tag:blogger.com,1999:blog-32636283.post7385237712959463545..comments2023-03-26T03:50:25.501-04:00Comments on David's Secret Blog: Darwin Disproved?Unknownnoreply@blogger.comBlogger56125tag:blogger.com,1999:blog-32636283.post-69176532832834624782012-02-16T00:14:45.822-05:002012-02-16T00:14:45.822-05:00How do you deal with the fact that Darwin himself ...How do you deal with the fact that Darwin himself stated that IF the single cell is found to be anything but a simple lump of protoplasm, that he would consider his own theory disproven, and microbiology has indeed proven that the single cell is a complex machine run by trillions of proteins interacting in a designed, purposeful manner. And this doesn't even address the advances in the other cutting edge science such as quantum physics and cosmology which also have found strong indications of design. And what about the Cambrian explosion? NO fossils have EVER been found indicating that several proto-species (before specific animals evolved into subspecies better suited for various ecosystems such as prototype fox became desert fox, arctic fox, etc.) did not just appeared from thin air. If there haven't been fossils found by now predating the Cambrian explosion, there never will be. There isn't and never will be real scientific evidence that all life evolved from a single blob of protoplasm. Like the Soviet Union and Communist China, politics in the US has censored science to suit its own ends.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-32636283.post-31116683327166831462007-12-06T14:21:00.000-05:002007-12-06T14:21:00.000-05:00paulj:I don't think we can conclude much yet excep...paulj:<BR/><BR/><I>I don't think we can conclude much yet except that there are as-yet unknown processes in genetics ...</I><BR/><BR/>Which is precisely the point I have tried to make several times. Their are two assertions required to make this extremely improbable result astonishing:<BR/><BR/>1. The conserved gene sequences have absolutely no function; and, <BR/><BR/>2. Piecemeal changes in those sequences will not have effects sufficiently deleterious to cause their disappearance from succeeding generations, even though the intact sequences themselves have no function.<BR/><BR/>There is very little evidence for the former assertion, and none for the latter. <BR/><BR/>If both could be demonstrated, then, and only then, will the random mutation portion of naturalistic evolution come into question, and in such a way as to quite possibly leave continuous supernatural intervention at the molecular level the best explanation.<BR/><BR/>David:<BR/><BR/><I>It does fit nicely with my understanding of natural selection, which is that, unless a mutation kills outright the phenotype will survive.</I><BR/><BR/>You need to work on your understanding. See, in particular, chronospecies.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-32636283.post-61183736396981035732007-12-05T17:32:00.000-05:002007-12-05T17:32:00.000-05:00We really don't know enough about how the genome f...We really don't know enough about how the genome functions to make any conclusions.<BR/><BR/>Cells tend to program in messiness and carry a lot of redundancy in them. They're not perfectly-engineered machines.Alihttps://www.blogger.com/profile/18230724707928518879noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-90108600483186670362007-12-05T15:46:00.000-05:002007-12-05T15:46:00.000-05:00Skipper: That really strikes me as whistling past...Skipper: That really strikes me as whistling past the graveyard. Any genetic mechanism that results in the most conserved genes being junk or only weakly related to fitness cannot be squared with any strong form of natural selection.<BR/><BR/>It does fit nicely with my understanding of natural selection, which is that, unless a mutation kills outright the phenotype will survive.Davidhttps://www.blogger.com/profile/16902329503560660425noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-1445174733824774902007-12-05T09:28:00.000-05:002007-12-05T09:28:00.000-05:00No. My experience has been that selection models a...No. My experience has been that selection models and independent coin flip models tend to have different amounts of clustering, which is a critical parameter.Susan's Husbandhttps://www.blogger.com/profile/02862667802025231163noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-31060799213507709342007-12-05T08:18:00.000-05:002007-12-05T08:18:00.000-05:00For the science-interested, here's an article indi...For the science-interested, here's an article indicating the lack of knowledge and uncertainties regarding the epigenetic role in genetics: <A HREF="http://www.sciencedaily.com/releases/2007/11/071130160450.htm" REL="nofollow">http://www.sciencedaily.com/releases/2007/11/071130160450.htm</A>. A quote:<BR/><BR/>“It’s like a puzzle where you only have a few pieces,” Pinto said. “There’s not a clear cut signal and consequence. We will learn new insights into the cellular mechanisms that govern the basic process of chromosome transmission from mother to daughter cell.”PaulJhttps://www.blogger.com/profile/06450891066260074318noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-43211366900653976682007-12-05T08:11:00.000-05:002007-12-05T08:11:00.000-05:00hey skipper - You lost me about three times in the...hey skipper - You lost me about three times in there. Darwin hasn't been disproved, but we can't really know whether he is disturbed, assuming God has told him about this finding.