191 thoughts on “But Is It Science”

  1. phoodoo: Rumraket,

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

    Yes, or at the very least you have to check the references. For example I have found many creationist edits in the articles. I prefer linking directly to the primary literature or college level textbooks.

    For the more mundane and basic stuff, like the basics of DNA replication, the function of the Lac-Operon, or how PCR works, it’s normally fine. When it comes to politically contentious stuff (such as evolution) or technical matters on the forefront of scientific knowledge, I absolutely agree, I’d find another source.

  2. colewd: I don’t see how you can have a solid tree without the nodes being solid.

    When it comes to universal common descent, the kingdoms clearly cluster together within domains, the phyla cluster together within kingdoms, classes cluster within phyla, orders cluster within classes, families cluster within orders, genera cluster within families, and species cluster within genera.

    Even if the arrangement of families (say) within the order rodentia is uncertain, it is still a fact that those families unambigously cluster together within rodentia. There isn’t a phylogeny constructed from any objective molecular or morphological data that puts a member of rodents within birds, or reptiles within cephalopods.

    Do you understand?

  3. colewd: 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?

    You first have to realize that trees don’t show who descended from who. That is, none of the species shown on the tree are ancestors to the others. What the trees show are closeness of relationship: A and B are more closely related to each other than to C. A node represent ancestors, and we can reconstruct their characteristics, but they are not species we can point to.

    Now of course you can’t have a solid tree without the nodes being solid. But certainly we don’t need every node in a large tree to be certain in order to have confidence in the rest. Each node is commonly tested independently of the rest. I could explain the methods, or you could read the methods section. Here are the three most important references:

    Felsenstein J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.

    Goldman N, Anderson JP, Rodrigo AG (2000) Likelihood-based tests of topologies in
    phylogenetics. Syst Biol 49:652–670.

    Shimodaira H, Hasegawa M (1999) Multiple comparisons of log-likelihoods with
    applications to phylogenetic inference. Mol Biol Evol 16:1114–1116.

    I think your “evidence of common genes” is another attempt to avoid the implications of a strong nested hierarchy. If you can think of another reason why there should be such a pattern of “common genes” than phylogeny, please state it now. If you can’t, you will have to accept that phylogeny is the only plausible explanation, which is as close as science can get to “true”.

  4. John Harshman,

    first have to realize that trees don’t show who descended from who. That is, none of the species shown on the tree are ancestors to the others. What the trees show are closeness of relationship: A and B are more closely related to each other than to C. A node represent ancestors, and we can reconstruct their characteristics, but they are not species we can point to.

    This now makes sense. The tree is showing the relationships of the species to each other. Given this, how do they fit in a nest hierarchy. How would you try to show this other than the observation of common genes or DNA?

    If you can’t, you will have to accept that phylogeny is the only plausible explanation, which is as close as science can get to “true”.

    I think in this case, I don’t know, is a better than making a hypothesis where you cannot validate a single node.

  5. Rumraket,

    When it comes to universal common descent, the kingdoms clearly cluster together within domains, the phyla cluster together within kingdoms, classes cluster within phyla, orders cluster within classes, families cluster within orders, genera cluster within families, and species cluster within genera.

    What does cluster together mean? What is the objective standard to do this.

  6. colewd: I think in this case, I don’t know, is a better than making a hypothesis where you cannot validate a single node.

    Well, unless we infer normal causes from their expected effects. Then we can validate away.

    Not something that IDists like.

    Glen Davidson

  7. colewd:
    John Harshman,
    This now makes sense.The tree is showing the relationships of the species to each other.Given this, how do they fit in a nest hierarchy.How would you try to show this other than the observation of common genes or DNA?

    You mean, how would one show this other than by presenting evidence that it’s true? Or are you asking for other sorts of evidence because you don’t believe that the evidence at hand is valid? One could of course appeal to other sorts of data, morphology for example, but I don’t see why you would accept a phylogenetic analysis based on morphological characters any more than one based on DNA sequences. One could look at other sorts of molecular data, e.g. LINE insertions, but again, why would you accept that? One could appeal to the fossil record, but birds are not all that well represented, for reasons that should be fairly obvious. Or is it a time machine you demand here? I just can’t tell.

