191 thoughts on “But Is It Science”

  1. John Harshman,

    Sometimes you evolutionists are just so pathetically predictable. Just throw out a cut and paste and pretend it supports your position, without saying why.

    Maybe the important parts of the paper John wanted to reference are in the very first paragraph:

    “Although well studied, the evolutionary relationships among avian groups are contentious.

    and

    “Little consensus exists regarding relationships within this clade”

    Gee John, that sounds like an exact contradiction of the point you are trying to make. Thanks for the link!!

    I guess you were once again hoping people wouldn’t actually read your links, and see how void of explanatory power they are-sort of like Nilsson Pelger, eh?

  2. John, you assume common descent a priori from similarity of DNA and I think that is where the science is and I support your conclusions.I have told you this several times.The science is not mature enough to show 95% statistical confidence that your conclusions are correct.The science is very immature IMHO and that is why I am skeptical.

    I recall it was Lizzie who pointed out, some while back, that well-supported evidence-based conclusions at one level, become input assumptions at a higher level. Science is hierarchical and cumulative in this respect – that bedrock conclusions at lower levels need not be retested ad infinitum.

    Almost any hypothesis can be supported by the combined techniques of ignoring uncongenial data and manufacturing ad hoc presumptions to create foregone conclusions. As Phoodoo and others have shown us, the real difficulty lies in noticing these techniques are being deployed when we like the conclusions. I suspect Gauger, Axe et. al. don’t even recognize that they apply these techniques iteratively in the formulation of their hypotheses and the structure of their methodologies.

    I also suspect mainstream scientists also often fall afoul of confirmation bias at all stages of their research. Peer review, replication, and poor predictions clean up some of this, but it’s always an uphill battle.

  3. phoodoo:
    John Harshman,

    Sometimes you evolutionists are just so pathetically predictable.Just throw out a cut and paste and pretend it supports your position, without saying why.

    Maybe the important parts of the paper John wanted to reference are in the very first paragraph:

    “Although well studied, the evolutionary relationships among avian groups are contentious.

    and

    “Little consensus exists regarding relationships within this clade”

    Gee John, that sounds like an exact contradiction of the point you are trying to make.Thanks for the link!!

    I guess you were once again hoping people wouldn’t actually read your links, and see how void of explanatory power they are-sort of like Nilsson Pelger, eh?

    I think you may be missing an important point here. Unlike fields where “truth” is received, perfect and immutable for those who accept it, everything in science is tentative, and the details at the cutting edge are always contentious.

    But your effort to conflate “there are disputed relationships in the clade details” with “clades themselves are arbitrary fictions” does you no credit. I may have no idea who my great-great-great-grandfather was, and I may have no way of ever identifying him, but I should not therefore jump to the conclusion that he never lived. I should be especially careful if I can recognize my powerful need to believe no such people existed.

  4. It should also be pointed out to colewd, yet again, that common descent is a conclusion, not an assumption, in these particular analyses. If one has 2 sequences with not just bitwise ‘similarity’ but with long runs of identity into which the differences are embedded, and a wider dataset giving strong coalescence on the same tree-like pattern of differences, what mechanisms can lead to that pattern?. I’ll start the list:

    1) Common descent.
    2) … ?

  5. phoodoo,

    Maybe the important parts of the paper John wanted to reference are in the very first paragraph:

    That would certainly save one the bother of reading further, O Quote-mining One.

  6. colewd: The science is very immature IMHO and that is why I am skeptical.

    And yet you keep ‘special creation’ open as a viable alternative on what evidentiary basis precisely?

    How mature is the science of ‘special creation’? How skeptical of that are you?

  8. Allan Miller:
    phoodoo,

    That would certainly save one the bother of reading further, O Quote-mining One.

    And as it happens, I’m Marshall McLuhan in this situation. The introduction of a paper is where you tell people what things were like before you published. Also as it happens, the introduction does mention that the part Bill and I were arguing about was one of the few points that was already settled. This sort of thing is why I ignore Phoodoo.

  9. GlenDavidson,

    2) Design that is magically indistinguishable from common descent. Because, you know, magic.

