Nested Hierarchies (Tree of life)

Moderator’s remark: this post is long enough to need a “more” tag.  But the wordpress editor will only allow me to add that at the very beginning or the very end.  So here it is at the very beginning.

Do you want to be my cousin?
Sure. If not me, then who?

  1. “Nested hierarchies” or “cladistic analysis” or “consilience of independent phylogenies” is often offered as support for Darwinist evolution. This is the idea that the “tree of life” classification of organisms is somehow objective despite being a creation of very zealous “evolution” advocates. The three basic assumptions of cladistics models are: a) Any group of organisms are related by descent from a common ancestor (UCD – universal common descent); b) There is a bifurcating pattern of cladogenesis; c) Change in characteristics occurs in lineages over time. Although not explicit, UCD (“descent from a common ancestor”) here means by a Darwinian “natural selection mechanism” and not by a process generated by a designer that also happens to make use of biologic reproduction.
  2. No assumption can be tested by the model that uses them. That is why they’re called ‘assumptions’ and not ‘conclusions’. Instead, assumptions have to be tested independently through an entirely separated method or be accepted as axioms. An UCD “mechanism” has never been observed or proved elsewhere and is not “self-evidently true”, therefore not a valid axiom. Because UCD is an assumption in “cladistic analysis”, it cannot be logically also a conclusion of any such analysis. Furthermore the conclusions of any “cladistic analysis” will always and trivially be compatible with the UCD assumption in that model.
  3. Hypothesis testing requires an alternative (null) hypothesis and a procedure that demonstrates how the data available is compatible with the successful hypothesis and at the same time is statistically incompatible with the alternative hypothesis. In the “cladistic analysis” case, the alternative hypothesis to UCD is “common design”, and of course UCD cannot be an assumption of such an analysis. However this rule is violated twice, first by the use of an assumption also presented as conclusion, and second by the prejudiced rejection of the alternative “common design” hypothesis before analysis. This clearly demonstrates that “cladistic analysis” can never be logically used as proof of UCD. What “cladistic analysis” is instead is ‘curve fitting’ where the cladistics model is best fitted to certain (conveniently selected!) morphologic/biochemical/genetic biologic data points.
  4. The ‘designer’ hypothesis cannot fail against the ‘no designer’ (Darwinist evolution) alternative in a biologic comparative analysis as designers have maximum flexibility. This is not surprising as designers are free to incorporate whatever mechanism they want, including intelligent “selection” (human breeders do!) and “common descent” (human breeders do!) if they so desire.
  5. The claim that cars and other entities cannot be uniquely and objectively classified (“nested hierarchy”), while organisms can, is false. On one hand, we do know the history of the automobile, so a proper classification must be able to reconstruct their unique “evolution”. Yes, vehicle share parts, so to get to the actual development tree, we must group them differently than organisms since mass production works differently than biologic reproduction. On the other hand, organisms may not be uniquely classified as demonstrated by the numerous revisions and exceptions to the “tree of life”, and in any case, “uniquely classified” is an absolute claim that can never be proven since it is impossible to compare the infinity of possible organism classifications.
  6. The claim that the “tree of life” based on anatomy is validated by the match with the tree based on biochemistry fails. Anatomy is not independent of biochemistry. Also, the oldest DNA ever found was 700k years old therefore any match between the independent trees is limited. This is not to say that the fossil record is complete, or that fossils can be positively linked to one another and the living without – once again – presupposing UCD. The claim that “there is no known biological reason, besides common descent, to suppose that similar morphologies must have similar biochemistry” is false as the ‘designer’ hypothesis produces the same result when one designer creates all morphologies, and furthermore “I cannot think of an alternative reason why…” is not a valid argument.
  7. A “tree of life” is an artificial human construct as organisms do not come labeled with their position in a cladistics hierarchical structure. To decide the position of a certain organism, the human creators of the “tree” have to decide which morphologic/biochemical/genetic characteristics to include and what weight to attach to each of those measures. This further supports the claim that “cladistic analysis” is ‘curve fitting’ rather than ‘hypothesis testing’ – if a tree must be built, a tree will be built as in this example: “The close relationship between animals and fungi was suggested by Thomas Cavalier-Smith in 1987, […] and was supported by later genetic studies. Early phylogenies placed fungi near the plants and other groups that have mitochondria with flat cristae, but this character varies. More recently, it has been said that holozoa (animals) and holomycota (fungi) are much more closely related to each other than either is to plants […].”

