most of the mutations

But not all of them. It’s interesting that even the most hardened creationists who have exposure to some science still cannot quite bring themselves to rule out the possibility of a beneficial mutation. Here’s Sal:

Much (not all) the heterozygosity and alleles were created and thus differences were strategically positioned to not cause functional compromise and most of the mutations thereafter are rare variants and slightly damaging.

So if most are slightly damaging then a few are beneficial. And if a few are beneficial then even fewer will be highly beneficial.

It’s not just Sal, but many IDCreationists seem to allow the possibility that a mutation may occur that is beneficial. Indirectly, of course, usually similarly phrased to the above. I don’t even think most of them know they are doing it.

So, Sal et al. What is it that is stopping the tiny number of beneficial mutations that you unwittingly admit happens spreading in a population? As presumably what you give with one hand you take away with the other. There must be some other mechanism preventing that, otherwise you are basically agreeing with the evilutionists. That is the topic of this thread.

Go team!

486 thoughts on “most of the mutations

  1. Joe Felsenstein: You seem incredibly reluctant to acknowledge that selection can be a consistent force increasing the frequencies of alleles that lead to higher fitness.

    Haven’t we had this conversation before? Fitter, ever fitter, maximize that fitness!

    I acknowledge that artificial selection can be a consistent force increasing the frequencies of alleles. 🙂

  2. Mung: I acknowledge that artificial selection can be a consistent force increasing the frequencies of alleles.

    But you don’t acknowledge that for natural selection. You are too busy portraying it as so uncertain of outcome as to be ineffective. Just like the creationist debaters do when they insist that evolutionary theory is one that involves only “chance”.

  3. Joe Felsenstein: But in that model the selection is a deterministic force.

    Are there no models at all of selection in which selection is not a deterministic force? Is selection never ever modeled as being stochastic?

  4. Mung: Are there no models at all of selection in which selection is not a deterministic force? Is selection never ever modeled as being stochastic?

    There is a nice body of theory on that. But the issue is whether, when it would be advantageous to go in one direction, natural selection will favor doing that. And you would go to almost any lengths to avoid acknowledging that.

  5. Joe Felsenstein: And you would go to almost any lengths to avoid acknowledging that.

    Well, I disagree with you about that. I have clearly agreed that natural selection is biased. To use your own analogy, it’s like a casino. There is a bias in favor of the casino due to their failure to pay out at the actual odds when the player wins.

    And yet people do in fact win at the casino. Would you call that a deterministic process?

    But the issue is whether, when it would be advantageous to go in one direction, natural selection will favor doing that.

    Natural selection doesn’t know that going in one particular direction will be advantageous, so it cannot favor going in any particular direction. You need to purge such teleological thinking because it bleeds over into your speech.

    Joe Felsenstein: You seem incredibly reluctant to acknowledge that selection can be a consistent force increasing the frequencies of alleles that lead to higher fitness.

    The alleles increase in frequency because they have a higher fitness. In what sense do they lead to higher fitness?

  6. Darwin recognized a crucial role of chance in evolution, but that role was limited to one part of the evolutionary process only: the emergence of changes (mutations, in the modern parlance). The rest of evolution was envisaged as a deterministic domain of necessity, with selection fixing advantageous mutations and the rest of mutations being eliminated without any long-term consequence. However, when population dynamics entered the picture, the situation changed dramatically.

    – The Logic of Chance, p. 10

    Now, given that the “random mutation” part of neo-Darwinian evolution has not changed, what part has changed dramatically? Rather obviously, it is the “deterministic” or “necessity” part.

  7. Mung,

    Well, big deal, all the change and new parts that get made are totally random, but after the eye gets made, natural selection helps keep it!

    Isn’t natural selection amazing!

  8. Let me deal with the two issues separately. I will comment about the casino example in another comment.

    Mung:
    Natural selection doesn’t know that going in one particular direction will be advantageous, so it cannot favor going in any particular direction. You need to purge such teleological thinking because it bleeds over into your speech.

    The alleles increase in frequency because they have a higher fitness. In what sense do they lead to higher fitness?

