladists treat these cladograms as gospel (until the next one appears), that they insist that everyone works to them and nothing else, and then, when pressed, they just turn round and lie that they themselves are just treating them as “…hypotheses liable to further testing”.

But then one day…

…I realised that just as big a problem is failure to understand what evidence is. Amazingly there are a lot of people who will agree that science is about finding the best explanations for the observations, but they don’t understand the significance of the fact that whether my theory or Naish’s is right, THE SAME CLADOGRAM WILL BE PRODUCED. It doesn’t act as a litmus test. But they just say “Well we’re going to take the cladogram literally”… even though both theories explain the evidence in the form of the cladogram, equally well (and other forms of evidence support me). Naish doesn’t understand this elementary issue, and neither do most DBPs – nor unfortunately do the funding bodies… yet – but that will change.

And if they don’t understand that elementary issue in philosophy of science, they don’t understand any philosophy of science at all. Not surprisingly it wasn’t realised, in the original Audubon piece, that since ostrich mimic dinosaurs (e.g. struthomimids) have brains that resemble in shape brains of birds that can fly, and also even dinosaurs nowhere near birds have feathers, and some e.g. Kulindadromeus, have blade shaped stalked feathers apparently originally designed for at least gliding flight, THE TRUE SCIENTIST WILL FAVOUR, ALL OTHER THINGS BEING EQUAL, THE THEORY THAT EACH HAD AERODYNAMIC ANCESTORS – and not stubbornly refuse to consider it till hell freezes over.

Most DBPs just shiftily look right and left to their colleagues, and try to guess which theory will look coolest to others, which is why new theories never seem to get accepted. And it’s why Sarepedon can say:

“Gregory S. Paul (who Jackson slavishly follows) does interesting and imaginative work on dinosaurs. However, most of Paul’s work has been comprehensively refuted – including the outlandish idea that non-avian coelurosaurs (such as Gallimimus) were secondarily flightless”

I’m a knowledge engineer, I’ve read all the relevant work on the subject, and I can tell you that Paul’s theory of secondary flightlessness has most certainly not been refuted. It makes as much sense to say that as to say that I slavishly follow Paul, since I also support Feduccia – in part. Of course they are, or were, on very different sides, but, perhaps uncomfortably for Paul, their positions are actually creeping together, and where I disagree with Paul (pre-Archaeopteryx) I tend to agree with Feduccia, and vice versa. I CAN’T AGREE HALF WITH PAUL AND HALF WITH AN OPPOSING THEORIST AND YET SLAVISHLY FOLLOW PAUL, CAN I?! And James Kirkland who is digging out and preparing the pit of Utahraptors, says they, which Sarepedon would call non-avian coelurosaurs, are secondarily flightless, so the expert Sarepedon had better get on the blower and inform James Kirkland right away that his idea is outlandish too.

But eventually…

…I became convinced that the real root of the whole dinobird palaeontology bullshit fiasco was groupism. Fix that and you could theroretically solve the rest. You see that it is groupism from the language used – not just the hatred expressed in the terms, but the way they denigrate outsiders. Now I know something about name-calling, and I know how often it involves groupism. When Archie Cochrane made criticisms of the way medicine was being practiced, and suggested that many were making the same mistakes, on his way to establishing the Evidence Based paradigm, Sarepedon would have called him too “a notorius troll and conspiracy theorist” – had his natural habitat of comment boxes in web-pages been invented then, and had he the wit to get into anything as serious as medicine himself. Of course the slogan “conspiracy theorist” is freely flung about wherever no-one knows what they’re talking about. You will find though that shouting “He’s just a conspiracy theorist” will get you no-where when defending in court a charge of conspiracy; nor will it work in social psychology where it is understood that humans are a social species.

The reasons groupism has taken hold here, include, I suggest, the following:

* Palaeontology is a historical science, and the philosophy of historical science isn’t well understood by almost anyone, including pretty well all palaeontologists. This allowed random meme evolution to develop driven merely by social dynamics and unconstrained by scientific reality.

* Palaeontology has traditionally been studied in geology departments (because that’s where the fossils are), so the idiotic practice of taking mainly geology students into palaeontology became accidentally established. Info. science, including training in the statistical behaviour of great swathes of numbers, and in the use of simulation particularly of evolution, and in graph theory, are all essential. Without them, even having a medical-based first degree wouldn’t make up the defecit. Having a reasonable percentage of psychologists might be expected to help the field avoid elementary errors in group and individual bias – which are actually the main driving forces within the three areas of palaeontology I’ve studied (dinobird, human, dog). Psychologists are also better at stats than geologists.

* Cladism is a form of groupism, and the social character of cladism arose because it was effectively born in the USA, where extreme groupism is not just common, but until recently was a way of life. Some would say it still is. Of course cladograms were invented in Germany but in the USA the cladists arose as a group because they opposed the pheneticists. That group battle, and the victory it won, set the style of the cladists, and ever since they’ve treated the supporters of every opposing idea as pretty well subhuman, and they expect to win every battle.

“I also fully concur with Darren that JJ’s perpetually condescending tone is really irritating and insulting.”

If you don’t want to be talked down to, get a relevant degree or two.

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