Evolution as natural history is psuedo-science

[busterdog]

A couple of recent beams of rarified starlight light into my existence: I met the guitarists and drummer from Switchfoot. I could have had a vomit soaked towel from the lead singer (stomach flu) for a sweet deal on ebay, but I was thinking with characteristic plodding. I also had an online conversation with Helen Fryman, wife to Barry Setterfield. Helen is a science writer, who was done a lot with genetics and written about the effects of mutation in populations: toward less vigor, less survivability. However, I also did learn that there are less events of speciation in evidence. I think it was a particular flower, where the mutation lead not to plants that were distinct in terms of their ability only to breed with each other. I think I understand this to have been a divergence in the functioning of the sexual organs, but not a true differentiation of species. This was fundamentally no different that a tendency toward a certain color of moth. The TEs claimed many examples of speciation.

As for the mutation rate, I don't think I follow you. The difference between 60 mutations per generation and 400 does not necessarily sound like a significant difference to me.

Edited to add: wait, I get it. The difference is 20/3 per generation over several million years, making the odds at best about 13.5M to one. Not sure about that odds figure, but the divergence occurring in every generation for millions of years does suggest a remarkably unlikely ,or indeed miraculous event. Maybe goddidit?

 

[mark kennedy]

A couple of recent beams of rarified starlight light into my existence: I met the guitarists and drummer from Switchfoot. I could have had a vomit soaked towel from the lead singer (stomach flu) for a sweet deal on ebay, but I was thinking with characteristic plodding. I also had an online conversation with Helen Fryman, wife to Barry Setterfield. Helen is a science writer, who was done a lot with genetics and written about the effects of mutation in populations: toward less vigor, less survivability. However, I also did learn that there are less events of speciation in evidence. I think it was a particular flower, where the mutation lead not to plants that were distinct in terms of their ability only to breed with each other. I think I understand this to have been a divergence in the functioning of the sexual organs, but not a true differentiation of species. This was fundamentally no different that a tendency toward a certain color of moth. The TEs claimed many examples of speciation.

As for the mutation rate, I don't think I follow you. The difference between 60 mutations per generation and 400 does not necessarily sound like a significant difference to me.

Edited to add: wait, I get it. The difference is 20/3 per generation over several million years, making the odds at best about 13.5M to one. Not sure about that odds figure, but the divergence occurring in every generation for millions of years does suggest a remarkably unlikely ,or indeed miraculous event. Maybe goddidit?

What was predicted for about half a century was that chimpanzees and humans diverved by less then 1% of their DNA. The mutation rate observed in primates (homimids) would get you about 35 million in 7 million years. What they found instead is 4x that amount and not even viruses mutate like that.

 

[Assyrian]

Bear with me here I am still learning.

Was the mutation rate they measured in primates the rate for single nucleotide mutations or did it include SNPs and other longer mutations like indels?

Now the 4x you quote that they actually found, is that SNPs only, or for combined SNPs and indels?

 

[RichardT]

Bear with me here I am still learning.

Was the mutation rate they measured in primates the rate for single nucleotide mutations or did it include SNPs and other longer mutations like indels?

Now the 4x you quote that they actually found, is that SNPs only, or for combined SNPs and indels?

indels are included in his figure..

btw, MK went offline right after I sent him a PM, I wanted him to answer it before he left oh well..

 

[sfs]

In September of 2005 the Chimpanzee Genome Project finished the Chimpanzee genome and published it in Nature Magazine. They found that the differences between chimpanzees and humans amounted to 145 million base pairs. There was just one problem with this, mutations (alterations of the DNA) happen at a measurable rate. Usually it averages around 2 x 10^-8 which means every human (ape or whatever) is born with 60 mutations permantly fixed in their genome.

This is the thing, it would require over 400 per generation (20 years) for 7 million years. Evolutionists have no answer for how this is possible so they lie about it or just don't talk about it at all. They also like to pretend that creationists don't know what they are talking about but the truth is they are pushing an impossible transition.

Mark has been corrected on this point literally dozens of times, but he keeps repeating it anyway. I guess he doesn't like the answer, since he insists that everyone (including the scientists) is lying to him.