    Suppose that we have a situation in which the mix of prey species has shifted to have mostly larger prey. There is genetic variation for size around in the predator population. Now at those loci, alleles that make the size bigger will have a higher fitness, and those that make it smaller will have a lower fitness. That is the sense of “lead to” that I am using.

    So now the size of the predator will shift, and in a particular direction. Measuring genetic variances and measuring the covariances between relatives in the population, and how survival and reproduction depends on size, we can predict how quickly the size will change.

    This is closely similar to what animal breeders do when they impose artificial selection and want to know how fast a response to expect.

    So since you say you “acknowledge that artificial selection can be a consistent force increasing the frequencies of alleles”, may I assume that you acknowledge that in this case we can expect that the alleles that lead to larger size will increase, and thus the size will increase?

    Or will you go to almost any lengths to avoid admitting that in this case natural selection (the differences in fitness among phenotypes, and thus among genotypes) will be a consistent force in increasing the frequencies of the large-size alleles?

  9. Mung: Well, I disagree with you about that. I have clearly agreed that natural selection is biased. To use your own analogy, it’s like a casino. There is a bias in favor of the casino due to their failure to pay out at the actual odds when the player wins.

    And yet people do in fact win at the casino. Would you call that a deterministic process?

    We’re going in circles here. The issue is not whether the overall process of change in the population is stochastic. The issue is whether the selection part is stochastic.

    The outcomes in gambling can be called stochastic, no problem there. (I was saying the same thing about individual survival and reproduction). But the bias is not stochastic, it is consistently in favor of the house, just as the natural selection (this differences in fitness among organisms) may be consistently in one direction.

    Casino management depends on the bias being consistently in their favor. Those odds are the deterministic part of the process, and the casino management would be very upset if they were stochastic.

    So I repeat, we are talking about whether the selection part of the process is stochastic, and in these simple cases it isn’t, just as the bias isn’t changing direction when one gambles at a casino.

  10. phoodoo: Oh Corneel this is a really bad argument on your part. You are referring to mutations in development, not NEW genes. All the genes for arms and legs and eyes already exist in the fruit fly.

    I wasn’t aware that my argument was required to include new genes. My aim with that comment was rather more modest; I merely wanted to show that the unlucky mutations in development, that you mentioned mockingly, were real. I also hoped to convey that the effects of mutations do not occur willy nilly across the body, but rather as modifications of coordinated developmental programs that are already in place.

    I do like to hear more about the genes for arms and legs in fruitflies. I wasn’t aware there were any.

  11. Mung: I think you’re cherry-picking. I think there are cases of the pupil developing before the eye ball. I mean, it makes sense to me that the hole came before what surrounds the hole.

    That sounds like impeccable logic. I bow to your superior reasoning skills.

  12. Corneel: I also hoped to convey that the effects of mutations do not occur willy nilly across the body, but rather as modifications of coordinated developmental programs that are already in place.

    The effects of mutations do not occur willy nilly across the body, but rather as willy nilly modifications of coordinated developmental programs that are already in place throughout the body?

    And not just the developmental programs are modified by willy nilly changes.

  13. What a creotard parade. Incredibly bright guys like Joe are kind enough to try to educate them and all they can do is waste the opportunity

  14. Joe Felsenstein: We’re going in circles here.

    A deterministic circle?

    ok, let me try to take another approach. I’m not arguing about what natural selection can or cannot do. I am trying to accurately describe the process. I am not arguing that each allele has the same probability of spreading throughout the population. For whatever reason some lineages may leave more offspring than others and the alleles they carry will perforce appear in higher frequency.

    In The Oxford Handbook of Probability and Philosophy Roberta L. Millstone writes that “evolution is probabilistic in the production of new variations (e.g., mutation; see Merlin 2010), in the microevolutionary perpetuation of those variations through natural selection and random drift, and even at the level of macroevolution… and also discusses “the probabilistic nature of fitness.”
    Do you agree that fitness is probabilistic, and if so why would I be mistaken to say that fitness is stochastic?

    If fitness is probabilistic then natural selection is probabilistic. If fitness is stochastic then natural selection is stochastic. Three is no logical conflict to speak of a process that is both biased and stochastic.

  15. dazz: What a creotard parade. Incredibly bright guys like Joe are kind enough to try to educate them and all they can do is waste the opportunity

    Shouldn’t you be off writing a program?

