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Author Topic:   Discussion of Phylogenetic Methods
RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 151 of 288 (796027)
12-21-2016 8:44 AM
Reply to: Message 147 by vaporwave
12-21-2016 7:25 AM


cytochrome b
Higher variation = increased deviation from a phylogenetic signal or pattern.
But it doesn't mean that the work is not being done nor that it does not support the phylogenetics. From the first hit on the search on cytochrome b phylogenetic:
quote:
The cytochrome b gene as a phylogenetic marker: the limits of resolution for analyzing relationships among cichlid fishes.
The mitochondrial cytochrome b (cyt-b) gene is widely used in systematic studies to resolve divergences at many taxonomic levels. The present study focuses mainly on the utility of cyt-b as a molecular marker for inferring phylogenetic relationship at various levels within the fish family Cichlidae. A total of 78 taxa were used in the present analysis, representing all the major groups in the family Cichlidae (72 taxa) and other families from the suborders Labroidei and Percoidei. Gene trees obtained from cyt-b are compared to a published total evidence tree derived from previous studies. Minimum evolution trees based on cyt-b data resulted in topologies congruent with all previous analyses. Parsimony analyses downweighting transitions relative to transversions (ts1:tv4) or excluding transitions at third codon positions resulted in more robust bootstrap support for recognized clades than unweighted parsimony. Relative rate tests detected significantly long branches for some taxa (LB taxa) which were composed mainly by dwarf Neotropical cichlids. An improvement of the phylogenetic signal, as shown by the four-cluster likelihood mapping analysis, and higher bootstrap values were obtained by excluding LB taxa. Despite some limitations of cyt-b as a phylogenetic marker, this gene either alone or in combination with other data sets yields a tree that is in agreement with the well-established phylogeny of cichlid fish.
bold added for emphasis.
Even a quick check with wikipedia shows it's usage:
quote:
Cytochrome b
Cytochrome b is a protein found in the mitochondria of eukaryotic cells. It functions as part of the electron transport chain and is the main subunit of transmembrane cytochrome bc1 and b6f complexes.[1][2]
So it would not be useful for prokaryotic cells which don't have mitochondria ... further:
quote:
Use in phylogenetics
Cytochrome b is commonly used as a region of mitochondrial DNA for determining phylogenetic relationships between organisms, due to its sequence variability. It is considered to be most useful in determining relationships within families and genera. Comparative studies involving cytochrome b have resulted in new classification schemes and have been used to assign newly described species to a genus as well as to deepen the understanding of evolutionary relationships.[6]
bold again for emphasis.
This is essentially an admission that cytochrome B data does not reinforce the preferred evolutionary relationships very well, or at least would not look as convincing when making a case to the public.
Except that this is a false conclusion you have reached based on your opinion instead of checking easily found facts. Sadly, for you, opinion has demonstrated a very poor record of affecting reality in any way shape or form.
This is why evolutionists, when trying to make their case, always focus on cytochrome C instead.
Or the reason is a simple matter of more universal applicability:
quote:
Cytochrome C
Cytochrome c is a highly conserved ~12 kDa protein consisting of a single 104 amino acid peptide with a single heme group, which is covalently attached to Cys14 and Cys17. Because of its ubiquitous nature and sequence homology, cytochrome c has been used as a model protein for molecular evolution.1
and bold again for emphasis.
So in summary, cytochrome b is useful in eukaryotes (with mitochondria) and cytochrome c is useful in eukaryotes and prokaryotes. In both cases the phylogenetic trees reinforce and fine-tune the previous derived trees.
Higher variation = increased deviation from a phylogenetic signal or pattern.
Or because there is more variation in cyt-b that it is better for fine detail within family and genus while cyt-c is better for larger scale detail ... ie cyt-c does not vary within a family or genus, so it cannot detail those branches, but cyt-b does vary and can be used to provide that detail.
I don't use a microscope to identify craters on the moon, and I don't use a telescope to identify moon dust.
Enjoy
Edited by RAZD, : .
Edited by RAZD, : .
Edited by RAZD, : added end
Edited by RAZD, : end analogy

