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Author Topic:   Discussion of Phylogenetic Methods
Taq
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Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


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Message 253 of 288 (796288)
12-28-2016 10:44 AM
Reply to: Message 239 by vaporwave
12-24-2016 5:11 AM


Re: templates and peripheral features
vaporwave writes:
One phylogeny has odd-toed and even-toed ungulates united
One phylogeny has odd-toed ungulates more closely related to bats
That's hardly drastic. That is a deep node in the placental phylogeny, and we would not expect there to be enough evidence for highly defined nodes that deep in the tree.
A drastic change would be putting a placental mammal in a cephalopod genus.
Edited by Taq, : No reason given.
Edited by Taq, : No reason given.

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 Message 239 by vaporwave, posted 12-24-2016 5:11 AM vaporwave has not replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 254 of 288 (796289)
12-28-2016 10:53 AM
Reply to: Message 246 by vaporwave
12-26-2016 3:50 PM


Re: templates and peripheral features
vaporwave writes:
That said, the nested design template idea does not seem significantly more ad-hoc than common ancestry.
The nested design template is light years more ad-hoc than common ancestry. We can directly observe common ancestry producing phylogenies. We can directly observe intelligent design not producing phylogenies.
You also gave no reason why templates would have to be nested. Why couldn't the templates not produce a nested pattern? You haven't given a reason. The only reason that you propose nested design templates is to produce a result similar to evolution. That makes it ad-hoc.
Sure, common ancestry "works" in that it's a flexible backdrop to work against. The very fact that it is so open-ended, and accommodating to diverse and contradictory narratives is what makes the idea work so well.
It isn't open ended. You keep making up stories.
Universal common ancestry, i.e. that all mammals share a common ancestor, that all vertebrates share a common ancestor, etc. has not been observed... obviously....
We have directly observed common ancestry producing phylogenies:
"Extensive data on genetic divergence among 24 inbred strains of mice provide an opportunity to examine the concordance of gene trees and species trees, especially whether structured subsamples of loci give congruent estimates of phylogenetic relationships. Phylogenetic analyses of 144 separate loci reproduce almost exactly the known genealogical relationships among these 24 strains."
Gene trees and the origins of inbred strains of mice - PubMed
Common ancestry has provided tons of predictions. It also has tons of excuses for when predictions fail. (e.g. well it must have evolved a lot sooner than we thought.... well those genes must not have been well-conserved.... well we'll have to move that node somewhere else on the tree of life... etc.)
We don't need excuses. The evidence supports common ancestry.
Not really. Common ancestry is mostly ad-hoc.
How is it ad hoc?

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 257 of 288 (796292)
12-28-2016 11:02 AM
Reply to: Message 249 by vaporwave
12-28-2016 7:09 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
vaporwave writes:
Pointing to the strength of current phylogenies is irrelevant.
Evolution did not predict those phylogenies.
Yes, it did.
"It will be determined to what extent the phylogenetic tree, as derived from molecular data in complete independence from the results of organismal biology, coincides with the phylogenetic tree constructed on the basis of organismal biology. If the two phylogenetic trees are mostly in agreement with respect to the topology of branching, the best available single proof of the reality of macro-evolution would be furnished. Indeed, only the theory of evolution, combined with the realization that events at any supramolecular level are consistent with molecular events, could reasonably account for such a congruence between lines of evidence obtained independently, namely amino acid sequences of homologous polypeptide chains on the one hand, and the finds of organismal taxonomy and paleontology on the other hand. Besides offering an intellectual satisfaction to some, the advertising of such evidence would of course amount to beating a dead horse. Some beating of dead horses may be ethical, when here and there they display unexpected twitches that look like life."
Emile Zuckerkandl and Linus Pauling, discussing the possibility of the twin nested hierarchy before the first molecular phylogenies had been made. (1965) "Evolutionary Divergence and Convergence in Proteins." in Evolving Genes and Proteins, p. 101.
Evolution could have occurred an infinite number of ways, producing a near infinite number of potential phylogenies.
But they would all have a phylogenetic signal. That is the prediction. Yes, evolution could have played out differently. However, whatever species did evolve they would produce a phylogeny.
For any one of these supposed "trends" you show me I could a fossil sequence that is out of order. One of the more interesting examples is advanced tetrapod footprints appearing in rocks roughly 20 million years older than the 'fishapods' that were supposed to just be starting to develop proto-limbs to walk on.
That is not out of order since those tracks appear after lobe finned fish appear.
You seem to be under the mistaken idea that Tiktaalik is a direct ancestor. Tiktaalik could have been a sister taxa that preserved some of the transitional features found in the direct lineage. Even Darwin addressed this:
"In looking for the gradations by which an organ in any species has been perfected, we ought to look exclusively to its lineal ancestors; but this is scarcely ever possible, and we are forced in each case to look to species of the same group, that is to the collateral descendants from the same original parent-form, in order to see what gradations are possible, and for the chance of some gradations having been transmitted from the earlier stages of descent, in an unaltered or little altered condition."--Charles Darwin, "Origin of Species"
The Origin of Species: Chapter 6
Your view of evolution is completely wrong. According to your misguided view, there should be just one species in the whole of Earth, the direct ancestor of a single lineage. Guess what? Lineages branch off and go in different directions. Some of those branched off lineages, what Darwin calls collateral descendants and what modern biologists call sister taxa, keep some of the ancestral features that are lost in the other taxa that have branched off. This makes them transitional species because they have preserved the mix of features that would have been found in the transition in the other lineages.