    Rumraket says selection is stochastic. Why aren’t you explaining to him why he is wrong and why your ignorance trumps his knowledge?

  16. For dazz:

    Rumraket: And that is despite the fact that selection events are also “random” or “stochastic”, they are still systematically biased towards fixation of fitness-increasing mutations.

  17. Mung: . I’m not arguing about what natural selection can or cannot do. I am trying to accurately describe the process. I am not arguing that each allele has the same probability of spreading throughout the population. For whatever reason some lineages may leave more offspring than others and the alleles they carry will perforce appear in higher frequency.

    If there is a direction of change in the phenotype that leads to greater adaptation, and thus greater fitness, natural selection will be biased in that direction. That is important, and it is important that people understand that. Creationist debaters endlessly tell their audiences that evolutionary biologists have a theory that explains adaptation by “chance” changes. They expect their audiences to contemptuously dismiss such a theory as obviously impossible.

    So how have you characterized the process? Look at what you’ve just said: “For whatever reason some lineages may leave more offspring than others and the alleles they carry will perforce appear in higher frequency.” It isn’t some “whatever reason” — it’s because the phenotypes of those lineages do better functionally. Wordings like that, and your implacable insistence that we describe natural selection as a stochastic force, seem to me to be a setup for saying that natural selection will cause the population to wander randomly among phenotypes and not prefer to go in the direction of greater adaptation.

    I very much doubt that you would call bullshit on those misleading statements by creationist debaters.

  18. Joe Felsenstein,

    If there is a direction of change in the phenotype that leads to greater adaptation, and thus greater fitness, natural selection will be biased in that direction. That is important, and it is important that people understand that. Creationist debaters endlessly tell their audiences that evolutionary biologists have a theory that explains adaptation by “chance” changes. They expect their audiences to contemptuously dismiss such a theory as obviously impossible.

    We have experimental evidence that an adaption occurred in bacteria via Lenski. Do we have any evidence that an adaption occurred in a multicellular organism that can be traced to genetic change as in the Lenski experiment?

  19. colewd: Do we have any evidence that an adaption occurred in a multicellular organism that can be traced to genetic change as in the Lenski experiment?

    Tons. Biston betularia, anyone? Sickle-cell anemia in West Africa?

  20. Joe Felsenstein,

    Ok. This is your argument that adaption can occur and is forced by the environment. Finch beaks are another example although the cause may have simply been from genetic variation due to reproduction and recombination of genes.

    Simple adaptions are real science.

    Where the argument breaks down is where you have to take a significant random walk through the genome to get your adaption.

  21. Joe Felsenstein: Tons.Biston betularia, anyone?Sickle-cell anemia in West Africa?

    This is the best Joe can do considering that 10 billion species on earth are evolving and transitioning into other species…
    I guess people like him never learn anything from the law of recurrent variation formulated and proven by mutagenesis experiments by Lonnig on over half a million plants…

    The foundation of the law of recurrent variation is that mutagenesis experiemtns produce similar or the same phenotypes…
    I’m not even going to mention duons and overlapping genes that restrict the possibilities of beneficial mutations…

    For those who care:

    http://www.weloennig.de/Loennig-Long-Version-of-Law-of-Recurrent-Variation.pdf

  22. Corneel: do like to hear more about the genes for arms and legs in fruitflies. I wasn’t aware there were any.

    So you think there aren’t any? You also think there aren’t genes for eyes?

    So how the heck did we get them?

    I am not sure what your fruit fly analogy is intended to reveal? That during development, all kinds of things can go wrong that can screw up the organism?

  23. colewd: Where the argument breaks down is where you have to take a significant random walk through the genome to get your adaption.

    I swear these retards falsify evolution, ugh!

  24. phoodoo: Corneel: do like to hear more about the genes for arms and legs in fruitflies. I wasn’t aware there were any.

    phoodoo: So how the heck did we get them?

    I didn’t know that you’re a fruitfly. First time I read about one with arms and legs.

  25. Groan.

    wdcole piped up in the middle of my exchanges with Mung, and asked the following simple, easily answered question:

    colewd: Do we have any evidence that an adapt[at]ion occurred in a multicellular organism that can be traced to genetic change as in the Lenski experiment?

