Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 08 2008,21:55    bFast proposes a simulation. Quote bFast: 1111111222 2212112211 1221212112 1112222121 1212221112 1112212112 1112122121 1122212212 1221122222 1121121121 2221122222 2221112122 1121121112 2221222212 1222211212 1221212121 1221111221 1122121111 1122212112 1212112222 SUM = 301 Bob O'H: you’re illustrating a well known problem, genetic drift. With a population size of 5, the relative fitness has to be very large to have a visible effect. Drift is a large factor in small populations, so even alleles which reduce fitness can become fixed. Bob O'H makes an important point. Some alleles will become fixed even without selection. Meanwhile, in a reasonable population of competitors, their overall fitness will tend to improve. That inevitably means more and more individual alleles will improve, even if particular alleles are gained or lost along the way. This is an example of how global pressure can bring about local changes. -- Update: The results are much as expected. In a recent run, I used a 100x100 grid for a population of 10000. Each genome is 100. When a replication occurs, there is a 10% chance of a mutation. Only 1's and 2's are allowed thus far. The child then displaces a weaker neighbor, if any. This creates a nice nested distribution of varieties across the grid. After 100 generations, the average fitness is about 1.8 per allele. The corners of the grid tend to have more primitive varieties. This is a typical genome: 1212112211 2122222212 2222212222 2222222221 2122222221 2212222122 2122122211 1222221212 1222222112 2122222222 Next step is to allow very rare 2-to-3 mutations. I'm also considering some sort of sexual recombination, but watching 1's doin' it doesn't strike me as particularly interesting. -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 08 2008,21:58    Quote (Zachriel @ Mar. 07 2008,06:47) bFast proposes a simulation. Quote bFast: 1111111222 2212112211 1221212112 1112222121 1212221112 1112212112 1112122121 1122212212 1221122222 1121121121 2221122222 2221112122 1121121112 2221222212 1222211212 1221212121 1221111221 1122121111 1122212112 1212112222 SUM = 301 Allele Blender uses a typical selection criteria called The Early Bird Gets the Worm, also known as I only need to outrun you, Albert. In other words, strong positive selection. Lately, I've allowed very rare 2-to-3 mutations. Of course, while some are lost, once established they tend to quickly dominate the population. I have tried to contact bFast to make sure I have represented his model correctly. The only contact I have found is at ISCID. Someone might want to give bFast a heads up. * Niels Bohr and Albert Einstein were taking a walk in the woods, vigorously debating the philosophical underpinnings of quantum theory, when a gigantic bear suddenly burst out of the underbrush and raced toward them. Niels immediately whipped out his fine running shoes and began lacing them up. Einstein, furrowing his brow at Bohr, said: "Niels, there's no way you can outrun that bear." "That's true," Bohr calmly replied, "but I don't need to outrun the bear. I only need to outrun you, Albert." -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 08 2008,21:59    Quote (Zachriel @ Mar. 07 2008,06:47) bFast proposes a simulation. Quote bFast: 1111111222 2212112211 1221212112 1112222121 1212221112 1112212112 1112122121 1122212212 1221122222 1121121121 2221122222 2221112122 1121121112 2221222212 1222211212 1221212121 1221111221 1122121111 1122212112 1212112222 SUM = 301 These are all adjustable, of course: * Alleles can now vary from 1 to 9. * Mutations occur every 10% of replications. * Only 10% of these 10% can cause an incremental improvement, most of the rest being detrimental. Fitness rapidly improves. Recombination with a random neighbor improves even faster. Recombination with the fittest available neighbor is faster still. But recombination with the most attractive neighbor still works very well, but has a peculiar effect. To simulate this, the Peahen chooses a mate from the immediate neighborhood—not based on fitness—but based on the one with the prettiest tail. The prettiest tail is defined as the longest length of trailing 1's—a trait which is actually detrimental to the overall fitness. The Peacocks Tail Notice the family resemblance among neighbors, and the small clan of uglies in the middle left column. This run has a genome of length twenty so you can more easily see the effect. -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 08 2008,22:19    Quote (bFast @ Mar. 08 2008,19:18) I have written my own sim at this point, and it fails miserably!  So bad, in fact, that I think it must have a bug. It isn't necessary to reinvent the wheel. I believe I have a working simulator. It's open source, and I'm more than willing to share. However, I want to make sure that the model correctly represents what you are trying to test. We have a population, each member represented by a genome. Each allele is a numeral. A member spawns a Child which then competes in the population. Fitness is determined by the sum of genes. In the Allele Blender, each member of the population is located on a grid. Each new Child will replace the weakest in the vicinity, assuming the Child is fitter. Is this correct? (By the way, starting with your original organisms, and assuming strong positive selection, Organism 2 will quickly dominate the population. The 3-allele in Organism 4 will almost definitely be lost.) Quote (bFast @ Mar. 08 2008,19:18) - No new alleles are created during the simulation.  I suspect that the addition of new alleles would increase the noise, therefore increasing the problem. I assume you mean more than two available versions at each locus. Using your concept, it was easy to have nine varieties, 1 through 9. If a given gene is a 2, then a standard mutation as described above would be either a 1 (detrimental) or a 2 (neutral). Very occasionally we might see a 2 increment to a 3. A novelty. Quote (bFast @ Mar. 08 2008,19:18) - The number of alleles per organism is small (initially 200).  I suspect that the more alleles, the worse the signal to noise problem. I think you mean the number of genes (each allele being represented by a numeral). It's just a parameter. I can adjust that to any reasonable number. There are several relationships that we can discover that will help us extrapolate to larger numbers. I'll provide some details later. Quote (bFast @ Mar. 08 2008,19:18) Selection is, well "pure", the definition of "fit" never changes, every organism death is determined by its ideally measured fitness compared to another organism.  This is a very positivistic model. That seemed to be your intent. But that can be easily adjusted. I have already added proximity, recombination, random mate selection, mate selection for fitness, and mate selection for an arbitrary trait (the peacock's tail). We could also add a random fudge factor. It doesn't really change the end result. Even with no selection, alleles become fixed. It's an important concept that I would be happy to discuss.        ' Recombine        For a = 1 To numAllele            If Rnd < 0.5 Then                Mid(Child, a, 1) = Mid(Mate, a, 1)            Else                Mid(Child, a, 1) = Mid(Parent, a, 1)            End If        Next a Quote (bFast @ Mar. 08 2008,19:18) I would love to hammer this challenge out with you to prove that in an ideal world a new mutation actually can catch on.  I would also love to see the sim prove that a mutation is more likely to fix in a large population.  So far my sim isn't doing any better with a large population (its a dog by about 50,000). Not only can new mutations fix, but they can do so in the absence of selection. -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 08 2008,22:19    Quote (bFast @ Mar. 08 2008,19:18) I would love to hammer this challenge out with you to prove that in an ideal world a new mutation actually can catch on.   Hi bFast! I have several open source projects that demonstrate various aspects of evolution. Nest of Letters shows how even neutral mutations can and will become fixated in populations. Killer Rabbits started with a very cool simulation by Wonders for Oyarsa posted on Telic Thoughts. Ironically, he overlooked the process of fixation that was staring him in the face. -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 09 2008,08:17    Neutral Drift and the Law of Small Numbers Consider a single locus in a population limited by circumstance to just two.        A, B Let them replicate.        A1, A2, B1, B2 Now, we keep two at random. These are the possibilities.        A1, A2        A1, B1        A1, B2        A2, B1        A2, B2        B1, B2 There is a one in three chance of forever losing one of the two alleles. But let's assume that we end up with both alleles. But then, over each succeeding generation, we are again faced with a one in three chance of forever losing one of the two alleles. Sooner or later, we will have A, A or B, B. Fixation. Now consider a population of three.        A, B, C Replicate.        A1, A2, B1, B2, C1, C2 Now choose three. There are twenty possibilities. Some of them include all three alleles. But some don't. Even if all three alleles make it into the next generation, we are again faced with a significant possibility of losing one of the alleles forever. Eventually, we will lose one allele. Such as this.        A, A, B Now replicate        A1, A2, A3, A4, B1, B2 Again, choose three. Notice that there is a finite chance of keeping both alleles. But there is also a finite chance of losing another allele forever. Eventually, this will happen. Fixation. Which allele will become fixed? It's random. So in the first case, it is 1/2. In the second case, it is 1/3. But notice that it takes longer with the larger population. Indeed, Hardy-Weinberg proved that in an infinite (undisturbed) population, the rate of fixation is zero. But no population is infinite. But we can make an even more powerful statement. Instead of a single allele, consider a genome of a 100 alleles. Assume, the rate of neutral mutation is 1 per 100 per allele per replication. That means each genome will have a single mutation. If it replicates a hundred children, then the average locus will have experienced one mutation (an average of one per child). What is the chance of a particular allele being fixed? One in a hundred. So what is the Expected Number of some mutation becoming fixed when we have a hundred mutations? 100*1/100 = 1. It's the same for any size genome, any size population. The rate of fixation of neutral mutations is equal to the rate of neutral mutations regardless of population size. This is not an empirical result. It's arithmetic, and is based on the assumption of neutrality. From what I gather, you are attempting to understand the case of nearly neutral evolution. -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 09 2008,08:43    In any case, you haven't provided us enough information to be sure we are properly simulating your model.  If we consider these two genomes:        1111111111111111111... and        1111121111111111111... You've defined fitness as the sum of the alleles. Assuming strong positive selection and a low mutation rate, the 2-mutation should quickly dominate the population. With a high mutation rate, then various mutants will compete to dominate the population, but any pure-strain will be quickly overwhelmed. Among your original organisms, Organism 2 will quickly dominate the population. The 3-allele in Organism 4 will almost definitely be lost. But then any future advantageous mutation to the dominant Organism 2 will then come to dominate the population:        xxxxxxxxxxxxxxxxxxxxxx... and        xxxxxXxxxxxxxxxxxxxxxx... Remember, Neils only has to outrun Albert. -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 09 2008,09:41    Quote (Zachriel @ Mar. 08 2008,22:19) I have already added proximity, recombination, random mate selection, mate selection for fitness, and mate selection for an arbitrary trait (the peacock's tail). I changed sexual selection for the tail to be a preference for a long tapering tail. I am allowing the 'head', the two leading loci, to mutate faster. This results in faster evolution in that region. (I'll probably fiddle with that feature. Maybe allow the head region to expand.) Here's a typical organism.       99544535322222111111 Notice the 'head' has hit the limit of 99. The tail is ...322222111111, but you can guess that some of its relatives probably have longer tails. (They do.) It's quite amazing how powerful sexual selection for an arbitrary trait can be at shaping the organism. — Update Took out the 'head'. Too contrived. Trying longer genomes. Works as before, with or without recombination, with or without mating selection for fitness, with or without mating selection for a beautiful tail.   ' Beauty is in the eye of the beholder   ' Long tapering tails preferred   Public Function calcBeauty(Mate) As Integer   Dim mv, mk As Integer         mk = Val(Right(Mate, 1))       calcBeauty = 0         For a = numGenes To 1 Step -1           mv = Val(Mid(Mate, a, 1))           If mv = mk Or mv = mk + 1 Then               calcBeauty = calcBeauty + 10 \ (mv + 1) ' Thinner the better               mk = mv           Else               Exit For           End If       Next a   End Function -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 09 2008,10:14    bFast emailed and said he has his simulator working. However, his email didn't reveal details sufficient to replicate his results. Unsurprisingly, he does say it confirms his suspicions. bFast, when you get the chance, maybe you could provide some examples using small genomes and populations so we can see how it works. Then it should be easy to scale it up once we understand what you are modeling. My first question has nothing with introducing the novel 3-allele mutation: Why doesn't Organism 2 quickly dominate the population? Why would you think that Organism 4 with the 3-allele would propogate? I would expect that line to die out and be replaced by Organism 2. Indeed, without new mutations being introduced, we would expect the entire population to be dominated by clones of Organism 2. Organism 4's only hope is to find a rock to hide under. -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

