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


Message 215 of 288 (796118)
12-22-2016 4:12 PM
Reply to: Message 204 by Dr Adequate
12-22-2016 8:34 AM


Re: The purpose of science
"So when you can see Saturn's rings you assume you're looking through a telescope.
And when you can't see Saturn's rings you assume you're not looking through a telescope.
Poor analogy. You don't have to assume or infer that the thing actually being observed through a telescope or microscope exists.
Evolutionists observe character traits and sequence data and have to make evolutionary assumptions or inferences about them, at times resulting in a great deal of controversy between themselves.
Edited by vaporwave, : No reason given.

This message is a reply to:
 Message 204 by Dr Adequate, posted 12-22-2016 8:34 AM Dr Adequate has replied

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


Message 216 of 288 (796119)
12-22-2016 4:41 PM
Reply to: Message 207 by Taq
12-22-2016 11:48 AM


Re: The purpose of science
We OBSERVE that it is well conserved due to the number of shared bases. There are no assumptions. It is a direct observation.
Why are you obfuscating? You know very well it is much more than the direct observation.
In evolutionary terminology, stating that a genetic sequence is 'conserved' is to make a claim about evolutionary relationships.
"Conservation across species indicates that a sequence has been maintained by evolution despite speciation. A highly conserved sequence is one that has remained unchanged far back up the phylogenetic tree, and hence far back in geological time."
Conserved sequence - Wikipedia
You don't observe geologic time in a genetic sequence. You observe the sequence and make inferences.
And so back to my last point:
Conflicting sequences can be accommodated into a preferred evolutionary narrative by simply assuming they were more or less conserved over deep time.
This is followed up by the usual circular reasoning whereby the conservation inference is considered self-evident because you *know* evolution is true.

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


Message 219 of 288 (796122)
12-22-2016 5:25 PM
Reply to: Message 208 by Taq
12-22-2016 11:50 AM


Re: The purpose of science
Linnaeus did not assume evolution in the 1700's, and he came to the same conclusion. The nested hierarchy is an observation
And a nested hierarchy is not evidence of evolutionary relationships unless you assume common ancestry.
You can't subjectively weigh a DNA base.
You can't subjectively measure a bone either. You make subjective inferences about why it looks the way it does.
Do you have to assume that a suspect is guilty in order to get a DNA match? No. The DNA match is what evidences guilt. The same process works with phylogenies and common ancestry. The phylogeny is evidence of common ancestry.
Oh that is just sad. You can be a bit more sophisticated than this I think.
Why not a vertebrate-cephalopod template? Why not a mammal-bird template? Why not a fish-jellyfish template?
Why didn't different types of animals evolve?
All of these would violate a nested hierarchy
Not necessarily. If there was a paleontological record of totally different types of animals, then it may have simply produced a different common ancestry narrative by those evolutionists studying them.
"Natural selection did it" is a surprisingly malleable explanatory device to wind a story around.
The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified.
There may be an objective data-set, but finding an animal's position within it is far from objective. (e.g. Evolutionists still can't decide whether or not birds nest in Theropoda. )

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


Message 220 of 288 (796123)
12-22-2016 5:41 PM
Reply to: Message 218 by Dr Adequate
12-22-2016 5:06 PM


Re: The purpose of science
That is certainly what conservation indicates, just as the article says, but it is not how it is defined or recognized
Oh, I see... so the term isn't recognized as what it typically indicates in the literature? Is that really your argument?
You should probably think your comments through a little more instead of just kicking up dust and making noise every time I post.

This message is a reply to:
 Message 218 by Dr Adequate, posted 12-22-2016 5:06 PM Dr Adequate has replied

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


Message 224 of 288 (796129)
12-23-2016 7:23 AM
Reply to: Message 205 by RAZD
12-22-2016 9:35 AM


Re: templates and peripheral features
So is the template that generates the gliding membranes in flying squirrel and sugar glider the same?
Depends. I suppose it could but I wouldn't necessarily expect it because those animals have very different underlying anatomy which may promote unique design decisions.
Evolution would say, if the genetic organization of the gliding membrane is different between both groups, then it independently evolved in eutheria and marsupialia.
On the other hand, if the genetic organization of the gliding membrane is the same or similar in both groups, then those particular gene sequences were inherited from a common mammalian ancestor and driven by natural selection to be recruited for a common function in different species.
Evolution would accommodate both observations in this case, just like design.
Help us understand how these traits are generated without evolution.
You mean a more complex explanation than "natural selection did it" ?