<BR/><BR/>I don't think we can conclude much yet except that there are as-yet unknown processes in genetics waiting to be discovered. Whether those processes have a bearing on phenotypic evolution is unknown.PaulJhttps://www.blogger.com/profile/06450891066260074318noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-53024530175173475112007-12-05T08:06:00.000-05:002007-12-05T08:06:00.000-05:00SH - Are you making the point that some base pairs...SH - Are you making the point that some base pairs will have mutated multiple times? Yes, but that's not going to affect the outcome much. We're still constrained by the observed mutation rates to end up with about 70% of the nucleotides unmutated. <BR/><BR/>Your more complex model only matters if you have a random process that is not identical for all base pairs and independent between base pairs. If you allow an independent random process to act on each base pair individually, then the outcome is adequately modeled by a Poisson process. And the point of the paper was that a Poisson process doesn't work, thus refuting the assumption of independent random events drawn from a uniform distribution.PaulJhttps://www.blogger.com/profile/06450891066260074318noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-85689509443147547082007-12-04T19:04:00.000-05:002007-12-04T19:04:00.000-05:00paulj:All of this is very dependent upon the suspi...paulj:<BR/><BR/>All of this is very dependent upon the suspicion that the gene sequences do not, in fact, have any function at all.<BR/><BR/>It is worth noting that conclusion is based upon deleting them in their entirety, not (IIRC) making changes in the way random mutations would.<BR/><BR/>My bet is that there is a reason -- other than highly fortuitous dice rolls -- these sequences are so highly conserved between disparate mammalian species.<BR/><BR/>Either they, in fact, do something; or, piecemeal mutations are very bad in ways that wholesale deletion is not.<BR/><BR/>Both leave Darwin undisturbed. <BR/><BR/>Of course, an intelligent designer could presumably manage wholesale deletions (which is, after all, the IC argument). But, It has not chosen to do so.Hey Skipperhttps://www.blogger.com/profile/10798930502187234974noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-56403264138303476712007-12-04T18:45:00.000-05:002007-12-04T18:45:00.000-05:00No, the process would pick a base pair at random r...No, the process would pick a base pair at random roughly 900,000,000 times and mutate it.Susan's Husbandhttps://www.blogger.com/profile/02862667802025231163noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-4807125702017860852007-12-04T13:58:00.000-05:002007-12-04T13:58:00.000-05:00I might add that in the model I've ascribed to you...I might add that in the model I've ascribed to you, the probability of getting a long run of non-mutations actually is less than in the Poisson process, because with every non-mutation added to a run of non-mutations the pool of available non-mutations is reduced and the probability of a non-mutation on the next try decreases. That doesn't happen in the Poisson process.PaulJhttps://www.blogger.com/profile/06450891066260074318noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-85879008124618871762007-12-04T13:55:00.000-05:002007-12-04T13:55:00.000-05:00SH - There is a "genetic clock" becuase in any ran...SH - There is a "genetic clock" becuase in any random process, if it goes on long enough, the number of mutations becomes strongly peaked around N mutations. For instance, in a sum over normally distributed events the width of the distribution scales as 1/sqrt(N), N the number of events; or, when rolling dice, the probability distribution is flat for one die, peaked at 7 for two dice, more strongly peaked at 10-11 for three dice, and so forth. The longer the time period, the more precise the evolutionary clock becomes (as long as the random process doesn't change its character -- not necessarily a good assumption).<BR/><BR/>Of course, the Poisson distribution they assumed also comes up with a distribution that is highly peaked around 30% of the genome being mutated. So, of 3 billion base pairs, 900 million +- a relatively small number will end up mutated.<BR/><BR/>Your alternative model is "we have N base pair mutations, randomly distributed." But "randomly distributed" usually means the next event is independent from previous events. If I understand you, your process will start with 3 billion base pair spots, run a random variable at each one, and assign either a mutation or non-mutation. At the first base pair the probability of mutation is N/(3 billion); if after y base pairs you've had x mutations, you want to make the probability of a mutation there as (N-x)/(3 billion - y), so that at the last base pair the probability of mutation is either 0 or 1 depending on whether you've previously used N or N-1 mutations.