Annyday Posts: 583 Joined: Nov. 2007 (Permalink) Posted: Mar. 09 2008,14:54    I am not in the least bit a programmer, but if you're actually getting funky results from a simulation, bFast, I'd like to see the simulator and the results. Mathematical modeling of changing populations is a mainstay of evolutionary theory, so funky results in simulations are pretty interesting. -------------- "ALL eight of the "nature" miracles of Jesus could have been accomplished via the electroweak quantum tunneling mechanism. For example, walking on water could be accomplished by directing a neutrino beam created just below Jesus' feet downward." - Frank Tipler, ISCID fellow

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 09 2008,18:06    The question that I present is, how easy is it for natural selection to favor an advantageous point mutation (signal) in light of the various destractions (noise)? I see noise in four areas: 1 - Allele populations.  Organisms, such as myself, consist of a mishmash of alleles that exist within the community of origin.  As such, any one individual will not have an ideal mix of alleles.  If an organism, such as myself, has the lucky slightly beneficial point mutation, will natural selection be able to favor it dispite all of the other alleles flying around in the population. 2 - New alleles.  Each individual organism will be hit with zero to a few mutations within the active DNA.  The fact that each organism is de-idealized by these mutations increases the noise, making it more difficult for natural selection to be able to favor a slightly beneficial point mutation. 3 - The fickleness of natural selection.  In two given contexts natural selection will favor different alleles.  For instance, I am more intelligent than most.  As such, I have a good allele set wrt intelligence.  I am decidedly less athletic than most.  As such, I don't have a good allele set wrt athletics.  If a given opportunity for selection involves me and a friend trying to outrun a hungry bear, in all likelihood my above average intelligence will do me no good, and I'll be lunch.  To make matters worse, I think that natural selection is probably best at ignoring allele mixes altogether, and causing one to be removed from the pool for no reason other than being in the wrong place at the wrong time. 4 - Bulk-editing.  Alleles come with an entire gene full of baggage.  Our dear lucky mutation has to happen within an existing allele.  This existing allele may not be a rising star.  Now a new allele exists which may be marginally better than its falling star cousin, but may not be sufficiently advantageous to beat out other alleles floating around in the population.  When organisms such as myself produce offspring, we generally exchange genetic data in bulk units called chromosomes.  So even if a gene is a particularly good one, I think that the fact that it is packaged up in a chromosome presents a challenge. Now, I have produced a simulation that selects out issue number 1.  The question is, is noise source 1 in itself sufficient to disable natural selection for a slightly beneficial mutation? My sim's algorithm is as follows: Initialization accepts 3 parameters: gene count, population, mutant count. - Per population, I create an organism -   Per organism, I create an array of 'gene count' elements. -   Each element is initialized with a random 0 or 1, representing allele #0 or allele #1 where we assume that the #1 allele is 'fitter' than #0. -   Each element is given a 'fitness' number -- the total of 1's in its genes. -   for 'mutant count', organisms are selected at random, and the first gene is boosted to allele #2.  The 'fitness' number is adjusted. Processing accepts 1 parameter: cycles and returns the total number of active mutants. - Per cycle: -    two organisms are selected at random -    the less fit of the two is decomissioned, and replaced by: -       two organisms are selected at random -       through the genes of these organisms, either the first or 2nd organism's allele will be selected. - the 'fitness' of the new organism is measured. One "generation" is considered to be Population cycles (on average, the death/replacement of each individual.) The general results of my sim are as follows (I haven't run lots of simulations yet, nor have I done careful logging yet.): - when there are 200 alleles per organism, the mutant dies very about 9 times out of 10.  If the mutant lives to get about 20 organisms to contain it, it rather quickly becomes fixed.  Dying or fixing doesn't seem to have much to do with population. - when there are 2000 alleles per organism, the mutant dies rather often, often enought that I have skipped past early processing and seeded the system with multiple mutants.  If it has 50 mutants in a 1000 population, the mutant usually survives, and fixes rather quickly. - when there are 20,000 alleles per organism, the population of the mutant seems to wander like it is influenced by the throwing of a dice -- genetic drift.  I have been seeding with 100 in a population of 1000, and have yet to be able to get it to fix.   NOTE: As all allele 1s are motivated to increase in popularity, one may consider that a bunch of them have fixed within this process.  As they fix, the amount of noise, the number of alleles in the population decreases.  I have not yet measured the number of fixed alleles in the calculation, but I suspect that with the small counts, the reason NS grabs the beneficial mutation so solidly at some point is because the noise has significantly decreased. Now, in real world organisms, there is (almost) always an abundance of available alleles.  In fact, when there are not, it is conserning.  This is caused, of course, by other organisms obtaining mutants that have infiltrated the population.  Populations always have many alleles, so the mutant of interest fixing because all of the nearby alleles fixing is an artificial situation. A major question that I have as I present this sim is, how many alleles are there in a population.  I could envision that there are a whole lot.  I know that I contain 2 sets of genes, each set has 25,000 coding genes.  My wife also has 2 sets of genes.  So between the two of us, let alone our neighbors, we have 100,000 coding genes.  But, for how many of those genes is there only one allele within the population?  For how many of those genes are there literlally hundreds of alleles?  Bottom line, how many alleles are disguising my lucky beneficial mutation.  My sim suggests that somewhere less than 20,000 is too many, that it produces too much noise for natural selection to filter out, when selecting a beneficial point mutation -- and that, dispite the other sources of noise as described above.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 09 2008,19:00    Zachriel, "Indeed, without new mutations being introduced, we would expect the entire population to be dominated by clones of Organism 2. Organism 4's only hope is to find a rock to hide under." In an asexual environment, this would obviously be so.  Which presents a problem.  It would seem that in an asexual environment, the signal to noise issue becomes very much stronger.  It is only in the most fit of organisms, that an advantageous mutation would stand a breath of a chance.

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 09 2008,21:31    Quote (bFast @ Mar. 09 2008,18:06) - Per cycle: -    two organisms are selected at random -    the less fit of the two is decomissioned, and replaced by: -       two organisms are selected at random -       through the genes of these organisms, either the first or 2nd organism's allele will be selected. - the 'fitness' of the new organism is measured. That's a rather odd selection method. You pit organism 1 against organism 2, but it's not the victor that reproduces, but a recombination of two other organisms. I suppose it should result in evolution towards higher fitness, though. I'll test it to be sure. Quote (bFast @ Mar. 09 2008,18:06) - when there are 200 alleles per organism, the mutant dies very about 9 times out of 10. Yes, of course. That's what we would expect for a near neutral mutation (your mutation only increases fitness by a small percentage) in the midst of chaos (randomized genomes). So? Quote (bFast @ Mar. 09 2008,18:06) As all allele 1s are motivated to increase in popularity, one may consider that a bunch of them have fixed within this process.  As they fix, the amount of noise, the number of alleles in the population decreases.  I have not yet measured the number of fixed alleles in the calculation, but I suspect that with the small counts, the reason NS grabs the beneficial mutation so solidly at some point is because the noise has significantly decreased. Again, of course. Try this. Assume there are no mutations. Run your simulation starting with your randomized genomes. Your population should evolve rapidly and fitness should fix at a high level. Then when you introduce your beneficial mutation, it will then tend to dominate because it will be distinguishing. Neils only has to outrun Albert. Quote (bFast @ Mar. 09 2008,18:06) Now, in real world organisms, there is (almost) always an abundance of available alleles. Quite the contrary, most organisms, including humans, share almost identical genomes. It's just that we happen to be most interested in the differences. Indeed, this is an important aspect of sexual selection. A seemingly minor difference (a bit better singing voice, an unusual coloration in plumage) can make the crucial difference between a successful mating or not. Quote (bFast @ Mar. 09 2008,18:06) This is caused, of course, by other organisms obtaining mutants that have infiltrated the population. Which is what Allele Blender simulates. New mutations are constantly being introduced. The amount of genetic diversity depends on several factors, including the mutation rate. Quote (bFast @ Mar. 09 2008,18:06) My sim suggests that somewhere less than 20,000 is too many, that it produces too much noise for natural selection to filter out, when selecting a beneficial point mutation -- and that, dispite the other sources of noise as described above. No. Rather, it demonstrates that a near neutral mutation may drift to extinction in a chaotic genomic population. This is what is expected. Quote (bFast @ Mar. 09 2008,19:00) In an asexual environment, this would obviously be so.  Which presents a problem.  It would seem that in an asexual environment, the signal to noise issue becomes very much stronger. Even without recombination, the Allele Blender quickly evolves higher fitness. (And it's much easier to distinguish the lines of descent, being uncrossed lines.) Without mutation also, the population will settle on a high fitness. With mutation, individual mutations, even if beneficial, may be lost, but other mutations will be found. Try your simulation again, without any mutation first. Take a look at how the  system evolves. Then add some fixed rate of mutation. You'll find that the population more closely resembles biological organisms, complete with families of varieties. -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 09 2008,22:42    Zachriel: Quote That's a rather odd selection method. You pit organism 1 against organism 2, but it's not the victor that reproduces, but a recombination of two other organisms. I suppose it should result in evolution towards higher fitness, though. I'll test it to be sure. This is certainly not sexual selection.  But why should we assume that the victor should also get the privelage of reproduction.  Am I to assume that shortly after my handicapped friend I get chased by the bear, and he gets eaten, I get to reproduce? You will note that when the allele count is 200, this sim works as expected, when it is 2000, it works as expected -- more slowly than the first, but it still evolves.   When the allele count gets to 20,000, genetic drift becomes the predominant paradyme.  This is what I would expect (exactly where the numbers lie is outside of my capacity to predict, but I expected that at some point genetic drift vastly dominates over selection.)  So, as expected, if there are too many alleles in a population, they act as noise, and the signal of the new mutation is drowned out by the noise of all the other alleles flying around everywhere. Now, the real question is how many alleles are in the average human population?  So far the answer you provided is, "most organisms, including humans, share almost identical genomes."  When the possibility exists of there being 100,000 alleles in the coding DNA of myslef and my wife, in addition there's the active, but not coding DNA (introns, etc.)  When that kind of numbers are being talked about, if 90% of our genes are identical, and the other 10% have an average of 5 alleles, that's still a lot of alleles.  Therefore, within the scope of the numbers that we are dealing with "almost identical" is a pretty mushy term. Is there a hard estimate of how many alleles are in the population of a typical human community?  (I assume that the alleles in my town are more important to me than additional alleles floating around darkest Africa somewhere.)

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Mar. 09 2008,23:36    Quote (bFast @ Mar. 09 2008,22:42) Now, the real question is how many alleles are in the average human population? Not at all. The real question is, how many SELECTABLE alleles are there versus how many alleles that produce no change in fitness?   Quote So far the answer you provided is, "most organisms, including humans, share almost identical genomes."  When the possibility exists of there being 100,000 alleles in the coding DNA of myslef and my wife,... My training is in mammalian genetics, and I have never heard the term "alleles" used in that context. I think you're missing the point. Quote ...in addition there's the active, but not coding DNA (introns, etc.)  When that kind of numbers are being talked about, if 90% of our genes are identical, and the other 10% have an average of 5 alleles, that's still a lot of alleles. But not all of them affect fitness. Moreover, there are genes for which selection drives polymorphism, such as those in the Major Histocompatibility Complex.   Quote Is there a hard estimate of how many alleles are in the population of a typical human community?  (I assume that the alleles in my town are more important to me than additional alleles floating around darkest Africa somewhere.) That's funny that you should put it in such disturbingly quasi-racist terms, as Africans, being from the cradle of mankind, tend to be much more polymorphic (they have lots more alleles/gene) than any of the human groups that left Africa.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 09 2008,23:59    JAM, "That's funny that you should put it in such disturbingly quasi-racist terms" I didn't mean slight.  I only was reaching for a population that was physically the farthest away from me.  I am likely to mate within my community, not a distant community.  The calculations need only reference the assessible genepool, not the total conceivable genepool. I am still not finding an answer to my question, however.  How many alleles are likely to exist within the human population in the average community.  I can accept that many alleles are "not selectable", "fully neutral".  Fine enough, how many "selectable" alleles are there in a typical community of humans?   I've been trying to find the answer to the question.  So far I've found the following site: http://books.google.ca/books?i....U&hl=en It says the following:   Quote Perhaps as many as half of the loci in the human population are polymorphic Quote the chances of two people who are both "Caucasoid" differing in genetic constitution at one site on a given chromosome are about 14.3 per cent. If I read this correctly, there's LOTS of alleles!!