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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


(1)
Message 152 of 288 (796028)
12-21-2016 9:20 AM
Reply to: Message 147 by vaporwave
12-21-2016 7:25 AM


Re: The purpose of phylogenetics
I accepted Taq's response. He said cytB has "higher variation" than cytC.
Higher variation = increased deviation from a phylogenetic signal or pattern.
No. Stop making shit up.
This is essentially an admission that cytochrome B data does not reinforce the preferred evolutionary relationships very well, or at least would not look as convincing when making a case to the public.
No. Stop making shit up.
This is why evolutionists, when trying to make their case, always focus on cytochrome C instead.
And now you are flatly lying, since you know that I linked you to innumerable articles on phylogeny done with cytochrome b. Unlike the other shit you made up this cannot be ascribed to your hopeless ignorance, it is a deliberate, willful lie.
And vaporware, when you have to lie to make your case, that's a sign that your case is not a good one.

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jar
Member (Idle past 394 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 153 of 288 (796029)
12-21-2016 9:36 AM
Reply to: Message 149 by vaporwave
12-21-2016 7:56 AM


the silence from the lambs
vaporwave writes:
I haven't said anything about creationist models, but it sounds like you're suggesting that one cannot group objects by shared traits (cladistics) unless those objects are related via common ancestry.
We have noticed that neither you or any other Creationist have ever said anything about creationist models.
Is there some reason no Creationist has ever been able to present a model, mechanism, plan, procedure, method or theory that explains the reality that is seen?
Edited by jar, : fix sub-title

My Sister's Website: Rose Hill Studios My Website: My Website

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Replies to this message:
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Coyote
Member (Idle past 2106 days)
Posts: 6117
Joined: 01-12-2008


(1)
Message 154 of 288 (796030)
12-21-2016 9:59 AM
Reply to: Message 153 by jar
12-21-2016 9:36 AM


Re: the silence from the lambs
Is there some reason no Creationist has ever been able to present a model, mechanism, plan, procedure, method or theory that explains the reality that is seen?
Of course there's a creationist model!
POOF!
That's it! Pretty simple, eh?

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
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jar
Member (Idle past 394 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 155 of 288 (796031)
12-21-2016 10:05 AM
Reply to: Message 154 by Coyote
12-21-2016 9:59 AM


Re: the silence from the lambs
Or make mud critters and then cough on them.

My Sister's Website: Rose Hill Studios My Website: My Website

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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 156 of 288 (796032)
12-21-2016 10:29 AM
Reply to: Message 149 by vaporwave
12-21-2016 7:56 AM


