Evolution and Probability

Fred: Your analogy is bogus. It is a bit similar to an analogy Thomas tried to pull at NaiG, but unfortunately I was too busy at the time to respond (Though I was itching to do so!)FK: Yes, I am sure that’s it. You had an answer but just didn’t have time to post it. But I am sure Thomas also had an answer to your answer, but he couldn’t answer since you never posted.Dillan: So therefore, how do we know that the other two nucleotides at each stage couldn't be beneficial as well? That would lower the probability to 1/3 x the original probability at each stage. At any rate, evolution is still improbable.FK: Most Creationists (and evolutionists, for that matter) say that beneficial mutations are extremely rare events. Yet you are proposing that 2 out of 3 possible point mutations at a specific site may have been beneficial. You seem to enjoy calculating probabilities. Set up that probability calculation, assuming that a beneficial mutation occurs once in every million or more mutations. I think you will see that what you are proposing is highly unlikely.Dillan: I know that parts of hemoglobin converged, because hemoglobin cannot be explained by common descent.FK: You are definitely going to have to explain that one.Dillan: From what we are able to calculate though, evolution is improbable.FK: How so?Dillan: By the way I would like to extend my gratitude to Fred for helping me out. I have read your article about evolution being thwarted by mutation rates. Has anyone totally refuted it?FK: Totally refuted it? No, because it does contain a few factual statements. On the other hand, it is riddled with errors, outdated arguments, and unwarranted conclusions. Fred has been promising to update it for quite some time, though. Some of what he cites has already been nullified by the sequencing of the human genome. For example, Crow’s estimates of U were based on an assumption that there would be more than 60,000 genes. So when Fred writes Widely recognized geneticist James Crow in an article in the same Nature issue agrees that the deleterious rate is more likely twice the rate cited by Eyre-Walker and Keightley, then this is just flat wrong since the number of genes is estimated to be 30,000 or so. There are several other examples like that in the article. I might comment when he updates it, but as it is it is not worth my time. You are easily impressed by Creationists arguments it seems. Maybe you should apply the same type of skepticism you seem to apply toward evolutionist’s arguments.FK

This was pointed out to him at NAIG. He replied with something along the lines of "Spetner's calculation disproved either speciation or convergent evolution. Since speciation has been observed, that means convergent evolution is disproven". I can honestly say that this didn't make a lick of sense to me.The funny thing is, though, if you follow Spetner's calculation, he does mathematically "disprove" the possibility of speciation. Since speciation has been observed, that pretty much nullifies Spetner's approach, which was a multi-level straw man anyway.FK

Dillan: According to Are Mutations Harmful?, "The average human being has about 50-100 mutations". I am not for sure about the langur, and I could not find the average number of mutations. However let us assume a number in range of humans-about 75. If I am not mistaking, there were 15 million yrs. for the convergent evolution of this lysozyme (I got this figure from a fellow named Thomas who posts on this board, and who I have discussed this issue with to before). If we assume a generation time of 7 years, that is 2,143,000 generations. If there are 10,000 in a population then there would be 750,000 total mutations. For the whole of langur evolution, it would be 750,000 x 2,143,000 = 1,607,250,000,000. This could overturn a genome of 3 billion nucleotides 535 times. However, we must divide this number by three to get the correct nucleotide, which would be about 179. Therefore the chance of fixation is 179/500^9, or 0.000096 (0.0096%). Even considering 5 yrs/generation and 100 mutations per individual this equals a 2% chance (0.026).There are two significant problems here, and this does not speak well toward your motives. I saw the exchange at NAIG. When Thomas did the calculation, he assumed a generation time of 5 years. In fact, langurs are sexually mature at the age of 3 or 4. Yet you have increased it to 7 years for a generation. I think the reason is quite obvious.2nd, you were shown recent estimates of mutation rates in humans. They range from 100 to about 175. Thomas used a recent estimate of 128. Yet you went with 75, from an outdated Talk.origins FAQ. Again, I think we can all see why.It appears to me you are less interested in performing a defensible calculation than you are in pushing an agenda. Otherwise you would not use outdated or flat out false numbers to push your case. You can't plead ignorance, because I know you were given references at NAIG. I don't even know why you want to persist with the lysozyme example. You got waxed on that one at NAIG. Perhaps another example might be better?FK