    I think in this case, I don’t know, is a better than making a hypothesis where you cannot validate a single node.

    What do you mean by “validate”? I’ve asked you this sort of question many times and you’ve never answered it. In what way does an appeal to a great many independent analyses of independently gathered data sets not count as validation? Is this in fact nothing more than a version of the creationist question “Were you there?”

  8. colewd:
    Rumraket,

    What does cluster together mean?What is the objective standard to do this.

    You are asking here for an education in phylogenetics, for which any comment here would be much too short. But if you read the various papers you have been directed to, and I mean actually read and attempt to understand them, you should get some idea.

  9. John Harshman: But if you read the various papers

    colewd is not interested in understanding. That’s become quite clear. He just want’s you to say “I don’t know” to everything then presumably once you’ve been broken down by realizing you don’t know anything at all the spirit of Jesus will enter into you to make you whole again.

    Or something, anyway.

  11. phoodoo,

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

    Along with ‘ad-hominem’, quote mine is a concept that Creationists really struggle to use correctly. Does the quote taken out of context mean anything different from the quote in its full context? No, it doesn’t. Hence, not a quote mine. A quote is not a quote mine.

    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.

    So you are doubling down on your lameness. You are arguing about the length of time monophyly has been accepted. And trying, lamely, to turn digs of mine against me. How lame can you get?

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

    Are you quite sure this remains the case.? I’m betting John knows pretty much everyone in this field, perhaps you could check with him, were it not for the fact that you rely solely on the authority of the not-John-Harshmans of this world.

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

    And your point – the one I am acknowledging – is?

  12. colewd,

    I think in this case, I don’t know, is a better than making a hypothesis where you cannot validate a single node.

    Essentially, you are saying that paternity and forensic tests should be thrown out of court. They use DNA evidence to validate node relationships. The node is the zygote in the case of the latter. You think nodes cannot be validated using that method. Give that argument a whirl next time you’re up before the beak.

    “Have you appointed no counsel Mr Cole?”
    “I am defending myself, Your Honor”
    “And what is your defence on the DNA evidence?”
    “I admit of no evidence that cannot be gained by direct observation and experiment”.

    Or you think something applies with validity within a species that does not apply outside it. Why? Where do we apply the razor? I frequently use the example of the Common and Spotted Sandpipers. What does their DNA commonality indicate – common ancestry, or your mysterious and STILL unstated ‘something else’. How far out do we go before it changes from one to the other?

    I already started drawing up the list of possible alternative causes for extensive DNA commonality for you to fill in. I’ll try again.

    1) Common Descent
    2) … ?

  14. phoodoo,

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

    The floor is open to anyone to find a way to make progress in understanding the world. As I’ve noted before, even you. Yet you appear to choose otherwise every time.

    In any case, as far as I know, you already dealt with Wikipedia’s untrustworthiness by creating a trustworthy alternative: http://www.conservapedia.com/Main_Page

    Do you think any of the biological science in Conservapedia is trustworthy?
    If you think belief in Evolution Boils Down to a Gut Feeling then the site is for you! If not, what other sources of information about biological sciences are worth listening to, according to phoodoo?

  15. Allan Miller: [Phoodoo:]Furthermore, it still does nothing to nullify the fact that there are avian biologists who disagree with this finding.

    Are you quite sure this remains the case.?

    It does not. The last publication I can think of that proposed non-monophyly of paleognaths was published 20 years ago [sorry, 28 years ago; I was thinking of Galloanserae there], and that was an outlier. Once more, check the references in Hackett et al. 2008, or anything else on paleognaths in the last 20 years.

  16. Bill Cole’s hyper-skepticism only applies to (macro) evolution for some weird reason (*scratches head*). I wonder why, after asking him so many times, he still can’t explain why he believes the mechanism of gravitational accretion can account for the formation of say, the rings of Saturn, and other “macro-gravitational” events. Why rule out special creation for celestial bodies? Does Bill have anything in terms of “direct observation and experiment” to support the claim that the Solar System formed by means of accretion from a nebula?

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

    That scientists are no more infallible than anyone else.

  19. Allan Miller: Essentially, you are saying that paternity and forensic tests should be thrown out of court.

    I love how because we can take DNA from a father and child or mother and child and compare it, this is proof of universal common ancestry, and if you don’t believe it, you must deny paternity testing.