Here's the situation: we do think that there are about 60 new mutations per generation in each copy of the genome. We also think there have been about 300,000 generations between us and the chimp-human common ancestor, so we would expect about 18 million new mutations have occurred since the common ancestor in our lineage, and another 18 million in the chimp lineage. So we would expect the human and chimpanzee genomes to differ by 35 or 40 million mutations (more or less -- with the uncertainty on the numbers, anything between 20 and 60 million would not have been very surprising). What we actually found when we compared the genomes was 40 million differences, i.e. just about exactly what we expected.

Those 40 million differences affected more than 40 million base pairs, however, since some of them (~5 million) were insertions or deletions of bits of DNA, which can affect many more than 1 base pair at a time. The total number of bases that differed was about 125 million (35 million single-base differences + 5 million insertions and deletions, with an average insertion/deletion size of 18 base pairs). Since 125 million (or 145 million, since Mark insists on including inversions for some reason) is larger than 40 million, Mark has decided there must be a terrible flaw in evolution here and that all of the scientists are lying to cover it up.

 

[busterdog]

Mark has been corrected on this point literally dozens of times, but he keeps repeating it anyway. I guess he doesn't like the answer, since he insists that everyone (including the scientists) is lying to him.

Here's the situation: we do think that there are about 60 new mutations per generation in each copy of the genome. We also think there have been about 300,000 generations between us and the chimp-human common ancestor, so we would expect about 18 million new mutations have occurred since the common ancestor in our lineage, and another 18 million in the chimp lineage. So we would expect the human and chimpanzee genomes to differ by 35 or 40 million mutations (more or less -- with the uncertainty on the numbers, anything between 20 and 60 million would not have been very surprising). What we actually found when we compared the genomes was 40 million differences, i.e. just about exactly what we expected.

Those 40 million differences affected more than 40 million base pairs, however, since some of them (~5 million) were insertions or deletions of bits of DNA, which can affect many more than 1 base pair at a time. The total number of bases that differed was about 125 million (35 million single-base differences + 5 million insertions and deletions, with an average insertion/deletion size of 18 base pairs). Since 125 million (or 145 million, since Mark insists on including inversions for some reason) is larger than 40 million, Mark has decided there must be a terrible flaw in evolution here and that all of the scientists are lying to cover it up.

So what did Nature say then? Presumptively they used one of these figures, 145M, 125M or 40M. What was it? And what about these figures of 60 and 400 mutations per generation? YOu haven't explained whether or which of those figures includes your inversions, insertions/deletions.

To my the difference between 40M and 145M is about 1 in 3M chance of the theoretical rate exceeding the observed rate.

 

[busterdog]

Mark has been corrected on this point literally dozens of times, but he keeps repeating it anyway. I guess he doesn't like the answer, since he insists that everyone (including the scientists) is lying to him.

Here's the situation: we do think that there are about 60 new mutations per generation in each copy of the genome. We also think there have been about 300,000 generations between us and the chimp-human common ancestor, so we would expect about 18 million new mutations have occurred since the common ancestor in our lineage, and another 18 million in the chimp lineage. So we would expect the human and chimpanzee genomes to differ by 35 or 40 million mutations (more or less -- with the uncertainty on the numbers, anything between 20 and 60 million would not have been very surprising). What we actually found when we compared the genomes was 40 million differences, i.e. just about exactly what we expected.

Those 40 million differences affected more than 40 million base pairs, however, since some of them (~5 million) were insertions or deletions of bits of DNA, which can affect many more than 1 base pair at a time. The total number of bases that differed was about 125 million (35 million single-base differences + 5 million insertions and deletions, with an average insertion/deletion size of 18 base pairs). Since 125 million (or 145 million, since Mark insists on including inversions for some reason) is larger than 40 million, Mark has decided there must be a terrible flaw in evolution here and that all of the scientists are lying to cover it up.

So what did Nature say then? Presumptively they used one of these figures, 145M, 125M or 40M. What was it? And what about these figures of 60 and 400 mutations per generation? YOu haven't explained whether or which of those figures includes your inversions, insertions/deletions.