<BR/><BR/>Well, your model isn't biologically realistic, but in any case it gives a very similar probability of not getting a 200 bp run as the model they used.PaulJhttps://www.blogger.com/profile/06450891066260074318noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-7025344139745338652007-12-04T12:21:00.000-05:002007-12-04T12:21:00.000-05:00No, I think the modeling problem is more subtle th...No, I think the modeling problem is more subtle than that.<BR/><BR/>The root is that in physical reality, the number of modified base pairs isn't variable, as it is in the Poisson model. We may not know precisely what it is, but it's effectively a fixed percent. If it wasn't, all of those "genetic clocks" would be hogwash. So I think the more accurate model is "we have N base pair mutations, randomly distributed". If we take that as basis, then we don't have independence of base pair mutations which is a significant difference.<BR/><BR/>My intuition is that such a model would be much clumpier than the Poisson model, i.e. have a much higher probability of long unmodified chains, but it's possible I am wrong about that as well. As I noted, I would need to run some simulations to get an order of magnitude sense of how much clumpier, which, sadly, I don't have time for right now.Susan's Husbandhttps://www.blogger.com/profile/02862667802025231163noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-36381064318338544312007-12-04T11:12:00.000-05:002007-12-04T11:12:00.000-05:00First, SH: You get clumping in any process. The ...First, SH: You get clumping in any process. The question is, what is the distribution of clumps, and is it consistent with a random process?<BR/><BR/>The model they used, a Poisson process, basically says: we going to run 3 billion events in succession, each with a 0.7 chance of non-mutation and 0.3 chance of mutation. Poisson statistics can calculate the frequency of "runs" of different length -- e.g. how many runs of 1 non-mutation, how many runs of 2 non-mutated base pairs, etc. It gives a probability of having even one run of 200 non-mutated base pairs of 10^(-22). So it seems Poisson statistics -- indicative of a random chance of mutation of 30% for each base pair, and independence of neighboring base pairs -- is not the right model. The mutations are too "clumped" for a Poisson process.<BR/><BR/>So, clearly, either: (1) the probability of mutation of certain base pairs is much less than 30%, or (2) the probability of mutation of one base pair, at least in certain regions of the genome, is not independent of the probability of mutation of neighboring base pairs, or both.<BR/><BR/>Peter - I didn't mean that there has to be a complete replacement/alternative to natural selection, only that some process must exist <I>besides selection</I> that makes the probability of mutation in a base pair correlated with the probability of mutation in its neighboring base pairs. Selection does this because it acts on genes (or transcriptional control regions of genes): the base pairs in a gene produce a specific protein whose function depends on every nucleotide, and if selection is conserving the protein, then it's conserving every base pair in the gene as a totality, i.e. blocking changes in any nucleotide.<BR/><BR/>But it's not selection that's enforcing the shared low mutation rate in this case. <BR/><BR/>As for other mechanisms, I am not a molecular biologist (though my wife is, and I stayed at a Holiday Inn Express), so I hesitate to make suggestions. I would guess that epigenetic transcriptional control mechanisms, which control the phenotype of cells (e.g. whether your cells, which all share the same genome, turn into heart, brain, muscle, or blood cells; or whether another genome forms a caterpillar or butterfly) are important. Epigenetic states are generally preserved through cell replication and can be inherited. If the mutation rate in this region is suppressed when genes are epigenetically silenced, and if these genes are silenced (explaining their lack of influence on the mice), it's possible they could have been silenced throughout the mammalian lineage going back tens of millions of years. In other words they might be "junk" genes that are silenced for reasons of energy-conservation.PaulJhttps://www.blogger.com/profile/06450891066260074318noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-69110887597215477212007-12-03T09:29:00.000-05:002007-12-03T09:29:00.000-05:00PaulJ;As far as I can tell from Mr. Cohen's quote ...PaulJ;<BR/><BR/>As far as I can tell from Mr. Cohen's quote and the numbers cited, their analysis was just what you wrote. What my experience of randomness tells me, though, is that you don't get such smooth distributions, you get a lot of clumping, which could easily yield sequences that this analysis would determine are extremely improbable. I would have to run some simulations to verify that, however.