Register | Sign In


Understanding through Discussion


EvC Forum active members: 65 (9162 total)
6 online now:
Newest Member: popoi
Post Volume: Total: 915,815 Year: 3,072/9,624 Month: 917/1,588 Week: 100/223 Day: 11/17 Hour: 0/7


Thread  Details

Email This Thread
Newer Topic | Older Topic
  
Author Topic:   Discussion of Phylogenetic Methods
Coyote
Member (Idle past 2106 days)
Posts: 6117
Joined: 01-12-2008


(1)
Message 91 of 288 (795939)
12-19-2016 9:21 PM
Reply to: Message 87 by vaporwave
12-19-2016 7:15 PM


Re: The purpose of phylogenetics
Animals that share similar anatomical systems tend to share similar genetic organization of that anatomy.
Not so.
There are three groups of humans with high altitude adaptations, and each uses a different method.
You can find the details here:
High-altitude adaptation in humans - Wikipedia
Also, human skin color is very dark among three (or four) different groups, but those groups are not closely related:
Dark skin - Wikipedia
The primary factor is intensity of UV radiation.

Religious belief does not constitute scientific evidence, nor does it convey scientific knowledge.
Belief gets in the way of learning--Robert A. Heinlein
In the name of diversity, college student demands to be kept in ignorance of the culture that made diversity a value--StultisTheFool
It's not what we don't know that hurts, it's what we know that ain't so--Will Rogers
If I am entitled to something, someone else is obliged to pay--Jerry Pournelle
If a religion's teachings are true, then it should have nothing to fear from science...--dwise1
"Multiculturalism" demands that the US be tolerant of everything except its own past, culture, traditions, and identity.

This message is a reply to:
 Message 87 by vaporwave, posted 12-19-2016 7:15 PM vaporwave has not replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


(2)
Message 92 of 288 (795947)
12-20-2016 2:45 AM
Reply to: Message 88 by vaporwave
12-19-2016 7:30 PM


Re: The purpose of phylogenetics
vaporwave writes:
Right, and to an evolutionist this is vindication of the theory.
Right, you see when two different methods of organising groups into sets produce the same result, it strengthens the idea that the sets are correct. Had molecular biology produced a different result, there would have been a lot of head scratching and you might have the beginnings of an argument. As it is, you're buggered.
Now how are you getting on disproving the ToE with evidence instead of words?

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 88 by vaporwave, posted 12-19-2016 7:30 PM vaporwave has replied

Replies to this message:
 Message 95 by vaporwave, posted 12-20-2016 6:59 AM Tangle has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 93 of 288 (795949)
12-20-2016 6:19 AM
Reply to: Message 76 by caffeine
12-19-2016 4:20 PM


Re: The purpose of phylogenetics
Phylogenetics does not make any sense as evidence for evolution. That's not what it's meant to be. Phylogenetics is what we do once we know evolution has occured. It's all about techniques to figure out how.
Eh, I mean that's kind of a sweeping statement. There are a number of ways phylogenetics makes sense as a confirmation of the broad theory of common descent.
E.g., I conducted molecular phylogenetics research on a set of prokaryotic transporters. The phylogenies weren't congruent with the species phylogeny as established by dozens of well-conserved proteins. This suggested horizontal gene transfer, and when I hunted for signs of HGT (based on GC content analyses), they showed up exactly where one would expect if the species phylogeny was correct (p = .04, based on independent samples t-test).
These results really only make sense under a model of common ancestry -- and it is, in fact, what one would predict under that model.
There's plenty of other examples that could be cited, too. Mol phylogenetics is widely used by evolutionary biologists as a tool within the theory of evolution, but it has also stridently confirmed the theory of common descent.

This message is a reply to:
 Message 76 by caffeine, posted 12-19-2016 4:20 PM caffeine has seen this message but not replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 94 of 288 (795950)
12-20-2016 6:27 AM
Reply to: Message 87 by vaporwave
12-19-2016 7:15 PM


Re: The purpose of phylogenetics
As I said, there is a pattern. Animals that share similar anatomical systems tend to share similar genetic organization of that anatomy.
Your problem is you cannot see the distinction between this observation and your assumption of common ancestry.
I can see that distinction, but that distinction has little merit. It doesn't explain the general concordance of various types of molecular phylogenies: protein sequence data, ERVs, phylogenies constructed from synonymous sites, etc. These sorts of molecular phylogenies all point to a conclusion as inescapable-as-a-spaceship-in-a-black-hole: that the theory of common descent is the most robust explanation for life's diversity.