To my eye the difference between 40M and 145M is generously, 1/4, which yields about 1 in 3M chance of the theoretical rate exceeding the observed rate. Or it exceeds the average rate by a factor of 3M over your 300,000 generations. For the theoretical rate to exceed the observed by 20/3 is not that huge of a difference. For it to happen 300,000 times in a row is a pretty good run.

 

[sfs]

So what did Nature say then? Presumptively they used one of these figures, 145M, 125M or 40M. What was it?

Nature says lots of things -- I'm not sure what you're asking about. The chimpanzee genome paper in Nature said, "we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements.

And what about these figures of 60 and 400 mutations per generation? YOu haven't explained whether or which of those figures includes your inversions, insertions/deletions.

The figure of 60 can include the insertions/deletions (usually known as "indels", since it's less to type) or not, according to taste. The total mutation rate includes single-base substitutions and indels. The single-base substitution rate was known to be 60 plus or minus at least 20. The indel rate was thought to be about one tenth the substitution rate, but is now estimated to be closer to 20% of the substitution rate. So you could use 50 as the substitution rate and 10 as the indel rate (giving 60 total), or 60 as just the substitution rate with 70 as the total. As I said originally, there was plenty of uncertainty about the exact numbers. The inversion rate can be ignored, since it is even lower than the indel rate.

As for the figure of 400 mutations per generation, that doesn't exist. Look back at what Mark wrote: he talked about "400 per generation", without saying what it was that was happening at a rate of 400 per generation. What he means is 400 base pairs per generation, not 400 mutations. Since a single indel can be hundreds, thousands or even hundreds of thousands of base pairs long, the number of base pairs mutated is generally larger than the number of mutations. (Presumably the 400 means 200 per generation in humans and 200 in chimpanzees, since that would add up to the total difference seen in the genome comparison.)

To my the difference between 40M and 145M is about 1 in 3M chance of the theoretical rate exceeding the observed rate.

I'm sorry, but I don't know what you mean. 40M and 145M are measuring different things. It's like comparing "number of car trips taken per year" and "miles travelled per year". There's no reason they should be the same.

 

[Deamiter]

I too wonder why Mark Kennedy is still making this mistake. If multiple people tell you that you're making a basic error in units, wouldn't you stop and sort it out before repeating your original argument again and again?

Anyway, it's VERY important to look closely at the units here precisely because people have been giving numbers without units, or giving numbers with the wrong units (on the board, not in the primary sources). ALWAYS check CAREFULLY to see if you're looking at base pair difference or number of mutations. Because indels are mutations of many base pairs, these can be very different.

Compounding the possible misunderstanding is the study of point mutations only. In my understanding (as a physicist mind you) point mutations are much more informative when it comes to divergence because it's much easier to count the number of point mutations than number of total mutations because indel length is extremely variable. Point mutations also happen at a more consistant rate, so they're more useful for trying to date divergence between populations.

Anyway, always look at the units. Scientists also sometimes cite how much the coding DNA (introns) vary from species to species (because coding DNA is much more important). The fixture rate in exons is invariably going to be lower than that for introns.

It's all compounded by imprecise or occasionally incorrect terminology by the media. Mark recently picked up on a poorly labeled figure in a reputable magazine (or was it Nature?) that cited a 1% difference, but didn't clarify what precisely it used was comparing. Mark almost always uses the largest percentage he can find (comparing each individual base pair to get around 4%) and started a thread on how they're lying to us because their number is different than his without ever (as far as I know) acknowledging that they might be using different units.

 

[shernren]

You should realize that you posts are becoming increasingly obscure. The specifics and particulars are getting harder and harder to find. I'm not chasing down every detail you challenge me on and begging the question of proof by refering to other discussions sounds like a diversionary tactic to me.

I'm not sure what the point of this quote is but notice the mutation rate is a per year substitution rate. Only viruses mutate on that level and that particular mutation rate is a virus. I'm still trying to figure out how you come to the conclusion that 8% of the human genome is the result of viruses for one thing. I am also wondering what possible arguement you think is concieved of here with the mutation rate of viruses.