 

1,059 Replies to “Nested Hierarchies (Tree of life)”

  1. Rumraket Rumraket
    Ignored
    says:

    Nonlin.org: What predictions?

    Consilience of independent phylogenies.

    Examples?

    http://www.talkorigins.org/faqs/comdesc/section1.html#independent_convergence

    To get specific examples I invite you to search for the DNA sequences of particular homologous genes from, say, 10 species of primates and infer a phylogenetic tree from them. Then pick another gene, find the homologoues of it from the same 10 species, infer a tree from that gene too. Do the same thing for 3 more different genes or so. Then compare the trees. Common descent predicts the trees you infer should be very similar to each other.

    You can probably find examples of genes (and species) to use in this paper: Perelman P, Johnson WE, Roos C, Seuánez HN, Horvath JE, Moreira MAM, et al. (2011) A Molecular Phylogeny of Living Primates. PLoS Genet 7(3): e1001342. https://doi.org/10.1371/journal.pgen.1001342/

  2. John Harshman John Harshman
    Ignored
    says:

    colewd:
    John Harshman,

    This is your assertion you keep repeating and not supporting.

    The argument that I make, which you generally ignore, is support for that assertion.

    I’ll ask you again how do you know differences are mutations unless you are in a controlled experiment.

    Experiment is not the only kind of science. How do you know the planets aren’t pushed around by angels? Have you done a controlled experiment with planets? Once again you attempt to hold evolution to a different standard than other science.

    No, it can’t.This is false equivalence.This is where your argument fails.

    If you say it’s false equivalence, you have to explain where the equivalence breaks down. I don’t think you can.

    I am asking you to show it is not likely the direct result of design.I know with reasonable certainty that you are not the direct result of design.

    How do you know that? How would I show that something was “not likely the direct result of design”? What does that even mean?

    The same requirement for the nested hierarchy.You need to show with REASONABLE CERTAINTY that it is not the direct result of design as I can show with REASONABLE CERTAINTY that you are not the direct result to design.

    I’d like to see you show that. I’d also like you to show with reasonable certainty (doesn’t have to be all caps) that angels don’t push the planets.

    The problem you are having is the process is underway to show with REASONABLE CERTAINTY the nested pattern is not the result of ancestry alone.

    The problem I’m having is that you are incapable of following an argument or of making one. Sometimes you’re incapable of so much as a coherent sentence, as the example just above. Whatever were you trying to say?

  3. Entropy Entropy
    Ignored
    says:

    colewd:
    Science is not about proofs.If you want to claim common descent based on a tree you need to show the alternative hypothesis (null) is highly unlikely.

    Nice cop-out., But sorry, you still need evidence for design. No way around this.

    colewd:
    The only competing hypothesis that can create a tree is design.

    At least you didn’t say “null” this time. That’s progress. However, as I explained to you before, It cannot be a competing hypothesis because it’s philosophically backwards and scientifically faulty.

    It cannot be a competing hypothesis because it’s not an actual explanation. “A designer made it appear as if things evolved” is not precisely convincing. It’s a ridiculous, philosophically bankrupt, excuse to bring your religious beliefs into the picture.

    colewd:
    There is no way around this.

    Of course there is. Where are those designers? What are they made of? How did they arise? If we, the only designers you can point to, had to be designed, then we should infer that designers have to be designed. So where does it stop? If it stops, and some designers are not the product of design, then considering that we were designed is adding layers without evidence for such layers, and without gaining any better understanding. We should therefore not consider design until there’s some actual evidence for such designers, starting with solving the philosophical and scientific problems, and with serious considerations about which designers could those be, which tools did they use, etc. No politically-inspired excuses like those from the IDIots.

    colewd:
    You can use your philosophical/materialist limitations argument to make your case but thats about it.Those arguments have very little meat on the bone.

