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Author | Topic: Discussion of Phylogenetic Methods | |||||||||||||||||||||||||||||||||||||||||||||
jar Member (Idle past 394 days) Posts: 34026 From: Texas!! Joined: |
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: |
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
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vaporwave Member (Idle past 2644 days) Posts: 66 Joined: |
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?
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jar Member (Idle past 394 days) Posts: 34026 From: Texas!! Joined: |
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.
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Dr Adequate Member (Idle past 284 days) Posts: 16113 Joined:
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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.
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Dr Adequate Member (Idle past 284 days) Posts: 16113 Joined: |
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.
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RAZD Member (Idle past 1404 days) Posts: 20714 From: the other end of the sidewalk Joined:
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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: 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. Enjoyby our ability to understand Rebel☮American☆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)
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RAZD Member (Idle past 1404 days) Posts: 20714 From: the other end of the sidewalk Joined: |
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. by our ability to understand Rebel☮American☆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)
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Tangle Member Posts: 9489 From: UK Joined: Member Rating: 4.9 |
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.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.
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Taq Member Posts: 9970 Joined: Member Rating: 5.6
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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:
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Taq Member Posts: 9970 Joined: Member Rating: 5.6
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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: 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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Dr Adequate Member (Idle past 284 days) Posts: 16113 Joined:
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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: Member Rating: 5.6
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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.
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Taq Member Posts: 9970 Joined: Member Rating: 5.6
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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.
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Taq Member Posts: 9970 Joined: Member Rating: 5.6 |
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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