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Author Topic:   Why can creationists give straight answers?
derwood
Member
Posts: 1457
Joined: 12-27-2001


Message 16 of 56 (15445)
08-14-2002 6:33 PM
Reply to: Message 14 by Fred Williams
08-13-2002 6:17 PM


quote:
Originally posted by Fred Williams:

quote:
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.

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.


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.

However, I admit that 'many' is not an accurate depiction. 'Some' is more in line. However, if we consider all mutations, then I would argue that indels contribute the largest per site numbers. For example, see this alignment. Follow the sequence for "Cja" (Callithrix jacchus) for about 300 bases. You will see a point at which Cja appears to have recieved an insertion of about 115 bases in length. This sort of occurrance is commonplace, especially in intergenic DNA and to a lesser (though not always - see the same alignment) extent in introns. Williams may now try to insert his recent claims about the functional importance of introns, but it is irrelevant. It has long been known that introns contain conserved sequence, particularly at the 'ends', where spliceosomes form on the mRNA transcript, for example. Obviously, mutations there can impact the expression of the protein. If the protein is involved in development, well, by golly...

quote:

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.

Fred:
This is not necessarily true. [SNIP most of attempt to make a point and fail]...I’d love to see him try to support this claim mathematically!... I’d be curious to know if Kimura or anyone else ever attempted this calculation ....


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."

Kimura had explained all this in his book and at least one other paper that I know of and have cited for Williams before. I find it astounding that someone that repeatedly claims to have read a "wealth of information" on this topic so frequently misrepresents or "forgets" such commonplace information.

quote:

Scott:
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.

Fred:

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 cannot believe that Williams is foolish enough to bring this up again. Tell me Willaims - are you hoping that a 'new' audience will not know about the previous instances in which you were shown to be completely in the dark on this?

Tell us all, Williams, How - EXACTLY - SNPs are then REMOVED from such analyses?

Do I really have to explain this to you AGAIN? Or how about quoting someone you love and respect?

"I am fully aware that past sequence comparisons must have included SNPs!"

This same person had previously written:

"THEY (SNPs) ONLY PLAY A ROLE IN INTRA-SPECIES COMPARISON."

Imagine that...

Oh - and this same person wrote;

"When informed evolutionists give estimates between chimp & man, they are referring to fixed differences. Trust me! "

That was BEFORE he wrote the quotes above.

But wait - the same person who wrote those quotes, also wrote this:

"I am not necessarily stating that "SNPs are excluded when scientists compare human and chimp sequences"
[/I]
Is it possible that I knew the scientists doing the comparisons did not filter out the noise (SNPs), realizing 1) there is not enough data to accomplish this, 2) the affect was negligible for their estimate anyway?"[/i]

And now, we have Williams most recent post in this thread, trying to say all over again that "An accurate measure of difference between chimps and man cannot, must not, include polymorphisms. "

Simply amazing....

Of course, an honest debater would see that I had already qualified my statement INDICATING THAT SOME OF THE INFERRED GENETIC DISTANCE WOULD CONSIST OF POLYMORPHISMS.

"Which means that roughly 17.5 million of these will be in each lineage, many of which are polymorphisms, most of which are neutral."

You have also admitted - under duress - that there is no way to identify and remove SNPs (not directly, anyway - more later) prior to typical phylogenetic analyses, so I have no clue whatsoever why you would even bring this up again, except perhaps as an attempt to make it appear as though 1. I made a mistake and 2. you know more than you really do...

Of course, those that are actually involved in perfroming relevant scientific research know that most phylogeny programs take polymorphisms into account during phylogenetic reconstruction. They are referred to as "phylogenetically uninformative sites". Gee... What a coincidnece that is!

I hope it does not come as a shock to the creationist Williams to be told that - believe it or not - such things have been taken into account long before he came on the scene...

quote:

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%.

Yes, it would, wouldn't it? As such, I am quite surprised that you and/or ReMine and or anyone else that tries to use sequence data and numbers to bluff their fantasies true have not as yet tried to 'prove' that 'huge' numbers of SNPs are not the norm and are in fact rare. Shame that actual data so often flubs up potential creation-friendly sound bites!...