    Au contraire. They show the nonsensical nature of your position. If to get to a designer you need “special” foundations, such as religious “non-materialistic” ones, then your case is even worse, since it depends on “foundations” that require, themselves, evidence, and that look like mere fantasies.

  4. Entropy Entropy
    Ignored
    says:

    Nonlin.org: Con: Every model contains assumptions, and the fit of the model to data can be used to test whether the assumptions are valid for the data. A chi square test is a simple example. And an inference made in one study can then be used as an assumption in another
    Pro: False. They’re called ‘assumptions’ and not ‘conclusions’ because they have to be tested independently through an entirely separated method or be accepted as axioms. as·sump·tion [əˈsəm(p)SH(ə)n] NOUN, a thing that is accepted as true or as certain to happen, without proof.

    Oh my fucking god Nonlin, you’re missing the fucking point. Here it goes again: we can start with the assumption that some fucking data fits some fucking curve. We can then try and fit the fucking data to such fucking curve. We can then test the fucking fit of the fucking data to the fucking curve and determine that the fucking data don’t fit the fucking curve, therefore showing that the curve is not proper for the fucking data. We can therefore conclude that what was initially an assumption was false.

    Things are dynamic Nonlin. We can start with something as a assumption, yet put it to the test and determine that the assumption was wrong, thus changing it’s status to false and go on with our lives. If the opposite happens, if the data fits the curve, then what was initially an assumption becomes a conclusion.

    This is fucking simple. I don’t understand, really, how your brain can misfire so badly.

    I’d explain the problems with the rest of your “points,” from false claims to further ignorance and incompetence on your part, but you cannot read. Maybe I’ll try this one for now and see if you can learn. I seriously doubt it though.

    Stop using words like retard for the people and their comments to you. You make your image worse, since your words backfire in the face of your incompetence. Pay attention instead and grow up.

  5. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    On the (side) issue of inferring genealogies,

    Nonlin.org: Is this not your comment:

    Joe Felsenstein: That is very odd. Given people’s DNA sequences, yes, we can infer their genealogy without any “labels” to help us. All we have to know is which DNA sequence came from which person.
    “?
    This is false as shown.

    I did respond to nonlin.org’s bringing up within-species genealogies. Mea culpa. Of course you can infer sets of siblings, sets of half-sibs, sets of cousins, etc. You cannot necessarily associate their parents with particular individuals in past generations, but you can reconstruct the shape of the genealogy.

    So not “false as shown”.

  6. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    nonlin.org keeps saying that we are assuming Universal Common Descent and therefore cannot test it.

    The consilience of phylogenies from different parts of the genome (say, different genes) shows that there is a common phylogeny affecting all these parts of the genome. In doing that, we do not assume that all these phylogenies are exactly the same — we check to what extent they are similar.

    Is having a common phylogeny “Universal Common Descent”? If so, did we assume a common phylogeny when we went to test it? There is nothing in our inferences of phylogenies that forces them to be the same for different loci.
    So are we assuming UCD? No! So nonlin.org is simply wrong about that.

  7. phoodoo
    Ignored
    says:

    Entropy: I’d explain the problems with the rest of your “points,” from false claims to further ignorance and incompetence on your part, but you cannot read. Maybe I’ll try this one for now and see if you can learn. I seriously doubt it though.

    Stop using words like retard for the people and their comments to you. You make your image worse, since your words backfire in the face of your incompetence. Pay attention instead and grow up.

    Do you like art?

  8. colewd
    Ignored
    says:

    John Harshman,

    Experiment is not the only kind of science.

    I understand but sometimes it is a critical tool in isolating cause. Like knowing the cause of observed genetic variation.

    If you say it’s false equivalence, you have to explain where the equivalence breaks down. I don’t think you can.

    You are comparing hypothesis that is modeled and tested with one that is not.

