Eye Mock Stupidity

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I’m all in favor of mocking stupidity, and here’s something definitely worth mocking.

In arguing for evolution, author Alan R. Rogers appeals to the Nilsson and Pelger paper on how simple it is to evolve an eye. He writes:

If eyes evolve, they must do so often and easily. Could it really be so easy?

Dan-Eric Nilsson and Susanne Pelger have answered this question. They constructed an evolutionary story much like the one that I told above.

– The Evidence for Evolution. p. 42.

And what did he write about the story that he told above?

This story is of course a fabrication. p. 40

I’m serious! Can it get any more stupid than that?

Do evolutionists believe fabrications? When it comes to how to evolve and eye it would certainly seem so.

524 thoughts on “Eye Mock Stupidity”

  1. colewd: How would you calculate probability based on genotype? I know there are possibilities based on beak size and moth color where the survival probability goes up but how much? Is the variation primary due to recombination or cross over? If so how is a speciation event ever going to occur?

    John has already responded to many of these. I’d say:

    How do we calculate probability based on genotype? We may or may not have information to do that. but we can ask what happens if Nature does. Different genotypes lead to different phenotypes, and they can have different probabilities of surviving (and different fertilities too). Section II.2 iin my text asks “what if”. I hope colew doesn’t think that all genotypes have the same fitnesses!

    “… but how much?” Well, the whole point of the math is to ask, what is the result of different values of fitness?

    “Is the variation primarily due to recombination or cross over?” At a single site, we are thinking about different alleles, which are primarily ultimately due to one having arisen by mutation. Of course the extent of recombination does affect outcomes when multiple sites are varying and when they are linked. But that is a more complicated case, for which see Chapter XIII.

    “If so how is a speciation event ever going to occur?” colew has something in mind here which neither I nor John Harshman can fathom, and in any case, that discussion is irrelevant.

    So all I can see that is relevant in colew’s response is that he imagines that we can’t discuss the effects of natural selection unless we actually know all the fitnesses of the genotypes. That is of course silly — who would complain to the author of a physics textbook that she had called the mass of an object m but did not actually know what the value of the mass actually was?

  2. Joe Felsenstein: So all I can see that is relevant in colew’s response is that he imagines that we can’t discuss the effects of natural selection unless we actually know all the fitnesses of the genotypes.

    Back to natural selection as a cause, I see.

  3. colewd:
    John Harshman,
    Natural Selection, Not Mutation: Recombination in Drosophila Increases Diversity
    Robin Mejia
    Published: November 13, 2012https://doi.org/10.1371/journal.pbio.1001423

    If you have a point, you need to say what it is. If.

  4. I would say that one potential cause of correlation between a population’s genetic diversity and recombination rate is that selective sweeps would produce smaller regions of reduced diversity if recombination were more frequent. Still don’t know what that would have to do with the source of variation, which was supposedly Bill’s question.

  5. Mung: Back to natural selection as a cause, I see.

    No one has persuaded me that it matters whether or not you say it is a “cause”. Still, the issue has great meaning to Miung.

  6. John Harshman:
    I would say that one potential cause of correlation between a population’s genetic diversity and recombination rate is that selective sweeps would produce smaller regions of reduced diversity if recombination were more frequent. Still don’t know what that would have to do with the source of variation, which was supposedly Bill’s question.

    Yes, the Hill-Robertson effect and its like underlay the papers that colew cited. But I agree with you, they are not about the source of variation so much as about the fate of variation. Which is a different discussion.

  10. Mung: Who here, when their phone rings, thinks that their phone number is what caused their phone to ring?

    Me, for one. If my phone number were instead on someone else’s phone, my phone would not ring when that phone number was dialed.

    Cause, schmause.

  11. Joe Felsenstein,

    Yes, the Hill-Robertson effect and its like underlay the papers that colew cited. But I agree with you, they are not about the source of variation so much as about the fate of variation. Which is a different discussion.

    I think we forget that we can have multiple causes. Just like a phone number is only one of the causes. The circuitry that causes a ring tone is another.

    How would you argue that for finch beaks and dark moths that random mutation was the cause vs genetic recombination?

  12. colewd:
    Joe Felsenstein,

    I think we forget that we can have multiple causes.Just like a phone number is only one of the causes. The circuitry that causes a ring tone is another.

