Genetics

The fine work of Joe Felsenstein and M. Wilson Sayres

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Joe Felsenstein is an evolutionist that has a unique distinction of having his work favorably cited by creationists and bible scholars (except where he disagrees). For example, religious scholars are using Joe’s work to find descendants of the line of priests from the time of the Bible’s King David. See: Y-Chromosomal Aaron.

Joe is also widely credited with coining the phrase “Muller’s ratchet”, a concept articulated in a paper 40 years ago! He must have written that when he was really young, 1973 was a while back.

The wiki entry on Muller’s ratchet:

In evolutionary genetics, Muller’s ratchet (named after Hermann Joseph Muller, by analogy with a ratchet mechanism) is the process by which the genomes of an asexual population accumulate deleterious mutations in an irreversible manner.

In other words, Darwinian evolution doesn’t always clean out the bad, real evolution ensures some of the bad becomes permanent!

Muller’s ratchet actually applies in sexually reproducing creatures if the genetic material has regions like the Y-Chromosome where material is passed off only from father to son. (More on that later as it relates to M. Wilson Sayres recent paper). And my best reading of Joe’s paper suggests that creatures with recombinatorial ability are not immune to getting twisted by problems similar to that of Muller’s ratchet, only that they have a better advantageous defense against it in small populations. So a “ratchet” is universal, just not as deadly in species with the ability to exchange genetic material. Whatever we wish to call it, the “ratchet” problem both in asexual and sexually reproducing species remains.

The paper is Evolutionary Advantage of Recombination .The paper is technical and apologies in advance to Joe if what I state mischaracterizes his position, but I will do my best to explain from my lay perspective.

But first, there is the problem of defining the notions of “deleterious” or “fit” mutations. If we define something as harmful or beneficial based only on the criteria of successful reproduction, we run in to some nasty paradoxes which Andreas Wagner, Lewontin, and others saw clearly. A quasi humorous take of this problem was pointed out in my discussion Survival of the sickest, Why we need Disease and a more technical discussion in Dennett’s strange idea is a bad idea for recognizing biological function . Simply stated, sickness and blindness in the Darwinian world can be viewed as “beneficial” and this leads to problems in defining what is actually “fit”, because the notion of “fit” is fluid. Lewontin pointed out in population genetics the notion of “beneficial” becomes so fluid as to become meaningless. Dennett’s strange idea goes into the details of this problem.

Secondly, because a population could be far sicker than its ancestors but still reproductively “fit” in terms of offspring, the problem of malfunction is equivocated away by “compensatory mutations” which enable more reproductive success but not restoration of function. Thus a population of blind cave fish in a dark cave can be viewed as supremely fit over the cave fish that have functioning eyes. The problem of Muller’s ratchet is alleviated through a process of implicit equivocation (I’m not saying it’s deliberate, but a serious oversight).

With those two caveats regarding the notion of “fit”, it is still helpful to see the effect of Muller’s ratchet. The paper delves into the notion of a bad mutation sweeping through a population and then becoming a feature of the entire population, a process we call fixation. When all the members of the population have the defective gene, the mutation is said to be “fixed”. How can selection fail? To understand the reasons selection can fail, see Gambler’s Ruin Is Darwin’s Ruin.

Problematic is that when this condition happens (where all individuals permanently have the bad mutation), the bad mutation by definition it is now the new baseline, and it ceases to be bad, just like blindness in cave fish. As long as we get some compensatory mutation to improve the number of offspring generated, the problem of lost function is equivocated away by the fluid notions of what it means for a population to be fit.

Joe’s paper goes into the problem of Muller’s ratchet instilling dysfunctional features into all members of population, the main point being that sexually reproducing creatures are better able to resist getting twisted by a ratchet than asexually reproducing creatures.

But Muller’s ratchet understates the problem of bad mutations, since the ratchet only deals with mutations that get fixed into every individual in a population, not ones that are in subsets of the population but are still harmful. Muller’s ratchet says some of the bad mutations become permanent, but another problem is that the number of bad mutations keep increasing even if they are not permanent.

Here is a conceptual cartoon of the problem in asexually reproducing genes. The red dots represent mutations, the broken ginger bread men represent serious expression of the bad gene. The broken ginger bread men are eliminated by selection, some of the bad genes are never purged, they accumulate over time. Humans may be subject to thousands of harmful mutations per individual per generation. The cartoon only uses one mutation per individual per generation to drive its point home.:

http://youtu.be/SrIDjvpx7w4

Muller’s ratchet delves into the likelihood the bad mutants will be “fixed” into a population, but that isn’t even the final problem, the problem is purging the bad mutations that aren’t even fixed. Muller’s ratchet guarantees some mutations will become more or less permanent, but with sufficient numbers of mutations per individual per generation, it is evident the deterioration and dysfunction will eventually become the norm even if Muller’s ratchet doesn’t infuse a given bad mutation into every member of the population. Only by allowing sickness to be redefined as “fit” does the problem really go away on paper.

The idea of Muller’s ratchet inspired creationists to begin investigating the problem of bad mutations. Unfortunately, creationists are not sufficiently recognizing the definitional difficulties that Lewontin realized when trying to define fitness, namely the statistical interpretation of “fit” leads to absurdities such as Survival of the sickest, Why we need Disease.

Regrettably, unlike most of my posts at UD, I don’t feel comfortable in asserting a black and white conclusion that Darwinism is definitely wrong based on Joe Felsenstein’s work (not that he would ever say that either). But Joe, like so many population geneticists (Haldane, Fisher, Crow, Kimura, Nachman, Crowell, Kondrashov, etc.) have a peculiar stature of commanding great admiration from ID proponents and creationists (i.e., Dembski frequently refers to Fisher in favorable terms). The population geneticists have unwittingly inspired creationists with the conviction that life was created.

Finally, I’d like to salute M. Wilson Sayres who reminded me by her published work that the human genome is showing signs of deterioration. This is consistent with findings in different areas of population genetics. See: Sanford’s pro-ID thesis supported by PNAS, read it and weep, literally. I quoted, Michael Lynch in that essay:

Unfortunately, it has become increasingly clear that most of the mutation load is associated with mutations with very small effects distributed at unpredictable locations over the entire genome, rendering the prospects for long-term management of the human gene pool by genetic counseling highly unlikely for all but perhaps a few hundred key loci underlying debilitating monogenic genetic disorders (such as those focused on in the present study).

Thus, the preceding observations paint a rather stark picture. At least in highly industrialized societies, the impact of deleterious mutations is accumulating on a time scale that is approximately the same as that for scenarios associated with global warming—perhaps not of great concern over a span of one or two generations, but with very considerable consequences on time scales of tens of generations.

Michael Lynch

M. Wilson Sayres reported publication of her paper here: Gene Survival and Death on the Y-Chromosome. Her work showed that even on the assumption of evolution, there seems to be substantial deterioration in the Y-chromosome.

In contrast, even without evolutionary assumption, Bryan Sykes at Oxford is noting emergence of irreversible dysfunction in the Y-Chromosome in the present day by comparing fathers to sons to grandsons etc. Sykes wrote the book Adam’s Curse: A future without men (a title that should no doubt be welcomed by the Feminist GNUs and Skepchicks). About the book:

Bryan Sykes follows up The Seven Daughters of Eve with the equally challenging and well-written Adam’s Curse. This time, instead of following humanity’s heritage back to the first women, Sykes looks forward to a possible future without men. The seeds of the book’s topics were sown when Sykes met a pre-eminent pharmaceutical company chairman who shared his surname. Using the Y chromosome, which is passed nearly unchanged from father to son, the author found that he shared a distant ancestor with the other Sykes. Along the way, he discovered that the Y chromosome was worth examining more closely. The first third of Adam’s Curse is devoted to a clear and comprehensive lesson about genetics, the second narrates several fascinating stories of tracing ancestry via the Y chromosome, and the last chapters explore the history of male humanity and its future. Some readers will eagerly skim until they reach Chapter 21, where Sykes gets to the heart of the matter–why and how the Y chromosome has created a world where men overwhelmingly own the wealth and power, commit the crimes, and fight the wars. He uses the structural puniness of the Y chromosome to demonstrate that men are as unnecessary biologically as they are dominant socially. Sykes’ provocative and quite personal book is likely to be unpopular among science readers who prefer their biology divorced from sociology, but his points taken in context will be difficult to refute.

Another relevant study is:
Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree.

Dr. Sayres was very kind to respond to my queries at Pandas Thumb. My question was:

Dr. Sayres,

Does your work agree with that of Bryan Sykes at Oxford who asserted that the Y-chromosome is dying quickly. He feels this could lead to extinction in about 100,000 years.

Some have argued that even thought humans reproduce sexually, that Muller’s ratchet applies to Y-chromosomes, and hence it’s unlikely that recovery will happen damaged genes as might be the case where genetic material can be exchanged and mixed from both parents.

Thank you in advance, and congratulations on your publication.

