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# Discussion of Phylogenetic Methods

Author Topic:   Discussion of Phylogenetic Methods
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 Message 7 of 288 (775822) 01-05-2016 12:56 PM

Member (Idle past 49 days)
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 Message 16 of 288 (776600) 01-17-2016 2:14 AM Reply to: Message 15 by herebedragons01-16-2016 4:57 PM

Re: Bayesian Inference I
 The prior probability of a particular tree is the probability that among all possible tree topologies it is the correct one. If we believed that all trees were equally likely, then we could assign a flat prior, where the prior probability of a tree equals one divided by the number of trees.

Why don't we believe that?

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 Message 18 of 288 (776611) 01-17-2016 10:33 AM Reply to: Message 17 by RAZD01-17-2016 8:57 AM

Re: Bayesian Inference I
I think we're meant to assume they're all bifurcating.

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 Message 31 of 288 (795858) 12-18-2016 1:01 PM Reply to: Message 26 by vaporwave12-18-2016 12:12 PM

Re: Introduction
 Evolutionists fall back on a strange sort of metaphysics... they work off the assumption that if common descent were false, the pattern of morphology and DNA would necessarily be in discord.

No, you have misunderstood the logic of the scientific method. Of any successful theory, we cannot (and no-one ever does) say for certain that if it was false, it would be falsified in any given way. What we can do is observe that there are many potential falsifications, none of which have come to pass.

(This of course has nothing to do with "metaphysics", it is an epistemological question.)

In the case of evolution, the fact that the study of DNA offers chance after chance of falsifying the theory, and that none of these chances comes up, must surely be regarded as confirmatory unless we are to descend into complete epistemological nihilism.

And yes, this is especially the case given that the only alternative hypothesis (and I use the term "hypothesis" loosely) gives us no inkling of a reason why this should be so.

 Ask an evolutionist what the evolutionary limits are to "Convergent Evolution", with regards to morphology. They won't be able to give you any kind of specific answer ...

I would rule out such things as a bat having wings just like a bird, or a duck-billed platypus having a bill actually identical in form and substance to that of a duck.

Perhaps, if you are a creationist, you could say what limits your hypothesis places on such things. Or indeed on anything else. What can God not do by magic?

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 Message 36 of 288 (795864) 12-18-2016 1:27 PM Reply to: Message 34 by vaporwave12-18-2016 1:15 PM

Re: Introduction
 Okay good that is pretty specific. Now just explain why it would be impossible for a mammalian lineage to convergently evolve feathers and wings.

It would be a fairly massive coincidence, don't you think? Since there are clearly lots and lots of ways to have wings, it would defy probability and beggar belief if, given the small number of times wings have evolved, they did so exactly the same way twice.

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 Message 37 of 288 (795865) 12-18-2016 1:36 PM Reply to: Message 35 by vaporwave12-18-2016 1:26 PM

Re: Introduction
 You trick yourself into pretending the core assumption of common ancestry isn't still there begging the question.

It isn't; it's manifestly falsifiable.

 DNA confirmed the pattern of shared physical features and functionalities of organisms.

No. For example, it puts a crocodile closer to a hummingbird than, for example, to a Komodo dragon. It puts a coelacanth closer to a dog than to a dogfish. We expect this on the basis of what we know of these organisms' evolutionary history, not their shared functionality.

And of course one could point to the consilience of the DNA evidence with itself. Evolutionary theory predicts that a cladogram constructed on the basis of one lot of DNA (say haemoglobin genes) will be in good accordance with one constructed on another basis, say ERVs.

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 Message 44 of 288 (795875) 12-18-2016 3:22 PM Reply to: Message 35 by vaporwave12-18-2016 1:26 PM

Re: Introduction
 You trick yourself into pretending the core assumption of common ancestry isn't still there begging the question.

I think I should expand on my response to this a little, since my response was in fact basically "nuh-uh".

It is, I suppose true that you could take any large set of objects with lots of measurable characteristics, assume common ancestry, and shoehorn them into a cladogram.

But the theory of evolution predicts that in the case of living organisms (or at least those which are complex, multicellular, and so not susceptible to lateral gene transfer) since they were produced by a process of copying with variation, the set should be robust with respect to the methods, by which I mean that the cladograms produced by the phylogenetic methods should not be highly sensitive to exactly which measurable characteristics of the set we use, so long as it is reasonably large.

If the set was not produced by copying with variation, there is only an infinitesimal chance that it would have this property of robustness by accident; so we would in fact (with overwhelming likelihood) notice if common ancestry was a false assumption. Unless you can hypothesize a reasonable alternative to evolution that would necessarily, and not just by chance, produce the same appearances ... in which case I would like to hear of it.

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 Message 45 of 288 (795876) 12-18-2016 3:25 PM Reply to: Message 43 by vaporwave12-18-2016 3:20 PM

Re: Introduction
 Convergent evolution is never chalked up to mere coincidence, but the product of similar functional constraints. Perhaps these constraints are so fine-tuned in the case of feathers/wings that natural selection only ever finds the same configurations in morphospace.

