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Author Topic:   Discussion of Phylogenetic Methods
vaporwave
Member (Idle past 2635 days)
Posts: 66
Joined: 12-17-2016


Message 24 of 288 (795846)
12-18-2016 9:47 AM
Reply to: Message 1 by herebedragons
01-01-2016 1:01 PM


Re: Introduction
A phylogeny is a hypothesis about the evolutionary history of a group of taxa and since the phylogeny we present is a hypothesis, we want to know how well our hypothesis is supported compared to other hypotheses. Thus, the various phylogenetic methods have been developed to provide researchers with ways to evaluate those hypotheses and determine which hypothesis is the best. In other words, phylogenetic programs don't just build trees but more importantly, they evaluate them so that researchers can present the most well supported hypothesis.
Phylogenetics asks: IF common ancestry is true, what is the most likely evolutionary relationship between living things?
But it does not investigate that core assumption that common descent has taken place.
Evolutionists paint a false picture for the public. They imply that if common ancestry were false, then assembling phylogenetic models would be impossible. The models would break down.
But this is not true.
Common ancestry could be false, and one could still derive phylogenetic models that gave the appearance of evolution.
There are a host of explanatory devices ready to deal with pieces that do not fit in any given phylogenetic model. e.g. If you have arranged branches based on genetic traits, but the morphology and anatomy don't reinforce it, then the evolutionists can propose that some of those traits must have evolved independently of each other... and voila, you have accommodated contradictory data into the model.
This is not to disparage the methodology... it is all very practical and extremely interesting. It is just dishonest to present such phylogenetic models as hard evidence that proves common ancestry is true.
I guess the idea is that if you present enough numbers, data matrices, complex diagrams, etc. then it will intimidate the opposition into silence. As I mentioned before, this all works off the implied evolutionist bluff that such diagrams would be impossible to generate if common ancestry were false.

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Replies to this message:
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vaporwave
Member (Idle past 2635 days)
Posts: 66
Joined: 12-17-2016


Message 26 of 288 (795849)
12-18-2016 12:12 PM
Reply to: Message 25 by Modulous
12-18-2016 10:33 AM


Re: Introduction
Of course, this doesn't explain how we can create those trees from morphology and from DNA evidence and come to very similar answers. This strongly suggests common descent is indeed correct.
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. This assumption cannot be demonstrated or tested in any way of course.
The typical rebuttal here has the evolutionist quickly retreating to teleological territory and he begins rambling about how a Creator could do X or Y, etc....
Furthermore, back to phylogenetics... when DNA and morphological traits actually are in conflict, evolutionists simply say the morphology evolved twice or more, significantly insulating the theory from potential falsification.
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, because tomorrow, in order to reconcile the phylogenetic data, they may have to assume an even more complex morphological trait evolved multiple times.
Again, the whole phylogenetic practice boils down to: IF evolution is true, this is likely how it happened. But it doesn't reveal more than that.
Edited by vaporwave, : No reason given.

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vaporwave
Member (Idle past 2635 days)
Posts: 66
Joined: 12-17-2016


Message 33 of 288 (795861)
12-18-2016 1:07 PM
Reply to: Message 28 by Modulous
12-18-2016 12:27 PM


Re: Introduction
There must not be a large path of reduced fitness through morphspace that can be achieved through incremental changes to the genome.
So, when identifying a convergent trait, you just have to assume evolution did not take such a pathway. Simple enough.
But you didn't answer the question. Specifically, what level of morphological complexity (edit: **the traits themselves** not supposed evolutionary pathways) would be impossible for convergent evolution and why?
Edited by vaporwave, : clarification

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Replies to this message:
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vaporwave
Member (Idle past 2635 days)
Posts: 66
Joined: 12-17-2016


Message 34 of 288 (795862)
12-18-2016 1:15 PM
Reply to: Message 31 by Dr Adequate
12-18-2016 1:01 PM


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

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vaporwave
Member (Idle past 2635 days)
Posts: 66
Joined: 12-17-2016


Message 35 of 288 (795863)
12-18-2016 1:26 PM
Reply to: Message 29 by Tangle
12-18-2016 12:39 PM


Re: Introduction
For example, taxomic trees were built based on the phyiscal features and functionalities of organisms and their assumed relationships. DNA came along and could have completely debunked the entire concept, yet it confirmed it.
DNA confirmed the pattern of shared physical features and functionalities of organisms. Dogs and cats remain more similar to each other than either is to a jellyfish or a reptile. Surprise surprise... I think evolutionists really make this discovery out to be more than it is.
You trick yourself into pretending the core assumption of common ancestry isn't still there begging the question.

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vaporwave
Member (Idle past 2635 days)
Posts: 66
Joined: 12-17-2016


Message 43 of 288 (795874)
12-18-2016 3:20 PM
Reply to: Message 36 by Dr Adequate
12-18-2016 1:27 PM


Re: Introduction
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.
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. That would be the inference.