    What a crock. Allan. Glen.

  20. Mung: I love how because we can take DNA from a father and child or mother and child and compare it, this is proof of universal common ancestry, and if you don’t believe it, you must deny paternity testing.

    But otherwise, you must pinpoint the place where such comparisons suddenly stop meaning what they do in paternity tests. If we compare, for example, DNA from the father with DNA from a chimpanzee, a chickadee, and a cichlid, what would degrees of similarity MEAN? If they mean something dispositive in paternity cases, are they meaningful between man and chimp but not between man and chickadee? Or is that comparison meaningful, but not the comparison with cichlid?

    Seems to me ancestry is implied by degree of DNA similarity or it isn’t. I don’t understand how you can say it’s implied in THIS case, but not in THAT case.

    At exactly what point does comparison become a crock?

  22. John Harshman,

    Yea, and how many years ago was it that people still thought ratites were monophyletic? 5? And now you don’t agree with that, right?

    And in Scientific American as recently as 2014 the author still disagrees with the idea of ratite polyphyly .

    So basically NOTHING is settled when it comes to avian relationships, except that we know birds are all birds-which is what creationists have been telling you for a long time.

    But more importantly, doesn’t it occur to you that the fact that flightless birds could have “evolved” multiple times to look nearly exactly alike give you pause to wonder about the whole idea of Darwinian evolution? Does the brushing under the carpet the problem of convergent evolution to the theory of evolution even make you think a little perhaps??

    Nearly identical functioning eyes could arise MULTIPLE TIMES? Huh? Its that ubiquitous? Why don’t we see new eyes evolving on elbows then? Just how ubiquitous is it? Just how bizarre is it that UNPLANNED, RANDOM mutations can create the exact same sculpture over and over?

    A blind watchmaker can make a whole line of Patek Philippe watches huh? If that doesn’t give you pause to wonder, I guess some people aren’t as curious as others.

  23. Phylogenetics assumes universal common descent. It does not “prove” it nor is it evidence for it. You need a mechanism that is capable of producing the changes required and the mechanism would say what pattern would be left behind.

    As for paternity tests the DNA sequences used to do that- show a man is the father of a child- would show that chimps are not related.

  24. Allan Miller:
    colewd,

    Essentially, you are saying that paternity and forensic tests should be thrown out of court. They use DNA evidence to validate node relationships. The node is the zygote in the case of the latter. You think nodes cannot be validated using that method. Give that argument a whirl next time you’re up before the beak.

    “Have you appointed no counsel Mr Cole?”
    “I am defending myself, Your Honor”
    “And what is your defence on the DNA evidence?”
    “I admit of no evidence that cannot be gained by direct observation and experiment”.

    Or you think something applies with validity within a species that does not apply outside it. Why? Where do we apply the razor? I frequently use the example of the Common and Spotted Sandpipers. What does their DNA commonality indicate – common ancestry, or your mysterious and STILL unstated ‘something else’. How far out do we go before it changes from one to the other?

    I already started drawing up the list of possible alternative causes for extensive DNA commonality for you to fill in. I’ll try again.

    1) Common Descent
    2) … ?

    2- Common Design- you still don’t have a mechanism for your 1) Common Descent

  25. Adapa,

    LoL! There aren’t any Nobel prize winning evos- that is no one has won a Nobel prize for any revelations into unguided evolution. OTOH ATP synthase is elucidated in peer-review and peer-review shows it is an irreducibly complex system. And no one can test the claim that natural selection and drift produced it.

    Genetic variations winnowed by selection pressure or passed via neutral drift and and carried forward as heritable traits

    Nice try but that has never been shown to do what you say. You lose, as usual

    It’s been empirically observed to work in the field, in the lab, and in simulations

    It has never been shown to produce the changes required. It only “works” on a very small scale.

    And if what you say is true then it is strange that evos had to lie and bluff their way through the Dover trial

  26. Frankie:
    Phylogenetics assumes universal common descent. It does not “prove” it nor is it evidence for it. You need a mechanism that is capable of producing the changes required and the mechanism would say what pattern would be left behind.

    As for paternity tests the DNA sequences used to do that- show a man is the father of a child- would show that chimps are not related.