Ok, it sounds like you are quoting me here but like I said your posts are getting increasingly obscure.

http://www.christianforums.com/showpost.php?p=28522578&postcount=9

[note: I have no intention of following this link]

Quit using circular arguements and I am not chasing your links in circles around arguements you couldn't make stick elsewhere. I have actually been looking at mutation rates for viruses, microbes, eukaryotes...etc. Obviously you have no clue what the signifigance of mutation rates are here so let me break it down to you. Humans and chimapnzees diverge by no less then 145 million bases. For that to happen it would require a mutation rate that is impossible for viruses or at least at their upper limit. Got it?

You are being irrelevant, whether or not retroviruses reproduce means absolutly nothing.

Alright, I'll talk on your terms. Please cite your source that viruses undergo mutation rates of less than 2x10^-8/bp/generation (units are important ). If I was wrong to assume that it was the same source you used in the debate with AEA, then my apologies.

 

[shernren]

Anyway, always look at the units. Scientists also sometimes cite how much the coding DNA (introns) vary from species to species (because coding DNA is much more important). The fixture rate in exons is invariably going to be lower than that for introns.

As far as I know, coding DNA between chimps and humans is 99.4% same. That's a statistic that mark the learned champion of chimp-human divergence never seems to bring up or deal with. Not that it contributes anything to his argument, but it's just a curious factoid which one would expect has some significance to the whole question of evolutionary origins of man.

 

[mark kennedy]

As far as I know, coding DNA between chimps and humans is 99.4% same.

If they weren't do you think they would come right out and tell us, because I don't. What I end up having to do is track it down one peice of the puzzle at a time.

"Point mutation rates in exons (synonymous sites) and noncoding (introns and intergenic) regions are generally assumed to be the same. However, comparative sequence analyses of synonymous substitutions in exons (81 genes) and that of long intergenic fragments (141.3 kbp) of human and chimpanzee genomes reveal a 30%–60% higher mutation rate in exons than in noncoding DNA. " (Neutral Substitutions Occur at a Faster Rate in Exons Than in Noncoding DNA in Primate Genomes, Letter Genome Research May 2003​

Why am I the only one in the world who finds this statement counter intuitive? Call me Mr. Incredulous but I just don't see how it is remotely reasonable to suggest introns higher mutation rates in expons than in noncoding DNA.

That's a statistic that mark the learned champion of chimp-human divergence never seems to bring up or deal with. Not that it contributes anything to his argument, but it's just a curious factoid which one would expect has some significance to the whole question of evolutionary origins of man.

Eventually I will find some time and get handy with a genome browser. Until then I will have to track this down one sequence or gene at a time. I have seen this 99% statistic applied to the entire genome before and since the Chimpanzee Genome was sequenced. Virtually all of the genes show divergance at an amino acid sequence level and we are not talking about minor variations.

Alright, I'll talk on your terms. Please cite your source that viruses undergo mutation rates of less than 2x10^-8/bp/generation (units are important ). If I was wrong to assume that it was the same source you used in the debate with AEA, then my apologies.

Viruses are the only sequences (they are not living systems) that undergo mutation rates on a per annum basis. I don't really have the details available at the moment but we can get into that later. I don't know why you think virus mutation rates would be less then the hominid mutation rate unless that is just an awkwardly worded statement.

 

[mark kennedy]

Mark has been corrected on this point literally dozens of times, but he keeps repeating it anyway. I guess he doesn't like the answer, since he insists that everyone (including the scientists) is lying to him.

I don't know what else to call it when you have a direct contradiction with only one of two statements being true. I was perfectly happy with the answer for months, it never set well with me but I figured you had your reasons.

Here's the situation: we do think that there are about 60 new mutations per generation in each copy of the genome. We also think there have been about 300,000 generations between us and the chimp-human common ancestor, so we would expect about 18 million new mutations have occurred since the common ancestor in our lineage, and another 18 million in the chimp lineage. So we would expect the human and chimpanzee genomes to differ by 35 or 40 million mutations (more or less -- with the uncertainty on the numbers, anything between 20 and 60 million would not have been very surprising). What we actually found when we compared the genomes was 40 million differences, i.e. just about exactly what we expected.

