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Author Topic:   Discussion of Phylogenetic Methods
RAZD
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Posts: 19231
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.6


Message 241 of 288 (796180)
12-24-2016 8:35 AM
Reply to: Message 231 by vaporwave
12-23-2016 1:28 PM


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.

Let's break this down:

  • "the genes were conserved" -- from what source? theria? or some other totally unknown and unevidenced gliding ancestor?
  • "for some other function" -- would this be the same function in possums and squirrels (eg - homologous genes)? or just somewhere in the DNA?
  • "later independently recruited for development of gliding membranes" -- by what process? mutation? or some other totally unknown unevidenced process
  • "because of similar selection pressures" -- ie - natural selection ... or some other unknown unevidenced process?

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.

Why is the membrane development in the Colugo different?

Enjoy


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This message is a reply to:
 Message 231 by vaporwave, posted 12-23-2016 1:28 PM vaporwave has responded

Replies to this message:
 Message 242 by herebedragons, posted 12-24-2016 8:55 AM RAZD has acknowledged this reply
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herebedragons
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Posts: 1413
From: Michigan
Joined: 11-22-2009
Member Rating: 2.8


(2)
Message 242 of 288 (796181)
12-24-2016 8:55 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.

Yea, this tactic has always puzzled me and it's pretty common. Just throw in a few buzz words like 'within a kind', 'designed', 'adapted' (instead of evolved) and 'irreducibly complex' and you have the creationist idea of a complete dismantling of the ToE.

Like this:

Independently adapted within a kind from a commonly designed DNA template through modification of an existing irreducibly complex system

Have a Merry Christmas and a happy New Year RAZD

HBD


Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca

"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.


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

  
Dr Adequate
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Posts: 15972
Joined: 07-20-2006
Member Rating: 4.7


Message 243 of 288 (796182)
12-24-2016 9:31 AM
Reply to: Message 239 by vaporwave
12-24-2016 5:11 AM


Re: templates and peripheral features
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.

'Cos neither phylogeny contradicts common ancestry.

Do you understand now? This is not that complicated...

Yeah, I should have figured out for myself that you were just blathering on about irrelevancies, but foolishly I tried to interpret your post is though it was relevant to the point under discussion, silly of me.

---

Are you going to answer my question? "Which animal, where on the tree of life?"

Edited by Dr Adequate, : No reason given.

Edited by Dr Adequate, : No reason given.


This message is a reply to:
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vaporwave
Member (Idle past 238 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 responded

Replies to this message:
 Message 245 by RAZD, posted 12-26-2016 7:43 AM vaporwave has responded

    
RAZD
Member
Posts: 19231
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.6


Message 245 of 288 (796231)
12-26-2016 7:43 AM
Reply to: Message 244 by vaporwave
12-26-2016 4:58 AM


Re: templates and peripheral features
Yes, that was my entire point and it sounds like you forgot the case you were making. ...

The one where I'm asking you to explain how your templates work? The one which has observed your explanation evolve to nested templates but where you won't commit to whether or not the templates for gliding membranes are the same or different? The one that has led you into a position of mirroring evolutionary processes with your use of templates? Seems to me I'm right on target, and now that you are in a box you try to pretend I'm arguing something else?

Sorry, that won't work.

... 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.

Curiously I'm the expert on what my argument is about, so like Dr A, I'll ask you to let me decide what my argument actually is.

You could of course use actual quotes instead of false claims ... if you can find them.

The story of common ancestry is far too pliable to be tested by phylogenetics.

Unlike your story of nested templates, which is scientifically completely useless for several reasons:

  1. they don't exist, there is no evidence for them
  2. there is no known process to apply them
  3. they provide no testable predictions
  4. doesn't provide any explanation that is not identical to evolution
  5. doesn't explain anything new that evolution does not explain

Nor does it matter what your opinion is regarding the pliability of phylogenetics, what matters is that it works. It has been observed, it has provided predictions, it has been tested.

It shows that the platypus are not closely related to ducks, and are only related by very distant non-duck billed common ancestors. It shows that the sugar gliders, and flying squirrels are not closely related, and are only distantly related by non gliding membrane common ancestors.

Enjoy

Edited by RAZD, : .


we are limited in our ability to understand
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RebelAmerican☆Zen☯Deist
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This message is a reply to:
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Replies to this message:
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vaporwave
Member (Idle past 238 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 responded

Replies to this message:
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RAZD
Member
Posts: 19231
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.6


Message 247 of 288 (796253)
12-26-2016 10:11 PM
Reply to: Message 246 by vaporwave
12-26-2016 3:50 PM


we have motive (survival) means (evolution) and opportunity (proximity)
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. ...

Except that templates are pure imagination with ad hoc peripheral features added to fit special cases, each time differently. It is useless.

Common ancestry does have evidence both of mechanism and observed occurrences. That is the difference between scientific hypothesis and theory from imaginary ad hoc fantasies.

... It's not something I'm committed to.

