Saturday, December 15, 2012

Ann Gauger Describes the Intelligent Design Creationist Version of Population Genetics

In lieu of Saturday morning cartoons, I offer this video. David Klinghoffer likes it [The Awkward Secret that Plagues Population Genetics and Darwinian Evolutionary Theory]. Enjoy.



70 comments:

  1. Is that a green screened image of a lab behind her? Instant credibility! Not.

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    1. have a look at the youtube comments--someone found out where they got the stock image that is sued in the video.

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    2. Incredible! They didn't even shoot their video at the vaunted "Bio-Logic" lab in Redmond, Wa.

      They stole a photo from a website. Pathetic. Just as fake as everything else they do. IDiots for sure.

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    3. Some of the most juvenile remarks are made on this blog. So who cares if the pictured lab is one where she works or not. She actually does work in a lab.

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  2. We laypeople are looking forward to a slightly more detailed critique of Gauger's views, Larry. Otherwise, we won't know if we're looking at a cartoon or a serious documentary.

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    1. Population genetics is the study of genes (alleles) in populations. It's the theoretical base of modern evolutionary theory and it encompasses things like natural selection and random genetic drift. The field was begun in the 1930s and most of the important concepts date back to that golden age. More recently, it covers coalescent theory and the genetics of complex populations with varying sizes and subpopulations.

      It has nothing to do with comparing DNA sequences and constructing trees.

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    2. Another great line was her bit about needing to look at the details of the chimp genome to test for common descent. Geneticists sequenced both the chimp and human genome years ago, and the details strongly confirm common descent. For example, we can see that two chimp chromosomes fused into one human chromosome. The genes in that human chromosome are in the same order as the genes on the two ancestral chimp chromosomes.

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    3. Re Lou Jost

      The latest ploy by the IDiots is to claim that the two structures in the middle of human chromosome 2 are not telomeres. Grasping at straws.

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    4. I think they argue that those are too short to be telomeres. But the most likely chromosomes to fuse are those with extra-short telomeres (chromosomes with long telomeres usually do not fuse), so shorter-than-normal leftover telomeres in the middle of the fused chromosome is what we expect. Have they made some other argument as well?

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    5. The problem with that argument is, the fusion responsible for human chromosome 2 (called a "centric fusion") involved breaks in the telomeric regions of both chromosomes, and a subsequent fusion of the chromosomes themselves at that point. However, the telomeric pieces that broke off are lost. So, we would not expect to see the original telomeric sequence lengths reproduced at the fusion point--we would expect LESS. Thus we can add basic cytogenetics to the list of disciplines about which IDers know nothing, and on which they constantly pontificate.

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    6. Quibble: coalescent theory does have something to do with constructing trees; there are a few recent phylogenetic methods that take it into account. In theory, these methods, when presented with a set of several loci, will deal with the problem of lineage sorting and the so-called "anomaly zone". In theory.

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  3. Common descent is not in any way an assumption in population genetics.

    Common descend is not an assumption anywhere, it's a conclusion based on comparative anatomy and phylogenetic reconstruction.

    Imperfect inheritance of sequences of genes over generations PREDICTS that you'll get nested hierarchies (from which you can construct trees), they are not ASSUMED.

    Jesus fucking Christ this woman is just ultra-clueless.

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    1. Jesus fucking Christ...

      An outbreak of coprolalia?

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    2. No no, it was entirely by intent.
      I dare you to google-image it. :)

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  4. It is true that both phylogenetics and population genetics start with the letter "P" and end with "genetics". But if you are interviewed as an "authority" on the subject, you should be expected to know the difference...

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  5. Yeah she seems confused about population genetics vs. phylogenetics. And confuses phylogenetics with "tree-drawing".

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    1. Aha! That comparison actually makes a whole lot of sense! I like it!

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    2. Cargo cult science

      Precisely. The cult members gather in mock laboratories full of imitation equipment, where they mimic the way scientists speak and behave. They believe that, if they do so regularly, God will appreciate their efforts, deprive the wicked scientists of the Scientific Results they have appropriated so unfairly, and pour them upon those who deserve them.