This message is a reply to:
 Message 249 by vaporwave, posted 12-28-2016 7:09 AM vaporwave has replied

Replies to this message:
 Message 260 by vaporwave, posted 12-29-2016 8:07 AM Taq has replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 261 of 288 (796368)
12-29-2016 10:43 AM
Reply to: Message 258 by vaporwave
12-29-2016 7:39 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
vaporwave writes:
So when fossil "transitions" lie in geologic order, then it is evidence for evolution and when the inferred transition is out of geological order then it is simply "not fully determined because evidence is lacking" ... seems convenient.
Your example is not out of order. Tiktaalik shows up well after the first lobe finned fish. You might as well claim that the platypus is out of order because it has outlived some placental mammal species. You might as well claim that a fish fossil is out of order if it is 10 million years old because mammals show up in the fossil record more than 60 million years ago. Do you see your flaw or not?
But the evolutionists in this discussion seem quite concerned about what 'could' occur, since your arguments continually circle back to how a designer 'could' create life, and why you claim this weakens the argument from design.
Dr Adequate explained it perfectly in post 255
quote:
And if biology was not constrained by evolution, there would be a still greater number of non-phylogenies.
Your argument is like saying that the theory of gravity isn't supported by observing the dynamics of the solar system, because we can imagine an infinite number of alternate solar systems with different planets at different distances from the sun which also obeyed the theory of gravity.
Well, this is true, the theory of gravity doesn't predict the number of the planets, or their distance from the sun, or their sizes. But it does predict, for example, that they will obey Kepler's laws --- and we can imagine many more solar systems that don't.
We put a theory to the test by testing the things it does predict; it is irrelevant to note that there are features of the solar system that it doesn't predict, that could be changed and still be compatible with the theory.
Is the theory of gravity falsified because another solar system has planets with different orbits than the ones found in this solar system? No.
The prediction for evolution is that whatever species do evolve they will fall into a nested hierarchy just as planets, no matter their composition or distance from their star, will follow the laws of gravity.
A designer has no such restrictions. A designer can design species so that they violate a nested hierarchy. We see that with human designs where paintings, buildings, computer programs, and automobiles do not form a nested hierarchy.
But nested hierarchies themselves are not evidence for evolution.
Yes, they are. When the pattern of shared derived features matches what evolution will produce then it is evidence for evolution.
And if common ancestry could potentially explain trillions of different nested hierarchies, then how strong of a theory is it really that it can explain one of them?
The same way that the theory of gravity can explain the orbits of trillions of different solar systems.
Edited by Taq, : No reason given.