Bob O'H Posts: 2561 Joined: Oct. 2005 (Permalink) Posted: Mar. 10 2008,01:21    bFast - just a couple of observations. 1. It would help if you could clarify your terminology.  I think when you write "alleles" you mean "genes".  In Zachriel's notation, when he has a string of numbers (1112111), each number is a "gene", and each value that a gene can take is an allele.  I think you're describing the same thing, but you're using "allele" when you mean "gene". Yeah, I know.  Terminology is a pain.  But it will help everyone understand what you're doing. 2. I agree with Zachriel that you have an odd selection scheme.  A "better" scheme might be to select an individual at random to die, and then select the replacement with a probability proportional to the individual's fitness (i.e. divide by the sum of the fitnesses).  Or have a discrete time model and at each generation pick N individuals with replacement with probabilities proportional to the individuals' fitnesses. 3. The reason the focal gene's frequency drifts when there are more genes is that it has a smaller effect on fitness.  If we just think of the binary case, the genetic variance for one gene is p_i(1-p_i) where p_i is the frequency of the 1 allele, and the total genetic variance is sum p_j(1-p_j).  The proportion of variance for one gene is then p_i(1-p_i)/(sum p_j(1-p_j)) and obviously the sum increases as each new gene is added, so the proportional effect of the ith allele get smaller.  Hence, the effect on fitness is less (because it is the absolute numbers you are using for that), so drift becomes more important. -------------- It is fun to dip into the various threads to watch cluelessness at work in the hands of the confident exponent. - Soapy Sam (so say we all)

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Mar. 10 2008,02:09    Quote (bFast @ Mar. 09 2008,23:59) JAM, "That's funny that you should put it in such disturbingly quasi-racist terms" I didn't mean slight. It sure seemed that way. You're ignoring my point, which is highly relevant to your question. Quote I only was reaching for a population that was physically the farthest away from me.  I am likely to mate within my community, not a distant community. Does your wife know about this? Seriously, do you not have any African-Americans in your community? Quote The calculations need only reference the assessible genepool, not the total conceivable genepool. Why? You're not making any sense. Quote I am still not finding an answer to my question, however. That's because, as Bob and I have noted, you are mangling the relevant terminology. Hint: geneticists don't use the term "genepool." Quote How many alleles are likely to exist within the human population in the average community. In Africa, or in North Dakota? I can't see how there wouldn't be "average communities" in both places. Or are you hinting at racism again? Quote I can accept that many alleles are "not selectable", "fully neutral". Those are generally described as polymorphisms. There are tens or hundreds of thousands. Quote Fine enough, how many "selectable" alleles are there in a typical community of humans? I don't know, but I know that each of us is heterozygous for 5-10 recessive lethal alleles. Does that help? The other place to look is in the huge study of Icelandic folks, which would only provide a lower bound, as they are very inbred. Quote If I read this correctly, there's LOTS of alleles!! Is that a problem? Google's not going to help if you use the wrong terminology.

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 10 2008,09:53    Quote (bFast @ Mar. 09 2008,22:42) Zachriel:       Quote That's a rather odd selection method. You pit organism 1 against organism 2, but it's not the victor that reproduces, but a recombination of two other organisms. I suppose it should result in evolution towards higher fitness, though. I'll test it to be sure. This is certainly not sexual selection.  But why should we assume that the victor should also get the privelage of reproduction.  Am I to assume that shortly after my handicapped friend I get chased by the bear, and he gets eaten, I get to reproduce? Thanks for providing your algorithm. I have reproduced your results. As I had expected, your selection method does result in strong positive selection. Starting from randomized genomes of 0's and 1's, the population rapidly evolves to maximum fitness. With recombination turned on, that's all 1's; 1111111111111111....    ' This one dies    If pFit < rFit Then        r = r1: c = c1    Else        r = r2: c = c2    End If -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 10 2008,09:53    JAM, you bore me.  You don't at all answer my real question, but spend all your energy trying to twist what I am saying into something racist.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 10 2008,09:59    Zachriel, "Starting from randomized genomes of 0's and 1's, the population rapidly evolves to maximum fitness." Yes. My algorithm works.  However, the greater the number of alleles, the more slowly any one evolves to maximum fitness.  By about 20,000 they all mostly just wander about aimlessly. How many alleles that actually do something exist in the average human community?  What is the reasonable number that I should be using when running my sim?

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 10 2008,11:39    Quote (bFast @ Mar. 09 2008,22:42) You will note that when the allele count is 200, this sim works as expected, when it is 2000, it works as expected -- more slowly than the first, but it still evolves.   When the allele count gets to 20,000, genetic drift becomes the predominant paradyme.  This is what I would expect (exactly where the numbers lie is outside of my capacity to predict, but I expected that at some point genetic drift vastly dominates over selection.)  So, as expected, if there are too many alleles in a population, they act as noise, and the signal of the new mutation is drowned out by the noise of all the other alleles flying around everywhere. Of course. So? With a (nearly) neutral mutation, we expect that most will be lost. (With your randomized genome with a size of 2000, the average fitness of each organism is 1000 with a standard deviation of ~22, so a single allele change from a 1 to a 2 is insignificant.) Keep in mind the chance of fixation of a (nearly neutral) mutation is (nearly) equal to the proportion in the population. If at a given locus, 1% of the population has the 2-allele, then we would expect the chance of fixation to be about 1% (perhaps a bit better because there is weak selection). However, if we introduce the occasional random mutation, the results are strikingly different. The population rapidly evolves by sorting through the randomized 0's and 1's of the genome. Once some order is imposed, the 2-allele then becomes a significant benefit and the selection becomes stronger. As to your question about natural genetic variations, not only do mutations add variation, but we also have variation due to geographic separation. Your simulation assumes random mating across the population, which will tend to lead to a monomorphic population. However, the Allele Blender uses proximity for both environmental and mating selection. This results in geographic patterns of diversity. It may be a few days, but I'll try to provide more specifics. -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 10 2008,12:34    It seems to me that there are three classes of alleles that are of interest: - Primarily beneficial alleles, those that have not yet fixed, but eventually will.  Probably a small number. - Alleles that cause differences between individuals, but are not easily rated as better or worse compared to their sibling alleles.  Like, who's to say that curly hair is better or worse than straight.  In some circomstances one will be favored over another, but hardly with universality. - Alleles that are functionally identical to their sibs even though they are technically different.  Such as an alternate amino within the same family, causing the same net result.  I think these can be ignored. So the two numbers of interest are: beneficial alleles, on the rise, and alleles that cause phenotypal differences, but not universal advantage. As human populations have, until the last couple of centries, been predominantly located into communities, I would assume that numbers from the Icelandic study mentioned by JAM would make sense.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 10 2008,13:14    Let me just also say, in case it makes for easier numbers, that we don't by any means need human numbers.  We could take numbers from any other species of mammal as far as I am conserned.

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 10 2008,13:22    Quote (bFast @ Mar. 10 2008,09:59) Zachriel, "Starting from randomized genomes of 0's and 1's, the population rapidly evolves to maximum fitness." Yes. My algorithm works.  However, the greater the number of alleles, the more slowly any one evolves to maximum fitness. By about 20,000 they all mostly just wander about aimlessly. That is not what my results show. With a randomized genome of 20,000 genes (0's and 1's), population of 100, no mutation, your selection algorithm, per generation,         G        Avr. Fit         0         10010         1         10038         2         10077         3         10121         4         10180         5         10220         10       10411         20       10741         30       10994         40       11216         50       11383 In other words, definitely not drift. It's easy to understand why you saw what you wanted to see within these long strings of numbers. Which brings us to a broader point. Try to hold your own views skeptically. Instead of trying to merely confirm them, try to falsify them. Even if you think you have demonstrated your point, someone might vary the selection algorithm slightly and produce a different result. You have to be able to explain not only your own results, but everyone else's too.         11326 11428 11409 11396 11408 11411 11333 11380 11334 11369         11325 11318 11455 11374 11370 11359 11361 11406 11338 11371         11373 11306 11412 11413 11382 11407 11414 11379 11373 11371         11407 11370 11387 11398 11326 11365 11417 11397 11405 11420         11376 11393 11421 11378 11389 11401 11371 11394 11437 11387         11383 11377 11381 11356 11379 11386 11381 11397 11372 11395         11339 11400 11383 11353 11351 11425 11411 11384 11408 11386         11404 11377 11388 11420 11375 11394 11345 11371 11397 11398         11426 11416 11368 11373 11414 11355 11385 11341 11377 11362         11383 11358 11408 11363 11355 11396 11345 11448 11362 11372 -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

J-Dog Posts: 4402 Joined: Dec. 2006 (Permalink) Posted: Mar. 10 2008,13:27    Quote (bFast @ Mar. 10 2008,13:14) Let me just also say, in case it makes for easier numbers, that we don't by any means need human numbers.  We could take numbers from any other species of mammal as far as I am conserned. Welcome to open posting, bfast.  I once was Glarson and DRat so that I could post at UD. And in honor of your attempt to break free of your brush with the Dark Side, I propose, as you suggested, a non-human mammal species to use with your sim.   I suggest a mammal covered with blubber, not a lot of brain power, and constantly attempting to increase its breeding opportunities through loud, agressive, and to us here, non-sensical chest beating behaviour.  Of course I am talking about a Walrus (aka DaveScot) and an Innuit woman. Please put this in your sim for me.  (Although I suspect this will not prove a very fruitful use of your time.) Thanks, J-Dog Banned Twice - And loving it. -------------- Come on Tough Guy, do the little dance of ID impotence you do so well. - Louis to Joe G 2/10 Gullibility is not a virtue - Quidam on Dembski's belief in the Bible Code Faith Healers & ID 7/08 UD is an Unnatural Douchemagnet. - richardthughes 7/11

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Mar. 10 2008,15:25    Quote (bFast @ Mar. 10 2008,09:53) JAM, you bore me.  You don't at all answer my real question, Really? How did you conclude that the three responses were not sincere efforts to answer your question at all? 1) There are tens or hundreds of thousands. 2) I don't know, but I know that each of us is heterozygous for 5-10 recessive lethal alleles. Does that help? 3) The other place to look is in the huge study of Icelandic folks, which would only provide a lower bound, as they are very inbred. Quote ...but spend all your energy trying to twist what I am saying into something racist. Then why not simply explain what you mean by "average community"? In the context of your question, I have no idea what you mean by that qualification. I don't think that any twisting is involved in concluding that your trying to exclude "darkest Africa" from your analysis *seems* racist.

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Mar. 10 2008,15:28    Quote (bFast @ Mar. 10 2008,12:34) As human populations have, until the last couple of centries, been predominantly located into communities, I would assume that numbers from the Icelandic study mentioned by JAM would make sense. So have you changed your mind since you wrote, "You don't at all answer my real question,..."? I still don't know what you mean by "communities," as average African communities would still be much more polymorphic than average European or Asian communities.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 10 2008,15:29    J-Dog: Quote Of course I am talking about a Walrus (aka DaveScot) and an Innuit woman. I was actually quite seriously thinking that we may know more about alleles that do stuff in dogs, as dogs have been bread from wolves into so many varieties.  So maybe we have a better logging of the effect of various alleles in dogs/wolves than in other mammals, such as walruses.  Oh yea, we'll have to include your genes.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 10 2008,15:32    JAM, the numbers available for the Icelandics seems just ducky as I suggested two posts back.  Though we may see the Icelandic community as "ingrown" by modern standards, I suspect that 200 years ago, (most of human evolution happened before 200 years ago, yes?) or 500 years ago, small, relatively isolated communities were much more common than they did now.  Selecting for an isolated community should produce a smaller allele count than would a count of all alleles within humanity.

