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Author Topic:   Discussion of Phylogenetic Methods
vaporwave
Member (Idle past 2645 days)
Posts: 66
Joined: 12-17-2016


Message 260 of 288 (796363)
12-29-2016 8:07 AM
Reply to: Message 257 by Taq
12-28-2016 11:02 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
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.
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.)
You can't say evolution predicted the general classification of animal groups since this was already achieved to a great degree before the theory was even off the ground. (And evolution couldn't predict this even in principle)
Evolution came along and constructed a narrative around that pattern of life. (as it could have a multitude of different patterns)
But they would all have a phylogenetic signal.
So what, a series of computer software has a "phylogenetic signal".
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.

This message is a reply to:
 Message 257 by Taq, posted 12-28-2016 11:02 AM Taq has replied

Replies to this message:
 Message 262 by Taq, posted 12-29-2016 10:45 AM vaporwave has not replied

  
vaporwave
Member (Idle past 2645 days)
Posts: 66
Joined: 12-17-2016


Message 267 of 288 (796442)
12-30-2016 7:08 AM
Reply to: Message 259 by JonF
12-29-2016 8:00 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
There are octillions to the octillionth power of possible patterns. The number of possible nested hierarchies is an infinitesimal fraction of the total. Nested hierarchies do not arise by chance. They are the result of a process.
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.

This message is a reply to:
 Message 259 by JonF, posted 12-29-2016 8:00 AM JonF has replied

Replies to this message:
 Message 269 by JonF, posted 12-30-2016 8:12 AM vaporwave has replied
 Message 273 by Dr Adequate, posted 12-30-2016 10:20 AM vaporwave has not replied
 Message 287 by Taq, posted 01-03-2017 2:57 PM vaporwave has not replied

  
vaporwave
Member (Idle past 2645 days)
Posts: 66
Joined: 12-17-2016


Message 268 of 288 (796443)
12-30-2016 7:18 AM
Reply to: Message 261 by Taq
12-29-2016 10:43 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
Your example is not out of order. Tiktaalik shows up well after the first lobe finned fish
So footprints showing up 10-20 million years before the limbs that would make them is not out of order. You have a strange definition of order.
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?
Obviously ancestors can live contemporaneously or outlast their descendants. I'm not arguing this is some kind of disproof of evolution.
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. So why were you arguing it in the first place? Just trying to make a sale?

This message is a reply to:
 Message 261 by Taq, posted 12-29-2016 10:43 AM Taq has replied

Replies to this message:
 Message 270 by JonF, posted 12-30-2016 8:31 AM vaporwave has not replied
 Message 285 by Taq, posted 01-03-2017 2:53 PM vaporwave has not replied

  
vaporwave
Member (Idle past 2645 days)
Posts: 66
Joined: 12-17-2016


Message 271 of 288 (796452)
12-30-2016 8:57 AM
Reply to: Message 261 by Taq
12-29-2016 10:43 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
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.
I think you're over-selling this nested hierarchy concept.
This nested hierarchy is as changeable as any common ancestry narrative will allow.
For example, an animal group with an even mix of bird and mammal traits would not necessarily violate a nested hierarchy, it would only require modeling the branches of the tree of life accordingly. Mammals and birds would now be placed much closer. Their relationship to dinosaurs would also likely be changed.
So yes, animals must fall into "a" nested hierarchy, but this is a very soft criteria to meet. Nothing like a law of physics that would be shattered if a parameter was slightly out of place.

This message is a reply to:
 Message 261 by Taq, posted 12-29-2016 10:43 AM Taq has replied

Replies to this message:
 Message 272 by Dr Adequate, posted 12-30-2016 10:19 AM vaporwave has not replied
 Message 277 by JonF, posted 12-30-2016 11:35 AM vaporwave has not replied
 Message 288 by Taq, posted 01-03-2017 3:33 PM vaporwave has not replied

  
vaporwave
Member (Idle past 2645 days)
Posts: 66
Joined: 12-17-2016


Message 274 of 288 (796471)
12-30-2016 11:22 AM
Reply to: Message 269 by JonF
12-30-2016 8:12 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
Nobody has proposed any other process that requires a nested hierarchy. If some other process produced what we see why did it produce a nested hierarchy instead of the almost innumerable other possibilities?
Nested hierarchies are an artifact of design. Human designers create nested hierarchies constantly without even thinking about it.
You may not like that because it undermines your entire argument, but it doesn't change the fact.
Your argument is only convincing if you assume the "random-creature-generator" absent of evolution, whereby you then invoke the "infinite possibilities" aspect, no one more likely then the other. Only against this contrived backdrop does common ancestry seem more likely.

This message is a reply to:
 Message 269 by JonF, posted 12-30-2016 8:12 AM JonF has replied

Replies to this message:
 Message 275 by Dr Adequate, posted 12-30-2016 11:26 AM vaporwave has not replied
 Message 276 by ringo, posted 12-30-2016 11:27 AM vaporwave has not replied
 Message 278 by JonF, posted 12-30-2016 11:44 AM vaporwave has replied

  
vaporwave
Member (Idle past 2645 days)
Posts: 66
Joined: 12-17-2016


Message 279 of 288 (796489)
12-30-2016 1:06 PM
Reply to: Message 278 by JonF
12-30-2016 11:44 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
No, human designers do not create nested hierarchies (of any significant numbers of items) because they are free to "cross-pollinate" characteristics from one item to an unrelated item.
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.
Maybe only 90% of the traits can be arranged in this hierarchy. That's still a dominant pattern of nested groupings.
Thus, nested hierarchies are a proven signal of design, whether you want to accept it or not.
This completely undermines your argument that non-evolutionary life should be a chaotic mish-mash with no decipherable phylogenetic signal.

This message is a reply to:
 Message 278 by JonF, posted 12-30-2016 11:44 AM JonF has replied

Replies to this message:
 Message 280 by Dr Adequate, posted 12-30-2016 1:36 PM vaporwave has not replied
 Message 281 by JonF, posted 12-30-2016 1:41 PM vaporwave has not replied
 Message 282 by Dr Adequate, posted 12-30-2016 5:30 PM vaporwave has not replied
 Message 284 by herebedragons, posted 12-31-2016 10:04 AM vaporwave has not replied
 Message 286 by Taq, posted 01-03-2017 2:55 PM vaporwave has not replied

  
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