191 thoughts on “But Is It Science”

  2. The key assumption that distinguishes our model from the standard ones is that we assume that the first pair started out with heterogeneous chromosomes — four distinct sets, two sets for each individual.

    It’s a question whether this is cargo-cult science?

    Glen Davidson

  3. Mung,

    Well you see Mung, this was posted in evolutionnews. And evolution news has an agenda to show evolution has problems. So if they write any articles which bring up problems with evolution, then it can’t be correct, because they have an agenda.

    However, when a site that is dedicated to promoting the belief in Darwinian evolution writes a science article about Darwinian evolution, they are doing science.

    So in answer to your question, if science is done that shows the problems in modern evolutionary beliefs, then of course its cargo science. Because they have an agenda. Its simple really.

  4. Hi Phoodoo,

    Everyone has an agenda. We’re all ideological animals. The real question is: is the model they propose mathematically rigorous, internally consistent and scientifically testable?

    One thing I would like to know is whether the ENV model makes any predictions regarding the age of the human race. I might email Dr. Gauger and find out.

  5. Its not science.

    Science creates models for understanding the world. To work the models must explain observations of the natural world. They gain power and validity when they predict phenomena that haven’t yet been observed. Science advances when the models dont quite fit observation. Sometimes the models are tweaked and then they work. Sometimes the models need major revision, and sometimes a completely new model is needed to fit all the observations.
    Gauger starts with a model of 2 original people. . What are the observations that lead her and others to prefer this model over the scientific consensus? There aren’t any. All of the observations confirm the consensus that the smallest the human population has ever gotten is a few thousand individuals. There’s absolutely no reason to question it except one: it contradicts Genesis from the Old Testament. Thats the only reason. Its also the reason people prefer models that involve the speed of light or radioactive decay being much faster in the past.

    This is trying to fit a square peg in a round hole to put it mildly, and its the reason it isnt science.

  6. Why yes, since you ask. It is cargo cult science. All the fancy math is window dressing that lets them ignore how bizarre their initial assumptions are. Recent, separate creation of two first parents, however heterozygous they might be, is incompatible with the morphological and genetic data relating us to other species, with the fossil record, with the coalescence of the uniparentally inherited bits of the genome, and, yes, with population genetics. A narrow focus to the exclusion of uncomfortable facts is indeed a feature of cargo cult science.

    By the way, since Eve was made from Adam’s tissue, how can there be complete four-way heterozygosity in the original pair?

    I would be fascinated to know what Joe Felsenstein thinks of their model.

  7. The first paper is mostly a review of population genetics. The second sets forth a very clever simulation technique called “backwards simulation”, using coalescents. Actually they did not invent this — it’s been around for 30 years or so.

    The whole point is to try to come up with a way that the level of genetic variability seen in present human populations is consistent with a scenario derived from the Bible. As John Harshman points out above, the two-person scenario did not arise because some group of scientists found it uniquely plausible, but to accommodate religion.

    Are they clear on how long ago these two people were? If they were 6000 years ago there is simply no way to get as much diversity as seen today. So they add:. “a second source of variation … created diversity.”. In other words, “poof!”.

  8. John Harshman: By the way, since Eve was made from Adam’s tissue, how can there be complete four-way heterozygosity in the original pair?

    Because the designer added variability? Or maybe they’re willing to compromise on the rib part.
    I’m wondering how they explain all the MHC complex alleles

  9. Joe Felsenstein: Are they clear on how long ago these two people were? If they were 6000 years ago there is simply no way to get as much diversity as seen today

    They say there are 2 possiblities. The 2 progenitors were created in Africa or the Middle East. The ME possibility would mean a much earlier creation. They dont say exactly ( although I mostly skimmed it) but I think they mean ‘much earlier’ than 50,000 years. Again, I’d have to go back and read more precisely but I think they suggest that both Africa and ME are possibilities and will require “more work” to distinguish. I wonder what observations led them to consider the Middle East as a starting point for humanity??

  10. Come to think of it, my cynical comment above about their motivations was unfair. They’re pretty upfront about admitting their religious motivations. Their reference list includes work by a YEC, J Sanford and they have several refs from the Answers in Genesis journal.