Dr. Sayres responded:

Hi Salvador,

I don’t think that there is clear evidence that the Y will become extinct in 100,000. There are many ways to avoid this. One of which has already occurred on the human sex chromosomes – the addition of a large autosomal segment to both the X and the Y (we call it the X-added or Y-added region). This region is autosomal in marsupials, but sex-linked in eutherian mammals. We have an extra table in the supplement of the paper discussed here that shows that gene loss occurs relatively quickly at first, then seems to slow down. This is consistent with previous work I did looking at substitution rates over evolutionary time in the X/Y-added regions (where we observe that very quickly after recombination is suppressed, the substitution rate increases on the Y, but then it does not continue to increase, at least for the surviving genes).

It is true that Muller’s ratchet applies to the Y chromosomes, but recent work I’m doing now (submitting a revised version in the next few weeks) shows that purifying selection, and specifically background selection, because nearly all of the content on the Y is linked, is quite strong on the human Y chromosome, acting to retain the little content it has left.

But, if we (humans) did “lose” the Y chromosome, we would still survive. The sex-determining region would likely jump to an autosomal chromosome, and the whole wonderful process would start all over again. Or, maybe some other mechanism we haven’t yet anticipated.

Best, Melissa

The issues raised do not have closure, and it is evident there are pointed disagreements on evolution, especially on the efficacy of “purifying selection”. Creationists argue purifying selection will never be sufficient (the cartoon above tries to display in simplest terms why purifying selection must logically fail).

The research and discussions will just have to keep moving forward, and hopefully more clarity will emerge in due time. I’ll just have to leave it at that for now.

Many kind regards to Dr. Felsenstein and Dr. Sayres for their willingness to dialogue.

96 Replies to “The fine work of Joe Felsenstein and M. Wilson Sayres

  1. 1
    NickMatzke_UD says:

    Hmm.

    Scientists find: Conversion of autosomes to sex chromosomes, followed by decay of one of the sex chromosomes, followed by the sex determining genes jumping to another chromosome (or the decayed chromosome fusing onto an autosome), has happened again and again in evolution, in many different lineages over millions of years.

    Sal concludes: Humans can only last thousands of years and evolution is wrong.

    Me: This is why creationists are a scientific joke and will never be taken seriously.

  2. 2
    scordova says:

    NickMatzke_UD,

    That conclusion by Dr. Sayres was derived by an evolutionary assumption, it is an inference, but not direct observation.

    Whereas, the deep pedigree study is very close to real-time evidence of what happens also Michael Lynch and Bryan Sykes work is real-time (in the present day) versus what is derived from evolutionary assumptions.

    This is why creationists are a scientific joke and will never be taken seriously.

    My my, this post is getting under your skin. 🙂

    So what if we’re never taken seriously, do you think evolutionary biology has much real rank in science except token homage?

    In sciences pecking order, evolutionary biology lurks somewhere near the bottom, far closer to phrenology than to physics.

    Jerry Coyne

    Thanks for you comments Nick.

  3. 3
    NickMatzke_UD says:

    That conclusion by Dr. Sayres was derived by an evolutionary assumption, it is an inference, but not direct observation.

    Says the young-earth creationist who believes YEC in spite of the evidence, and who ignores that common ancestry and phylogenetic methods can be tested, have been tested, and have passed with flying colors.

    Ask Joe Felsenstein, he’ll tell you the same thing. Better yet, read his book, “Inferring Phylogenies”. I read it for my qualifying exam. Why should I take you seriously when you have basic misunderstandings that would get you failed in phylogenetics 101?

  4. 4
    scordova says:

    Why should I take you seriously when you have basic misunderstandings that would get you failed in phylogenetics 101?

    You shouldn’t take me seriously. 🙂 But you should take the problems of the theories of evolutionism very seriously, and the problems are legion.

    Better yet, read his book, “Inferring Phylogenies”.

    Joe Felsenstein is a fine scientist, I’ve never argued otherwise. Dr. Sayres is too. You’re pretty sharp yourself, I just don’t share every idea you all subscribe to.

    But since you’re here, Nick, the substance of my objection can essentially be distilled in this peer-reviewed paper by Kondrashov:
    Why Haven’t we died 100 times over

    Kondrashov didn’t answer the question himself except some by some unproven speculative mechanism of “synergistic epistasis”. The problems articulated by Konrashov are not over come by the mechanisms Dr. Sayres mentioned.

    I appreciate her kind and cordial response, and I’m sorry that I disagree with her since she’s a lot nicer to me than you are.

  5. 5
    scordova says:

    Kondrashov’s abstract is below. Note, his paper describes mutations that selection can’t see.

    Some of the mutations he describes are approximately in-line with my thesis that the notion of “fit” is suspect if one defines “fit” only by statistics instead of function.

    If something is functional but will not be selected against when it becomes dysfunctional, it leads to serious problem. We know on mathematical grounds such functions have to exist since the force of selection must be diluted in some proportion by the number of traits (or even nucleotides).

    The problem of purging out the bad is awful, not just because problems get infused into the population by Muller’s ratchet but even non-fixed mutation just linger only to be replaced by other bad mutations.

    Abstract

    It is well known that when s, the selection coefficient against a deleterious mutation, is below approximately 1/4Ne, where Ne is the effective population size, the expected frequency of this mutation is approximately 0.5, if forward and backward mutation rates are similar. Thus, if the genome size, G, in nucleotides substantially exceeds the Ne of the whole species, there is a dangerous range of selection coefficients, 1/G < s < 1/4Ne. Mutations with s within this range are neutral enough to accumulate almost freely, but are still deleterious enough to make an impact at the level of the whole genome. In many vertebrates Ne approximately 10(4), while G approximately 10(9), so that the dangerous range includes more than four orders of magnitude. If substitutions at 10% of all nucleotide sites have selection coefficients within this range with the mean 10(-6), an average individual carries approximately 100 lethal equivalents. Some data suggest that a substantial fraction of nucleotides typical to a species may, indeed, be suboptimal. When selection acts on different mutations independently, this implies too high a mutation load. This paradox cannot be resolved by invoking beneficial mutations or environmental fluctuations. Several possible resolutions are considered, including soft selection and synergistic epistasis among very slightly deleterious mutations.

    Nonetheless Nick asserts:

    This is why creationists are a scientific joke and will never be taken seriously.

    Nick could of course offer his superior learning of phylogenetics to quell the questions that Kondrashov has raised.

    It is irrelevant that I may not know much, what is relevant is DarwinDefender’s like Nick don’t have answers to such basic problems.

    And even more basic than Kondrashov’s problem, has he resolved Lewontin’s problem regarding the fluid nature of the meaning of “fit”? That problem was enough for Stanley Salthe to quit defending Darwinism.

    Why should I take you seriously when you have basic misunderstandings that would get you failed in phylogenetics 101?

    It’s true, I didn’t study phylogentics 101, I thought Quantum Mechanics 400 or General Relativity 700 was a more important topic for a bystander to the world of science than studying phylogenetics 101 — phylogenetics, a discipline that has yet to make a conflict-free phylogenetic tree above the trivial for Darwin’s grand claim of Universal Common Ancestry. What were you saying again about phylogenetics passing with flying colors?

  6. 6
    NickMatzke_UD says:

    by some unproven speculative mechanism of “synergistic epistasis”

    Do you even understand what “synergistic epistasis” of deleterious mutations means? It’s not some wild, crazy, unproven idea.

    E.g., pop quiz: is epistasis thought to be common or rare in biology?

    It’s true, I didn’t study phylogentics 101, I thought Quantum Mechanics 400 or General Relativity 700 was a more important topic for a bystander to the world of science than studying phylogenetics 101 — phylogenetics, a discipline that has yet to make a conflict-free phylogenetic tree above the trivial for Darwin’s grand claim of Universal Common Ancestry. What were you saying again about phylogenetics passing with flying colors?

    I say you don’t understand the fact that phylogenetic incongruence has degrees, and typically the degree of observed incongruence is remarkably, amazingly, small — in a rigorous statistical sense — given just how big incongruence would be if there were no phylogenetic signal in the data (either genetic, morphological, or both compared with each other).

    Making the argument you are making about phylogenetics is about as silly as if I argued that various fundamental theories of physics were wrong because various measurements of physical constants disagreed by 0.000001% or whatever. All measurements in science have error. Phylogeneticists know how to measure this and assess the degree of disagreement between independent datasets. You guys have no idea, and instead just cherry-pick and quote-mine from other people who are not statistical phylogeneticists.

  7. 7
    scordova says:

    Do you even understand what “synergistic epistasis” of deleterious mutations means? It’s not some wild, crazy, unproven idea.

    E.g., pop quiz: is epistasis thought to be common or rare in biology?

    The existence of epistasis (expression of one gene dependent on others) is not what is questioned, it is whether it answers Kondrashov’s question. Kondrashov postulates this, but if this were so, Lynch wouldn’t have to be fanning the flames of eugenics would he?

    You guys have no idea, and instead just cherry-pick and quote-mine from other people who are not statistical phylogeneticists.

    One way to settle this is if we see increased deterioration not only in the Y-chromosome but the human genome on the whole. So far, the real-time evidence (versus evolutionary speculations of the distant past) is that the human genome is deteriorating at an alarming rate.

    So how many deleterious mutations do you think each human on average is creating for each generation?