    Someone Very Powerful has gone to such enormous lengths to make it look like common descent that it would be churlish, nay, downright disrespectful, not to play along and reach that conclusion.

  10. Allan Miller: Someone Very Powerful has gone to such enormous lengths to make it look like common descent that it would be churlish, nay, downright disrespectful, not to play along and reach that conclusion.

    That’s the spirit!

  11. OMagain,

    How mature is the science of ‘special creation’? How skeptical of that are you?

    I am skeptical of all arguments that come form a historic inference vs direct observation and experiment.

  14. colewd,

    Geology consists of far more than ‘ooh look, basalt!’ It is concerned with reconstruction of ancient landscapes, continental movements, historic process, as inferred from present materials and process. It is as much based on a combination of observation and inference as is pattern analysis among modern DNA sequence datasets.

  15. colewd:
    OMagain,

    I am skeptical of all arguments that come form a historic inference vs direct observation and experiment.

    And the direct observation and experimental support for Magic Creation is, apparently, sufficient for you to regard as a compelling alternative. Right?

  19. colewd:
    OMagain,

    I am skeptical of all arguments that come form a historic inference vs direct observation and experiment.

    You might as well just come out and say you have no idea how science works. And your argument here is one that in my experience only committed creationists make. Might as well admit that too.

  22. Allan Miller:
    phoodoo,

    That would certainly save one the bother of reading further, O Quote-mining One.

    So people are supposed to guess where in the paper is the point he was trying to make, since he won’t say it himself?

    Maybe the point doesn’t exist?

    However, I wonder if in the future someone posts a ten page link to a query of yours and says go find the answer if you can, you will oblige. You seem to think its a worthy response. Or maybe you know its not a worthy response , but you are a team player.

  23. phoodoo,

    So people are supposed to guess where in the paper is the point he was trying to make, since he won’t say it himself?

    No. But I would certainly expect an honest reader to get past the frigging abstract, and not try to make a point on the historical notes. It is a quote mine. An honest-to-goodness, red-handed, shameless quote mine. ‘Noted evolutionist John Harshman says that avian relationships are controversial’. Which must mean they are wrong, his paper has no light to shed on the subject, and he’s so embarrassed about the fact that he both mentioned it in the paper and linked to it here.

    […] you are a team player.

    I understand the points John makes. If that makes me a team player, so be it. You’d have me react with drooling incomprehension occasionally, just to avoid the slur?

  24. Darwin:

    To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree.

    Case closed eh Phoodoo?

  25. Allan Miller,

    Where in the paper does it show that ” the monophyly of paleognaths had been well established long previously.”? What is the evidence in that paper?

    Have you found where it exists? What are the exact words in that paper that count as evidence for this?

    In fact if you read the whole paper, which I doubt you have, the authors are pretty clear to state that there is no definitive way to classify all birds, and they state:

    “Decipering the roots of the avian tree of life has been a lingering problem in evolutionary biology.”

    That is a far cry from John boastful premise that the “monophyly of paleognaths had been well established long previously.” Nothing in the tree of life has been well established Allan, that is a pure lie, NOT a quote mine!

  27. colewd:
    OMagain,

    I am skeptical of all arguments that come form a historic inference vs direct observation and experiment.

    Are you against forensic science in general, or just when it shows that evolution occurred?

    IOW, can DNA really show relatedness, or should that be thrown out of court?

    Glen Davidson

  28. colewd,
    Is there anything in science which you are sufficiently confident of to build upon? If so, what is it?

  29. OMagain,

    Is there anything in science which you are sufficiently confident of to build upon? If so, what is it?

    Yes, I have confidence in the scientific method that includes testing a hypothesis that is derived from observation.

  30. phoodoo,

    Pure bullshit. You are using quotes by John Harshman regarding avian phylogeny to support the contention that John Harshman is not in a position to offer an opinion on paleognath monophyly. You realise it’s the same person, right?

    And you cling to the desperate hope that birds are not related at all because .. … well, beats me. Why would anyone give that much of a shit? Oh yeah, evolution, decline of the western world, all that crap. But of course they are. What would lead one to think otherwise, given the wealth of data on the matter? The fact that John Harshman says certain relationships remain controversial?

