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Author Topic:   Discussion of Phylogenetic Methods
jar
Member (Idle past 394 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 106 of 288 (795964)
12-20-2016 9:12 AM
Reply to: Message 105 by vaporwave
12-20-2016 9:08 AM


Re: The purpose of phylogenetics
vaporwave writes:
Can you give an example of what you're talking about....
Consider hippopotamus and whale.

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


Message 107 of 288 (795965)
12-20-2016 9:12 AM
Reply to: Message 102 by Tangle
12-20-2016 8:38 AM


Re: The purpose of phylogenetics
Darn... Tangle, you were just teasing I see.
You refuse to back up this claim... just like Dr. Adequate...
But without common descent there's no reason for DNA and form based taxonomy to agree on their classification

This message is a reply to:
 Message 102 by Tangle, posted 12-20-2016 8:38 AM Tangle has replied

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


Message 108 of 288 (795967)
12-20-2016 9:21 AM
Reply to: Message 104 by RAZD
12-20-2016 8:58 AM


Re: The purpose of science
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.
Or maybe they are left-over from a previously served function.
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.
Why'd you dodge the question? You're telling me you couldn't make a guess before you dissected them?

This message is a reply to:
 Message 104 by RAZD, posted 12-20-2016 8:58 AM RAZD has replied

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


Message 109 of 288 (795968)
12-20-2016 9:22 AM
Reply to: Message 107 by vaporwave
12-20-2016 9:12 AM


how to converse, the 101 level course
You really don't understand even the very basics of communication do you?
vaporwave writes:
Darn... Tangle, you were just teasing I see.
You refuse to back up this claim... just like Dr. Adequate...
Tangle writes:
But without common descent there's no reason for DNA and form based taxonomy to agree on their classification
If someone makes a statement that you think might be incorrect your job is to present an example that you believe might refute the position not simple play the three year old at the playground tactic of telling the other kid to prove it and then sticking out your tongue.
If you have some reason to expect DNA and form taxonomy to agree then you should present your reason.

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

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


(1)
Message 110 of 288 (795969)
12-20-2016 9:59 AM
Reply to: Message 105 by vaporwave
12-20-2016 9:08 AM


Re: The purpose of phylogenetics
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....
Well, what about genes which don't organize anatomy?
Consider for example the gene for cytochrome c. This does nothing to control anatomical development, is not even nuclear, but mitochondrial, and does exactly the same thing in every organism, functioning as part of the electron transport chain in mitochondria.
Here's a cladogram produced just by applying phylogenetics to this one gene. (Schwartz and Dayhoff, "Origins of prokaryotes, eukaryotes, mitochondria, and chloroplasts", Science, 27 Jan 1978 Vol. 199, Issue 4327, pp. 395-403.)
Tthat's a pretty good fit with evolution for just one gene. And that gene is not organizing anatomy.

This message is a reply to:
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Replies to this message:
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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 111 of 288 (795970)
12-20-2016 10:05 AM
Reply to: Message 107 by vaporwave
12-20-2016 9:12 AM


Re: The purpose of phylogenetics
You refuse to back up this claim... just like Dr. Adequate...
I suppose your petulant dishonest whining about me is intended to be tiresome. But it is also unconvincing. If that too is your intent, by all means continue.

This message is a reply to:
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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 112 of 288 (795971)
12-20-2016 10:17 AM
Reply to: Message 108 by vaporwave
12-20-2016 9:21 AM