  13. John Harshman,

    Why yes, since you ask. It is cargo cult science. All the fancy math is window dressing that lets them ignore how bizarre their initial assumptions are.

    I think they are testing the assumption of 2 original humans. If they are simply testing the assumption is that really “cargo cult science”. The paper says that the model is new and they are working to refine it.

  14. Joe Felsenstein,

    Are they clear on how long ago these two people were? If they were 6000 years ago there is simply no way to get as much diversity as seen today. So they add:. “a second source of variation … created diversity.”. In other words, “poof!”.

    Can you show me in the paper where they are doing this?

  15. REW: I’m wondering how they explain all the MHC complex alleles

    Especially the ones shared with chimps.

  16. colewd:
    John Harshman,

    I think they are testing the assumption of 2 original humans.If they are simply testing the assumption is that really “cargo cult science”.The paper says that the model is new and they are working to refine it.

    You seem remarkably flexible in your positions. You would strongly criticize any mainstream science that did what they did. In fact, you have strongly criticized mainstream science that did what they claimed to. It seems that your critical faculties depend on the conclusion more than the process.

  17. John Harshman,

    You would strongly criticize any mainstream science that did what they did

    No, I would not. I would criticize any assumption that is called a fact without direct observation or testing. Since they are attempting to test, I acknowledge that they are using the scientific method I was taught. If the result of that test was inconclusive and they claimed otherwise, then I would criticize.

  19. I agree, if it’s testable, it’s science.

    A model designed to explain an existing data set, is tested by the modesty of it’s assumptions and proposed mechanisms (supposing it really does actually predict the observed data set). A model that explains the data by invoking observed mechanisms, is preferred over a model invoking unobserved or very unlikely mechanisms.

    Technically it is always possible to come up with a model that explains the data, you can just invent whatever ad-hoc unlikely mechanisms you desire to explain the observations. But the more you do this, the less likely your model becomes.

    So extant human populations have far more genetic diversity than could have evolved from 2 humans in a few tens or hundreds or thousands of years? Ok, so we just invoke extremely unlikely mutational events along the way. Massive chromosomal rearrangements, dusins of duplications, a twentyfold point mutation rate etc. etc. Oh look, now our model works, it “fits” the data.

    Could extant human genetic diversit have been created 6000 years ago by two humans? Technically yes, if you suppose there were some absurdly unlikely genetic mutations happening along the way. Like, every few generations, whole chromosomes got rearranged, lots of new alleles created by duplication, tonnes of mutations happening in all of them and so on and so forth. Can such a model explain the data? Yes. But it’s an absurd model, the invoked mechanisms would be rejected by any and all IDcreationists, as bordering on miraculous, if proposed as an explanation in an evolutionary model.

  20. Rumraket: I agree, if it’s testable, it’s science.

    But shouldn’t science be more than just whether its testable or not? Shouldnt it include the actual test and its interpretation?
    If archaeologists thought that a particular passage in Genesis described an historical event they could actually test that by looking for evidence in historical artifacts and sites and writings. This would be science. But if they decided a priori that some event in Genesis must be true because the Bible is the inerrant word of God and ignored all negative evidence and relied on endless ad hoc interpretations to support their preferred conclusion this wouldnt be science.
    But ‘science’ doesn’t have a precise definition. This is just my preferred definition

  21. John Harshman: REW: I’m wondering how they explain all the MHC complex alleles

    Especially the ones shared with chimps

    Yes. And some loci have over 1600 alleles. Thats a lot of mutation in ~10,000 years.

  22. REW: But shouldn’t science be more than just whether its testable or not? Shouldnt it include the actual test and its interpretation?

    In the longer term, sure. So let’s modify it to say it’s a scientific claim, rather than just “science”.

  23. colewd:
    John Harshman,

    No, I would not.I would criticize any assumption that is called a fact without direct observation or testing. Since they are attempting to test, I acknowledge that they are using the scientific method I was taught.If the result of that test was inconclusive and they claimed otherwise, then I would criticize.

    You have criticized a number of papers that did testing. You wouldn’t believe that they tested what they tested, possibly because you didn’t think they involved “direct observation”. Now what are Gauger et al. attempting to test? I haven’t been able to find any tests of hypotheses there. How would they even test their model against others?