<BR/><BR/>The other thing that bothers me is that their universe of outcomes varies along the number of mutations axis, i.e. every possible number of mutations is an outcome. I would think that a better model would restrict the universe to outcomes with a relatively constant number of mutations. I.e., presume 30% mutations and then modify that many pairs.Susan's Husbandhttps://www.blogger.com/profile/02862667802025231163noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-56332436789364892932007-12-03T06:44:00.000-05:002007-12-03T06:44:00.000-05:00paulj:What's missing is a theory of the mechanism....paulj:<BR/><BR/><I>What's missing is a theory of the mechanism. It could be a host of things.</I><BR/><BR/>Can you suggest some possibilities? In previous discussions about how Darwinism is ultimately tautological, we've tried to think of theoretical alternatives without much success. If the whole game is about survival by definition, how can the mechanism be anything other than a drive to survive without bringing the whole ediface down?Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-32636283.post-15514695382803354532007-12-02T22:26:00.000-05:002007-12-02T22:26:00.000-05:00SH - They estimate a 30% change that any one base ...SH - They estimate a 30% change that any one base pair is mutated. Then, crudely, in a single 200-bp segment the chance of it being ulta-conserved is (.7)^200 = 10^(-31). There are 3 billion such segments in the genome, to take your number, so, ignoring overlap, no more than 3 billion (3 x 10^9) 200-bp segments; so the chance of an ultra-conserved 200-bp sequence in the genome is on the order of 3 x 10^(-22).<BR/><BR/>So their number of 10^(-22) is plausible, presumably their calculation was more realistic than the above.<BR/><BR/>Clearly, the assumption that base-pair mutations are random events independent of the mutation status of their neighbors is wrong. So far, the only mechanism accepted for non-independence is selection, and there seems to be no phenotypic event for selection to act on. So there must be some unknown non-selection effect that makes the probability of a mutation on one bp of this sequence correlated with the probability of a mutation in its neighbor. <BR/><BR/>That's the state of affairs. What's missing is a theory of the mechanism. It could be a host of things. <BR/><BR/>I don't take it as a refutation of the existence of either "random" mutations or selection, but as a proof that some other effects also exist.PaulJhttps://www.blogger.com/profile/06450891066260074318noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-30452088098515881252007-11-26T13:39:00.000-05:002007-11-26T13:39:00.000-05:00Much too much. Evolution isn't a science. It is n...Much too much. Evolution isn't a science. It is natural history.<BR/><BR/>But natural selection is a scientific theory. A flimsy one.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-32636283.post-55218437672923306302007-11-26T11:32:00.000-05:002007-11-26T11:32:00.000-05:00Is it too much to suppose we shall never hear agai...Is it too much to suppose we shall never hear again that evolution is not a science because it can't be disproved?Hey Skipperhttps://www.blogger.com/profile/10798930502187234974noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-91458154257775522022007-11-25T09:53:00.000-05:002007-11-25T09:53:00.000-05:00Elaborate, Joe.Elaborate, Joe.Duckhttps://www.blogger.com/profile/08852569465893563139noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-50427232664594760502007-11-24T15:11:00.000-05:002007-11-24T15:11:00.000-05:00I don't know of any souls that are at stake in the...<I>I don't know of any souls that are at stake in the debate over natural selection.</I><BR/><BR/>Yes, you do.joe shropshirehttps://www.blogger.com/profile/12183662262318452612noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-81140113242099609872007-11-24T14:59:00.001-05:002007-11-24T14:59:00.001-05:00This comment has been removed by the author.Duckhttps://www.blogger.com/profile/08852569465893563139noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-69170354248671606902007-11-24T14:59:00.000-05:002007-11-24T14:59:00.000-05:00This comment has been removed by the author.Duckhttps://www.blogger.com/profile/08852569465893563139noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-41285501853326467222007-11-24T14:58:00.000-05:002007-11-24T14:58:00.000-05:00And don't worry! I imagine we will continue to fi...And don't worry! I imagine we will continue to find subjects to disagree over. ;-)Duckhttps://www.blogger.com/profile/08852569465893563139noreply@blogger.comtag:blogger.com,1999:blog-32636283.post-88465975091620059982007-11-24T14:57:00.000-05:002007-11-24T14:57:00.000-05:00The problem with theologians being proved wrong is...The problem with theologians being proved wrong is that they are purportedly inspired by divine revelation to get it right. The whole enterprise is built upon revelation. If you can't get revelation right, it sorta destroys all credibility for the enterprise.<BR/><BR/>And the stakes being what they are, salvation or damnation, their little mistakes cost souls. I don't know of any souls that are at stake in the debate over natural selection.Duckhttps://www.blogger.com/profile/08852569465893563139noreply@blogger.com