Re: The purpose of science
Or maybe they are left-over from a previously served function.
Every part of DNA is either left-over (inherited), regardless of functionality, or new mutation. Whether it is left-over or not is irrelevant.
Any difference in the same DNA location, if common to two species but not others, would also imply descent from an ancestor that first had the altered DNA.
quote:
Evidence of common descent
Cytochrome c and b
A classic example of biochemical evidence for evolution is the variance of the ubiquitous (i.e. all living organisms have it, because it performs very basic life functions) protein Cytochrome c in living cells. The variance of cytochrome c of different organisms is measured in the number of differing amino acids, each differing amino acid being a result of a base pair substitution, a mutation. If each differing amino acid is assumed the result of one base pair substitution, it can be calculated how long ago the two species diverged by multiplying the number of base pair substitutions by the estimated time it takes for a substituted base pair of the cytochrome c gene to be successfully passed on.
The cytochrome c molecule has been extensively studied for the glimpse it gives into evolutionary biology. Both chicken and turkeys have identical sequence homology (amino acid for amino acid), as do pigs, cows and sheep. Both humans and chimpanzees share the identical molecule, while rhesus monkeys share all but one of the amino acids:[22] the 66th amino acid is isoleucine in the former and threonine in the latter.[21]
What makes these homologous similarities particularly suggestive of common ancestry in the case of cytochrome c, in addition to the fact that the phylogenies derived from them match other phylogenies very well, is the high degree of functional redundancy of the cytochrome c molecule. The different existing configurations of amino acids do not significantly affect the functionality of the protein, which indicates that the base pair substitutions are not part of a directed design, but the result of random mutations that aren't subject to selection.[23]
Being neither selected for nor selected against, they would be neutral mutations, and the fact that they are shared by some (humans, chimps) but not all primates (humans, chimps, rhesus monkeys) would imply descent from an ancestor (for chimps and humans) that first had the altered DNA.
Likewise the sharing of all but one amino acids with the rhesus monkey implies a more ancient common ancestor than the one for chimps and humans, but not for a species with a second altered amino acid.
Why'd you dodge the question? You're telling me you couldn't make a guess before you dissected them?
Because science doesn't guess, it formulates hypothesis based on objective empirical evidence.
If you like, you can call an hypothesis an "educated guess" because it is informed by the objective empirical evidence.
Science also places the additional constraint on the "educated guesses" -- that they are testable.
Guesses based solely on opinion (no matter how well informed) can interfere with scientific study if the evidence points to that opinion being wrong.
Enjoy

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This message is a reply to:
 Message 108 by vaporwave, posted 12-20-2016 9:21 AM vaporwave has not replied

Replies to this message:
 Message 119 by Taq, posted 12-20-2016 11:19 AM RAZD has replied

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


Message 113 of 288 (795972)
12-20-2016 10:24 AM
Reply to: Message 110 by Dr Adequate
12-20-2016 9:59 AM


Re: The purpose of phylogenetics
hint: if you use [blockcolor=white][img](gif or png image) [/blockcolor][/img] you get
which is more readable. you can also center it if like.

we are limited in our ability to understand
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to share.


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


Message 114 of 288 (795973)
12-20-2016 10:31 AM
Reply to: Message 107 by vaporwave
12-20-2016 9:12 AM


Re: The purpose of phylogenetics
vaporwave writes:
Darn...
It's kind of obvious, but hey ho.
Suppose this God guy designed every single organism on the planet individually, he could just as easily mix and match all sorts of components from all sorts of models - just like car manufacturers. In that case the eye of a gibbon could be made from molecules he used for the eye of a squid - maybe with a tweak here and there. Of course, what you don't find are things like teats on turtles, 'cos we know that teats hadn't been invented for reptiles - they came later whem mammals came along Just like you don't find autoparking on a 1955 Ford.
For DNA itself, the rules of base pairing (or nucleotide pairing) are:
A with T: the purine adenine (A) always pairs with the pyrimidine thymine (T)
C with G: the pyrimidine cytosine (C) always pairs with the purine guanine (G)
But uracil also pairs with adenine, so why not use that combo in, say cows and only cows, just for a laugh. That'll screw those evil evolutionist up.
My apologies to real molecular biologists.

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Faith is the denial of observation so that Belief can be preserved."
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This message is a reply to:
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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 115 of 288 (795974)
12-20-2016 10:38 AM
Reply to: Message 76 by caffeine
12-19-2016 4:20 PM