Dillan: I do not assume that 2 out of there point mutations at a specific site are beneficial, just like I don't assume that 1/3 mutations at a specific site are beneficial (as someone may have inferred from my calculations). I just said that there is no way of knowing that the other two couldn't have been beneficial.FK: There is also no way of knowing whether Pluto is covered with a fine layer of cheddar cheese. But I think you would agree that it would be highly unlikely. Again, I asked you to make a probability calculation so we can have some idea of the odds. You seem reluctant to do so in this case. I do wonder why (not really).I snipped the hemoglobin stuff, because there is really nothing there that we can apply any calculations to. It is not stated how many nucleotides are believed to have converged. Surely you don’t believe that evolutionists think the entire molecule converged? All you have done is show that evolutionists believe that hemoglobin is descended from an ancient ancestor of hemoglobin. You are going to have to do a lot better than that if you want to make the same type of argument that you did about lysozyme.Dillan: I do think that creationists devastate evolution at some points.FK: You will have to turn me on to some of these devastating arguments. I have been debating this for 10 years and have never seen one.Dillan: However when this happens convergent evolution has a number of paths to take. This means that the probability that two species will take the same path is very slim.FK: That all depends. If you mean that there are slim odds that two species’ genomes would converge to a large degree, then you are correct. No evolutionist, however, would suggest such a thing. To present this as a refutation of evolution is certainly attacking a straw man.Dillan: The reason I used 7 is because I searched for the relevant material on the internet but could not find any information on the generation time. I didn't know if Thomas had made an error or not. However, I used 5 yrs. below. If you want I can recalculate using 3 or 4.Yes, why don’t you recalculate it using 4 years per generation and 128 mutations per generation? I don’t think you will be pleased with the result.Dillan: So now you can discern my intentions?FK: Yes, I can. When Creationists ignore certain bodies of evidence that don’t support their preconceived notions, I question their motives. If you read Fred’s article, you will see that he is guilty of the same. Did you know that Eyre-Walker has updated their estimate of U, and that there are a number of estimates out there, lower than the ones Fred uses? Did you see how Fred ignored lower estimates and only did calculations with the higher estimates? Fred ignores all of that in favor of any estimates that tend to support his position. That’s why he is an engineer, and not a scientist. A scientist engaged in such behavior would have zero credibility. (Not that Fred has credibility anyway).Dillan: As far as getting "waxed" on NAiG-I have participated in my fair share of debates. I can assure you that I hardly ever get completely waxed-just ask Asmodean, Butch, Prof Weird, Roland (rjw), skepticboy, etc.. In fact, I wanted to discuss the issue more but Thomas decided he did not want to. I am NOT saying that he ran away-I am merely saying that I did not get a chance to completely corroborate to develop my model.FK: No, you were pretty well manhandled. It looked to me like Thomas just got bored.Dillan: If you want, we can again set up the calculation: 100 mutations per individual (Crow's estimate)FK: Or, you could use Nachman’s estimate that you linked to of 175. This completely changes the outcome. Now you are looking at about 100% probability of convergence. What you can conclude from this is that the probability of convergence in this case is somewhere between 2% and 100%. This is not exactly a damning argument against convergent evolution. Do you have a better example?Dillan: First of all, just because an animal is able to reproduce at 4yrs. old doesn't mean that it is going to. A 14 yr. old human can reproduce, but the average generation time is around 20 years.FK: But it wasn’t always. A couple of hundred years ago the generation time was about 14 years. As soon as women came of age, they married and began to reproduce. This is still the case in 3rd world countries. But nowadays in the U.S., we don’t have too many marriages before girls turn 18. In fact, the average age at marriage is 24. That’s why the average generation time is 20 years or so. But as late as 1950, the average marrying age for a girl in India was 13 years.Dillan: Using Haldane's number, if 1 mutation can be fixed every 300 generations, this is 1 mutation per 1200 years.FK: I am not really seeing how Haldane is relevant here. Are you sure you understand Haldane’s argument?Dillan: For example, if rhodopsins of the eye converged in a similar manner (I don't have the actual figures), then the probability would be 0.19x0.19= 0.036, or about 3%. When other convergences are considered, the numbers drop.FK: And by slightly changing the assumptions, the probability will again go to 100%. Perhaps you need some new material. I have yet to see one of these mathematical disproofs of evolution that stood up to scrutiny.FK