    If you say, 1 per human per generation, you might have to deal with this from Muller himself:

    it would in the end be far easier and more sensible to manufacture a complete man de novo, out of appropriately chosen raw materials, than to try to fashion into human form those pitiful relics which remained…

    it is evident that the natural rate of mutation of man is so high, and his natural rate of reproduction so low, that not a great deal of margin is left for selection…

    it becomes perfectly evident that the present number of children per couple cannot be great enough to allow selection to keep pace with a mutation rate of 0.1..if, to make matters worse, u should be anything like as high as 0.5…, our present reproductive practices would be utterly out of line with human requirements.

    Hermann Muller quoted by John Sanford
    Appendix 1, Genetic Entropy

    The cartoon above showed the difficulty of even dealing with 1 novel bad mutation per individual per generation. So what if the mutations don’t even go to fixation, they can just keep piling up where new problems arise after old ones are tossed via neutral mechanisms.

    You’re invited to provide for the reader your estimate for the number of mutations per person per generation.

    Of course, Darwinists can hide behind reproductive success even though humans are suffering from disease. That’s why “sickness” (like sickle cell anemia and tay-sachs disease and blindness in cave fish) can be called be a favored trait in the world of Darwin. Indeed selection favors such traits in certain circumstances, but rather than vindicate Darwinian evolution, it only shows how natural selection favors making defective organisms, not making functional ones.

    So, feel free to reassure readers the mutation rate per human per generation is some low number like .01, that human genome isn’t deteriorating and that Darwinian evolution will keep improving us as it did from our ape ancestors. Feel free to provide that number, I’m sure the UD readers and your colleagues would be interested to hear a figure.

  8. 8
    NickMatzke_UD says:

    The existence of epistasis (expression of one gene dependent on others)

    That’s not epistasis, in the sense we are discussing here. You still aren’t getting the basics.

    Another example: Eugenic-type arguments, whatever their worth (minimal IMHO) aren’t particularly relevant here. Neither the modern situation in industrialized societies (low birth rates and super-high childhood survival rates), nor the situation in the last 10,000 years (dramatic population growth due to agriculture) reflects the long-term equilibrium condition of the human species and its ancestral species.

    The long-term, roughly-equilibrium condition of the human species and its ancestral species was basically: flat population, and a high number of deaths every generation (an average of 2 surviving offspring per adult woman, but perhaps 4-8 babies per adult woman). Many of those deaths would have been selective due to disease, starvation, etc.

    It’s quite possible that the more recent situations encourage the spread of deleterious mutations, but the ancient long-term situation did not. You can’t use quote-mines and arguments about the recent situations to try to prove something about the ancient situation.

  9. 9
    scordova says:

    It’s quite possible that the more recent situations encourage the spread of deleterious mutations, but the ancient long-term situation did not. You can’t use quote-mines and arguments about the recent situations to try to prove something about the ancient situation.

    Thank you for your response, but do you have a figure for the number of bad mutations per person per generation?

    You can set the record straight. How many bad mutation per person per generation on average. Muller provided his figures, do have any?

    Thanks for taking time to comment on my discussion.

  10. 10
    Mung says:

    Welcome back Sal!

  11. 11
    Mung says:

    Dear Nick,

    I apologize if I missed your post answering my previous questions. I admit my failure to closely scrutinize all of your posts here at UD due to the history of lack of relevant content.

    Your field is macro-evolutionary theory?

    What was your primary text during your “macro-evolutionary studies?

    You proposed to represent the “field” of macro-evolutionary theory to Prof Tour?

    Assume I’m a fresh college student who wants to become familiar with the latest research in macro-evolutionary theory.

    What textbook on macro-evolutionary theory would you recommend?

    Does a textbook on macro-evolutionary theory even exist?

    I want to be like you, Nick. I want to become an expert in Macro-Evolutionary Theory. I want to be able to debate Emeritus Professors and set them straight about their misunderstandings.

  12. 12
    bornagain77 says:

    Mr. Matzke, seeing as you are obsessed and driven by the singular purpose to prove we have no true purpose to our lives, I would like to help you in your endeavor. I have a few questions about this epistasis thing you are talking about that maybe you can help us IDiots understand. You see Mr. Matzke,,

    Mutations : when benefits level off – June 2011 – (Lenski’s e-coli after 50,000 generations)
    Excerpt: After having identified the first five beneficial mutations combined successively and spontaneously in the bacterial population, the scientists generated, from the ancestral bacterial strain, 32 mutant strains exhibiting all of the possible combinations of each of these five mutations. They then noted that the benefit linked to the simultaneous presence of five mutations was less than the sum of the individual benefits conferred by each mutation individually.
    http://www2.cnrs.fr/en/1867.htm?theme1=7

    New Research on Epistatic Interactions Shows “Overwhelmingly Negative” Fitness Costs and Limits to Evolution – Casey Luskin June 8, 2011
    Excerpt: In essence, these studies found that there is a fitness cost to becoming more fit. As mutations increase, bacteria faced barriers to the amount they could continue to evolve. If this kind of evidence doesn’t run counter to claims that neo-Darwinian evolution can evolve fundamentally new types of organisms and produce the astonishing diversity we observe in life, what does?
    http://www.evolutionnews.org/2.....47151.html

    Mr. Matzke, The preceding experiment was interesting, for they found, after 50,000 generations of e-coli which is equivalent to about 1,000,000 years of ‘supposed’ human evolution, only 5 ‘beneficial’ mutations. Moreover, these 5 ‘beneficial’ mutations were found to interfere with each other when they were combined in the ancestral population. Needless to say, this is far, far short of the functional complexity we find in life that neo-Darwinism is required to explain the origination of. For instance, over 1000 orphan genes are now found to be in humans that are not present in chimps (and this number is growing). Even more problematic for neo-Darwinism is when we realize that Michael Behe showed that the ‘beneficial’ mutations of Lenski’s e-coli were actually loss or modification of function mutations. i.e. The individual ‘beneficial’ mutations were never shown to be in the process of building functional complexity at the molecular level in the first place! This is not good for neo-Darwinism Mr. Matzke!

    Moreover,,,

    Epistasis between Beneficial Mutations – July 2011
    Excerpt: We found that epistatic interactions between beneficial mutations were all antagonistic—the effects of the double mutations were less than the sums of the effects of their component single mutations. We found a number of cases of decompensatory interactions, an extreme form of antagonistic epistasis in which the second mutation is actually deleterious in the presence of the first. In the vast majority of cases, recombination uniting two beneficial mutations into the same genome would not be favored by selection, as the recombinant could not outcompete its constituent single mutations.
    http://www.uncommondescent.com.....ach-other/

    Response from Ralph Seelke to David Hillis Regarding Testimony on Bacterial Evolution Before Texas State Board of Education, January 21, 2009
    Excerpt: He has done excellent work showing the capabilities of evolution when it can take one step at a time. I have used a different approach to show the difficulties that evolution encounters when it must take two steps at a time. So while similar, our work has important differences, and Dr. Bull’s research has not contradicted or refuted my own.
    http://www.discovery.org/a/9951

    Where’s the substantiating evidence for neo-Darwinism?
    https://docs.google.com/document/d/1q-PBeQELzT4pkgxB2ZOxGxwv6ynOixfzqzsFlCJ9jrw/edit

    I know Mr. Matzke, you are probably just shaking your head at how we IDiots can miss something so obvious to you, but please be patient with us, I’m trying my best to understand how randomly colliding particles can create information processing mechanisms that greatly outclass our best computers, but I just can’t seem to find that one piece of evidence that would make me such a zealot as you are (are at least not such a skeptic). Tell you what Mr. Matzke, I know what would do it. Show me the laboratory work where one molecular machine was arrived at by neo-Darwinian processes:

    Michael Behe on Falsifying Intelligent Design – video
    http://www.youtube.com/watch?v=N8jXXJN4o_A

    Orr maintains that the theory of intelligent design is not falsifiable. He’s wrong. To falsify design theory a scientist need only experimentally demonstrate that a bacterial flagellum, or any other comparably complex system, could arise by natural selection. If that happened I would conclude that neither flagella nor any system of similar or lesser complexity had to have been designed. In short, biochemical design would be neatly disproved.- Dr Behe in 1997

  13. 13

    Mung, welcome back! Still on your quest to understand macroevolution, I see. 🙂

  14. 14
    CharlieD says:

    Oh yeah, hiding behind the “irreducibly complex” argument. Why am I not surprised? You ask questions that no one has an answer to right now, and think you’ve won the argument. What a joke.

  15. 15
    Robert Byers says:

    Genetics has never provided evidence for evolution.
    Its all presumed that genetics can’t change from other mechanisms and so its a true trail of descent.
    Its all guessing.
    Its like saying all white people come from a original white Adam/eve or white tribe.
    When in fact whiteness was a common reaction to different unrelated peoples.

    Seems unlikely any connection can be made by genetics from present Jews to the priests back in old israel. It would be cool but even the purest of race would not show this in genes I think.
    Genes are just a atomic score for biology but not indicator for genetic change.
    People changed colour soon after Babel and it would be shown in the genes but it wasn’t due to the genes.

  16. 16
    Upright BiPed says:

    Charlie,

    No one needs to “hide behind” irreducible complexity. IC systems are incontrovertibly present in biological systems (i.e genetic translation). And saying that “no one has an answer right now” is called assuming your conclusion. First you must assume that volitional agency isn’t the cause of an effect, and then you must assume that a non-agency cause exists, for which you have no confirming evidence.