But that's not remotely credible, and could indeed be demonstrated to be false on theoretical grounds --- we know how wings work, after all.

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 Message 50 of 288 (795881) 12-18-2016 3:59 PM Reply to: Message 48 by vaporwave12-18-2016 3:44 PM

Re: Introduction
 But for all you know, the types of wings we see in nature are the only configurations that natural selection is able to find in actual animal populations. Slight deviations may cause fitness to plummet drastically. That would be the inference.... and however surprising or unlikely, you would know it happened... because 'evolution is true.

That's an interesting fantasy you have there about what people would think if it looked like evolution was false. In fact, if it looked like it was false no-one would have thought of it or believed it in the first place. However, this fact, like your self-serving daydream, is by-the-by, because it doesn't look like it's false.

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 Message 55 of 288 (795886) 12-18-2016 4:39 PM Reply to: Message 53 by vaporwave12-18-2016 4:19 PM

Re: Introduction
 There is a robust relationship between genetic information and the type of morphology that it organizes. I don't doubt that.

As that is not remotely what I said, I suggest that you read my post again.

 That is a completely non-testable metaphysical/philosophical claim. You can't calculate the chances of such a thing unless you assume some kind of random creature generator in the absence of universal common ancestry.

And yet I do not. The alternative hypothesis doesn't have to be a "random creature generator"; but if there is no reason why it should produce robustness, then it would be a matter of chance if it actually did.

I am mildly curious to know what you think "metaphysical" means. You are wrong. Again, this has nothing to do with metaphysics: this is epistemology; this is the scientific method.

 This is a bizarre assumption, yet your whole defense hinges on this "what are the chances" claim which evolutionists try to smuggle in as scientific evidence.

And since all science is done this way, it would seem that this is the very essence of scientific reasoning.

I must go out now, but I shall be happy to disabuse you of any further errors you may have perpetrated by the time I get back.

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 Message 62 of 288 (795899) 12-18-2016 7:06 PM Reply to: Message 59 by vaporwave12-18-2016 6:15 PM

Re: More nonsense.
 Let me rephrase that. No matter how weak naturalistic origin of life theories may become, no matter how much that claim may appear to be false, the academic community will never consider the central idea of a naturalistic origin of life to be disproved.

Well, again, that's a self-serving fantasy about a universe very different to the one we live in.

It is in fact normal for people to adjust their beliefs in accordance with the evidence. Creationists don't, but that's because they work using the rules of religion rather than science.

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 Message 64 of 288 (795901) 12-18-2016 7:12 PM Reply to: Message 57 by vaporwave12-18-2016 4:58 PM

Re: Introduction
 Yes indeed. If.Let me know when you're able to demonstrate the reasoning or lack of reasoning of this non-evolutionary creature generator.Until then you're just philosophically speculating to the extreme... Which is totally fine, just don't try to smuggle it in as scientific evidence for your theory.

I demonstrate it like this. You can't think of an alternate theory that would produce the same evidence. You can't begin to think of such a thing. So merely speculating that there might be one which you can't even think of would be idle and vacuous pseudoscientific speculation which can have no place in science. We can't base scientific reasoning on a daydream which you haven't even had yet --- on a daydream that one day you might have a daydream --- on something you can't even imagine, but you can imagine being able to imagine it. In science such speculation about speculation is worthless, no matter how much it may comfort the religious.

It says a great deal about the weakness of the creationist view that you find it necessary to attack the scientific method itself, and to adopt rhetorical positions that would render all of science impossible ... just so's you can dispute evolution. It's like someone adopting a philosophy that nothing is true just so he can say that "It's not true that I took the cookies from the cookie jar".

Edited by Dr Adequate, : No reason given.

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 Message 69 of 288 (795914) 12-19-2016 9:12 AM Reply to: Message 66 by vaporwave12-19-2016 7:33 AM

Re: Introduction
And vaporwave's prolonged futile assault on the scientific method itself continues.

 But you are the one guilty of this so far.

No.

 You've claimed to hold insight into the probabilities of how life would look if common ancestry were false.

No.

 Earlier here you stated that genetic/morphological concordance of life would be "accidental" if not for evolution.

No.

If you don't understand my point, why don't you ask me to explain it instead of making up crazy stuff in your head?

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 Message 72 of 288 (795917) 12-19-2016 9:59 AM Reply to: Message 71 by vaporwave12-19-2016 9:52 AM

Re: Introduction

No.

 Go ahead and explain how you didn't mean what you plainly wrote.

No.

You're doing such a good job of explaining how I didn't mean what I plainly wrote that you hardly need any help.

I don't know who you can actually hope to deceive on this subject, which I think makes this kind of a strange hobby for you to have. But we are obviously two very different people.

Edited by Dr Adequate, : No reason given.

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 Message 77 of 288 (795925) 12-19-2016 5:03 PM Reply to: Message 76 by caffeine12-19-2016 4:20 PM

Re: The purpose of phylogenetics
Gaylord Simpson wasn't using molecular phylogeny, though, was he? He died in 1984.

I'm not responsible for, nor will I defend, vaporwave's strawman of my argument.

Edited by Dr Adequate, : No reason given.

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