Tuesday, April 15, 2014

Branko Kozulic has questions about fixation

Branko Kozulic is trying to understand how so many neutral alleles could be fixed in the human and chimpanzee populations (species) over the past five million years. He's not happy that Vincent Torley conceded the point that it was possible.

There are two relevant posts on Uncommon Descent: Branko Kozulic Responds and Branko Kozulic responds to Professor Moran, Part II.

I'll respond to the second one since it is more specific. He begins with ...
The idea of 100 mutations being fixed in the human population in each generation over a period of 185,000 generations, or 5,000,000 years, has always appeared intuitively unrealistic to me, possibly because I am primarily a practical scientist.
Many things in science seem counter-intuitive. That's why you have to make an effort to understand the science. In this case, you've been arguing against evolution for many years so you've had plenty of opportunity to get beyond intuition.
My first question was: How many mutations are fixed now, in my generation? I am pretty sure that the answer is zero. Fixation means, we agree, that all individuals in the human population acquire the same mutation in a generation, or, equivalently, that the other allele is completely lost. If so, then the question logically follows: When did this change from 100 to zero fixed mutations per generation take place? Alternatively, is there perhaps something wrong with my initial assumptions?
Your definition of fixation leaves a lot to be desired. I do not agree with it.

I'll use the definition on Wikipedia [Fixation (population genetics)].
In population genetics, fixation is the change in a gene pool from a situation where there exists at least two variants of a particular gene (allele) to a situation where only one of the alleles remains.[1] The term can refer to a gene in general or particular nucleotide position in the DNA chain (locus).

In the process of substitution, a previously non-existent allele arises by mutation and undergoes fixation by spreading through the population by random genetic drift and/or positive selection. Once the frequency of the allele is at 100%, i.e. being the only gene variant present in any member, it is said to be "fixed" in the population.
It wasn't very hard to find this definition. In future, I suggest you check Wikipedia when you are tempted to make up definitions. It will save time.

The situation with humans gets a bit complicated because the population has expanded so much in the past 100,000 years. If we think about the simple situation in the past when the effective population size was about 10,000, there were about 100 alleles fixed (and lost) per generation. In each generation there would have been a very small number of individuals who carried an ancient allele and a very large number (99.9%) who carried an allele that first appeared one million years earlier. By chance, the individuals carrying the ancient allele failed to pass it on to their offspring. The result is that the other allele becomes fixed in the population (100%). This happens, on average, 100 times in each generation.
After wandering around, a solution entered my mind while reading the following sentence in Professor Moran’s reply: "In my calculation, the values of Ne are irrelevant, so any value will work equally well, as long as you realize that you are starting with an ancestral population containing existing variation." Here, the key phrase is "containing existing variation." That is the essential assumption. What it means in reality is this: throughout the whole period leading up to the fixation – i.e. in the case we are considering, a population of 10,000 individuals over 40,000 (=4N) generations (which, when multiplied by 20 years/generation, equals 800,000 years) – a group of individuals may split off from the population, but no newcomers are allowed to enter it – that is, the population must remain closed in terms of mating. Here, a newcomer is defined as any individual from a group that had lived separately, say on an adjacent island or across a mountain, for some generations. Whenever a newcomer joins the population, the fixation process is broken, because migrants bring with them new variation that did not exist initially. Migration is a powerful force acting against genetic divergence among sub-populations (Hartl & Clark, Principles of Population Genetics, pp. 295-309).
In my example we were dealing with the entire species and not subpopulations.

There has to be some gene flow between subpopulations otherwise they become equivalent to species (in the strict sense of the biological species concept). So, you are correct. There will be migrants and subpopulations. What this means is that the actual path to fixation (or elimination) gets complicated as it becomes fixed in one subpopulation then spreads to another. However, that doesn't affect the overall averages. There will still be about 100 "new" alleles fixed in the species per generation.
Herein lies the weak point in Professor Moran’s calculations. Based on our knowledge of human history and behavior, we know that groups of people grow in numbers, split in two and merge, repeatedly. This commonly known fact has to be ruled out, in order to allow for the fixation of 100 mutations per generation. And now we can see that the value of Ne will have a major impact: a large Ne makes it more likely that a newcomer will join the population, and also that a group will split away from it and then re-enter it (in part) later on.
Like I said earlier, the math gets more complicated with subpopulations but I think you can see that the sizes of the individual subpopulations don't have a significant effect on the big picture. They cancel out for the subpopulations just as they do for the species as a whole.
In view of the above, I believe I am entitled to continue rejecting the feasibility of 22,000,000 mutations being fixed in the human population over a period of 5,000,000 years, or 100 mutations each generation.
You are entitled to reject all of population genetics for all I care. What you are NOT entitled to do is pretend that you have refuted all of the textbooks by just thinking about subpopulations and migrants. Do you honestly think that no population geneticist has ever thought about these things—and dealt with them— in the past 100 years?
Here it is appropriate to mention a reservation relating to the exact number of fixed differences between the human and chimp genomes that has been expressed by Professor Felsenstein: the actual number might be lower than 22,000,000.
We don't know the exact number but 22 million seems like a pretty good approximation in order to illustrate the point.

I don't think Joe Felsenstein really questions this value for the species as a whole. What he points out is that you don't really need to emphasize fixed alleles in order to show that the population genetics equations work for humans and chimpanzees. The equations, and our understanding of evolution, work even if you just compare the differences between any randomly chosen human and a randomly chosen chimpanzee.

The entire field of molecular evolution is based on the idea that a lot of evolution occurs by fixation of nearly neutral alleles by random genetic drift. It's the reason why there's an approximate molecular clock and it's the reason why we can construct phylogenetic trees based on sequence comparisons. There's a massive amount of data supporting the basic concepts of population genetics. This is not just something that scientists made up to confuse creationists with counter-intuitive ideas.