This message is a reply to:
 Message 258 by vaporwave, posted 12-29-2016 7:39 AM vaporwave has replied

Replies to this message:
 Message 268 by vaporwave, posted 12-30-2016 7:18 AM Taq has replied
 Message 271 by vaporwave, posted 12-30-2016 8:57 AM Taq has replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 262 of 288 (796369)
12-29-2016 10:45 AM
Reply to: Message 260 by vaporwave
12-29-2016 8:07 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
vaporwave writes:
This is a prediction that the already observed pattern of life will be maintained with increased data. (e.g. mammals will continue to find highest trait similarity among mammals, etc.)
That is false. In 1965 they had barely discovered DNA. They had no real data demonstrating that DNA phylogenies would match phylogenies based on morphology.
So what, a series of computer software has a "phylogenetic signal".
Prove it. Until you do, the evidence is in support of evolution.
To rule out evolution, there would have to be a significant enough violation of the signal to be irreconcilable to any potential common ancestry narrative, something that couldn't be dismissed as a lack of data.
Precisely. Such violations would be child's play for a designer. In fact, humans do it all of the time.

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Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


(1)
Message 285 of 288 (796715)
01-03-2017 2:53 PM
Reply to: Message 268 by vaporwave
12-30-2016 7:18 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
vaporwave writes:
So footprints showing up 10-20 million years before the limbs that would make them is not out of order.
You haven't shown that limbs show up after footprints. Tiktaalik does not establish the earliest limbed fish. Tiktaalik only establishes that there were limbed fish at a precise time in history.
Your argument boils down to the old "if men evolved from apes, where are there still apes?" fallacy. Are chimps out of order because they exist after H. erectus? No. Is the platypus out of order because it exists after the extinction of many placental mammal species? No. Is the frog out of order because it exists after the extinction and evolution of more derived amniotes? No.
Guess what? Sister taxa branch off of other lineages and preserve less derived characteristics. That is what Tiktaalik is. It is a side branch on the tetrapod lineage.
It's funny you guys make such a big deal out of these supposed chronological fossil transitions and then when a counter-example is pointed out you start hand-waving that the specific order actually doesn't matter.
You haven't produced a counter-example.

This message is a reply to:
 Message 268 by vaporwave, posted 12-30-2016 7:18 AM vaporwave has not replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 286 of 288 (796716)
01-03-2017 2:55 PM
Reply to: Message 279 by vaporwave
12-30-2016 1:06 PM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
vaporwave writes:
So what.. for argument's sake let's say you find "cross-pollinated" violations, it's still true that designed traits tend to fall into nested hierarchies, especially models that are based off small variations of a basic design.
I call Bullshit!. Either you support this claim or admit that you have no such evidence.

This message is a reply to:
 Message 279 by vaporwave, posted 12-30-2016 1:06 PM vaporwave has not replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 287 of 288 (796719)
01-03-2017 2:57 PM
Reply to: Message 267 by vaporwave
12-30-2016 7:08 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
vaporwave writes:
Another invocation of the hypothetical 'random-creature-generator' - (If not evolution, then we should expect the pattern of life to look like spaghetti thrown against the wall)
If that's the bizarre comparison you need to draw to make common ancestry seem more likely, then have at it.
It isn't hypothetical. Organisms designed by humans do just that. We constantly violate a nested hierarchy when we design organisms.
You still haven't come up with a single reason as to why we see a nested hierarchy, out of the octillion to octillionth power other possible patterns that a designer could produce.

This message is a reply to:
 Message 267 by vaporwave, posted 12-30-2016 7:08 AM vaporwave has not replied

  
Taq
Member
Posts: 9973
Joined: 03-06-2009
Member Rating: 5.7


Message 288 of 288 (796720)
01-03-2017 3:33 PM
Reply to: Message 271 by vaporwave
12-30-2016 8:57 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
vaporwave writes:
This nested hierarchy is as changeable as any common ancestry narrative will allow.
Prove it.
For example, an animal group with an even mix of bird and mammal traits would not necessarily violate a nested hierarchy,
It would violate a nested hierarchy. Period.
So yes, animals must fall into "a" nested hierarchy, but this is a very soft criteria to meet.
It isn't soft at all. Your criticisms have all been off the mark.

This message is a reply to:
 Message 271 by vaporwave, posted 12-30-2016 8:57 AM vaporwave has not replied

  
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