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Author Topic:   molecular genetic proof against random mutation (1)
Dr_Tazimus_maximus
Member (Idle past 3304 days)
Posts: 402
From: Gaithersburg, MD, USA
Joined: 03-19-2002


Message 196 of 274 (19702)
10-11-2002 11:07 PM
Reply to: Message 195 by derwood
10-11-2002 1:15 PM


[QUOTE]Originally posted by SLPx:
Looks pretty random to me - even within species (see Ptr1 and 2, Pan troglodytes).
Of course, the 'non-random' distributions are what we call synapomorphies.[/B][/QUOTE]
I thought that synapomorphies dealt more with phenotypic traits than genotypic traits. Is this a recent use of the term. I have to admit that I am behind on the changes in molecular biology terms as my current work is much more into physical biochem and biochem engineering as they relate to the production and definition of biopharm products than I am into the straight molecular bio. By the way, thanks for the reference earlier.
------------------
"Chance favors the prepared mind." L. Pasteur
Taz

This message is a reply to:
 Message 195 by derwood, posted 10-11-2002 1:15 PM derwood has replied

Replies to this message:
 Message 197 by derwood, posted 10-13-2002 1:33 PM Dr_Tazimus_maximus has not replied

derwood
Member (Idle past 1963 days)
Posts: 1457
Joined: 12-27-2001


Message 197 of 274 (19786)
10-13-2002 1:33 PM
Reply to: Message 196 by Dr_Tazimus_maximus
10-11-2002 11:07 PM


quote:
Originally posted by Dr_Tazimus_maximus:
[B][QUOTE]Originally posted by SLPx:
Looks pretty random to me - even within species (see Ptr1 and 2, Pan troglodytes).
Of course, the 'non-random' distributions are what we call synapomorphies.[/B][/QUOTE]
I thought that synapomorphies dealt more with phenotypic traits than genotypic traits.
It seems that the term is ubiquitous. Basically, for those that do no tknow, a synapomorphy is what is also referred to as a 'shared deerived trait' in cladistics. In other words, a trait (in this case, a mutation at a specific locus/site) that is due to common descent.
quote:
Is this a recent use of the term. I have to admit that I am behind on the changes in molecular biology terms as my current work is much more into physical biochem and biochem engineering as they relate to the production and definition of biopharm products than I am into the straight molecular bio. By the way, thanks for the reference earlier.
My pleasure.
I don't know if the term has been 'recently' adopted by molecular ststematists or not - I think rather not, as I have several publications form the 80s that use the term. Perhaps it was limited to 'specialists' until relatively recently?

This message is a reply to:
 Message 196 by Dr_Tazimus_maximus, posted 10-11-2002 11:07 PM Dr_Tazimus_maximus has not replied

peter borger
Member (Idle past 7752 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 198 of 274 (19800)
10-13-2002 8:22 PM
Reply to: Message 194 by derwood
10-11-2002 11:31 AM


Dear Dr Page,
You say:
quote:
--------------------------------------------------------------------------------
Originally posted by peter borger:
dear Dr Page,
I know these articles. Actually, I got a personal copy from Dr Kim. However, the authors do not show the sequences, only the percentages. I was curious whether or not the muations were introduced at random ar not. It didn't show these data.
Furthermore 0.026 and 0.033 is both 0.03. So what's your point w.r.t common descent?
best wishes,
Peter
[This message has been edited by peter borger, 10-10-2002]
--------------------------------------------------------------------------------
The genetic distance reflects the evidence-supported hypotheses of descent.
Should have been obvious.
I say:
If so, than it would also be expected for the ZFX region (albeit less pronounced since it has chromosomal back up). However, in the article by Kim et al the comparison between human and chimp, human & gorilla, human & orangutan, human & agile gibbon, and human and siamang demonstrates 0.008, 0.008, 0.008, 0.008 and 0.008, respectively. Common descent?
best wishes,
Peter

This message is a reply to:
 Message 194 by derwood, posted 10-11-2002 11:31 AM derwood has not replied

derwood
Member (Idle past 1963 days)
Posts: 1457
Joined: 12-27-2001


Message 199 of 274 (19846)
10-14-2002 9:38 AM


Interesting how science actually tries to solve problems, while pseudoscience tries to use them to support pet beliefs....
J Mol Evol 1994 Dec;39(6):569-78
Contrasting rates of nucleotide substitution in the X-linked and Y-linked zinc finger genes.
Shimmin LC, Chang BH, Li WH.
Human Genetics Center, University of Texas Houston Health Science Center, 77225.
We have sequenced the entire exon (approximately 1.180 bp) encoding the zinc finger domain of the X-linked and Y-linked zinc finger genes (ZFX and ZFY, respectively) in the orangutan, the baboon, the squirrel monkey, and the rat; a total of 9,442 bp were sequenced. The ratio of the rates of synonymous substitution in the ZFY and ZFX genes is estimated to be 2.1 in primates. This is close to the ratio of 2.3 estimated from primate ZFY and ZFX intron sequences and supports the view that the male-to-female ratio of mutation rate in humans in considerably higher than 1 but not extremely large. The ratio of synonymous substitution rates in ZFY and ZFX is estimated to be 1.3 in the rat lineage but 4.2 in the mouse lineage. The former is close to the estimate (1.4) from introns. The much higher ratio in the mouse lineage (not statistically significant) might have arisen from relaxation of selective constraints. The synonymous divergence between mouse and rat ZFX is considerably lower than that between mouse and rat autosomal genes, agreeing with previous observations and providing some evidence for stronger selective constraints on synonymous changes in X-linked genes than in autosomal genes. At the protein level ZFX has been highly conserved in all placental mammals studied while ZFY has been well conserved in primates and foxes but has evolved rapidly in mice and rats, possibly due to relaxation of functional constraints as a result of the development of X-inactivation of ZFX in rodents. The long persistence of the ZFY-ZFX gene pair in mammals provides some insight into the process of degeneration of Y-linked genes.
So, yes, common descent.