    How would you argue that for finch beaks and dark moths that random mutation was the cause vs genetic recombination?

    I think you’re confused about levels. The ultimate source of variation is mutation. Recombination puts mutations into different genetic contexts, which may produce new features at the phenotypic level, but not new features at the genetic level.

    I don’t know if anyone knows the genetic basis of finch beak differences, but we do know what causes industrial melanism, and it’s not recombination. It’s a single mutation at a single locus.

    Now if you’re just trying to say that some phenotypic differences within species result from recombination of previously existing alleles, that’s true. But those previously existing alleles arose by mutation, and recombination is not the main source of variation.

  13. John Harshman,

    I don’t know if anyone knows the genetic basis of finch beak differences, but we do know what causes industrial melanism, and it’s not recombination. It’s a single mutation at a single locus.

    If that was one of a few genes responsible for the color wouldn’t recombination be responsible for generating more copies of that gene in the population?

    Now if you’re just trying to say that some phenotypic differences within species result from recombination of previously existing alleles, that’s true. But those previously existing alleles arose by mutation, and recombination is not the main source of variation.

    We have hard evidence for genetic variation from in species reproduction.

    You are a long way from demonstrating that existing alleles arose by mutation.

  14. colewd:
    If that was one of a few genes responsible for the color wouldn’t recombination be responsible for generating more copies of that gene in the population?

    No. Recombination doesn’t make more copies of anything. It just moves copies from one chromatid to another.

    We have hard evidence for genetic variation from in species reproduction.

    Yes, and mutations happen within species. What are you actually trying to say there?

    You are a long way from demonstrating that existing alleles arose by mutation.

    What is your alternative? How do you imagine recombination generates new alleles. Here:

    These are two alleles:

    AAAGAAAA

    AAAAACAA

    Recombination might produce two new alleles

    AAAAAAAA

    AAAGACAA

    Now if that happened, we ought to see both the original alleles in the population in addition to the two new ones. But if we see just

    AAAAAAAA

    AAGAAAAA

    that didn’t happen by recombination. That was a mutation.

  15. John Harshman,

    Yes, and mutations happen within species. What are you actually trying to say there?

    That we know recombination is responsible for variation in sepecies. Mutation certainly has the possibility to represent some level of variation but it is more likely to break down sequences then improve them. Recombination transfers genes between chromatid and so it is not a destructive process like mutation.

    The other issue is how many long term mutations are really generated as some are eliminated by purifying selection and some are eliminated by DNA repair which is constantly finding and eliminating them.

  17. colewd: Recombination transfers genes between chromatid and so it is not a destructive process like mutation.

    What!? You’re not aware of all those recombination repair enzymes?

  18. John Harshman: I would be particularly interested in the claims that choanoflagellates and sponge collar cells are only convergently similar. That seems odd, since choanoflagellates are the sister group of metazoans.

    John should stick to birds.

    While this catalogue of shortcomings represents a substantial rebuttal of Kent’s (1880-2) hypothesis, nevertheless the view persists, and is still reported in textbooks, that sponges are derived from choanoflagellates.

    – The Choanoflagellates. p. 13

    There’s no reason to doubt convergent evolution. Just look at the eye. Evolution makes convergence highly probable.

    #EmbraceConvergence

  19. colewd:
    John Harshman,
    That we know recombination is responsible for variation in sepecies.Mutation certainly has the possibility to represent some level of variation but it is more likely to break down sequences then improve them.Recombination transfers genes between chromatid and so it is not a destructive process like mutation.

    I don’t think you have a clue what either mutation or recombination is, even after I showed you an example. Recombination is also just as likely to “break down” (by which I assume you mean reduce fitness), by changing the genetic background of a particular bit of DNA.

    The other issue is how many long term mutations are really generated as some are eliminated by purifying selection and some are eliminated by DNA repair which is constantly finding and eliminating them.

    We’ve been over this before. Most mutations are neutral, and the observed mutation rate already takes DNA repair into account. If it gets repaired, you never see it.

  21. John Harshman,

    I don’t think you have a clue what either mutation or recombination is, even after I showed you an example. Recombination is also just as likely to “break down” (by which I assume you mean reduce fitness), by changing the genetic background of a particular bit of DNA.