We can quibble about the details, as you are about to see in the comments, but the fundamental principles are sound. It's about time that creationists start to accept population genetics and move on to other complaints. Why not start by reading Nature's Destiny by Intelligent Design Creationist, Michael Denton? He has a pretty good description on page 277 where he says ...
Another example is the very great similarity of the DNA sequences in the human and chimpanzee genomes. In fact, extensive comparisons of long sections of the DNA of man and chimpanzee show that the differences are extraordinarily trivial. Human and chimpanzee sequences differ on average at only one base per hundred. As far as we can tell, not only are the DNA sequences virtually identical, but every gene identified in the human genome has its counterpart in the chimpanzee genome. So all the morphological differences between man and chimpanzee, involving the form and relative shape of the limbs, the genital organs, sperm morphology etc., and all the mental differences are generated from DNA sequences which are virtually identical. The distance between man and chimp which seems so significant at a gross morphological level is trivial in DNA sequence space. In fact, the differences between the DNA of man and chimp can be accounted for by simple well-known mutational processes which are occurring all the time in nature at present.

HTH HAND


142 comments :

  1. Apart from prejudice, the problem appears to be that he does not understand that many alleles that arose a very long time ago will in this generation be very close to fixation already, and that those are the ones that get fixated and not those that still have to spread from, say, Africa to Japan.

    I am not really a population geneticist but I would assume that the rate of fixation would slow down in a massively expanding population such as ours in the last few hundred years, but that it would speed up to the same degree once the population contracts again in the future, evening out in the long run average?

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    1. I'm no population geneticist either. But I think you're broadly correct. When a population expands, there is a lag while Ne expands - the extra mutations produced by the larger population take time to establish, and the variation from its prior Ne has a much bigger field to colonise. Eventually, at a new steady state, Ne would top out at a level appropriate to that census size. Reduction, however, reduces Ne immediately. If you plotted census size and Ne on the same graph, smooth fluctuations in census size would produce a 'sawtooth' pattern in Ne, as it crawled in the direction of census size on expansions but dropped suddenly on contractions. This is additional to the geographic effect.

      I think people sometimes misinterpret the now-classical population-size-independence of neutral alleles. It doesn't mean that population size is irrelevant. When a population has had time to equilibrate at a particular size, neutral alleles will fix at the mutation rate regardless of that size. But when changing size, this no longer holds. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3374318/ (I present the link for those up to following the maths - I can barely handle 4Ne myself!).

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    2. Yes, that is more or less what I was thinking. The contraction side is relatively straightforward - if you kill all members of a species except one you have thereby immediately fixed all alleles that this last individual is homozygous for. Extending from that extreme scenario to less extreme ones it seems obvious that our rate of fixation would be above average for the next five hundred years if over that time we contracted down to, say, only one billion people.

      Conversely, I would assume that individual alleles are less likely to get lost as long as they have an ever expanding number of individuals to survive in, so that an expanding population such as we had over the last few thousand years (and especially the last two hundred) would have a below average rate of allele fixation.

      However, because no population can expand infinitely and the only populations that contract infinitely go extinct, it would have to even out in the end.

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    3. We also have to wonder what fixation means if the population size is near to (or greater than) 1/mu. Pretty much every site in every generation must be polymorphic, as pretty much every site undergoes multiple mutations in the population.

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    4. (PS John you can type Greek mu by typing μ).

      True, you won't get fixation in that case, but if you are using the mutation rate per base, then effective N would have to be about 10^8. Which can be reasonable for small organisms. For the case of comparing the reference sequences of two species, you don't really need to calculate chances of fixation anyway.

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    5. So you would agree that there probably (under the definition we happen to be using at the moment) are no fixed alleles in the current human population? (Well, there doubtless are, in for example the second positions of many sites in many exons. But those are rare exceptions.) μ?

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    6. (Yes, you got the Greek μ right!) I seem to recall that if 4Nμ < 1, that the diffusion process approximating the drift-with-mutation process can actually reach the boundary. When this condition does not hold, there are enough new mutations in the population that it never hits the boundary.

      For humans or chimps N is very much smaller than the value of μ for one site, so there would have been many sites actually fixed. For modern humans N is large enough that probably few sites are fixed.

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  2. You are missing the real whopper in that. Sure, changing the population structure doesn't affect substitution rates. But in Kozulic argument there's the notion that mean times to fixation would increase if you had subpopulations with reduced gene flow. That's basically stating that the effective population size goes up with more inbreeding, rather than down.

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    1. Sorry to "pull rank" but I am a professional population geneticist. Mean times to fixation will increase with population subdivision. There is some ambiguity whether we should use the notion of effective population size to describe this. But if we do, yes, some overall effective population size will increase with subdivision.

      For technical details see pages 263 - 280 of my free downloadable book Theoretical Evolutionary Genetics.

      Branko Kozulić was not telling a "whopper" -- he just missed the fact that population structure would also increase the amount of neutral genetic variation that would build up in those populations, enough to cancel out the effect of it taking longer to fix any one variant.

      And when we look at the reference sequences of human and chimpanzee, the amount of difference between those that is expected from neutral mutation is independent of any issues of fixation. It depends on the time since the species separated, plus the time to coalescence of two copies in the ancestor species, one ancestral to each reference sequence.

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    2. Hmm, that section addresses a different question though, the time to fixation of a novel mutant allele in a subdivided population is conditioned on the novel allele getting fixed. I have to admit I MC this and might have fallen prey to heavy tails.

      My population genetics is certainly getting rusty.

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    3. That section calculates time to fixation once the variants are segregating in the populations. But I don't see that it conditions on fixation, since in those sections "fixation time" means time to fixation or loss, i.e. time until the locus is fixed for one allele or another. See page 271 where we cailculate in terms of the rate of loss of heterozygosity between and within populations.

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    4. Precisely. I was thinking of the conditional expected time to fixation and it's not conditioned in that section. The mean time to fixation or loss is a weighted average of the mean time to fixation and the mean time to loss and this weighting heavily favors the loss case. I'll try to work out the conditional case when I have some more time on my hands.

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  3. The abbreviated answer: Kuzolic is wrong because math.

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  4. Some quibbles:

    There has to be some gene flow between subpopulations otherwise they become equivalent to species (in the strict sense of the biological species concept).

    I don't think you mean that. Biological species require that the (relative) absence of gene flow be due to genetically-based isolating mechanisms. If isolation is strictly geographic, we merely have subspecies. Now, if you want to talk about phylogenetic species, your claim would be approximately correct given enough time for private alleles to arise.