  24. Rumraket: In the longer term, sure. So let’s modify it to say it’s a scientific claim, rather than just “science”.

    But then just about everything is a scientific claim.
    I’ve found that drinking diet Root Beer allows me to read peoples minds. This is a scientific claim

  25. REW: But then just about everything is a scientific claim. I’ve found that drinking diet Root Beer allows me to read peoples minds. This is a scientific claim

    Yes, all empirical claims are scientific claims. If we can test them by observation or experiment, it’s a scientific claim. That’s really all there is to it.

    Yes, that means even such things as astrology is potentially scientific, since it makes testable claims that people’s personality traits should strongly correlate with their date of birth. It so happens to be FALSE scientific claims, in that they have in fact been tested and found to be false. But just because it was tested and found false, no less scientific a claim does that make it.

  26. A farmer asks an engineer and a physicist to help improve the efficiency of his dairy.

    The engineer says, “I can re-design your system to boost profits by 20% and reduce waste by 10%. It’ll cost you 3,000 and take two months". The physicist says, "well, I can re-design your system to boost profits by 200%, reduce waste by 90%, and it'll cost you250 and take two weeks.”

    The farmer says, “how is that possible?” “Ah,” the physicist says, “first, assume a spherical cow . . . ”

    This is “first, assume a spherical cow” science. How did the genetic diversity of seven billion human beings come into existence from an original pair of only two? By having already been there to begin with.

    Now that’s what I call science with a capital S!

  27. Hi everyone,

    I emailed Ann Gauger, and she told me that the model does not make any prediction regarding the antiquity of the human race. So it’s quite consistent with the idea of an original couple who lived hundreds of thousands of years ago.

  28. Splitting this work into two papers was a stroke of genius. In doing so they are now solely responsible for 50% of the papers published this year in Bio-Complexity.

    I would mention that two of the authors are on the editorial board, and the author of one of the other papers is also on the editorial board, but that would be beneath me.

  29. colewd:

    Joe Felsenstein,

    Are they clear on how long ago these two people were? If they were 6000 years ago there is simply no way to get as much diversity as seen today. So they add:. “a second source of variation … created diversity.”. In other words, “poof!”.

    Can you show me in the paper where they are doing this?

    You’re right and I’m wrong. They didn’t invoke “poof”. I read superficially and reacted impulsively. Apologies.

    They are instead referring by “created diversity” to the diversity among the initial 4 copies (at an autosomal locus) or 2 copies (allowing for the cloning of Eve from Adam).

    If the ancestral couple were 6000 years ago, one would need to show that ancestral diversity, acted on by recombination and a bit of further mutation, would explain present levels of diversity. If the ancestral couple were 1,000,000 years ago, mutation since then would play a larger role, and the ancestral diversity might not be critical.

    The objections raised by Francisco Ayala and others were in regard to the HLA (MHC) genes, which maintained large numbers of haplotypes which it would be very difficult to explain if there were a bottleneck of the population 6000 years (250-300 generations) ago. Even a bottleneck 1,000,000 years (40,000 generations) ago would make it hard to imagine that level of diversity.

  31. Joe Felsenstein,

    So they add:. “a second source of variation … created diversity.”. In other words, “poof!”.

    A convenient ‘poof’ in multiple lineages at once for each shared variant, in order to make it appear they commonly descended. Or maybe generations were telescoped and people reached reproductive maturity about 10 days after birth.

  32. phoodoo,

    So in answer to your question, if science is done that shows the problems in modern evolutionary beliefs, then of course its cargo science. Because they have an agenda. Its simple really.

    An agenda. The fact that 2 starting individuals accords with nothing about reality not a problem, then?

    It’s rejected because it’s hogwash, not because it appears in ENV. Still, when Pence is running science in the US, we won’t have to worry about concordance with reality.

  33. colewd,

    Can you show me in the paper where they are doing this?

    If you paste a portion of text you wish to find into the ‘search’ box of your pdf reader and click ‘next’, purpose-built software navigates you to the point in the document where that text appears.

  34. Allan Miller,

    Actually, reading the subsequent comments, I can see we have misinterpreted. Oddly phrased to place original diversity as the second source of variation, though, no?