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 10 2008,20:25    Quote (bFast @ Mar. 09 2008,22:42) (I assume that the alleles in my town are more important to me than additional alleles floating around darkest Africa somewhere.) Quote (bFast @ Mar. 10 2008,12:34) As human populations have, until the last couple of centries, been predominantly located into communities, I would assume that numbers from the Icelandic study mentioned by JAM would make sense. There is more variation within human populations (~85%) than between human populations (~15%). Any two random humans has about 99.99% sequence similarity. Most of these differences are biologically insignificant, a point that JAM alluded to above. -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 10 2008,22:09    1, You seem to be saying that local community or scope of humanity makes little difference.  Fine enough. 2, You suggest that you and I are 99.99% identical.  If there are 25,000 genes, with an average of 100 aminos per gene, that would mean that there's about 250 alleles.  From my understanding there are at least seven alleles that control for eye color (I recognize that these alleles may have other effects, as is so common.)  So eye color eats up 35% of the available alleles.  I don't believe it for a moment.  My bet is that there is no less than 1000 alleles that affect the phenotype within humanity.  Even 1000 would be an amazingly small number considering the amount of variance within humanity.  Further, if there really are this few alleles, getting to an accurate cause for all genetically caused diseases should be pretty darn easy. "There are over 6000 genetic disorders that can be passed down through generations." (http://www.geneticdiseasefoundation.org/) That would indicate that there are 6 genetic disorders for every allele. ;)

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 10 2008,22:27    Oops, math error.  7 in 250 is about 2.8% of the alleles that control eye color.

Henry J Posts: 5760 Joined: Mar. 2005 (Permalink) Posted: Mar. 10 2008,23:13    Quote If there are 25,000 genes, with an average of 100 aminos per gene, that would mean that there's about 250 alleles. Wouldn't that 250 be only the ones that happen to differ between the two individuals being compared? Other individuals could have different alleles for those 250 genes or for other genes that were the same in the two that were being compared here. Henry

Wesley R. Elsberry Posts: 4966 Joined: May 2002 (Permalink) Posted: Mar. 10 2008,23:19    Quote (bFast @ Mar. 10 2008,22:09) 1, You seem to be saying that local community or scope of humanity makes little difference.  Fine enough. 2, You suggest that you and I are 99.99% identical.  If there are 25,000 genes, with an average of 100 aminos per gene, that would mean that there's about 250 alleles.  From my understanding there are at least seven alleles that control for eye color (I recognize that these alleles may have other effects, as is so common.)  So eye color eats up 35% of the available alleles.  I don't believe it for a moment.  My bet is that there is no less than 1000 alleles that affect the phenotype within humanity.  Even 1000 would be an amazingly small number considering the amount of variance within humanity.  Further, if there really are this few alleles, getting to an accurate cause for all genetically caused diseases should be pretty darn easy. "There are over 6000 genetic disorders that can be passed down through generations." (http://www.geneticdiseasefoundation.org/) That would indicate that there are 6 genetic disorders for every allele. ;) Amino acids are specified by 3 nucleotide bases. 25,000 * 100 * 3 / 10,000 = 750 Edit: I missed another obvious factor: two copies per individual, thus: 25,000 * 100 * 3 * 2 / 10,000 = 1,500 That would be the estimate given the numbers you give for the expected number of nucleotide bases different between any two members of the population in question, and not an estimate of the total number of alternative alleles in the population. That number would be far, far larger for any reasonable-sized population. I also think the average AA length of proteins is skimpy in your estimate, but that's a really minor error, comparatively.   Quote From my understanding there are at least seven alleles that control for eye color (I recognize that these alleles may have other effects, as is so common.) Here's a useful piece of trivia: Between any two organisms whose genetics are based on paired chromosomes, the total number of alleles that they can possibly represent at any one locus is four. Edited by Wesley R. Elsberry on Mar. 11 2008,00:08 -------------- "You can't teach an old dogma new tricks." - Dorothy Parker

Richard Simons Posts: 425 Joined: Oct. 2006 (Permalink) Posted: Mar. 11 2008,05:31    bfast, I am not convinced that you have the concept of alleles completely straight as you use the word in an idiosyncratic manner. Quote My bet is that there is no less than 1000 alleles that affect the phenotype within humanity. Here you seem to be using allele when you actually mean locus. If we think of genes as being strung out along a chromosome, each position is referred to as a locus. At some of the loci there may be variants in the gene, called alleles. In a diploid organism, such as humans, each individual can, at most, have just two alleles for any one trait even though in the population as a whole there may be hundreds of alleles for this trait. It is not normal to refer to people as differing by a certain number of alleles, partly because what do you if two people are heterozygous and have three alleles between them? I suspect part of the problem may be that the word 'gene' is used in two ways. It usually means 'locus' but is also used to mean 'allele' so whenever you see it you need to be sure which meaning is intended. I am writing this in the middle of the night because I could not sleep. I hope I don't look at it in the morning and realize it is really obtuse. -------------- All sweeping statements are wrong.

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 11 2008,07:03    bFast, this was an interesting project. I just don't think it shows what you think it does. Nor have you cast the skeptical eye towards your preconceived notions, as I suggested you do. Quote (bFast @ Mar. 10 2008,22:09) 1, You seem to be saying that local community or scope of humanity makes little difference.  Fine enough. They are certainly not negligible, not to humans anyway. Some non-humans might have trouble telling the difference. Unlike Allele Blender, your simulation does not account for proximity. This tends to mix and homogenize the population. Quote (bFast @ Mar. 10 2008,22:09) If there are 25,000 genes, with an average of 100 aminos per gene, that would mean that there's about 250 alleles. Between two individuals, not throughout the population. Gene size is usually in the few kilobyte range. Of course, we are only concerned with environmentally selectable differences, so there may be innumerable flavors all represented by 1's. In any case, unlike Allele Blender, your simulation only allows for three selectable alleles per locus throughout the population. Quote (bFast @ Mar. 10 2008,22:09) From my understanding there are at least seven alleles that control for eye color (I recognize that these alleles may have other effects, as is so common.)  So eye color eats up 35% of the available alleles. I don't believe it for a moment. Many alleles may be neutral. Other alleles may be partially or wholly due to mating selection. Again, unlike Allele Blender, your simulation does not account for mating selection (for fitness or arbitrary trait). There are also other polymorphisms, such as duplications, insertions, deletions, rearrangements, and linked traits that are not considered in either simulation. This doesn't mean the simulations are without value. But even within the limited venue of your own simulation, you have yet to justify your preconceived conclusions. SOME OUTSTANDING QUESTIONS: * You claim that some beneficial mutations can be lost in genomes that vary wildly in fitness. So!? This is the expected result. * You claimed, incorrectly, that your random genomes of sufficiently large size would not evolve directionally. This was incorrect. * Mating selection in Allele Blender for a non-beneficial trait still allows for rapid improvement in fitness. * If we introduce the occasional random mutation, the results are strikingly different. The population rapidly evolves by sorting through the randomized 0's and 1's of the genome. Once some order is imposed, the 2-allele then becomes a significant benefit and the selection becomes stronger. * The real question is, how many SELECTABLE alleles are there versus how many alleles that produce no change in fitness? — JAM * As to your question about natural genetic variations, not only do mutations add variation, but we also have variation due to geographic separation. Your simulation assumes random mating across the population, which will tend to lead to a monotypic population. However, the Allele Blender uses proximity for both environmental and mating selection. This results in geographic patterns of diversity. I'll try to clean up the code on Allele Blender in a few days, so you can experiment with it.    ' Child's Fitness    cFit = calcFitness(Child)    ' Find weakest in area, including Parent    minFit = pFit    For f = 1 To 9        fit(f) = Fitness(r + ro(f), c + co(f))        If fit(f) > 0 And fit(f) < minFit Then minFit = fit(f)    Next f    ' If Child is better than anyone in the Neighborhood,    '   then replace the weakest    If cFit > minFit Then        ' Count weaklings in Neighborhood        w = 0        For f = 1 To 9            If fit(f) = minFit Then                w = w + 1                weak(w) = f            End If        Next f        ' Replace the weakest in Neighborhood        If w > 0 Then            weakest = Random(1, w)            rx = r + ro(weak(weakest))            cx = c + co(weak(weakest))            ' Update Array            Population(rx, cx) = Child            Fitness(rx, cx) = cFit            Beautiful(rx, cx) = calcBeauty(Child)            ' Update Display            Worksheets("Fitness").Cells(rx, cx) = Fitness(rx, cx)            Worksheets("Sequence").Cells(rx, cx) = Population(rx, cx)            Worksheets("Beauty").Cells(rx, cx) = Beautiful(rx, cx)        Else            Stop    ' Just checking        End If    End If -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 11 2008,07:38    Quote (Zachriel @ Mar. 11 2008,07:03) * You claim that some beneficial mutations can be lost in genomes that vary wildly in fitness. So!? This is the expected result. Perhaps some examples would help. * A hunting dog with a refined sense of smell but who would rather sleep than hunt. * A graceful gazelle without a sense of danger. * A smart kid with a reckless streak regarding cars. (Each of these traits might be beneficial in certain environments.) -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

slpage Posts: 349 Joined: June 2004 (Permalink) Posted: Mar. 11 2008,08:29    [quote=bFast,Mar. 10 2008,22:09][/quote] Wow... bfast: Quote 2, You suggest that you and I are 99.99% identical.  If there are 25,000 genes, with an average of 100 aminos per gene, that would mean that there's about 250 alleles. What does the average amino acid number have to do with it?  How you get 250 alleles out of that is a mystery of creationist math and biology. Quote From my understanding there are at least seven alleles that control for eye color (I recognize that these alleles may have other effects, as is so common.)  So eye color eats up 35% of the available alleles.  I don't believe it for a moment. What you 'believe' or not is immaterial. Quote My bet is that there is [sic] no less than 1000 alleles that affect the phenotype within humanity.  Even 1000 would be an amazingly small number considering the amount of variance within humanity. Why is that?  Do you have a rationale for that statement?  How much change does an allele produce?  Is it quantifiable?  Do all alleles produce the same or similar amount of change?  And how do you know? Quote  Further, if there really are this few alleles, getting to an accurate cause for all genetically caused diseases should be pretty darn easy. "There are over 6000 genetic disorders that can be passed down through generations." (http://www.geneticdiseasefoundation.org/) That would indicate that there are 6 genetic disorders for every allele. ;) You demonstrate nicely a common problem with IDcreationists with no biology background attempting to pontificate on biological matters.   For starters, why do you assume a completely uniform distribution of allelic difference?

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 11 2008,11:30    Richard Simons: Quote bfast, I am not convinced that you have the concept of alleles completely straight as you use the word in an idiosyncratic manner. Quote My bet is that there is no less than 1000 alleles that affect the phenotype within humanity. Here you seem to be using allele when you actually mean locus. No, I actually mean allele.  An allele is a variant of the same protein.  Somewhere in the genome there is a protein that controls for eye color.  One variant produces blue eyes, the other produces brown eyes.  Likely the allele producing green eyes is a third allele of the same protein.  Honest, I doubt if I could have carried this conversation on this long with Zachriel if I was unaware of what an allele is.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 11 2008,11:35    Zachriel, this conversation really needs a hard (or reasonably hard) number of how many alleles affect the phenotype of the human population.  I would suggest that any allele that produces a noticeable effect of any sort should be counted.  Though eye color may not affect one's ability to fight a bear, it may may a big difference with any one mating opportunity. Zachriel: [QUOTE]bFast, this was an interesting project/QUOTE] I am working on a more advanced sim that integrates two of the other sources of noise that I suggested in the beginning. Quote I just don't think it shows what you think it does. Nor have you cast the skeptical eye towards your preconceived notions, as I suggested you do. This sword cuts both ways.  I don't see you risking your preconceived notions on this sim any more than I am.

oldmanintheskydidntdoit Posts: 4999 Joined: July 2006 (Permalink) Posted: Mar. 11 2008,11:40    Quote (bFast @ Mar. 11 2008,11:35) I don't see you risking your preconceived notions on this sim any more than I am. For the benefit of the reader who is not familiar with the background here, why not list these "preconceived notions" to ensure no misunderstandings arise? If they are contributing to the design of the sim anyway.... -------------- I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies". FTK if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand Gordon Mullings

