Monday, May 11, 2009

More Medical Quackery

I didn't have the energy to find these links before, when I was talking about idiots who treat their kids with homeopathy and/or prayer, but I've since run across them.

Prayer does not cure diabetes, Part the First.
Prayer does not cure diabetes, Part the Second.
Herbs and ionized water probably aren't going to help with cancer.
Here's the proof.

If you read some of those links, you'll notice that in many cases the parents are being strung up on criminal charges, which I support entirely. The child's rights are being quashed by the religious/nutjob beliefs of the parents, who are voluntarily sending their spawn to an early grave. On the one hand, this does get rid of idiots from the gene pool (parents die and they killed their offspring already), but on the other hand, I really hate these people. My desire to see justice done outweighs my apathy towards the death of morons.

So again I ask: what drives people to such incredible acts of cognative dissonance? When your daughter is days from death's door, what moves you to email your friends and ask for "emergency prayers?" Because prayer worked so well until that point! A few emergency prayers will do the trick! ACK!

*storms out of the room*

As a brief aside, here's a great Discover magazine story about those moronic anti-vaccine activists and why, even after all their claims have been discredited, they still parade their cause.

ANGRY POSTSCRIPT: Look, just because your fringe, nutcase belief is not supported by science or, perhaps, the public in general, does not mean that there's a gigantic conspiracy going on to subdue said belief. Life is not the The X-Files. Here's how science works: If you don't have a falsifiable theory to support your claim, you MUST defer to the theory that DOES have the evidence, at least until you can present actual evidence to your claim. This is a principle I really want to hit the BAND members over the head with (among other groups). If you can't show me a basal crurotarian or archosaur who shares multiple non-convergent synapamorphies with birds that are not plesiomorphies, shut the fuck up and move on. Merely trying to poke holes in established theories is NOT science. You have to come up with a falsifiable alternative yourself, too. If all available evidence shows that vaccines do NOT cause autism, get the fuck over it and move on with your life. Why is it so difficult for people to accept falsifiability? ARGH!

*storms out of room again*

14 comments:

John Jackson said...

“Merely trying to poke holes in established theories is NOT science.”

Well, someone who’s read as many books around the subject as you would know, wouldn’t he?! And in which year exactly did you read Popper’s “Conjectures and Refutations”? You’ve just advertised to the world that you are angrily insisting people follow your advice in an area where you haven’t read the basic text - anyone can tell that. Your version has come third or fourth hand from uninformed conversations you’ve heard about the subject, and you just know that your colleagues and yourself are above needing to read the book. Did you know the most prominent book by the most prominent figure in the field over the last 70 years states that science is pretty well exactly the opposite to what you just said? And did you know that far from being an irrelevant old fool, Popper’s insight is honoured by scientists - that’s REAL scientists - whenever we carry out scientific experiments, since the statistics is based entirely on the Popperian approach... to repeat - the opposite to what you said? Although many scientists don’t quite understand the theory, they cannot help following it because the statistical tests are Popperian whether the experimenters understand it or not.

Did you design the statistical model for your last experiment and carry it out after reading your last book on the philosophy of science or before? Oh - let me guess - neither applies to you.

“Here's how science works: If you don't have any falsifiable evidence to support your claim, you MUST defer to the theory that DOES have the evidence, at least until you can present actual evidence to your claim.”

No. Here’s how real science works: We seek theories that explain the most. My theory - yes - that’s BAND - DOES explain the most. You should forget your usage of “falsifiable” concerning evidence - it’s confusing you and it’s wrong. It’s not falsifiable evidence you should be worrying about but the business of falsifying theories. The two prongs of real scientific research are comparing the evidence and the theories. Theories that don’t explain the evidence at all fail on their own, and theories that don’t explain as well as others lose out to them.

Whether you realise it or not, you are using the principle of positive evidence, which is possibly the most insidious and damaging error infecting the thinking of the non-religious sane today, and you claim you’re crusading for falsifiability. Just in that alone you’re insulting people who’ve gone to the trouble of finding out how things really work and then taking the effort to explain them properly.

To demonstrate the case against you, it is merely necessary to point out that you and the people you choose to be influenced by, have gained no useful ability, through study or experience, of the basis of the subject you rant about. The knowledge you lack has been sought in vain for thousands of years by people far brighter than you, and was only discovered through the development of statistics in the last century or two, and then noticed, utilised and proselytised by Popper. Like evolution it is simple, but not obvious, and is widely misunderstood and resented.

The basic problem with you is that you can’t imagine the possibility that so many of your co-theorists are wrong, and that others, whose ideas you don’t have the patience ever to try to understand, could ever be right. You don’t realise the difference is that we understand your ideas and you don’t understand ours. That’s a huge imbalance you haven’t noticed - along with the difference in qualifications - at least in my case.