    I’d like to see you show that. I’d also like you to show with reasonable certainty (doesn’t have to be all caps) that angels don’t push the planets.

    By showing an alternative mathematical model that we can test or has been tested. In this case general relativity.

  9. colewd
    Ignored
    says:

    Entropy,

    Nice cop-out., But sorry, you still need evidence for design. No way around this.

    What do you consider evidence?

  10. colewd
    Ignored
    says:

    Joe Felsenstein,

    So are we assuming UCD? No! So nonlin.org is simply wrong about that.

    What is your null hypothesis for the cause of the tree?

  11. John Harshman John Harshman
    Ignored
    says:

    colewd: Me: Experiment is not the only kind of science.

    Bill: I understand but sometimes it is a critical tool in isolating cause. Like knowing the cause of observed genetic variation.

    Once again, you are unclear. What “observed genetic variation”? Are you claiming that we don’t know the cause of variation within species? Between parents and children? What, in regard to mutation, even counts as “observing”?

    Me: If you say it’s false equivalence, you have to explain where the equivalence breaks down. I don’t think you can.

    Bill: You are comparing hypothesis that is modeled and tested with one that is not.

    What modeling and testing are you talking about?

    Me: I’d like to see you show that. I’d also like you to show with reasonable certainty (doesn’t have to be all caps) that angels don’t push the planets.

    Bill: By showing an alternative mathematical model that we can test or has been tested. In this case general relativity.

    How has general relativity been tested in the laboratory as an explanation for planetary movement? How have angels been ruled out? I’m afraid all this post shows is that you haven’t thought about the matter at all.

  12. John Harshman John Harshman
    Ignored
    says:

    colewd:
    Joe Felsenstein,

    What is your null hypothesis for the cause of the tree?

    The null hypothesis would be no tree or a star tree: the hypothesis that the data do not support any tree over any other tree. I will also point out that the null hypothesis model is not the only model of scientific testing.

    Now, your null hypothesis, “design”, just doesn’t work as a null hypothesis at all. A null hypothesis, in the first case, must be well characterized. We have to know what we expect if it’s true and what we expect if it’s false. The point of a null hypothesis is that if the data fall outside the expected range, we can reject it. Design isn’t characterized at all, there are no expectations, there are no data that could fall outside its range, and therefore it’s impossible for it to be rejected. Every time you use the term you demonstrate that you understand nothing about statistical testing.

  13. colewd
    Ignored
    says:

    John Harshman,

    Are you claiming that we don’t know the cause of variation within species?

    I am not claiming any specific cause in this case. I am simply pointing out that it is an important tool used in science.

    What modeling and testing are you talking about?

    In the case of the ball falling off the table newtons model works fine. The test would be to measure if the model predicts the outcome properly.

    How have angels been ruled out?

    On what basis would you consider “angels”a hypothesis to be considered.

  14. colewd
    Ignored
    says:

    John Harshman,

    I will also point out that the null hypothesis model is not the only model of scientific testing.

    Why was the model introduced?

  15. colewd
    Ignored
    says:

    John Harshman,

    Design isn’t characterized at all, there are no expectations, there are no data that could fall outside its range, and therefore it’s impossible for it to be rejected.

    Design in biology is characterized by the observation of functional information. It is also characterized by trees that don’t follow a strict inheritance pattern.

    A lack of functional information in the genome would be grounds to reject design as a cause.

    A pattern that strictly follows inheritance would be grounds to reject design as a cause for the tree-like pattern.

  16. Rumraket Rumraket
    Ignored
    says:

    colewd: It is also characterized by trees that don’t follow a strict inheritance pattern.

    So you’re saying design predicts the absense of converging phylogenetic trees?

  17. Rumraket Rumraket
    Ignored
    says:

    colewd: Design in biology is characterized by the observation of functional information.

    Why? Can the designers not elect to design organisms without it?

  18. Rumraket Rumraket
    Ignored
    says:

    colewd: What do you consider evidence?

    Data that is more likely on a particular hypothesis, is evidence for that particular hypothesis.