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Mar. 11 2008,12:25    Quote (bFast @ Mar. 11 2008,11:30) Richard Simons:       Quote bfast, I am not convinced that you have the concept of alleles completely straight as you use the word in an idiosyncratic manner.     Quote My bet is that there is no less than 1000 alleles that affect the phenotype within humanity. Here you seem to be using allele when you actually mean locus. No, I actually mean allele. No, you don't.   Quote An allele is a variant of the same protein. Wrong. Alleles are variants of genes. We've since expanded the definition to refer to polymorphisms outside of genes, like SNPs. Only a minority of alleles cause the production of different proteins. Only a minority of those alleles change the function of proteins.   Quote Somewhere in the genome there is a protein that controls for eye color. Your terminology is completely wrong, and it prevents you from understanding and communicating the most basic concepts. There are no proteins in the genome. There are genes throughout the genome that encode proteins involved in eye color. To say that this "controls" eye color is, strictly speaking, incorrect. The products of two genes are simply required to produce pigment in the iris. People who are homozygous null at both loci have blue eyes.   Quote One variant produces blue eyes, the other produces brown eyes. That's an oversimplification.   Quote Likely the allele producing green eyes is a third allele of the same protein. No, for two reasons. There's no such thing as "an allele of a protein," because alleles are versions of genes (aka loci). The second reason is that there is a second locus, EYCL1, to which green color is largely (but not completely) attributed. Then, there's epistatic interactions.   Quote Honest, I doubt if I could have carried this conversation on this long with Zachriel if I was unaware of what an allele is. That's why we're laughing at you.

slpage Posts: 349 Joined: June 2004 (Permalink) Posted: Mar. 11 2008,13:09    [quote=bFast,Mar. 11 2008,11:30][/quote] Clueless creationist.... Quote Richard Simons:   Quote bfast, I am not convinced that you have the concept of alleles completely straight as you use the word in an idiosyncratic manner.   Quote My bet is that there is no less than 1000 alleles that affect the phenotype within humanity. Here you seem to be using allele when you actually mean locus. No, I actually mean allele.  An allele is a variant of the same protein.   Do you even know what a GENE is for christ's sake? No, an allele is a variant form of a GENE. You should stick to whatever it is you think you actually understand, because this ain't it. Quote Somewhere in the genome there is a protein that controls for eye color. Clueless.  I may be distracting from is topic, but you should not even be discussing it with this level of ignorance. Quote  Honest, I doubt if I could have carried this conversation on this long with Zachriel if I was unaware of what an allele is. Well, you have been yet you are very clearly unaware. Creationists have never let their ignorance stop them from pontificating, though.  So keep going - it is entertaining to see someone so clueless carry on as if they have some sort of in-depth understanding.

Wesley R. Elsberry Posts: 4966 Joined: May 2002 (Permalink) Posted: Mar. 11 2008,13:11    Here's the t.o. jargon file entry: Quote :Allele:    (n) [FAQ] 1. One of two or more forms [of a {gene}] that can exist at a single locus. [den., from Suzuki et al. 1989] "If one of your parents has blue eyes and yours are brown, then you have two different alleles of the eye color gene -- one for blue and one for brown." -------------- "You can't teach an old dogma new tricks." - Dorothy Parker

Wesley R. Elsberry Posts: 4966 Joined: May 2002 (Permalink) Posted: Mar. 11 2008,14:12    Researchers aren't confused about what an allele is...   Quote The presence of a multitude of protein isoforms, such as splice variants, combinatorial variants, post-translational modifications, specific proteolysis, and genetic variability (alleles), makes the human proteome space huge, and the initial ambition of a genome-wide antibody-based proteomics effort has therefore been suggested to be directed to the non-redundant proteome defined as a representative protein from every gene locus (3). The current estimate of the size of the non-redundant proteome is ~23,000 proteins (Ensembl, www.ensembl.org), and at present more than 16,000 of those have been manually annotated by the Swiss-Prot/UniProt effort (www.uniprot.org). Emphasis added. -------------- "You can't teach an old dogma new tricks." - Dorothy Parker

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 11 2008,14:19    Wesley Elsberry, thanks for getting to a real number to my question. Based upon this information, it it reasonable to use the number 16,000 as the number of alleles in the human population?

Wesley R. Elsberry Posts: 4966 Joined: May 2002 (Permalink) Posted: Mar. 11 2008,14:21    If bFast hasn't read it yet, it is time to dig into Chris Colby's "Introduction to Evolutionary Biology", one of the "must-read" FAQs on the TalkOrigins Archive. Quote Evolution requires genetic variation. If there were no dark moths, the population could not have evolved from mostly light to mostly dark. In order for continuing evolution there must be mechanisms to increase or create genetic variation and mechanisms to decrease it. Mutation is a change in a gene. These changes are the source of new genetic variation. Natural selection operates on this variation. Genetic variation has two components: allelic diversity and non- random associations of alleles. Alleles are different versions of the same gene. For example, humans can have A, B or O alleles that determine one aspect of their blood type. Most animals, including humans, are diploid -- they contain two alleles for every gene at every locus, one inherited from their mother and one inherited from their father. Locus is the location of a gene on a chromosome. Humans can be AA, AB, AO, BB, BO or OO at the blood group locus. If the two alleles at a locus are the same type (for instance two A alleles) the individual would be called homozygous. An individual with two different alleles at a locus (for example, an AB individual) is called heterozygous. At any locus there can be many different alleles in a population, more alleles than any single organism can possess. For example, no single human can have an A, B and an O allele. Considerable variation is present in natural populations. At 45 percent of loci in plants there is more than one allele in the gene pool. [allele: alternate version of a gene (created by mutation)] Any given plant is likely to be heterozygous at about 15 percent of its loci. Levels of genetic variation in animals range from roughly 15% of loci having more than one allele (polymorphic) in birds, to over 50% of loci being polymorphic in insects. Mammals and reptiles are polymorphic at about 20% of their loci - - amphibians and fish are polymorphic at around 30% of their loci. In most populations, there are enough loci and enough different alleles that every individual, identical twins excepted, has a unique combination of alleles. That essay has been there since the mid-1990s. -------------- "You can't teach an old dogma new tricks." - Dorothy Parker

Wesley R. Elsberry Posts: 4966 Joined: May 2002 (Permalink) Posted: Mar. 11 2008,14:25    Quote (bFast @ Mar. 11 2008,14:19) Wesley Elsberry, thanks for getting to a real number to my question. Based upon this information, it it reasonable to use the number 16,000 as the number of alleles in the human population? No. The very paragraph quoted notes that their research is ignoring the various sources of variation listed, including allelic variation. They just want to accumulate one representative protein per genetic locus, and thus will take the result of protein assembly from only one allele per locus. Nor is 16,000 even the number to use for that limited prospect, since that just happens to be how many proteins have been manually annotated so far in one project. ETA: For the eye color example, the project quoted would likely register only two proteins for the two major loci known for eye color, though we happen to know that there are more protein products associated with those loci. Edited by Wesley R. Elsberry on Mar. 11 2008,14:29 -------------- "You can't teach an old dogma new tricks." - Dorothy Parker

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 11 2008,14:29    Quote (bFast @ Mar. 11 2008,11:35) Zachriel, this conversation really needs a hard (or reasonably hard) number of how many alleles affect the phenotype of the human population.  I would suggest that any allele that produces a noticeable effect of any sort should be counted.  Though eye color may not affect one's ability to fight a bear, it may may a big difference with any one mating opportunity. You are getting a bit ahead of yourself. Biology is far more complicated than these sorts of simulations which are only tangentially related to living organisms. You haven't even been able to sustain your simple point concerning noise within the toy universe. Quote (bFast @ Mar. 11 2008,11:35) Zachriel:     Quote I just don't think it shows what you think it does. Nor have you cast the skeptical eye towards your preconceived notions, as I suggested you do. This sword cuts both ways.  I don't see you risking your preconceived notions on this sim any more than I am. Huh? I even replicated your own algorithm so that I could study its behavior in detail. Moreover, for some reason, you seem to have forgotten to address these points: * You claimed that some beneficial mutations can be lost in genomes that vary wildly in fitness. So!? This is the expected result. * You claimed, incorrectly, that your random genomes of sufficiently large size (20K) would not evolve directionally. This was incorrect. * If we introduce the occasional random mutation, the results are strikingly different. The goal isn't to prove that a particular system works the way you think it should. You need to generalize your results to include a sufficiently large class of evolutionary algorithms that is might reasonably shed light on the behavior of biological systems. I would suggest you continue to study your simple system to better understand how it works and why you were wrong about its behavior. It's sufficient to its purpose. -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 11 2008,14:50    I have added a few features to my sim.  Most noteably I have added an excel compatible summary output.  The computer is now producing a mass simulation.  When we get real data to work with, we can examine the results with a higher data to presumption ratio.

Wesley R. Elsberry Posts: 4966 Joined: May 2002 (Permalink) Posted: Mar. 11 2008,15:04    One could get a back-of-the-envelope guess for a minimum number of alleles in the human population by combining Colby's information with that of the quoted proteomic project. I worked that out, but I figure that maybe I can pose it as an exercise for the reader here. I don't get, though, what a "estimated total number of alleles" is supposed to do for you once you've got it. AFAICT, one cannot use the number in a unitary fashion. -------------- "You can't teach an old dogma new tricks." - Dorothy Parker

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 11 2008,15:17    Wesley R. Elsberry, "one cannot use the number in a unitary fashion." Why not?

Wesley R. Elsberry Posts: 4966 Joined: May 2002 (Permalink) Posted: Mar. 11 2008,15:24    Quote (bFast @ Mar. 11 2008,15:17) Wesley R. Elsberry, "one cannot use the number in a unitary fashion." Why not? Tell me how you propose using it and I'll tell you whether that makes sense to me. -------------- "You can't teach an old dogma new tricks." - Dorothy Parker

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Mar. 11 2008,16:31    Quote (bFast @ Mar. 11 2008,14:19) Wesley Elsberry, thanks for getting to a real number to my question. But no thanks to those who corrected your gross misunderstanding of the fundamentals you need to understand to construct a useful model. Never admit an error, bfast. That does wonders for your credibility.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 11 2008,18:30    Wesley R. Elsberry, "Tell me how you propose using it and I'll tell you whether that makes sense to me." Please read my original post, post #19 on page 1.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 11 2008,18:31    JAM, and the other peanut gallery critics,  has it dawned on you that Zachriel, an actual Ph.D. biologist, has not questioned my understanding of what an allele is.  Convince him that I misunderstand or SHUT UP!!

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 11 2008,18:53    Quote (bFast @ Mar. 11 2008,18:31) JAM, and the other peanut gallery critics,  has it dawned on you that Zachriel, an actual Ph.D. biologist, has not questioned my understanding of what an allele is. Convince him that I misunderstand or SHUT UP!! I think you're confused. Zachriel is the angel that rules over memory, presides over the planet Jupiter. Crystal spheres, that sort of thing. JAM, on the other hand, says he's trained in mammalian genetics. Of mice and men. -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Mar. 11 2008,18:57    Quote (bFast @ Mar. 11 2008,18:31) JAM, and the other peanut gallery critics,  has it dawned on you that Zachriel, an actual Ph.D. biologist, has not questioned my understanding of what an allele is.  Convince him that I misunderstand or SHUT UP!! bFast, It's clear to me that Zachriel knows full well that you don't understand what an allele is. Given your petulant whining, that would be clear to me even if I was a lay observer instead of the Ph.D. biologist that I actually am. It's hysterically funny that you take the fact that Zachriel didn't correct you as some sort of endorsement of your false claim that alleles are versions of proteins. bFast, Mar. 10 2008,09:53   "JAM, you bore me.  You don't at all answer my real question..." bFast, less than 3 hours later: "I would assume that numbers from the Icelandic study mentioned by JAM would make sense."

