molecular genetic proof against random mutation (1)

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Originally posted by peter borger:
dear Monkenstick,

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There will be a day that YOU have to apologize.

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best wishes,
Peter

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Because you are RIGHT, right? And all those thousands of others in relevant fields are all just wrong, right?I have to agree with Monken....

Dear dr Page,You reply:quote:
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Originally posted by peter borger:
The ZFX gene has about 20% neutral positions on third codon position. No variation in these position during 20 million years simply overturns molecular evolution. Today is just another bad day for evolutionism, I guess.
--------------------------------------------------------------------------------So Peter B. thinks that evolution is overturned becasue about 80 nucleotides in 'neutral' positions did not exhibit substitution in 20 million years.Of course, where is Borger's evidence that there were no back mutations?MY RESPONSE:
If there were, it would only confirm non-random mutations. I don't mind non-random mutations. That is what I am telling you all the time.YOU SAY:
Not that it matters, really.MY RESPONSE:
I think it does matter a lot.YOU SAY:
No, if there were an intergenic locus of 5kb that showed no change between species in 20 million years, I would be a bit suspicious. But nothing in 300+ bps? Chance alone can probably explain that...I SAY:
Chance alone? Calculate a bit on it, please. Demonstrate the odds.But....That is about 0.0000025 % of the genome.I guess we should ignore the fact that most of the remaining 99.9999975% doesn't show anything out of the ordinary (at least according to asthma guy creationist Borger)."ASTMA GUY CREATIONIST BORGER" RESPONSE:
As a matter of fact within a species the major part of the DNA sequences do not change at all. So, in contrast to what evolutionism requires (change), DNA sequences are stable. Stability of DNA sequences is the rule, not the exception.Best wishes,
Peter

Since Peter ignored it (and most of my comments) the last time I bump this again....

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Originally posted by Mammuthus:
Why would the ZFX region be neutral? Destruction of this region would lead to inablitity of the X and Y to pair and thus lead to male sterility and extinction....I would be surprised to find much change at all for this region.

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MY RESPONSE:

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The ZFX gene has about 20% neutral positions on third codon position. No variation in these position during 20 million years simply overturns molecular evolution. Today is just another bad day for evolutionism, I guess.

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Best wishes,
Peter
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ZFX is not so static as you make it seem

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Mol Biol Evol 2000 May;17(5):804-12 Related Articles, Links

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Sex chromosomal transposable element accumulation and male-driven substitutional evolution in humans.

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Erlandsson R, Wilson JF, Paabo S.

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Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany. riker1@biochem.kth.se

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We sequenced the genomic region containing the human Y-linked zinc finger gene (ZFY). Comparison of ZFY to the related region on the X chromosome (ZFX) and to autosomal sequences reveals a significant accumulation of transposable elements on the sex chromosomes. In addition, five times as many retroviruslike elements (RLEs) are present in the ZFY region as in the ZFX region. Thus, transposable elements accumulate more rapidly on the sex chromosomes, and the insertion of RLEs may occur more frequently in the male than in the female germ line. When the accumulation of substitutions in Alu elements was analyzed, it was found that the Alu elements at the Y-chromosomal locus diverged significantly faster than those at the X-chromosomal locus, whereas the divergence of autosomal Alu elements was intermediate. The male-to-female mutation rate ratio was estimated to be 2.5.