  35. colewd,

    How did you get on with the ‘SINE’ data in whale phylogeny? This might have some relevance in this discussion too …

  36. John Harshman,

    You have criticized a number of papers that did testing. You wouldn’t believe that they tested what they tested, possibly because you didn’t think they involved “direct observation”. Now what are Gauger et al. attempting to test? I haven’t been able to find any tests of hypotheses there. How would they even test their model against others?

    As far as I can tell Ann is testing multiple hypothesis. She has not given a conclusion as far as I can tell. My criticism was simply part of the conclusion did not match the data. I never challenged whether the papers were scientific.

  37. Joe Felsenstein,

    You’re right and I’m wrong. They didn’t invoke “poof”. I read superficially and reacted impulsively. Apologies.

    They are instead referring by “created diversity” to the diversity among the initial 4 copies (at an autosomal locus) or 2 copies (allowing for the cloning of Eve from Adam).

    If the ancestral couple were 6000 years ago, one would need to show that ancestral diversity, acted on by recombination and a bit of further mutation, would explain present levels of diversity. If the ancestral couple were 1,000,000 years ago, mutation since then would play a larger role, and the ancestral diversity might not be critical.

    The objections raised by Francisco Ayala and others were in regard to the HLA (MHC) genes, which maintained large numbers of haplotypes which it would be very difficult to explain if there were a bottleneck of the population 6000 years (250-300 generations) ago. Even a bottleneck 1,000,000 years (40,000 generations) ago would make it hard to imagine that level of diversity.

    Thanks. I will look up the HLA argument. These ID guys have been criticized for not using scientific arguments. Its good to see them attempting to model and test their assumptions.

  38. Allan Miller,

    How did you get on with the ‘SINE’ data in whale phylogeny? This might have some relevance in this discussion too

    I have not had a chance. Any possibility you could create an op on this subject?

  39. colewd:
    John Harshman,

    As far as I can tell Ann is testing multiple hypothesis.She has not given a conclusion as far as I can tell.My criticism was simply part of theconclusion did not match the data.I never challenged whether the papers were scientific.

    So far, Gauger et al. have tested nothing. They have a model which they have not used. I don’t see how they would test their hypothesis against any other. But if you can see, tell me.

    Your criticism was ill-informed, as you never actually managed to look at the data.

    colewd: Any possibility you could create an op on this subject?

    Why, when it’s already been done in the various papers that have been cited for you? Why, when you won’t even read those papers or try to understand them?

  40. vjtorley: I emailed Ann Gauger, and she told me that the model does not make any prediction regarding the antiquity of the human race. So it’s quite consistent with the idea of an original couple who lived hundreds of thousands of years ago.

    If you put Adam/Eve at about 2 million years ago (when Homo habilis was around, by the way) then going back from the present, essentially all loci would coalesce before then. Thus the variability of present-day humans is predicted provided we have about 10-20,000 people most of the way back, with more recently. All the variability would come from mutation since Adam/Eve. No “created variability” necessary.

    This would still not explain the HLA data or the similarities to chimpanzees, but it would be basically indistinguishable from most recent theories.

  41. colewd,

    Any possibility you could create an op on this subject?

    My own time is limited, though it would actually be a useful OP subject. You could profitably try this undergrad-level exercise. It mentions both casein and SINEs, and is an accessible hands-on way in to the concepts.

    You might think it irrelevant here, since that is about broader phylogeny, but it does have relevance to human variation. SINEs are part of the variation that must be accounted for, because the jumping that is fixed in the case of the cetartiodactyla is still polymorphic in many instances within a species (such as ours). The amount of polymorphism, particularly when one considers multiple loci and nesting, must be capable of being generated by your process of descent, absent a mechanism for generating the same traits independently. In the case of SINEs, there appears to be no such mechanism that operates down to individual dinucleotide level, so they are a very useful marker – hence their use in paternity tests for example. The big problem with 2 starting individuals is getting enough generations, given present rates of transposition. If one supposed rates elevated in the past (ad hoc), one would wonder why that was not cripplingly mutagenic.

  42. John Harshman,

    Your criticism was ill-informed, as you never actually managed to look at the data.

    My criticism was certainly ill informed because your paper only had very small subset of all the DNA data. We all have limited time and I did not go through the raw data sets. Your weakness John is you are long on personal “put downs” and short on solid arguments that support your conclusions. Since you wrote the paper my expectation is that you would argue your position backed up with data.