    It was obvious that wdcole thought that it was somehow impossible in principle for there to be an adaptation in a multicellular organism that was the result of genetic changes.

    So I tossed off an answer. Even a single example would refute the idea that this was impossible. But I provided two:

    Joe Felsenstein: Tons. Biston betularia, anyone? Sickle-cell anemia in West Africa?

    But nnnoooo … wdcole does not recognize being totally refuted by one counterexample, or even two. wdcole won’t admit being refuted until much more evidence is provided:

    [oops, sorry, previous version of this comment quoted a response by J-Mac, not by wdcole.]

    wdcole: Where the argument breaks down is where you have to take a significant random walk through the genome to get your adapt[at]ion.

    No, I answered, refuted the argument by providing an example of a genetically-based adaptation in multicellular organisms.

    wdcole’s further issue is a different question. I’m not sure what wdcole’s new question is, but I totally refuted his previous assertion.

    So people, whenever you are tempted to answer a question from wdcole, keep in mind that whatever your answer, wdcole will declare it inadequate. If you, like me, are dumb enough to try to answer his question, that is a neverending fall down into the bottomless pit of “you haven’t answered me enough yet”.

    Lesson learned.

    So my question for wdcole is: Is that a European swallow or an African swallow?

  26. Joe Felsenstein,

    It was obvious that wdcole thought that it was somehow impossible in principle for there to be an adaptation in a multicellular organism that was the result of genetic changes.

    I thought you were trying to validate a simple adaption and was trying to help. If you are trying to now say a simple adaption validates all evolution then I disagree but if you are simply trying to say, as I thought, that the creation argument implying that natural selection is useless is nonsense then I do agree with your argument.

  27. I was looking for information on explanations for the evolution of the magnificent plumage of peacocks and I came across this piece by Carrie Arnold with the heading, “Mystery Solved: Why Peacocks Got Their Eyespots”. She said:

    When a peacock struts his stuff, our attention immediately turns to his elaborate plumage with its colorful eyespots. Why and how these dazzling “eyes” evolved has been a mystery—until now.

    It was a review of an article from The Royal Society. Had the mystery of the evolution of these plumage patterns really been solved? I had my doubts. And my doubts were confirmed by the article itself. Nowhere did the authors claim to have solved the mystery. It was another of the all too frequent misleading and exagerated claims written by a reviewer for public consumption. Here are some quotes from the actual article:

    The close relationship between taxa with and without ocelli suggests multiple gains or losses. Independent gains, possibly reflecting a pre-existing bias for eye-like structures among females and/or the existence of a simple mutational pathway for the origin of ocelli, appears to be the most likely explanation…

    Darwin’s hypothesis predicts that modern, phylogenetic analyses should strongly support a close relationship among galliforms having ocelli. However, the inferred relationships among these taxa remain controversial…

    The difficulties in resolving phylogenetic relationships among the ocellated galliforms combined with the potential loss of ocelli within genera have made it unclear whether ocelli are homologous (with subsequent loss in some taxa) or whether ocelli arose independently in each ocellated genus…

    These differences in distribution could be suggestive of multiple origins. Indeed, given the differences among taxa in the distribution of ocelli, the hypothesis of a single origin would require either (i) an ancestor with ocelli on multiple feather types (similar to most Polyplecton species) combined with loss on most feather types in Pavo and Argusianus or (ii) an ancestor with ocelli on a single feather type combined with shifts among feather types (i.e. the development of ocelli on a novel feather type combined with the loss of expression on the original feather type). Thus, even if Darwin’s [1] hypothesis of homology were correct (hypothesis 1), the evolution of galliform ocelli must be more complex (and therefore even less parsimonious) than a single origin and five losses.

    It does not touch upon how ocelli (eyespots) were formed, it just accepts that they were formed somehow or other. It looks at probable evolutionary paths for their formation and decides that their appearance in galliformes is complex.