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Dear mammuthus,You posted:Originally posted by Mammuthus:
Why would the ZFX region be neutral? Destruction of this region would lead to inablitity of the X and Y to pair and thus lead to male sterility and extinction....I would be surprised to find much change at all for this region.
MY RESPONSE:The ZFX gene has about 20% neutral positions on third codon position. No variation in these position during 20 million years simply overturns molecular evolution. Today is just another bad day for evolutionism, I guess.Best wishes,
Peter
*************************ZFX is not so static as you make it seemMol Biol Evol 2000 May;17(5):804-12 Related Articles, LinksSex chromosomal transposable element accumulation and male-driven substitutional evolution in humans.Erlandsson R, Wilson JF, Paabo S.Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany. riker1@biochem.kth.seWe sequenced the genomic region containing the human Y-linked zinc finger gene (ZFY). Comparison of ZFY to the related region on the X chromosome (ZFX) and to autosomal sequences reveals a significant accumulation of transposable elements on the sex chromosomes. In addition, five times as many retroviruslike elements (RLEs) are present in the ZFY region as in the ZFX region. Thus, transposable elements accumulate more rapidly on the sex chromosomes, and the insertion of RLEs may occur more frequently in the male than in the female germ line. When the accumulation of substitutions in Alu elements was analyzed, it was found that the Alu elements at the Y-chromosomal locus diverged significantly faster than those at the X-chromosomal locus, whereas the divergence of autosomal Alu elements was intermediate. The male-to-female mutation rate ratio was estimated to be 2.5.MY RESPONSE:I didn't forget about this reference. I read it last weekend and the content of the article simply doesn't rebut my observation that the ZFX gene is completely stable during '20 million' years. That there are genetic elements jumping around in the genome and accumulate on the X chromosome in this region is in accord with the vision of a multipurpose genome where variation is induced by such elements, not by accumulation of SNPs or other mutations. These jumping elements affect gene expression and thus induce phenotypic variations.Best wishes,
Peter

Dear mammuthus,You posted:Originally posted by Mammuthus:
Why would the ZFX region be neutral? Destruction of this region would lead to inablitity of the X and Y to pair and thus lead to male sterility and extinction....I would be surprised to find much change at all for this region.
MY RESPONSE:The ZFX gene has about 20% neutral positions on third codon position. No variation in these position during 20 million years simply overturns molecular evolution. Today is just another bad day for evolutionism, I guess.Best wishes,
Peter
*************************ZFX is not so static as you make it seemMol Biol Evol 2000 May;17(5):804-12 Related Articles, LinksSex chromosomal transposable element accumulation and male-driven substitutional evolution in humans.Erlandsson R, Wilson JF, Paabo S.Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany. riker1@biochem.kth.seWe sequenced the genomic region containing the human Y-linked zinc finger gene (ZFY). Comparison of ZFY to the related region on the X chromosome (ZFX) and to autosomal sequences reveals a significant accumulation of transposable elements on the sex chromosomes. In addition, five times as many retroviruslike elements (RLEs) are present in the ZFY region as in the ZFX region. Thus, transposable elements accumulate more rapidly on the sex chromosomes, and the insertion of RLEs may occur more frequently in the male than in the female germ line. When the accumulation of substitutions in Alu elements was analyzed, it was found that the Alu elements at the Y-chromosomal locus diverged significantly faster than those at the X-chromosomal locus, whereas the divergence of autosomal Alu elements was intermediate. The male-to-female mutation rate ratio was estimated to be 2.5.MY RESPONSE:I didn't forget about this reference. I read it last weekend and the content of the article simply doesn't rebut my observation that the ZFX gene is completely stable during '20 million' years. That there are genetic elements jumping around in the genome and accumulate on the X chromosome in this region is in accord with the vision of a multipurpose genome where variation is induced by such elements, not by accumulation of SNPs or other mutations. These jumping elements affect gene expression and thus induce phenotypic variations.Best wishes,
Peter

quote:

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Originally posted by peter borger:
Dear mammuthus,

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You posted:

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Originally posted by Mammuthus:
Why would the ZFX region be neutral? Destruction of this region would lead to inablitity of the X and Y to pair and thus lead to male sterility and extinction....I would be surprised to find much change at all for this region.
MY RESPONSE:

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The ZFX gene has about 20% neutral positions on third codon position. No variation in these position during 20 million years simply overturns molecular evolution. Today is just another bad day for evolutionism, I guess.