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  7. Since the IDiot discusses the homoplasy of the octopus eye and the vertebrate eye, I guess it would be useful to give a recent reference on this.

    Kozmik et al., PNAS July 1, 2008 vol. 105 no. 26 8989-8993

    http://www.pnas.org/content/105/26/8989.long

    They conclude:

    In conclusion, the present study uncovers a surprising molecular parallelism in the eye design of vertebrates and cubozoan jellyfish. Although the current data do not distinguish unambiguously between the common-ancestry and independent-recruitment scenarios, we propose that they lean in the direction of the latter, favoring multiple independent reorganizations of common elements and independent recruitments of similar suites of genes during evolution of the diverse eyes.

    They point out:

    That vertebrates and Cnidaria share many more genes than anticipated, including pax, mitf, c-opsin, pde's, phosducin, guanylate cyclase, and oca2, supports the notion that both animal groups use similar sets of genes to generate significantly different body plans. It follows that changes in gene regulation, rather than “new” genes, may drive novelties such as eyes during evolution.

    Overall they show how molecular similarity can arise in this case of convergent evolution.

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    1. Don't you mean "how molecular similarity can arise in this case from symplesiomorphy"? The molecular similarity is homologous. It's the recruitment to performing similar signalling functions that's convergent. But I suspect that, if our source is right, there's an element of parallelism too: something about the original functions of those genes that makes them particularly likely to be recruited.

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    2. How nice of @chemicalscum to reply with a reference and more. I wish I was as diligent. All that I did was just smacked my forehead with mine own palm. But she is only lying so hard to get the Templeton. Ayala did it, why can't she?

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  8. Homoplasies are such a secret we teach about them in all introductory biology courses, including those for nonmajors.

    She's a dishonest hack.

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  9. But note that population genetics make the unwarranted assumption that those individual organisms that can interbreed and share essentially the same genome are actually related to each other. The notion of a "species" is a construct that scientists place on the organisms. Organisms don't come with a label telling you what species they are, or even what population they belong to --- it's the godless scientists who make this determination, and then engage in completely circular reasoning with their studies of "alleles within populations".

    (Christine Janis --- have problems with posting to this cite under my own ID)(And I think I've been reading too many things posted by creationists on the web, I'm finding only too easy to make up stuff like this.)

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  10. I must be totally confused. I wrote a book on reconstructing evolutionary trees -- and it's the standard textbook in that area. But it does not mention many basic population genetics concepts. I have another book (a free downloadable e-book) that is a textbook of theoretical population genetics. And it does not mention homoplasy at all.

    So I must misunderstand what "population genetics" is. And here I've been giving courses on it for the last 44 years. At the university where Ann Gauger got her Ph.D. degree, for that matter.

    Silly me.

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    1. http://24.media.tumblr.com/tumblr_lzifjhU2uv1qituqxo1_500.jpg

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    2. Joe,

      You're not far away from that famous research institute where she works. Maybe you could meet up and she could teach you a thing or two about tree making and about the true meaning of population genetics?

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    3. LOL, she must be proud of the University of Washington if she still gives it (and not the Biologic Institute) as her affiliation:

      http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=660

      Or at least she realises that UW dignifies her more than that other institution. Gosh, there are more talks by Ann Gauger on Youtube. It's really crrrrreepy stuff!

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    4. According to Wikipedia she also got her BS from MIT and did a postdoc at Harvard...

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    5. I don't know where her degrees are from, but I'm pretty sure she grows her own BS.

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  11. More to the point (aside from the definition of population genetics, she is asserting that homoplasy is ignored and similarity is used for evidence of common ancestry. In fact everyone working on reconstructing phylogenies is painfully aware that reversals and parallelisms that we see in evolution create homoplasy and that we have to take this into account in evaluating the statistical evidence for common ancestry.