    What should the data look like on design? What pattern should there be in the data and why?

  19. J-Mac
    Ignored
    says:

    Neil Rickert: intelligent

    Congratulations Neil!!! You have become the first product of this OP that has shown some “flexibility”, or reason, among the rest of egocentric, narcissistic and self-absorbed crowd here… I like your “truth” response too….

  20. John Harshman John Harshman
    Ignored
    says:

    colewd:
    John Harshman,

    I am not claiming any specific cause in this case.I am simply pointing out that it is an important tool used in science.

    I have no idea what that was supposed to mean. Are you capable of clarity?

    In the case of the ball falling off the table newtons model works fine.The test would be to measure if the model predicts the outcome properly.

    But common descent predicts the tree properly, and you reject that. Why?

    On what basis would you consider “angels”a hypothesis to be considered.

    It’s design, and you have alleged that design is the proper null model.

    Nothing you have said here is a a response to my request that you explain the difference between testing the gravity hypothesis and testing the descent hypothesis.

  21. John Harshman John Harshman
    Ignored
    says:

    colewd:
    John Harshman,

    Why was the model introduced?

    Because it’s useful. Sometimes.

    Design in biology is characterized by the observation of functional information.It is also characterized by trees that don’t follow a strict inheritance pattern.

    A lack of functional information in the genome would be grounds to reject design as a cause.

    A pattern that strictly follows inheritance would be grounds to reject design as a cause for the tree-like pattern.

    Several flaws in your “argument:. 1) Those are criteria you just made up. I don’t think you can justify them. 2) A designer could as easy follow inheritance as not, and a genome with no functional information could not exist, as it wouldn’t support life. 3) None of that is a prediction of design, nor does it distinguish design from common descent. 4) The first bit isn’t even relevant to common descent; you have once again confused the source of variation with descent. 5) The data are as predicted by common descent; homoplasy is expected. 6) You have not dealt with the basic fact that nested hierarchy is not a prediction of design; it’s only compatible with design because everything is compatible with design.

  22. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    colewd’s statement that functional information indicates Design is absurd. Functional information can (also) come to be in the genome as a result of natural selection. After all, all functional information indicates is that the genome is has higher function (of some sort that we have chosen in advance) than would be expected in a random genome.

    colewd needs to justify his statement by explaining why natural selection cannot be the reason functional information is in the genome, why it can only come from Design.

  23. John Harshman John Harshman
    Ignored
    says:

    Joe Felsenstein,

    He also needs to explain why nonfunctional information in the genome (i.e. junk DNA) is also a prediction of design. Design, apparently, predicts that we will see whatever we see. Since we see what we see, design is confirmed.

  24. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    John Harshman: Since we see what we see, design is confirmed.

    Yes, I was astonished to see colewd take that as a strength of the Design hypothesis.

  25. colewd
    Ignored
    says:

    John Harshman,

    But common descent predicts the tree properly, and you reject that. Why?

    If it predicts the tree we are observing then build a mathematical model that re creates the tree through a process of inheritance.

    It’s design, and you have alleged that design is the proper null model.

    I do not consider my 17 month old grandson pushing his toy truck across the floor design. If you do maybe I have underestimated him 🙂

  26. colewd
    Ignored
    says:

    John Harshman,

    He also needs to explain why nonfunctional information in the genome (i.e. junk DNA) is also a prediction of design.

    Since you made up this claim maybe you can deal with it.

  27. colewd
    Ignored
    says:

    Joe Felsenstein,

    colewd needs to justify his statement by explaining why natural selection cannot be the reason functional information is in the genome, why it can only come from Design.

    I think the burden of proof is on you since we know conscious intelligence can create FI. Natural Selection can only select information that already exists.

    Maybe you can generate a competitive inference to the origin of FI.

  28. colewd
    Ignored
    says:

    Rumraket,

    What should the data look like on design? What pattern should there be in the data and why?

    A functional sequence. A sequence that can create another functional sequence. A repair mechanism that is made of a functional sequence that is created from another functional sequence.