    The entire field of molecular evolution is based on the idea that a lot of evolution occurs by fixation of nearly neutral alleles by random genetic drift.

    You say "nearly neutral" a lot. But in nearly neutral evolution, Ne matters a lot. It's only in strictly neutral evolution that it doesn't matter.

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    1. What I meant was that the only time you can be sure there's no gene flow between populations is when they become true biological species.

      I use "nearly neutral" because when I'm talking about the mutations that have become fixed in real populations (e.g. humans and chimps) I can't assume that they were all neutral in the strict sense of the word. If I said "neutral" all the time someone would surely try to correct me in the comments. Believe it or not, there are quite a few Sandwalk readers who enjoy that kind of nitpicking. :-)

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    2. What I meant was that the only time you can be sure there's no gene flow between populations is when they become true biological species.

      Sorry, but if that's what you meant, it's wrong. We can be sure there's no gene flow if no individuals ever come into contact, as for example in populations on isolated islands or mountain peaks. And of course separate biological species can have gene flow between them, so that's really not a way of being sure.

      I can't assume that they were all neutral in the strict sense of the word.

      My point is that you can't talk about nearly neutral evolution and simultaneously claim that Ne is irrelevant.

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    3. In the right hands, nitpicking becomes an art form. It's marvelous to behold. :-)

      You are setting yourself up to be a reviewer of my book on Evolution by Accident, if I ever get around to finishing it.

      One of the reasons why Dawkins is such a successful writer is that he deals in generalities and avoids exceptions and qualifying explanations. One of the reason why Gould is harder to read is than he doesn't.

      I find it hard to write like Dawkins and whenever I try to do so, there are always people like you to remind me that I've over-simplified.

      And of course separate biological species can have gene flow between them ...

      I thought that the very definition of Biological Species (as in Biological Species Concept) was that there cannot be any gene flow between them? Or are you referring to another, more common, definition of biological species?

      Paging John Wilkins ....

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    4. Any reasonable definition of species should allow some gene flow, albeit at a very low rate. The question is: Given the maximum possible rate of gene flow (i.e. ignoring extrinsic factors), are they expected to diverge.

      The ISC still uses the BSC to define start and endpoints, which means that molecular clocks have a systematic error in that they date divergence, which usually precedes speciation (in the same way the fossil record has a systematic error towards younger ages - the oldest fossil representative is usually preceded by speciation).

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    5. Larry, I can see that you don't deal with species much. Yes, the commonly understood version of the BSC, at least among systematists and anyone who has to deal with species concepts, does allow for some gene flow. Again, as I generally do, I will point out that if no gene flow were allowed, there would be only one biological species in the family Anatidae. And nobody wants that.

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    6. That's really interesting. I was under the impression that the Biological Species Concept referred specifically to species that cannot interbreed. A quick scan of the internet indicates that this is a very common definition of BSC dating back to Ernst Mayr (and earlier).

      I'm aware of the fact that it's a theoretical ideal that's not very practical in the real world but I didn't know that the definition had been revised. I thought that systematicists used some of other 27(?) species concepts in their everyday work.

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    7. Mayr didn't phrase it that way. He said "...interbreeding or potentially interbreeding populations...". That doesn't quite say that there must be zero introgression. And in fact Mayr at one point worked on ducks, and despite the fact that he was well aware of hybridization did not merge them all into a single species. Clearly even Mayr thought there was some give in the definition.

      So is it your fallback position that nobody actually uses the BSC? I would agree that nobody does if we accept your version as the real one. But most systematists at least claim to use the BSC, even though they allow for hybridization. Consider, for example, all the work on hybrid zones between species. Under your BSC, that was a nonsense sentence.

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    8. "I thought that systematicists used some of other 27(?) species concepts in their everyday work."

      Are all of them species concepts though? Arguably a lot of the "species concepts" are better refered to as type concepts. Generally we can take an approach that defines sets of organisms through some dynamical properties - in that case there is uncertaincy on which organisms belong to a particular set - or we can define a set of organisms through some diagnostic criteria - in which case there is uncertaincy about the dynamics.
      Some authors would reserve the term species for the former and assign type to the latter and I agree with that position. The minimal position is that there should be separate terms.
      Now type concepts are used, because they allow other people to identify what you are working on. If somebody works on E.coli, somebody else can figure out what that is. That doesn't imply that E.coli meets the criteria of a species concept. Generally a taxonomic paper will describe types and then present the hypothesis that these are also species. The former isn't testable - there's nothing that would falsify a type, but species status is. And hypotheses about the species status of some set of organisms generally are hypotheses about the species status of a particular type.

      The language convention has been somewhat popular in German literature and isn't really doing a lot of work in the english literature. But it is a useful convention and an awful lot of the discussions about species concepts get very clear once you adopt it.

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    9. Some thoughts:

      John is right about the BSC. Even in Coyne and Orr's recent Speciation book, they modify the Mayrian definition to include some introgression. Systematists have an operational concept of a "good species" which is a meld of morphological, genetic, reproductive and ecological conceptions, and these things (if they are things at all) are allowed to share genes via hybridisation. I was at a conference on hybridisation in primates, held in Göttingen a while back, and every specialist (in macaques, baboons, etc.) described repeated hybrids that were interfertile with one of the parental species.

      The BSC is not an operational definition, by the way. Almost no studies are done on introgressive breeding before identifying a species. This was an early critique of Mayr's definition by none other than Paul Ehrlich.

      As to "type concepts", I think this is an artificial distinction. I do think there are some "pure" notions of species (phylogenetic, genetic, ecological, etc.) and most "definitions" are a mix of criteria from these, but the notion that "species" applies solely to a class of multicellular sexual organisms is not now nor ever has been the standard rule. Instead, it is because people who describe species dealing with multicellular sexual organisms tend to overgeneralise from their own experience. Bacteriologists have troubles defining what counts as a species, to be sure, but nevertheless, they describe them. Likewise, some species (e.g., of lichens) are obligate or even facultative mutualisms between vastly different organisms.

      Finally I note that there is only one "concept": species. These are not concepts of species, but criteriological or theoretical *definitions* of species. A species has always been a sort of organism in which progeny resemble parents more than they resemble organisms from other sorts of organisms. All the rest is argument over preferred criteria for delimitation.