    The evidence for common ancestry has to do with the reinforcement of features of the tree by looking at the trees obtained for many genes. That's how we can know that even though sharks and dolphins look similar in exterior form, dolphins are much more closely related to cows than to sharks. This issue is fudged in descriptions of homoplasy, such as this one from Gauger.

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    1. Don't forget bootstrapping as an index of support from a single gene and thus as evidence of common ancestry. I'm surprised you're unfamiliar with the technique. It amounts to the same thing, more or less: consilience of multiple lines of evidence, whether they're genes in genomes or sites in genes.

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    2. I'm pretty sure that Dr. Felsenstein is familiar with the bootstrap.

      http://www.hum.utah.edu/~mhaber/Documents/Course%20Readings/Felsenstein-Bootstrap-Evol1985.pdf

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    3. Yeah John Harshman had to be making a joke. Joe, I'm surprised you're not familiar with this "zone" where parsimony is misleading. It's called the Frankenstein Zone or something.

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    4. Sorry. I should remember to put in a :) for the benefit of the differently clued. But the comment was meant for Joe.

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    5. One gets forgetful at this age, but I do remember the bootstrap. I should have worded my comment to allow for conflict within as well as between genes.

      One also gets given credit for things other people did even earlier. For example some people have actually credited me with inventing likelihood (to my intense embarrassment). Some people have also argued that when the sites analyzed exclude the invariable ones, that the bootstrap will be miseading. But John Harshman disposed of that argument in a very nice paper years ago.

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  12. What really blows my mind is how the Discovery Institute chooses to introduce this video:

    Frankly, I have been struck dumb all day by the events in Connecticut. Parents in particular will understand.

    So it's a blessing to be able to present a brief video in which Biologic Institute's Ann Gauger, coauthor of the Discovery Institute Press book Science and Human Origins, clears the mind, changes the subject, and answers a good question....



    W.
    T.
    F.

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  13. It amazes and saddens me when I hear creationists use the fact that different data sets can produce different phylogenetic trees to call the whole idea of phylogenetic reconstruction into doubt. They apparently think that congruence between trees is an all or nothing issue. In fact, most studies show areas of the trees that disagree along with many areas of congruence. Consider how many phylogenetic trees are possible from a given date set. It’s much higher than most people realize. For example, for ten taxa there over 292,137,824 possible trees ! (Joe Felsenstein figured this out back in 1978). So, the levels of congruence we do see in most phylogenetic studies are really amazing even when there is some disagreement between trees. This screams out for the reliability of our phylogenetic methods and for common descent. Either that or the Intelligent Designer is being deliberately deceptive.

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    1. Although I published that number in 1978, my method was a simpler algorithm to do a calculation that had been done by generating function methods by a (major) German mathematician, Ernst Schröder, in 1870 and published in the Zeitschrift für Mathematik und Physik. Schröder did not carry out his calculation as far as 10 species, so I guess I am the first to calculate that number, but not the first to know how to.

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    2. Thanks for the clarification Joe. You are a national treasure.

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    3. I get the number of possible rooted binary trees for ten taxa to 17!! = 34,459,425. Thus I reckon you must be talking about something else, but I can't figure out what.

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    4. That's what I get too. And the number for 11 taxa is already 654,729,075.

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  14. Is that the kind of lab where they make edible gummy bugs? Sweet!

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  15. Since the trackback I threw from a Thumb post pointing to this one generated an error message, I'll insert it as a comment: If they both begin with “P” and end with “genetics,” they must be the same thing, right?.

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  16. Ann Gauger wasn't even in a lab when she made her statement. As I already mentioned at PT the background is definitively green screened. You will find the picture "lab at night" at shutterstock (http://www.shutterstock.com/pic-862039/stock-photo-biological-science-laboratory-at-night.html).
    Please be aware that you will have to pay for any use of the picture.

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    1. Thanks, it's made my day! The Biologic Institute hasn't even got a lab where its "scientists" could be video'd (never mind doing any work).

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    2. I wonder if the "Biologic Institute" paid for the use of this picture ?