This is where you flew off into obscurity with no apparent motive other then contradicting me. In your discussion on the mutation rate with details virtually identical to this one you actually measured the mutation in terms of base pairs. When you talk about the indels suddenly it can be one base pair or a million which is absurd.

Using this technique, it has been estimated[1] that the single-base substitution rate for humans is approximately 1.7 x 10^-8 substitutions/nucleotide/generation, that is, 17 changes per billion nucleotides. That translates into ~100 new mutations for every human birth. (17 x 3, for the 3 billion nucleotides in the genome, x 2 for the two genome copies we each carry). At that rate, in 350,000 generations a copy of the human genome should have accumulated about 18 million mutations, while the chimpanzee genome should have accumulated a similar number.

Common ancestry of humans and chimpanzees: mutations

What is so hard to understand, you want a mutation a million base pairs and one base pair to be counted the same. I'm not buying it, in fact, I don't think you have a clue how to reconcile the divergance between chimpanzees and humans to the known mutation rate.

Those 40 million differences affected more than 40 million base pairs, however, since some of them (~5 million) were insertions or deletions of bits of DNA, which can affect many more than 1 base pair at a time.

That's 35 million single base substitutions and 5 million indels adding up to 90 million bases. This is in addition to the 20 million base pairs due to chromosomal rearrangements but they don't count, just like indels irregardless of lenth, only count as one.

The total number of bases that differed was about 125 million (35 million single-base differences + 5 million insertions and deletions, with an average insertion/deletion size of 18 base pairs). Since 125 million (or 145 million, since Mark insists on including inversions for some reason) is larger than 40 million, Mark has decided there must be a terrible flaw in evolution here and that all of the scientists are lying to cover it up.

There is a flaw in evolution as a theory, the most important is that the facts are twisted to fit the theory. What ends up happening is the facts get distorted, perhaps not purposely but inevitably. The biggest problem mainstream science seems to have no answer for is the rate at which they were accumulated.

Let's say these indels average 20 base pairs and we have 90 million base pairs that diverge in 7 million years (it's less the 5 mya but that's not important yet). Each generation you would need one indel per year for 7 million years fixed every generation for 7 million years.

You guys tell us that each human being has maybe 120 mutations in their genome that is unique to them. With the differences between chimpanzees and humans it would have to be at least three times that. When explaining this the first mistake is that mainstream evolutionists simply ignore the amount of divergance, or worse they lie about it.

Then you come along and act as it it's not problem. I can accept that you have an answer for it and that it is actually a complicated issue, I'll buy that. It's when you act like it's not problem and then treat an indel 18 bases long as it it were the same as a single substitution one base long.

I think I can make a prediction based on the pattern I'm seeing here. We are going to find out that the genes are actually showing vastly more differences then we are currently being told exist. My prediction is that the truth will come out and no one will even notice.

 

[Deamiter]

Let's say these indels average 20 base pairs and we have 90 million base pairs that diverge in 7 million years (it's less the 5 mya but that's not important yet). Each generation you would need one indel per year for 7 million years fixed every generation for 7 million years.

Do you see a problem with this? An average of one fixed indel per year in a population of 10,000 would be trivial.

 

[mark kennedy]

Do you see a problem with this? An average of one fixed indel per year in a population of 10,000 would be trivial.

Your not getting the big picture here, indels when comparing human and chimpanzee genome sequences are 3x larger, as measured in base pairs then single nucleotide insertions. However, the way they happen in human polymorphisms is the single nucleotide insertions or polymorphisms will will represent 10x more of the diversity.

There are two major problems here, one there would have to be a disproportionate number of indels and two they would have to be a permentant part of the genomic architechture. What you don't seem to understand is that everyone of the 10,000 would have the same forces generating the same level of genetic diversity.

There is no problem with this, it's impossible.

 

[Deamiter]

Your not getting the big picture here, indels when comparing human and chimpanzee genome sequences are 3x larger, as measured in base pairs then single nucleotide insertions.

About what I've heard.