​

Best wishes,
Peter
*************************

​

ZFX is not so static as you make it seem

​

Mol Biol Evol 2000 May;17(5):804-12 Related Articles, Links

​

Sex chromosomal transposable element accumulation and male-driven substitutional evolution in humans.

​

Erlandsson R, Wilson JF, Paabo S.

​

Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany. riker1@biochem.kth.se

​

We sequenced the genomic region containing the human Y-linked zinc finger gene (ZFY). Comparison of ZFY to the related region on the X chromosome (ZFX) and to autosomal sequences reveals a significant accumulation of transposable elements on the sex chromosomes. In addition, five times as many retroviruslike elements (RLEs) are present in the ZFY region as in the ZFX region. Thus, transposable elements accumulate more rapidly on the sex chromosomes, and the insertion of RLEs may occur more frequently in the male than in the female germ line. When the accumulation of substitutions in Alu elements was analyzed, it was found that the Alu elements at the Y-chromosomal locus diverged significantly faster than those at the X-chromosomal locus, whereas the divergence of autosomal Alu elements was intermediate. The male-to-female mutation rate ratio was estimated to be 2.5.

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MY RESPONSE:

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I didn't forget about this reference. I read it last weekend and the content of the article simply doesn't rebut my observation that the ZFX gene is completely stable during '20 million' years. That there are genetic elements jumping around in the genome and accumulate on the X chromosome in this region is in accord with the vision of a multipurpose genome where variation is induced by such elements, not by accumulation of SNPs or other mutations. These jumping elements affect gene expression and thus induce phenotypic variations.

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Best wishes,
Peter

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*****************************************Hi Peter,
However, that is completely false...the ZFX region is NOT completely stable. There is also a ZFY microsatellite that varies and is used in studying evolution of male lineages. Thus, your argument that ZFX/ZFY is absolutely stable is falsified.PB
"These jumping elements affect gene expression and thus induce phenotypic variations"M: However, there is no evidence for this...most elements do nothing. However, even if retrotranposition events were the only mutations occurring..they are still significant mutations and a major component of genetic variability. And there is extremely strong selectional constraints in the ZFX/ZFY regions because destroying this region would prevent XY chromosomal pairing thus limited diversity in this region is fully expected by evolutionary theory. oh yes, and you ignored the following...from Erlandsonn et al. "When the accumulation of substitutions in Alu elements was analyzed, it was found that the Alu elements at the Y-chromosomal locus diverged significantly faster than those at the X-chromosomal locus, whereas the divergence of autosomal Alu elements was intermediate. The male-to-female mutation rate ratio was estimated to be 2.5." Thus SNP's and other mutations that you dismissed for this region are happening at a nice clip.So the data are not compatible with your Lamarkian pseudo pre-adaptation hypothesis.Hopefully we can continue to discuss some of the other points as well.Best wishes,
M

Dear Mammuthus,
Thanks for the swift reponse, but could you please point out where exactly your reference falsifies the observation that the ZFX gene is completely stable, i.e. NO mutations on neutral positions. According to molecular evolution variation is expected to be found on these silent positions.
In addition, you suggest that the invariability may be due to alignment of X and Y chromosome during cell divisions. Although it could potentially explain non-variablity within species, it doesn't explain the non-variability between the primates. Besides, a couple of weeks ago you mailed references regarding these regions and it turned out that they are not at all crucial for chromosomal alignment, since several species simply lack them ( for instance marsupials if I recall properly).
Bottomline is, you still didn't rebut the observations of high stability of the ZFX gene. In my opinion its is a 'inert DNA location', i.e. mutations have never been 'dragged' to this spot. (Q: Dragged by what? A: Unknown mechanism/force?)Peter

quote:

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Originally posted by peter borger:
Dear Mammuthus,
Thanks for the swift reponse, but could you please point out where exactly your reference falsifies the observation that the ZFX gene is completely stable, i.e. NO mutations on neutral positions. According to molecular evolution variation is expected to be found on these silent positions.

