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Author Topic:   Discussion of Phylogenetic Methods
caffeine
Member (Idle past 1024 days)
Posts: 1800
From: Prague, Czech Republic
Joined: 10-22-2008


(1)
Message 76 of 288 (795924)
12-19-2016 4:20 PM
Reply to: Message 27 by jar
12-18-2016 12:21 PM


The purpose of phylogenetics
vaporwave writes:
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.
Several of you have criticised vaporwave for this point, but it strikes me that on this point he is entirely correct. Phylogenetics is precisely what he says. Phylogenetic methods are means of calculating the most probable tree topologies given that a group of organisms share a common ancestor. These are not techniques to establish that evolution occured, but rather the means to figure how it did once we've taken that for granted.
I think we need to get away from the idea that the robustness of phylogenetic trees is a massive support for evolution, since a lot of phylogenies have turned out to be not very robust at all. The molecular revolution in phylogenetics has transformed our understanding of the tree of life. Consider the traditional classification of mammals as exemplified by Gaylord-Simpson's. He divided Eutherian mammals into four cohorts, only two of which are monophyletic based on our current understanding. At the order level he did better - only two of his 15 orders of extant eutherians were non-monophyletic; but this is not so impressive. Most of these are relationships which are obvious to the naked eye; and sometimes match with the idea of creationist kinds. His concepts of the interrelationships between these orders, however, bears very little relationship to modern systematics.
Phylogenetics does not make any sense as evidence for evolution. That's not what it's meant to be. Phylogenetics is what we do once we know evolution has occured. It's all about techniques to figure out how.

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Replies to this message:
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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 77 of 288 (795925)
12-19-2016 5:03 PM
Reply to: Message 76 by caffeine
12-19-2016 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.

This message is a reply to:
 Message 76 by caffeine, posted 12-19-2016 4:20 PM caffeine has not replied

Replies to this message:
 Message 81 by vaporwave, posted 12-19-2016 5:54 PM Dr Adequate has replied

  
vaporwave
Member (Idle past 2644 days)
Posts: 66
Joined: 12-17-2016


Message 78 of 288 (795926)
12-19-2016 5:10 PM
Reply to: Message 72 by Dr Adequate
12-19-2016 9:59 AM


Re: Introduction
No.
So that's two replies now you've avoided clarifying what you allege is a misunderstanding on my part. I guess you're bowing out of our discussion.

This message is a reply to:
 Message 72 by Dr Adequate, posted 12-19-2016 9:59 AM Dr Adequate has replied

Replies to this message:
 Message 79 by Dr Adequate, posted 12-19-2016 5:14 PM vaporwave has not replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 79 of 288 (795927)
12-19-2016 5:14 PM
Reply to: Message 78 by vaporwave
12-19-2016 5:10 PM


Re: Introduction
So that's two replies now you've avoided clarifying what you allege is a misunderstanding on my part. I guess you're bowing out of our discussion.
No.
You didn't ask me for a clarification. What you said was, and I quote: "Go ahead and explain how you didn't mean what you plainly wrote."
Do you now want a clarification instead?
Edited by Dr Adequate, : No reason given.

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Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


Message 80 of 288 (795928)
12-19-2016 5:33 PM
Reply to: Message 76 by caffeine
12-19-2016 4:20 PM


Re: The purpose of phylogenetics
caffeine writes:
Several of you have criticised vaporwave for this point, but it strikes me that on this point he is entirely correct.
One of the good things about this forum is that people get picked up and corrected on facts and bad argument - regardless of sides. Though I have to say, I see less of it on the creo side, just disagreement.
And you're at least mostly correct on this point. Science considers evolution settled so it's no longer concerned with proving it, it rightly wonders about how the most recent developments fit with it. So when taxonomy based almost entirely on form met DNA, errors were found and corrected. But molecular biology could have totally trashed the entire tree - it didn't, it confirmed it in spades.
The phylogenetic tree IS a massive support for the ToE, the fact that science now takes it for granted is not an argument against it.

Je suis Charlie. Je suis Ahmed. Je suis Juif. Je suis Parisien.
"Life, don't talk to me about life" - Marvin the Paranoid Android
"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.