    Congratulations, you’re a standard issue ID critic.

  17. 17
    Upright BiPed says:

    Hey Mung. 🙂

  18. 18
    CharlieD says:

    Irreducible complexity is an idea based on an absence of scientific knowledge and simply plays on the lack of knowledge that most people have in the field of Biology. Yes there are many complex structures in nature, is there any reason why natural methods could not produce these structures? No there isnt. My saying that no one has the answer right now is not an assumption. You saying something is irreducibly complex is an assumption and an absolute, of which there are never any absolutes in biology.

  19. 19
    bornagain77 says:

    CharlieD you state,

    Yes there are many complex structures in nature, is there any reason why ‘natural’ methods could not produce these structures? No there isn’t.

    So your argument for Darwinism is not an empirical demonstration that molecular machines can arise by purely material means but is this instead?

    Darwinism Not Impossible Therefore It Must Be True – Plantinga – video
    http://www.metacafe.com/watch/10285716/

    Notes:

    Programming of Life – Probability – Defining Probable, Possible, Feasible, etc.. – video
    http://www.youtube.com/watch?v=kckv0wVBYpA

    The Universal Plausibility Metric (UPM) & Principle (UPP) – Abel – Dec. 2009
    Excerpt: Mere possibility is not an adequate basis for asserting scientific plausibility. A precisely defined universal bound is needed beyond which the assertion of plausibility, particularly in life-origin models, can be considered operationally falsified. But can something so seemingly relative and subjective as plausibility ever be quantified? Amazingly, the answer is, “Yes.”,,,
    c?u = Universe = 10^13 reactions/sec X 10^17 secs X 10^78 atoms = 10^108
    c?g = Galaxy = 10^13 X 10^17 X 10^66 atoms = 10^96
    c?s = Solar System = 10^13 X 10^17 X 10^55 atoms = 10^85
    c?e = Earth = 10^13 X 10^17 X 10^40 atoms = 10^70
    http://www.tbiomed.com/content/6/1/27

    Could Chance Arrange the Code for (Just) One Gene?
    “our minds cannot grasp such an extremely small probability as that involved in the accidental arranging of even one gene (10^-236).”
    http://www.creationsafaris.com/epoi_c10.htm

    Probabilities Of Life – Don Johnson PhD. – 38 minute mark of video
    a typical functional protein – 1 part in 10^175
    the required enzymes for life – 1 part in 10^40,000
    a living self replicating cell – 1 part in 10^340,000,000
    http://www.vimeo.com/11706014

    The math just doesn’t work out CharlieD. Which reminds me:

    “Nothing in evolution can account for the soul of man. The difference between man and the other animals is unbridgeable. Mathematics is alone sufficient to prove in man the possession of a faculty unexistent in other creatures. Then you have music and the artistic faculty. No, the soul was a separate creation.”
    Alfred Russell Wallace, New Thoughts on Evolution, 1910, co-discoverer of natural selection

    The Unreasonable Effectiveness of Mathematics in the Natural Sciences – Eugene Wigner – 1960
    Excerpt: ,,certainly it is hard to believe that our reasoning power was brought, by Darwin’s process of natural selection, to the perfection which it seems to possess.,,,
    http://www.dartmouth.edu/~matc.....igner.html

  20. 20
    Joe says:

    CharlieD:

    Irreducible complexity is an idea based on an absence of scientific knowledge and simply plays on the lack of knowledge that most people have in the field of Biology.

    Now THAT is based on an absence of knowledge. IC is based on our knowledge of casue and effect relationships, Charlie. And no one can demonstrate unguided evolution can produce it.

    So don’t blame us because unguided evolution doesn’t have any support.

  21. 21
    Joe says:

    Nick matzke:

    Says the young-earth creationist who believes YEC in spite of the evidence, and who ignores that common ancestry and phylogenetic methods can be tested, have been tested, and have passed with flying colors.

    Only within species common ancestry can be tested, Nick. Common Design employs the same type of tests as universal common ancestry. So by Nick’s “logic” Common Design has been tested and passed with flying colors!

  22. 22
    scordova says:

    That’s not epistasis, in the sense we are discussing here. You still aren’t getting the basics.

    For one, you asked about epistasis not “synergistic epistasis” which Kondrashov used to argue for the sudden synergy of several weakly selective mutations becoming collectively more deleterious than their individual weak selection values. It was speculative, and no proof. John Sanford pointed that out in his book Genetic Entropy. So the existence of epistasis is not in question, the efficacy of “synergistic epistasis” to remove deleterious mutations is. The deep pedigree study, and even M. Wilson Sayres study give good reasons to say “synergistic epistasis” works only to remove weakly deleterious mutation in ones imagination, not in the nature.

    Nick fumed:

    Hmm.

    Scientists find: Conversion of autosomes to sex chromosomes, followed by decay of one of the sex chromosomes, followed by the sex determining genes jumping to another chromosome (or the decayed chromosome fusing onto an autosome), has happened again and again in evolution, in many different lineages over millions of years.

    Sal concludes: Humans can only last thousands of years and evolution is wrong.

    Me: This is why creationists are a scientific joke and will never be taken seriously.

    Nick, the highlighted part demonstrates circular reasoning. At issue is the very question of what exactly happened in the past, and you are assuming the very thing you are trying to prove. I only pointed out, even with evolutionary assumptions, M. Wilson Sayres reported substantial damage to the Y-Chromosome, and that Muller’s ratchet applies to the Y-chromosome. I pointed out there are disagreements and I implied it wasn’t for me to try to argue against everything I might disagree with in Dr. Sayres work or her response to me, more research will hopefully clarify the issue, but I have a suspicion of what will be discovered…

    Circular reasoning is no proof, you never seem to have figured that out because you keep using circular reasoning to defend your claims, and you have the gall to say something about scientific jokes?

    Muller (of Muller’s ratchet fame) won the Nobel Prize for his research related to the mutational damage of radiation on offspring. He had some knowledge about how many mutations a population could endure before it could no longer purge the bad out of the population.

    So now, regarding the Y-chromosome, if we assume that it has been losing function over millions of years, did it ever occur to you this raises the question of how it got their in the first place? 🙂

    So now, here is your chance to set the record straight for the readers.

    I asked:

    You can set the record straight. How many bad mutation per person per generation on average. Muller provided his figures, do have any?

    Crickets.

  23. 23
    scordova says:

    Nick wrote:

    You guys have no idea, and instead just cherry-pick and quote-mine

    It’s true, I have a collection of quotes from evolutionists from Richard Dawkins, to Jerry Coyne, to PZ Myers, and Abbie Smith:

    Nick Matzke is a deliberate, intentional, unrepentant liar.

    Richard Dawkins

    and

    [Matzke is] a nasty piece of work

    Matzke has apparently made stuff up

    Jerry Coyne

    and

    Yeah, I’m looking at you, Nick Matzke. …sleazy.

    PZ Myers

    and

    Nick completely and utterly slighted me, in what I viewed as a sexist manner

    Abbie Smith

  24. 24
    Upright BiPed says:

    CharlieD,

    You saying something is irreducibly complex is an assumption and an absolute, of which there are never any absolutes in biology.

    Spoken like someone who would like the freedom to ignore inexorable law whenever it’s convenient.

    Allow me to ask a question about absolutes. Darwinian evolution is based on the presence and transference of recorded heritable information (leading to specified effects among prodigy). Do you think it’s possible to have and transfer heritable recorded information without using an arrangement of matter or energy as a medium of that information? By what other means would it be accomplished?

    Is this an absolute?

    And if you have an arrangement of matter or energy as a medium of heritable recorded information, do you think it is possible to produce specified effects from that arrangement without the presence of a second arrangement of matter to establish what the effect will be? In other words, in genetic translation systems, the medium of information is the arrangement of a nucleic sequence, and the second arrangement of matter (a protocol to locally establish what the effect will be) is the aminoacyl tRNA synthetase. If you take away the second arrangement of matter, the system will fail because you’ve removed a requirement from within the system – that requirement is the physical establishment of a pathway to locally achieve the specified effect from the medium. So is a second arrangement of matter necessary to the first?

    Is this another absolute?

    If these are not absolutes, then how would you record and transfer heritable information without using an arrangement of the matter/energy within in the cosmos as a medium? And how would you achieve a specified effect from that arrangement without using a second arrangement of matter to establish what the effect will be?

    On the other hand, if these are real world absolutes, are they irreducibly complex?

  25. 25
    CharlieD says:

    Like I said, there are no absolutes in Biology and there is no scientific basis behind irreducible complexity.

  26. 26
    bornagain77 says:

    as to “there is no scientific basis behind irreducible complexity.”

    Then there is no scientific basis to Darwinism either since ID is based on the same method of science as Darwinism was:

    Stephen Meyer – The Scientific Basis Of Intelligent Design – video
    https://vimeo.com/32148403

  27. 27
    CharlieD says:

    For the last time, irreducible complexity has no scientific basis. Evolution, however is backed by an overwhelming amount of evidence gathered by scientists for over the last hundred years. In fact I sat in on a seminar today about the genomic convergence of the thylacine and dog, and in just a half hour more science was presented than can be found on this entire site.

