Summations Only

After reading TheArtists recent topic proposal I think that an explanation of the mainstream pro-evolution position is needed. I will try to be uncontroversial in that but if anyone on the evolution side objects to this characterisation (which is not intended to include fringe positions) please speak up.1) Evolution is not an all-encompassing belief system, it is a scientific theory with a limited scope. In particular, it is not a source of moral or ethical values. There are many Christians on the pro-evolution side.2) Science is the best way to learn about and understand the physical universe, both how it operates and its history. A well-established scientific theory should be accepted as a good approximation of the truth. (And no more than that - nobody on the mainstream pro-evolution side would claim that the current theory was absolutely correct in every little detail)3) Evolution is a well-established scientific theory (this should be uncontroversial to anyone, since it is a clear fact)

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Natural selection is totally relevant. Natural selection must do something very specific in order to improve the probability that a beneficial mutation will occur

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Natural selection does not improve the probability of beneficial mutations occurring. If you think that evolutionary theory claims otherwise you really need to take a step back and apologise for running through this silly routine of yours.

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If natural selection is not altering the probabilities that a particular mutation will occur at a particular site in a genome, then what do you think that natural selection does?

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Natural selection increases the probability that a beneficial mutation will be retained (and spread) in a population and the probability that deleterious mutations will be lost.

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I have nothing to apologise for here. You have something to apologise for by not correctly describing how rmns works.

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You have been extremely evasive about your argument and now it turns out that you have made a basic error. And I am certainly not going to apologise for disagreeing with your erroneous opinion.

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Ok, so those members with a beneficial mutation will increase in number. How large does that lineage have to be in order for there to be a reasonable probability of another beneficial mutation occurring on a member of that lineage?

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Obviously that depends on the number of beneficial mutations available. But bear in mind that bacteria have very large populations, very short generation times and can share genetic material quite freely.

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My argument is not complicated but it is not trivial. I'm trying to teach you something about rmns that you have missed. Your above quote is taking you on the correct path to understand this phenomenon. If you think I have made an error, feel free to post my quote.

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At this point it looks more like an attempt to get other people to do the work that you have not (and assuming the result). Anyway, your assertion that natural selection "must" increase the probability of a beneficial mutation occurring is an obvious error.

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If you are going to consider the mathematics of rmns, you have to consider the size of lineages in populations, not the entire population size when computing probabilities.

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That is obviously incorrect. It is not true when you are considering the probability of a mutation appearing in a population, nor is it true when there is exchange of genetic material between lineages.

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I assure you that I have already done the mathematics for rmns.

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I rather doubt that.However, your private probability argument is completely irrelevant to your assertion that the theory of evolution is nor a well established theory. so that claim remains completely unsupported.

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If you want to peer review my work, you had better have a good understanding of probability theory.

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I suspect that if you honestly describe your argument a decent understanding of evolutionary theory will be sufficient to see the error. Nevertheless I believe that my understanding of probability theory will be adequate.

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Here's the short answer why the theory of evolution is not true, it's the multiplication rule of probabilities which makes the theory of evolution not true.

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Perhaps you can explain the model of evolution that you use to make those calculations. Because without that all you have is an assertion.

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Do you think that every mutation is beneficial? If lineages are exchanging genetic material, why can HIV evolve resistance efficiently to combination therapy?

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The first question is an obvious non-sequitur- although for the record most mutations are neutral.The second question is foolish. Saying that another factor must be considered in the general case obviously does not mean that it will make enough of a difference in a particular case.And when do you intend to start supporting your claim that the theory of evolution is not well-established ?

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My argument is totally public and shows both mathematically and empirically why the theory of evolution is not true.

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Really ? Has it been published in a peer-reviewed journal ? Has it been cited by other papers ? Do you have any reason to believe that it is widely accepted in the scientific community? Even if your assertion were true (and it doesn't look at all likely) it would not be sufficient to support your assertion.