It needn’t matter that you don’t have any science degree at all, or any experience of doing science, and have never read a book on the principles of developing scientific knowledge, if your arguments were good. But when you clearly don’t understand the thinking behind the beliefs of others vastly more knowledgeable than you, but insist they stop expressing their beliefs, you reduce yourself to the level of a religious fanatic. You’ll have noticed that people are often allowed to behave as ignorant fanatics, but that’s only because stopping them sometimes seems a bit complicated.

Take care. The world is not as you understand it.

Will Baird said...

Mr (Dr?) Jackson:

You have some valid points that Zach needs to address in how he sees how science is conducted. Pointing this out to him was a very important thing to do.

However...

Your manner of doing so is extraordinarily unbecoming. In fact, I would say that you are bordering on frothing at the mouth with your comments. My recommendation is to go back, delete the original comment, and revise what you have said.

I understand that BAND isn't doing well these days. Frustration can cause people to be intemperate. Since its the hope of most bloggers that their blogs last a long time and be used as references, your comment will last a loooong time. That means your comment will be here for a while too.

It's perfectly possible to have discussions between the sides that differ on theories. There's one going on between an individual and myself over the KT and other extinctions. It's slow and ongoing, but very civil.

Please revise your comment.

Raymond said...

To Mr. Jackson

I agree with much of what you say here. Yet I can't agree with the concept of BAND or MANIAC. Over three hundred characteristics are shared between Aves and Basal Maniraptora. At least 100 with the rest of Dinosauria within Ornithodira IIRC. Crurotarsa, the next out-group, shares quite a bit less.

What exactly do you propose as an alternative for maniraptora as the basal ancestral clade of Aves?

lantaro said...
This comment has been removed by the author.
lantaro said...

To quote a nun on House, "If I break my leg, I believe that God allowed it to happen for a reason. But I also believe He wants me to go to the hospital to have it fixed."

I agree with a lot of what you had going on there, good sir! And Mr. Jackson, my god, you are an angry person.

ScottE said...

John,

Much of your response makes no sense to me. You appear to venerate Popper, but reject positive evidence as being an insiduous something in the same comment. Surely your comment on positive evidence is overblown.

Perhaps admitting that you don't regard birds as dinosaurs isn't the best way to come out as pro-science. Birds are dinosaurs, and only positive evidence (at this point, lots of it) is going to disprove that. Complaining that your ideas are just misunderstood impresses nobody (especially if we've already had plenty of prior contact with them).

I think you also misidentify Zach's basic problem. Maybe it isn't fair to lump BAND groupies together with homeopaths and other quacks (and I don't think it is either), but based on both our experiences, it seems very few BANDers really understand or grasp that science is primarily an evidence-based discipline. (Look at the claims made by Fedducia, Martin et al. every time they wind up another response. After a point, it becomes perfectly fair to question wether or not their ideas are science.)

John Jackson said...

Hi Bill- (reply to Raymond at the end)

Thanks for commenting; as you say, there were errors in the way he sees science. And yes, I am angry about it because I’ve had to say the same thing several times a year for the past ten years, and not one of these characters has ever bothered themselves to pick up the book that I (as thousands of others would) recommend as essential. It’s worth remembering, very few of the important beneficial changes we see around us got done without someone getting angry. There’s no point accusing someone of being angry if they have every right to be. Doing so tends to put the blame on the person solving the problem, and doesn’t help. As a psychologist (and a sometime successful teacher of a martial art), I know what anger is and what it’s worth. Imagine how pointless it would be, saying to Parks, Huxley or von Stauffenberg “but you’re just angry!”

As it happens, I am keener on calm, careful discussion than 99% of those I see around me. I’ve put a lot of effort into learning how to explain and discuss complex issues over the years, I’ve been paid for various version of teaching, and I still am. The cladists however are hard to work with since they feel they have nothing to learn. But that’s only the start of it. Since three separate areas of their understanding (knowledge engineering whether by humans or machines, dinobird evolution, and the way scientists should operate) are so cluttered with mistakes, you can’t offer one correction since on its own it wouldn’t fit with the rest of their beliefs even in one of the three areas. All the areas need vast simultaneous replacements - and of course, you can’t get any of these people to concentrate for longer than it takes to think up some facile retort before flouncing off. You can tell how interested they are in developing their ideas by the way nothing remotely significant has changed in the way most of them do phylogenesis in over 20 years. Try comparing that to a genuine intellectual field.

Looked at from a selling point of view, trying to offer them some kind of a reward is intrinsically doomed since their having done everything completely wrong for decades is always going to be part of the package. There is no way of getting people to accept their ideas are rubbish that could be called “becoming” - and that is no reason to stop doing it. But don’t tell me discussions work best without pressure, since the problem is that there is no discussion.