Obviously.

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.

You have every right to express your opinion, but you do not have the right to have it considered as anything other than ad hoc fantasy unless and until you provide objective empirical evidence to support your opinion. Opinion, historically, as a very poor record of altering reality in any way shape or form.

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.

A claim you have failed to substantiate in any way. There are a couple of examples that other people have brought up showing some small difficulty in determining lineage, as in the frogs above, and the reasons for those difficulties are also documented - their evolution was too rapid to show up in the markers.

Your argument is that this invalidates all the rest of the phylogeny where no such problems exist. It doesn't, and it doesn't even bring the methodology into question.

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.

It isn't a willy nilly ad hoc arrangement either, as the evidence has to fit the requirement to be near in time and space ... there has to be motive (survival) means (evolution) and opportunity (proximity ... there had to be contact).

For example in Pelycodus we see

quote:
A Smooth Fossil Transition: Pelycodus, a primate

The dashed lines show the overall trend. The species at the bottom is Pelycodus ralstoni, but at the top we find two species, Notharctus nunienus and Notharctus venticolus. The two species later became even more distinct, and the descendants of nunienus are now labeled as genus Smilodectes instead of genus Notharctus.

As you look from bottom to top, you will see that each group has some overlap with what came before. There are no major breaks or sudden jumps. And the form of the creatures was changing steadily.


There is the evidence of generation by generation of evolution from common ancestor populations to younger populations, and the division at the top into two reproductively isolated daughter species.

From a common ancestor population, Pelycodus jarrovii.

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....

And yet we have the fossils that show the appropriate evolutionary changes at the appropriate times and in the appropriate locations ... we have motive (survival) means (evolution) and opportunity (proximity).

And we have the evidence that what is observed in the world today, and what is supported by the fossil evidence like Pelycodus (and others) provide is sufficient to explain the rest of the fossil record using the same processes. We don't have to invent any new or different process to explain the vast record of natural life on earth.

it has provided predictions,

Common ancestry has provided tons of predictions. ...

Agreed.

... 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....

Two very strong reasons why genetic phylogenies are innaccurate in a small number of cases ... ones we can test in the lab.

AND last time I checked two <<<<< tons.

... well we'll have to move that node somewhere else on the tree of life... etc.)

And curiously this is the scientific process when new information becomes available. This happens in ALL science.

, it has been tested.

Not really. Common ancestry is mostly ad-hoc.

Repeating your fallacious opinion doesn't make it any more correct.

If it were ad hoc, then two different groups would arrive at two different conclusions almost every time. Clearly that does not happen.

Enjoy

Edited by RAZD, : proximity


we are limited in our ability to understand
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This message is a reply to:
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Replies to this message:
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Dr Adequate
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Posts: 15972
Joined: 07-20-2006
Member Rating: 4.7


(1)
Message 248 of 288 (796254)
12-26-2016 10:43 PM
Reply to: Message 246 by vaporwave
12-26-2016 3:50 PM


Re: templates and peripheral features
I note from your latest inane ramblings that you still don't know what a conserved sequence is and that we can tell whether a gene is well-conserved by looking at it.

While concepts as simple as this escape you, you should not be lecturing us on any aspect of genetics, evolution, or biology.


This message is a reply to:
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vaporwave
Member (Idle past 238 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


This message is a reply to:
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JonF
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Posts: 3993
Joined: 06-23-2003
Member Rating: 2.6


Message 250 of 288 (796282)
12-28-2016 7:54 AM
Reply to: Message 249 by vaporwave
12-28-2016 7:09 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
Evolution predicted a nested hierarchy phylogeny, but not a specific phylogeny. Any nested hierarchy phylogeny is a very unlikely event, and demands explanation.
This message is a reply to:
 Message 249 by vaporwave, posted 12-28-2016 7:09 AM vaporwave has not yet responded

  
RAZD
Member
Posts: 19231
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.6


(2)
Message 251 of 288 (796285)
12-28-2016 10:07 AM
Reply to: Message 249 by vaporwave
12-28-2016 7:09 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
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.

You mean this?

quote:
Oldest Land-Walker Tracks Found--Pushes Back Evolution

An undetermined species of tetrapod (illustrated) created tracks in what's now a Polish quarry (bottom), a new study says.

The first vertebrates to walk the Earth emerged from the sea almost 20 million years earlier than previously thought, say scientists who have discovered footprints from an 8-foot-long (2.4-meter-long) prehistoric creature.

Discovered in an abandoned mountain quarry, the tracks suggest that tetrapods were traipsing the planet 18 million years earlier than previously indicated by the fossil record.

Dozens of the 395-million-year-old fossil footprints were recently discovered on a former marine tidal flat or lagoon in southeastern Poland (prehistoric time line).

The tracks are also ten million years older than the oldest known fossils of lobe-finned fishes called elpistostegids, which are widely considered to be transitional forms between fish and tetrapods.