Re: The purpose of phylogenetics
caffeine writes:
Phylogenetics is precisely what he says. Phylogenetic methods are means of calculating the most probable tree topologies given that a group of organisms share a common ancestor. These are not techniques to establish that evolution occured, but rather the means to figure how it did once we've taken that for granted.
From my understanding, that simply isn't true. Phylogenetics is a test for common ancestry and evolution through vertical inheritance. The various methods for detecting phylogenies return values that measure the phylogenetic signal. A result with low statistical significance indicates a lack of phylogenetic signal. This can be due to a lack of data or a lack of common ancestry and evolution.
For example, you could list the physical characteristics of cars and measure the phylogenetic signal (which should be low). You don't have to assume common ancestry or evolution. People have also measured the phylogenetic signal for groups of languages and found a strong phylogenetic signal, as would be expected since many languages evolve much like biological species.
From the classic 29+ Evidences for Macroevolution Talkorigins page:
quote:
The degree to which a given phylogeny displays a unique, well-supported, objective nested hierarchy can be rigorously quantified. Several different statistical tests have been developed for determining whether a phylogeny has a subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a chance process instead of a genealogical process (Swofford 1996, p. 504). These tests measure the degree of "cladistic hierarchical structure" (also known as the "phylogenetic signal") in a phylogeny, and phylogenies based upon true genealogical processes give high values of hierarchical structure, whereas subjective phylogenies that have only apparent hierarchical structure (like a phylogeny of cars, for example) give low values (Archie 1989; Faith and Cranston 1991; Farris 1989; Felsenstein 1985; Hillis 1991; Hillis and Huelsenbeck 1992; Huelsenbeck et al. 2001; Klassen et al. 1991).

This message is a reply to:
 Message 76 by caffeine, posted 12-19-2016 4:20 PM caffeine has replied

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


(1)
Message 116 of 288 (795976)
12-20-2016 10:49 AM
Reply to: Message 110 by Dr Adequate
12-20-2016 9:59 AM


Re: The purpose of phylogenetics
Dr Adequate writes:
Consider for example the gene for cytochrome c. This does nothing to control anatomical development, is not even nuclear, but mitochondrial, and does exactly the same thing in every organism, functioning as part of the electron transport chain in mitochondria.
To help drive this point home, for 30 taxa there are over 1 x 10^38 possible trees. That is over 10^38 different ways to organize 30 taxa into a branching tree. When you organize 30 different taxa by morphology and by cytochrome c you get a perfect match between them:
quote:
So, how well do phylogenetic trees from morphological studies match the trees made from independent molecular studies? There are over 10^38 different possible ways to arrange the 30 major taxa represented in Figure 1 into a phylogenetic tree (see Table 1.3.1; Felsenstein 1982; Li 1997, p. 102). In spite of these odds, the relationships given in Figure 1, as determined from morphological characters, are completely congruent with the relationships determined independently from cytochrome c molecular studies (for consensus phylogenies from pre-molecular studies see Carter 1954, Figure 1, p. 13; Dodson 1960, Figures 43, p. 125, and Figure 50, p. 150; Osborn 1918, Figure 42, p. 161; Haeckel 1898, p. 55; Gregory 1951, Fig. opposite title page; for phylogenies from the early cytochrome c studies see McLaughlin and Dayhoff 1973; Dickerson and Timkovich 1975, pp. 438-439). Speaking quantitatively, independent morphological and molecular measurements such as these have determined the standard phylogenetic tree, as shown in Figure 1, to better than 38 decimal places. This phenomenal corroboration of universal common descent is referred to as the "twin nested hierarchy". This term is something of a misnomer, however, since there are in reality multiple nested hierarchies, independently determined from many sources of data.
29+ Evidences for Macroevolution: Part 1
There is absolutely no reason that a creator would be forced to match cytochrome c sequences to morphology. None. As you mention, the function of cytochrome c has nothing to do with having fur, gills, feathers, or eyes. To stress this again, out of 10^38 possible ways that cytochrome c could have been arranged in a phylogeny, we see the single tree out of those 10^38 that we would expect to see from evolution.
Edited by Taq, : No reason given.
Edited by Taq, : No reason given.

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


(1)
Message 117 of 288 (795979)
12-20-2016 10:52 AM
Reply to: Message 115 by Taq
12-20-2016 10:38 AM


Re: The purpose of phylogenetics
Several different statistical tests have been developed for determining whether a phylogeny has a subjective or objective nested hierarchy, or whether a given nested hierarchy could have been generated by a chance process instead of a genealogical process.
But you're forgetting that a comparison with the null hypothesis is not a standard statistical technique used constantly in science, as statisticians and scientists would have you believe, but is in fact unscientific because something something philosophical, blah blah metaphysics.
Edited by Dr Adequate, : No reason given.