Wesley R. Elsberry Posts: 4966 Joined: May 2002 (Permalink) Posted: Mar. 11 2008,19:07    Quote (bFast @ Mar. 11 2008,18:30) Wesley R. Elsberry, "Tell me how you propose using it and I'll tell you whether that makes sense to me." Please read my original post, post #19 on page 1. Yes. What you want is the proportion of polymorphic loci, not the absolute number of alleles. There are broad numbers in the Colby FAQ. Alleles are not variants of proteins, they are variants of genes. I am a Ph.D. biologist, by the way. -------------- "You can't teach an old dogma new tricks." - Dorothy Parker

Wesley R. Elsberry Posts: 4966 Joined: May 2002 (Permalink) Posted: Mar. 11 2008,20:24    By the way, Sir Ronald Fisher has analytic solutions for many of the problems proposed in this thread. See "The Genetical Theory of Natural Selection", 1930. -------------- "You can't teach an old dogma new tricks." - Dorothy Parker

Richard Simons Posts: 425 Joined: Oct. 2006 (Permalink) Posted: Mar. 11 2008,21:00    Quote (bFast @ Mar. 11 2008,11:30) An allele is a variant of the same protein.  Somewhere in the genome there is a protein that controls for eye color. No, alleles are not proteins. Although in the 1950s it was thought that the genetic material might be protein it has been known for over 40 years that is nucleic acids.   Quote (bFast @ Mar. 11 2008,18:31) JAM, and the other peanut gallery critics,  has it dawned on you that Zachriel, an actual Ph.D. biologist, has not questioned my understanding of what an allele is.  Convince him that I misunderstand or SHUT UP!! That Zachriel has not blatently criticized your use of allele does not make it correct. I too have a Ph.D., perhaps not in genetics but I have taken several post-graduate courses in plant breeding. Your usage of 'allele' has been, shall we say, different. -------------- All sweeping statements are wrong.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 11 2008,21:28    Wesley R. Elsberry, "Alleles are not variants of proteins, they are variants of genes. I am a Ph.D. biologist, by the way." I am aware that alleles are variants of genes. But genes make proteins, amongst other stuff that they do.  Often coding genes vary in a way that doesn't affect the resultant protein.  As such, the variant is not selectable, and is ignorable in this context.  Often the resultant change in the protein is the switch of one amino for another which does not affect the protein in any way.  I also respect the hypothesis that about 95% of DNA does absolutely nothing for the organism, therefore any change in that 95% does nothing. Only alleles of genes (two variants of the same gene) which actually affect the phenotype of the organism need be considered in this context.  I actually understand all of that. Now, back to the first question.  How many alleles are there which affect the organism's phenotype (in this case a mammal, I don't care which one) in any measurable way?   JAM: Quote bFast, less than 3 hours later: "I would assume that numbers from the Icelandic study mentioned by JAM would make sense." You still haven't given me the darn number!! I understand perfectly what an allele is.  You all are just playing the "creationists aren't evolutionists because they don't understand the basics" card.  It is bull! If I get any more of it, I will end this thread.  I am getting interesting results on my extended simulation, but I think I'll find a less rejecting audience.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 11 2008,21:31    Oh, by the way.  I am also aware that genes often code for more than one protein, that genes sometime code for active RNA sequences, and that genes play various "control" roles.  Any of these genes could have multiple versions floating around, each "multiple version" is an allele.  If the versions affect the organism's phenotype in any way, whether it be the organism's fight/flight respons, or the length of its eye-lashes then it should "count" in this context.  If two alleles make no difference to the phenotype they should be ignored.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 11 2008,21:40    And, gentlemen, if my understanding of alleles is so messed up, why could Zachriel simulate my ideas in his pre-built allele simulating software?  Answer me that one?

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 11 2008,22:00    I ran a very interesting trial with bFast's simulator. Population 400, genes 500. At generation 71, all 500 genes were 1's. Doing a little ID math, that's 2^500. The Universal Probability Bound! And not just once! The entire population. (By the way, if the population is too small, there's a significant chance that a particular locus will not have an available 1-allele. His simulation does not allow novel mutations.) Now with Allele Blender, we can mutate from a 1-allele to a 2-allele with a probability of 20%. From a 2-allele to a 3-allele also with a probability of 20%. And stepping up to the 9-allele. For any particular gene to reach the 9-allele is eight steps or ~10^-6. Population 400, genes 100. At generation 369, we reached saturation. All 9's. Every gene throughout the population. The ID math is 10^-600.    ' Fitness and Beauty Stats    cntFitness = 0: minFitness = Fitness(1, 1): maxFitness = minFitness    cntBeauty = 0: minBeauty = Beautiful(1, 1): maxBeauty = minBeauty    For r = 1 To numRows      For c = 1 To numCols        f = Fitness(r, c)        cntFitness = cntFitness + f        If f > maxFitness Then maxFitness = f        If f < minFitness Then minFitness = f        b = Beautiful(r, c)        cntBeauty = cntBeauty + b        If b > maxBeauty Then maxBeauty = b        If b < minBeauty Then minBeauty = b      Next c    Next r    avrFitness = cntFitness / (numRows * numCols)    avrBeauty = cntBeauty / (numRows * numCols) And it took less than zillions of years ™ -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

digitus impudicus Posts: 62 Joined: Feb. 2008 (Permalink) Posted: Mar. 11 2008,22:01    At first guess, I would say that he made a decision to use the appropriate definition of an allele in the model..... We now return you to your lurker free channel

slpage Posts: 349 Joined: June 2004 (Permalink) Posted: Mar. 12 2008,08:08    Quote (bFast @ Mar. 11 2008,18:31) JAM, and the other peanut gallery critics,  has it dawned on you that Zachriel, an actual Ph.D. biologist, has not questioned my understanding of what an allele is.  Convince him that I misunderstand or SHUT UP!! Sorry, bfast, I too have a PhD in biology (anatomy and cell biology, to be precise) and you clearly don't even really understand what a gene is, much less an allele. Here, I will prove it: "An allele is a variant of the same protein. " An allele is not a protein.  Nor is a gene.  You clearly don't know, whether Zachrial pointed it out or not.  Maybe he just has a higher tolerance for arrogant ignorance. Perhaps YOU should SHUT UP since you are clearly well out of your league on this basic issue.

slpage Posts: 349 Joined: June 2004 (Permalink) Posted: Mar. 12 2008,08:11    Quote (bFast @ Mar. 11 2008,21:40) And, gentlemen, if my understanding of alleles is so messed up, why could Zachriel simulate my ideas in his pre-built allele simulating software?  Answer me that one? Simulators do not rely on erroneous understandings, they use numbers.  Pretty simple, really. But, you are a computer technician creationist, and you know everything about everything.

slpage Posts: 349 Joined: June 2004 (Permalink) Posted: Mar. 12 2008,08:22    Quote (bFast @ Mar. 11 2008,21:28) bfast: Quote I am aware that alleles are variants of genes. But genes make proteins, amongst other stuff that they do. Yes, but they are not proteins. Google expertise is not real expertise. Quote Only alleles of genes (two variants of the same gene) which actually affect the phenotype of the organism need be considered in this context.  I actually understand all of that. Yet you wrote that alleles are variations of proteins, so clearly you don't.  If it had been a mere misstatement, then you would have had no problem admitting the error and moving on. But you actually expanded on the error: No, I actually mean allele.  An allele is a variant of the same protein.  Somewhere in the genome there is a protein that controls for eye color.  One variant produces blue eyes, the other produces brown eyes.  Likely the allele producing green eyes is a third allele of the same protein. And now you are attempting to minimize/equivocate by offering up some Wiki expertise (that still seems to ignore the resources Wes provided). Quote Now, back to the first question.  How many alleles are there which affect the organism's phenotype (in this case a mammal, I don't care which one) in any measurable way?   Who knows?  Maybe you can ask DaveScot - he has a high IQ. Quote I understand perfectly what an allele is.  You all are just playing the "creationists aren't evolutionists because they don't understand the basics" card.  It is bull! An allele is a variant of the same protein.  Somewhere in the genome there is a protein that controls for eye color.  One variant produces blue eyes, the other produces brown eyes.  Likely the allele producing green eyes is a third allele of the same protein. 'Bull' must be creationese for 'true'. Quote If I get any more of it, I will end this thread.  I am getting interesting results on my extended simulation, but I think I'll find a less rejecting audience. You mean like a bunch of sycophantic know-nothing fellow creationists who seem to live to pat each other on the back for spewing nonsense on moderator-protected creationist havens like UD? What a spoiled baby.

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 12 2008,09:08    Quote (slpage @ Mar. 12 2008,08:08) You clearly don't know, whether Zachrial pointed it out or not.  Maybe he just has a higher tolerance for arrogant ignorance. I did try to clarify bFast's terminology earlier in the thread in order to fully comprehend what he was trying to claim. However, he hasn't been too forthcoming on answering my questions. I am still willing to give him a chance to make his point. (The problem remains of how to generalize the results sufficiently as to make a valid claim about biology. I remain very doubtful. The results so far actually contradict bFast's understanding—even within the toy universe. But first things first.) -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

slpage Posts: 349 Joined: June 2004 (Permalink) Posted: Mar. 12 2008,09:22    Quote (Zachriel @ Mar. 12 2008,09:08) Quote (slpage @ Mar. 12 2008,08:08) You clearly don't know, whether Zachrial pointed it out or not.  Maybe he just has a higher tolerance for arrogant ignorance. I did try to clarify bFast's terminology earlier in the thread in order to fully comprehend what he was trying to claim. However, he hasn't been too forthcoming on answering my questions. I am still willing to give him a chance to make his point. (The problem remains of how to generalize the results sufficiently as to make a valid claim about biology. I remain very doubtful. The results so far actually contradict bFast's understanding—even within the toy universe. But first things first.) Indeed. This reliance upon 'toy' examples has a long history in the IDcreationist realm.  I am reminded of Cordova's insistence that his "toy example" (his words) of molecular phylogenetics - employing a whopping 10 letters, 'mutating' 1 per round of 'evolution', and showing that after only a few such rounds, hierarchies were impossible to make - proved that molecular phylogenetics was unrelaiable and also, of course, that somehow this showed evolution was wrong.  This occurred on the old version of the KCFS forum.  To employ a hackneyed phrase, it wasn't even wrong, and here we have a simulator violating Borel's theorem right before the creationist's eyes.  Amazing. In the end, my 'predicition' was right - you just have a higher tolerance for arrogant ignorance. :p

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 12 2008,10:41    Zachriel, "I am still willing to give him a chance to make his point." As I mentioned earler, I have modified my sim to log its results, and to do a run, advance, run cycle.  I am also running a pure-random baseline, so that we can see exactly what genetic drift will do.  When I have a package of serious data, then there will be results to talk about. Zachriel: Quote I did try to clarify bFast's terminology earlier in the thread in order to fully comprehend what he was trying to claim. However, he hasn't been too forthcoming on answering my questions. Which question have I not been forthcoming about? I have placed one question before you all that I haven't had an answer to yet.  How many alleles are there in the human, or another mammal's, population that directly affect the phenotype.  What number should I be using for my gene count?  So far I have numbers from the unbelievably low 250, to a high of 16,000.  However, whether the 16,000 all register a difference in the human phenotype is not clear.

oldmanintheskydidntdoit Posts: 4999 Joined: July 2006 (Permalink) Posted: Mar. 12 2008,10:55    Quote (oldmanintheskydidntdoit @ Mar. 11 2008,11:40)   Quote (bFast @ Mar. 11 2008,11:35) I don't see you risking your preconceived notions on this sim any more than I am. For the benefit of the reader who is not familiar with the background here, why not list these "preconceived notions" to ensure no misunderstandings arise? If they are contributing to the design of the sim anyway.... Hi bFast, I asked you what preconceived notions were feeding into the design of your sim. What notion is it that you hope your sim will support, once sufficient data is available? -------------- I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies". FTK if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand Gordon Mullings