“BAND isn’t doing well these days”? Evolution isn’t doing well these days. There have never been more people who do not believe in evolution than there are now. (99% of those haven’t read any of Darwin’s books. [My recommendation? Read “The Voyage of the Beagle”. “...The Origin...” is boring if you’re a believer.]) Almost all new theories start with just one believer, and at that time, just as at any other, there is no point counting heads unless you are not going to consider the arguments. The only people who count in getting to the bottom of an evolutionary puzzle are those who amongst other things understand the importance of correct philosophy of science in historical science - and that’s not many.

I’d like to think our internet utterances are permanent, but discovering that my Geocities site will not just be swamped by trillions of competitors but will actually disappear later this year reminds me that anything we commit to it is doomed, like all our thoughts, be “lost in time like tears in rain” :-) .

But until then, there is still just time to catch my
http://www.geocities.com/strangetruther/pottedpopper.html
for those who haven’t time to read the most important book that’s ever been written. I felt I had to start writing my survey of it in 2000 since even by then I’d got fed up with having to teach the same first lesson over and over and over and over again.

Again, thanks for your comment. As for revising it, I am happy to progress a real discussion on the subject but I meant what I said.

Raymond: thanks for your comment too. How on earth can I not believe that birds came from dinosaurs when the two groups are so similar they are clearly related? Well, if “mammals” contains humans, humans are mammals, but it is not right to say “mammals are humans” - and some “dinosaurs”, for example Cretaceous maniraptorans, look to many like flightless birds. That last bit is GSP’s view (and, now, Feduccia’s) but I agree that you can, like GSP, force yourself to believe the first flying birds sprang, via arboreal versions, originally from ground-living theropods... if you’re willing to sacrifice explanations for waggonloads of evidence that BAND alone can explain and which my forthcoming book is a better place to expand on than here.

Suffice it to say first that your three hundred characteristics shared between Aves and Basal Maniraptora which I won’t dispute, say nothing about the direction of descent between Aves and those basal manis. It’s a mystery to me why people keep thinking it does. I do hope you’ll either stop thinking it does, or explain why you won’t stop.

Then, we have a lineage of small tree-dwelling fossils a few of which have miraculously survived despite living exclusively in forests, which are an important part of what only BAND explains. Their significance is tied up with the bizarre parallel lines of epidermal structures shared by birds, crocs, dinosaurs, Longisquama, and almost certainly the drepanosaurs too. Yes, BAND alone explains the spinal structures of Megalancosaurus.

In case you’re interested, I left BADD for BAND when I discovered that feathers could not have evolved from fur-like material initially designed for insulation.

I’m afraid I wouldn’t know where to begin to reply to your comment Scott E - we just start form too far apart - but thanks anyway.

Finally, thanks to Zach for not blocking this.

Zach said...

Okay, John. You want to have a go? Let's do it. Karl Popper, a European philosopher, wrote a book called "Conjectures & Refutations" in which he argues that no scientific theory is true. We can never assert truth, only whether one theory is more correct than another based on available data. Moreover, a hypothesis is only scientific and viable if it is falsifiable.

So, in fact, it seems like Popper honors the traditional scientific method, that is evidence leads to conjecture leads to experiment leads to hypothesis leads to vigorous, brutal re-examination. Theories that do not survive repeated testing are thrown by the wayside.

The way Popper differentiates himself (and rightly hits the nail on the head) is that general statements cannot be upheld. If, for example, we were to find a single example of Sinosauropteryx with protofeathers, we could not say with certainty that all Sinosauropteryx individuals had protofeathers, much less all compsognathids. And that's completely true. To say otherwise would be silly. But we can infer, from a great number of protofeathered specimens, that most Sinosauropteryx animals probably did have feathers. And if other compsognathids are discovered with them, we can begin to state that protofeathers may have been a common feature to all those animals.

Here's the point. Popper in fact advocates a scientific method that rejects theories the second new evidence supports a new theory. The old theory is thrown out, the new one is brought in. Example: back when dinosaurs were first discovered, they were thought to be giant lizards because there was nothing else to compare them to. As more material was discovered, it became clear that these were not big lizards, but a unique group of animals. As cladistics came to the fore, it became clear that Dinosauria is a monophyletic group. So we've gone from a bunch of big lizads to a bunch of big potentially unrelated animals to a monophyletic group. That's Popperian falsification right there.

If a theory is falsifiable, it is scientific. That is Popper's criteria. And the second it is falsified, it is thrown out with the bathwater and replaced by whatever theory explains the evidence better.

And besides, where do we get theories? From available evidence! Theories would not exist without evidence. We create theory to explain what's in front of us. In refuting a theory, you are refuting the explaination for the evidence.

Of course, you're leaning on the teachings of just one philosopher when there exist many others. Kuhn, for instance, has been incredibly influencial in scientific circles. What's more, a simple Wikipedia search shows that Popper is in fact strongly criticized by his peers. Why should I listen only to Popper? Is he Jesus?