  31. colewd,

    Yes, I have confidence in the scientific method that includes testing a hypothesis that is derived from observation.

    So if we observe that intra-species common descent produces sequence alignment and a tree pattern, and we have numerous pairs of highly aligned genomes in a tree pattern between broader clades, are we justified in our suggestion that we have tested the hypothesis that we are directly observing genetically related sequences, and the test has been passed to a high degree of confidence?

    What other hypotheses should we consider? What pattern do they predict? Is it the same one? Why?

  32. Allan Miller,

    So if we observe that intra-species common descent produces sequence alignment and a tree pattern, and we have numerous pairs of highly aligned genomes in a tree pattern between broader clades, are we justified in our suggestion that we have tested the hypothesis that we are directly observing genetically related sequences, and the test has been passed to a high degree of confidence?

    Would you agree that the confidence of that accuracy of the tree is the cumulative probabilities of the accuracy of all the nodes of the tree? What is the probability that specie A and B descended from common ancestor C?

    I agree that we have tested successfully that there is genetic relationships among species.

  33. colewd: Would you agree that the confidence of that accuracy of the tree is the cumulative probabilities of the accuracy of all the nodes of the tree? What is the probability that specie A and B descended from common ancestor C?

    I agree that we have tested successfully that there is genetic relationships among species.

    The hypothesis of common descent has been tested to 38 decimal places. It is the most statistically well-supported theory in all of science. http://www.talkorigins.org/faqs/comdesc/section1.html#independent_convergence

    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.

    …

    Nevertheless, a precision of just under 1% is still pretty good; it is not enough, at this point, to cause us to cast much doubt upon the validity and usefulness of modern theories of gravity. However, if tests of the theory of common descent performed that poorly, different phylogenetic trees, as shown in Figure 1, would have to differ by 18 of the 30 branches! In their quest for scientific perfection, some biologists are rightly rankled at the obvious discrepancies between some phylogenetic trees (Gura 2000; Patterson et al. 1993; Maley and Marshall 1998). However, as illustrated in Figure 1, the standard phylogenetic tree is known to 38 decimal places, which is a much greater precision than that of even the most well-determined physical constants. For comparison, the charge of the electron is known to only seven decimal places, the Planck constant is known to only eight decimal places, the mass of the neutron, proton, and electron are all known to only nine decimal places, and the universal gravitational constant has been determined to only three decimal places.

    The idea that common descent is on a weaker footing than other theories in science is the most wrong position it is possible to take.

  34. colewd: I agree that we have tested successfully that there is genetic relationships among species.

    Given your ability to write unclearly, I have no idea what you have just agreed to.

  35. Allan Miller:
    phoodoo,

    Pure bullshit. You are using quotes by John Harshman regarding avian phylogeny to support the contention that John Harshman is not in a position to offer an opinion on paleognath monophyly. You realise it’s the same person, right?

    And you cling to the desperate hope that birds are not related at all because .. … well, beats me. Why would anyone give that much of a shit? Oh yeah, evolution, decline of the western world, all that crap. But of course they are. What would lead one to think otherwise, given the wealth of data on the matter? The fact that John Harshman says certain relationships remain controversial?

    Uh no Allan. I am using quotes from the paper he referenced! You are off your rocker Allan. But since you have not read the paper, I guess you are in no position to say how the paper supports his premise. According to you, quoting from the paper that HE posted is quote mining. Totally off your rocker.

    But he is on your team, so you like him, rah, rah, rah….!

  36. Allan Miller: You are using quotes by John Harshman regarding avian phylogeny to support the contention that John Harshman is not in a position to offer an opinion on paleognath monophyly.

    To be fair, I didn’t write those quotes. One or more of the first three authors did. The rest of the authors put together the data, did some of the analyses, suggested changes, and approved the final product. But I think that’s close enough; I certainly don’t disagree with what was written. I don’t think Phoodoo has yet realized that I’m one of the authors.

  37. John Harshman,

    How does you being one of the authors of the paper change anything? The paper doesn’t prove the claim that the “monophyly of paleognaths had been well established long previously.”