    Yes, that’s right. Furthermore, when we try to understand relationships between many animals the picture is so murky, that we can draw almost no conclusions, without first knowing some recorded history with which to work off of. For instance, if we found fossils of a shar-pei and of a wolf, would we know we are looking at the same animal? If we didn’t know the history of dog breeding, wouldn’t we call these totally different animals? A chihuahua and a wolf, the same ?

    Even when we check their DNA, the results we get is basically that ALL dogs have the same amount of common DNA with wolves. Why should that be, they were all bred at the same time? And yet even to this day, virtually all dogs can still breed with wolves. So no new species? How long does this speciation thing take?

    As a researcher put it: “One of the most interesting questions still to understand … is why did the wolf keep locked in its genome everything that was necessary to make a Pekingese to a Great Dane,” said Elaine A. Ostrander of the Fred Hutchinson Cancer Research Center in Seattle.

    Why indeed.

  27. phoodoo

    Even when we check their DNA, the results we get is basically that ALL dogs have the same amount of common DNA with wolves.Why should that be, they were all bred at the same time? And yet even to this day, virtually all dogs can still breed with wolves. So no new species?How long does this speciation thing take?

    Speciation isn’t defined by an inability to produce viable offspring. Lions and Tigers can mate and produce Ligers – do you think lions and tigers are the same species?

  28. And if what you say is true then it is strange that evos had to lie and bluff their way through the Dover trial

    I see the truth hurts. Good

  30. Adapa,

    Well in those 15 years I have never been refuted. Attacked and insulted but never refuted. and I am more than OK with that.

  31. The Nobel Prize is in Physiology and Medicine. Evolutionary biology isn’t physiology and it isn’t medicine. Nobody has ever won it for work on “unguided evolution” for the same reason nobody has won the physics prize for such work, and the same reason that Albert Einstein never won the Boston Marathon.

    Why are creationists so certain about science about which they are completely ignorant?

  32. John Harshman:
    The Nobel Prize is in Physiology and Medicine. Evolutionary biology isn’t physiology and it isn’t medicine. Nobody has ever won it for work on “unguided evolution” for the same reason nobody has won the physics prize for such work, and the same reason that Albert Einstein never won the Boston Marathon.

    Why are creationists so certain about science about which they are completely ignorant?

    Umm at least TRY to follow along. It was one of yours that brought up the Nobel Prize stupidity. That means it was an evo who is completely ignorant in this case.

    Nice own goal

  33. John Harshman,

    Physiology is biology and medicine has to do with biology. That means that someone could very well use unguided evolution to elucidate something about physiology or come up with a new medicine.

    Who is the ignorant one now, John…

  34. Frankie:
    Adapa,

    Well in those 15 years I have never been refuted. Attacked and insulted but never refuted. and I am more than OK with that.

    LOL! “Completely deluded” has always been first on your list of YEC attributes.

  35. John Harshman,

    Well, I agree with you that physiology and medicine has absolutely nothing whatsoever to do with evolution. I wish all evolutionists would acknowledge this.

  36. Adapa,

    I think the concept of species has no real meaning whatsoever. Lions and Tigers are cats. Just like wolves and chihuahuas are dogs.

    Get it?

  37. Mung,

    I love how because we can take DNA from a father and child or mother and child and compare it, this is proof of universal common ancestry, and if you don’t believe it, you must deny paternity testing.

    What a crock. Allan. Glen.

    Well, it is exactly the same analysis. If you were presented with blind DNA sequences, without knowing that one came from within a species and one from outside it, they would differ only in degree – the percentage alignment possible, or the numbers of transposon inserts that differ, that sort of thing. I am certainly not leaping from paternity tests to universal common descent. Let’s start with the Common and Spotted Sandpipers. What say you? Related or not?

  38. phoodoo,

    2. Common genes for common purposes….

    Well, that doesn’t really work, but let’s say it does, at what point does 2) take over from 1) in a taxonomic series, starting with intra-species sibling relationships and working out? Is there a sharp transition or a fuzzy one? How come we can’t see it?

  39. Frankie: Well in those 15 years I have never been refuted.

    To be refuted first you have to say something that can be refuted. Ramblings don’t count.