And no, I've never developed a statistical model before. I'm too busy. I merely read and internally criticize (and read the responses to) my colleague's analyses. So sorry. I don't think my non-BAND colleagues are wrong because they've got the evidence. They've got feathered raptors, compsognathids, and Archaeopteryx. What does BAND have? Euparkeria? Megalancosaurus? Can you imagine a more inappropriate avian ancestor?

And sure, I've never read a book about science. Should I take a photo of my book shelf? Of my five-drawer filing cabinet packed the brim with scientific papers?

Every theory starts with one believer. That's true--but if a theory doesn't stand up to scrutiny, it must be discarded or put on the backburner while more evidence can be dug up. I think we can both agree that Proavis is a joke, and that those aren't collagen fibers sticking out of Tianyulong and Sinornithosaurus. Show me a Triassic avian ancestor (it's going to look a lot like Archaeopteryx, and I'll take a serious look. But nobody's done that yet.

Yes, some maniraptors look like secondarily flightless birds. GSP did come up with that one. And for the most part he's probably wrong. Countless papers written since that time, and a better understanding of theropod anatomy, has suggested that while microraptorines may have been gliders, the vast majority of these animals were happily terrestrial. I used to be the world's biggest "secondarily flightless dromaeosaur" guy (ask Scott!) but I haven't seen any good evidence to support it that has stood up to scientific rigor. Just because it's awesome doesn't mean it's right.

Epidermal structures shared by crocs, birds, dinosaurs, Longisquama, and monkey-lizards? You can't be serious. You know what...plesiomorphy means, right? Hmmm...it's really wierd how I have hair and so do platypuses. I know you don't mean integumentary structures. You can't possibly. Crocs share basic pedal scale patterning with birds because...it's a plesiomorphy. I'm not sure what "spinal structures" you're talking about in regards to Megalancosaurus. No such epidermal structure were mentioned by Renesto (2000), Renesto & Vecchia (2005), or Senter (2004). If you mean the scratches on the matrix of one or two specimens (I can see what you might be talking about in Renesto (2000), but it's probably not integumentary structures or muscle fibers. If it was, I think one of the three papers would've mentioned them. None of them do. Maybe I don't know what stuctures you're referring to. And what spinal structures? The tall neural spines above the pectoral girdle? Have you ever seen a chameleon skeleton? Drepanosaurs were Triassic chameleons, not birds. Drepanosaurs are horrible avian ancestors. Senters' 2004 phylogeny places them WAY outside Archosauria proper, and closer to Tanystropheus.

Finally, the epidermal structures of Longisquama: I quote here from Voigt, et al. (2008):
"In contrast to earlier suggestions, we find no close morphological similarity of the proximal rugae to feather pulp chambers and caps...remaining discrepancies, in particular the flexible enveloping membrane and the lateral position of the middle axis, demonstrate the phylogenetic distance of Longisquama's appendages to avian feathers...we agree with others that the dorsal appendages are unlikely to be homologous with avian feathers."

Those authors present a very detailed analysis of the structure and potential function of Longisquama's dorsal appendages which explain their occurance and morphology better than previous theories. According to The Lamb of...I mean, Popper, the feather theory would be thrown out in the face of new, more conclusive evidence.

And of course I'm not going to block this. Everybody gets a chance to chime in.

ScottE said...

John: "I’m afraid I wouldn’t know where to begin to reply to your comment Scott E - we just start form too far apart - but thanks anyway."

Start with evidence. The burden of proof lies with you, and yes, that means you get to do most of the work.

Raymond said...

A very nice reply Zach.

I don't agree with your assessment of Medicine as "easily" falsifiable. It is field that varies often in methods of treatments and approaches to illness. More an art than science.
Not to mention that there is a huge social, political and economic aspect that inevitably corrupts it.

Paleontology seems to be not quite as bad, great changes in thinking can happen within a generation or two due to the enthusiasm of questioning minds. Medicine on the other hand, often takes decades or centuries to turn tack.

Perhaps the key difference is, if you're wrong about your interpretation of fossils, dating times, ultimately, no one is likely to be seriously hurt or die for it. (SVP meeting fisticuffs aside ;)

John Jackson said...

“Karl Popper, a European philosopher, wrote a book called "Conjectures & Refutations" in which he argues that no scientific theory is true. We can never assert truth, only whether one theory is more correct than another based on available data. Moreover, a hypothesis is only scientific and viable if it is falsifiable.”

That’s largely how I see his view. In terms of truth though, I think he’d prefer the idea that truth could never be demonstrated, rather than that something couldn’t actually be true. Humans (and animals) seem to use a concept of truth which is useful for them, perhaps like mathematicians using the concept of i. Behaving as though something is true might be more central than actually saying it is true.