JAM Posts: 517 Joined: July 2007 (Permalink) Posted: Mar. 12 2008,11:47    Quote (bFast @ Mar. 12 2008,10:41) Zachriel, "I am still willing to give him a chance to make his point." As I mentioned earler, I have modified my sim to log its results, and to do a run, advance, run cycle.  I am also running a pure-random baseline, so that we can see exactly what genetic drift will do.  When I have a package of serious data, then there will be results to talk about. Does that mean you'll be interested in discussing the real sequence data too? Quote I have placed one question before you all that I haven't had an answer to yet. That's not true, bFast. I was completely forthcoming and answered it as completely as possible. Quote How many alleles are there in the human, or another mammal's, population that directly affect the phenotype. I answered, "I don't know, but I know that each of us is heterozygous for 5-10 recessive lethal alleles. Does that help? The other place to look is in the huge study of Icelandic folks, which would only provide a lower bound, as they are very inbred." Quote What number should I be using for my gene count? That's a completely different question. You have conflated "allele" with both "version of a protein" and "gene," and neither is correct. Quote So far I have numbers from the unbelievably low 250, to a high of 16,000.  However, whether the 16,000 all register a difference in the human phenotype is not clear. For genes, I would start with dozens and gradually increase until the answer is clear. The real number of genes (30000) seems like too much for your sim to handle.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 12 2008,15:10    JAM:   Quote The other place to look is in the huge study of Icelandic folks, which would only provide a lower bound, as they are very inbred." I do not have access to the journals.  Is the information on the Icelandic folks published on the net?   Quote You have conflated "allele" with both "version of a protein" and "gene," and neither is correct. I understand that an allele is a version of a gene.  I understand that there are non-coding genes.  I understand that introns, for instance, often affect the phenotype.  I would assume that an intron would be seen as a non-coding gene.  However, I may be incorrect when I assume that an intron would be seen as a gene, or a portion of a gene even though it is not a gene that codes to protein.  Alas, this only goes to the question of exactly how the word "gene" is defined by biologists, not to my understanding of what an allele is.   Is it safe to say that an allele is a variant of a segment of DNA that acts as a unit, where a coding gene is an example of a segment of DNA that acts as a unit -- translating into protein. If a gene codes to a protein, as somewhere between 20,000 and 30,000 do, then any two versions of that protein would indicate two versions of the gene, two alleles, would they not?  I agree that I sometimes refer to two versions of proteins because the proteins are closer to the phenotype, and it is only the phenotype that natural selection works on.  However, I do recognize that the "alleles" are the variants of the genes involved. Quote For genes, I would start with dozens and gradually increase until the answer is clear. The real number of genes (30000) seems like too much for your sim to handle. I am starting with 200.  There are surely 200 phenotype affecting alleles in the human population.  My simulator can probably handle about 5,000, maybe 10,000.  However, I think that the range of 200 to 2000 will produce an algebraic curve that will allow for reasonable extrapolation.   I am of the impression that for most genes there is only one allele, or if there are more, that the other alleles don't affect the phenotype.  If there is only one allele, it doesn't count in my sim, its only the multiple-allele genes, introns, etc., where the two alleles produce differences in the phenotype that should count for my sim.   Further, when I consider the 6000 disease producing alleles, I assume that they have very low rates in the population.  As I consider this, it becomes clear to me that some reasonable level of "rare allele" can be dismissed. Quote For genes, I would ... gradually increase until the answer is clear. By time I have run my sim, I will have an algebraic expression that follows the curve.  Is that what you mean by "until the answer is clear", or are you suggesting that once I determine the point when natural selection no longer grabs the mutation as proof of how many phenotype affecting alleles the human family has?

Wesley R. Elsberry Posts: 4966 Joined: May 2002 (Permalink) Posted: Mar. 12 2008,16:12    Quote (bFast @ Mar. 12 2008,10:41) Zachriel, "I am still willing to give him a chance to make his point." As I mentioned earler, I have modified my sim to log its results, and to do a run, advance, run cycle.  I am also running a pure-random baseline, so that we can see exactly what genetic drift will do.  When I have a package of serious data, then there will be results to talk about. Zachriel:     Quote I did try to clarify bFast's terminology earlier in the thread in order to fully comprehend what he was trying to claim. However, he hasn't been too forthcoming on answering my questions. Which question have I not been forthcoming about? I have placed one question before you all that I haven't had an answer to yet.  How many alleles are there in the human, or another mammal's, population that directly affect the phenotype.  What number should I be using for my gene count?  So far I have numbers from the unbelievably low 250, to a high of 16,000.  However, whether the 16,000 all register a difference in the human phenotype is not clear. 250 was unbelievable because it was premised upon - the false belief that characterizing the degree of genetic difference between two individuals was also a characterization of total variation in the population from which the individuals were taken - the false belief that alleles were proteins - the false belief that each amino acid represented one opportunity for genetic change - the false belief that each individual carried only one copy of the genetic information - the false belief that 100 amino acids is an average length of proteins in the proteome A correction concerning the 250 number followed shortly after it was first posted. There seems to be some fixation on the 16,000 number, though it was clearly stated that was merely the number of proteins currently annotated in a particular database and not the total number of proteins (or, more precisely, representative proteins) in the human proteome.     Quote The current estimate of the size of the non-redundant proteome is ~23,000 proteins (Ensembl, www.ensembl.org), and at present more than 16,000 of those have been manually annotated by the Swiss-Prot/UniProt effort (www.uniprot.org). They were only interested in collecting one protein per locus, which  completely blows off the issue of prevalence of alternatives due to allelic variation. I already pointed out that the 16,000 number wasn't what bFast wanted. I also pointed out that one could derive an estimate of the minimum number of alleles in the human population based upon the information in two comments, this one and this one. I get 27,600 on the back on my envelope for that figure. -------------- "You can't teach an old dogma new tricks." - Dorothy Parker

C.J.O'Brien Posts: 395 Joined: Aug. 2005 (Permalink) Posted: Mar. 12 2008,16:17    Quote If a gene codes to a protein, as somewhere between 20,000 and 30,000 do, then any two versions of that protein would indicate two versions of the gene, two alleles, would they not?  I agree that I sometimes refer to two versions of proteins because the proteins are closer to the phenotype, and it is only the phenotype that natural selection works on.  However, I do recognize that the "alleles" are the variants of the genes involved. Your terminology is still confused. An allele that results in a different sequence of amino acids by definition codes for a different protein, not a different "version" of the same protein. Not being well-versed in biochemistry, I'm not even sure that terminology is ever used, but I suspect that if it is, it refers to the same sequence of amino acids folded differently. You're still not dealing with the idea of loci, which is the concept underlying alleles as "different versions" of the same gene. We consider them different versions of the same gene because they are two different sequences at exactly the same locus on the same chromosome. -------------- The is the beauty of being me- anything that any man does I can understand. --Joe G

swbarnes2 Posts: 78 Joined: Mar. 2006 (Permalink) Posted: Mar. 12 2008,16:41    [quote=bFast,Mar. 12 2008,15:10] Quote I understand that there are non-coding genes. Non-coding gene?  I've never heard the term.   Sure there are non-coding sequences of DNA that have important functions, but we don't call promotors genes, for instance.   Can you give us, say, the name of an non-coding gene in any organism? Quote I would assume that an intron would be seen as a non-coding gene.  However, I may be incorrect when I assume that an intron would be seen as a gene, or a portion of a gene even though it is not a gene that codes to protein. You assume wrong.  Introns aren't genes.  They are non-coding parts of genes. Quote Alas, this only goes to the question of exactly how the word "gene" is defined by biologists, not to my understanding of what an allele is. Well, why don't you start there? Why didn't you start there in the first place? Quote Is it safe to say that an allele is a variant of a segment of DNA that acts as a unit, where a coding gene is an example of a segment of DNA that acts as a unit -- translating into protein. Don't be silly.  The segments of DNA that are transcribed into t-RNAs are certainly called genes. Quote If a gene codes to a protein, as somewhere between 20,000 and 30,000 do, then any two versions of that protein would indicate two versions of the gene, two alleles, would they not? Nope.  You can have different splicing of the same mRNA sequence in eukaryotes.   Quote There are surely 200 phenotype affecting alleles in the human population. There are about that many alleles of the MCH locus, which affects the phenotype of tissue matching. Quote However, I do recognize that the "alleles" are the variants of the genes involved. See, your "200 alleles" phrasing is what's making people think that you don't. If it were me, I'd be saying "I'm simulating with 100 genes, each of which has 5 alleles", so as to distinghush between simulating with 5 genes of 50 alleles, or 250 genes with 2 alleles.  And I bet almost everyone else on this board would describe the experiment the same way. Those are all different simulations, and just saying "I'm simulating a genome with X alleles" doesn't say much about the experiment, and suggest that you aren't differentiating between genes and alleles.   Quote However, I think that the range of 200 to 2000 will produce an algebraic curve that will allow for reasonable extrapolation.   Are you relaly talking about that many alleles at only one locus?  One gene? Simulating 2000 alleles at one gene isn't going to tell you much.  Simulate 5 alleles at 10 genes, with some way to simulate interaction between the gene products, that will be interesting.

Albatrossity2 Posts: 2780 Joined: Mar. 2007 (Permalink) Posted: Mar. 12 2008,17:03    Quote (bFast @ Mar. 11 2008,21:28) I understand perfectly what an allele is.  You all are just playing the "creationists aren't evolutionists because they don't understand the basics" card.  It is bull! And of course this is completely unlike the folks on UD and other venues who demand that you read all of the books written by Behe, Dembski and Wells before they will discuss CSI with you. Sauce for the goose, etc. Oh, BTW, I am a Ph.D. biologist too, and I am only delurking here to let you know that I find your blustering about biology to be quite hilarious. Carry on. -------------- Flesh of the sky, child of the sky, the mind Has been obligated from the beginning To create an ordered universe As the only possible proof of its own inheritance.                         - Pattiann Rogers

jeannot Posts: 1201 Joined: Jan. 2006 (Permalink) Posted: Mar. 12 2008,17:24    Quote (swbarnes2 @ Mar. 12 2008,16:41) [quote=bFast,Mar. 12 2008,15:10]   Quote I understand that there are non-coding genes. Non-coding gene?  I've never heard the term.   Sure there are non-coding sequences of DNA that have important functions, but we don't call promotors genes, for instance.   Loci that produce RNAs are non-coding, but are still called "genes". At least, the locus for 16S RNA is referred to as a gene. Still, I'm not sure what this simulation is about. It looks like the problem of natural selection in a population has been solved long ago.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 12 2008,17:29    Gentlemen, A common definiton of evolution is, "change in allele frequency over time", correct? Please, gentlemen, hash out between yourselves a comprehensive definition of allele, I will happily use your definition.

C.J.O'Brien Posts: 395 Joined: Aug. 2005 (Permalink) Posted: Mar. 12 2008,17:36    Why don't you just start using the only definition there is? Don't project your confusion onto us. -------------- The is the beauty of being me- anything that any man does I can understand. --Joe G

jeannot Posts: 1201 Joined: Jan. 2006 (Permalink) Posted: Mar. 12 2008,17:49    Quote (bFast @ Mar. 12 2008,17:29) Gentlemen, A common definiton of evolution is, "change in allele frequency over time", correct? Please, gentlemen, hash out between yourselves a comprehensive definition of allele, I will happily use your definition. Our discussion over non-coding genes has very little to do with the definition of allele that you could to use. Take the one provided by wikipedia. It looks good enough. Technically, alleles are not limited to genes. Microsatellites aren't genes, but they have plenty of alleles. I would say that an allele is every intraspecific form of a locus produced by a "local" mutation (i.e not a major indel, duplication, chromosomal change... although this could be discussed). Update: A broader definition would cover every copy of a locus that exist within a species, but between haploid genomes, considering that a diploid has only 2 haploid genomes (and not 2 genomes per cell). This broad definition is implicit when you consider that every locus has two alleles in a diploid organism. In that case, between-cell copies of a locus within an individual are not considered as alleles, neither are the copies carried by the two chromatids produced during replication. Actually, the definition can be slightly altered for convenience, depending on your problem.

swbarnes2 Posts: 78 Joined: Mar. 2006 (Permalink) Posted: Mar. 12 2008,18:19    [quote=jeannot,Mar. 12 2008,17:24 Quote Loci that produce RNAs are non-coding I'll buy that, if that's how people really use the term.  I just never thought of them that way.  Sure, they don't get translated into amino acids, but the data is in the form of DNA, and it get 'encoded' into RNA to be functional. But, if the definition is indeed that RNA genes don't make the cut, then I stand corrected.

slpage Posts: 349 Joined: June 2004 (Permalink) Posted: Mar. 12 2008,18:34    [quote=bFast,Mar. 12 2008,15:10][/quote] bfast: Quote I understand that an allele is a version of a gene.  I understand that there are non-coding genes.  I understand that introns, for instance, often affect the phenotype. Who wrote this: "No, I actually mean allele.  An allele is a variant of the same protein.  Somewhere in the genome there is a protein that controls for eye color.  One variant produces blue eyes, the other produces brown eyes.  Likely the allele producing green eyes is a third allele of the same protein. " Quote  I would assume that an intron would be seen as a non-coding gene. No, an intron is part of a gene. Quote However, I may be incorrect when I assume that an intron would be seen as a gene, or a portion of a gene even though it is not a gene that codes to protein. No, an intron is a part of a gene. Quote  Alas, this only goes to the question of exactly how the word "gene" is defined by biologists, not to my understanding of what an allele is.   "No, I actually mean allele.  An allele is a variant of the same protein.  Somewhere in the genome there is a protein that controls for eye color.  One variant produces blue eyes, the other produces brown eyes.  Likely the allele producing green eyes is a third allele of the same protein. " I don't think it is the biologists that have the problem. It is the non-biologists that think they can gain google or wiki expertise or read a few creationist books and pontificate on biology on par with actual biologists.

slpage Posts: 349 Joined: June 2004 (Permalink) Posted: Mar. 12 2008,18:37    Quote (bFast @ Mar. 12 2008,17:29) bfast: Quote Gentlemen, A common definiton of evolution is, "change in allele frequency over time", correct? Yes - not protein, not intron. Quote Please, gentlemen, hash out between yourselves a comprehensive definition of allele, I will happily use your definition. Nice way to cover your ignorance. Stick to writing scanning software.