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    10. I take issue with the idea that the BSC isn't operational. At least, it can be. If there's any sympatry at all you can investigate gene flow, and this happens often enough. You can investigate selection against hybrids, and this too happens often enough. And if you know the nature of the isolating mechanism (which you frequently can in some taxa, e.g. birds) you can test whether that mechanism is operating in the present case, and this too happens often enough.

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    11. @John Wilkins,

      Thanks, but now I'm even more confused. If I want to refer to the idealized definition of species as populations that cannot interbreed, as I wanted to do in this post, is there a term I can use? Apparently the old term "Biological Species Concept" has been modified. It's a shame that most internet sites are using it in the old way but I've seen lots of examples where bad definitions are widely used.

      I hope everyone reading this understands that I was not trying to pretend that real species were defined that way. I've written many posts about the problems of defining species and how scientists in different fields use different ways of defining a species.

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    12. @John S. Wilkins:
      Well, your post does provide ample reason to make the distinction between type and species.
      Using potential gene flow as a definition is universal - you can easily apply this to bacteria (you've got different mechanisms of gene flow, but that's not something the definition can't handle). And it might turn out that some types consist of multiple species or that a species contains multiple types. In the extreme cases, most of non-multicellular life is one species, or conversely you get species consisting of a single individual. Neither of these is a problem for the concept.

      In the rest of your post you define something that definitely falls under the type label and is in fact close to the "cynical species concept": A species is whatever a competent taxonomist declares to be a species (in the common case of multiple opinions, pick a side). Types are useful, arguably even indispensable. But we do need a species concept to adequately adress questions about speciation and even to give a solid definition of macroevolution. You try to do these things with types and you end up with fuzzy nonsense.
      A chemist picks up a bottle labeled "Water". The content has a density of 0.789 g/cm³ and it burns. The chemist should conclude that the bottle contains ethanol and was mislabeled. Instead he publishes a paper saying that water sometimes has the property of burning and can have lower densities. Spectral analysis also shows that water sometimes contains carbon. In short: There's something wrong with the usual concepts of water...

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  5. Branko Kozulić is correct that the number of fixed differences between human and chimpanzee might be less than the 22 million figure. The 22 million figure is not all fixed differences, it is simply the difference between the reference genomes.

    But saying that they might all not be fixed does not cast Larry Moran's original calculation into question. Larry used inferred mutation rates and numbers of generations of divergence and showed that 22 million differences between the reference genomes was a plausible figure. Actually, taking into account also the coalescence times (in effect the genetic variability within the human/chimp ancestor at the time of the speciation), we might expect more than 22 million on the assumption of neutrality -- the fact that we get 22 million might mean that some of the observed new mutations were disadvantageous (or that other estimates in the calculation are a bit off).

    Though Branko Kozulić may refuse to accept it, there is not sign of some impossibility of the figure of 22 million differences in the reference sequences, based on the population genetics.

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    1. Typo: " .. there is no sign of some impossibility ..."

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    2. Typo: "...Though Branko "Numerous Patents" Kozulić may refuse to accept it..."

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  6. What is this alleged science behind neutral allele fixation? Has this been observed? Has it been tested? That is with respect to unguided evolution?

    The point being is my bet is it is all post hoc and ad hoc reasoning.

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    1. And all we have left of Tyrannosaurus rex is fossils...hardly evidence of living T. rex.

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    2. And what about random segregation of genes? Not directly observed by Gregor Mendel and those other folks!! And electrons? Shame on all those physicists 100 years ago for imagining them without actually observing them! And gravity acting at a distance? Isaac Newton was widely criticized for assuming it without a mechanism for it to act across space. And Dalton? Why did he assume all those atoms when you could not see a single one?

      Oh, how the world eagerly awaits Joe G's reformulation of physics, chemistry, and biology without all those purely-ad-hoc, post-hoc equations.

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    3. LoL! @ Joe Felsenstein- No evidence then Joe, is that right?

      We can actually test the atomic theory and for electrons, Joe.

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    4. If we didn't observe it, it's not science ... not the strongest card for a proponent of Detectable ID.

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    5. Design is observed. Unguided evolution has never been observed to produce anything beyond disease and deformities.

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    6. @JoeG The mechanisms of random genetic drift are (1) random Mendelian segregation, (2) random deaths of individuals, (3) random variation from individual to individual in numbers of births. Guess we've never seem those!

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    7. I guess those who cover their eyes won't see them.

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    8. OMG!!! Joe F still has not evidence...neither anybody else... Speculation without evidence is a new name for population genetics "science"... LMAO ;)

      Way to go boys...That's the way to go...;)

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    9. Mutations are an observed fact. Genetic drift is an observed fact. Natural selection is an observed fact.

      But according to Joe "so nuts there's a thread on panda's thumb just dedicated to stupid shit he says" G, we should now conclude it's the work of an invisible designer who designs with an unknown method, at unknown times, trying to achieve unknown results, who has survived for billions of years, been unaffected by mass extinctions, which can reach into the genomes of living organisms and cause individual mutations, know what effects they will have millions of years and generations into the future and has been doing so for the entire history of life.

      And then to top it all off, the observed mechanisms mentioned he now declares are erected ad-hoc to explain genetic patterns.

      And that, my dear Joe, is why you have that thread on panda's thumb. When we need a good laugh at the inanity of IDiot acolytes, you're the default go-to for quotes. Between you, Quest and Robert Byers I cannot think of a better advertisement for the brainlessness of the average IDcreationist.

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    10. Strange that the thread you mention doesn't have anything that supports unguided evolution- no models, no math, no research, nothing.

      And that makes me very happy.

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    11. Joe G Design is observed.

      So what? We observe X therefore it is the cause of Y? Think again, grasshopper.

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    12. Yes design always means there was a designer- always. OTOH you still cannot model unguided evolution. I take it that bothers you

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    13. Yes design always means there was a designer- always.

      Who said anything about a designer? We observe design therefore everything was designed? That's a seriously dumb argument. But you knew that already.

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    14. joey g says: "Design is observed."