Re: pro template and con template and taxon arguments
Only if you assume shared traits are the product of common inheritance. The traits themselves don't show you that.
It's what we observe happening in every species known. You have traits your parents had (and some they didn't). You have the same DNA for those shared traits. You get your DNA from your parents in the process of reproduction. Thus we know from observation that they are inherited.
What we hypothesis is that this pattern of inherited traits holds for all life, from the fossil record, the historic record and the genetic record.
That's how science works -- it observes objective empirical evidence and then posits an explanation for how the evidence came to be, then it tests that hypothesis.
"Did the squirrel become a possum or did the possum become a squirrel?"
Honestly I have no idea what you're talking about.
The argument was: dogs will always be dogs (descendants will still be dogs), so when will "macro"evolution be observed? -- when they no longer look like dogs, but look like something else; flying squirrels look like sugar gliders (and vice-versa), therefore "macro"evolution (by this creationist mis-definition) has occurred, agreed? So:
Has the flying squirrel become a look-alike to the sugar glider possum ... or has the sugar glider possum become a look-alike to the flying squirrel? (Or do they both look like something new?)
Are you under the impression that templates can only be used exclusively of each other? You can't use more than one when building something? That would be a bizarre thing to assume from a design perspective.
And now your argument is totally bizarre and useless. You can't predict a single thing from it, not sister species similarities (the original purpose of this creationist concept) nor the differences between sequoia trees slime molds and elephants. There is no time or location restriction on their use. Rabbits in the cambrian or on the moon, it's all good ... except it's just hand-waving, and it's denial of the strong evidence for evolution of inherited traits.
I haven't said anything about creationist models, but it sounds like you're suggesting that one cannot group objects by shared traits (cladistics) unless those objects are related via common ancestry. Is that really what you're saying?
Again, the definition of cladistics is that you start with a breeding population and then all the descendants are members of that parent population clade. By definition you start with a common ancestor for all the descendants:
quote:
Clade
A clade (from Ancient Greek: κλάδος, klados, "branch") is a group of organisms that consists of a common ancestor and all its lineal descendants, and represents a single "branch" on the "tree of life".[1]
Definitions
A clade is by definition monophyletic, meaning that it contains one ancestor (which can be an organism, a population, or a species) and all its descendants.[note 1][7][8] The ancestor can be known or unknown; any and all members of a clade can be extant or extinct.
If you are going to use a science term, you need to use it the way it is defined in the science and not for something else -- that's how you communicate without confusion.
You can't do cladistics without a common ancestor BY DEFINITION.
Perhaps you should use the old term taxon instead of clade
quote:
Taxon
In biology, a taxon (plural taxa; back-formation from taxonomy) is a group of one or more populations of an organism or organisms seen by taxonomists to form a unit. ...
Although preceded by Linnaeus's system in Systema Naturae (10th edition, 1758)[1] and unpublished work by Bernard and Antoine Laurent de Jussieu, the notion of a unit-based "natural system" of biological classification was first made widely available in 1805 ...
Definition
A taxonomic unit, whether named or not: i.e. a population, or group of populations of organisms which are usually inferred to be phylogenetically related and which have characters in common which differentiate (q.v.) the unit (e.g. a geographic population, a genus, a family, an order) from other such units. A taxon encompasses all included taxa of lower rank (q.v.) and individual organisms. [...]"
ie -- that's the way we used to do it, then it was discovered that cladistics and the nested hierarchies from common ancestors was a better predictor of actual phylogenetic relationships.
But hey, go back to the 1850's if that whets your whistle.
... you're suggesting that one cannot group objects by shared traits ...
Like the shared traits between sugar gliders and flying squirrels, which you have previously rejected in favor of the hereditary traits of metatherians and eutherians?
See, this is the kind of mistaken relationships that the old taxonomy system tended to make. This is where phylogenetics based on cyt-c and cyt-b help to strengthen the cladistic relationships.
Are you under the impression that templates can only be used exclusively of each other? ...
The only "template" that we have any objective empirical evidence for is DNA, inherited from parents and modified by mutations. These individual "templates" are exclusive to, and guide the development of, each and every organism. We have observed it happen. We don't need multiple templates to explain the diversity of life as we know it, from the fossil record, to the historic record, from the genetic record to the record of life today.
Enjoy

we are limited in our ability to understand
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Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


(2)
Message 157 of 288 (796033)
12-21-2016 10:36 AM
Reply to: Message 136 by vaporwave
12-20-2016 6:04 PM


Re: The purpose of phylogenetics
vaporwave writes:
So in other words.... cytochrome B isn't something you want to show off when trying to sell evolution to people... so you cherry-pick cytochrome C instead.
That isn't true at all. The higher rate of change in the cytB gene means it is more useful for more closely related species.