      For folk who hide behind a veneer of faux scientific victimhood they seem to be pretty free and easy with the intellectual property of others.

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  17. That's an ABI3130 sequencer in the background, circa 1996, I think. Not too many of those are still active. Some, yes, but not that many.

    She's clearly been green-screened into a lab. Why doesn't that embarrass them to point this out? Hell, I made a video pointing out the sloppy green-screening of Stephen C Meyer into a LIBRARY (http://www.youtube.com/watch?v=t4l0T31ovP0) They couldn't find a real library that allowed him in?

    My only conclusion: In much the same way that a proton and antiproton collide and annihilate, ID creationism and real research or scholarship... well, you get the idea. For all our sakes, let's be grateful they favor safety in their videography.

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  18. Larry, instead of firing spitballs from your sandbox...er walk, why don't you invite your colleague Ann Gauger to respond directly?

    You know what they say about ASS-U-MEing.

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    1. Larry, instead of firing spitballs from your sandbox...er walk, why don't you invite your colleague Ann Gauger to respond directly?

      Or even better, why not just go onto their website and make the comments directly. After all, that would be in the spirit of collegial scientific discussion, right? Any real scientist would welcome comments and corrections. In fact, maybe I'll go ahead and do that right now.

      Hey, wait a minute. Where's the comment section? It has to be here somewhere....

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    2. Steve says,

      Larry, instead of firing spitballs from your sandbox...er walk, why don't you invite your colleague Ann Gauger to respond directly?

      Ann Gauger is not my colleague.

      Many IDiots read my blog. They frequently reply to my criticism by posting responses on the main creationist blogs. I'm looking forward to seeing Gauger's response to the charge that she doesn't understand population genetics.

      I'm guessing that her reply will consist mostly of an attack on my use of "Saturday morning cartoons" and my reference to IDiots as "creationists."

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    3. It's interesting that they so frequently make reference to this blog, but rarely if ever take advantage of the comments section to dialogue directly with Larry. They really are afraid of direct confrontation of their ideas.

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    4. Maybe Ann Gauger has too much class to stoop to the level of name calling and acting like elementary kids on Facebook. I was surprised to the total lack of civility and respect for anybody who has a varying viewpoint. How are laypeople like myself really supposed to know what to believe. I find her more credible and believable just by the way she conducted herself. If you cannot clearly and respectfully discuss and explain why she is wrong and give references, then don't be surprised that people will take Intelligent Design seriously.

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    5. Kristen Mayeaux:
      I find her more credible and believable just by the way she conducted herself.

      Babbling on about things she doesn't understand in front of a green-screened 'lab' that's actually a stock photo? Yeah, that just screams credibility.

      If you cannot clearly and respectfully discuss and explain why she is wrong and give references, then don't be surprised that people will take Intelligent Design seriously.

      References? You want references to why population genetics and phylogenetics are two almost wholly independent scientific fields? Any introductory text for either field will do. If someone claimed that classical history and the history of science were the same thing, would you demand piles of references showing that each discipline has a distinct focus?

      This isn't about her "varying viewpoint"; it's about her abysmal ignorance, despite which she still feels perfectly entitled to lecture to people who know more than she does.

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  19. No need to invite Ann over for cookies and chocolate. She knew you were too stingy to cough them up. But anyway, she was polite enough to reply.

    And as usual her clarity and calm demeanor slaps down the silliness coming from the evolution blogsphere.

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    1. How's that bluepill working out for ya, pure bliss right?

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    2. lutesuite, you can catch her reply on the shopping channel.

      Her clarity and calm demeanor is a big hit with the rubes there.

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    3. Steve wrote "Ann...was polite enough to reply."

      Where? Got a URL? Did she mention her laboratory background?

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    4. Talking of labs:
      http://www.idthefuture.com/2010/05/testing_evolution_in_the_lab_w.html

      Now we know it was virtual research green-screened into a virtual lab.

      ...a new article she and Dr. Ralph Seelke have in the peer-reviewed journal BIO-Complexity...