“So, in fact, it seems like Popper honors the traditional scientific method, that is evidence leads to conjecture leads to experiment leads to hypothesis leads to vigorous, brutal re-examination. Theories that do not survive repeated testing are thrown by the wayside.
The way Popper differentiates himself (and rightly hits the nail on the head) is that general statements cannot be upheld. If, for example, we were to find a single example of Sinosauropteryx with protofeathers, we could not say with certainty that all Sinosauropteryx individuals had protofeathers, much less all compsognathids. And that's completely true. To say otherwise would be silly. But we can infer, from a great number of protofeathered specimens, that most Sinosauropteryx animals probably did have feathers. And if other compsognathids are discovered with them, we can begin to state that protofeathers may have been a common feature to all those animals.”

I agree with that, but I think this is a weak point of Popper - his view on creating theories in the first place. He didn’t seem to consider any method respectable. Here posterity will help him. Animals have evolved to assume something will be a certain way after observing it some number of times - especially when no different version is seen. (The exact type of confidence will depend on how many standard examples there have been, how many counter examples, type of animal, type of circumstance etc.) He’s right that general statements cannot be upheld, but of course absolute certainty is not the main criterion by which humans, animals or any agents must rule their lives, or even their knowledge systems. (Shame we seldom seem to have enough info before we have to make a decision!) But the truth concept can be pushed further than I might have suggested; when it is though, the way we discover truth isn’t quite as most people think. Saving your life by predicting correctly that there is no black swan around the next corner, is one thing. Announcing to the world that people are unscientific and on the lunatic fringe because they suspect adult swans might not be white everywhere is another. Science is a bit unnatural in that it tries to find truth, and often has to look in some annoyingly unpromising places to find it.

Going further back, your comment on evidence leading to conjecture is not false but it is not entirely true, and accepting it unquestioningly as part of the scientific method leads to problems. What should generate candidate theories, and what actually does, are both black arts. In particular, a huge mistake is made when insisting that candidate theories be made in a certain way.

“Here's the point. Popper in fact advocates a scientific method that rejects theories the second new evidence supports a new theory. The old theory is thrown out, the new one is brought in. Example: back when dinosaurs were first discovered, they were thought to be giant lizards because there was nothing else to compare them to. As more material was discovered, it became clear that these were not big lizards, but a unique group of animals. As cladistics came to the fore, it became clear that Dinosauria is a monophyletic group.”

Yes, the lizard theory was perhaps justifiably considered refuted (depending on definitions and what certainty they can lend). At some stage “it became clear” to some people that big sauropods spent most of their time in deep water, and that idea came to the fore. Some of the paths popular belief followed (including that of “experts”) was sound and some wasn’t - for example firm beliefs that cladograms could refute anything.

“So we've gone from a bunch of big lizads to a bunch of big potentially unrelated animals to a monophyletic group. That's Popperian falsification right there.”

The theory that dinosaurs are not monophyletic may be wrong or it may not be, but I don’t think your use of it contributes to a good example of Popperian falsification.

“If a theory is falsifiable, it is scientific. That is Popper's criteria. And the second it is falsified, it is thrown out with the bathwater and replaced by whatever theory explains the evidence better.”

Largely, I’d agree that is basically it. (Confusing complications that shouldn’t be brought up here are: “near-refutation”, “what when no theory quite fits but you have to do something”, and “can failed theories be adjusted”.)

“And besides, where do we get theories? From available evidence! Theories would not exist without evidence. We create theory to explain what's in front of us. In refuting a theory, you are refuting the explaination for the evidence.”

At least you have reached the stage where you can say this, but it is a classic error. First, we do not just get theories “from evidence”. Doing this point justice would take forever. Second, there is no “the” explanation for evidence. The whole point about competing theories is that there is often more than one candidate theory for any set of evidence. If I was being paid to teach an enthusiastic student who had said what you just said I would be delighted since it shows he was good enough to conceive of that idea, and had obviously put some effort into thinking about it. Getting closer to the true situation, I might even be pleased that you had at least registered on the radar screen so we could get a good plot of how far you’d got in this subject - which is the pitfall on square one. But we recall how all this started. You were criticising people who believed as I did, and suggesting we were so intransigently stupid that the best thing to do was hit us with something. In fact my beliefs incorporate a truer understanding of the point you have just messed up along with dozens of other insights some of which you will probably never reach.

“Of course, you're leaning on the teachings of just one philosopher when there exist many others.”

It’s convenient to use it’s inventor as a handle for a theory but however it arose it simply does the job. Do you want to throw that comment at anyone who uses statistics consistent with the Popperian view?

“Kuhn, for instance, has been incredibly influencial in scientific circles.”

Do you suppose every philosopher offers his own unique account inconsistent with every other? Popper suggests how scientists should handle their theorisation and why. Kuhn works at a higher level and gives an explanation for the way beliefs spread through a scientific community. I own a book called “Popper vs. Kuhn”. It’s rubbish.

“What's more, a simple Wikipedia search shows that Popper is in fact strongly criticized by his peers.”