This message is a reply to:
 Message 205 by RAZD, posted 12-22-2016 9:35 AM RAZD has replied

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


Message 230 of 288 (796154)
12-23-2016 1:21 PM
Reply to: Message 228 by Dr Adequate
12-23-2016 9:55 AM


Re: templates and peripheral features
But it can't. Gliding is not in fact an ancestral characteristic of mammals,
That's not what I said. I said the genes would be inferred to have served a different purpose in the ancestor and been independently recruited for a similar function in the later separated descendants, (via similar selection pressures.)
Gene recruitment is a phenomenon in which a particular gene becomes used during evolution as a gene with a totally different function. The term "gene recruitment" was coined because a gene has evolved as if it had been recruited to exhibit a different or another function.
Gene Recruitment (Molecular Biology)
That's how evolution could accommodate similar genetic organization of gliding membranes in marsupials and eutherians. It would not disprove common ancestry.
Edited by vaporwave, : No reason given.

This message is a reply to:
 Message 228 by Dr Adequate, posted 12-23-2016 9:55 AM Dr Adequate has replied

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


Message 231 of 288 (796155)
12-23-2016 1:28 PM
Reply to: Message 229 by RAZD
12-23-2016 10:42 AM


Re: templates and peripheral features
Except that the membranes did not occur in older ancestors, and so would not expect them to be a conserved DNA section.
Unless the genes were conserved for some other function in the mammal line and later independently recruited for development of gliding membranes in the separate branches, because of similar selection pressures.

This message is a reply to:
 Message 229 by RAZD, posted 12-23-2016 10:42 AM RAZD has replied

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


Message 233 of 288 (796164)
12-23-2016 3:39 PM
Reply to: Message 226 by herebedragons
12-23-2016 9:38 AM


Re: The purpose of phylogenetics
3) The job of a phylogenetic program is to create phylogenetic trees... that's what it does. You will NEVER get a result of "No suitable tree exists." no matter what data set you use. You may have a lot of unresolved branches, but we often do with real biological data anyway. A phylogenetic program builds and evaluates phylogenetic trees from a given data set - that's it.
Yes, though so many evolutionists believe that it would be impossible to generate phylogenetic trees in the first place if common ancestry was false... that a giant red flag would pop up and the application would break down if any data were out of place of a rigorously defined evolutionary order.
2) As much as it sounds wrong, common ancestry IS a basic assumption of phylogenetics.
That fact seems to be quite the heretical statement around here.
But before someone like vaporwave completely misunderstands this statement, I am using assumption in the way scientists use it: An assumption is a premise that must be true in order for your conclusions to be accurate. It is NOT something taken for granted, or taken without evidence, or taken by faith, or a wild-ass guess... that is not how we use assumptions in science. You must always be ready to justify your assumptions and sometimes even test them.
I actually think common ancestry is a reasonable assumption, just not nearly as strong as evolutionists make it out to be. Their whole schtick is selling the idea that common ancestry is scientifically ironclad and beyond reasonable doubt, which it isn't.

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


Message 234 of 288 (796165)
12-23-2016 3:57 PM
Reply to: Message 232 by Dr Adequate
12-23-2016 1:30 PM


Re: templates and peripheral features
the gene (or pseudogene) would have to be spread throughout the clade.
Just curious, why is this necessarily so? Wouldn't unique traits simply indicate the animal was actually more distant from the clade in question?
It would simply mean re-positioning the animal on the tree of life. Perhaps if it were unique enough it would be classified as a member of a new order of mammals, like monotremes were.

This message is a reply to:
 Message 232 by Dr Adequate, posted 12-23-2016 1:30 PM Dr Adequate has replied

Replies to this message:
 Message 235 by Dr Adequate, posted 12-23-2016 4:22 PM vaporwave has replied

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


Message 236 of 288 (796167)
12-23-2016 5:35 PM
Reply to: Message 235 by Dr Adequate
12-23-2016 4:22 PM


Re: templates and peripheral features
Well, the clade that includes flying squirrels and sugar gliders would in fact be theria, i.e. all the mammals that aren't monotremes. If, then, the flying squirrels and sugar gliders inherited a gene from a common ancestor, it would also be the common ancestor of all the other theria.
Assuming the Theria clade is correct and doesn't need to be revised.
Evolutionists are prepared to make some fairly drastic cladistic revisions if they need to.
Just a few years ago, based on genetic sequences, an evolutionary clade was proposed that would put Horses (odd-toed ungulates) closer to Bats (the flying things) than to Cows (even-toed ungulates)...
Pegasoferae is a proposed clade of mammals based on genomic research in molecular systematics by Nishihara, Hasegawa and Okada (2006).
To the surprise of the authors, their data led them to propose a clade that includes bats (order Chiroptera), carnivores such as cats and dogs (order Carnivora), horses and other odd-toed ungulates (order Perissodactyla) and pangolins (order Pholidota) as springing from a single evolutionary origin within the mammals.
Pegasoferae - Wikipedia
This clade has since been rejected but that it was seriously proposed highlights how resistant common ancestry is to being falsified by contradictory data.
Phylogenetics is not testing common ancestry.
Edited by vaporwave, : No reason given.
Edited by vaporwave, : No reason given.