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Replies to this message:
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vaporwave
Member (Idle past 2635 days)
Posts: 66
Joined: 12-17-2016


Message 46 of 288 (795877)
12-18-2016 3:38 PM
Reply to: Message 38 by Modulous
12-18-2016 1:41 PM


Re: Introduction
You don't assume evolution did not take a pathway
Well, if a particular evolutionary pathway is deemed impossible, then obviously the evolutionist will not assume it. That much is certain. The evolutionist will assume whatever he needs in order to reconcile the theory.

This message is a reply to:
 Message 38 by Modulous, posted 12-18-2016 1:41 PM Modulous has replied

Replies to this message:
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vaporwave
Member (Idle past 2635 days)
Posts: 66
Joined: 12-17-2016


Message 48 of 288 (795879)
12-18-2016 3:44 PM
Reply to: Message 45 by Dr Adequate
12-18-2016 3:25 PM


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

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Replies to this message:
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vaporwave
Member (Idle past 2635 days)
Posts: 66
Joined: 12-17-2016


Message 49 of 288 (795880)
12-18-2016 3:58 PM
Reply to: Message 47 by Modulous
12-18-2016 3:42 PM


Re: Theory, not isms
If a pathway is known to be impossible, it will be ruled out. What on earth are you trying to say?
If an interpretation of the data leads to a conclusion that Common Descent did not take place, then the evolutionists will obviously dismiss this interpretation.
Bringing it back to your example, an evolutionist would simply never assume a large path of reduced fitness through morphospace in order to explain the existence of a character trait. By definition of being an Evolutionist he can't assume this.

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vaporwave
Member (Idle past 2635 days)
Posts: 66
Joined: 12-17-2016


Message 53 of 288 (795884)
12-18-2016 4:19 PM
Reply to: Message 44 by Dr Adequate
12-18-2016 3:22 PM


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

This message is a reply to:
 Message 44 by Dr Adequate, posted 12-18-2016 3:22 PM Dr Adequate has replied

Replies to this message:
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vaporwave
Member (Idle past 2635 days)
Posts: 66
Joined: 12-17-2016


Message 56 of 288 (795887)
12-18-2016 4:46 PM
Reply to: Message 50 by Dr Adequate
12-18-2016 3:59 PM


Re: Introduction
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.
Interesting take. I think if you're committed enough to an evolutionary worldview then it doesn't matter how false it looks.
Look at the related field of Origin of Life studies to get some inkling of the metaphysical commitment. It doesn't matter how much the various OoL theories may struggle, the general academic community knows with complete certainty that it happened completely naturally somehow.
Edited by vaporwave, : No reason given.

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vaporwave
Member (Idle past 2635 days)
Posts: 66
Joined: 12-17-2016


Message 57 of 288 (795888)
12-18-2016 4:58 PM
Reply to: Message 55 by Dr Adequate
12-18-2016 4:39 PM


Re: Introduction
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.
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.

This message is a reply to:
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Replies to this message:
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vaporwave
Member (Idle past 2635 days)
Posts: 66
Joined: 12-17-2016


Message 59 of 288 (795895)
12-18-2016 6:15 PM
Reply to: Message 58 by jar
12-18-2016 5:13 PM


Re: More nonsense.
What is actually said is that so far no examples of non-natural causes have ever been found. Until someone actually presents a non-natural cause for examination and can explain how such non-natural causes work there is no reason to suggest non-natural causes.
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. Perhaps rethought entirely but never dismissed or replaced... (indeed the alternative is not even to be considered)
I don't want to get off-topic from phylogenetics here. I'm just offering it as an example of the type of commitment someone may hold to an evolutionary style worldview.

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 Message 58 by jar, posted 12-18-2016 5:13 PM jar has replied

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vaporwave
Member (Idle past 2635 days)
Posts: 66
Joined: 12-17-2016


Message 66 of 288 (795905)
12-19-2016 7:33 AM
Reply to: Message 64 by Dr Adequate
12-18-2016 7:12 PM


Re: Introduction
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.
But you are the one guilty of this so far. You've claimed to hold insight into the probabilities of how life would look if common ancestry were false.
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
Earlier here you stated that genetic/morphological concordance of life would be "accidental" if not for evolution. I'm still waiting for you to explain how you got this knowledge.

This message is a reply to:
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vaporwave
Member (Idle past 2635 days)
Posts: 66
Joined: 12-17-2016


Message 67 of 288 (795906)
12-19-2016 7:44 AM
Reply to: Message 60 by Tangle
12-18-2016 6:44 PM


Re: More nonsense.
Do you accept that common descent is falsifiable?
Yes. But practically every idea is falsifiable in some way so this isn't saying much. It's like the bare minimum requirement in science. Falsifiability doesn't necessarily translate to a robust ironclad theory that no reasonable person can question.

This message is a reply to:
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