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Author | Topic: Discussion of Phylogenetic Methods | |||||||||||||||||||||||||||||||||||||||
RAZD Member (Idle past 1395 days) Posts: 20714 From: the other end of the sidewalk Joined: |
The prior probability of a particular tree is the probability that among all possible tree topologies it is the correct one. If we believed that all trees were equally likely, then we could assign a flat prior, where the prior probability of a tree equals one divided by the number of trees. Why don't we believe that? Well I would think that the probability of the first two of these | | | would be the same but different from the probability of third, (which I would expect to be lower). Enjoy Edited by RAZD, : .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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RAZD Member (Idle past 1395 days) Posts: 20714 From: the other end of the sidewalk Joined: |
Dr. A is right, only bifurcating trees are evaluated for likelihood. ...Tree number 3 above would be an unresolved trichotomy, not that 3 lineages diverged from the same ancestor. This would occur when there are not enough differences between two or more taxa to completely resolve the relationship. Interesting, thanks. So what about:
vs | | a a / \ / \ / \ / \ / \ b \ / b / \ \ c / \ c \ \ / \ / \ / \ \ \ d e f g d e f g I would think the first is more probable than the second as I would not expect all the "activity" to be on one branch. Thoughts? Edited by RAZD, : .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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RAZD Member (Idle past 1395 days) Posts: 20714 From: the other end of the sidewalk Joined: |
Well, let's think about what this means phylogenetically. In the figure on the left, both lineages have diverged at roughly the same rate. In the figure on the right, lineage 'd' has diverged at a much higher rate than has lineage 'g'. What a priori belief about evolution or about this system would cause us to believe that the first tree is more likely? ... Indeed, and if we assume that -- all things being equal -- the rates of evolution should be about the same, then the left model seems more likely, but we'd have to evaluate the probabilities of the rates to determine an approximation of the difference (similar to greatest likelihood?).
... It is quite plausible that a North American species, 'f', is more closely related to the Australian species 'd' and 'e' than it is to another N. American species 'g'. Indeed. Any marsupial (opposums for example) should relate to 'd' or 'e' more than 'g' and any placental mammal in Australia should relate more to N.American taxa. But I would also expect the genetics to provide this information.
For now, I think the important "take-away" is that Bayesian statistics allows us to incorporate our prior knowledge of a system into the calculation of the posterior probability. Because of the way the formula is structured, the posterior probability becomes the probability that our hypothesis is true. Maximum-likelihood does not calculate the probability of the hypothesis, but the probability that the hypothesis could produce the given data - which is kind of backwards from what we really want to know. We want to know if our hypothesis is correct or what the probability is that it is correct. That is the big advantage of Bayesian statistics over ML. Can you combine these? ie - use ML as a gage of prior probability? or is there a conflict? 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 1395 days) Posts: 20714 From: the other end of the sidewalk Joined:
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Hi vaporwave, and welcome to the fray.
Message 24 Evolutionists paint a false picture for the public. They imply that if common ancestry were false, then assembling phylogenetic models would be impossible. The models would break down. But this is not true. Common ancestry could be false, and one could still derive phylogenetic models that gave the appearance of evolution. Please provide an example. Note that the phylogenetic models can be used to predict new finds, and they are tested everytime a new fossil is found.
If you have arranged branches based on genetic traits, but the morphology and anatomy don't reinforce it, then the evolutionists can propose that some of those traits must have evolved independently of each other... and voila, you have accommodated contradictory data into the model. When the model fails the hypothesis is reevaluated and altered to fit the new data -- that is how science works.
This is not to disparage the methodology... it is all very practical and extremely interesting. It is just dishonest to present such phylogenetic models as hard evidence that proves common ancestry is true. There is no proof of scientific hypothesis or theory, just disproof and validation. Validation is where all the evidence is explained by the hypothesis\theory, including new information from testing results. The theory of common ancestry is derived from the theory of evolution:
(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. This process has been observed to occur in virtually every living species, and it is a FACT. This is also called "microevolution."
(2) Speciation is the process whereby parent populations are divided into two or more reproductively isolated, independently evolving, daughter populations. This process has been also observed to occur, and it is a FACT. This process forms nested hierarchies of species, which is what biologists mean by "macroevolution."