As is every philosopher, to a degree dependent on their prominence. His advice doesn’t take us all the way. Some of what he does say is imperfect, and all of what he said has been criticised and will continue to be so. One could point out that Darwin didn’t give the last word on his subject, but his not killing evolution or biology stone dead shouldn’t be seen as a fault. Admittedly Popper’s contribution to his field isn’t quite as absolute as Darwin’s, but you can explain the way creatures from humans to viruses use knowledge, you can incorporate Shannon’s definition of information, and you can make a working thinking machine all based on Popperian principle, and you can’t do all that with anything else. Oh - did I mention that whatever scientists might say, statistical tests are based heavily on the Popperian principle?

“Why should I listen only to Popper?”

For the answer, see above.

“And no, I've never developed a statistical model before. I'm too busy.”

Yes - too busy to get the basics right.

“I merely read and internally criticize (and read the responses to) my colleague's analyses. So sorry. I don't think my non-BAND colleagues are wrong because they've got the evidence.”

You’ve got an obsession with positive evidence, which assumes evidence you don’t have yet has already been proved completely absent. There are stretches of more than a billion years where there is no direct evidence for life on earth, yet we don’t say it didn’t exist. You haven’t even got a proper definition of evidence.

“They've got feathered raptors, compsognathids, and Archaeopteryx”.

I think here and now would be a good time for you to answer the point I made with Raymond in an earlier comment. Given two types of animals which are clearly related, A (Archaeopteryx), and say M (for manirap..s), why does the mere similarity between them intrinsically determine a direction of descent? And in the direction of the later-occuring being ancestral to the earlier! Until you can do that convincingly, the similarity is not evidence for your theory since it is equally or better explained by mine. I don’t have an ideal close ancestral genus for Archaeopteryx unless Scansoriopteryx or Anchiornis actually lived earlier. But they or something very like them offer a much better explanation for the ancestry of Ax than your compsognathid. And any claim you might make that we haven’t got a fossil from a poorly preserved part of the Jurassic (when the animal must have lived in forests and been subject to acid soils) would merely highlight your poor understanding of the nature of evidence.

“What does BAND have? Euparkeria? Megalancosaurus? Can you imagine a more inappropriate avian ancestor?”

Oh, you still insist on an immediate ancestor? And then presumably the immediately ancestral species and indeed actual parent to that, and so on, like the creationists? I’m sorry to tell you, but a compsognathid was not the ancestral genus to Archaeopteryx, but my two suggestions are better candidates for near ancestry. However Megalancosaurus, though not any kind of ancestor, is a useful window on the bauplan a couple of significant steps prior to Archaeopteryx - and also a useful pointer to the origin of feathers. That does however require a feather theory that explains Meg. well, but then you don’t, even now, understand the link between evidence and explanation.

“And sure, I've never read a book about science. Should I take a photo of my book shelf? Of my five-drawer filing cabinet packed the brim with scientific papers?”

How many electric motors do you have in your various appliances? Does that number say anything about how well you understand the way they work? Does a creationist who has seen a million animals in his life understand their origins better than an evolutionist who has seen a fraction of that number? Does someone who has offered up ten thousand prayers in their lifetime understand their significance better than someone who gave up after just ten? There’s a saying: You may have been doing it that way for 40 years but then you’ve been doing it wrong for forty years.

“Every theory starts with one believer. That's true--but if a theory doesn't stand up to scrutiny, it must be discarded or put on the backburner while more evidence can be dug up.”

Stand up to scrutiny by whom? That counts. Just as importantly, a theory that explains some evidence, but also predicts other evidence that has not yet been found is not weakened if that evidence is not necessarily expected to have been found, or has not been sought, or exists but has been misinterpreted.

“I think we can both agree that Proavis is a joke, and that those aren't collagen fibers sticking out of Tianyulong and Sinornithosaurus.”

Fibres? Not all of my new-found stable-mates are quite up to speed with the new programme. Most theories have a central core, as BAND has, and other parts of the story had to be generated to complete a full picture. Similarity between birds and manirap...s was handled one way for a long time, until Allan Feduccia replaced the one major area that he had wrong by the one major area that GSP had right, and hit the jackpot. The first professional to do so, he’ll go down in history as the winner of one of the big three or four games in tetrapod palaeontology. He no longer actually needs those daft “collagen fibres” since he can now count feather-related fibres as homologous between birds and mani.s. I’m not sure exactly where he is on this at the moment but I suspect he’s ahead of most of the rest of his lot. In time, everyone will be able to look back on the collagen days and chuckle, but I never subscribed. CFs are not central to BAND, never have been in principle, and BAND should not be judged by them.

Substantial fibres on non-mani.s is well explained by my theory.

Protoavis wasn’t preserved as well as we might have liked but we’re still very lucky to have it. Maybe Sankar’s restoration and commentary is not to everyone’s taste but at least two things are worth mentioning. If you want to say something is a chimera, you have to make sure the contribution by various animals of various parts, without duplication, is statistically plausible. Needless to say, no member of the SVP has gone into this as far as I know. Then, when you’ve accepted the picture for one individual, start worrying about compounding these numbers for when two different-sized individuals are present, or are also a compound of various types, this time actually substituting the same parts from each contributor species. Chimera-hood can get close to being refuted. The fairly brisk look I took at Protoavis in this light still left some scope for a chimera, but you shouldn’t assume that it is one.