      Peer-reviewed by themselves, it seems, as both authors are members of the editorial board... but then bloody well everything that gets published in that travesty of a journal is contributed by the editorial team. There isn't much of it anyway.

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  20. If we replace "population genetics" by "phylogenetics", her argument becomes that models of evolution assume there's a tree to reconstruct. And that is indeed the case. All phylogenetic analysis programs will give you one or more trees from an input data set, but what they won't do is give you two or more entirely unconnected trees. But this is a limitation of the programs, not of the models. All you have to do to test the disconnected tree hypothesis is apply the same model to two trees vs. one tree and see which fits the data better. Now in practice nobody does this, because it's a stupid hypothesis. But Doug Theobald did it anyway.

    Theobald, D. 2010. A formal test of the theory of universal common ancestry. Nature 465: 219–222.

    Can you guess the result? It turns out that the data are much more likely under a hypothesis of common ancestry than under one of separate ancestry. Humans are not only related to chimps, but to Eubacteria and Archaea. Shocking that a biologist of Geiger's stature would not be acquainted with this paper. (Do I need the smiley this time?)

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    1. Geiger, Gauger, tomato, tomahto.

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    2. Oh I see. That's how science is done. The data are 'more likely' under a hypothesis of common ancestry. That settles that.

      All we need to do is offer the opinion that something is more likely and we can close the book on the question.

      I had no idea it was that easy!

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    3. I know you don't care and are merely a creationist troll, but I'll explain anyway. "More likely" is a technical term here. Under a particular model, any data set has a probability of being observed that can be quantified. That's what a model does: it tells us the probability of observing particular events if the model is true. In Theobald's case, the probability of observing the data he tested was much higher under a model that supposed a single tree than under any model that supposed disconnected trees. Conditional probabilities (in this case conditional on the model being used) are called likelihoods. If you read Theobald's paper, which of course you never will, you will be able to see the actual, numerical likelihoods and statistical tests of whether they are significantly different (they are) -- that is, whether the common descent model is "much more likely" than the separate creation model (it is).

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  21. It's like the DI isn't even trying anymore.

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  22. Dr. Jerry Bergman has made an argument that the evidence is not conclusive for the fusion event and here is one reason:
    1. The purported fusion site on human chromosome 2 is actually located in a different position on chromosome 2 than predicted by the fusion model. The hypothetical fusion site is also in an area with suppressed recombination (meaning that the fusion sequence should be very pristine) and should exhibit very little degeneracy, compared to standard telomere sequence. Telomere sequences in humans normally consist of thousands of repeats of the standard 6-base sequence “TTAGGG.” We found that the hypothetical fusion region is completely degenerate and vaguely represents anything close to intact and fused telomeres. An earlier 2002 research report by molecular evolutionists also made note of this extreme sequence degeneracy and the obvious discrepancies it presented for the evolutionary model.

    Here is the paper from Genome Research and a quote from it:

    "The head-to-head arrays of repeats at the fusion site in RP11-395L14 have degenerated significantly (14%) from the near perfect arrays of (TTAGGG found at telomeres."

    Fan, Y. et al. 2002. Genomic Structure and Evolution of the Ancestral Chromosome Fusion Site in 2q13-2q14.1 and Paralogous Regions on Other Human Chromosomes. Genome Research. 12 (11): 1651-1662.

    http://www.evolutionnews.org/2012/07/what_the_litera_1062521.html
    http://www.icr.org/article/new-research-undermines-key-argument/

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    1. Pathetic. Jerry Bergman is not a scientist. He is a pathological liar posing as a scientist.

      It's pathetic to quote mine the Yuxin Fan 2002 paper yet again, pathetic to tell real scientists that 11-year old results are "recent research."

      The Yuxin Fan paper presents evidence that SUPPORTS chromosome fusion. They were quoted out of context by ID creationist Casey Luskin and Jerry Bergman, both pathological liars, neither a scientist.

      For a thorough refutation, Google Carl Zimmer's smack down of Luskin, "And now the hounding duck can rest."

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