  29. colewd
    Ignored
    says:

    Joe Felsenstein,

    colewd’s statement that functional information indicates Design is absurd. Functional information can (also) come to be in the genome as a result of natural selection. After all, all functional information indicates is that the genome is has higher function (of some sort that we have chosen in advance) than would be expected in a random genome.

    Joe, do you believe that we can explain the eukaryotic genome with random variation and natural selection?

  30. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    colewd: Maybe you can generate a competitive inference to the origin of FI.

    Sorry, I forgot that colewd uses the gpuccio definition of “functional information”. We have discussed this here ad nauseam.

    There is of course the old original definition of “functional information” by Jack Szostak, also used by Robert Hazen. Derived from Leslie Orgel’s “specified information”. Those can get into the genome by natural selection acting on mutations.

    The gouccio/colewd version only calls it functional information if it can’t come about by natural selection, if there is an isolated “island” of functional sequences that is too far from the starting point to be reached by mutation with natural selection. Not going to discuss that further here, especially since it is off-topic.

    For those who want to see the extremely long discussion of “FI” and its supposed use by gpuccio to infer Design, try this thread, all 1,971 frustrating comments of it.

  31. John Harshman John Harshman
    Ignored
    says:

    colewd:
    John Harshman,

    If it predicts the tree we are observing then build a mathematical model that re creates the tree through a process of inheritance.

    I do not consider my 17 month old grandson pushing his toy truck across the floor design.If you do maybe I have underestimated him

    I do not know what you intended to say in any of those sentences. Please try much harder to communicate intelligibly.

  32. John Harshman John Harshman
    Ignored
    says:

    colewd:
    John Harshman,

    Since you made up this claim maybe you can deal with it.

    This is you refusing to consider the implications of what you say. If genomes are created, then the functional sequences are designed, but so are the non-functional ones. Think.

  33. Entropy Entropy
    Ignored
    says:

    colewd:
    Entropy:
    Nice cop-out., But sorry, you still need evidence for design. No way around this.

    Bill:
    What do you consider evidence?

    You stoped reading right there, didn’t you?

  34. Rumraket Rumraket
    Ignored
    says:

    colewd: A functional sequence.

    This is a meaningless “prediction” as in so far as some sort of living organism exists, there are going to be functional polymers of some sort. That’s not a prediction of design, it is as best we know, a requirement of life. And that might even be wrong. How do we really know that some sort of self-sustaining and reproducing chemical reaction not involving polymer chemistry isn’t possible? How do we know a designer can’t make such an entity? Why would it want to make sequences of polymers in particular?

    In any case, if polymers are fundamental to life, that would make it equally predicted on all hypotheses that attempt to account for life, and therefore can’t be evidence for any of them over another.

    Also, I don’t see the model that actually predicts this. You just declare that design predicts it, but where is your mechanism? What is it about the design process that entails functional sequences?

    You can’t just skip the why. Otherwise they’re not predictions you are stating, they are just claims.

    There’s a mechanism involved in common descent (splitting lineages, incremental independent change in isolated subpopulations) from which the pattern (tree-like structure in the data, consilience of independent phylogenies) inexorably follows. It explains WHY we expect the pattern that we do. It gives a REASON FOR the pattern. It effectively says why that pattern should form over time if the mechanism is operating.

    You are not giving any of that on your design “predictions”. Because they’re not actually predictions, let’s be real. You just declare that something we see in living organisms is what the designer wanted. There is no why, or how, no rhyme or reason involved. You just point to something fancy you like and say “yeah the designer would want to make that”.

    Sorry, not buying it.

    A sequence that can create another functional sequence.

    Please elaborate. What do you mean by a sequence that can create another functional sequence, and why is that a prediction on design?

    Look, any idiot can point to something in life as we know it and just declare that their pet hypothesis predicts it. What you need to explain is WHY that is a prediction.

    If you disagree, then imagine if I was to do what you’re doing. I could just sit here and declare that evolution predicts all the molecules and polymers we see. Ribosomes, ATP synthases, flagella, spiceosomes and so on to pick your favorites. Evolution predicts all of them. Oh look, they really exist, well then evolution must be true.

