Why can creationists give straight answers?

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Mark:: My point above was, if human/chimp divergence was 5 mya (or whatever),

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The assumption is 10mya to arrive at 1667. If we assume 5 mya the number is 833.

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Mark: Today, his the maximum number of fbm has been shown to have have been exceeded experimentally.

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This is big news! Please provide the experimental study that has shown this.

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Scott: The 1667 figure represents only fixed, beneficial (adaptive) mutations. These are not necessarily point mutations (indeed, many are probably not), nor are all of them necessarily in coding regions.

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Why would many probably not be point mutations? From what we know of mutations, by far the best candidates are point mutations because 1) they are the most frequent, 2) the other types are far more likely to be harmful. Regarding transposons (which are also infrequent), they give all the appearances of non-random mutation. I think very few would be non-point mutations.

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Scott: Neutral mutations (those changes that do not affect fitness) can reach fixation in a population at a rate comparable to the rate of occurrance of these mutations, that is, at a much higher rate than adaptiove mutations.

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This is not necessarily true. To illustrate, consider a clade that regularly receives two new mutations each generation, a beneficial mutation and a neutral mutation. If one were to take Scott’s statement above at face value, the neutral mutations will fix at a greater rate than the beneficial ones. I’d love to see him try to support this claim mathematically! The qualifier that needs mentioning is that in order for neutrals to fix faster than adaptive mutations, you need a higher ratio of neutrals to adaptives to begin with. There is some ratio of neutrals to adaptives that represents the threshold where neutrals surpass adaptives in fixation rate. I’d be curious to know if Kimura or anyone else ever attempted this calculation (the key dependency would of course be the adaptive mutations’ assumed selection value).

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So, when we look at a human and a chimp genome, they differ by about 1.1%, or roughly 35 million bps total. Which means that roughly 17.5 million of these will be in each lineage, many of which are polymorphisms, most of which are neutral.

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Not this again! An accurate measure of difference between chimps and man cannot, must not, include polymorphisms. The differences must be in fixed bps in order for it to count as a difference between chimp/man. SNPs (single-nucleotide polys) represent noise, so they are useless in such a comparison. The only time I think you could consider an SNP is if it is at a high frequency, while its corresponding SNP in the other species is at a low frequency. Only then should it be logged as a difference.I realize that the 1.1% estimate is not based on a complete sequence comparison of the two. But if it were, any bp counted as a difference that was later discovered to be an SNP would have to be removed from the difference ledger. So, if 1/5th of the bps counted as different turned out to be SNPs, this would reduce the difference number from 1.1% to .088%.[I have family in town, so may not be able to respond for a while]

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Page: Frankly, considering the fact that you 'think' that the ancient Hebrews knew all about bacteria (see the "Medical Evidence" section at the "Bible Evidences" link - it is all pretty funny!) because in Leviticus they are told to wash the tapestries in the home of the leper, I am not all that concerned about what you think.

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You have brought this up before, always with the usual sarcasm, yet never an argument as to why the leprosy paragraph is flawed. What is your specific complaint? Do you deny that leprosy can survive on walls and garments?

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Fred: I’d be curious to know if Kimura or anyone else ever attempted this calculation ....
Page: Kimura, M. 1987. "Molecular Evolutionary Clock and the Neutral Theory." "If the mutant is selectively neutral, the probability of ultimate fixation is equal to its initial frequency , that is, u=1/(2N) in the diploid population... In other words, for neutral alleles, the rate of evolution is equal to the mutation rate."

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No kidding Sherlock! That is not what I asked. I’ll ask again, but re-word it. We know that a specific adaptive mutation will fix faster than a specific neutral mutation. But neutrals overall fix at a greater rate than adaptives because there are presumably many more of them. Each generation there is some number of new neutral mutations and some number of new adaptive mutations (assuming evolution for the moment). What ratio of neutral to adaptive mutations is required to get more neutrals fixing than adaptives? That is what I was asking. It’s really not very important, just a curiosity on my part whether or not this calculation has been attempted, and if so what was the assumed selective value, etc.

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Tell us all, Williams, How - EXACTLY - SNPs are then REMOVED from such analyses?The curious reader should wonder why it is that Williams - like many other creationists - simply re-asks, re-claims, re-states, and especially, re-asserts the same things over and over

