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Author Topic:   Discussion of Phylogenetic Methods
herebedragons
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Posts: 1341
From: Michigan
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(1)
Message 226 of 288 (796137)
12-23-2016 9:38 AM
Reply to: Message 212 by Taq
12-22-2016 1:01 PM


The purpose of phylogenetics
caffeine writes:

I'm taking issue with the point I've seen Taq and others make more than once on these forums, that phylogenetics by itself is a test of common ancestry. Since we don't reject common ancestry when we cannot produce a well supported phylogeny, it seems dishonest to say we're testing evolution this way.

But we do produce well supported phylogenies all over the place. I have already cited the cytochrome c example.

I agree with Caffeine on this, and we have had this discussion before but I have been too busy to participate much and really didn't finish up our last exchange. By itself phylogenetics are not a true test of common ancestry. Here is my reasoning:

1) When we do a phylogenetic analysis we don't have a null hypothesis - especially one that says that there is no common ancestor for the taxa. A true test of common ancestry would involve a hypothesis such as "these taxa are related by common ancestry" and a null hypothesis such as "these taxa are not related by common ancestry." Instead the question that a phylogeny asks is "What is the BEST hypothesis as to how these taxa are related by descent."

2) As much as it sounds wrong, common ancestry IS a basic assumption of phylogenetics. 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.

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.

4) Phylogenetic signal or phylogenetic support is a statistical methodology that is used like other statistical methodologies - essentially they state how likely the data is to be non-random. When you see 95% support for a particular branch, that means there is a 5% chance that the data is just random and only appears to fit that pattern (phylogenetic support is a little more nuanced than that, but that is essentially what the support value tells us). No tree has 100% support for all branches, it just doesn't happen. In fact, I would say that it is more typical for 1/3 or more of the branches to have support values below the reporting threshold (usually 70%) and when they don't report them they can be anywhere below that threshold, even say 10%.

5) Related to #4, what threshold of phylogenetic signal or phylogenetic support would cause the researcher to conclude that there is no common ancestor between the two taxa? There is NOTHING in the tree itself that would lead you to conclude there is no common ancestor. I think this is the strongest point for my case.

The key to my argument is that phylogenetic trees are not support for common ancestry by themselves, but must be coupled with other data to be useful. And that is where phylogenetics provide real support for common ancestry - we can produce meaningful reconstructions!

For example, I am certain that I could develop a data set for cars that would result in a decent phylogram. But it would be completely meaningless from any evolutionary perspective. For instance, it might group a 1927 Ford model T with a 2010 Ford Focus because they are both Fords, have 4 cylinder engines and the same horsepower rating . But that is completely meaningless from an evolutionary standpoint - that is they are not related in time or space.

Biological phylogenies, on the other hand, produce meaningful hypotheses that can be used to make predictions and further develop understanding. For example, it seems just about as daft to group hippos and whales together as it does to group the model T and the Ford Focus together, unless you know more about the biology of the organisms. The whale - hippo relationship also makes specific predictions about what intermediate forms should be found and where we expect to find them in relation to time and space.

Phylogenetics also makes predictions about physiological characteristic of closely related taxa as opposed to more distantly related taxa. We use this information to make investigating biological function more productive. I used a phylogenetic approach to look for disease resistance in a dry bean diversity panel. It improved my success rate 4 fold, although I never really found anything that was suitably resistant.

Vaprowave mentioned that molecular phylogenies were overturning long standing morphological phylogenies. In this he is largely correct, especially in plants and fungi. The problem with morphology is that it can be very difficult to know what traits are evolutionary important so that those traits are chosen to construct phylogenies. Molecular work has made those relationship much less subjective (there is still some subjective nature to molecular work, but much, much less so than with morphological data). Phylogenetics has given us significant insight into how evolutionary mechanisms work. Again, they lead to hypotheses about evolutionary mechanisms that can be tested and verified.

Bottom line: being able to construct phylogenetic trees from biological data is not in and of itself a true test of common ancestry. It is the meaningful insights that come from phylogenetic reconstructions and the resulting hypothesis testing that provides support for common ancestry.

Maybe this is semantics, or a highly technical perspective on the subject, but I think it is important to recognize the weaknesses and limitations of our methodologies as well as the strengths. For the most part you are doing great at explaining the strengths of phylogenetics and have given good examples. Good job on the protein alignment - I thought about doing something like that but it was just too time consuming.

And just to be clear to all, despite my minor disagreement with Taq on this, vaporwave's overall assessment of phylogenetics, as presented on this thread, is uninformed and just plain wrong, even though he may have some of the general points more or less right. This is so typical of creationists who get their biological training from creationist websites and books rather than learning any real biology.

Merry Christmas and have a happy New Year...