Dillan: Please do not put words in my mouth. I never said 'to a large degree'. I will attempt to show why that convergence is slim in a moment.FK: Perhaps you have a reading comprehension problem, because I didn't say this is what you said. I said If you mean that there are slim odds that two species’ genomes would converge to a large degree You are going to have to clarify how much of the genome you think evolutionists believe converged. Please don’t make up numbers. Show me some hard evidence.Dillan: By the way, what is the new estimate for U?FK: The last time I spoke with Adam his estimate of U was 2.2. This was after the human genome was decoded. But you can e-mail him at a.c.eyre-walker@sussex.ac.uk and ask him yourself. The implications of this are that it would make the number of conceptions (not births as Fred writes) less than 20 instead of the 60 Fred wishes you to believe.Dillan: True, I could use Nachman's estimate. Then again instead of using 0.1% as a typical selective value I could use 0.01%. This does not require any leap out of logic-in fact G.G. Simpson said it could work for evolution.FK: Yes, or we could use 0.3% or 0.7% which would also require no leap of logic. All of which will vary your probability between effectively 0% and 100%. So what must I conclude from this? Attempting to disprove evolution, when so little is known about the actual values needed to plug into the model, is a completely worthless approach. You can’t really say anything at all about whether or not convergent evolution is possible. You have waffled all over the place on the assumptions, and this renders the output meaningless. The only conclusion I can accept based on this exercise is that the probability of convergent evolution for the 9 nucleotides in lysozyme is somewhere between 0% and 100%. So we learned exactly nothing.Dillan: 1). If the webpage for talkorigins has been updated this year, why have they not changed their figure for mutations per individual.FK: I am not associated with Talk.Origins, so maybe you should write and ask them. Maybe they are just unaware of the fact. But you have been given more up to date estimates from the literature, so you really have no excuse for using lower numbers. Genetics is a very fast moving field. Relying on old data in this field is a fool’s errand.Dillan: 2). The paper whose numbers you embrace also agrees with a higher mutation rate also agree that U=3,FK: That estimate of U was made before the human genome was decoded. The number of genes was believed to be higher in the past, which would render estimates of U too high. Most estimates of U that I have seen over the past two years are between 1.5 and 3. Adam’s group is on the cutting edge in this field, so he probably has better numbers than you will find anywhere else. But don't expect to see Fred update his argument anytime soon, as most of the newer estimates are going against him.Dillan: However, have you thought that this short generation time has anything to do with the length of their lives? Early American colonists died in their 30's and 40's. You could pick any isolated example to prove your point, as could I. The fact is that you do not have to reproduce once you attain the ability to. Some may be able to reproduce at 12. I have heard of several cases where girls around 12 have had kids. Does this negate your postulation that the generation time used to be 14? No, just as your postulation does not negate my original position.FK: My postulation absolutely negates your assertion. Without birth control, when sexually reproducing species reach reproductive age they start to reproduce. Female langurs become sexually active as young as 3. I can assure you that the generation time is not 7 years. Or do you think they became sexually mature and decided to postpone having offspring until they were more financially secure? In humans, the generation time is going to closely correspond to the average age at marriage.Dillan: If I wanted, I could change the calculation around to where evolution is extremely improbable.FK: Which renders it absolutely useless. Your problem is that you are trying hard to plug in numbers that give you a preconceived low probability. This was obvious from your first post, where you ignored recent estimates in favor of those you felt lowered the probability.FK

Peter: I read an article a while ago that said it had been
found that each of us has as many as four genetic
differences from our parents.FK: To clarify, that was probably "expressed" differences, or differences in coding regions. The actual mutation rate is quite a bit higher than 4 per generation, but most mutations are in non-coding regions.A comment that I missed earlier:Dillan: Let's say only 3% of the mutations are in the coded region.FK: If only about 1% of the genome is coding, why would 3% of all mutations fall in coding regions?FK

Fred: They are? Which ones? Surely you would not just say this without being expected to produce evidence?FK: Well, let’s have a look. From your article at 404 Not Found :

quote:

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Now consider that extremely favorable assumptions for evolution were used in the Eyre-Walker & Keightley article. If more realistic assumptions are used the problem gets much worse. First, they estimate that insertions/deletions and some functional non-genic sequences would each independently add 10% to the rate. Second, and more importantly, they assume a functional genome size of only 2.25% (60K genes). When they assume a more widely accepted 3% functional genome (80K genes), they cite U = 3.1, which they admit is "remarkably high" (even this may be a favorable assumption, considering Maynard Smith estimates the genic area to be between 9 — 27%.