      Hey joey, are you claiming that you or someone else has observed the 'intelligent designer' (allah in your case) designing life and evolution? You expect and demand that all steps/processes/events/changes/mutations/origins, etc., etc., etc., of life and evolution MUST be observed AS they were/are happening in order to verify that 'intelligent design' was/is not involved.

      So, joey, since you're making the claim that 'intelligent design' was/is involved, you should provide what you expect and demand from 'evos'. Can you do that, joey? Can you show that you or someone else has actually observed the 'intelligent designer' (allah in your case) designing all (or any) of the steps/processes/events/changes/mutations/origins, etc., etc., etc., of life and evolution as they were/are happening?

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    15. We observe the DESIGN, moron. And YOURS is the position that sez it has an incremental mechanism. Don't blame me because no one can demonstrate it.

      It's as if you are proud to be an ass

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    16. Allan Miller:
      Who said anything about a designer?

      YOU asked about a cause.

      We observe design therefore everything was designed?

      What?

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    17. "And Dalton? Why did he assume all those atoms when you could not see a single one?"

      Just a slight nitpick - you can see individual atoms within magneto-optic traps (MOTs). Usually the light intensity is too low and there are a lot of other atoms within the limits of spatial resolution, so you don't see an isolated one. But in a MOT light intensity is high and particle densities are so low, that you often get to see a single atom (occasionally more than one gets trapped, so you have to check that).

      I've been to a lab, where they have a MOT and got to see a single atom with the naked eye. That is rather impressive.

      "Gravity acting at a distance". Yea, that's been gone for a while now, hasn't it? Relativity doesn't have it (and maybe that's the problem with relativity).

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    18. "Design is observed."

      This is a standard (and pathetic) argument via strained analogy so common in IDiots. The 'design' Gallien is referring to is HUMAN deign. An honest and intelligent IDiot would realize that human design is not the same thing as their mythical, mystical Ultimate Designer's (wink wink Jesus) design. These fools actually seem to think analogies are evidence.

      As Larry says - no wonder we call them IDiots.

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    19. LoL! Sam your position doesn't have any arguments. It is pure dogma. And the design I am referring to is biological, chemical and cosmological.

      No wonder we call you asshole cowards.

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    20. @Simon Gunkel: Yes, but Dalton couldn't see the atoms. Nevertheless using them was very helpful.

      As for JoeG's endless attempts to divert the thread (which was originally discussing the process of substitution and fixation of neutral alleles) while simultaneously lecturing people that they should stay on topic, if people want to really see what he is like see his own blog Intelligent Reasoning, easily found by searching on that phrase. Here he is a pale shadow of his actual self.

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    21. YOU asked about a cause.

      I wasn't asking about the designer, but the design.

      Your initial argument was about observation, that the absence of certain 'observational' evidence on the part of conventional theory is a flaw. In attempting to evade the equivalent problem for your own pet theory, you merely mumbled something about the fact that we can 'observe design'. Again: so what? I can observe a banana, it doesn't make it a cause of earthquakes.

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    22. The cause of the design is the designer's actions. And I asked about more than observation.

      We can't test neutral theory. It hasn't been observed, it can't be tested and its equations have never been verified.

      And you still can't model unguided evolution

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    23. Joe Felsenstein- How am I diverting the thread? I asked about the fixation of neutral mutations. Don't blame me because you are too much of a coward to answer my questions.

      Some "expert" you are.

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    24. "An honest and intelligent IDiot would realize that human design is not the same thing as their mythical, mystical Ultimate Designer's (wink wink Jesus) design."

      Indeed. The ID logic runs '(1) We can tell the difference between something that's designed and something that isn't, (2) Everything, without exception, is designed'.

      It is either a self-defeating argument, or just a gibberish one. Those are the only two options available.

      Delete
    25. Jem spews gibberish and thinks he has an argument. No one says that everything is designed

      Delete
    26. The cause of the design is the designer's actions.

      So? That does not make design, or a designer, the cause of evolution. If you didn't observe it happening, your 'were you there' critique applies to ID just as much as to evolution. Yeah, I know, forensics and Stonehenge. Yawn.

      Delete
    27. "No one says that everything is designed"

      Ooh, show and tell, brilliant. Please show us something in nature God didn't design, and explain how you know he didn't design it.




      Delete
    28. Allan- unguided evolution is not scientific. No one can model it for anything but diseases and genetic breakdowns. We can use design detection techniques in biology and they say design

      Delete
    29. joey g said:

      "We observe the DESIGN, moron. And YOURS is the position that sez it has an incremental mechanism. Don't blame me because no one can demonstrate it."

      So, you admit that no one has ever actually observed the 'intelligent designer' (allah in your case) designing life, evolution, or anything else.

      Hey joey, you constantly say that 'ID' is NOT anti-evolution. You don't know what MY position is but you're obviously saying that non-IDiot evolutionary theory relies on "an incremental mechanism". What mechanism does IDiot evolutionary theory rely on, joey? Is the IDiot mechanism "incremental"? If not, what is it, magical? You say that 'ID' is not anti-evolution but doesn't 'evolution' imply (or require?) increments, at least in a general sense? And even if the IDiot mechanism is magical, wouldn't it still be incremental, and in an extremely 'specified' sense?

      Tell me, joey, how exactly did/does evolution occur via 'intelligent design' without "an incremental mechanism"?

      Delete
    30. "Ooh, show and tell, brilliant. Please show us something in nature God didn't design, and explain how you know he didn't design it."

      Joe G. Still waiting. Or has a miracle happened, and you realized you couldn't open your mouth without sounding foolish? If so, now you've got proof of that concept, why not apply it more generally?

      Delete
    31. if people want to really see what he is like see his own blog Intelligent Reasoning, easily found by searching on that phrase.

      Thanks, Joe F. Wowee. I see over in Joe G's alternate universe that Michael Behe is "correcting" Judge Jones (of the Kitzmiller v. Dover trial) with regard to evolution.

      Here in the real world, Behe's credibility was so thoroughly destroyed at that trial on cross-examination it's been suggested it should be used as a teaching example in law schools.

      Delete
    32. The level of invective there (much of it reflecting hatred of gays and the tactic of baiting men by calling them women) has always been remarkable. JoeG is a Real Man™, obviously.