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:
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herebedragons
Member
Posts: 1341
From: Michigan
Joined: 11-22-2009
Member Rating: 4.9


(1)
Message 227 of 288 (796140)
12-23-2016 9:51 AM
Reply to: Message 225 by RAZD
12-23-2016 8:36 AM


Re: metaphysics and morphology and macroevolution
no alternate hypothesis or theory provides the detail explanation for the observed objective empirical evidence that evolution theory provides. No alternative hypothesis\theory has made testable predictions that don't falsify them, or they have failed entirely to make testable predictions.

To me, this is by far the strongest point in favor of evolutionary theory. I do feel that evolutionary theory has some weak areas... areas that are pretty much biological black boxes, and I would love for a revised or new theory to come out that could fill in those gaps. And I would especially love to be the one who made those revisions. But for now the ToE is the absolute BEST explanation for the diversity of life on earth that we have. There isn't even a close second - there isn't even a semi-viable alternative.

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 225 by RAZD, posted 12-23-2016 8:36 AM RAZD has acknowledged this reply

  
Dr Adequate
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Posts: 15948
Joined: 07-20-2006
Member Rating: 4.3


Message 228 of 288 (796141)
12-23-2016 9:55 AM
Reply to: Message 224 by vaporwave
12-23-2016 7:23 AM


Re: templates and peripheral features
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.

But it can't. Gliding is not in fact an ancestral characteristic of mammals, and if it was then the genes would be found throughout the mammal class if only as pseudogenes. If they weren't there, that would destroy any such hypothesis.

Unlike "design"/magic, evolution is testable.

You mean a more complex explanation than "natural selection did it" ?

You should really find out what the theory of evolution is, it's fascinating.

An alternative hypothesis doesn't necessarily have to be complex. If you like it could be as simple as the theory of evolution or even as simple as the theory of gravity. What we should require of it is first that it should actually exist, second, that it should be predictive, third, that its predictions should be correct. If it does better than the theory of evolution, we'll adopt it.

So far you're stuck on not even having anything with enough content to qualify as a hypothesis. Let us know.

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 224 by vaporwave, posted 12-23-2016 7:23 AM vaporwave has responded

Replies to this message:
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RAZD
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Posts: 18855
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Joined: 03-14-2004
Member Rating: 3.5


Message 229 of 288 (796145)
12-23-2016 10:42 AM
Reply to: Message 224 by vaporwave
12-23-2016 7:23 AM


Re: templates and peripheral features
So is the template that generates the gliding membranes in flying squirrel and sugar glider the same?

Depends. ...

On what? Whim? We're looking for a theory that can be tested and one that makes predictions, not one that depends on some arbitrary application of an untested concept.

... 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.

We are talking about flaps of skin, not internal structure.

Or is this why the skin flaps on the frog are just between toes? Because the internal anatomy of flying frogs is so different from the mammals?

Can those internal differences predict which template causes this group of frogs to grow membranes between toes or not?

quote:
Or even for Wallace's Frog

quote:
Wallace's flying frog or the Abah River flying frog (Rhacophorus nigropalmatus) is a moss frog found at least from the Malay Peninsula into western Indonesia. It is named for the biologist, Alfred R. Wallace, who collected the first specimen to be formally identified.


picture source

Help us understand how these traits are generated without evolution.


So is the template that generates the gliding membranes in flying squirrel and sugar glider the same? And is it the same for the colugo and the flying frog?

Is the template for webbed frog feet also used to generate webbed feet in Newfoundland and some other dogs?

quote:
5 Dog Breeds With Webbed Feet

This black wooly giant of a dog was bred to help Newfoundland fishermen work in the cold waters of Canada. Nearly every one of their traits is perfectly suited to make them experts at that duty. Their thick fur is water resistant, their muscular build lets them haul in fishing nets and carts, and their size and loyalty make them perfect for lifesaving should a man fall overboard. And, of course, they have thick, webbed paws and the longest toes of any breed that let them tear through the water. They also use those paws to swim in a unique way, with a down-and-out motion, rather than an ordinary dog paddle. This lets them power through waves and surf. They’re so good at being water companions that a Newfoundland named Seaman accompanied Lewis and Clark as they explored and mapped the rivers of the American frontier.


Or the webbed feet of ducks? the platypus?

people?

(image source)

Is that from the same template as the flying squirrel and sugar glider?

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 ...

Except that the membranes did not occur in older ancestors, and so would not expect them to be a conserved DNA section.

You mean a more complex explanation than "natural selection did it" ?

It is a common mistake of creationists to equal natural selection with evolution, and anyone saying this just demonstrates ignorance of how evolution actually works (and has been observed to work).

Remember this?

(1) The process of evolution involves changes in the composition of hereditary traits, and changes to the frequency of their distributions within breeding populations from generation to generation, in response to ecological challenges and opportunities.

and this?

Evolution is a two-step feedback response system that is repeated in each generation, like walking on first one foot and then the next.