    To understand how they originated would require an understanding the formation of multiple features which combine in the context of the whole. Here are a few:

    1. The irredescent colours of the feathers are obtained by thin-film interference caused by the shape and thickness of the barbules. To produce a single colour the thickness of the barbules need to be accurate to within one twenty thousandth of one millimetre.
    2. The positioning of the colours on each individual barbule, barb and feather needs to be precise so that when the feathers unfurl and emerge the overall pattern appears. In the peacock there are around around 200 tailfeathers, 170 eye, 30 ‘T’ and there relative lengths need to be accurate.
    3. There is uniform distribution of ‘eyes’ so that they are all visible when displayed and held in position by individual muscles.
    4. The feature is not only visual it is also aural as the bird makes the tail vibrate and hum during display.

    The tail feathers should not and cannot interfere with the day to day life of the bird. The result of the overall pattern, colours and coordination of individual components is truly a work of art.

    Talbott says

    The biologist does possess what Portmann calls a “curio cabinet” containing various examples of protective coloration, warning coloration, mimicry, and the pollination of flowers by insects and other organisms. These cases certainly point to a legitimate role for natural selection. But after we have identified the utility of some trait, the specific form itself remains to be accounted for. Why this particular pattern for performing the function, when an infinite variety of other patterns could achieve the same thing? The specific form of a bird’s feathery crest or a butterfly’s wing, the shape of antlers or horns, the patterns on a zebra’s head “are by no means explained” by the function (Portmann 1967, pp. 208-9).

    Every organism “speaks itself into the world” as a unity of expressive form. That’s what we see. And we will never understand a unified form by talking about how its parts are tinkered together or what purposes they come to serve. We have to find a language that matches the phenomena we observe. In every organism we see parts that are themselves expressions of the form of the whole. In our attempts to understand, we cannot escape the language of form, so we might as well start learning how to use this language in an accurate and revelatory way.

    It would be very difficult to make the case that the form of the peacock is determined by accidental mutations combined with natural selection.

    No one seems to be arguing with J-Mac: on the limits accidental mutations as he linked to here

  28. Gee, you sound like a real non-skeptic Charlie.

    I like this line:

    CharlieM: The biologist does possess what Portmann calls a “curio cabinet” containing various examples of protective coloration, warning coloration, mimicry, and the pollination of flowers by insects and other organisms. These cases certainly point to a legitimate role for natural selection.

    They exist, so they are legitimate.

  29. CharlieM,

    Evolution must be right even if it has been proven wrong by thousands of mutagenesis experiments…. Faith and belief drives the Darwinian propaganda…not evidence…

  30. phoodoo: So you think there aren’t any? You also think there aren’t genes for eyes?

    So how the heck did we get them?

    Return question: do you think that “genes for eyes” function exclusively in eye development?

    I’ll let you figure out the genes for arms in fruit flies for yourself.

  31. phoodoo: I am not sure what your fruit fly analogy is intended to reveal? That during development, all kinds of things can go wrong that can screw up the organism?

    You mockingly brought up unlucky mutations in which eye sockets developed in limbs and pupils wandered all over the body in search for the right place. I just wanted to show that 1) pretty bizarre things do happen when mutations are introduced in developmental genes but 2) that the effects of such mutations can not manifest just anywhere but happen in the context of a developmental program. The transformation of antennae to legs is possible because they derive from homologous structures, evolved from a common ancestral appendage.

  32. Mung: The effects of mutations do not occur willy nilly across the body, but rather as willy nilly modifications of coordinated developmental programs that are already in place throughout the body?

    Exactly. I knew you was smart.

    Mung: And not just the developmental programs are modified by willy nilly changes.

    I’d rather stick to more simple examples but it seems that these kind of discussions always gravitate to the evolution of complex structures, like vertebrate eyes.

  33. colewd: Where the argument breaks down is where you have to take a significant random walk through the genome to get your adaption.

    What is a “significant random walk through the genome”?

    Bill why do you just type shit?

  34. J-Mac: Evolution must be right even if it has been proven wrong by thousands of mutagenesis experiments…. Faith and belief drives the Darwinian propaganda…not evidence…

    Evolution must be wrong even if it has been proving right by thousands of mutagenesis experiments…. Faith and belief drives the anti-Darwinian propaganda…not evidence…

  35. dazz,

    I promised I’d get back to you.