However, the way they happen in human polymorphisms is the single nucleotide insertions or polymorphisms will will represent 10x more of the diversity.

What diversity? Do you mean they're 10x more prominent in coding regions, or in the entire genome? Is there some reason you DON"T think point insertions are more likely to be fixed?

There are two major problems here, one there would have to be a disproportionate number of indels and two they would have to be a permentant part of the genomic architechture. What you don't seem to understand is that everyone of the 10,000 would have the same forces generating the same level of genetic diversity.

Um... that last statement is quite bogus. I KNOW you understand the concept of averages -- you don't need every member to have exactly the same forces because that would be silly.

One of these days, it'd be VERY helpful if you'd write out your argument in a properly cited report that gives units and sources for each of your numbers. Then give units and sources for the numbers that show the measured numbers to be impossible.

As it is, I've seen you, on multiple occasions, contrasting the number of mutations to the number of base pair differences and claiming that because the second is higher, the first is impossible...

Anyway, I WANT to be able to go through the entire discussion, but in the forums, you tend to talk past other people when they point out math errors and I'm never quite satisfied that your numbers are on the right order of magnitude. Since you've apparently already done the research, why not just write it all down in one place (on the web or in a document you could email)? If everything is as shocking as you claim, I, for one, would love to be converted to the truth! I just haven't seen a rigorous treatment of your claims.

 

[shernren]

If they weren't do you think they would come right out and tell us, because I don't. What I end up having to do is track it down one peice of the puzzle at a time.

"Point mutation rates in exons (synonymous sites) and noncoding (introns and intergenic) regions are generally assumed to be the same. However, comparative sequence analyses of synonymous substitutions in exons (81 genes) and that of long intergenic fragments (141.3 kbp) of human and chimpanzee genomes reveal a 30%–60% higher mutation rate in exons than in noncoding DNA. " (Neutral Substitutions Occur at a Faster Rate in Exons Than in Noncoding DNA in Primate Genomes, Letter Genome Research May 2003​

Why am I the only one in the world who finds this statement counter intuitive? Call me Mr. Incredulous but I just don't see how it is remotely reasonable to suggest introns higher mutation rates in expons than in noncoding DNA.

Please define an exon in your own terms, and then explain why exons cannot have higher mutation rates than non-coding DNA.

Eventually I will find some time and get handy with a genome browser. Until then I will have to track this down one sequence or gene at a time. I have seen this 99% statistic applied to the entire genome before and since the Chimpanzee Genome was sequenced. Virtually all of the genes show divergance at an amino acid sequence level and we are not talking about minor variations.

(emphasis added) Please substantiate the bolded portion. If you are referring again to the PTR22q data from here:

[FONT=times, times new roman, serif]Human–chimpanzee comparative genome research is essential for narrowing down genetic changes involved in the acquisition of unique human features, such as highly developed cognitive functions, bipedalism or the use of complex language. Here, we report the high-quality DNA sequence of 33.3 megabases of chimpanzee chromosome 22. By comparing the whole sequence with the human counterpart, chromosome 21, we found that 1.44% of the chromosome consists of single-base substitutions in addition to nearly 68,000 insertions or deletions. These differences are sufficient to generate changes in most of the proteins. Indeed, 83% of the 231 coding sequences, including functionally important genes, show differences at the amino acid sequence level. Furthermore, we demonstrate different expansion of particular subfamilies of retrotransposons between the lineages, suggesting different impacts of retrotranspositions on human and chimpanzee evolution. The genomic changes after speciation and their biological consequences seem more complex than originally hypothesized.[/FONT]​

http://www.nature.com/cgi-taf/DynaP...full/nature02564_r.html&filetype=&dynoptions=
with my post discussing it: http://www.christianforums.com/showpost.php?p=24830925&postcount=56

please define a "difference at the amino acid sequence level", including on average how many nucleotides' worth of difference would be necessary to constitute one.

Viruses are the only sequences (they are not living systems) that undergo mutation rates on a per annum basis. I don't really have the details available at the moment but we can get into that later. I don't know why you think virus mutation rates would be less then the hominid mutation rate unless that is just an awkwardly worded statement.