  28. 28
    Upright BiPed says:

    Like I said, there are no absolutes in Biology and there is no scientific basis behind irreducible complexity.

    So… when confronted with contrary evidence which you cannot handle, you simply close your eyes to it and repeat yourself.

    How empirically convincing.

  29. 29
    CharlieD says:

    Uh, you havent provided any scientific evidence for irreducible complexity whatsoever. That would be because there is none.

  30. 30
    Upright BiPed says:

    …in just a half hour more science was presented than can be found on this entire site.

    Uh huh.

    And yet, you can’t even answer the simplest of questions, i.e. #24

  31. 31
    bornagain77 says:

    CharlieD, no one has ever seen Darwinian processes produce a single molecular machine, but ID has produced as such:

    “There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject.”
    James Shapiro – Molecular Biologist

    Michael Behe – No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines
    http://www.metacafe.com/watch/5302950/

    of related note to the fact that Darwinists have ZERO empirical evidence of Darwinian processes EVER producing a molecular machine, here are several examples that intelligence can do as such:

    (Man-Made) DNA nanorobot – video
    https://vimeo.com/36880067

    Whether Lab or Cell, (If it’s a molecular machine) It’s Design – podcast
    http://intelligentdesign.podom.....3_41-08_00

  32. 32
    Upright BiPed says:

    Uh, you havent provided any scientific evidence for irreducible complexity whatsoever. That would be because there is none.

    You simply ignored it.

    Far be it for me to confuse you with the facts, but you can’t record and transfer heritable information without an arrangement of matter to be a medium of the information, and a second arrangement of matter to establish what the effect of that medium will be within a system. Without both roles, it is not possible to transfer form though a material medium.

  33. 33
    CharlieD says:

    Oh yeah, ask a question that nobody knows the answer to right now and pretend you’ve stumped me. Congrats. You did the exact same thing to me a month ago. Doesnt it get old? Pretending to be an intellectual by hiding behind a facade of pseudoscience?

  34. 34
    scordova says:

    CharlieD wrote:

    In fact I sat in on a seminar today about the genomic convergence of the thylacine and dog,

    Convergence isn’t proof of evolution. It’s proof of similarity when similarity can’t be explained by common descent. Well done.

    and in just a half hour more science was presented than can be found on this entire site.

    Wonderful, perhaps then you can tell us what the average number of mutations per generation per individual is.

    I mean, if Darwin claimed evolution builds up the good and eliminates the bad, evolutionists should have some estimate of how much bad and how much good is made from which evolution constructs a human since they are so sure of their theory.

    If evolutionists assert evolutionism is true, surely it’s not too much to ask them how many bad mutations are being generated in the human genome per individual per generation.

    So how many bad mutations are appearing in the human genome today per individual per generation. You’re invited to provide and answer because Dr. Matzke is awfully silent on a matter which ought to be trivial. Here is your chance to provide some real science. What range are we talking about in terms of a number?

    .001
    .01
    .1
    1.0
    10
    100
    1000

    Any figures that interested readers can take away from this discussion?

    If that’s too much for your evolutionist database, here is a thought. Consider that in the genetic difference between humans and chimps is 9,000,000 base pairs (a figure that can be defended based on another post at UD), if you assume that this implies 9 million mutations were then fixed from the most recent comment ancestor are neutral to good, that implies how many bad mutations per individual had to be ejected? If even assuming you get as many bad mutations as non-bad mutations (an extraordinarily generous assumption), that should give you a figure of the same magnitude of 9,000,000.

    If we take the number of generation since the Last Common Ancestor (LCA) at about 7 million years ago, that’s about 350,000 generations. That implies evolution would have to be purging about 25 new BAD mutations per person per generation.

    Don’t like those figures? Then provide the correct ones. Mr. Phylogenetics Matzke seems awfully reluctant to provide a figure. I mean, didn’t they teach him that in phylogenetics or population genetics 101?

    So even if I’m incorrect, I took a stab at an estimate, which is more than I can say for Mr. Phylogenetics Nick Matzke.

  35. 35
    CharlieD says:

    The fact that you are using the phrase “bad mutation” right off the bat tells me you should not be talking about evolution. You, like your buddies here, are asking a question that is extremely complex. The estimate you provided is a wild guess at best. The amount of information to get a reliable estimate requires a huge amount of data collection and interpretation. You are oversimplifying a very complex process.

  36. 36
    Joe says:

    CharlieD,

    If there isn’t any scientific basis for irreducible complexity, then why are evos spending so much time and effort trying to refute it?

    And why do all observations confirm its existence? See ATP synthase for starters. I bet I could find one for every letter in the alphabet.

  37. 37
    Upright BiPed says:

    #33

    Are you actually suggesting that asking ‘if its possible to record and transfer heritable information without using the matter in the universe as a medium’ is too difficult of a question to answer?

    Pffft.

  38. 38
    scordova says:

    The fact that you are using the phrase “bad mutation” right off the bat tells me you should not be talking about evolution.

    Really, from Darwin’s Origin

    Natural Selection is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good.

    C.DARWIN sixth edition Origin of Species — Ch#4 Natural Selection

    So by your twisted logic neither should Darwin. Well done.

    So what’s the figure, Muller provided figures, and he didn’t even go into the notion of bad vs good, because his research and numerous other research discovered, the vast majority of mutations are harmful. He realized this grim fact since it was his research on the effects of radiation on offspring that won him the Nobel Prize.

    The fact that you are using the phrase “bad mutation” right off the bat tells me you should not be talking about evolution.

    Do you like the word “deleterious” better, but the problem then is you have to define “beneficial” and as was pointed out earlier, doing this strictly through statistics leads to absurdities such as saying sickle-cell anemia, tay-sachs disease, diabetes, blindness in cave fish aren’t defects they are advantageous beneficial features.

    So provide some figures, and if you can’t, just say so and admit no evolutionists has ever bothered to explain it to you. Here is your chance to shine and educate the readers or at least demonstrate the concerns expressed here are
    without basis.

    Let me make it easer for you:

    1. what is the mutations per human per generation. That’s not so hard is it? Neutralists like Kimura can provide a figure where fixation rate is roughly equal to mutation rate.

    2. Some fraction of those mutations are bad. Which leads to : bad mutations per human per generation.

    But to assume mutation rate is approximately fixation rate implies neutrality in mutations and this has been experimentally refuted. If most mutations were really neutral, Muller would not have won the Nobel Prize.

    The amount of information to get a reliable estimate requires a huge amount of data collection and interpretation. You are oversimplifying a very complex process.

    So no one knows, is that fair? Would Nick Matzke agree with you?

    The estimate you provided is a wild guess at best.

    Good, so was my number too high, too low, or you don’t know?

    To your credit you are at least doing better than Mr. Phylogenetics Nick Matzke who is always verbose when he gets riled and thinks he can score a debate point, but is strangely silent now.

    I don’t think the questions raised are outrageous. How many mutations per individual per generation? How many bad (or deleterious) mutations per individual per generation?

    Not too much to ask is it?

  39. 39
    CharlieD says:

    No one is “trying to refute irreducible complexity,” you jackass. Science studies what is discovered and draws conclusions from the information gathered. Stop making it seem like there are battle lines, there are none. Science doesnt need to refute your claims, it just laughs at you.
    Sorry, I wasnt clear enough, the context you are using the phrase “bad mutation” in is incorrect. Darwin was being extremely general, you however are asking for exact numbers, details, etc in a question about the entire human population. What may be beneficial to some, can be bad for others. You simply have no idea what you are talking about.

  40. 40
    Joe says:

    No one is “trying to refute irreducible complexity,” you jackass.

    All evidence to the contrary, of course. And it still stands that science says that unguided evolution has nothing.

    I see that bothers you. Good

  41. 41
    CharlieD says:

    Give me one scientific article that is specifically trying to refute irreducible complexity.
    “Unguided evolution” is a bullshit term also. Evolution is guided by natural selection among other factors.

  42. 42
    scordova says:

    For the reader’s benefit, if mutations are neutral, the rate at which the entire human population will get a new nucleotide is equal to the neutral mutation rate. That was highlighted in this wiki article with supporting calculations:

    http://en.wikipedia.org/wiki/F....._genetics)

    The problem is that, well….most mutations aren’t neutral, but harmful. If we suppose the ratio of harmful (even slightly harmful) number of mutations per neutral mutation is even 1-to-1, this is a serious problem since slightly harmful mutations even if they leave the population are replaced by other harmful mutations, and as the cartoon above illustrated, the harmful ones will just keep accumulating.

  43. 43
    scordova says:

    Give me one scientific article that is specifically trying to refute irreducible complexity.

    Take a look at this one by Thornhill and Ussery, page 1 🙂

    http://www.cbs.dtu.dk/staff/da.....Darwin.pdf

    Given that I responded to you querry, you are invited to respond to mine.

    1. How many mutations per human per generation
    2. How many bad mutation per human per generation

    If you don’t know, just say so.

  44. 44
    CharlieD says:

    Wow a six page paper that talks about some types of evolution. Thats a real comprehensive study that tries to refute irreducible complexity. Please. That probably took the guy a day to write up. It doesnt even have a methods section, it is not a scientific experiment aimed at refuting irreducible complexity, its a compilation of ideas to sum up and try to help show how ridiculous the idea of irreducible complexity is. Nice try though.
    Again, those questions are ridiculous. Youre going to need to be much more specific if you want me to answer.