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Oops. There’s a paragraph you can throw in the trash. That’s one estimate from your article that is no longer valid. Of course you admitted earlier that you are aware of this, which makes me wonder why it’s still there.Here’s another paragraph:

quote:

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Widely recognized geneticist James Crow in an article in the same Nature issue agrees that the deleterious rate is more likely twice the rate cited by Eyre-Walker and Keightley. So if we use Crow's revised rate of U=3, we get:

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B = 2e^3 = 40 births before we get one offspring that escapes a new defect!

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There’s two estimates from your article you can throw in the trash. If you read Dr. Crow’s article, he is assuming the rate is higher because he felt like 60,000 was an underestimate of the number of genes. Of course you know this, which makes me wonder why you haven’t updated the article. Crow’s estimate is no longer valid.Now, that is not to say that U might not actually be 3. It could be. But not based on the logic Dr. Crow was using.Fred: My queries show three new estimates since my article: the slightly lower Keightley-revised number, and two studies that support U=3 or higher.FK: Were you planning on sharing these queries with us? I am aware of a single study that estimated that U was 3 (or even greater). This was a pre-HGP study published 3 years ago by Nachman and Crowell. They were assuming that there were 70,000 genes in the human genome. Of course they also estimate that the total mutation rate was 175 base pairs per individual per generation. This is on the high side of most estimates, and would make their estimate of U on the high side (as would the too high estimate of the number of genes). If you have an estimate from a post-HGP study, I would certainly be interested in reading it.FK

Dillan: There can be selection coefficients this high, but can this be used in the working of natural selection?FK: Didn’t Thomas point out to you that in the case of the peppered moth the selection coefficient had actually been measured to be slightly greater than 0.5? That’s real experimental data for you, not some ancient quote based on incomplete information. I think I would go with the recent data instead of using old quotes to lower the estimate as needed.Dillan: Using mainstream numbers, I have constructed a probability.FK: No, you have constructed a probability using outdated numbers. You have two recent estimates of the mutation rate; 128 and 175. You used 100 to lower the probability, and that’s also why you used the 7 year generation time.Dillan: (This would even prove to be true if the probability was 49% in favor of evolution-as there would be a greater chance-51%-that it wouldn't occur.)FK: Do you even understand what these probabilities mean? If the true probability were 10%, that would mean that 1 out of every 10 cases we look at will be successful. That means that we would see cases of this in the animal world. Your original argument would have been powerful if indeed the probabilities had been set up correctly and they were actually something like 1 in 100 billion. But if you are retreating to arguments like 49% means it probably wouldn’t occur then it’s time to give up this argument and move on to the next one.Dillan: If we only incorporate numbers that are beneficial to evolution, like a 0.7% selection coefficient, and a mutation rate of 175 mutations per individual, then you will get your desired result. However this follows an element of just so story telling. (I apologize to the administator, however I felt that this must be said. If you prefer, I could say that this is a 'possibly how' story). Using realistic numbers I calculated that the chances are more likely than not that the mutation won't occur.FK: That’s quite misleading on your part. You don’t have to plug in both; if you plug in either you will get the desired result (assuming you don’t change your other initial assumptions). We also get the desired result by assuming more langur generations (more than 15 million years), or a 3-4 year generation time.So, what can one conclude from this? Pretend for a moment that you are a practicing scientist, and you are presenting conclusions. Here is your major conclusion: Based on the uncertainty in mutation rate and in the selection coefficient, no conclusion can be made regarding whether convergence in the case of the langur is probable. Using the most recent estimates available, convergence appears to be likely. That’s it.Dillan: First of all, evolutionists refer to talkorigins articles often, as I did. Talkorigins updates their webpages often, and they have very competent evolutionists monitoring the website. Second, I know that there are higher estimates. In fact, I made reference to this in one of my posts. However I also made references to a lower mutation rate. In fact, if we use 100 mutations per individual, like Crow did, then this can coincide with the talkorigins article range of 50-100 mutations per individual.FK: You don’t seem to get it. Crow’s estimate was also pre-HGP. Yes, Talk.Origins updates their website often, but as you can see the text in that article has not been updated since 1999. These guys are not getting paid for this, so it is possible to have information in an article that has been superceded by more recent data. By insisting on using a mutation rate from that article, when more recent estimates are available, demonstrates that you are not really interested in doing this problem with the highest possible level of accuracy.Dillan: Are you refering to Smith's estimate? Why is it out of date? What is the most commonly accepted percentage of the coded portion of the DNA?FK: I explained why it was out of date above. Almost all of these estimates (all of them?) were made prior to the sequencing of the genome when it was believed that there were more genes and a higher coding percentage. The most recent estimates, from the Human Genome Project website at Page Not Found | ORNL are Less than 2% of the genome codes for proteins and The total number of genes is estimated at 30,000 to 35,000much lower than previous estimates of 80,000 to 140,000 that had been based on extrapolations from gene-rich areas as opposed to a composite of gene-rich and gene-poor areas.Dillan: Oh, and by the way, where did you get the information that langurs sexually mature at three to four years old? I am not saying that this is untrue, but I would like to read the material for myself.FK: Let me get this straight. You are pushing this argument, and you don’t actually know the langur generation time? I have a better idea. Start doing better background checks before pushing an argument. It is pretty easy to find out about langurs. You should have no problem confirming this.FK