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Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 158 of 288 (796034)
12-21-2016 10:38 AM
Reply to: Message 137 by vaporwave
12-20-2016 6:08 PM


Re: Introduction
vaporwave writes:
This is a really interesting subject, but don't you find it strange that evolutionists are so quick to wander into teleology when making their case for common ancestry? I thought it was strictly all about the science with you guys?
I seems in every defense of evolution I've heard, within 3 or 4 posts the evolutionists are always making implications about what God would or wouldn't do...
Is this an admission that creationism is incapable of making any predictions about what we should or shouldn't observe?

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Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


(1)
Message 159 of 288 (796035)
12-21-2016 10:40 AM
Reply to: Message 138 by vaporwave
12-20-2016 6:20 PM


Re: pro template and con template
vaporwave writes:
Cladistics actually works just fine without assuming common ancestry.
The point we are making is that only common ancestry can explain why species fit into clades. You have been incapable of explaining why creationism would produce clades, such as the mammal clade that humans belong to.

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Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 160 of 288 (796037)
12-21-2016 10:41 AM
Reply to: Message 142 by vaporwave
12-20-2016 6:41 PM


Re: The purpose of science
vaporwave writes:
But I think if an individual coder designed many variations of a web browser in short span of time, then it could pretty easily be interpreted as an evolutionary pattern.
How so? Why would an individual coder produce code so that it falls into a nested hierarchy?

This message is a reply to:
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Replies to this message:
 Message 176 by vaporwave, posted 12-21-2016 4:43 PM Taq has replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


(1)
Message 161 of 288 (796040)
12-21-2016 10:47 AM
Reply to: Message 147 by vaporwave
12-21-2016 7:25 AM


Re: The purpose of phylogenetics
vaporwave writes:
Higher variation = increased deviation from a phylogenetic signal or pattern.
No, it doesn't. It means a loss of phylogenetic signal for distantly related species.
"There is one caveat to consider with this prediction: if rates of evolution are fast, then cladistic information can be lost over time since it would be essentially randomized. The faster the rate, the less time needed to obliterate information about the historical branching pattern of evolution."
29+ Evidences for Macroevolution: Part 1
This is why strongly conserved sequences of DNA are used for phylogenetic reconstruction of species that share a distant common ancestor. For more closely related species, the phylogenetic signal in the cytB gene is still there. For more distantly related species, the phylogenetic signal in cytC is still there.
We could use a crime scene as an analogy. If an expert shows up at a crime scene within hours of a murder then the expert can collect evidence such as fresh tire tracks, fresh shoe prints, and so forth. If the expert shows up weeks after a murder that evidence will be gone, but there will still be other evidence such as DNA and fingerprint evidence. Just because some evidence has disappeared does not make all of the evidence disappear.

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Replies to this message:
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Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


(1)
Message 162 of 288 (796041)
12-21-2016 10:52 AM
Reply to: Message 149 by vaporwave
12-21-2016 7:56 AM


Re: pro template and con template
vaporwave writes:
Only if you assume shared traits are the product of common inheritance. The traits themselves don't show you that.
The pattern of shared derived characteristics (i.e. an objective phylogeny) do show us that they share a common ancestor in the same way that a fingerprint shows us that someone touched a surface.
Are you under the impression that templates can only be used exclusively of each other? You can't use more than one when building something? That would be a bizarre thing to assume from a design perspective.
Isn't that the impression you have been pushing all along? If a designer can mix and match design units freely, then creationism should not produce a nested hierarchy.
I haven't said anything about creationist models, but it sounds like you're suggesting that one cannot group objects by shared traits (cladistics) unless those objects are related via common ancestry. Is that really what you're saying?
We are saying that only common ancestry is able to explain why shared derived characteristics found in biological species form an objective phylogeny. Creationism can't explain it.