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The reason I have to re-ask over and over again is because you refuse to see the point I am trying to make. I’ll give it one last shot. Say a specific base-pair site on a chimp has an SNP where 50% of the population has an ‘A’, and 50% of the population has a ’G’. The corresponding site on human has the same distribution. If we assume Hardy-Weinberg equilibrium (H-W specifically deals with alleles, but it applies equally well to haplotypes such as my example above) then the shared ancestor would have had the same ratio. Thus, this would represent a site that does not represent a difference between the two species. However, if we do a direct sequence-to-sequence comparison between chimps & humans, we have a 50% chance we will log a difference where there is no difference. If the SNP ratio is 75% ‘A’ and 25% ‘G’, the odds are 3/8 (.375) that we will incorrectly log a difference. The point is, SNPs introduce error into these difference estimations. It would be very difficult to remove the SNP-induced errors with precision, but its impact can be reasonably estimated if we have a good idea of the average distribution of SNPs and the ratio of SNPs to the genome portion being compared.My point all along is that a precise difference calculation requires accounting for the noise introduced by SNPs. I will again stress that I realize that this SNP noise has not been directly removed, or even accounted for via estimations, when difference estimations have been made. When I argued that scientists were referring to fixed differences when they talk of differences that separate chimp/human, I was stating that I assumed they knew that SNPs inflict noise that distorts the difference estimation to some unknown extent, but must be negligible enough to ignore. I admitted this sentence was confusing, but I still stand by it. If a scientist tells us there is a 1% difference between chimps and man, we must assume these differences pertain to fixed sites, and assume the SNP impact is negligible.So, when you say many of the bp sites in the difference ledger are polymorphisms, we should raise our eyebrows because SNPs impact the accuracy of the difference estimate. If you had said some, then my eyebrow would have remained in stasis.

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Given that the coalescent point of two homologous alleles is likely to be after speciation,

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What? Would you care to elaborate further?

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Wouldn't it therefore be sensible to arrive at a consensus sequence before performing the analysis? What I mean by this, is to take (for the sake of argument) 100 sequences from humans, 100 from chimps, then orangutans etc. in order to eliminate SNPs. That is, if 99 samples say A at a particular locus, & one says G, then G can be thrown out, & A taken as the consensus for that loci.

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Exactly! My point is that if there truly are many polymorphisms within the 1% estimate as Page claims, then such an analysis would indeed be sensible and necessary. But I think Page is mistaken, and should have said some instead of many. I’ve seen estimates of SNPs ranging from 1 SNP per 1200-1900 base pairs in humans, so the SNP impact on the difference is probably negligible (SNPs are not uniform across the genome and occur in hot spots, but I doubt Page is relying on this when he says many reside within the 1% difference estimate; perhaps Scott still thinks SNPs are fixed? )

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It is flawed because you wildly and illogically extrapolate some commonplace activities as 'proof' that the ancient Hebrews had in-depth knowledge about microbes.

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You still have failed to give a decent rebuttal (only a strawman) why my leprosy claim is flawed. For anyone interested, here is the passage in question:

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Bacteria
Some time after I wrote these web pages, a Bible skeptic unwittingly showed me yet another example of advanced scientific/medical knowledge in the Bible. He posted a message on a discussion board that ridiculed some verses in Leviticus 13 and 14 that mention leprosy on walls and on garments. He felt this was silly and an error since leprosy is a human disease. What this skeptic was unaware of is the fact that leprosy is a bacteria, a living organism, that certainly can live on walls and garments! How often and how sweet it is when we see skeptic's attempts to denigrate God and the Bible turned around such that they end up glorifying God!

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[/I]Scott, the onus is on you to show this was not advanced knowledge of that time. Here is one of many web sites regarding leprosy:Inquire About This DomainFrom the above article:The bacteria can survive three weeks or longer outside the human body, such as in dust or on clothing.It was not until 1873 that leprosy could be shown to be infectious rather than hereditary.Now don’t you think it was a good thing that God commanded the Levitical priests to isolate lepers, and burn their garments? What other culture prior to the 1800s, let alone 4000 years ago, practiced safe leprosy? Feel free to chalk this up to yet another coincidence or blind luck. You guys ought to be exhausted constantly having to explain away the myriad of supernatural evidences within the Bible.Can you find another religious book that consistently gets these things right?

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Oh - and Fred - did you follow the link to the alignment?

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Yes I did, but it didn’t have much bearing on the debate since you already admitted some was the more appropriate depiction. Besides, I didn’t have a problem with your belief that indels (specifically insertions) represent the largest per site numbers. I would suggest however that this particular insertion was likely a non-random mutation.

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But the real issue is whether or not the Isrealites had advanced knowledge of microbes.

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I am not saying Isrealites had advanced knowledge of microbes. This is Scott Page’s strawman. I am saying the Bible’s treatment of leprosy is yet another example where the Bible provides knowledge not available to man at the time. I’m sure the Isrealites had no idea why God commanded them to take certain actions regarding leprosy.

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This is not supported by the fact that they burned houses and clothing. Such action is a pretty normal reaction to combatting disease where the source is not known. The same reactions are observed during the various plagues of the middle ages.

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Same reactions? Please provide your evidence for this. The only documented evidence I have from the middle ages is that some church fathers in Vienna began quarantine based on Leviticus, and their success was recognized and copied in other areas.

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Here is a problem. The Egyptians, Indians and Chinese all knew that leprosy was an infectious disease.

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Please provide evidence for this. I have heard examples where some cultures would isolate whole families, but this obviously was not the ideal solution. The Bible got it precisely right, isolating only the patient and requiring the attending priest to wash himself.

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By the way, the word 'leprosy' used in the Bible covered a many different diseases, not just the one known as leprosy today.