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 12 2008,19:11    Quote (bFast @ Mar. 12 2008,10:41) Zachriel:   Quote I did try to clarify bFast's terminology earlier in the thread in order to fully comprehend what he was trying to claim. However, he hasn't been too forthcoming on answering my questions. Which question have I not been forthcoming about? Well, let's start with what I consider the most important question.   * You claim that some beneficial mutations can be lost in genomes that vary wildly in fitness. So!? This is the expected result. Allele Blender is still a few days away. But here's a very stripped down version that only does bFast's basic algorithm. You have to set the parameters in the Declarations module of the VBasic editor. Press ctrl-g to cycle through generations.    ' Parameters    Public Const maxGenerations As Integer = 1    Public Const maxGenes As Integer = 20    Public Const maxRows As Integer = 20    Public Const maxCols As Integer = 10    Public Const Mutants As Single = 1 / 20 maxGenes is the number of genes in each genome. maxRows * maxCols is the population. Mutants is the proportion of the population born with a single 2-allele. -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 12 2008,19:24    Hmmm, no takers on a definition of allele?  Let me try someone else's for you gurus to shoot apart: Dictionary.com: Quote any of several forms of a gene, usually arising through mutation, that are responsible for hereditary variation. American Heritage Dictionary: Quote One member of a pair or series of genes that occupy a specific position on a specific chromosome. 'Seems that every variant of formal definition that I can find on dictionary.com all include "gene" in their definition.  Now, either my definition is plenty right enough, or the 7 dictionaries sited on dictionary.com are all wrong. Now, ladies and gentlemen, give me a working definition of allele that isn't bickered with, or accept the American Heritage Dictionary's definition. Honest folks, I think that this thread has meandered into people finding fancy ways of telling other people that they are stupid becuase either you all have narcisistic personality disorder, or because you fear that I have your pet theory by the short hairs.

Wesley R. Elsberry Posts: 4966 Joined: May 2002 (Permalink) Posted: Mar. 12 2008,19:48    Quote (bFast @ Mar. 12 2008,19:24) Hmmm, no takers on a definition of allele?  Let me try someone else's for you gurus to shoot apart: Dictionary.com:   Quote any of several forms of a gene, usually arising through mutation, that are responsible for hereditary variation. American Heritage Dictionary: Quote One member of a pair or series of genes that occupy a specific position on a specific chromosome. 'Seems that every variant of formal definition that I can find on dictionary.com all include "gene" in their definition.  Now, either my definition is plenty right enough, or the 7 dictionaries sited on dictionary.com are all wrong. Now, ladies and gentlemen, give me a working definition of allele that isn't bickered with, or accept the American Heritage Dictionary's definition. Honest folks, I think that this thread has meandered into people finding fancy ways of telling other people that they are stupid becuase either you all have narcisistic personality disorder, or because you fear that I have your pet theory by the short hairs. I provided two already. It seems a bit tendentious to claim that things haven't been provided when it is easy to confirm that they exist in the thread. Perhaps reading what other people write in responses might prove, hmmm, instructive? -------------- "You can't teach an old dogma new tricks." - Dorothy Parker

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 12 2008,20:03    Wesley R. Elsberry   Quote I provided two already.  The first problem is that you provided two.  I only want one! I have found no definition of allele on this site that has been provided by you or any one else on this site and approved by the others on this site  I am fed up with this "you don't know what you are talking about" bit.  I want to work with one definition of allele that all of you can agree on.  That will end the bickering about the definition of the term.  Then we might be able to get to a number of how many phenotype affecting alleles there are in a typical population of mammals.  Then I will have a useful number to put into my sim.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 12 2008,20:57    Let me try again. If we accept dictionary.com's definiton of allele   Quote any of several forms of a gene, usually arising through mutation, that are responsible for hereditary variation. And if we also accept a very broad definition of gene, such as provided by American Heritage Dictionary:   Quote A hereditary unit consisting of a sequence of DNA that occupies a specific location on a chromosome and determines a particular characteristic in an organism. Genes undergo mutation when their DNA sequence changes. We end up with fairly close to what I have always understood an allele to be: Quote any of several forms of a hereditary unit, usually arising through mutation, that are responsible for hereditary variation.

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 12 2008,21:24    Quote (bFast @ Mar. 12 2008,20:57) Let me try again. Tough audience. Please provide your current algorithm. Please restate your claim. -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 12 2008,21:28    Zachriel: Quote Tough audience. Thank you. Quote Please provide your current algorithm. Please restate your claim. My dear computer crashed.  I had a memory leak in my dll.  I should get a good spectrum of well summarized results by morning.  (Some of these cycles take half an hour to run, and I'm running about 100 cycles.) I would rather provide my algorithm (slightly modified from the original) and will restate my claim when I post my data.

bFast Posts: 44 Joined: Mar. 2008 (Permalink) Posted: Mar. 12 2008,21:31    Nope, 50 cycles, 12 are already done, and some of them take less than half an hour.  The worst case, random drift took half an hour.

oldmanintheskydidntdoit Posts: 4999 Joined: July 2006 (Permalink) Posted: Mar. 13 2008,03:49    Quote (bFast @ Mar. 12 2008,19:24) you fear that I have your pet theory by the short hairs. A Nobel awaits then, once you disprove "evolution". -------------- I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies". FTK if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand Gordon Mullings

Wesley R. Elsberry Posts: 4966 Joined: May 2002 (Permalink) Posted: Mar. 13 2008,05:53    bFast: Quote We end up with fairly close to what I have always understood an allele to be: The fact is that you provided math that demonstrated vividly that you did *not* always have that understanding. Either you are continuing with the same erroneous math, indicative of erroneous understanding, or you have adopted more accurate math indicating a difference between your previous understanding and the state you are in now. Anybody can correct personal ignorance. Admitting that one is actually learning from experience is not a bad thing. Failing to admit that, though, is both transparently obvious and annoying. -------------- "You can't teach an old dogma new tricks." - Dorothy Parker

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 13 2008,06:57    A randomized genome of 0's and 1's with an initial smattering of 2's is not what we would expect. In nature, traits tend to vary as a probability distribution about a mean. bFast is imposing a contrived situation to match his expectations. But regardless of whether we start with a random distribution or a flat one, if we allow occasional mutations to occur, the population spontaneously evolves towards a mass probability distribution about the mean.  Genes = 20  Population = 10000  Generations = 20  A sample gene:  Allele    Count     0       140     1      5603     2      3825     3       416     4        16  mean ~1.46 The result of random mutation in the toy universe resembles (in this one aspect) what we observe in nature. This example only allows 0's, 1's and 2's.  Genes = 20  Population = 10000  Generations = 20  A sample gene:  Allele    Count     0       370     1      6700     2      2930  mean ~1.26 It's a result of historical evolution, not due to anyone's expectations or preconceptions. -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.

slpage Posts: 349 Joined: June 2004 (Permalink) Posted: Mar. 13 2008,07:49    Quote (bFast @ Mar. 12 2008,19:24) Honest folks, I think that this thread has meandered into people finding fancy ways of telling other people that they are stupid becuase either you all have narcisistic personality disorder, or because you fear that I have your pet theory by the short hairs. The irony is rich. The creationist not only projects, but then goes on to engage in the rampant megalomania that seems nearly endemic in those that inhabit protected pro-creationism blogs and forums. Let us not forget that bfast the computer tech not only claimed that alleles are proteins, but EXPANDED on that theme: No, I actually mean allele.  An allele is a variant of the same protein.  Somewhere in the genome there is a protein that controls for eye color.  One variant produces blue eyes, the other produces brown eyes.  Likely the allele producing green eyes is a third allele of the same protein.

slpage Posts: 349 Joined: June 2004 (Permalink) Posted: Mar. 13 2008,07:50    Quote (bFast @ Mar. 12 2008,20:03) I am fed up with this "you don't know what you are talking about" bit. You are fed up with the truth? Too bad.

slpage Posts: 349 Joined: June 2004 (Permalink) Posted: Mar. 13 2008,07:51    Quote (oldmanintheskydidntdoit @ Mar. 13 2008,03:49) Quote (bFast @ Mar. 12 2008,19:24) you fear that I have your pet theory by the short hairs. A Nobel awaits then, once you disprove "evolution". But, but - Warren Bergerson already did that!

slpage Posts: 349 Joined: June 2004 (Permalink) Posted: Mar. 13 2008,08:00    Quote (Zachriel @ Mar. 13 2008,06:57) bFast is imposing a contrived situation to match his expectations. Well, of course. That is what these people do. I mentioned Warren Bergerson (aka 'LifeEngineer')above - surely most of us remember him? If not, he is a retired actuary who claimed for years that he had disproved evolution using 'actuarial math.'  And, after years of claiming this, it was drawn out of him, on ARN, that he had in fact never done any calculations at all, he just "knew" that if he had done so, it would have disproved evolution. After some prodding, he finally revealed his math on Terry Trainor's MSN group, Talkorigins (note that the guy that pointed out Bergerson's stupidity was eventually railroaded and banned - just like what happens at UD).  His claims were challenged, and he ended up changing his formulae and inputs 3 times when shown to be in error (never admitting it, of course), each time coming up with the same answer.  That is, he rigged the formulae repeatedly to get the results he wanted, to include doing a simple probability calculation backwards. Same thing with this UD denizen.  He's just making it up as he needs it to be.

Cedric Katesby Posts: 55 Joined: Aug. 2006 (Permalink) Posted: Mar. 13 2008,08:35    bFast, have you read the "Uncommonly Dense" thread at After the Bar Closes? If so, what do you think of the comments/threads preserved there that UD tried to flush down the memory hole because they got embarrassing? Are you really comfortable associating with such a crowd? P.S. I will say I am surprised that you have ventured out of the echo-chamber.  Good for you. I hope you'll stay the course and not disappear.

Zachriel Posts: 2722 Joined: Sep. 2006 (Permalink) Posted: Mar. 13 2008,09:17    Quote (Cedric Katesby @ Mar. 13 2008,08:35) bFast, have you read the "Uncommonly Dense" thread at After the Bar Closes? If so, what do you think of the comments/threads preserved there that UD tried to flush down the memory hole because they got embarrassing? Are you really comfortable associating with such a crowd? P.S. I will say I am surprised that you have ventured out of the echo-chamber.  Good for you. I hope you'll stay the course and not disappear. The Uncommonly Dense thread has a high snark-to-content ratio — which is quite appropriate for the subject matter. However, I would like to keep this thread close to topic. BFast should understand that in an open forum, we have to be somewhat tolerant. My efforts to test bFast's claims should be sufficient evidence of my willingness to consider his views. I, too, am glad that bFast has ventured outside the cloister. He has yet to be forthcoming in his responses, but I assume that's because he is still attempting to understand how his toy world works. --------------- * You claim that some beneficial mutations can be lost in genomes that vary wildly in fitness. So!? This is the expected result. * You claimed that your random genomes of sufficiently large size would not evolve directionally. My results were different. How can you explain this? * Your randomized population rapidly evolves by sorting through the 0's and 1's of the genome. If we introduce the occasional random mutation, the results tend towards a mass probability distribution (most apparent with a wide variety of available alleles in any given locus). Once some order is imposed, then selection works as expected. -------------- You never step on the same tard twice—for it's not the same tard and you're not the same person.