  45. 45
    Joe says:

    Give me one scientific article that is specifically trying to refute irreducible complexity.

    They only publish successes, Charlie.

    “Unguided evolution” is a bullshit term also.

    Nope. THAT is what is being debated. So how stupid is it of you to not even undersatnd the debate?

    Evolution is guided by natural selection among other factors.

    Whatever works survives and reproduces, Charlie. So all you are saying is that evolution is guided by the reproducing survivors.

    Ya see Charlie, natural selection is blind and mindless. Not much guidance there. Only artificial selection has guidance, Charlie.

    I take it that you didn’t read any biology text books…

  46. 46
    Joe says:

    Dear Nature,

    Please accept my following paper that shows I could not evolve an IC system.

    Thank You,

    Joe Biologist

  47. 47
    scordova says:

    Youre going to need to be much more specific if you want me to answer.

    How many DNA point muatations per human per generation. 🙂

  48. 48
    CharlieD says:

    Joe, you couldnt be more wrong. Im not surprised that I can come on here and find people telling me I havent opened a biology book while at the same time I am majoring in molecular and cell biology. You dumbasses think youre so smart, but anyone with a decent science background can see right through you. Lucky for you guys, most people are just as lacking in science or even more so than you.

  49. 49
    CharlieD says:

    Not even close to specific enough.
    How about this, I believe DNA duplication results in an error once every million base pairs or so. Run with that, let me know where it takes you.

  50. 50
    Joe says:

    Charlie,

    Your ignorance of natural selection is very telling. Don’t blame me for your ignorance. Biology 101 should have covered natural selection. Maybe you just haven’t got to that part yet.

    Let us know when you catch up.

  51. 51
    CharlieD says:

    You are soooo funny! Man you must be the center of attention when everyone is standing around the koolaid cooler. Im ignorant? Youre the ones talking about science when you know nothing of it.

  52. 52
    Arthur Hunt says:

    How many DNA point muatations per human per generation.

    Explained here and in the accompanying links.

    As far as beneficial vs neutral vs deleterious, one way to explain the contingent nature of mutations is to use the analogy of a hand of bridge. Say one has, among other cards, the ace and deuce of spades. If the contract is, say, 4 spades, then both cards are beneficial. If the contract is, conversely, 5 diamonds, then the ace may be beneficial (but much less so), but the deuce is deleterious (a sure loser). Etc. for other cards, contracts, and hands. (What is the value of the ace of spades in a hand where the contract is 5 diamonds and dummy has a void in spades?)

    It’s possible to explain epistatic effects using this example, but that’s for another time, I’m afraid.

  53. 53
    Joe says:

    Your distractions don’t work here, Charlie.

    Natural selection doesn’t do anything. Whatever is good enough gets through that “filter”. Lenski has 50,000+ generations with nothing to brag about wrt evolution.

  54. 54
    CharlieD says:

    Natural selection doesnt do anything? Yeah thats all I need to hear. You guys just love to twist things how you see fit, it great. Keep up the good work! Anyone with an iota of intelligence in biology can see what you are doing, but unfortunately the world is filled with people unwilling to put the effort in to really get into the biological sciences. Keep preying on the scientifically illiterate, youre doing a great job

  55. 55
    Barb says:

    Also, it is revealing to see what has happened to Darwin’s long-accepted idea regarding the “survival of the fittest.” This he called “natural selection.” That is, he believed that nature “selected” the fittest living things to survive. As these “fit” ones supposedly acquired new features that worked to their advantage, they slowly evolved. But the evidence of the past 125 years shows that, while the fittest may indeed survive, this does not explain how they arrived. One lion may be fitter than another lion, but that does not explain how he got to be a lion. And all of his offspring will still be lions, not something else.

    Darwin recognized the need for some designing force and gave natural selection the job. “Natural selection,” he said, “is daily and hourly scrutinising, throughout the world, the slightest variations; rejecting those that are bad, preserving and adding up all that are good.”1 That view, however, is now losing favor. Stephen Gould reports that many contemporary evolutionists now say that substantial change “may not be subject to natural selection and may spread through populations at random.” Gordon Taylor agrees: “Natural selection explains a small part of what occurs: the bulk remains unexplained.” Geologist David Raup says: “A currently important alternative to natural selection has to do with the effects of pure chance.” But is “pure chance” a designer? Is it capable of producing the complexities that are the fabric of life?

  56. 56
    bornagain77 says:

    CharlieD states incredulously

    “Natural selection doesnt do anything? Yeah thats all I need to hear.”

    yet

    “Natural selection does not act on anything, nor does it select (for or against), force, maximize, create, modify, shape, operate, drive, favor, maintain, push, or adjust. Natural selection does nothing…. Having natural selection select is nifty because it excuses the necessity of talking about the actual causation of natural selection. Such talk was excusable for Charles Darwin, but inexcusable for evolutionists now. Creationists have discovered our empty “natural selection” language, and the “actions” of natural selection make huge, vulnerable targets.”
    The Origin of Theoretical Population Genetics, 2001 (pp. 199-200) William Provine – Professor of Evolutionary Biology – Cornell University

  57. 57
    scordova says:

    CharlieD wrote:

    Not even close to specific enough.
    How about this, I believe DNA duplication results in an error once every million base pairs or so. Run with that, let me know where it takes you.

    Human genome size at roughly 3.5 giga base pairs. At 1 error per million that’s 3,500 errors. Are you sure you’re on the Dariwnist side? 🙂

  58. 58
    CharlieD says:

    Let me spell out the process of natural selection for you:
    1. Organisms produce far more offspring each generation than can possibly survive, given limited resources (from Malthus)
    2. Individuals within a population VARY in their traits.
    3. Some of this phenotypic variation is heritable, and can therefore be handed down to descendants (genetic & epigenetic factors).
    4. In a particular environment or habitat, certain variants will be better able to SURVIVE and REPRODUCE than others, because their traits are more suitable (FIT) for that habitat.
    5. The “fitter” variants will, on average, produce more (most) of the next generation – g and these offspring will also tend to possess the special “fit” trait, because offspring tend to resemble their parents.
    6. Over time, that trait (or traits) will increase in frequency in the population. It will be SELECTED by the environment for survival and reproduction.

    And do you have a point cordova?

  59. 59
    CharlieD says:

    I think its pretty funny that I can come on here and be told that I dont know anything about biology. Im not really surprised though because what you guys call biology and what everyone else calls biology are two very different things it would seem.

  60. 60
    scordova says:

    HT JoeCoder!

    Larry Moran gives an estimate of 160 mutations per human per generation

    http://sandwalk.blogspot.com/2.....-rate.html

    This estimate assumes molecular evolution happened under mostly neutral (not Darwinist) conditions.

    Using the fixation model from the wiki link, this implies 160 mutations per human per generation that are neutral or nearly neutral. See:

    http://en.wikipedia.org/wiki/F....._genetics)

    So the responses to the question of how many mutations per individual per generation

    Nick Matzke: refuses to answer
    me: 25
    larry: 160
    charlieD: 3500

    Even assuming that for ever neutral mutation, there is a bad mutation, this is very bad.

    How many bad ones can we tolerate according to Muller? .5
    How many bad ones can we tolerate according to the cartoon? 1.0

    Every number provided for mutation rates is far above Muller’s figure and the simplified cartoon model. If anything the cartoon model was generous….

    Further, it was I that gave the most favorable figure for Darwinists, and even that was too high.

    But Larry’s figure is 160 mutations assumed to be neutral, no figure is given as to their harmful level. As I said, and as Kondrashov points out, mutations can be harmful without having much selective effect (or even having positive selective effect but being harmful such as sickle cell anemia).

    Muller said .5 mutations per individual would result in irreversible damage to humans. If the 90% of mutations are harmful then from Moran’s figure we get 144 bad mutations per human per generation. Deadly. Think of that cartoon with the red dots and instead of 1 red dot per generation, think of 144 red dots per generation.

    One problem the neutral model poses for mindless evolution. If we find that the majority of genome is functional and more in accord with the Neutral Model than the Selectionist Model, that implies the majority of the function evolved without selection, hence selection is ruled out as the major cause of design for most of the genome, hence Darwin is wrong and so is Dawkins. QED.

  61. 61
    scordova says:

    Art Hunt weighed in but his comment was trapped in the queue. See above.

    PS
    Art, I had no involvement in how you got put in the queue. I’ll release your comments as quickly as I’m aware of them. Thanks for your patience.

  62. 62
    Phinehas says:

    AH:

    As far as beneficial vs neutral vs deleterious, one way to explain the contingent nature of mutations is to use the analogy of a hand of bridge. Say one has, among other cards, the ace and deuce of spades. If the contract is, say, 4 spades, then both cards are beneficial. If the contract is, conversely, 5 diamonds, then the ace may be beneficial (but much less so), but the deuce is deleterious (a sure loser). Etc. for other cards, contracts, and hands. (What is the value of the ace of spades in a hand where the contract is 5 diamonds and dummy has a void in spades?)