The other thing is the feather bumps on the hand. They are pretty believable.

Finally, I do hope you’re not presuming the correctness of your own theory when judging Protoavis’ significance - and then using this to bolster your own theory? I suspect you are, and if Protoavis didn’t exist, it would still have been predicted by my theory. Sure, it stinks in your theory but that’s your problem.

“Show me a Triassic avian ancestor (it's going to look a lot like Archaeopteryx, and I'll take a serious look. But nobody's done that yet.”

Whether you like it or not, a-Protoavis-like form of a suitable age is a good ancestor for both Archaepoteryx and Coelophysis. It’s even got features of C’s legs. The ancestry doesn’t have to be immediate, and none the arboreal fossils I favour are likely to be ancestral genera, they’re more likely offshoots representing bauplans of truly ancestral genera.

“Yes, some maniraptors look like secondarily flightless birds. GSP did come up with that one. And for the most part he's probably wrong. Countless papers written since that time, and a better understanding of theropod anatomy,...”

“...he’s probably wrong...”
...says which “expert”? No-one has a better understanding of theropod anatomy than GSP, and he hasn’t changed his mind yet. Countless papers may have been written but no matter how high a pile of crap gets, it’s still a pile of crap. And the number of supporters of neoflightlessness is large and growing.

“...has suggested that while microraptorines may have been gliders, the vast majority of these animals were happily terrestrial.”

Even if your view of the way evolution works allows you to see a creature like M. gui with all it needs to be able to fly down to every aerodynamic feature and skeletal structure, but still call it a glider, why on earth do you think it wouldn’t evolve just that last little bit that is so small we can’t even identify it, and achieve powered flight?! Not even over 80 million years?! And where were the birds of prey at that time? Your theories sometimes don’t even pretend to try to explain. And if James Cunningham says Microraptors could have been perfectly good powered fliers, you disagree because of...who?...what?...why?

“I used to be the world's biggest "secondarily flightless dromaeosaur" guy (ask Scott!) but I haven't seen any good evidence to support it that has stood up to scientific rigor.”

You and most members of the SVP wouldn’t know scientific rigour if it sat on you.

“Epidermal structures shared by crocs, birds, dinosaurs, Longisquama, and monkey-lizards? You can't be serious.”

And you explain pterylae in crocs, dinosaurs, Longisquama and birds how?

“I'm not sure what "spinal structures" you're talking about in regards to Megalancosaurus.”

The pair of hinged bones attached to the top of the neural spines. What did it use those - and the extraordinary neural spines themselves - for? And don’t say flinging the head forward.

“And what spinal structures? The tall neural spines above the pectoral girdle? Have you ever seen a chameleon skeleton?”

You mean something like this:?
http://www.outdoorphoto.co.za/forum/photopost/showphoto.php?photo=154442
Funnily enough a special development of the anterior neural spines aren’t apparent in this picture, not any of the others I found. Compare to the first and particularly the last pics in this page from Silvio’s Meg. site:
http://dipbsf.uninsubria.it/paleo/megalancosaurus3.htm

“Drepanosaurs were Triassic chameleons, not birds. Drepanosaurs are horrible avian ancestors.”

Forget about ancestors. We don’t have ancestors. We don’t need ancestors. Cladists aren’t even supposed to like ancestors. The ancestor of all archosaurs was a fairly unspecialised lizard-shaped form with a long enough neck for flicking the head forward, and paired non-fibrous plumes down it’s back. Of course if you don’t believe in anything you can’t see, you won’t like this idea. You will though if you understand that theory choice is based on explanatory power.

“Senters' 2004 phylogeny places them WAY outside Archosauria proper, and closer to Tanystropheus.”

You may have guessed by now I’m not terribly impressed by the opinions of cladists, particularly on the subject of cladograms.

“Finally, the epidermal structures of Longisquama: I quote here from Voigt, et al. (2008):”

I read that paper too. They pointed out similarities and differences between the plumes and modern feathers. That’s exactly what evolution gives you when you compare an earlier form with a later homologue (though Longisquama itself will have been a blind offshoot). I can hardly believe the attempts people make to cash in on differences, and say they mean these plumes can’t be related to feathers. There are differences between humans and the platypus. What else would you expect? The killer point of that paper was when they said the main reason they didn’t think the plumes could be homologous with feathers was... because they considered Longisquama and birds to be too distantly related!! SO?! That just means, if they are homologous - and the paper went no-where near disproving this (quite the opposite in fact) - plumes are hugely ancestral! They didn’t like that theory because they didn’t like the theory! And sure enough - here’s you quoting that paper as though it said anything valid about the phylogeny.