      Delete
    33. Well, joey g, are you going to respond to my points and questions? How about Jem's request? Name some things (How about 5?) in nature that were/are not designed by the 'intelligent designer' (allah in your case) and how you know. I've asked you and other IDiots to do that many times and NONE of you ever do it. You all just ignore it and run away.

      Come on joey g, be a Real Man™ (LOL) and let's see what you've got.

      Delete
    34. The level of invective there (much of it reflecting hatred of gays and the tactic of baiting men by calling them women) has always been remarkable.

      I mentioned this regarding JoeG on another thread as well. As a generality, its perhaps not remarkable how often things like hostility toward science and emotional immaturity go together.

      Delete
    35. I see JoeG is a 'Field Service Engineer' and fixes things "mechanical, electrical, electronic and personal". Washing machine repair man? Eminently qualified to contradict those who have actually been educated in biology.See rationalwiki for 'the salem hypotheses'. "engineers as a group have a noted tendency to pontificate on things well outside their area of expertise, to the point of actual fallacy. This phenomenon is so prevalent that users of talk.origins have come up with the Salem Hypothesis, which predicts that any creationist claiming scientific expertise or advanced degrees is likely to be an engineer."

      A sample of his blogging style:-
      "Larry Moran- The Idiot Who Refuses to Get It"
      "Kevin R, McCarthy- Still a Lying Little Bitch"
      "A Dog is Still a Dog and Kevin McCarthy is Still a Moron"

      Delete
    36. Joe Gallien repeatedly threatens scientists and/or atheists with violence and/or extermination, at the Intelligent Design website Uncommon Descent, where name-calling, insults and threats of violence or persecution are applauded-- as long as they're directed at scientists. UD treats Joe Gallien as their greatest intellectual. Here's his evidence against evolution:

      Joe Gallien: "If this is true, that he [Mark Armitage] was fired for writing that paper and questioning evolutionism, then it is time for a war- a bloody war at that because this crap has to stop and obvioulsy the only way to stop it is to rid the world of all the cry-baby loser materialists."
      [Joe G comments at UD, August 6, 2013 at 7:15 am ]

      Delete
    37. JoeG in a hilarious exchange with his arch enemy "Thorton". I'm sure the accusations made against him are totally without foundation.
      http://tinyurl.com/lclqzck

      Delete
  7. Joe F sez:
    The mechanisms of random genetic drift are (1) random Mendelian segregation, (2) random deaths of individuals, (3) random variation from individual to individual in numbers of births. Guess we've never seem those!

    1- You have no idea which mutations are random
    2- All of that still doesn't help with respect to getting neutral changes fixed.

    At least TRY to stay focused on the discussion

    ReplyDelete
  8. What can natural selection do? Nothing Genetic drift? More of nothing.

    Still no model for unguided evolution- no predictions, no math, no research, nothing. You chumps need to focus on the lameness of your position before you attack ID with your ignorance.

    ReplyDelete
    Replies
    1. No math Joe G says, in the very same thread where Joseph Felsenstein linked this: Theoretical Evolutionary Genetics.

      Delete
    2. JoeG does know that there is some math there but declares it all irrelevant.

      Delete
    3. What math supports unguided evolution? Please be specific,
      (hey reply worked)

      What is the model for unguided evolution?

      Delete
    4. A mathematical treatment of the consequence of random birth and death (nothing else) in a finite population: http://www.genetics.org/content/61/3/763.full.pdf

      Delete
    5. LoL! So no model for unguided evolution. Figures...

      Delete
    6. Maybe you should actually read the book Felsenstein linked? That's what you're claiming doesn't exist.

      Delete
    7. The book has NOTHING to do with unguided evolution. You are an ignorant as

      Delete
    8. LoL! So no model for unguided evolution. Figures...

      Lol! So you don't think that Kimura's mathematical model (or any other) is 'unguided'? Someone reaches into the formulae and twiddles with them while we're scanning past the equals sign? Heh heh.

      Delete
    9. Allan, you are lame. How does Kimura model unguided evolution? Have his equations been verified? No

      Does Kimura model the evolution of a bacterial flagellum via unguided evolution? No. Does he model anything or just provide unverified equations?

      Delete
    10. I'm lame! Lol! The post, and your initial enquiry, were about neutral fixation in primates. Now you're gibbering about the frigging flagellum! You asked for a mathematical model of unguided evolution. I provided one. Bet you didn't read it.

      Does he model anything or just provide unverified equations?

      Laugh my hairy ass off!

      Delete
    11. No Allan. I never asked about neutral mutations in primates. I asked a GENERAL question about neutral theory. And I NEVER asked for a mathematical model for unguided evolution. You are just an obtuse ass.

      Delete
    12. I NEVER asked for a mathematical model for unguided evolution.

      This is you not-asking for a mathematical model:

      Still no model for unguided evolution- no predictions, no math, no research, nothing.[...]
      What math supports unguided evolution? Please be specific,

      You are just an obtuse ass.

      Finally, you get something right!

      Delete
    13. LoL! Nothing in what I said says I wanted a mathematical model. I asked for math that supports unguided evolution and I asked for a model for unguided evolution- you have provided neither.

      Delete
    14. So ... the math that deals with the population-level consequences of random birth and death is not "math that supports unguided evolution", and such a treatment is not a "model". Got it.

      Delete
  9. Again, I ask:

    What is this alleged science behind neutral allele fixation? Has this been observed? Has it been tested? That is with respect to unguided evolution?

    ReplyDelete
    Replies
    1. 1. Observation. 2. Yes. 3. Yes. 4. Yes.

      See: Lenski's long-term evolution experiment with E coli. Most of the mutations fixed were neutral. It was an experiment to see what would happen, so yes, it was observed and tested. They can directly compare independent lineages and ancestral frozen stages from the population to each other, in order to gauge the effect of various mutations. That's how they know most of them were neutral, by directly observing and comparing the fitness of carriers. Yes, it was unguided evolution, noone's forcing the bacteria to evolve in any specific direction. This is shown among other things by the fact that all the independent lineages evolved according to different mutational trajectories, despite starting from the same original clonal population and in the same environment, for the same amount of time. It doesn't get any more observed, tested and unguided than this.

      Delete
    2. LoL! Neutral theory pertains to neutral alleles (genes for the moron), not just mutations that don't do anything.