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M:
Hi Peter,
"When the accumulation of substitutions in Alu elements was analyzed, it was found that the Alu elements at the Y-chromosomal locus diverged significantly faster than those at the X-chromosomal locus, ...what is it here that you do not understand regarding substitutions at neutral positions?

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PB:
In addition, you suggest that the invariability may be due to alignment of X and Y chromosome during cell divisions. Although it could potentially explain non-variablity within species, it doesn't explain the non-variability between the primates. Besides, a couple of weeks ago you mailed references regarding these regions and it turned out that they are not at all crucial for chromosomal alignment, since several species simply lack them ( for instance marsupials if I recall properly).

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M: First, I am not claiming it is the only reason for primate speciation. However, the region is more similar among primates as they are related and the region is similar within primate groups because it is conserved.....and the region is critical for chromosomal alignment..try pairing a marsupial X with mammalian X chromosome of choice. The reference to marsupials had to do with the content of the X chromosomes by the way and not ZFX if I recall. Marsupials have a large chunk of eutherian X linked genes on their autosomes.

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PB:
Bottomline is, you still didn't rebut the observations of high stability of the ZFX gene. In my opinion its is a 'inert DNA location', i.e. mutations have never been 'dragged' to this spot. (Q: Dragged by what? A: Unknown mechanism/force?)

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M: This last paragraph makes no sense. The region is not inert (whatever that means). And I have not suggested that mutations are dragged there...rather most large scale mutations are not tolerated and are selected out....not an uknown mechanism or force....but I am not sure what you where trying to say in the last paragraph...could you elaborate.

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Cheers,
M

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Peter

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quote:

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Originally posted by peter borger:
I didn't forget about this reference. I read it last weekend and the content of the article simply doesn't rebut my observation that the ZFX gene is completely stable during '20 million' years.

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I think I see the problem - Peter B - Do you know the difference between a gene and an exon?It is an honest question. After all, a PhD-holding creationist once appeared on a discussion board, claiming that his doctorate was in microbiology and genetics, and launched into a diatribe about the human genome having 3 billion codons...

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Originally posted by peter borger:
PB:
quote:----------------------------------------------------------------
Originally posted by peter borger:
The ZFX gene has about 20% neutral positions on third codon position. No variation in these position during 20 million years simply overturns molecular evolution. Today is just another bad day for evolutionism, I guess.
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SLP: So Peter B. thinks that evolution is overturned becasue about 80 nucleotides in 'neutral' positions did not exhibit substitution in 20 million years.

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Of course, where is Borger's evidence that there were no back mutations?

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MY RESPONSE:
If there were, it would only confirm non-random mutations. I don't mind non-random mutations. That is what I am telling you all the time.

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Only if one were to employ your naive 'definition' of non-random. Why you keep ignoring the fact that you do not seem to understand what 'random' means in terms of genbetics is beyond me.

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YOU SAY:
No, if there were an intergenic locus of 5kb that showed no change between species in 20 million years, I would be a bit suspicious. But nothing in 300+ bps? Chance alone can probably explain that...

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I SAY:
Chance alone? Calculate a bit on it, please. Demonstrate the odds.

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Mutation rate estimates are along the lines of 1 mutation per 10^9 bps per generation. At a 20 year generation time, that amounts to 1 million mutations in 20 million years. So any given site in a 3.2 billion bp genome has about a 0.03125% chance of 'suffering' a mutation in that time frame. That works out to less than 1 in 300 bases.
Very rough estimate and calculation, but it demonstrates my point.How about you - lets see your calculations.

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But....

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That is about 0.0000025 % of the genome.

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I guess we should ignore the fact that most of the remaining 99.9999975% doesn't show anything out of the ordinary (at least according to asthma guy creationist Borger).

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"ASTMA GUY CREATIONIST BORGER" RESPONSE:
As a matter of fact within a species the major part of the DNA sequences do not change at all. So, in contrast to what evolutionism requires (change), DNA sequences are stable. Stability of DNA sequences is the rule, not the exception.