Please Fred - in the future, at least make an attempt to keep your own arguments constant. You might try to make light of the fact that some evolutionists save the internet posts of you and other creationists, but I show above the real reasons...

Goodbye, Fred.

[This message has been edited by SLPx, 08-14-2002]


This message is a reply to:
 Message 14 by Fred Williams, posted 08-13-2002 6:17 PM Fred Williams has not yet responded

Replies to this message:
 Message 17 by derwood, posted 08-16-2002 12:27 PM derwood has not yet responded

    
derwood
Member
Posts: 1457
Joined: 12-27-2001


Message 17 of 56 (15529)
08-16-2002 12:27 PM
Reply to: Message 16 by derwood
08-14-2002 6:33 PM


I was casually perusing some other threads, and came across an exchange that I had with Williams - on the VERY TOPIC that he rants about above! Amazingly, I had already explained all this - for about the 10th time - in that thread. Williams, as he has a tendancy to do, ignored that message. Perhaps so that he can later claim that no one rebutted him?

www.evcforum.net/cgi-bin/dm.cgi?action=page&f=5&t=53&p=5 -->www.evcforum.net/cgi-bin/dm.cgi?action=page&f=5&t=53&p=5">http://www.evcforum.net/cgi-bin/dm.cgi?action=page&f=5&t=53&p=5

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 despite the fact that they have had the realities explained to them on many occasions.

I think that I know why...


This message is a reply to:
 Message 16 by derwood, posted 08-14-2002 6:33 PM derwood has not yet responded

Replies to this message:
 Message 18 by Fred Williams, posted 08-19-2002 8:55 PM derwood has responded

    
Fred Williams
Member (Idle past 2966 days)
Posts: 310
From: Broomfield
Joined: 12-17-2001


Message 18 of 56 (15719)
08-19-2002 8:55 PM
Reply to: Message 17 by derwood
08-16-2002 12:27 PM


quote:

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.”

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?

quote:

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."

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.

quote:

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

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.


This message is a reply to:
 Message 17 by derwood, posted 08-16-2002 12:27 PM derwood has responded

Replies to this message:
 Message 19 by mark24, posted 08-19-2002 9:39 PM Fred Williams has responded
 Message 20 by derwood, posted 08-20-2002 1:23 AM Fred Williams has not yet responded

    
mark24
Member (Idle past 3305 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 19 of 56 (15723)
08-19-2002 9:39 PM
Reply to: Message 18 by Fred Williams
08-19-2002 8:55 PM


quote:
Originally posted by Fred Williams:

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.


Good question, one that I will leave to Scott to answer in depth, if I may.

That said...

Firstly, if you have ANYTHING in Hardy Weinberg equilibrium, then it's an allele. It MAY be the result of an SNP, but not necessarily (no biggie). Therefore, assuming you can identify the different (homologous) alleles, who cares? As long as you don't mix them up, it shouldn't make much difference. Given that the coalescent point of two homologous alleles is likely to be after speciation, the derived phylogeny (inter-species) should be identical.

There are exceptions that spring to mind, alpha/beta heamaglobins for example, that are extant in both humans & chimps (coalescence occurred before speciation). In this case, choose which allele from which to infer a phylogeny from, ie don't use alpha from humans & beta from chimps. If you can't tell the difference between alleles, then there's not likely to be an appreciable affect on any derived phylogeny, is there?

Regarding SNPs...... 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.

Mark

------------------
Occam's razor is not for shaving with.


This message is a reply to:
 Message 18 by Fred Williams, posted 08-19-2002 8:55 PM Fred Williams has responded

Replies to this message:
 Message 21 by derwood, posted 08-20-2002 1:31 AM mark24 has responded
 Message 24 by Fred Williams, posted 08-20-2002 5:19 PM mark24 has not yet responded

    
derwood
Member
Posts: 1457
Joined: 12-27-2001


Message 20 of 56 (15741)
08-20-2002 1:23 AM
Reply to: Message 18 by Fred Williams
08-19-2002 8:55 PM


Originally posted by Fred Williams:

Dr.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.”