  40. Frankie: We have established design for living organisms and many of their systems and subsystems.

    Who is ‘we’? Can you provide references to this design determination? What date was design established for living organisms? Who did that? Who determined design for biological systems? And subsystems? When did they do that?

    If you have established design for many systems and subsystems, what work remains to establish design for the rest? Who is doing that work? How? Why are the remaining systems and subsystems different from the ones that design has already been established for? Why was it not possible to determine design for those?

    If your claim had any basis in reality you’d be able to answer all of these questions.

  43. Mung: I love how because we can take DNA from a father and child or mother and child and compare it, this is proof of universal common ancestry, and if you don’t believe it, you must deny paternity testing.

    The inference is the same. It’s a distance-based inference in both cases. Which is why Allan keeps asking people like colewd where the cutoff lies, and why there?

    Mung, you accept common descent right? Why? For what other reason than the patterns of distance-based relationships could you possibly infer common descent?

  44. phoodoo: Frankie:
    “Phylogenetics assumes universal common descent. It does not “prove” it nor is it evidence for it. You need a mechanism that is capable of producing the changes required and the mechanism would say what pattern would be left behind.

    As for paternity tests the DNA sequences used to do that- show a man is the father of a child- would show that chimps are not related.”
    Yes, that’s right.

    No, that’s not right. Paternity tests do not give conclusions such as “you are not related”. They effectively give you distance-based relationships* and then in comparison to an expectation (if you are the persons cousin, brother, mother or child, or great great great great grandfather for example) tell you how like it is you are one of those, given how well the observation (some particular piece of your DNA known to be diagnostic in accumulating change in a few short generations) matches the expectation. And in fact, the particular method by which this is elucidated differs between the type of paternity tests.

    Christ, here you are agreeing with Frankie and I’m instantly reminded why I’ve put you on ignore 3 times before. I can’t help it, I keep thinking there’s hope and take you off my ignore list, only to immediately rediscover how naive of me. You are truly an amazing individual phoodoo.

    * If you don’t know what this means, ask.

  45. Suppose I took 3 genome sequences from 3 individuals. Being a sneaky bastard, I’ve discarded all differences, and am left with 3 billion or so base pairs that align exactly in each genome. Being double-sneaky, I have ensured that contiguous sequences in all 3 datasets break when there is a difference in any. So basically, I have ended up with the same incomplete genome 3 times, by scrubbing them of difference. One would be sure that I have in my residual data loads of ‘common design for common purpose’ genes. I’ve thrown away all the differences.

    Now, as a further piece of information, the 3 samples were taken from 2 species. Furthermore, 2 of the samples were taken from father and son. No, I’m not telling you which. I must have, in my 3 pieces of data, all the common-descent data AND all the ‘common-design-for-common-purpose’ data. One is descended from one of the others; one is a different species from 2 of the others. Which is which?

  47. Allan Miller: Well, it is exactly the same analysis.

    I’m no expert, but I don’t believe it is “exactly the same analysis” Allan. In fact, I believe the analysis is actually quite different.

  48. Allan Miller: Let’s start with the Common and Spotted Sandpipers. What say you? Related or not?

    I have no problem with all birds sharing a common ancestor and it really puzzles me why even the most ardent YEC would have a problem with it either. It seems to me they accept common descent, except when they don’t.

  49. Rumraket: Mung, you accept common descent right? Why? For what other reason than the patterns of distance-based relationships could you possibly infer common descent?

    Yes, I accept common descent as the current best explanation, but I can tell you it isn’t based on examining and comparing DNA sequences of every species. Which of us has actually done that?

  50. Mung,

    I’m no expert, but I don’t believe it is “exactly the same analysis” Allan. In fact, I believe the analysis is actually quite different.

    OK, scrub ‘exactly’ and replace with ‘pretty much’.

    If one is taking any interest in comparing 2 sequences, one has to do some kind of 2-sequence analysis, no? One could do sequence alignment, or use endonucleases and electrophoresis, or PCR for specific targets, RNA probes, melting-point hybridisation, chip arrays etc. All different ways of analysing the DNA for commonality – and difference, of course. All can be used on any 2 DNA samples, whether forensic or phylogenetic. Some techniques are too coarse or fine for some resolutions, is all.

    But the differences are embedded in a sea of sameness. That’s how they stick out.

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