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So I have to wonder why you have tried to make such a big deal out of this. It looks to me like you just contradicted your original hyperbole.

dear Dr Page,You write:quote:
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Originally posted by peter borger:
I didn't forget about this reference. I read it last weekend and the content of the article simply doesn't rebut my observation that the ZFX gene is completely stable during '20 million' years.
--------------------------------------------------------------------------------I think I see the problem - Peter B - Do you know the difference between a gene and an exon?It is an honest question. After all, a PhD-holding creationist once appeared on a discussion board, claiming that his doctorate was in microbiology and genetics, and launched into a diatribe about the human genome having 3 billion codons...MY RESPONSE:
Dr Page I am always so impressed by your honest questions. (Does it implicate that your other questions are dishonest questions?)I have the opinion --honestly-- that evolutionism is an outdated theory and I mentioned that several times. Why do I have this opinion? In my discussion over the last couple of years I discovered that most evolutionist do not know anything on contemporary biology besides their own field. Contemporary biology demonstrates that the complexity of life is beyond any expectation and it is simply not known (remember aditinal DNA associated codes I mentioned before) or denied (common habit throughout this site).
In looking for truth I discovered that evolutionism does not provide anything close to solutions except just-so stories. Example, recently I looked into the origin of the invariable histons H3 and H4 (human, trout and chicken have exacly the same), ubuiquinon, TCR (T cell receptor) and ribunucleases since they seem to drop out of the sky and stay unchanged for 1.000.000.000 years or so. Explanation: birth-and-death-evolution, or another just-so story. (It used to be concerted evolution, but that vision has been abondoned recently).
I don't believe these stories any more. I prefer creaton interactions with matter in a morphogenetic field, abbreviated: creation. It is not a better or worse explanation you provide me with in evolutionism. So, in my example of unchanged proteins it is B-a-D evolution versus Creation. I prefer creatons.Now, regarding your question whether I know the difference between exons and introns. I often wonder whether evolutionary biologist know about the difference, since the simply compare them to assess neutral evolution in genes. They have the tacit assumption that introns do not serve functions and are able to change over time with a neutral rate. However, this vision is highly disputable. Often we see fixed introns in genes between distinct species meaning in evolutionary vision that they should be under selective constraint. (I think that introns can fullfil important regulatory functions). Therefore, if introns aren't neutral we can skip the major part of evolutionary publications that compare introns and exons to assess neutral evolution. So, my question to you do you know the difference/similarities between introns and exons??Best wishes,
Peter[This message has been edited by peter borger, 10-22-2002]

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Originally posted by peter borger:
You write:

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quote:
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Originally posted by peter borger:
I didn't forget about this reference. I read it last weekend and the content of the article simply doesn't rebut my observation that the ZFX gene is completely stable during '20 million' years.
----------------------------------------------------------------------

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I think I see the problem - Peter B - Do you know the difference between a gene and an exon?

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It is an honest question. After all, a PhD-holding creationist once appeared on a discussion board, claiming that his doctorate was in microbiology and genetics, and launched into a diatribe about the human genome having 3 billion codons...

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MY RESPONSE:
Dr Page I am always so impressed by your honest questions. (Does it implicate that your other questions are dishonest questions?)

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You did not answer the question. The reader can draw his or her own conclusions. And hey - I liked that snide redirect....

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I have the opinion --honestly-- that evolutionism is an outdated theory and I mentioned that several times.

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Yes I know you have that opinion. You and every other creationist.

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Why do I have this opinion? In my discussion over the last couple of years I discovered that most evolutionist do not know anything on contemporary biology besides their own field.

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But YOU do, right? it is amazing at how well-rounded creationist scientists are. Why, not only are they 'experts' in their own fields, but they can speak with authority on nearly ANY field of science! It is amazing.

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Contemporary biology demonstrates that the complexity of life is beyond any expectation and it is simply not known (remember aditinal DNA associated codes I mentioned before) or denied (common habit throughout this site).