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?

It is flawed because you wildly and illogically extrapolate some commonplace activities as 'proof' that the ancient Hebrews had in-depth knowledge about microbes.
M. leprae, by the way, does not in fact live very long outside of a host.
Do you really think that the only 'ancient' peoples to engage in hygiene were the Hebrews?


Fred: …I’d be curious to know if Kimura or anyone else ever attempted this calculation ....
Dr.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."

No kidding Sherlock! That is not what I asked. I’ll ask again, but re-word it.

Let me guess - one of those "shortcomings of the medium" schticks?

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.

Then perhaps that is what you actually should have asked.

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.


Oh really? Just curious? Odd - I fouond your phrasing to be somewhat different than that which is normally associated with mere curiosity...


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

The reason I have to re-ask over and over again is because you refuse to see the point I am trying to make.

That is because you never seem to be able to make a point, and what point you do make (I will be generous here) is that you don't have a clue as to how molecular phylogenetic analyses are done.

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.


You belabor the obvious, oh Grand Wizard of Undereducated Creationists! What a splendid point! I'll bet all the creationists are hanging on your every word....

My point all along is that a precise difference calculation requires accounting for the “noise” introduced by SNPs.

Amazingly, did I not state when I mentioned this that SNPs are in the mix? Why, yes I did! My original assessment (in this thread) is on the mark... AGAIN!

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.


Translation: I have no clue what I am talking about, but I have ot say SOMETHING!

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.

You stand by everything you say.write. That is, obviously, no indicator of correctness.

So, again, I see absolutley no reason whatsoever for you to have brought up your usual bullshit, except a sad attempt to look smarter than you are.


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.

Give me a friggin break....

Your eyebrow is where is usually is - ticking Wally Kuckoo's glutes...

Informed cretins know that difference estimates are raw estimates because, as has been explained to you numerous times, such differences are gleaned using single or a few specimens of each taxon. Therefore, informed cretins know that there is no way to know exactly how many fixed v. unfixed differences there are. Informed cretins also know that whether or not a site is fixed in a species is essentially irrelevant in performing phylogenetic analyses (Poor Johnny Paul really stepped in it on that issue...).

By the way all - this is how Freddie 'admits' error....

[This message has been edited by SLPx, 08-20-2002]


This message is a reply to:
 Message 18 by Fred Williams, posted 08-19-2002 8:55 PM Fred Williams has not yet responded

    
derwood
Member
Posts: 1457
Joined: 12-27-2001


Message 21 of 56 (15743)
08-20-2002 1:31 AM
Reply to: Message 19 by mark24
08-19-2002 9:39 PM


quote:
Originally posted by mark24:
Fred:
My point all along is that a precise difference calculation requires accounting for the “noise” introduced by SNPs...

Good question, one that I will leave to Scott to answer in depth, if I may.


Sorry to disappoint - but there was no need to go into any depth - red herrings and all. One thing - informed cretins know that '% differences' are not meant to be "precise"...

quote:

Regarding SNPs...... 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.

In a perfect world, sure. Sequencing is EXPENSIVE, even if you have your own sequencers (around $125,000 and up), reagents are on the order of 300-500 dollars for 100 or so reactions...

However, phylogeny analysis does not really need consensus sequences to work. Consensus sequences would provide greater resolutiom and stronger results in most cases, but if your locus contains enough phylogenetically informative sites, it doesn't matter.

[/B][/QUOTE]


This message is a reply to:
 Message 19 by mark24, posted 08-19-2002 9:39 PM mark24 has responded

Replies to this message:
 Message 23 by mark24, posted 08-20-2002 7:09 AM derwood has not yet responded

    
derwood
Member
Posts: 1457
Joined: 12-27-2001


Message 22 of 56 (15744)
08-20-2002 1:33 AM


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

I wish you would. I have always found that seeing actual data strengthens one's understanding....