Dillan: Oh, and by the way, where did you get the information that langurs sexually mature at three to four years old? I am not saying that this is untrue, but I would like to read the material for myself.FK: Here is your last freebie. I would expect, as I am sure others would, that you research these issues in depth before developing your argument. Relying on 2nd hand or outdated sources for your information is not the way to conduct research.For the Hanuman Langur:"Sexual maturity is achieved after 3 years".ADW: Semnopithecus entellus: INFORMATIONFor the Douc Langur:"Females reach sexual maturity at about 4 years, while the males reach it at 4-5 years".Blue Planet Biomes - Red-shanked Douc LangurFK

Dillan: You said that the mutation estimate of 175 per individual was a "more recent" estimate, yet you imply the U estimate is oudated.FK: It is clear that you don’t really understand how these estimates work. An estimate of the overall mutation rate will not necessarily be affected by a lowered estimate of the total amount of coding DNA. However, the value of U depends directly on the amount of coding DNA, so post-HGP estimates will be lower. In other words, the 175 estimate could be just fine, but the estimate of U is outdated because it is based on the assumption that there are 70,000 genes.Dillan: The authors of the paper at Page not found - Biozentrum
suggest that the mutation rate is around 100 per individual and give an estimate of U that is around 3. This would justify Fred's number.FK: Because someone on the Internet says U=3 does not justify Fred’s number. You need to go to the primary literature; that is where you will find the most recent research. Your link gives no reference for this estimate. Most likely they got this from one of the outdated estimates. This is from a teaching lecture in Switzerland, and there is no indication (and it is highly unlikely) that they measured the value themselves. There is also no indication when they last updated the slides. If you really want to make a case with these slides, you need to write and find out their source for the estimate. I am afraid you will be disappointed. On the other hand, the mutation rates that you have been given (128 and 175) are the most recent estimates, based on actual measurements.Dillan: 'The genomic deleterious mutation rate is likely much larger given our estimate that 80% of amino acid mutations are deleterious and given that it does not include deleterious mutations in noncoding regions, which may be quite common. [emphasis mine].'Using their estimates, the required offspring number rises to at least 60 offspring per breeding couple! (for explanation, see my opening comments in my debate with Dr Page.)"This is fairly recent. Heck, even if U was 1.6 as suggested by Adam that is still means that 10 conceptions just to keep the genetic degradation near equilibrium! I don't think that primates conceive this much on average, but I am not for sure. (Humans can, but it is very rare when they do.)FK: I really think you should try to focus on one argument at a time. If you want to discuss Fred’s misconceptions and erroneous conclusions, maybe you should start a new thread. If you really think that 10 conceptions for a primate is too much, I suggest you do a little more background work. How many conceptions do you think occur today in 3rd world countries among humans? Do you have any idea as to how high the spontaneous abortion rate is?Dillan: I don't remember Thomas saying this, but he could have. It doesn't matter, because we cannot base all of evolution on just one example. Besides, even with the selection coefficient this high the variety of colors in the peppered moths stayed the same-that is that there were still black and white variations. The frequency of each color changed, but the colors involved remained constant. Therefore the variation did not take over the population. If it did take over the population, you may have a point. However it didn't. (By the way, I thought the 0.1%-0.01% values were just for beneficial mutations, not necessarily the variations between the two species. There are black and white colored humans, but did not necessarily achieved by mutation and