This message is a reply to:
 Message 87 by vaporwave, posted 12-19-2016 7:15 PM vaporwave has replied

Replies to this message:
 Message 96 by vaporwave, posted 12-20-2016 7:41 AM Genomicus has replied

  
vaporwave
Member (Idle past 2644 days)
Posts: 66
Joined: 12-17-2016


Message 95 of 288 (795951)
12-20-2016 6:59 AM
Reply to: Message 92 by Tangle
12-20-2016 2:45 AM


Re: The purpose of phylogenetics
Right, you see when two different methods of organising groups into sets produce the same result, it strengthens the idea that the sets are correct
The "sets are correct" ? What does that mean?
Had molecular biology produced a different result, there would have been a lot of head scratching
Debatable. The common ancestry narrative is surprisingly malleable.
Also, I asked you to explain how you knew this:
But without common descent there's no reason for DNA and form based taxonomy to agree on their classification
It seems a lot of your case hinges on this claim.

This message is a reply to:
 Message 92 by Tangle, posted 12-20-2016 2:45 AM Tangle has replied

Replies to this message:
 Message 102 by Tangle, posted 12-20-2016 8:38 AM vaporwave has replied

  
vaporwave
Member (Idle past 2644 days)
Posts: 66
Joined: 12-17-2016


Message 96 of 288 (795953)
12-20-2016 7:41 AM
Reply to: Message 94 by Genomicus
12-20-2016 6:27 AM


Re: The purpose of phylogenetics
It doesn't explain the general concordance of various types of molecular phylogenies: protein sequence data, ERVs, phylogenies constructed from synonymous sites, etc.
Eh... I don't see that concordance as confirming much of anything but the concordance itself.
You seem to be making the same leap in logic and just assuming common ancestry.
You are selecting a group of shared traits (e.g. mammals: endothermy, hair, neocortex, mammary glands, etc.) and bringing them into deeper focus on a molecular level, and finding the pattern of similarity to persist.
Why would it not persist?

This message is a reply to:
 Message 94 by Genomicus, posted 12-20-2016 6:27 AM Genomicus has replied

Replies to this message:
 Message 97 by Genomicus, posted 12-20-2016 7:48 AM vaporwave has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 97 of 288 (795954)
12-20-2016 7:48 AM
Reply to: Message 96 by vaporwave
12-20-2016 7:41 AM


Re: The purpose of phylogenetics
You are selecting a group of shared traits (e.g. mammals: endothermy, hair, neocortex, mammary glands, etc.) and bringing them into deeper focus on a molecular level, and finding the pattern of similarity to persist.
It's not the similarity that matters here. It is the concordant nested hierarchies of similarities that exist between disparate sequence data. Why would primate phylogenies created from synonymous sites match protein phylogenies if not for common descent? It's exactly what we'd expect from the thesis of shared ancestry among primates.

This message is a reply to:
 Message 96 by vaporwave, posted 12-20-2016 7:41 AM vaporwave has replied

Replies to this message:
 Message 99 by vaporwave, posted 12-20-2016 8:08 AM Genomicus has replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 98 of 288 (795955)
12-20-2016 7:51 AM
Reply to: Message 82 by vaporwave
12-19-2016 6:11 PM


The purpose of science
What he's saying is that because DNA didn't group giraffes with turtles instead of other mammals, Common Ancestry was totally vindicated.
Well grouping giraffes with turtles would have falsified that section of the morphology phylogenetic tree hypothesis, wouldn't it? Would not whole scale scrambling of all the branches have falsified the whole thing?
That's how science tests of hypothesis work -- they either falsify or don't falsify the hypothesis\theory.
Evolutionists really set the bar high.
No different than any other science. There is no "proof" in science, it's all built up on hypothesis and theory that have not been falsified, and all falsified concepts are discarded.
I refer you to the diagram in Message 70 on the scientific method and the red box in the diagram:
Is Hypothesis invalidated?
and then again to the green box at the end:
Are results replicated?
The options are "yes" or "no" ... no proof, just invalidation or not.
And what we see is that the DNA evidence did not invalidate the morpological evidence across the board, although there were some minor adjustments that were turned up.
And this again is part of the general scientific process: when new evidence shows the previous concept was wrong it is either adjusted to fit the new data or it is discarded in favor of a new concept that explains all the evidence.
Enjoy

we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
to share.


Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)

This message is a reply to:
 Message 82 by vaporwave, posted 12-19-2016 6:11 PM vaporwave has replied

Replies to this message:
 Message 101 by vaporwave, posted 12-20-2016 8:31 AM RAZD has replied

  
vaporwave
Member (Idle past 2644 days)
Posts: 66
Joined: 12-17-2016


Message 99 of 288 (795956)
12-20-2016 8:08 AM
Reply to: Message 97 by Genomicus
12-20-2016 7:48 AM


Re: The purpose of phylogenetics
It's not the similarity that matters here. It is the concordant nested hierarchies of similarities that exist between disparate sequence data.
What do you mean similarity doesn't matter? The nested hierarchies are arranged based off similarity to begin with.

This message is a reply to:
 Message 97 by Genomicus, posted 12-20-2016 7:48 AM Genomicus has replied

Replies to this message:
 Message 100 by Genomicus, posted 12-20-2016 8:30 AM vaporwave has replied

  
Genomicus
Member (Idle past 1941 days)
Posts: 852
Joined: 02-15-2012


Message 100 of 288 (795958)
12-20-2016 8:30 AM
Reply to: Message 99 by vaporwave
12-20-2016 8:08 AM


Re: The purpose of phylogenetics
It's the concordant nested hierarchy of similarities that matters, because randomly distributed similarities would be rather contrary to the evolutionary synthesis. Of course, convergences will emerge throughout the evolutionary bush, but a clear pattern of nested hierarchies exists.
So why do primate phylogenies created from synonymous sites match phylogenies generated from amino acid sequence data?

This message is a reply to:
 Message 99 by vaporwave, posted 12-20-2016 8:08 AM vaporwave has replied

Replies to this message:
 Message 105 by vaporwave, posted 12-20-2016 9:08 AM Genomicus has replied

  
vaporwave
Member (Idle past 2644 days)
Posts: 66
Joined: 12-17-2016


Message 101 of 288 (795959)
12-20-2016 8:31 AM
Reply to: Message 98 by RAZD
12-20-2016 7:51 AM


Re: The purpose of science
Well grouping giraffes with turtles would have falsified that section of the morphology phylogenetic tree hypothesis, wouldn't it?
Probably, yea. I just think it's lame to consider it a stunning victory of evolution theory.
I think even if molecular researchers had no concept of common ancestry they could have made similar predictions based off the simple idea that beings of similar anatomical properties are going to be more similar to each other in additional ways than not.
If you had no concept of evolutionary relationships and furthermore knew absolutely nothing about internal anatomy and saw a dog, a cat, and a turtle. Which ones would you guess to be more similar to each other if you dissected them?

This message is a reply to:
 Message 98 by RAZD, posted 12-20-2016 7:51 AM RAZD has replied

Replies to this message:
 Message 103 by Tangle, posted 12-20-2016 8:47 AM vaporwave has not replied
 Message 104 by RAZD, posted 12-20-2016 8:58 AM vaporwave has replied
 Message 125 by Taq, posted 12-20-2016 12:31 PM vaporwave has replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


(1)
Message 102 of 288 (795960)
12-20-2016 8:38 AM
Reply to: Message 95 by vaporwave
12-20-2016 6:59 AM


Re: The purpose of phylogenetics
vaporwave writes:
The "sets are correct" ? What does that mean?
It means that common descent has been shown by two different and distinct methods. Species that look related at a level of physical sructure have been shown to be related at a molecular level too. And this relationship is demonstrable over time. The molecular analysis also reveals when species diverged.
It seems a lot of your case hinges on this claim.
It does, or rather it did - had DNA not supported the theory, it would have been devastating for it. But it did. You lose.
Still no actual evidence I see, you're still dicking about with error-ridden pseudologic.