This message is a reply to:
 Message 76 by caffeine, posted 12-19-2016 4:20 PM caffeine has not replied

Replies to this message:
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vaporwave
Member (Idle past 2644 days)
Posts: 66
Joined: 12-17-2016


Message 81 of 288 (795929)
12-19-2016 5:54 PM
Reply to: Message 77 by Dr Adequate
12-19-2016 5:03 PM


Re: The purpose of phylogenetics
Gaylord Simpson wasn't using molecular phylogeny, though, was he?
I think you're missing caffeine's point.
You guys are constantly stressing the supposed "consilience" of data, yet the history of evolution theory shows conflict, e.g. molecular data causing major revision of evolutionary relationships that had been inferred from fossil morphology.
And the fossil data alone had already produced all sorts of conflicting interpretations.... and no, not at the "tips of the branches", but among entire classes of animals like mammals.
The rosy picture that evolutionists paint for the public tends to be a world apart from the picture they discuss among themselves in the literature.

This message is a reply to:
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Replies to this message:
 Message 83 by Dr Adequate, posted 12-19-2016 6:24 PM vaporwave has replied
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 Message 86 by Dr Adequate, posted 12-19-2016 6:53 PM vaporwave has not replied

  
vaporwave
Member (Idle past 2644 days)
Posts: 66
Joined: 12-17-2016


Message 82 of 288 (795930)
12-19-2016 6:11 PM
Reply to: Message 80 by Tangle
12-19-2016 5:33 PM


Re: The purpose of phylogenetics
So when taxonomy based almost entirely on form met DNA, errors were found and corrected. But molecular biology could have totally trashed the entire tree - it didn't, it confirmed it in spades.
What he's saying is that because DNA didn't group giraffes with turtles instead of other mammals, Common Ancestry was totally vindicated.
Evolutionists really set the bar high.

This message is a reply to:
 Message 80 by Tangle, posted 12-19-2016 5:33 PM Tangle has replied

Replies to this message:
 Message 84 by Tangle, posted 12-19-2016 6:49 PM vaporwave has replied
 Message 98 by RAZD, posted 12-20-2016 7:51 AM vaporwave has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 83 of 288 (795931)
12-19-2016 6:24 PM
Reply to: Message 81 by vaporwave
12-19-2016 5:54 PM


Re: The purpose of phylogenetics
You guys are constantly stressing the supposed "consilience" of data ...
I stressed the consilience of the molecular data.
And I gave examples of how this didn't agree with morphology when you, vaporwave, you said "DNA confirmed the pattern of shared physical features and functionalities of organisms." And then even after I had pointed out your mistake you continued to asset "There is a robust relationship between genetic information and the type of morphology that it organizes. I don't doubt that."
And now that we've finally convinced you that you were mistaken, you're trying to ascribe your own mistake to us, and blame us evolutionists for you making it! Sheesh, vaporwave, are you a man or a weasel?
Edited by Dr Adequate, : No reason given.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 81 by vaporwave, posted 12-19-2016 5:54 PM vaporwave has replied

Replies to this message:
 Message 87 by vaporwave, posted 12-19-2016 7:15 PM Dr Adequate has replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


Message 84 of 288 (795932)
12-19-2016 6:49 PM
Reply to: Message 82 by vaporwave
12-19-2016 6:11 PM


Re: The purpose of phylogenetics
vaporwave writes:
What he's saying is that because DNA didn't group giraffes with turtles instead of other mammals, Common Ancestry was totally vindicated.
I guess we'll have to wait and see what caffeine says he's saying, but I can't make any sense out of that sentence.
Neither taxonomy, nor DNA groups turtles with mammals. But without common descent there's no reason for DNA and form based taxonomy to agree on their classification. Molecular biology confirmed common descent.
Evolutionists really set the bar high.
There is no bar.

Je suis Charlie. Je suis Ahmed. Je suis Juif. Je suis Parisien.
"Life, don't talk to me about life" - Marvin the Paranoid Android
"Science adjusts it's views based on what's observed.
Faith is the denial of observation so that Belief can be preserved."
- Tim Minchin, in his beat poem, Storm.