Are you referring to this source?

"By contrast, HERV-K18, RTVL-Ha, and RTVL-Hb are found only in humans, chimpanzees, and gorillas, which are thought to have diverged around 5 million years ago. To estimate the age of each provirus the human/chimpanzee distances from each tree were used to calibrate the rate of molecular evolution at each locus. The most recent common ancestor of humans and chimpanzees lived approximately 4.5 mya, so divedin the distance between the huyman and chimpanzee siquences (substitutions per site) by this numbner gives rates ranging from 2.3 to 5.0 x 10^-9 substitutions per site per year. These numbers are simular to the estimated rates of evolution for pseudogenes and noncoding regions of mammalian genes.(PNAS Constructing primate phylogenies from ancient retrovirus sequences, 2006)


or something else?

Forgive the unwieldy trail of requests for definitions, but ever since watching your style on EvC I've come to realize that I can no longer assume that you use standard definitions or concepts of any biological terminology.

 

[shernren]

Your not getting the big picture here, indels when comparing human and chimpanzee genome sequences are 3x larger, as measured in base pairs then single nucleotide insertions. However, the way they happen in human polymorphisms is the single nucleotide insertions or polymorphisms will will represent 10x more of the diversity.

There are two major problems here, one there would have to be a disproportionate number of indels and two they would have to be a permentant part of the genomic architechture. What you don't seem to understand is that everyone of the 10,000 would have the same forces generating the same level of genetic diversity.

There is no problem with this, it's impossible.

(emphasis added)
Please cite source for the bolded portion. If you are referring to this:

Together with previous studies, our analysis indicates that SNPs, indels, and transposon insertion polymorphisms represent significant sources of genetic variation in humans. Human populations are estimated to harbor ∼10 million common SNPs (Judson et al. 2002), ∼2 million common indels (our unpublished data), and ∼2000 common transposon insertion polymorphisms (this study). Therefore, with 10 million bases of variation, SNPs account for the majority of common human genetic variation, followed by indels and then transposon insertion polymorphisms. On the other hand, if we assume that the average transposon polymorphism in humans is ∼500–1000 bp in length, then the total amount of variation caused by common transposon insertions is 1–2 million base pairs (equivalent to 10–20% of the base pair variation caused by SNPs). Thus, in terms of the number of base pairs, common transposon insertions cause significant levels of human genetic variation.

http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15514065
​

(emphasis added) then you have again misinterpreted. The bolded words represent an important transition.

 

[mark kennedy]

About what I've heard.

What diversity? Do you mean they're 10x more prominent in coding regions, or in the entire genome? Is there some reason you DON"T think point insertions are more likely to be fixed?

What I mean is that single nucleotide substitutions (1 nucleotide/base pair) taken together are ten times greater in cumulative size then indels (insertions/deletions of length). That is normal in human genomics, single nucleotide substitutions/polymorphisms are far more common then indels.

What has been found to be the case is that there are 4x more indels (measured in base pairs) then single nucleotide substitutions. To put this in perspective the averge person has about 60 germline mutatoins in their genome at birth. These are inheritable and as far as anyone knows they accumulate from one generation to another. In order to account for the divergance between chimpanzees and humans you would need 400 per generation permenantly fixed every generation (20years).

This is not only a strong arguement against common ancestry, I have not heard a single arguement that it's even concievable that the mutation rate could be sustained. The problems with this are ignored, in fact, Time magazine and Nature magazie have both said that the Chimpanzee Genome Consortium found that the DNA of chimpanzees and humans was 98% the same. This is simply not true and they are well aware of this fact.

Think I'm exaggerating, type 'Chimpanzee Genome' into your google search engine and you will find this webpage:

"What makes us human? We share more than 98% of our DNA and almost all of our genes with our closest living relative, the chimpanzee. Comparing the genetic code of humans and chimps will allow the study of not only our similarities, but also the minute differences that set us apart."