  38. Phoodoo, against my better judgment I’m not going to ignore you this once. I encourage you to actually read the paper rather than looking for quote mines; and yes, it’s a quote mine. Notice that right after the bit you quote we get this: “Only two nodes at the base of the avian tree are consistently supported by both molecular and morphological phylogenetic studies (2–5, 10–14). The first divides the Paleognathae (ratites and tinamous) and Neognathae (all other birds), and the second splits the neognaths between the Galloanserae (chickens, ducks, and allies) and Neoaves (other neognaths).”

    Now, if you see the “2-5, 10-14”, that means that support for the claim is found in the references at the end of the paper with those numbers. Then the paper goes on to support that claim itself with its analyses of DNA sequences. You would have to read the whole thing for full details, but Fig. 2 is the simplest thing to look at.

  39. Phoodoo is doing the classic error of confusing the level of support for universal (or even within-group) common descent, with the level of support for a particular phylogeny within some particular group. He latched onto a statement about common descent, then cherry picked a sentence about a within-group phylogeny thinking the latter throws doubt on the former.

    We can know with great certainty, that all the members of a group are related, without knowing with great certainty exactly how that particular phylogeny resolves.

    Another good example besides birds would be rodents. There is no doubt the members of rodentia are related, but the exact relationships between them (whether two particular species of mice are more closely related to each other, than to some third mouse species) is hard to pin down. Nevertheless, they are all clearly more closely related to each other, than they are to bovines, birds, cephalopods etc.

  40. John Harshman:
    Phoodoo, against my better judgment I’m not going to ignore you this once. I encourage you to actually read the paper rather than looking for quote mines; and yes, it’s a quote mine. Notice that right after the bit you quote we get this: “Only two nodes at the base of the avian tree are consistently supported by both molecular and morphological phylogenetic studies (2–5, 10–14). The first divides the Paleognathae (ratites and tinamous) and Neognathae (all other birds), and the second splits the neognaths between the Galloanserae (chickens, ducks, and allies) and Neoaves (other neognaths).”

    Now, if you see the “2-5, 10-14”, that means that support for the claim is found in the references at the end of the paper with those numbers. Then the paper goes on to support that claim itself with its analyses of DNA sequences. You would have to read the whole thing for full details, but Fig. 2 is the simplest thing to look at.

    I guess you disagree with Wikipedia that this is in question then. Why should we accept you are right. It certainly doesn’t sound well established to say the least. When you claim that Nilsson Pelger is a great paper on how novel features develop, I think your judgement deserves to be questioned.

    Other authors questioned the monophyly of the Palaeognathae on various grounds, suggesting that they could be a hodgepodge of unrelated birds that have come to be grouped together because they are coincidentally flightless. Unrelated birds might have developed ratite-like anatomies multiple times around the world through convergent evolution. McDowell (1948) asserted that the similarities in the palate anatomy of paleognathes might actually be neoteny, or retained embryonic features. He noted that there were other feature of the skull, such as the retention of sutures into adulthood, that were like those of juvenile birds. Thus, perhaps the characteristic palate was actually a frozen stage that many carinate bird embryos passed through during development. The retention of early developmental stages, then, may have been a mechanism by which various birds became flightless and came to look similar to one another.[11]

    Hope (2002) reviewed all known bird fossils from the Mesozoic looking for evidence of the origin of the evolutionary radiation of the Neornithes. That radiation would also signal that the paleognaths had already diverged. She notes five Early Cretaceous taxa that have been assigned to the Palaeognathae. She finds that none of them can be clearly assigned as such. However, she does find evidence that the Neognathae and, therefore, also the Palaeognathae had diverged no later than the Early Campanian age of the Cretaceous period

  41. colewd,

    Would you agree that the confidence of that accuracy of the tree is the cumulative probabilities of the accuracy of all the nodes of the tree? What is the probability that specie A and B descended from common ancestor C?

    You wouldn’t conclude that all relationships are false. One can have robust support for the base of a clade without having robust support for a particular node within it. For example, we have robust support for the base of the mammal clade – all mammals are commonly descended – but there might be dispute about the branching order of civets, mongooses and cats, or whatever, which has no bearing.