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dwise1
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Posts: 5930
Joined: 05-02-2006
Member Rating: 5.8


(1)
Message 163 of 288 (796042)
12-21-2016 11:31 AM
Reply to: Message 142 by vaporwave
12-20-2016 6:41 PM


Re: The purpose of science
But I think if an individual coder designed many variations of a web browser in short span of time, then it could pretty easily be interpreted as an evolutionary pattern.
No, not really.
I've been a practicing professional software engineer since 1982, so I might have some familiarity with the process in question.
It is true that we often do take what we refer to as an evolutionary approach. That is to say that we will copy some existing code that operates similarly to what we want and then we modify it. Copy-and-modify is basically how evolution works. Code reuse is also a very important concept in software design. Management comes to expect you to work that way and the time that we are given to complete the software design pretty much forces us to copy and modify old code. When we create a new member to our product line, we use an existing product as the baseline and start modifying it and adding to it.
We should note here that a by-product of that "evolutionary" process is that the code's complexity increases rapidly. It turns out that great complexity is a sure sign that evolutionary processes were used, as has been verified by experiments using evolutionary processes to engineer functional designs. So if you see something complex in nature, you can be sure that it had evolved.
Now the analogy with evolution starts to fall apart. During the maintenance phase of the product's life we are constantly required to add new features which are often incompatible with the original design, so we have to burrow back into the code and change the fundamental ways that the software works at its lowest levels. That cannot happen in nature. It would be like the evolution of a new species requiring completely changing how DNA works. Cannot happen. Evolution can only work with what it starts with; you cannot completely reinvent entire systems on the fly.
But wait, there's more! In software, we can also reach in, rip out whole sections of code, and replace it with completely foreign code. For example, you start with a software product that communicates with another program on another computer via the serial port. Then you migrate it to a Netware network, so you rip out all the serial port code and replace it with some Netware code you bought from a third-party vendor. Then you migrate to an internet connection, so you rip out the Netware code and replace it with TCP/IP code. This is facilitated by the object-oriented-design principle of encapsulation (ie, an object has an interface which the other objects use to communicate with it, such that that interface does not depend on the object's internals, on how it processes those inputs and generates those outputs. That means that you can completely replace the object's internals and have it work completely differently, and the overall design will never notice as long as the interface still works the same. This is called pin-for-pin compatibility, a hardware concept that also works in software with encapsulation.
Evolution does not support pin-for-pin compatibility. Web browsers do. Cars do. Life does not.
An "Intelligent Designer" would be perfectly capable of using pin-for-pin compatibility, yet we never see it happening in nature. It would be a very desirable practice, since many of the "designs" that have evolved are so convoluted and overly complex because of the constraint on evolution that it cannot completely replace entire sections but rather can only work with what's already there by copying and modifying.

This message is a reply to:
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Replies to this message:
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RAZD
Member (Idle past 1404 days)
Posts: 20714
From: the other end of the sidewalk
Joined: 03-14-2004


(1)
Message 164 of 288 (796043)
12-21-2016 11:41 AM
Reply to: Message 161 by Taq
12-21-2016 10:47 AM


levels of observation
This is why strongly conserved sequences of DNA are used for phylogenetic reconstruction of species that share a distant common ancestor. For more closely related species, the phylogenetic signal in the cytB gene is still there. For more distantly related species, the phylogenetic signal in cytC is still there.
We don't use a microscope to identify craters on the moon, and we don't use a telescope to identify the moon dust in the craters.
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 161 by Taq, posted 12-21-2016 10:47 AM Taq has not replied

  
Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


(2)
Message 165 of 288 (796044)
12-21-2016 11:45 AM
Reply to: Message 163 by dwise1
12-21-2016 11:31 AM


Re: The purpose of science
dwise1 writes:
But wait, there's more! In software, we can also reach in, rip out whole sections of code, and replace it with completely foreign code.
That is probably the most important point. You can take modules from several other programs and meld them into a new program. This would produce numerous and obvious violations of a nested hierarchy. Contrary to vaporwave's claims, if we took the tools we use to analyze phylogenies in biological species and applied them to software we would not conclude that software evolved through common ancestry and vertical inheritance.

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