    I’m not a bridge player, but I think I get what you are saying having played various other card games. Despite the fact that different cards can have different values in different circumstances, I can still look at my hand and bid on its likely value. In general, I’ll be bidding much higher on a hand with four aces than I will on a hand with four twos.

    The point is this: statistics can handle the contingent nature of cards, and I’m pretty sure it can do the same with mutations. If nature is dealing lots of twos, does it really matter greatly that there are a few obscure cases where the two may be a winner?

  63. 63
    JoeCoder says:

    scordova @60

    I don’t think it’s fair to cite Larry Moran for 160 mutations per generation. His overview of studies ranges from 56 to 160. So let’s give the benefit of the doubt and go with 56. Or perhaps 112, which was the lower bound of the phylogenetic method, which would be the average rate if evolution is true.

    So what percentage of these are deleterious? Even in an ID model it’s reasonable to think that some nucleotides are there for structural purposes and can take on any value without being deleterious. So let’s take some numbers from recent studies:

    “our results suggest that between 200 and 300 Mb (6.7%–10.0%) of the human genome is under functional constraint. This estimate was arrived at as follows. First, the amount of human genome under functional constraint is at least 200 Mb, the upper-bound estimate for human and horse made in a divergence regime associated with conservative estimations, according to our simulations. Second, the indicative higher estimate of 300 Mb was obtained by extrapolating the trend for lower-bound estimates involving human … methods for inferring quantities of functional DNA rest upon the hypothesis that in functional sequence most nucleotide changes are detrimental, causing such changes to be purged from the species’ populations, which results in evolutionarily conserved sequence. … the true quantity of functional material in mammalian genomes may be around 300 Mb (10% of the human genome) … these values may underestimate the true level of constraintMassive turnover of functional sequence in human and other mammalian genomes, Genome Research, 2010

    “…all ENCODE classes display evidence of negative selection in these unique-to-primate elements. Furthermore, even with our most conservative estimate of functional elements (8.5% of putative DNA/protein binding regions) and assuming that we have already sampled half of the elements from our transcription factor and cell-type diversity, one would estimate that at a minimum 20% (17% from protein binding and 2.9% protein coding gene exons) of the genome participates in these [primate] specific functions, with the likely figure significantly higher.” An Integrated Encyclopedia of DNA Elements in the Human Genome, Nature, 2012

    So based on phylogeny 10% to 20% are deleterious. So we can calculate a possible range of the del mutation rate:

    10% * 56 = 5.6 del mutations per generation
    20% * 160 = 32 del mutations per generation

    So how many per generation can we tolerate? More than 1.0 under strong selection. If you have a large family chance alone will cause some to get 2 del mutations while others none at all. Keightley and Eyre-Walker give an equation for calculating this:

    It has been estimated that there are as many as 100 new mutations in the genome of each individual human. If even a small fraction of these mutations are deleterious and removed by selection, it is difficult to explain how human populations could have survived. If the effects of mutations act in a multiplicative manner, the proportion of individuals that become selectively eliminated from the population (proportion of `genetic deaths’) is 1-e^-U, where U is the deleterious mutation rate per diploid, so a high rate of deleterious mutation (U>>1) is paradoxical in a species with a low reproductive rate.

    Taking their same probability distribution formula and using U=6, that means 1-e^-6 = 99.752% of the population will have to be selected away each generation for one to survive. That’s one out of 403 chance. Or 806 offspring required to maintain constant population size.

    Ah yes, but what about synergistic epistasis removing deleterious mtuations faster? This is the idea that del. mutations are only slightly bad on their own but when they pair together they’re really bad, so that selection can remove them in clumps and allow for higher U values.

    According to Keightly and Eyre-Walker 2012:

    there is little empirical evidence that synergistic epistasis is more frequent than diminishing returns epistasis

    Note that this paper purports to finally resolve the mutational load paradox. However, as best I can tell their solution is an accounting trick–they ignore absolute fitness and calculate relative fitness instead. Basically that larger families in the current generation will be more fit than smaller families. While ignoring that both are less fit than the starting population.

  64. 64
    scordova says:

    6. Over time, that trait (or traits) will increase in frequency in the population. It will be SELECTED by the environment for survival and reproduction.

    And do you have a point cordova?

    If you think selectively advantage traits will always be selected in favor of those with disadvantaged traits, you’re extremely naïve. Muller’s ratchet basically is one example of such a process where bad traits go on to dominate a population.

    So yes, I have a point: Darwin was wrong.

  65. 65
    JoeCoder says:

    Based on my comment @63 I don’t know of a way out of the mutational load paradox even under artificial selection and sequencing the genome of every offspring to find del. mutations. Moreso, this problem would affect any large-genome species with low reproductive rates–any of our would-be ancestors over the last 300m years–all birds, reptiles, and mammals.

  66. 66
    JoeCoder says:

    Also above, that should be “Or 806 offspring per female required to maintain constant population size.” Important difference 🙂

  67. 67
    scordova says:

    Or 806 offspring required to maintain constant population size.

    Assuming strong selection, so I presume a human mom will actually have to have make more than 806 kids if selection is weak because this presumes the eugencally clean individual will be selected rather that genetically damaged individual who goes around making lots of babies.

    If supposing random chance (like natural accidents or predators or Jodi Arias) happen to wipe out 805 of the kids, the eugenically clean individual has a less than 99% chance of surviving.

    Every human mom will have to be an Octo mom times a hundred and then some. And again, we are still making generous assumptions of strong selection of 100% efficacy which isn’t really seen in nature.

    Thanks for your input and constructive criticism. You’re more versant at this than any one at UD! Thanks for posting.

  68. 68
    JLAfan2001 says:

    JoeCoder@63

    UUHHH, in layman’s terms is that a good thing or a bad thing? Are you saying common descent isn’t possible using those numbers?

  69. 69
    JoeCoder says:

    It’s a bad thing because evolution destroys faster than it creates and this will eventually lead to the extinction of higher animals including us. Bad mutations arrive faster than selection can remove them. Common descent isn’t possible unless a creator continually intervenes to fix things up. So it invalidates an “unbroken natural law” view of evolution, but not common descent with intervention as some ID’ers believe.

    To throw in a source here as evidence that I’m not just blowing smoke: This is from geneticist and atheist to creationist convert John Sanford, whose invention of the gene gun led to the production of most of the world’s GM food:

    Our numerical simulations consistently show that deleterious mutations accumulate linearly across a large portion of the relevant parameter space. This appears to be primarily due to the predominance of nearly-neutral mutations. The problem of mutation accumulation becomes severe when mutation rates are high. Numerical simulations strongly support earlier theoretical and mathematical studies indicating that human mutation accumulation is a serious concern. … Intensified natural selection only marginally slows the accumulation of deleterious mutations.”, Using computer Simulation to Understand Mutation Accumulation Dynamics and Genetic Load, Intl. Conf. Computational Science, 2007

    Mendel’s Accountant, the free/open source program they wrote for the simulation, is peer reviewed and used/cited by other geneticists. You can try it yourself and reproduce their results.

  70. 70
    bornagain77 says:

    JLAfan2001, this video may make it easier for you to understand (it made the issue clearer for me):

    Human evolution or extinction – discussion on acceptable mutation rate per generation (with clips from Dr. John Sanford) – video
    http://www.youtube.com/watch?v=aC_NyFZG7pM

  71. 71
    JoeCoder says:

    @BA77

    I disagree with your video at 4:28. In the third generation, some will have 4 and some will have 2. Some may even revert back 1 due to shuffling of alleles. They say “one mutation per person per generation would doom the human race”. But it has to be higher than an average of 1 for it to be a problem, since the average means that in large families some will have 2 or 3 and others will have 0. To calculate how much is too high, see the 1-e^-U equation in my post @63.

  72. 72
    JoeCoder says:

    it has to be higher than an average of 1 for it to be a problem

    Assuming artificial selection at least, which isn’t realistic.

  73. 73
    scordova says:

    The easiest way to understand some of the problems is the cartoon I provided above. One of John Sanford’s associates that co-authored that paper and software presented at the conference, Walter ReMine, helped me to synthesize the conceptual basis of the cartoon. It shows how natural selection, or any sort of selection will ultimately fail for sufficiently high mutation rates.

    Again, the cartoon is here. It is only 2-minutes long.

    http://youtu.be/SrIDjvpx7w4

    The cartoon approximates the problem of mutation but many of the details simplified out.

    The math that JoeCoder provided deals with sexually reproducing species, but for even moderately bad mutation rates of 5.6 per individual per generation, the cartoon model is a good approximation.

  74. 74
    bornagain77 says:

    scordova and Joecoder thanks for the links and correction. scordova, I don’t know if you’ve heard this interview with Walter ReMine yet, but I saw it this morning and set it aside, due to the tremendous respect I’ve seen for his work on UD, so as to listen to this evening.

    Interview (with) electrical engineer and information expert Walter ReMine to identify the specific illusions offered by evolutionists when they claim to have established ancestors and evolutionary lineage. ReMine’s classic book, The Biotic Message, makes a significant contribution to the anti-evolution literature.
    http://kgov.com/Walter-ReMine

  75. 75
    scordova says:

    But it has to be higher than an average of 1 for it to be a problem, since the average means that in large families some will have 2 or 3 and others will have 0. To calculate how much is too high, see the 1-e^-U equation in my post @63.