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Do you have a specific Bible verse where the use of leprosy appears to cover a different disease? My search yielded 28 hits of the word leprosy, and a quick check of each context appeared to support the modern version, though I’m no leprosy expert. I looked up the Hebrew word used, and it is defined in Strong’s Hebrew dictionary as leprosy. That’s it. Normally this dictionary is very reliable, so I would have expected to find additional definitions, such as or pertaining to skin disease if what you claim is valid.

Hello Randy! There are two things that drag you out of the woodwork, 2LOT and Noah’s ark. You must have only two books on your shelf: 2LOT for Dummies, and Noah’s ark for Dummies.

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I should point out that while leprosy (from Mycobacterium leprae) is an infectious disease it is in fact very difficult to contract. It requires long and intimate contact with infected people and even then not all contract it. I have asked some dermatologists who have experience with this disease and they agree that it would not be possible to contract it from walls.

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Impossible? If the bacteria can live for 3 weeks or more, it is certainly possible. Unlikely? Perhaps. Question: If you were forced to live with a leper, would you regularly wash yourself, your clothes, and anything in your room you think he might have rubbed up against? Case closed.(BTW, there are also symbolic reasons for cleaning the walls that have to do with sin and atonement, but no need to get into that Bible study here).

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If you are going to put forward some supposed Biblical knowledge of leprosy one might also point out that the Biblically prescribed treatment is totally worthless.

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It is? You must have missed the part where Hyssop oil has been shown to contain 50% antifungal and antibacterial agents.

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BTW which of Noah's children or daughters-in-law do YECs think was the leper? I don't see how else the disease could have survived the worldwide flood.

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Who said the disease existed before the flood? Surely you are aware the vast majority of bacteria are beneficial ecological agents? You are also surely aware that mutation occurs? I submit that the Mycobacterium leprae bacillus is a bacteria that was once a useful ecological agent before the flood, and mutated after the flood into its nasty form we see today.I believe the post-flood environment resulted in an increase in harmful mutations. There is both Biblical and scientific evidence for this, but I obviously cannot be dogmatic on it. It is entirely reasonable and possible that a post-flood world would see a rapid increase in mutated bacteria, including undesirables such as Mycobacterium leprae.

As is common my young apprentice ran out of steam, so he returned to ole-reliable: blame it on ‘debate’ tactics. LOL!

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I will be archiving this thread, too, for future use, as I am confident that I will, at some time, have to drag it out again to show your underhanded 'debate' tactics to a new audience.

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No, I suspect you will be true to form and save if for some future misrepresentation. Even your protg Robert, who I originally went round-and-round on the SNP noise issue, did not resort to making things up, like your allegation I claimed SNPs could be removed via a single taxon DNA sequence. That was some twisting of my words. You da man!But on to more important matters. I must say I continue to be thrilled and flattered that you take such great interest and hang on my every word. My sincerest appreciation, my young apprentice.Your idol,
Fred
PS to evos: Things are heating up at work again, so I may not be able promptly respond. This thread is pretty much exhausted anyway.

Scottie?

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There is no forum rule obligating anyone to reply to messages, and I offer no assessment as to the content of SLPx's replies (in other words, perhaps replies are called for, perhaps not, I am not saying either way), but within the bounds of available time meaningful threads of discussion should not be purposefully left hanging.

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Well stated. It boils down to subjective opinion whether or not a thread is exhausted. In my opinion this thread is exhausted. Here is a summary from my POV:1) Scott claimed my leprosy bit at my bibleevidences.com site was bogus.
2) I supported my claim with citations showing that leprosy can survive outside of the body for three weeks or more. It further puts into favorable light the associated Biblical requirements such as burning garments.
3) Scott then turned to a strawman argument by incorrectly claiming I said the Hebrews were educated in microbiology.
4) John, then later Randy if I recall, point out that the word leprosy in the Bible may cover a variety of diseases. This may be so, it may not. Regardless, it does not impact my original argument.
5) Randy protests that leprosy is not that contagious and requirements such as cleaning walls is not necessary. Perhaps, perhaps not. If #3 is valid and some other disease (or perhaps some other form of leprosy) is more contagious, it is very reasonable that walls also be cleaned. But again, this does not impact my original argument much if at all. The Biblical passage implies that leprosy can live on garments and walls, and we know that indeed it can. Whether or not washing the walls is worthwhile is not that crucial to my core argument. Burning the garments certainly makes perfect sense, but even it is not crucial to my argument. They are merely icing on the cake.
6) The thread moved to hyssop oil. Randy agrees it has some anti-bacterial agents, but claims it is a worthless remedy against leprosy. Perhaps, but perhaps not, particularly if claim #3 above is valid. Randy acknowledges hyssop would be effective against ailments that could easily be confused with leprosy. Moreover, in reading the Bible passage one gets the impression that in the case of leprosy hyssop is part of the ceremonial cleaning, and that shaving and washing is the medical prescription. However, in Numbers 19:18 hyssop oil is clearly part of the medical prescription, in the cleaning of vessels and people who come into contact with dead corpses.What else is there to add? Nothing, really, other than to add that there is mounting evidence that non-random mutations occur.