    It’s pretty obvious why those aren’t genuine predictions. And yours aren’t for the same reason. You understand this right? You can see the problem now?

    A repair mechanism that is made of a functional sequence that is created from another functional sequence.

    Same thing, explain why those are predictions of design.

    I have to note here that at the very least, your declaration of these as “predictions” of design are historically implausible, as these have all suddenly become “predictions” after their discovery in living organisms.

    In order to make these predictions into genuine predictions, you need a model of design that has a design-mechanism from which they follow.

  35. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    Rumraket:

    colewd: A functional sequence.

    This is a meaningless “prediction” as in so far as some sort of living organism exists, there are going to be functional polymers of some sort.

    You have fallen into the same trap that I did, just a little upthread. To colewd (and gpuccio) “functional” does not just mean that it functions. It means that it is part of a group of sequences which is rare and is isolated from any other functional sequence, so much so that you can’t get there from here, because the neighboring sequences to that island have no function at all, so natural selection cannot climb the fitness surface onto that island.

    colewd thinks that we see lots of cases of this. All this was gone over endlessly at this thread not too long ago. I doubt that rehashing that discussion here will help this one.

  36. John Harshman John Harshman
    Ignored
    says:

    Joe Felsenstein,

    And let us note again that this has nothing at all to do with the ostensible subject, common descent, but with the origin of novelty. As we know, Bill can’t tell the difference.

  37. petrushka
    Ignored
    says:

    Getting from there to here does impinge on common descent.

    It’s true that analysis of similarities and differences leads to the inference of common descent, but if you can’t get here from there, the inference falls flat.

    It’s half empty vs half full.

    One side says the evidence for common descent is beyond a reasonable doubt. The other side says you can’t get here without miracles.

    The problem I see with the miracle argument is leads nowhere and produces no research proposals.

    Whereas the argument for continuity has made progress for hundreds of years.

  38. colewd
    Ignored
    says:

    petrushka,

    The problem I see with the miracle argument is leads nowhere and produces no research proposals.

    When you study the eukaryotic cell to try and understand such hard things as human disease, and if it is indeed designed, you will get much further if you make design you’re working assumption.

  39. colewd
    Ignored
    says:

    Joe Felsenstein,

    there from here, because the neighboring sequences to that island have no function at all,

    Or the functional sequences are too far away for evolutionary resources to find.

    Do you believe that the tree of life can be explained by descent with modification?

  40. Entropy Entropy
    Ignored
    says:

    colewd:
    When you study the eukaryotic cell to try and understand such hard things as human disease, and if it is indeed designed, you will get much further if you make design you’re working assumption.

    This must be the worst attempt at justifying the philosophically and scientifically bankrupt “design” “inference.”

    Such a thing would be disastrous. We find no repair factories with replacement parts. We’d be cutting arms and legs thinking that they attache precisely, rather than organically messy, and would get people bleeding profusely, interrupting their blood flows, never finding the screws and easy-to-detach points, and assuming that replacing pieces is a question of going to the factory.

    We’d go as far as detaching heads, considering them also replaceable and easy to detach from carefully designed attachment points. Who cares? They’re designed, they must be easy to exchange.

    We’d think that human diseases are just about worn but replaceable parts, never to consider parasites, from viruses to bacteria to fungi to protozoa. Just add water, or oil here and there, some coolant, perhaps, and be done.

    I could continue, but this is too ridiculous.

  41. Rumraket Rumraket
    Ignored
    says:

    colewd: When you study the eukaryotic cell to try and understand such hard things as human disease, and if it is indeed designed, you will get much further if you make design you’re working assumption.

    Cool story bro.

  42. John Harshman John Harshman
    Ignored
    says:

    petrushka:
    Getting from there to here does impinge on common descent.

    It’s true that analysis of similarities and differences leads to the inference of common descent, but if you can’t get here from there, the inference falls flat.

    It’s half empty vs half full.

    One side says the evidence for common descent is beyond a reasonable doubt. The other side says you can’t get here without miracles.