selection. If you take just two moderately dark people you can produce much variation in the offspring as far as 'color' is concerned. This is just a result of sexual recombination.)FK: Frankly, I can’t make any sense out of this. You seem content to run with a very old estimate, based on zero experimental data over an actual experimental finding. What is your evidence that the proper estimate in the lysozyme case is 0.1, or 0.01? None, you are just relying on outdated quotes. This is no way to develop a model. On the other hand, the one actual measured value of a selection coefficient that has been provided was 0.53. IF you want to challenge that, you need to come up with a measurement, not a quote dating to before the discovery of DNA.Dillan: I never said that when a probability is 49% that it couldn't occur. In fact it could. I just said that in the isolated case of the langur, it probably wouldn't. You seem to want to incorporate more examples into the equation.FK: Along the same lines, in the isolated case of a single person buying a lottery ticket, the odds of winning are slim. But we can find cases where someone won, can’t we? That’s one point. You really don’t seem to understand what this probability means. If 49% was the exact number (which it’s not) then we could say for every 2 cases we consider with these same assumptions, we will find one case of convergence. However, as I have amply demonstrated, you don’t have enough certainty in several of your model parameters to make any conclusion. The key point you need to consider is: What is your margin of error? Based on what I have seen, it is huge.Dillan: I just used estimates from Simpson about the average selective value for mutations. I think that my results can be just as valid as yours. So which is correct? I don't know. We need more information about a concensus of opinion on what these numbers should be.FK: Actually you just need the most recent estimates you can find. Remember, the moon dust argument was once a staple among Creationists. The reason it disappeared is because better estimates became available. You seem dead set on ignoring recent estimates.Dillan: The article that I listed above includes HGP. In fact, that is the main theme of the paper is to give an update and summary of it. It uses the estimate of 100 mutations per individual (or possibly less-so when I used 75 mutations per individual I was not necessarily completely wrong).FK: I suggest you reread the article. The 100 estimate is from the 1999 paper by Eyre-Walker. It is not a post-HGP estimate.Dillan: So which numbers should we use? 4, 5, or 7? I think that the average would be around 5. After all, the females can't mate until males mature sexually. However the number 7 was included in one of the papers above, so I wasn't deliberately avoiding the hard facts.FK: Your main problem is that you are demanding precision where precision is not available. There is no magic number here for the number of generations. It may range from 3 to 6, which means your answer is going to have a large error associated with it. By the way, the number 7 was for a specific case of the maturity of males in one species. The maturity of males is going to have little to do with the length of a generation; the sexual maturity of females is the key.Dillan: Using 5 yrs/generation, 100 mutations per inidividual, we still only get a probability of a 2% chance (0.026), or about 1/50. Not impossible, but still not very likely. I do believe these numbers are reasonable. I have yet to see a reason why they are not.FK: They are not reasonable because you are still ignoring the most recent estimates we have of the mutation rate in favor of older estimates that support your argument. This is just moon dust revisited. In addition, you have provided no justification at all that 15 million years is all that would be available. You have not come close to making a case. But even if your numbers were accurate and the probability was 2%, that says that 1 in 50 cases we examine with these parameters would result in convergence. So, 15 million later when we find a case of convergence, how can you argue that this was not the 1 in 50? Your entire argument is going nowhere.FK