The age of the newfound tracks suggest that "these transitional fish continued to exist alongside the tetrapods for quite some period of time," said Per Ahlberg, a paleontologist at Uppsala University in Sweden, who led the new research.

It's not so strange for one type of animal to live alongside its evolutionary successors, Ahlberg noted. Several feathered dinosaurs, for example, "continued to exist alongside the birds for millions of years."


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.

Pointing to the strength of current phylogenies is irrelevant.

Pointing to small numbers of seeming anomalies out of thousands and thousands of non-anomalous phylogenies is irrelevant.

Evolution could have occurred an infinite number of ways, producing a near infinite number of potential phylogenies.

And your templates could have produced fire breathing flying dragons and an infinite number of fantasies. After all they produced over 99% of the beasts whose only record is the fossils they left behind ... were they designed\created just to fill voids in rocks?

However, reality cares not a whit for how evolution could occur, and that is irrelevant to what did occur. Fossils are the record of what did occur, and evolution with nested hierarchies explain the evidence better than any other theory or hypothesis.

Evolution does not mean that anything that could be imagined would occur, only what survives and reproduces and evolves from ancestors that provide the base for modification and adaptation. Evolution cannot create wings without adapting an existing structure and modifying it to suit.

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.

Let me fix that for you:

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.

Correct. And it would still show the patterns of evolution and nested hierarchies ... because the mechanisms and processes that cause these are well known, observed and documented, and no other process that has been suggested explains the evidence any where near as well.

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.

No, it is an example of the fossil evidence available, one that shows the development of a nested hierarchy by common descent from ancestor populations.

Another example is foraminifera:

quote:
A Classic Tale of Transition

Drs. Tony Arnold (Ph.D., Harvard) and Bill Parker (Ph.D., Chicago) are the developers of what reportedly is the largest, most complete set of data ever compiled on the evolutionary history of an organism. The two scientists have painstakingly pieced together a virtually unbroken fossil record that shows in stunning detail how a single-celled marine organism has evolved during the past 66 million years. Apparently, it's the only fossil record known to science that has no obvious gaps -- no "missing links."

"It's all here -- a complete record," says Arnold. "There are other good examples, but this is by far the best. We're seeing the whole picture of how this organism has changed throughout most of its existence on Earth."

The pattern is exactly what Arnold and Parker have found in the forams. It is but one of a number of observations that the FSU team has made thus far about what arguably is nature's crowning achievement -- the act of speciation itself.

"We've literally seen hundreds of speciation events," Arnold added. "This allows us to check for patterns, to determine what exactly is going on. We can quickly tell whether something is a recurring phenomenon -- a pattern -- or whether it's just an anomaly.


That's 66 million years of continuous evolution documented in the fossil record and hundreds of speciation events that form nested hierarchies.

... This is a good example of cherry-picking data. Fossils do not typically follow such a trend, ...

This level of detail is not always available, but whenever the detailed evidence exists, it shows the same patterns of evolution and the formation of nested hierarchies from common ancestor populations.

So .. we have the evidence (fossils), motive (survival) means (evolution) and opportunity (proximity).

Enjoy

Edited by RAZD, : .


we are limited in our ability to understand
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RebelAmerican☆Zen☯Deist
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This message is a reply to:
 Message 249 by vaporwave, posted 12-28-2016 7:09 AM vaporwave has responded

Replies to this message:
 Message 258 by vaporwave, posted 12-29-2016 7:39 AM RAZD has responded

  
Taq
Member
Posts: 7263
Joined: 03-06-2009
Member Rating: 3.7


(1)
Message 252 of 288 (796286)
12-28-2016 10:42 AM
Reply to: Message 233 by vaporwave
12-23-2016 3:39 PM


Re: The purpose of phylogenetics
vaporwave writes:

Yes, though so many evolutionists believe that it would be impossible to generate phylogenetic trees in the first place if common ancestry was false...

You have been incapable of explaining why something other than common ancestry would necessarily produce a nested hierarchy. If you can't come up with a logical and valid reason why a process other than common ancestry would necessarily produce a nested hierarchy, then our point stands.

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.

Doesn't change the fact that all of the evidence supports common ancestry.


This message is a reply to:
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Taq
Member
Posts: 7263
Joined: 03-06-2009
Member Rating: 3.7


(1)
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.


This message is a reply to:
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Taq
Member
Posts: 7263
Joined: 03-06-2009
Member Rating: 3.7


(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."
https://www.ncbi.nlm.nih.gov/pubmed/1948030

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?


This message is a reply to:
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Dr Adequate
Member
Posts: 15972
Joined: 07-20-2006
Member Rating: 4.7


(2)
Message 255 of 288 (796290)
12-28-2016 10:54 AM
Reply to: Message 249 by vaporwave
12-28-2016 7:09 AM


Re: we have motive (survival) means (evolution) and opportunity (proximity)
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.

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.

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 249 by vaporwave, posted 12-28-2016 7:09 AM vaporwave has not yet responded

  
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