    The problem I see with the miracle argument is leads nowhere and produces no research proposals.

    Whereas the argument for continuity has made progress for hundreds of years.

    I think you’re making the same mistake Bill does. It’s still common descent even if every mutation is directly zapped into existence by God. The mechanism of innovation is not relevant to common descent.

  43. Joe Felsenstein Joe Felsenstein
    Ignored
    says:

    colewd: Do you believe that the tree of life can be explained by descent with modification?

    Yes. Though of course I cannot provide detailed explanations for all characters in all species, as we know too little. And of course the “modification” that occurs on lineages as they diverge can be anything, even Design (as John Harshman has just noted, and as he and others have pointed out to you many times).

  44. OMagain
    Ignored
    says:

    colewd: When you study the eukaryotic cell to try and understand such hard things as human disease, and if it is indeed designed, you will get much further if you make design you’re working assumption.

    Then why are you not heading up a premier research department curing disease with ease?

    You think that scientists are clinging on to orthodoxy when it’s their dream to destroy it. It means their names live forever. They seek what is productive. What works. If what you say is true it’d be happening, right now.

    It’s not.

  45. J-Mac
    Ignored
    says:

    OMagain: Then why are you not heading up a premier research department curing disease with ease?

    Why would he? Evolution explains everything…even the evolutionary “advantage” of cancer… as it should…
    I think a prominent theistic evolutionists has a “respectable” article about that at peaceful science fiction blog…

    I’m sure you will like it:
    http://peacefulscience.org/cancer-evolution/

  46. Nonlin.org
    Ignored
    says:

    Rumraket: To get specific examples I invite you to search for the DNA sequences of particular homologous genes from, say, 10 species of primates and infer a phylogenetic tree from them. Then pick another gene, find the homologoues of it from the same 10 species, infer a tree from that gene too. Do the same thing for 3 more different genes or so. Then compare the trees. Common descent predicts the trees you infer should be very similar to each other.

    And why not? These are based on the same UCD assumption and your genes are not proven independent of each other.

  47. Nonlin.org
    Ignored
    says:

    Entropy: We can start with something as a assumption, yet put it to the test and determine that the assumption was wrong, thus changing it’s status to false and go on with our lives. If the opposite happens, if the data fits the curve, then what was initially an assumption becomes a conclusion.

    No, you cannot. Since this is not going anywhere, go ahead and ask someone else. This is 100% retard: “what was initially an assumption becomes a conclusion”. Anyone else wants to chime in on this?

    Even better, look up a situation outside of the Darwinism pseudoscience where someone builds a model based on an assumption and then tries to justify that assumption based on the model’s output. And stick with the hard sciences.

  48. Nonlin.org
    Ignored
    says:

    Joe Felsenstein: Of course you can infer sets of siblings, sets of half-sibs, sets of cousins, etc. You cannot necessarily associate their parents with particular individuals in past generations, but you can reconstruct the shape of the genealogy.

    Huh? What does this mean?

  49. Nonlin.org
    Ignored
    says:

    Joe Felsenstein: So are we assuming UCD? No! So nonlin.org is simply wrong about that.

    Berkeley thinks you’re wrong:
    http://www.ucmp.berkeley.edu/clad/clad1.html assumptions
    http://www.ucmp.berkeley.edu/clad/clad2.html method

  50. Nonlin.org
    Ignored
    says:

    John Harshman: The null hypothesis would be no tree or a star tree: the hypothesis that the data do not support any tree over any other tree. I will also point out that the null hypothesis model is not the only model of scientific testing.

    Now, your null hypothesis, “design”, just doesn’t work as a null hypothesis at all. A null hypothesis, in the first case, must be well characterized. We have to know what we expect if it’s true and what we expect if it’s false. The point of a null hypothesis is that if the data fall outside the expected range, we can reject it. Design isn’t characterized at all, there are no expectations, there are no data that could fall outside its range, and therefore it’s impossible for it to be rejected.

    As explained many times, what you do is curve fitting, not hypothesis testing.

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