(3) The Theory of Evolution (ToE), stated in simple terms, is that the process of evolution, and the process of speciation, are sufficient to explain the diversity of life as we know it, from the fossil record, from the genetic record, from the historic record, and from everyday record of the life we observe in the world all around us. So we see that common ancestors are predicted by this theory, and this then makes a testable hypothesis.
Message 26 Ask an evolutionist what the evolutionary limits are to "Convergent Evolution", with regards to morphology. They won't be able to give you any kind of specific answer, because tomorrow, in order to reconcile the phylogenetic data, they may have to assume an even more complex morphological trait evolved multiple times. Convergent evolution is limited by the ability of mutation and selection to achieve adaptation to a current ecology (see (1) above). As soon as that need is filled stasis would likely set in.
Message 33 So, when identifying a convergent trait, you just have to assume evolution did not take such a pathway. Simple enough. But you didn't answer the question. Specifically, what level of morphological complexity (edit: **the traits themselves** not supposed evolutionary pathways) would be impossible for convergent evolution and why? Curiously I was just posting on this issue on another thread ... see The Great Creationist Fossil Failure, Message 1121. Note that the internal differences are not being selected to change, there is no pressure for them to do so.
Message 34 Okay good that is pretty specific. Now just explain why it would be impossible for a mammalian lineage to convergently evolve feathers and wings. Because there is no selection pressure for that to happen. Bats are sufficiently successful with the wings they have, and going towards a bird like wing would mean a devolution, which would be selected against (less fit than the existing species). Enjoy
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RAZD Member (Idle past 1395 days) Posts: 20714 From: the other end of the sidewalk Joined:
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DNA confirmed the pattern of shared physical features and functionalities of organisms. Dogs and cats remain more similar to each other than either is to a jellyfish or a reptile. Surprise surprise... I think evolutionists really make this discovery out to be more than it is. Except that the science behind the phylogenies is much much more than this. Again if you look at the breakdown between flying squirrel and sugar glider in Message 1140 you will get an inkling of the depth of evidence being significantly more than you appear to assume. The same kind of break-down can be done for dogs and cats, if you are interested, but there is more ...
The Great Creationist Fossil Failure, Message 1143: We can also think of fossils as embedded in a matrix of time and space, a 4D supercube, and the critical element in this view is that for species (A) to evolve from species (B) they must be located closely nearby in both time and space. This holds for all species, so you have to be able to link one to the other with both location and time. Note that a prediction from the 4D supercube model was used to find Tiktaalik:
quote: Located the right time and place in the 4D supercube and voila: the intermediate fossil between fish and quadruped is found .... That is a prediction from the phylogenetic tree common ancestry hypothesis.
You trick yourself into pretending the core assumption of common ancestry isn't still there begging the question. Not an assumption, a scientific hypothesis based on observed empirical evidence, and tested by each new find, whether genetic or fossil. If it is constantly being tested then that hardly qualifies as "pretending" now, does it? 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 1395 days) Posts: 20714 From: the other end of the sidewalk Joined:
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DNA confirmed the pattern of shared physical features and functionalities of organisms. Dogs and cats remain more similar to each other than either is to a jellyfish or a reptile. Surprise surprise... There are actually 3 different lines of evidence leading to our current understanding of the natural history of life on earth:
To fit an organism into the phylogeny these 3 things must agree. The DNA structure must be more similar than other less closely related species; the fossil morphology must be more similar than other less closely related species; the location must be more congruent or connected than other less closely related species. When these 3 bits of evidence from entirely different sets of information come together then their concilience provides added confidence to the validity of the hypothesis or theory:
quote: 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 1395 days) Posts: 20714 From: the other end of the sidewalk Joined:
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Convergent evolution is never chalked up to mere coincidence, but the product of similar functional constraints. ... Which can be observed and documented. They are mutation and selection (survival and reproduction). Again, there has to be some selection pressure and ecological opportunity:
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. This can be illustrated as a two-step feedback response system that is repeated in each generation:
Like walking on first one foot and then the next. If there is no selection pressure for convergence, it won't happen. When an existing organism already fills an ecological niche, another organism will be under strong pressure to avoid that niche unless it has superior survival and reproductive success. Convergent evolution occurs when neither of these constraints exist, and even then, rarely is the convergence as complete as seen in the flying squirrel and sugar glider -- both evolved from sap and insect diets and the opportunity provided by forest ecology and the pressure to avoid ground predators ... and they live in entirely separate geological locations. ie there was opportunity and there was no conflict. btw - the species don't know they are converging, being totally ignorant of each other. They are just filling an available niche by improving their adaptation to it via (micro)evolution.