  43. Allan Miller,

    My own time is limited, though it would actually be a useful OP subject. You could profitably try this undergrad-level exercise. It mentions both casein and SINEs, and is an accessible hands-on way in to the concepts.

    Thanks, I will look into this. The SINE argument is interesting for more transitions than just whale evolution.

  44. colewd: Your weakness John is you are long on personal “put downs” and short on solid arguments that support your conclusions. Since you wrote the paper my expectation is that you would argue your position backed up with data.

    The solid arguments are in the paper. The data aren’t in the paper — there’s too much data for that — but the trees shown result from well-explained and rigorous analyses of the data; in other words, the conclusions are backed up with data. If you really wanted to see the raw data it would be easily downloaded from the site mentioned in the paper or from the one I’ve linked for you before.

    These are not personal put downs; they’re attempts to get you to realize your biases. You aren’t reading papers given to you for comprehension. You’re searching them for reasons to doubt their conclusions, and you seize upon those reasons even if they result from your misunderstandings. Haven’t I shown you exactly how you have misunderstood a number of things that you have used as objections?

  46. dazz: Wouldn’t a population of two be doomed to die out because of mutational meltdown?

    They started out with a very low entropy.

  47. Mung: They started out with a very low entropy.

    Is that supposed to be one of those assumptions immune to scrutiny and evidence?

    BTW, just Googled genetic entropy and see what’s there in the Wikipedia article

    “An important corollary to genetic entropy is that “beneficial mutations are so rare as to be outside of consideration.”[4]:23 Therefore, natural selection is considered too slow to allow evolution.”

    reference? John C. Sanford. LMFAO

  49. John Harshman,

    These are not personal put downs; they’re attempts to get you to realize your biases. You aren’t reading papers given to you for comprehension. You’re searching them for reasons to doubt their conclusions, and you seize upon those reasons even if they result from your misunderstandings. Haven’t I shown you exactly how you have misunderstood a number of things that you have used as objections?

    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 do not a priori discount special creation. That would makes common descent a conclusion without an alternative.

    I agreed with you that except for the ostrich, none of your arguments would stop me from supporting a common descent hypothesis among paleognaths. I understand that that you think that I should include the ostrich but you have not yet made an argument that convinces me. This is not bias. It is looking at a intron sequence that does not overlap with other flightless birds. Please show me the argument in your paper that explains how this exception still supports a common descent hypothesis.

  50. colewd: 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’ve told you this several times: common descent isn’t assumed; it’s concluded. If you can think of another explanation, we could test that. In fact, Theobald explicitly did just that. You have no basis for supposing that the science is immature; your opinion should be much more humble than it is.

    I do not a priori discount special creation. That would makes common descent a conclusion without an alternative.

    It’s a conclusion without a viable alternative. There’s a difference. Separate creation can’t explain the data.

    I agreed with you that except for the ostrich, none of your arguments would stop me from supporting a common descent hypothesis among paleognaths. I understand that that you think that I should include the ostrich but you have not yet made an argument that convinces me. This is not bias. It is looking at a intron sequence that does not overlap with other flightless birds. Please show me the argument in your paper that explains how this exception still supports a common descent hypothesis.

    Once again you indulge in word salad, but I will try to address what I imagine you may be trying to say. If you look at the trees you will note that the ostrich appears in a consistent position on the tree, and all the data support that position. Granted that isn’t a focus of the paper, because the monophyly of paleognaths had been well established long previously. If you need some evidence of that try this paper:

    Hackett S.J., Kimball R.T., Reddy S., Bowie R.C.K., Braun E.L., Braun M.J., Chojnowski J.L., Cox W.A., Han K.-L., Harshman J., Huddleston C.J., Marks B.D., Miglia K.J., Moore W.A., Sheldon F.H., Steadman D.W., Witt C.C., Yuri T. A phylogenomic study of birds reveals their evolutionary history. Science 2008; 320:1763-1768.

    As for the word salad, “It is looking at a intron sequence that does not overlap with other flightless birds.” makes absolutely no sense. You’re still paying attention only to one figure that you misinterpret, and which I have explained to you at length, and ignoring all the rest of the paper. You prove my point.

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