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


(2)
Message 118 of 288 (795981)
12-20-2016 11:00 AM
Reply to: Message 114 by Tangle
12-20-2016 10:31 AM


Re: The purpose of phylogenetics
Tangle writes:
But uracil also pairs with adenine, so why not use that combo in, say cows and only cows, just for a laugh. That'll screw those evil evolutionist up.
Or better yet, why not change the codon tables for each species? You could produce the same exact proteins but with completely different DNA sequences. I am not going to do the math here, but I would strongly suspect there are more than enough possible combinations between codons and amino acids to go around, even with 3rd base wobble. In fact, why not have some species where they have 1st base wobble, or 2nd base wobble? That would greatly increase the number of combinations.
For an all powerful and all knowing deity with unlimited time and resources, this would be child's play. I have always found it fascinating that creationists insist that God would have to reuse designs. They claim that humans reuse designs, so it would make sense that God would too. What they don't seem to realize is that humans reuse designs because we are not all powerful, not all knowing, and are limited in both time and resources. What they are saying is that God is as limited as human beings, which makes sense to atheists since we have long suspected that God was invented by humans.

This message is a reply to:
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Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


(2)
Message 119 of 288 (795982)
12-20-2016 11:19 AM
Reply to: Message 112 by RAZD
12-20-2016 10:17 AM


More Fun With Cytochrome C
RAZD writes:
Being neither selected for nor selected against, they would be neutral mutations, and the fact that they are shared by some (humans, chimps) but not all primates (humans, chimps, rhesus monkeys) would imply descent from an ancestor (for chimps and humans) that first had the altered DNA.
Continuing with the cytochrome c theme . . .
There is another feature of cladistics that is called genetic equidistance. Here is a model phylogeny to work from:
In this phylogeny we can see that A and B share a recent common ancestor. A and B also share the SAME common ancestor with C. When you trace the phylogeny to where B and C meet it is the same node where A and C meet. Therefore, the genetic (i.e. evolutionary) distance between A and C is the same as that for B and C. A and B are genetically equidistant from C. We should see this equidistance in genetic data if evolution is true.
Using cytochrome c as our model gene, here are the pairwise alignment scores for human, mouse, and chicken DNA (from Homologene at NCBI, don't know if that link will work or not)
H.sapiens vs. Mouse = 90.5%
H. sapiens vs. Chicken = 81.6%
Humans and mice are the A and B in our model. Chickens are the C. Therefore, we should see similar genetic distance between humans and chickens as we see for mice and chickens. So do we? We sure do:
Chicken vs. Mouse = 81.9%
They are just 0.3% off. We see nearly the same genetic distance between humans and chickens as we see between mice and chickens. I have yet to find a single creationist who can explain this. Only evolution can explain this.
Edited by Taq, : No reason given.
Edited by Taq, : No reason given.
Edited by Taq, : No reason given.

This message is a reply to:
 Message 112 by RAZD, posted 12-20-2016 10:17 AM RAZD has replied

Replies to this message:
 Message 122 by jar, posted 12-20-2016 11:50 AM Taq has replied
 Message 133 by RAZD, posted 12-20-2016 4:39 PM Taq has replied

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


Message 120 of 288 (795983)
12-20-2016 11:39 AM
Reply to: Message 66 by vaporwave
12-19-2016 7:33 AM


Re: Introduction
vaporwave writes:
But you are the one guilty of this so far. You've claimed to hold insight into the probabilities of how life would look if common ancestry were false.
We can directly observe what common ancestry, vertical inheritiance, and evolution would look like because we can watch it in real time. It produces a phylogenetic signal.
"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."
Gene trees and the origins of inbred strains of mice - PubMed
The ancestral history of these lab strains of mice are known. We know exactly how each strain is related to another, and they have been kept separate from one another. When we look at the phylogeny based on their DNA, it almost exactly matches the known relationships. We know what evidence common ancestry and evolution produces because we can directly observe it.
Earlier here you stated that genetic/morphological concordance of life would be "accidental" if not for evolution. I'm still waiting for you to explain how you got this knowledge.
We are still waiting for you to explain why an omnipotent and omniscient creator would be forced to fit DNA and morphology into the same nested hierarchies.

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