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Denied? Don't you mean exposed? Or perhaps refuted?

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In looking for truth I discovered that evolutionism does not provide anything close to solutions except just-so stories.

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Just-so stories? You mean like how all those articles demonstrating that directed mutations are artifacts of genome-wide hypermutation were claimed ot be evidence FOR directed mutations? Something like that?

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Example, recently I looked into the origin of the invariable histons H3 and H4 (human, trout and chicken have exacly the same), ubuiquinon, TCR (T cell receptor) and ribunucleases since they seem to drop out of the sky and stay unchanged for 1.000.000.000 years or so. Explanation: birth-and-death-evolution, or another just-so story. (It used to be concerted evolution, but that vision has been abondoned recently).

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Creationists like those 'anomalies'. After all, they PROVE evolution wrong... Right?

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I don't believe these stories any more. I prefer creaton interactions with matter in a morphogenetic field, abbreviated: creation. It is not a better or worse explanation you provide me with in evolutionism. So, in my example of unchanged proteins it is B-a-D evolution versus Creation. I prefer creatons.

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Of course you 'prefer' creations. That is what creationists do. They prefer to posit a miracle rather than try to find out a real answer.

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Now, regarding your question whether I know the difference between exons and introns.

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That was not my question. My question was do you know the difference between an exon and a gene. I asked that because you keep referring to the ZFX/ZFY as 'genes' when the papers you cite deal with only the sequence from one exon of around 300 bps - the exon that encodes the portion of the protein that is the binding site, i.e., the protion that is under great selective constraint. You apparently totally ignored the alignment I took the time to make for you, as the creationist is wont to do, as well as the other references provided (that you just blew off or twisted around).

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I often wonder whether evolutionary biologist know about the difference, since the simply compare them to assess neutral evolution in genes. They have the tacit assumption that introns do not serve functions and are able to change over time with a neutral rate.

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Now you are just blowing more smoke. Going off on a tangent of your own creation to try to prove some vacuous point. To claim that evolutionists think that introns serve no function is to display YOUR ignorance, not ours.[quote] So, my question to you do you know the difference/similarities between introns and exons?? [QUOTE] Yes I do. You did not answer my question, and you deigned not to respond to anything else you 'requested' of me before. Typical.Do you get your information on what 'evolutionists' know from evolutionists, or creationists?The answer to that question will clear several things up.

Dear Dr Page,You wonder:"Do you get your information on what 'evolutionists' know from evolutionists, or creationists?"I say:You should know by now that I am perfectly able to read scientific manuscripts and analyse the data by myself. I don't require either creationists or evolutionists opinions on science. Ever heard of objective unbiased data analysis?Best wishes,
Peter

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Originally posted by peter borger:
Dear Dr Page,

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You wonder:

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"Do you get your information on what 'evolutionists' know from evolutionists, or creationists?"

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I say:

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You should know by now that I am perfectly able to read scientific manuscripts and analyse the data by myself. I don't require either creationists or evolutionists opinions on science. Ever heard of objective unbiased data analysis?

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Best wishes,
Peter

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Well, I know how you analyze papers.Oh - I wasn't aware that locus control regions had genes in them...Citation please?

Dear Dr Page,Often I have the feeling that I am waisting my time here on this board. If you for instance started to look up the papers I refer to, it certainly would improve our discussion.
Weeks and weeks ago I referred to a Nature paper on the gene in LCR16a region. You even commented on it, and now I have to inform you again on the same topic. But, for the purposes of discussion, you can find the reference in: Nature 2001, volume 413, pp514-519.The paper is on the morpheus gene family and the authors conclude:...some genes emerge and evolve very rapidly, generating copies that bear little similarity to their ancestral precursors. Consequently, a small fraction of human genes may not possess discernible orthologues within genomes of model organisms.Random mutation and selection?I don't think so, the odds are against it.Best wishes,
Peter