Replies to this message:
 Message 25 by Fred Williams, posted 08-20-2002 5:54 PM derwood has responded

    
mark24
Member (Idle past 3305 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 23 of 56 (15770)
08-20-2002 7:09 AM
Reply to: Message 21 by derwood
08-20-2002 1:31 AM


quote:
Originally posted by SLPx:
quote:
Originally posted by mark24:
Fred:
My point all along is that a precise difference calculation requires accounting for the “noise” introduced by SNPs...

Good question, one that I will leave to Scott to answer in depth, if I may.


Sorry to disappoint - but there was no need to go into any depth - red herrings and all. One thing - informed cretins know that '% differences' are not meant to be "precise"...

quote:

Regarding SNPs...... 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.

In a perfect world, sure. Sequencing is EXPENSIVE, even if you have your own sequencers (around $125,000 and up), reagents are on the order of 300-500 dollars for 100 or so reactions...

However, phylogeny analysis does not really need consensus sequences to work. Consensus sequences would provide greater resolutiom and stronger results in most cases, but if your locus contains enough phylogenetically informative sites, it doesn't matter.


I figured as much re. Not necessary to eliminate SNPs.

For the benefit of creationists, here’s why.

When performing phylogenetic analysis, you are deriving a divergence (coalescence) tree of XX number of organisms. An SNP in a gene that appeared a generation ago should still return the same tree as the fixed allele. Even if the SNP occurs at a phylogenetically informative site, providing you have enough of those sites, it won’t make an appreciable difference.

Mark

------------------
Occam's razor is not for shaving with.


This message is a reply to:
 Message 21 by derwood, posted 08-20-2002 1:31 AM derwood has not yet responded

    
Fred Williams
Member (Idle past 2966 days)
Posts: 310
From: Broomfield
Joined: 12-17-2001


Message 24 of 56 (15799)
08-20-2002 5:19 PM
Reply to: Message 19 by mark24
08-19-2002 9:39 PM


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

What? Would you care to elaborate further?

quote:
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.

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? )


This message is a reply to:
 Message 19 by mark24, posted 08-19-2002 9:39 PM mark24 has not yet responded

    
Fred Williams
Member (Idle past 2966 days)
Posts: 310
From: Broomfield
Joined: 12-17-2001


Message 25 of 56 (15800)
08-20-2002 5:54 PM
Reply to: Message 22 by derwood
08-20-2002 1:33 AM


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

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:

quote:

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!

[/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:

http://www.medic-planet.com/MP_article/article_num/Leprosy/5

From 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?

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

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.


This message is a reply to:
 Message 22 by derwood, posted 08-20-2002 1:33 AM derwood has responded

Replies to this message:
 Message 26 by John, posted 08-20-2002 9:55 PM Fred Williams has responded
 Message 31 by derwood, posted 08-21-2002 11:18 AM Fred Williams has responded

    
John
Inactive Member


Message 26 of 56 (15806)
08-20-2002 9:55 PM
Reply to: Message 25 by Fred Williams
08-20-2002 5:54 PM


quote:
Originally posted by Fred Williams:
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!

No problem. The person to whom you were reponding was wrong. But the real issue is whether or not the Isrealites had advanced knowledge of microbes. 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.

quote:
Scott, the onus is on you to show this was not advanced knowledge of that time.

Scott, if I may....

quote:
“The bacteria can survive three weeks or longer outside the human body, such as in dust or on clothing.”

No problem so far.

quote:
“It was not until 1873 that leprosy could be shown to be infectious rather than hereditary.”

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

quote:
Now don’t you think it was a good thing that God commanded the Levitical priests to isolate lepers, and burn their garments?

Sure, its a good thing that the Levitical priests included this injucntion, but it is hardly the result of advanced medical knowledge. It isn't a big leap of logic. Sick person. Another person comes in contact with sick person and thereafter gets sick as well. Solution: Don't come in contact with sick people, or people who have particular symptoms. And burn their stuff just to be safe.

quote:
What other culture prior to the 1800s, let alone 4000 years ago, practiced “safe leprosy”?

hmmm.... every culture where the disease is prevalent.

http://www.slic2.wsu.edu:82/hurlbert/micro101/pages/Chap1.html

quote:
Feel free to chalk this up to yet another “coincidence” or “blind luck”.