    But that assumes strong selection, no? The formula only says how many offspring are needed to create a eugenically fit kid, it doesn’t say much about the survival of that kid.

    Here the problem of gambler’s ruin asserts itself, even with advantage, there is no guarantee the eugenically fit kid will live, and especially since we are talking slightly deleterious mutations.

    Random events can take the fit kid out of the population. This is especially true if we have 99 defective kids and 1 fit kid in a slightly selective advantage. Since this is a slightly selective scenario, it would be fair to say, his chances of survival are around 1%.

    The more mutations and the weaker they are, the stronger the problem of gambler’s ruin becomes.

    That’s how I see it. Is my reasoning incorrect? Thanks in advance.

  76. 76
    JoeCoder says:

    CharlieD wrote:

    In fact I sat in on a seminar today about the genomic convergence of the thylacine and dog

    I would really like more information on this if you can link me. I’m not trying to troll or debate you on this, but am genuinely interested in the wold/thylacine convergence. This is the first time I had ever heard anything about genomic convergence.

  77. 77
    JoeCoder says:

    Yes, it assumes strong/artificial selection. Under realistic parameters a rate of 1.0 is probably still too high. Sorry for the confusion.

  78. 78
    Axel says:

    ‘I want to be like you, Nick. I want to become an expert in Macro-Evolutionary Theory. I want to be able to debate Emeritus Professors and set them straight about their misunderstandings.’

    Nick is still sulking because the God he doesn’t believe in, isn’t as nice as, ihvho, He should be. In fact, he thinks He’s downright nasty.

  79. 79
    JoeCoder says:

    I wish we wouldn’t mock those that disagree with us, even when they start it. Let’s be bigger than that. Besides it wastes space that could be used for fruitful dialog.

  80. 80
    computerist says:

    The Darwinian process is simply too volatile (ie: it can quickly lose even a “well adapted” state, never mind a state which hasn’t yet “adapted” or formed). Take RM’s which is indiscriminate; that is it doesn’t “care” about the current state of the system. The environment in turn acts as another indiscriminate factor with respect to the current state of the system. We find that internal bottom-up (RM) and external top-down (environment) dynamics are acting against the possible net increase in FCSI.

    CharlieD, perhaps you would like to explain how the Darwinian mechanism gets around this?

  81. 81
    JoeCoder says:

    @computerist, what are RM’s?

  82. 82
    computerist says:

    @JoeCoder, RM’s = random mutations

  83. 83
    scordova says:

    regarding this

    1-e^-U

    I said

    The formula only says how many offspring are needed to create a eugenically fit kid, it doesn’t say much about the survival of that kid.

    based on intuition, not any formal derivation.

    I looked on the net and I saw something looking like that in Luria and Delbruck’s work, and then that led me to the Poisson distribution, so it looks like that paper is merely using the Poisson distribution

    http://en.wikipedia.org/wiki/Poisson_distribution

    I used a k-parameter of zero (for zero mutants), and then substituting the mutation rate as the lambda-parameter.

    So let
    k = 0
    lamda = mutation rate = u

    That is:

    percent of population with no mutation =

    P(k,lambda) = P(0,u) = (U^0)(e^-U)/0! = e^-U

    Hence the number of mutated individuals is

    1-e^-U

    http://www.umass.edu/wsp/stati.....n/#classic

  84. 84

    computerist @80:

    Good point.

  85. 85
    JoeCoder says:

    I believe the formula dates back to a 1966 paper by Kimura. That’s what Nachman & Crowell 2000 cite for it (last paragraph). But I haven’t made an attempt to follow the math within Kimura’s paper.

  86. 86
    JoeCoder says:

    But I’m impressed scordova that you derived it on your own. I have a minor in math but I barely remember anything about the Poisson distribution. I wasn’t sure which one it was.

  87. 87
    scordova says:

    JoeCoder

    WHOA!

    Look at equation 1.4 in Kimura’s paper. Thanks a million!!!!

    Under free recombination between mutant genes, i may be distributed with a Poisson distribution,

    fi = e^-lambda lambda^i/i!

    where lambda is the average number of mutant genes per individual before selection

    It’s the same formula in Kimura’s paper, just different symbols!

  88. 88
    scordova says:

    It now totally makes sense that Kimura used the Poissan distribution.

    This is a beautiful illustration:

    The classic Poisson example is the data set of von Bortkiewicz (1898), for the chance of a Prussian cavalryman being killed by the kick of a horse. Ten army corps were observed over 20 years, giving a total of 200 observations of one corps for a one year period. The period or module of observation is thus one year. The total deaths from horse kicks were 122, and the average number of deaths per year per corps was thus 122/200 = 0.61. This is a rate of less than 1. It is also obvious that it is meaningless to ask how many times per year a cavalryman was not killed by the kick of a horse. In any given year, we expect to observe, well, not exactly 0.61 deaths in one corps (that is not possible; deaths occur in modules of 1), but sometimes none, sometimes one, occasionally two, perhaps once in a while three, and (we might intuitively expect) very rarely any more. Here, then, is the classic Poisson situation: a rare event, whose average rate is small, with observations made over many small intervals of time.

    Let us see if our formula gives a close fit for the actual Prussian data, where r = 0.61 is the average number expected per year for the whole sample, and the successive terms of the Poisson formula are the successive probabilities. Remember that our formula for each term in the distribution is:

    p(k) = r*k / (k!)(e*r)(5)

    We may start by asking, given r = 0.61, what is the probability of no deaths by horse kick in a given year (module of observation)? For k = 0, we get by substitution

    p(0) = (0.61)*0 / (0!)(e*0.61) = 1 / (1)(1.8404) = 0.5434

    Given that probability, then over the 200 years observed we should expect to find a total of 108.68 = 109 years with zero deaths. It turns out that 109 is exactly the number of years in which the Prussian data recorded no deaths from horse kicks. The match between expected and actual values is not merely good, it is perfect.

    http://www.umass.edu/wsp/stati.....n/#classic

  89. 89
    JoeCoder says:

    Sorry, I should’ve made it clear in the beginning this was before selection. Or to put it another way, assumes omniscient artificial selection.

  90. 90
    bornagain77 says:

    Okie Dokie scordova, now that you are getting the math of evolution down pat, can you finally give me a ballpark prediction on a burning question I have that Mr. Matzke refused to give me an answer for. Please tell me, using all the power of artificial selection, approximately how many generations it will take me to get a bird-dog. I mean a real bird-dog that flies not one that hunts birds! 🙂

  91. 91
    bornagain77 says:

    sure would make Frisbee in the park a blast! 🙂

  92. 92
    JoeCoder says:

    lol @ ba77

  93. 93
    scordova says:

    As difficult as Kimura’s math is, for high mutation rates, a lot of issues become pretty much moot. For example, in the case of U=5.6, does it really matter that one has moderate selective advantage over his peers through “synergistic epistasis” or that the worst individual is guaranteed to die via “synergistic epistasis”.

    From JoeCoder’s calculation above, if only one individual lived out of 806, a random chance of survival is 0.12%. If the eugenically clean individual is 5 times better than the sick individual to survive, his chance of survival is only in the ball park of .60% (approximately). So let’s be generous and say he has a 1% chance of survival, that’s not very good. The next generation will thus have a 99% chance of being defective, and that is on the generous assumption that human females can give birth to 806 children!

    I have friends who have genetic mutations that are slightly deleterious (allergies, myopia, etc.) who have children, and sadly some very fine healthy people who died early due to car accidents, etc. If mutation rates are high enough relative to birth rates, it really doesn’t matter how advantaged one individual may be over another if the selective advantage is moderate.

    The discussion has helped justify extending the cartoon model of asexually reproducing species to sexually reproducing species in principle.

    In other words, it was quite legitimate to be putting red dots (mutations) in all the gingerbread kids. One can’t run away from the concept conveyed by the cartoon because it is now backed up with the math.

    Dawkins weasel has now been defeated by ReMine’s gingerbread kids. 🙂

    PS
    If someone wants to volunteer to redo the cartoon (to make it a little more entertaining) that would be great. Hint hint!

  94. 94
    Mung says:

    Eric, UPB,

    thanks mates!

    lack of response from nick noted.

    Yes, the search for truth never ends.

    I’d just love to know what the “truth” was that Nick discovered in his “macro-evolutionary” studies and why he is so unwilling to share it with the rest of us?

    I guess I am just naturally skeptical of those who claim to know truth but are not willing to share it or how they arrived at it. Sounds cultish, yes?

  95. 95
    Mung says:

    Nick Matzke:

    Ask Joe Felsenstein, he’ll tell you the same thing. Better yet, read his book, “Inferring Phylogenies”. I read it for my qualifying exam. Why should I take you seriously when you have basic misunderstandings that would get you failed in phylogenetics 101?

    OMG!

    That must be one of “the golden books of knowledge” I’ve been asking you to reveal to us ignorant “creationists.”

    I can buy this book and learn all about the truth of your alleged field of “macro-evolutionary theory?”

    But it’s a bit dated, isn’t it?

  96. 96
    Mung says:

    Is Nick still pretending that he can educate James Tour?

    What a laugh.

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