    November 15, 2017 at 9:08 pm

    stcordova:
    dazz,

    Mendel’s Accountant by Sanford and Sons simulates Kimura’s famous equations quite well.Maybe someday they’ll make their latest freely available as the old versions are retired.

    Is this the one? https://sourceforge.net/projects/mendelsaccount/

    And I responded:

    November 16, 2017 at 4:35 am

    Dazz,

    I’ll have to ask John Sanford. I’ll back to you about it. Thank you for your interest.

    Sal

    So, I spoke to John this morning on the phone, and your request was on my list of things to ask! See, you’re special. 🙂

    The public server has been taken offline and we’re in the middle of moving Mendel’s Accountant to the cloud. It could take a while. Although I might recommend they move the thing to the NIH Biowulf Server. Bwahaha!

    The way things go, the public server could be on the back burner unless I personally get involved. I may bring up the issue personally when John’s team has their giant get-together from around the world in July/August 2018. So, sorry for the news of the delay.

    But speaking of that giant get-together, I’m inviting you to the get-together and anyone here at TSZ. It will be at the 8th International Conference of Creationism July 29, 2018 – Aug 1, 2018. I offer you and others at TSZ a personal invitation to hang out with us there. You’ll have to pay your way for transportation and lodging and conference registration, probably at least $500 total excluding air fare. One evolutionary biologist showed up in 2013, in 2008 even Jason Rosenhouse was there!

    http://www.creationicc.org/icc18_registration.php

    •On Monday, July 30, 2017 Dr. Kevin Anderson will present a Creation Biology Update where he will cover the current scientific findings on soft dinosaur tissue being studied at the Van Andel Research Facility and any other findings that correlate and better explain what we see in created organisms and how they better fit the creation model.

    •On Tuesady, July 31, 2018 Dr. Steve Austin will discuss Building a Machine that Deposits Mud Layers Rapidly. His talk will focus on recent scientific findings of creation scientists and how those findings better explain and correlate with the fossil evidence and geologic formations;

    •On Wednesday, August 1, 2018 Dr. Jason Lisle will present Cosmology: Evolutionary Model and Problems -Suggestions by Creation Scientists. This talk will focus on recent scientific findings that question the current standard theory of the cosmological origin of the universe – The Big Bang. In addition, a discussion of the answers that creation scientists have for scientific findings like the cosmic background radiation and speed of light travel / time questions raised by evolutionary cosmologists.

  36. Corneel: I’d rather stick to more simple examples but it seems that these kind of discussions always gravitate to the evolution of complex structures, like vertebrate eyes.

    I hear you. I’d prefer to stick to single celled asexually reproducing prokaryotes.

    Then we could talk about willy nilly changes throughout the cell instead.

    🙂

  37. Corneel: Return question: do you think that “genes for eyes” function exclusively in eye development?

    Yes, otherwise they would be “genes for eyes and other stuff” by accident.

  38. Allan Miller:
    (Edit) Sorry, I started to type something but I’m losing the will to live …

    You don’t actually mean there is a will to live, right? You mean, the position of chemicals floating around inside a membrane, that creates the illusion that the chemicals want to live, right?

    But often its troublesome for materialists to write what they actually mean, so they take shortcuts, and say what they don’t mean.

  39. Rumraket: Evolution must be wrong even if it has been proving right by thousands of mutagenesis experiments…. Faith and belief drives the anti-Darwinian propaganda…not evidence…

    really? Don’t overwhelm us with too many examples of mutagenesis experiments that lead to new species that could survive in the wild without life support like corneel shocked us with the fruit fly full of defects…. lol

    Any idea how beneficial mutations happen in duons and overlapping genes?

  40. phoodoo: You don’t actually mean there is a will to live, right?

    It’s one of the doctrines of the Church of Allan. As a religious doctrine it doesn’t have to make sense.

  41. J-Mac: Any idea how beneficial mutations happen in duons and overlapping genes?

    Exactly in the same way that beneficial mutations happen anywhere else.

  42. J-Mac: Don’t overwhelm us with too many examples of mutagenesis experiments that lead to new species that could survive in the wild without life support like corneel shocked us with the fruit fly full of defects…. lol

    J-Mac I am not sure who you are referring to but it sure as hell isn’t me, because I have never tried to show that.

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