Thanks for the offer, but there is no need for luck or coincidence. Common sense works just fine.

quote:
You guys ought to be exhausted constantly having to explain away the myriad of supernatural evidences within the Bible.

... constantly having to explain over and over and over and over

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

------------------
www.hells-handmaiden.com


This message is a reply to:
 Message 25 by Fred Williams, posted 08-20-2002 5:54 PM Fred Williams has responded

Replies to this message:
 Message 27 by gene90, posted 08-20-2002 11:36 PM John has responded
 Message 33 by Fred Williams, posted 08-21-2002 7:15 PM John has not yet responded

  
gene90
Member (Idle past 1933 days)
Posts: 1610
Joined: 12-25-2000


Message 27 of 56 (15811)
08-20-2002 11:36 PM
Reply to: Message 26 by John
08-20-2002 9:55 PM


[QUOTE][B]Here is a problem. The Egyptians, Indians and Chinese all knew that leprosy was an infectious disease.[/QUOTE]

[/B]

I'm a little confused. Do you mean the condition caused by Mycobacterium leprae or just some skin disease? I thought we weren't sure that "leprosy" in the Bible is what we call "leprosy" today?


This message is a reply to:
 Message 26 by John, posted 08-20-2002 9:55 PM John has responded

Replies to this message:
 Message 28 by Randy, posted 08-21-2002 12:54 AM gene90 has not yet responded
 Message 29 by John, posted 08-21-2002 8:23 AM gene90 has not yet responded

  
Randy
Member (Idle past 4357 days)
Posts: 420
From: Cincinnati OH USA
Joined: 07-19-2002


Message 28 of 56 (15814)
08-21-2002 12:54 AM
Reply to: Message 27 by gene90
08-20-2002 11:36 PM


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.

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.

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. Armadillos are the only animal carrier and they die pretty quickly when they get it so I don't think they could have gotten from the middle east to Texas if infected.

Randy


This message is a reply to:
 Message 27 by gene90, posted 08-20-2002 11:36 PM gene90 has not yet responded

Replies to this message:
 Message 30 by mark24, posted 08-21-2002 10:29 AM Randy has not yet responded
 Message 34 by Fred Williams, posted 08-21-2002 7:57 PM Randy has responded

    
John
Inactive Member


Message 29 of 56 (15823)
08-21-2002 8:23 AM
Reply to: Message 27 by gene90
08-20-2002 11:36 PM


quote:
Originally posted by gene90:
[QUOTE][B]Here is a problem. The Egyptians, Indians and Chinese all knew that leprosy was an infectious disease.[/QUOTE]

[/B]

I'm a little confused. Do you mean the condition caused by Mycobacterium leprae or just some skin disease? I thought we weren't sure that "leprosy" in the Bible is what we call "leprosy" today?


That is a very good question. What information I found on leprosy in the ancient world was not terribly clear on this, but I kinda doubt that anyone had it narrowed down to one species of bacteria. The 'collection of skin disease' definition seems likely.

Here is a pretty good history of the disease.

http://www.webspawner.com/users/LEPHISTORY/

------------------
www.hells-handmaiden.com


This message is a reply to:
 Message 27 by gene90, posted 08-20-2002 11:36 PM gene90 has not yet responded

  
mark24
Member (Idle past 3305 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 30 of 56 (15834)
08-21-2002 10:29 AM
Reply to: Message 28 by Randy
08-21-2002 12:54 AM


quote:
Originally posted by Randy:

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. Armadillos are the only animal carrier and they die pretty quickly when they get it so I don't think they could have gotten from the middle east to Texas if infected.

Randy


Same goes for syphilis, gonorrhoea (sp?), etc.

In fact, we might ask was it Adam, Eve, or both, that had the above?

Mark

------------------
Occam's razor is not for shaving with.


This message is a reply to:
 Message 28 by Randy, posted 08-21-2002 12:54 AM Randy has not yet responded

Replies to this message:
 Message 32 by derwood, posted 08-21-2002 11:21 AM mark24 has not yet responded

    
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