... Perhaps these constraints are so fine-tuned in the case of feathers/wings that natural selection only ever finds the same configurations in morphospace. That would be the inference. Alternatively, the inference would be that such a result is not necessary to the continued survival and reproduction of either species. Evolution is the survival of those able to survive and breed, it has no goal and nor purpose, nor does it have any need to reproduce something that worked somewhere else. Your fixation on re-evolving feathers is curious and seems to demonstrate a failure to understand how evolution actually works rather than offer a critique of evolution. 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 1395 days) Posts: 20714 From: the other end of the sidewalk Joined:
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But for all you know, the types of wings we see in nature are the only configurations that natural selection is able to find in actual animal populations. ... Dinosaurs had feathers before some developed wings. There were a variety of feathered wing patterns tried, but one was more successful at survival and reproduction than the others. Being more successful at survival and reproduction than the others is all that matters in evolution. Reaching some alternate goal envisaged by a novice understanding of evolution is certainly not in the cards. Pterosaurs developed skin wings to fly and soar, and they were successful for a while.
quote: In other words, totally different from bird and bat wings, and in no need to have feather wings, in spite of being closer to wing evolution in dinosaurs than bats are.
quote: Once the niche was occupied there was no need to develop further, certainly no need to develop entirely different systems, as all they needed was to become more successful at survival and reproduction than the others. Being more successful at survival and reproduction than the others is all that matters in evolution. Reaching some alternate goal envisaged\imagined by a novice understanding of evolution is certainly not in the cards. 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 1395 days) Posts: 20714 From: the other end of the sidewalk Joined: |
Look at the related field of Origin of Life studies to get some inkling of the metaphysical commitment. It doesn't matter how much the various OoL theories may struggle, the general academic community knows with complete certainty that it happened completely naturally somehow. Again you demonstrate ignorance regarding science, moving from your ignorance of how evolution actually works now to more general ignorance of all science. Ignorance is not a crime, nor is it derogatory, it is just unawareness of things (undereducated might be a better term), it is curable with education.
Here's a little chart of the scientific method for your use:
Note it is a continual feedback loop, testing keeps being done and each successful test leads to more tests. Nothing is ever proved. Now we come to Origins of Life, which is not part of evolution (evolution is the change in a living population -- no living population no evolution), And this leads to all kinds of questions (not least of which is "what is the definition of life?" -- try it -- give us your definition). Another is "what is the evidence for origin of life?" ... and the evidence is:
Therefore somewhere between ~4.5 byr and ~3.5 byr ago life began. So the next question is "How can that occur?" And that is being tested with a wide variety of hypotheses that posit different scenarios, and that provide tests using objective empirical evidence to see if they work. A couple of old threads discussing these are:
Panspermic Pre-Biotic Molecules - Life's Building Blocks (Part I) and Self-Replicating Molecules - Life's Building Blocks (Part II) Now a question for you: IFF we posit that "God did it" then how do we test that? Enjoy Edited by RAZD, : .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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RAZD Member (Idle past 1395 days) Posts: 20714 From: the other end of the sidewalk Joined: |
You're doing such a good job of explaining how I didn't mean what I plainly wrote that you hardly need any help. I don't know who you can actually hope to deceive on this subject, which I think makes this kind of a strange hobby for you to have. But we are obviously two very different people. Apparently what we are seeing is a creationist devolving into a troll. With no cogent argument and no response to the several posts pointing towards erroneous and false arguments, the poster falls back on twisting words to get a rise out of people rather than a discussion. Waste of bandwidth, imho. But still a good foil to speak to the peanut gallery, demonstrating the failure of these purported "arguments" -- most of which are pratts (more like coming to an axe fight without an axe). 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 1395 days) Posts: 20714 From: the other end of the sidewalk Joined:
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It's really simple, there is ample evidence of natural causes but no one has ever presented any evidence of any un-natural causes. Simple -- as soon as something is observed and verified it becomes natural caused ...
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RAZD Member (Idle past 1395 days) Posts: 20714 From: the other end of the sidewalk Joined:
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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. 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 1395 days) Posts: 20714 From: the other end of the sidewalk Joined: |
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. 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 1395 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 1395 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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