    Do you really think recombination is an exchange of single bits?

    We’ve been over this before. Most mutations are neutral, and the observed mutation rate already takes DNA repair into account. If it gets repaired, you never see it.

    I understand this but it is based on a large quantity of junk DNA which is a best a controversial claim. What is the observed mutation rate? How has it been validated?

    The junk DNA hypothesis is based on a large mutation rate which does not make sense to me based on the accuracy of the repair mechanism and its constant scanning of DNA during the cell, before transcription and in areas that are not being transcribed and between cell divisions.

  22. colewd:
    John Harshman,

    Do you really think recombination is an exchange of single bits?

    No, I don’t. I think you are misunderstanding my little example. Perhaps you can describe what you think recombination is. Everything you say seems to suggest that you can cut & paste but don’t understand the words you are pasting.

    I understand this but it is based on a large quantity of junk DNA which is a best a controversial claim.What is the observed mutation rate?How has it been validated?

    No, the observed mutation rate is not based on the assumption of junk DNA. It’s based on actual observation of mutation rates.

    The junk DNA hypothesis is based on a large mutation rate which does not make sense to me based on the accuracy of the repair mechanism and its constant scanning of DNA during the cell, before transcription and in areas that are not being transcribed and between cell divisions.

    The junk DNA hypothesis is not based on a mutation rate. And you just said that mutation rates are based on junk DNA. Are you saying that it’s all circular, or do you just not pay attention to what you say from one sentence to the next?

    Larry Moran had several articles on how mutation rates are estimated. Perhaps you could read a few. As it is you just seem to have a blanket denial of the data, purely because the data don’t fit what you are sure must be true.

  24. Mung: There’s no reason to doubt convergent evolution. Just look at the eye. Evolution makes convergence highly probable.

    Imagine if we had no examples of convergent evolution. Wouldn’t that be pointed out as great evidence for evolution? “Well, of course no two organisms evolve the same way, how could they. That just goes to show that evolution is true, because everything evolves independently.”

    And now that we find that, miraculously, things that look and function exactly the same, can have completely different origins, THAT TOO IS EVIDENCE FOR EVOLUTION!

    Convergent evolution is one of the biggest farces people are forced to swallow.

  25. phoodoo,

    Convergent evolution is one of the biggest farces people are forced to swallow.

    Unlike your religion, nobody is forced to swallow anything. If people have reasoned objections to convergent evolution they are free to make them.

    However, the interpretation of convergent evolution is not without controversy. Some view convergent evolution as ubiquitous across the tree of life, thus marking the predictability of evolution even over long time scales. Others view convergent evolution as a rare fluke of evolution, and believe that evolution is dominated by chance events. Additionally, some evolutionary biologists view convergent evolution as the result of deterministic natural selection and adaptation, while others see the mark of genetic and/or developmental constraints.

    http://www.oxfordbibliographies.com/view/document/obo-9780199941728/obo-9780199941728-0038.xml

    But before you get all excited, read the next sentence:

    Recent advances in evolutionary developmental biology and genomics have given us a wealth of new information about the mechanisms of convergent evolution.

    So you see phoodoo, there is always controversy if you look. As such you are always free to take part in the process and refine our understanding. Or you could just do what you are doing…..

  26. phoodoo,

    And now that we find that, miraculously, things that look and function exactly the same, can have completely different origins, THAT TOO IS EVIDENCE FOR EVOLUTION!

    Whereas of course you have an explanation that explains all the observed data better then anything currently available?

  27. phoodoo,

    Imagine if we had no examples of convergent evolution.

    So you admit such examples exist? Progress I suppose.

  28. OMagain: Whereas of course you have an explanation that explains all the observed data better then anything currently available?

    Yes of course, everything that we see is exactly what the designer wanted. If it was different, that was what the designer wanted.

  29. OMagain: If people have reasoned objections to convergent evolution they are free to make them.

    Here is a reasoned objection. If you believe in Darwinian evolution, random mutations over billions of years making exactly the same thing is the dumbest fucking idea on the planet.

  30. John Harshman,

    This is recombination per wiki: Do you disagree? This confirms that recombination occurs at the gene level.