Each generation builds on the generation before to adapt to their ecological challenges and opportunities.

Evolution would accommodate both observations in this case, just like design.

Evolution does indeed accommodate observed objective empirical evidence, that is the nature of science. It also makes testable predictions.

So far I have not seen any predictions from your nested templates concept, you haven't shown how it is activated or instigated, and you can't even decide whether or not one is used for both the webbed membranes of sugar gliders and flying squirrels. It's appears more like waving hands than providing a usable concept.

So I'm still trying to understand how these traits are generated by templates without evolution.

Enjoy


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This message is a reply to:
 Message 224 by vaporwave, posted 12-23-2016 7:23 AM vaporwave has responded

Replies to this message:
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vaporwave
Member (Idle past 139 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.

http://what-when-how.com/...ne-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 responded

Replies to this message:
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vaporwave
Member (Idle past 139 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 responded

Replies to this message:
 Message 241 by RAZD, posted 12-24-2016 8:35 AM vaporwave has responded

    
Dr Adequate
Member
Posts: 15948
Joined: 07-20-2006
Member Rating: 4.3


Message 232 of 288 (796156)
12-23-2016 1:30 PM
Reply to: Message 230 by vaporwave
12-23-2016 1:21 PM


Re: templates and peripheral features
That's how evolution could accommodate similar genetic organization of gliding membranes in marsupials and eutherians. It would not disprove common ancestry.

Your excuse might be somewhat plausible if they were just vaguely similar, but not if they were the same. And either way or your excuse to hold water the gene (or pseudogene) would have to be spread throughout the clade.

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 230 by vaporwave, posted 12-23-2016 1:21 PM vaporwave has responded

Replies to this message:
 Message 234 by vaporwave, posted 12-23-2016 3:57 PM Dr Adequate has responded

  
vaporwave
Member (Idle past 139 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 139 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 responded

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

    
Dr Adequate
Member
Posts: 15948
Joined: 07-20-2006
Member Rating: 4.3


Message 235 of 288 (796166)
12-23-2016 4:22 PM
Reply to: Message 234 by vaporwave
12-23-2016 3:57 PM


Re: templates and peripheral features
Just curious, why is this necessarily so?

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.

It would simply mean re-positioning the animal on the tree of life.

Which animal, where on the tree of life?


This message is a reply to:
 Message 234 by vaporwave, posted 12-23-2016 3:57 PM vaporwave has responded

Replies to this message:
 Message 236 by vaporwave, posted 12-23-2016 5:35 PM Dr Adequate has responded

  
vaporwave
Member (Idle past 139 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.

https://en.wikipedia.org/wiki/Pegasoferae

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 responded

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

    
Dr Adequate
Member
Posts: 15948
Joined: 07-20-2006
Member Rating: 4.3


Message 237 of 288 (796168)
12-23-2016 6:14 PM
Reply to: Message 236 by vaporwave
12-23-2016 5:35 PM


Re: templates and peripheral features
Assuming the Theria clade is correct and doesn't need to be revised.

Revised how? By putting a marsupial next to a squirrel? What do you have in mind? 'Cos that wouldn't work either.

This clade has since been rejected but that it was seriously proposed highlights how resistant common ancestry is to being falsified by contradictory data.

In what sense was that "contradictory data"?

Phylogenetics is not testing common ancestry.

Assertion is not argument.

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

Edited by Dr Adequate, : No reason given.


This message is a reply to:
 Message 236 by vaporwave, posted 12-23-2016 5:35 PM vaporwave has responded

Replies to this message:
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Tangle
Member
Posts: 4950
From: UK
Joined: 10-07-2011
Member Rating: 3.1


Message 238 of 288 (796176)
12-24-2016 3:35 AM
Reply to: Message 237 by Dr Adequate
12-23-2016 6:14 PM


Re: templates and peripheral features
Dr. A writes:

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

I'll sure he'll get round to that just after he's provided evidence against common descent and just before he confirms he not a creationist.

Like never. He prefers waffle to fact.


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 237 by Dr Adequate, posted 12-23-2016 6:14 PM Dr Adequate has not yet responded

  
vaporwave
Member (Idle past 139 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 responded

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Tangle
Member
Posts: 4950
From: UK
Joined: 10-07-2011
Member Rating: 3.1


Message 240 of 288 (796178)
12-24-2016 5:49 AM
Reply to: Message 239 by vaporwave
12-24-2016 5:11 AM


Re: templates and peripheral features
vaporwave writes:

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.

And you do understand that when your god gave us this jigsaw puzzle to figure out he didn't provide the picture on the box lid, left 90% of the parts out and scattered the rest across and inside the globe creating an almost never ending treasure hunt?

Gonna help with those other questions yet?


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 239 by vaporwave, posted 12-24-2016 5:11 AM vaporwave has not yet responded

  
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