Fortunately, mutations are rare. They occur on an average of perhaps once in every ten million duplications of a DNA molecule (10^7, a one followed by seven zeroes). On the other hand, it's not that rare. Our bodies contain nearly 100 trillion cells (10^14). So the odds are quite good that we have a couple of cells with a mutated form of almost any gene. A test tube can hold millions of bacteria, so, again, the odds are quite good that there will be mutatant forms among them.The mathematicaal problem for evolution comes when you want a series of related mutations. Teh odds of getting two mutations that are related to one another is the product of the separate probabilities: one in 10^7 x 10^7, or 10^14....Any two mutations might produce no more than a fly with a wavy edge on a bent wing....So what are the odds of getting three mutations in a row? That's one in a billion trillion (10^21)....It was at this level (just four related mutations) that microbiologists gave up on the idea that mutations could explain why some bacteria are resistant to four different antibiotics at the same time....So even by the wildest 'guesstimates', the universe isn't old enough or big enough to reach odds like the 1 in 10^3,000,000 that Huxley, an evolutionist, estimated as the odds against the evolution of the horse."FK: Actually, this is just plain wrong. False inputs lead to faulty conclusions. The mutation rate is wrong, and I don't even know what "The odds of getting two mutations that are related to one another" is supposed to mean.FK

Since the only estimate of U=3 that I am aware of was in the Genetics paper by Nachman and Crowell, I wrote to Dr. Nachman and asked whether the HGP would affect his estimate. He responded:

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With the newer estimates of the total number of genes, yes, it is certainly possible that U is about half of the estimate I provided in the Genetics paper. But it is important to keep in mind that these numbers are quite rough; I wouldn't place too much significance on differences of a factor of two.

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FK

I am going to try and summarize some of the key points. Dillan, if I didn’t address something you felt was important, please bring it up again.The mutation rate came up several times in your post, so I will just address it a single time here: Whether it is 64, 100, 128, or 175 is clearly uncertain. The rate will vary across the genome and from individual to individual. These are different estimates based on different studies. It just so happens that the two most recent ones are 128 and 175. But there is still no way of knowing that this is representative of the entire genome, and is a good number to use as a long term average. All we can say is that this range poses no problem for the example of lysozyme convergence. If the actual mutation rate was 1/10th this, then it could pose a problem.Dillan: Okay, in the future I will perhaps discuss Fred's 'misconceptions'. However if Fred represented the authors of the Wu paper correctly, then this could have severe consequences for evolutionary theory-namely that there must be 60 births per individual just to maintain genetic equilibrium!FK: But Fred did not represent the authors correctly. The 60 births per individual comes from an error that Fred made which lead to a faulty conclusion. We can get into it if you like, but the findings of the HGP nullify Fred’s claim.Dillan: Well, if I am to challenge something I need the original source to refer to. What source said the selection coefficient was .53?FK: You were given the source, an actual literature reference if I recall correctly, at NAIG. You should have saved it. Or, you could try to find some actual experimental evidence to suggest that 0.1 is a good selection coefficient to use in this case. It doesn’t really matter, because convergence in this case is not a problem even if the selection coefficient is 0.1. It would only become a problem if you reduced it to 0.01, but you have no justification for doing so (other than you need to).Dillan: In langurs, the entire population has the nucleotides that converged on lysozyme.FK: Do you have a reference that says the entire langur population has all 9 nucleotides? I am surprised that someone has sequenced the entire langur population. That must have cost several trillion dollars. But even if they all did have the 9, that would argue for a larger than average selection coefficient. You do understand that the selection coefficient will be larger when the mutation is more beneficial than average?Dillan: However if convergence is so likely, as you suggest, why do we not see more cases of it? I am only aware of a few examples of genetic convergence.FK: It is going to depend. Here we are considering 9 nucleotides. We can see that this would take a few million generations to have a decent chance of convergence. But if we assumed 15 nucleotides, the number of required generations goes way up. But if you have the same initial conditions as in the langurs, convergence would be a fairly likely occurrence for a small number of nucleotides, just not a long string of nucleotides. I doubt that many studies have been done looking for small strands of convergence among various species.Dillan: I would say it is likely that the Eyre-Walker estimate is closer to being correct since the authors of the paper that was written post-HGP used it. If it had been incorrect, or if somehow the HGP suggested that the number was wrong, then I do not know why they would use it.FK: That’s a pretty weak argument. There are all kinds of reasons they could have used the older estimate. The main reason they probably used it is they weren’t aware of the other estimates. Also, as far as most people are concerned there is not that much difference than approximately 100 and 128. It just turns out in the case we are arguing that it makes an order of magnitude difference in the probability calculation.Dillan: I do not see a problem with me using the 100 estimate.FK: I bet you don’t, since it lowers the probability (given all the other assumptions) from about 25% (in the case of 128) to 2%. I would use that estimate too if I had interest in merely trying to win an argument as opposed to getting to the truth of the matter.Dillan: I thought that the mutation rate was around 1 copying error every 10 million replications. However Nachman (whose estimate you like) estimated "The average mutation rate was estimated to be approximately 2.5 x 10(-8) mutations per nucleotide site or 175 mutations per diploid genome per generation."FK: The phrase 1 copying error every 10 million replications is nonsensical in the context in which he used it. If he had written 1 copying error every 10 million nucleotides then the statement makes more sense. But the original phrase that you wrote, They occur on an average of perhaps once in every ten million duplications of a DNA molecule is completely incorrect. The correct phrasing is that there are lots of mutations during every duplication of a DNA molecule. A reading of the paragraph you posted indicates that this guy doesn’t know what he is talking about and no business critiquing genetics.FKP.S. Your "number of conceptions" argument is really steering the topic in a different direction. I would prefer to focus on one subject at a time, or at the very least dedicate another thread to that argument.