This message is a reply to:
 Message 82 by vaporwave, posted 12-19-2016 6:11 PM vaporwave has replied

Replies to this message:
 Message 88 by vaporwave, posted 12-19-2016 7:30 PM Tangle has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 85 of 288 (795933)
12-19-2016 6:52 PM
Reply to: Message 81 by vaporwave
12-19-2016 5:54 PM


Re: The purpose of phylogenetics
d.p.
Edited by Dr Adequate, : No reason given.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 81 by vaporwave, posted 12-19-2016 5:54 PM vaporwave has not replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 86 of 288 (795934)
12-19-2016 6:53 PM
Reply to: Message 81 by vaporwave
12-19-2016 5:54 PM


Re: The purpose of phylogenetics
d.p.
Edited by Dr Adequate, : No reason given.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 81 by vaporwave, posted 12-19-2016 5:54 PM vaporwave has not replied

  
vaporwave
Member (Idle past 2644 days)
Posts: 66
Joined: 12-17-2016


Message 87 of 288 (795935)
12-19-2016 7:15 PM
Reply to: Message 83 by Dr Adequate
12-19-2016 6:24 PM


Re: The purpose of phylogenetics
And I gave examples of how this didn't agree with morphology when you, vaporwave, you said "DNA confirmed the pattern of shared physical features and functionalities of organisms." And then even after I had pointed out your mistake you continued to asset "There is a robust relationship between genetic information and the type of morphology that it organizes. I don't doubt that."
As I said, there is a pattern. Animals that share similar anatomical systems tend to share similar genetic organization of that anatomy.
Your problem is you cannot see the distinction between this observation and your assumption of common ancestry.

This message is a reply to:
 Message 83 by Dr Adequate, posted 12-19-2016 6:24 PM Dr Adequate has replied

Replies to this message:
 Message 89 by Dr Adequate, posted 12-19-2016 7:30 PM vaporwave has not replied
 Message 91 by Coyote, posted 12-19-2016 9:21 PM vaporwave has not replied
 Message 94 by Genomicus, posted 12-20-2016 6:27 AM vaporwave has replied

  
vaporwave
Member (Idle past 2644 days)
Posts: 66
Joined: 12-17-2016


Message 88 of 288 (795936)
12-19-2016 7:30 PM
Reply to: Message 84 by Tangle
12-19-2016 6:49 PM


Re: The purpose of phylogenetics
I guess we'll have to wait and see what caffeine says he's saying, but I can't make any sense out of that sentence.
Sorry I was referring to you not caffeine.
Neither taxonomy, nor DNA groups turtles with mammals.
Right, and to an evolutionist this is vindication of the theory. Because if DNA had grouped one family of mammals closer to reptiles than other mammals, then Common Ancestry would have been falsified. Evolutionists use examples like this to celebrate how amazing the theory it is.
But without common descent there's no reason for DNA and form based taxonomy to agree on their classification
Oh good. I'd love to know how you've arrived at this special knowledge of how life would or would not appear absent of common descent.
Dr. Adequate vaguely alluded to calculating the chances of this scenario but he kinda clammed up when I pressed him for details.

This message is a reply to:
 Message 84 by Tangle, posted 12-19-2016 6:49 PM Tangle has replied

Replies to this message:
 Message 90 by Dr Adequate, posted 12-19-2016 7:32 PM vaporwave has not replied
 Message 92 by Tangle, posted 12-20-2016 2:45 AM vaporwave has replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 89 of 288 (795937)
12-19-2016 7:30 PM
Reply to: Message 87 by vaporwave
12-19-2016 7:15 PM


Re: The purpose of phylogenetics
As I said, there is a pattern. Animals that share similar anatomical systems tend to share similar genetic organization of that anatomy.
Your problem is you cannot see the distinction between this observation and your assumption of common ancestry.
One of your problems is that you almost continually lie to me about what I think. But you have others.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 87 by vaporwave, posted 12-19-2016 7:15 PM vaporwave has not replied

  
Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 90 of 288 (795938)
12-19-2016 7:32 PM
Reply to: Message 88 by vaporwave
12-19-2016 7:30 PM


Re: The purpose of phylogenetics
Dr. Adequate vaguely alluded to calculating the chances of this scenario but he kinda clammed up when I pressed him for details.
You know how Tangle can actually read this thread on which he is a participant? So you are unlikely to deceive him.
Edited by Dr Adequate, : No reason given.

This message is a reply to:
 Message 88 by vaporwave, posted 12-19-2016 7:30 PM vaporwave has not replied

  
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