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 95 by vaporwave, posted 12-20-2016 6:59 AM vaporwave has replied

Replies to this message:
 Message 107 by vaporwave, posted 12-20-2016 9:12 AM Tangle has replied

  
Tangle
Member
Posts: 9489
From: UK
Joined: 10-07-2011
Member Rating: 4.9


Message 103 of 288 (795961)
12-20-2016 8:47 AM
Reply to: Message 101 by vaporwave
12-20-2016 8:31 AM


Re: The purpose of science
vaporwave writes:
If you had no concept of evolutionary relationships and furthermore knew absolutely nothing about internal anatomy and saw a dog, a cat, and a turtle. Which ones would you guess to be more similar to each other if you dissected them?
And that child, is how it all began 150 years ago. And here you are 150 years later still making the same mistakes.
You realise that relatedness is not restricted to modern animals? Descent means that relationship can be derived backwards in time through the fossil record.
Now, you've admitted that common descent is falsifyable, why then haven't you falsifyed it?

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 101 by vaporwave, posted 12-20-2016 8:31 AM vaporwave has not replied

  
RAZD
Member (Idle past 1405 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


Message 104 of 288 (795962)
12-20-2016 8:58 AM
Reply to: Message 101 by vaporwave
12-20-2016 8:31 AM


Re: The purpose of science
Probably, yea. I just think it's lame to consider it a stunning victory of evolution theory.
Well, it IS probably the biggest hard test of evolution theory so far, and it united the genetic branch with the natural science branch to form the synthesis approach to evolution.
I think even if molecular researchers had no concept of common ancestry they could have made similar predictions based off the simple idea that beings of similar anatomical properties are going to be more similar to each other in additional ways than not.
But they could not have surmised that genetic markers would provide evidence of ancestry to the detail we have. Markers in non-coding sections of the DNA that could only be preserved by descent from an individual that first had the mutation, and no reason for it to occur other than random mutation.
Thus our relationship to chimpanzees is a lot closer than to gorillas because of a higher degree of shared markers. Going on just similar anatomical properties would not necessarily produce that significant level of difference. You could put them in the correct general order, but not provide the different distances (Those come from their ancestors places in the temporal\geological matrix of the fossil record).
If you had no concept of evolutionary relationships and furthermore knew absolutely nothing about internal anatomy and saw a dog, a cat, and a turtle. Which ones would you guess to be more similar to each other if you dissected them?
So now we go back to Linnaeus and early taxonomy to reinvent the wheel?
If I dissected them and used the results to form an hypothetical relationship, I would not be guessing I would be comparing empirical objective data and using that as the basis for the hypothesis.
This could be repeated with different sets of 3 animals and then an overall synthesis of the data to see if there were any conflicts in the overall pattern of relationships.
Enjoy

we are limited in our ability to understand
by our ability to understand
RebelAmerican☆Zen☯Deist
... to learn ... to think ... to live ... to laugh ...
to share.


Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)

This message is a reply to:
 Message 101 by vaporwave, posted 12-20-2016 8:31 AM vaporwave has replied

Replies to this message:
 Message 108 by vaporwave, posted 12-20-2016 9:21 AM RAZD has replied

  
vaporwave
Member (Idle past 2644 days)
Posts: 66
Joined: 12-17-2016


Message 105 of 288 (795963)
12-20-2016 9:08 AM
Reply to: Message 100 by Genomicus
12-20-2016 8:30 AM


Re: The purpose of phylogenetics
It's the concordant nested hierarchy of similarities that matters because randomly distributed similarities would be rather contrary to the evolutionary synthesis.
I'm still not getting the distinction you're making. I thought that's what I was saying with the mammal example... that the similarities clearly are not random. We find similar anatomy tends to be organized by similar genes.
Can you give an example of what you're talking about....

This message is a reply to:
 Message 100 by Genomicus, posted 12-20-2016 8:30 AM Genomicus has replied

Replies to this message:
 Message 106 by jar, posted 12-20-2016 9:12 AM vaporwave has not replied
 Message 110 by Dr Adequate, posted 12-20-2016 9:59 AM vaporwave has not replied
 Message 146 by Genomicus, posted 12-21-2016 3:36 AM vaporwave has not replied

  
Newer Topic | Older Topic
Jump to:


Copyright 2001-2023 by EvC Forum, All Rights Reserved

™ Version 4.2
Innovative software from Qwixotic © 2024