      Delete
    3. An allele is just a variant of a locus. How do loci differ from each other(what is the source of the variation)? Mutations.

      Care to try again Joe?

      Delete
  10. Umm Lenski's was artificial selection and no one knows if the mutations were random, as in chance events.

    ReplyDelete
    Replies
    1. He's right, you know. All mutations could be carefully crafted by god to look just like random events. I understand he moves in mysterious ways, his wonders to perform. He could easily make anything look just like anything else. There's really no point in trying to find any regularities in the world; science is futile.

      Delete
    2. Only ignorance sez they look like random events. Heck the 1s and 0s on a computer buss look random but they ain't.

      And science, under materialism, is futile.

      Delete
    3. Isn't science futile under any conceivable epistemic regime? If god is running everything, and we can't understand god, how can we know anything at all? How can you tell the world wasn't created last Thursday? How do you know every third tree isn't a lobster wearing a magical disguise? How do you know there are mutations at all rather than god messing around with the sequencing machines? Knowledge is a delusion.

      Delete
    4. Joe, what does it mean when evolutionary biologists say mutations are random? Explain it in your own words.

      Testable Prediction: you will fail to produce an accurate description, but will instead regurgitate mindless creationist nonsense.

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    5. They mean the mutations are chance/ happenstance events. They are all accidents/ errors/ mistakes. Mayr, "What Evolution Is"

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    6. Yep, that's a fail right there. Prediction: confirmed.

      Delete
    7. How do you know there are mutations at all rather than god messing around with the sequencing machines?

      Because I tried praying once while waiting for sequencing results, and still didn't get the results I wanted.

      Delete
    8. Looks like Mikkel is ignorant of biology. According to Mayr, et al., random wrt mutations means they are chance/ happenstance events. They are accidents, errors or mistakes.

      I can support that and Mikkel can't support anything it spews

      Delete
    9. Joe "Clueless about the subject he's attempting to criticize" G fails as usual. Mutations are only said to be random with respect to their effect on fitness and even that statement is subject to some debate.

      "Patterns of mutation
      The direction of mutation is nonrandom. In particular, transitions were found
      to occur more frequently than transversions. In animal nuclear DNA, transitions were found to account for about 60-70% of all mutations, whereas the proportion of transitions under random mutation is expected to be only 33%. Thus, in animal nuclear genomes, transitional mutations occur twice as frequently as transversions. In animal mitochondrial genomes, the ratio of transitions to transversions is about 15 to 20. Some nucleotides are more mutable than others. For example, in nuclear DNA of mammals, G and C tend to mutate more frequently than A and T.

      Are mutations random?
      Mutations are commonly said to occur "randomly." However, as we have
      seen, mutations do not occur at random with respect to genomic location, nor do all types of mutations occur with equal frequency. So, what aspect of mutation is random? Mutations are claimed to be random in respect to their effect on the fitness of the organism carrying them (Chapter 2). That is, any given mutation is expected to occur with the same frequency under conditions in which this mutation confers an advantage on the organism carrying it, as under conditions in which this mutation confers no advantage or is deleterious. "It may seem a deplorable imperfection of nature," said Dobzhansky (1970), "that mutability is not restricted to changes that enhance the adeptness of their carriers." And indeed, the issue of whether mutations are random or not with respect to their effects on fitness is periodically debated in the literature, sometimes with fierce intensity (see, e.g., Hall 1990; Lenski and Mittler 1993; Rosenberg et al. 1994; and Sniegowski 1995).
      "
      Graur, D. and W-H. Li, 2000. Fundamentals of Molecular Evolution;
      Second Edition. Link to a freepdf version of the book.

      Delete
    10. There's an eternal discrepancy between what 'random' means when biologists typically say it, and what mathematicians (including many population geneticists) mean. Li and Graur (somewhat surprisingly) seem to be treating 'nonrandom' as 'not equiprobable'. But that's still 'random', in a probabilistic sense, regardless of the importing of yet another definition, approximately according with 'unplanned, 'aimless'.

      Delete
    11. That's a good point and unfortunately there's quite a lot of ambiguity going around concerning the meaning of the word 'random'. If we go by Li and Graur's implied definition being 'evenly distributed across the total space of outcomes(with respect to fitness)', then mutations definitely aren't random, since they're mostly (nearly)neutral. A better word to use then would be 'stochastic', which basically means they must be analysed in terms of probability theory.

      Delete
  11. For whatever reason the reply doesn't seem to work-

    What is this alleged math from unguided evolution? How many mutations does it take to get a vision system starting from a population tat doesn't have one, via unguided evolution?

    ReplyDelete
    Replies
    1. Nilsson, D., and S. Pelger. 1994. A pessimistic estimate of the time required for an eye to evolve. Proceedings of the Royal Society of London, Series B 256:53-58.

      Delete
    2. LoL! There isn't any science in that paper and nothing tat supports unguided evolution.

      Delete
    3. But the paper specifically answered exactly the question you asked. Why are you complaining?

      Delete
    4. No, it didn't answer anything. Did you even read it?

      Delete
    5. I did. Did you? OK, it starts from a eye spot. Is that your problem?

      Delete
  12. I've always enjoyed following the arguments of ID proponents. Other people like to do crossword puzzles, but I think its fun to come up with clear concise ways of explaining the flaws in ID arguments and explaining the more subtle aspects of evolution. I teach biology at the college level so I guess all that makes sense

    But there are other times when I wonder why the hell I waste my time with this when I could be reading real science. Now is one of those times

    ReplyDelete
    Replies
    1. Perhaps you should focus on the flaws with evolutionism before having a go at ID.

      Delete
    2. But there are other times when I wonder why the hell I waste my time with this when I could be reading real science.

      I'm sure most everyone here wonders that, but few can resist the temptation. Its a charming diversion, in the Victorian sense of the phrase.

      Delete
  13. This comment has been removed by the author.

    ReplyDelete
    Replies
    1. Hey Joe, look, that raindrop is rolling down the window pane.

      Joe: LOL, you have no science to prove God didn't make it move in that path!

      Delete
    2. judmarc LoL! how does materialism explain rain and gravity?