You were writing to PaulK here, but let me throw in a couple of comments.Dillan: The only problem that I have with this is that evolution depends in nearly every evoluitonary sequence of some kind of pattern of mutations. For one thing nearly all of them must be beneficial.FK: Profoundly untrue. Do the terms genetic drift or neutral theory mean anything to you?Dillan: For example, ReMine states, "...in flies there is a gene affecting eye color that also afects the reproductive organs."FK: I would take anything Remine says with a grain of salt. He has made some fundamental errors in his book, perhaps because he is unqualified to write about biology. He is an electrical engineer, for crying out loud. When you have no training in a specific area, it is quite easy to make mistakes if you are attempting to critique it. I am just trying to say that you should be careful when putting Remine out there as an authority. His musings will carry no weight with the scientifically literate.Dillan: Since evolution almost relies on related mutations, it is the rule rather than the exception.FK: You really have some serious misconceptions about evolutionary theory. I recommend that you take a break from the Creationist literature and read an actual mainstream science book about evolution. You don't have to accept it or agree with it, but at least you might understand it.FK

Dillan: As for Parker's number, it may be a powerful argument yet, but I need to develop it some more. As for now, I will say that both of you have indeed given some very powerful criticisms to my model and both of you are worthy opponents. The question now is, where do we go from here? I am going to try to gather some evidence for Parker's calculation. If you would, help me use Parker's number to set up a correct calculation. It is clear that his calculations have no contraints involved.FK: I am not really sure why you think Parker’s argument is meaningful. First, based on the excerpt you provided, he knows very little about genetics. 2nd, I looked up his book and it was published in 1980. If he is using mutation estimates that are that old, they are frankly worthless. 3rd, he is obviously a Creationist with an agenda. I don’t trust those types of sources.There could be a simple solution to all of this Dillan. The reason that these Creationists arguments fall apart under the microscope is because evolution really happened. Don’t you think there are mathematically competent scientists working in the field? Do you know what a coup it would be to disprove evolution? It would have enormous implications. I would love to publish a paper along those lines; it would make me rich and famous. But the fact is that you only see Creationists doing so, because Creationists have an agenda to protect.I would recommend that you go to the primary literature and develop your own argument. Even though his argument has been superceded by more recent data, I think that’s what Fred Williams did with his work on U and the number of required births. But you are never going to get anywhere with the approach you are taking, especially if you try to develop an argument now based on Parker’s number. You are once again starting off with an incorrect premise.Good luck. I sincerely mean it when I say I think it would be cool if one of these mathematical arguments ever held up to close scrutiny, but I don’t see it happening. There is just too much evidence from too many fields that indicate that evolution is true.FK