This message is a reply to:
 Message 235 by Dr Adequate, posted 12-23-2016 4:22 PM Dr Adequate has replied

Replies to this message:
 Message 237 by Dr Adequate, posted 12-23-2016 6:14 PM vaporwave has replied

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


Message 239 of 288 (796177)
12-24-2016 5:11 AM
Reply to: Message 237 by Dr Adequate
12-23-2016 6:14 PM


Re: templates and peripheral features
In what sense was that "contradictory data"?
One phylogeny has odd-toed and even-toed ungulates united
One phylogeny has odd-toed ungulates more closely related to bats
These phylogenies heavily contradict each other and tell totally different stories about the evolution of ungulate traits, yet common ancestry could potentially accommodate either one.
The common ancestry story can change significantly if it is discovered an animal group's position on the tree of life needs to be changed.
Do you understand now? This is not that complicated...

This message is a reply to:
 Message 237 by Dr Adequate, posted 12-23-2016 6:14 PM Dr Adequate has replied

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


Message 244 of 288 (796230)
12-26-2016 4:58 AM
Reply to: Message 241 by RAZD
12-24-2016 8:35 AM


Re: templates and peripheral features
Because it sure looks to me like you are saying "independently evolved from existing DNA from their common therian ancestor by mutation and selection" while trying desperately to make it sound like not-evolution.
Yes, that was my entire point and it sounds like you forgot the case you were making. You act like such discoveries (e.g. the gliding membrane example) would blow evolution out of the water and falsify it immediately, but then actually it wouldn't.
The story of common ancestry is far too pliable to be tested by phylogenetics.

This message is a reply to:
 Message 241 by RAZD, posted 12-24-2016 8:35 AM RAZD has replied

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


Message 246 of 288 (796246)
12-26-2016 3:50 PM
Reply to: Message 245 by RAZD
12-26-2016 7:43 AM


Re: templates and peripheral features
Unlike your story of nested templates, which is scientifically completely useless for several reasons:
It's not something I'm committed to. I only brought it up in the first place because evolutionists here insisted on driving the discussion towards creation/design.
That said, the nested design template idea does not seem significantly more ad-hoc than common ancestry. With either origins model, it's basically just grouping shared traits and then pinning on a fanciful story to add some dramatic scenery.
Nor does it matter what your opinion is regarding the pliability of phylogenetics,
Well... this is a public discussion thread on phylogenetics.... I don't know where else I'd share my opinion on it.
what matters is that it works.
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 has been observed
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....
it has provided predictions,
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.)
, it has been tested.
Not really. Common ancestry is mostly ad-hoc.

This message is a reply to:
 Message 245 by RAZD, posted 12-26-2016 7:43 AM RAZD has replied

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


Message 249 of 288 (796280)
12-28-2016 7:09 AM
Reply to: Message 247 by RAZD
12-26-2016 10:11 PM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
There are millions of species arranged in quantifiably strong phylogenies, so a handful of indeterminates is not surprising nor unexpected -- because that's science in the real world.
Pointing to the strength of current phylogenies is irrelevant.
Evolution did not predict those phylogenies.
Evolution could have occurred an infinite number of ways, producing a near infinite number of potential phylogenies.
If the traits of animals happened to be different than what we see today, then we'd simply have a different story of common descent.
For example in Pelycodus we see
This is a good example of cherry-picking data. Fossils do not typically follow such a trend, and even this one I bet is questionable.
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.
http://news.nationalgeographic.com/...evolution-walking-land

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


Message 258 of 288 (796359)
12-29-2016 7:39 AM
Reply to: Message 251 by RAZD
12-28-2016 10:07 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
Please note that this is ~18 million years older than previous tetrapod finds, not the transitional "fishapods" -- that difference is ~10 million years.
Curiously, that is not so much "out of order" as it is that the "order" (sequence) is not fully determined, because evidence is lacking.
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.
Actually this wouldn't really bother me except evolutionists are constantly showing off cherry-picked examples of the former while concealing the latter, (providing they are not ignorant of it themselves.)
However, reality cares not a whit for how evolution could occur, and that is irrelevant to what did occur.
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.
All I'm doing is applying the same standard to common ancestry.
If the traits of animals had evolved to be different than what we see today, then we'd simply have a different story of common descent.
... And it would still show the patterns of evolution and nested hierarchies
But nested hierarchies themselves are not evidence for evolution. They may be a requirement of evolution, but that doesn't mean they explicitly point to 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?

This message is a reply to:
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Replies to this message:
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