While Kleinman has yet to reveal his argument we have some clues to the way it goes - and I can see some quite serious problems.From the side of probability theory - aside from the difficulty of calculating the probability of feathers evolving - there is the problem that that is very likely the wrong probability.Sequences of random events naturally have low probabilities. It is trivial to generate incredibly low probability sequences just by tossing a coin. The probability of the sequence is unimportant, it is necessary to extract some special feature, and - unless there is a justification for choosing that particular feature - it is necessary to also include the possibility of getting other, equally special features.To take a simple example, suppose you toss a coin and it comes up Heads each time. Unless there is some reason that Heads is more significant than Tails, the relevant probability would be the probability of getting the same result on each toss - which is twice the probability of getting all Heads.Now, there is no good objective way of choosing which features of the sequence count as "special" in more complicated cases, but it seems rather unlikely that the producing feathers rather than some other adaption is really special enough.From the side of evolutionary theory, there is also a problem. Combination therapy for HIV works by confronting the virus with an array of threats which must be overcome independently. The fact that the drugs are killing the virus is a very important part of the reason that the virus cannot adapt to counter them all. From the standpoint of evolutionary theory it is hardly surprising that it does work - a sufficiently large array of lethal threats should be enough to drive a population to extinction.But that is a rather atypical situation, especially when we are considering long timespans. Normal evolution has considerable scope for neutral drift (at the level of gene sequences it is the dominant form of change). Selection may be positive rather than strongly negative - favouring new traits rather than eliminating those without them. Even if we consider antibiotic use - which is very similar - the existence of multiply-resistant bacteria should alert us to the fact that combination therapy is a special case and is designed to be a special case.Certainly we cannot use combination therapy against HIV as a model for evolution in general. Even if it were only an example of the application of probability to evolution it is poor - because survival is one of the few outcomes that could be classed as "special" enough that we can use the full probability.So, Kleinman's argument is not looking at all promising which makes the delay in revealing it quite annoying - pure time wasting.

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PaulK, the reason there is no rational way that feathers can evolve from scales by rmns is there are too many genetic loci which must be transformed simultaneously

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Are there ? How do you know that ? And I note that none of the three papers you list addresses the topic.

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Every evolutionary step (beneficial mutation) must amplify in order to improve the probability of another beneficial mutation occurring on some member of the lineage with that particular mutation. rmns only works efficiently when a single selection pressure targets a single gene at a time

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That is really only true in cases of "hard selection". As Haldane showed, hard selection has a limit on the speed of selection, which cannot be overcome by selecting in parallel. Soft selection - and neutral drift - are not subject to this limit.And that is why relying on antibiotic resistance as a paradigm is inadequate. You only deal with hard selection - which is not the most efficient. As I recall rapid evolution can occur from relaxing selection.So, nothing you have said gives me any confidence that you have answered either of the concerns I raised in Message 95. Indeed, my concern that the argument relied on attempting to apply the atypical situation of antibiotic resistance to all evolution is reinforced.

Perhaps a simpler take on the issues.Hard selection is the fastest way to achieve fixation of a single allele. However, because it relies on a declining population - and the rate of decline is directly tied to the strength of selection - it does not work any faster in parallel, nor is it sustainable.Soft selection is slower but it does not rely on a declining population. So it is sustainable and it can work in parallel. Soft selection, then, can be more efficient than hard selection because it can work sustainably and in parallel.

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The theory of evolution doesn't explain anything. It doesn't explain how rmns works, it doesn't explain how recombination works. It's a theory which takes the concept of common descent and says every living thing we see today came from some replicator from the primordial soup. This is a belief system made up by someone who doesn't understand the consequences of the multiplication rule of probabilities.

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This is hardly the sort of thing we can expect from someone who really had a scientific disproof of the theory of evolution. Universal common descent is not even a very important part of the theory - and it would be dropped if the evidence went against it, with very little effect on evolutionary theory. It is not even what I would expect from somebody who understands how to apply probability theory to long sequences of events.

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Fixation is neither necessary nor sufficient for rmns to work. This notion of fixation is based on an erroneous application of a physical principle. Do you think that natural selection is a conservative phenomenon?

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What a bizarre thing to say! Would you not agree that the alleles to create feathers are fixed in every bird population ? And obviously in at least many other dinosaur populations ? It is rather important to evolution that fixation does occur, and natural selection is one of the mechanisms by which it does occur.And I will add that frequency could be considered a conserved quantity for the simple reason that the sum of the frequencies (of alleles of a gene) must be 1. As you must surely know, through the connection to probability theory at least.Spouting nonsense does not help your case.Edited by PaulK, : No reason given.

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However, once mutation A occurs, that member becomes the progenitor for a new lineage which are candidates for mutation B

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As I stated earlier it is often not the case that two beneficial mutations have to occur in the same lineage. Therefore any equation that assumes otherwise cannot represent the general case as you claim.

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The mathematics I'm presenting here is the mathematics of rmns by common descent. How do you think replicators accumulate the mutations necessary to adapt to selection pressures by rmns?

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Sexually reproducing creatures - like dinosaurs - receive genetic material from both parents. Thus it is possible to inherit advantageous mutations from both parents.