Perhaps you would now like to point out exactly where it is in whatever I’ve said above, that makes me and people who think like me, deserve to be “hit over the head”? I intensely resent people of inferior education rehearsing violent sentiments on those they don’t understand, and I also resent the way people starting to get into palaeontology will visit your blog and be put off what happen to be the best theories, because you think the average cladist has a better understanding of the way science works than the world’s top philosophers of science; also that views that are in a minority for any reason ought to be snuffed out without bothering to understand them first.


@ScottE :
“The burden of proof lies with you”

EXACTLY WHAT PART OF “THEORIES CANNOT BE PROVED, ONLY DISPROVED” DO YOU NOT UNDERSTAND?!

ScottE said...

John Jackson: "Second, there is no “the” explanation for evidence. The whole point about competing theories is that there is often more than one candidate theory for any set of evidence."

This is only true where competing theories have not yet been sussed out against incoming evidence. Where there is a clear and clean synthesis, while there may be competing theories in the sense of a theory being a related set of ideas, it will be obvious in many many cases that they will never retain anything but a minority acceptance--and the bulk of that may even be amongst those who are less than familiar with the subject.

The fact that any given theory will continue to be tweaked to fit new evidence will ensure this remains the case.

As time goes on, there will be fewer and fewer theories to compete against each other. Either they will merge and cover all the bases as best as can be expected (possibly forming a synthesis), or one will win out.


And: "EXACTLY WHAT PART OF “THEORIES CANNOT BE PROVED, ONLY DISPROVED” DO YOU NOT UNDERSTAND?! "

Gosh, John. Absolutely nobody here is saying otherwise.

When I tell you where the burden of proof lies (with you), I mean you have to perform the work necessary to disprove a very well-supported (current) theory (such as birds are dinosaurs).

That's what "burden of proof" means.

And really, shouting seldom makes anything better here. (There's also a point to be made here about snagging more flies with honey than with vinegar. Also: it helps to not look all mouth-foamy on the internet if you disdain the caps-lock key on your keyboard.)

Michael BW said...

J. Jackson on Longisquama-Paper by Voigt et al.:

"The killer point of that paper was when they said the main reason they didn’t think the plumes could be homologous with feathers was... because they considered Longisquama and birds to be too distantly related!! SO?! That just means, if they are homologous - and the paper went no-where near disproving this (quite the opposite in fact) - plumes are hugely ancestral! They didn’t like that theory because they didn’t like the theory!"

...it was surely not the main intention of a paper entitled "Feather-like development of Triassic skin appendages" to show that these appendages are non-homologous to feathers - (otherwise at least the title would have been different I assume)

...if the authors say they find such a relationship (high-level homology of the two integument types) unlikely if Longisquama's few discernible osteological features shows few/no indications that it sides with birds they (intentionally) do not rule out the alternative if Longisquama is shown to be closely related to birds some day

...and I understood that they do not oppose the homology of avian feathers and Longisquama appendages below the level of branched follicular structures (let's say on the level of the filament/ unbranched "plume")

Nima said...

Gentlemen, the right honorable Mr. Jackson has shown us exactly a textbook case of the quintessential BAND methods and ideology - for BAND doesn't just stand for "Birds Are Not Dinosaurs" - it also sums up their self-righteous philosophy of escalating their commitment to a tottering wisp of a theory for all eternity:

B: Bark louder than anybody else
A: Angrily vent at all who disagree
N: Never admit flaws in your theory
D: Denigrate and insult any human (not dinosaur or bird, but fellow HUMAN) who finds said flaws and points them out, as part of some grand Bakkerian/Machiavellian/Marxist/Terrorist/Masonic/Illuminati conspiracy!

Honestly I can't say much for the future of BAND - they are becoming more wacko and less and less relevant every year. Feduccia is their only well-known figure, and he's already wrecked his own credibility with at least five sledgehammers.

The fact that he's so stuck on the 2,3,4, pattern of chicken embryo fingers as his main line of "proof" for the BAND theory, is a DEAD giveaway that he doesn't even accept the evolutionary FACT of genetic retention and NON-mutated developmental throwbacks.

That's essentially rejecting one of the most critical parts of evolution - the very STOREHOUSE of genes for natural selection.

And much like those hot-headed preachers who reject evolution as a complete fantasy altogether, BAND members often have a very abrasive and personally incendiary way of getting their increasingly spurious message out. Thanks to the esteemed Mr. Jackson, for promptly reminding us in no uncertain terms, of precisely what sort of wonderfully arrogant demagogues we're talking about.

BAND looks like it's rapidly heading the way of Eugenics, Creation science, and Ptolemaic epicycles. Global warming denial, deregulanomics, and the SNAP (Sauropod Necks Ain't Priapic!) movement of Kent Stevens, are soon to follow. I'd also add the Flat Earth Society, but last time I checked their membership actually seems to be on the rise.