      Delete
    3. LoL! You enjoy being an asshole. Nice. Gravity would be a design parameter and rain, well that would be a consequence of this designed planet

      Delete
    4. so you have never designed anything in your life. and you think your ignorance means something- strange

      Delete
    5. judmarc LoL! how does materialism explain rain and gravity?

      I have no idea at all what you're trying to ask here. I'm assuming you're aware of the science of how precipitation occurs, and general relativity (gravity).

      Delete
    6. and you think your ignorance means something- strange

      Just when one thinks the irony can't get any richer, the fellow who's unaware of 170 years of science regarding "unguided evolution," and thus confidently proclaims there is none, says to someone else that they think their ignorance is meaningful.

      Delete
  14. Joe G: And science, under materialism, is futile.

    Right Joe. That's why when you repair your toasters you use MAGIC instead of materialistic tools and processes.

    ReplyDelete
  15. No dumbass, I use immaterial information to repair anything. Without that tools are useless. And guess what? Immaterial information was used to design the tools.

    ReplyDelete
    Replies
    1. What do you mean by "information"?

      Delete
    2. Are you retarded? Information is what makes the world work. We use it every day. Communication would be impossible without it. Trade would be impossible without it.

      Delete
    3. "Immaterial" information. What the fuck does that even mean?

      Delete
    4. Sam Harris,

      What do I mean when I write toilet paper...? Do I mean I Indian food...?

      Delete
    5. Mikkel, your ignorance, while amusing, means nothing

      Delete
    6. Rum,

      Shouldn't you be by the vents recreating life...?

      Delete
    7. LOL! Joe once again chickens out, can't give his definition of "immaterial information".

      Maybe you can tell the immaterial information in an object by counting the letter in its description. That's how you did it for 'aardvark' and 'caek', right Chubs?

      Delete
    8. Timmy chokes on information. Timmy is software material or immaterial? Are thoughts material or immaterial?

      "Information is information, neither matter nor energy" Norbert Weiner

      Delete
    9. " Information is neither a physical nor a chemical principle like energy and matter, even though the latter are required as carriers" J Piel

      Delete
    10. Maybe I could take you seriously if you could show me a thinking entity without a physical brain, or a piece of software not stored and run on on a physical computer.

      Your participation here is golden, Joe. Keep banging the rocks together, will quickly fill my "stupid shit IDiots say"-folder.

      Delete
    11. Joe G

      "Information is neither a physical nor a chemical principle like energy and matter, even though the latter are required as carriers"


      OK Joe, you've told us what information isn't.

      Now tell us what "immaterial information" is.

      Delete
    12. " Information is neither a physical nor a chemical principle like energy and matter, even though the latter are required as carriers" J Piel

      Who, or what, is, or was, J Piel?

      Delete
    13. Immaterial information is what you use every day, Timmy. It is used to communicate, trade, build, travel- just about everywhere.

      Are you really that retarded?

      Delete
    14. J Peil- scientist from E Germany

      Delete
    15. Googling it appears to be a typo. J. Peil was an eastern German biomathematician, wrote some decent textbooks in the 1980s. The quote is a translation from an article written in 1973 "Einige Bemerkungen zu Problemen der Anwendung des Informationsbegriffs in der Biologie I. Der Informationsbegriff und seine Rolle im Verhältnis zwischen Biologie, Physik und Kybernetik", Biometrische Zeitschrift, 15, 117–128, which is a conference paper. Peil mainly discusses how population genetics and statistical mechanics are related, mainly in that they are both stochastic theories and therefore can make use of the same mathematical tools in a lot of cases.

      It's worth noting that the ie is flipped in Wieners name as well. Here's the thing, I don't get Joe - if these points about information somehow are in conflict with population genetics, why didn't Wiener ever tell Haldane, who was a personal friend (and in fact Wiener got a lot of flak for it during the McCarthy era)? Why did Peil write textbooks on population genetics?

      Delete
    16. Joe G

      Immaterial information is what you use every day, Timmy. It is used to communicate, trade, build, travel- just about everywhere.


      People use you for a chew toy every day too Chubs but you're not "immaterial information".

      We'll just note that you have no definition and are talking out of your ass again as per usual.

      Delete
    17. Simon- I never said nor implied that immaterial information is in conflict with pop gen

      Delete
    18. Poor Chubs has no definition of "immaterial information".

      Hey Chubs, can you eat information? Is that why you're so roly poly?

      Delete
    19. Still no definition of "immaterial information" from Chubs.

      Are you saying now you can't eat information?

      Delete
    20. J. Peil was an eastern German biomathematician, wrote some decent textbooks in the 1980s.

      Well, I know, because I've also googled up Jürgen Peil. JoeG doesn't, because he only copied the out-of-context quote (together with the typo in Peil's name) from creationist pages that toss it around. They first quote-mined it from a 2006 book by Gitt. They neither know nor care who Peil was and do not bother to refer to the original article. Gitt mentions Peil as a former East German scientist, and that's the only information repeated by those "sources".

      Delete
    21. "Who, or what, is, or was, J Piel?"

      Joe G *meant* 'Peil', but a random transcription error changed the function of his sentence.


      Delete
    22. Creationists who quote Peil somehow fail to reflect that, since information requires "matter" (mass/energy) as its vehicle, it must be an emergent property, presupposing the existence of mass/energy. It can't come from an immaterial god.

      Delete
    23. @Simon Gunkel: Peil mainly discusses how population genetics and statistical mechanics are related, mainly in that they are both stochastic theories and therefore can make use of the same mathematical tools in a lot of cases.

      So, unlike JoeG, Peil did not reject the relevance of population genetics to the study of evolution. Maybe JoeG would accept population genetics equations if they came from Peil.

      Delete
    24. It seems like a bit of a hurdle. Have him learn to read German, then track down Peils "Grundlagen der Biomathematik" which has been out of print for a while...

      @Piotr Gąsiorowski
      I don't think it makes sense to think of it as an emergent property. A more apt relation migh tbe analogous to - say - differential equations. There are no "naked" differential equations in nature. A lot of natural processes can be described using differential equations, but if one was to say that differential equations were energy or matter one would be wrong. Information as a mathematical concept can be used to describe things in nature, but it isn't itself nature.

      Delete