    In eukaryotes, recombination during meiosis is facilitated by chromosomal crossover. The crossover process leads to offspring having different combinations of genes from those of their parents, and can occasionally produce new chimeric alleles. The shuffling of genes brought about by genetic recombination produces increased genetic variation. It also allows sexually reproducing organisms to avoid Muller’s ratchet, in which the genomes of an asexual population accumulate genetic deletions in an irreversible manner.

    Chromosomal crossover involves recombination between the paired chromosomes inherited from each of one’s parents, generally occurring during meiosis. During prophase I (pachytene stage) the four available chromatids are in tight formation with one another. While in this formation, homologous sites on two chromatids can closely pair with one another, and may exchange genetic information.[4]

    Lets table the mutation rate discussion for now. I don’t see Larry’s assumptions well supported and I think the current accuracy and frequency of the repair mechanisms puts a 100 mutations per generation claim into question.

  31. colewd:
    John Harshman,
    This is recombination per wiki:Do you disagree?This confirms that recombination occurs at the gene level.

    To quote from my favorite author: “Everything you say seems to suggest that you can cut & paste but don’t understand the words you are pasting.” In this particular case, the wikipedia page uses the word “gene” and you seem to think that proves some point you want to make. But recombination occurs both within and between genes. It occurs at some particular spot in the chromosome, between two particular adjacent bases. Because genes are a fairly small portion of the chromosome, recombination within genes is less common than recombination between genes. And none of this has anything to do with my point, though you seem to think it does.

    Lets table the mutation rate discussion for now.I don’t see Larry’s assumptions well supported and I think the current accuracy and frequency of the repair mechanisms puts a 100 mutations per generation claim into question.

    I don’t think you have any idea what Larry’s assumptions are, what the data are, or much of anything else. Reading with intent to understand rather than to reject by reflex might help.

  32. John Harshman,

    I don’t think you have any idea what Larry’s assumptions are, what the data are, or much of anything else. Reading with intent to understand rather than to reject by reflex might help.

    I understand this is your preconception. I accepted Larry’s explanation for over a year until I began to better understand DNA repair.

  33. phoodoo: Here is a reasoned objection. If you believe in Darwinian evolution, random mutations over billions of years making exactly the same thing is the dumbest fucking idea on the planet.

    LoL. But you don’t understand. If A is improbable. 2A is even more improbable. Unless evolution. Then 2A = 1/2A.

  34. colewd,
    I have sincere doubts that you ever accepted Larry’s explanation, and you do not at all understand DNA repair.

  35. Mung: LoL. But you don’t understand. If A is improbable. 2A is even more improbable. Unless evolution. Then 2A = 1/2A.

    Getting heads on a coin is more improbable if your first toss is a heads?

  36. Tossing “heads” 100 times in a row with a fair coin is highly improbable. After you’ve done it once do it again. Of course, with evolution, all that improbability doesn’t multiply. Heck, it doesn’t even become additive. Doing it once actually makes doing it twice even more probable! Absolutely hilarious. Really.

  37. Mung: Doing it once actually makes doing it twice even more probable! Absolutely hilarious. Really.

    Don’t you get it, that’s why eyes are so easy. If they only evolved once, of course that would be unlikely, but they have evolved like 18 times or so. So by now nature knows exactly how to do it.

    If you don’t believe it, just look at how many things have eyes. That’s proof right there that it is inevitable. See? See! Of course you see, everything sees!

  39. Mung,

    Doing it once actually makes doing it twice even more probable!

    Has anyone actually advanced this reverse gambler’s fallacy? You and phoodoo seem to have descended into shadow boxing strawmen. It’s fun to watch, for a while.

  40. Mung: Tossing “heads” 100 times in a row with a fair coin is highly improbable. After you’ve done it once do it again. Of course, with evolution, all that improbability doesn’t multiply. Heck, it doesn’t even become additive. Doing it once actually makes doing it twice even more probable! Absolutely hilarious. Really.

    In the frequentist interpretation of probability theory, probabilities are obtained by observing the frequency with which certain events occur.

    If something evolves over and over again, then yes obviously it is evident that the event is increasingly likely for every time it occurs. The assumption that the evolution of eyes must be very unlikely is contradicted by real-world evidence.