Nature, Web Focus, The Chimpanzee Genome​

The publishers of Nature know that this is not true, the paper they are announcing says something very different:

On the basis of this analysis, we estimate that the human and chimpanzee genomes each contain 40–45 Mb of species-specific euchromatic sequence, and the indel differences between the genomes thus total 90 Mb. This difference corresponds to 3% of both genomes and dwarfs the 1.23% difference resulting from nucleotide substitutions; this confirms and extends several recent studies. Of course, the number of indel events is far fewer than the number of substitution events (5 million compared with 35 million, respectively).​

Initial sequence of the chimpanzee genome and comparison with the human genome


My opinion is that they are simply unprepared to deal with the indels, the mutation rate is too high for them to have accumulated naturally.

Um... that last statement is quite bogus. I KNOW you understand the concept of averages -- you don't need every member to have exactly the same forces because that would be silly.

Evolutionists no longer have any moral authority with regards to bogus information. Nature magazine has deliberatly misrepresented the evidence and there is an identical statement in Time magazine. This is the partyline of evolutionists, they are saying 98% homology across the board. This is more then a perspective problem, they are lying through their teeth.

One of these days, it'd be VERY helpful if you'd write out your argument in a properly cited report that gives units and sources for each of your numbers. Then give units and sources for the numbers that show the measured numbers to be impossible.

Allright brother, I will be quite happy to submit all the particulars for your review. I'll post them both here and in the common forum so they are free to correct any discrepancies. The truth is that they can't and if you want the details I am delighted to provide them unambiquisly and I'm perfectly willing and able to defend my position.

As it is, I've seen you, on multiple occasions, contrasting the number of mutations to the number of base pair differences and claiming that because the second is higher, the first is impossible...

That is a good concise summary.

Anyway, I WANT to be able to go through the entire discussion, but in the forums, you tend to talk past other people when they point out math errors and I'm never quite satisfied that your numbers are on the right order of magnitude. Since you've apparently already done the research, why not just write it all down in one place (on the web or in a document you could email)? If everything is as shocking as you claim, I, for one, would love to be converted to the truth! I just haven't seen a rigorous treatment of your claims.

That's a great idea, I'll have something up in a day or two covering the whole gambit. Just off the top of my head I can think of 6 papers that will need expostitive reviews. I look forward to the review, thanks for the suggestion.

 

[sfs]

What I mean is that single nucleotide substitutions (1 nucleotide/base pair) taken together are ten times greater in cumulative size then indels (insertions/deletions of length). That is normal in human genomics, single nucleotide substitutions/polymorphisms are far more common then indels.

This is wrong -- Mark has misunderstood something he read. Within the modern human population, one particular class of indels (transposons) accounts for 10-20% as many variable bases as single base substitutions (SNPs). Transposons are, however, only 0.5% of all indels. Combined, all indels account for many more variable bases than do SNPs.

In "An initial map of insertion and deletion (INDEL) variation in the human genome" (Genome Research 2006 16:1182-1190) the authors found 3.3 million SNPs and 534,000 indels in a survey of variation in the genome. That is, indels are 16% as common as SNPs in modern humans. Recall from the chimpanzee genome that when comparing humans and chimpanzees, indels are 14% as common as single-base substitutions. Quite consistent, I'd say, and a good indication that the human/chimp indel differences are the result of mutation.

As for the total number of bases involved in indels, we still do not have a very good estimate. The chimpanzee genome paper found that indels accounted for 2.3 - 2.6 times as many bases (different between the two species) as single-base substitutions. The indel map cited above found in modern human variation that indels accounted for 1.3 times as many bases as single-base substitutions. That study was limited to indels shorter than 10,000 base pairs, however, and is therefore a lower limit on the total number. Indels are known to be as long as hundreds of thousands of base pairs; even small numbers of these large indels contribute enormously to the total number of bases affected by indels. When a complete survey can be done, finding that indels contribute at least 2.5 times the variation (in base pairs) as SNPs will be consistent with everything we've seen so far. (In fact, I suspect we will find that indels contribute a larger fraction to modern variation than they do to between-species differences, since they are somewhat more likely to be deleterious and thus not to stick around.)

In any case, it is clear that the number of bases that vary between humans as a result of indels is larger than the number that vary because of SNPs. In short, Mark's entire line of argument here is wrong.