    You are kind of chucking Ann Gauger’s analysis of Adam and Eve out with the bathwater too. The probablity of ‘accuracy’ is the cumulative probability of the accuracy of all descendant nodes, sez you. Do you have that data?

  42. phoodoo,

    Uh no Allan. I am using quotes from the paper he referenced!

    And demonstrating your profound ignorance in the process. There is absolutely no conflict between the statement that monophyly of paleognaths is well-supported with any statement regarding nodal uncertainties within it. It’s the same mistake as colewd’s.

    You are off your rocker Allan.

    That much, you have right.

    But since you have not read the paper, I guess you are in no position to say how the paper supports his premise.

    Hey, if I didn’t know better I’d say you were deliberately trying to get a rise out of me! I have read the paper. You have yet to demonstrate you have got more than 3 paragraphs in.

    According to you, quoting from the paper that HE posted is quote mining. Totally off your rocker.

    So it’s not quote mining by taking a segment out of its wider context if it’s in a paper one of the authors has linked?

    But he is on your team, so you like him, rah, rah, rah….!

    boing-fwip

  43. Allan Miller,

    We have no idea what part of the paper John wanted highlighted, because all he did was say the proof is in there somewhere.

    I have just shown you from Wikipedia that a number of biologists disagree with this conclusion. So that doesn’t sound like its long established at all. Now, If you think Wikipedia is wrong about science, well, at least we are making some progress.

  44. phoodoo,

    It says here: “Recent research has indicated that paleognaths are monophyletic”. It rather seems to hinge on how recent is recent, which is possibly the lamest point one could pick, among the various choices. But hey, anything to avoid admitting error.

  45. phoodoo,

    We have no idea what part of the paper John wanted highlighted, because all he did was say the proof is in there somewhere.

    I looked, and I found it in a moment, using the handy looking-glass icon that someone left lying around for some obscure purpose in Adobe. Look harder. And, for fucksake, John just told you above. You saw it, because you replied, quoting Wikipedia as your authority, irony upon irony. You don’t even believe Wikipedia, but … you see the links referring to one J. Harshman?

  46. Allan Miller:
    phoodoo,

    It says here: “Recent research has indicated that paleognaths are monophyletic”. It rather seems to hinge on how recent is recent, which is possibly the lamest point one could pick, among the various choices. But hey, anything to avoid admitting error.

    Why that’s just a pure bald-faced quote mine Allan.

    If I didn’t know better I might think you are trying to get a rise out of me there partner!

    Recent research is not even close to meaning something has long been established. If you are arguing that this means the same, well, that’s the lamest point ever.

    Furthermore, it still does nothing to nullify the fact that there are avian biologists who disagree with this finding.

    So I am not sure your point, other than to acknowledge my point.

  47. phoodoo: Furthermore, it still does nothing to nullify the fact that there are avian biologists who disagree with this finding.

    Ahh, the argument from “there are people who disagree”. By that standard, nothing is well supported.

    There are people who believe the Earth is flat. I guess all the certainty in the world on the part of people with satellite pictures makes no difference. Some idiot just has to say “nay” and ta-dah, we’re in a quagmire with no way to tell.

  48. Rumraket,

    So you also share the opinion that Wikipedia is very untrustworthy on matters of biological sciences.

    Cool, glad we found some common ground.

    Let’s remember that.

  49. Allan Miller,

    You wouldn’t conclude that all relationships are false. One can have robust support for the base of a clade without having robust support for a particular node within it. For example, we have robust support for the base of the mammal clade – all mammals are commonly descended – but there might be dispute about the branching order of civets, mongooses and cats, or whatever, which has no bearing.

    I don’t see how you can have a solid tree without the nodes being solid. Yes, you can have evidence of common genes but how do you know who descended from who. If you were to choose one node to work on from John’s 2008 paper to show 95% confidence of A and B descending from C what would be your methodology?

  50. colewd,

    For example, we have robust support for the base of the mammal clade – all mammals are commonly descended

    What robust support?

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