    If you toss heads 100 times in a row with a coin, twice, you should start to consider the option that the coin isn’t fair. In other words, that the assumption that the outcomes are equiprobable, is mistaken.

    https://plato.stanford.edu/entries/probability-interpret/#FreInt

    3.4 Frequency Interpretations
    Gamblers, actuaries and scientists have long understood that relative frequencies bear an intimate relationship to probabilities. Frequency interpretations posit the most intimate relationship of all: identity. Thus, we might identify the probability of ‘heads’ on a certain coin with the frequency of heads in a suitable sequence of tosses of the coin, divided by the total number of tosses. A simple version of frequentism, which we will call finite frequentism, attaches probabilities to events or attributes in a finite reference class in such a straightforward manner:

    the probability of an attribute A in a finite reference class B is the relative frequency of actual occurrences of A within B.

    Thus, finite frequentism bears certain structural similarities to the classical interpretation, insofar as it gives equal weight to each member of a set of events, simply counting how many of them are ‘favorable’ as a proportion of the total. The crucial difference, however, is that where the classical interpretation counted all the possible outcomes of a given experiment, finite frequentism counts actual outcomes. It is thus congenial to those with empiricist scruples. It was developed by Venn (1876), who in his discussion of the proportion of births of males and females, concludes: “probability is nothing but that proportion” (p. 84, his emphasis). Finite frequentism remains the dominant view of probability in statistics, and in the sciences more generally.

    You might have some ideas about how unlikely some things are, given some set of assumptions you have about how the world works. But if evidence keeps contradicting what your assumptions lead you to conclude about how unlikely those things are, perhaps it is time to reevaluate your assumptions?

  41. Allan Miller:

    Mung,

    Doing it once actually makes doing it twice even more probable!

    Has anyone actually advanced this reverse gambler’s fallacy? You and phoodoo seem to have descended into shadow boxing strawmen. It’s fun to watch, for a while.

    Um. maybe you and Rumraket could shadow box.

    Rumraket
    In the frequentist interpretation of probability theory, probabilities are obtained by observing the frequency with which certain events occur.

    If something evolves over and over again, then yes obviously it is evident that the event is increasingly likely for every time it occurs.

  42. Hey phoodoo, I have never won the lotto. I am due brother!

    Send me your money so I can buy tickets.

  43. Even Stephen Jay Gould:

    We gain some sense of probabilities for repetition of a basic theme (but not of specific details) from the phenomenon known as “convergence.” … Since adaptive themes are limited and animals so diverse, convergence of different evolutionary lineages to the same general solution (but not to detailed repetition) are common. Highly adaptive forms that are easy to evolve arise again and again.

    – The Flamingo’s Smile p. 411-412

    LoL!

    Evolutionary theory at it’s best.

  44. Mung: Even Stephen Jay Gould:

    We gain some sense of probabilities for repetition of a basic theme (but not of specific details) from the phenomenon known as “convergence.” … Since adaptive themes are limited and animals so diverse, convergence of different evolutionary lineages to the same general solution (but not to detailed repetition) are common. Highly adaptive forms that are easy to evolve arise again and again.

    – The Flamingo’s Smile p. 411-412

    LoL!

    Evolutionary theory at it’s best.

    What are evolutionists to do when faced with things that aren’t sensible, based on their theory? Embrace them!

    We find out some things arise suddenly, and not the gradual small step modifications like Darwin proposed? Who cares, call it punctuated equilibrium, who will know what that means!

    The same things keep forming again and again? Great, convergence! There are only so many ways to be the best!

    Life is teleological? Ok, how about Natural Genetic Engineering, how does that sound?

  46. Rumraket: No you idiot, there is evidence for the common descent of the gradual morphological change of eyes.

    Evidence of eyes evolving from other eyes? Where?

  47. Rumraket: If something evolves over and over again, then yes obviously it is evident that the event is increasingly likely for every time it occurs.

    If the events are independent the probability is multiplicative. More unlikely.

    Please explain and/or clarify what you mean.

  48. Poor Mung is as baffled by probability as he is by math generally.

    Pretty amusing in a thread he titled “Eye Mock Stupidity.”

  49. Mung:
    Hey phoodoo, I have never won the lotto. I am due brother!

    Send me your money so I can buy tickets.

    I suggest the more tickets you buy the more probable the improbable event is

  50. newton: I suggest the more tickets you buy the more probable the improbable event is

    Is that how evolution works?

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