Replies to this message:
 Message 200 by peter borger, posted 10-14-2002 9:44 PM derwood has replied

peter borger
Member (Idle past 7752 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 200 of 274 (19889)
10-14-2002 9:44 PM
Reply to: Message 199 by derwood
10-14-2002 9:38 AM


dear Dr page,
You write:
Interesting how science actually tries to solve problems, while pseudoscience tries to use them to support pet beliefs....
J Mol Evol 1994 Dec;39(6):569-78
Contrasting rates of nucleotide substitution in the X-linked and Y-linked zinc finger genes.
Shimmin LC, Chang BH, Li WH.
Human Genetics Center, University of Texas Houston Health Science Center, 77225.
We have sequenced the entire exon (approximately 1.180 bp) encoding the zinc finger domain of the X-linked and Y-linked zinc finger genes (ZFX and ZFY, respectively) in the orangutan, the baboon, the squirrel monkey, and the rat; a total of 9,442 bp were sequenced. The ratio of the rates of synonymous substitution in the ZFY and ZFX genes is estimated to be 2.1 in primates. This is close to the ratio of 2.3 estimated from primate ZFY and ZFX intron sequences and supports the view that the male-to-female ratio of mutation rate in humans in considerably higher than 1 but not extremely large. The ratio of synonymous substitution rates in ZFY and ZFX is estimated to be 1.3 in the rat lineage but 4.2 in the mouse lineage. The former is close to the estimate (1.4) from introns. The much higher ratio in the mouse lineage (not statistically significant) might have arisen from relaxation of selective constraints. The synonymous divergence between mouse and rat ZFX is considerably lower than that between mouse and rat autosomal genes, agreeing with previous observations and providing some evidence for stronger selective constraints on synonymous changes in X-linked genes than in autosomal genes. At the protein level ZFX has been highly conserved in all placental mammals studied while ZFY has been well conserved in primates and foxes but has evolved rapidly in mice and rats, possibly due to relaxation of functional constraints as a result of the development of X-inactivation of ZFX in rodents. The long persistence of the ZFY-ZFX gene pair in mammals provides some insight into the process of degeneration of Y-linked genes.
So, yes, common descent.
MY RESPONSE:
Ever heard of neutral theory?
Best wishes,
Peter

This message is a reply to:
 Message 199 by derwood, posted 10-14-2002 9:38 AM derwood has replied

Replies to this message:
 Message 201 by derwood, posted 10-15-2002 1:57 PM peter borger has replied

derwood
Member (Idle past 1963 days)
Posts: 1457
Joined: 12-27-2001


Message 201 of 274 (19939)
10-15-2002 1:57 PM
Reply to: Message 200 by peter borger
10-14-2002 9:44 PM


quote:
Originally posted by peter borger:
So, yes, common descent.
MY RESPONSE:
Ever heard of neutral theory?
Yes, of course I have. I own a collection of Kimura's works and have read his book.
What about it?

This message is a reply to:
 Message 200 by peter borger, posted 10-14-2002 9:44 PM peter borger has replied

Replies to this message:
 Message 202 by peter borger, posted 10-15-2002 7:31 PM derwood has replied

peter borger
Member (Idle past 7752 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 202 of 274 (19957)
10-15-2002 7:31 PM
Reply to: Message 201 by derwood
10-15-2002 1:57 PM


Dear Dr Page,
It is hard to make links, isn't it?
In a previous mail you admitted that neutral positions are able to change over time more rapidly than non-neutral position. Kim et al demonstrate that the ZFX region doesn't change at all over 20 million years or so, not even on neutral positions. I find this a bit suspicious. What kind of evolution is this? Non-random evolution? Maybe you can help out?
Best wishes,
Peter

This message is a reply to:
 Message 201 by derwood, posted 10-15-2002 1:57 PM derwood has replied

Replies to this message:
 Message 203 by Mammuthus, posted 10-16-2002 4:21 AM peter borger has replied
 Message 209 by derwood, posted 10-18-2002 10:56 AM peter borger has not replied

Mammuthus
Member (Idle past 6562 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 203 of 274 (20001)
10-16-2002 4:21 AM
Reply to: Message 202 by peter borger
10-15-2002 7:31 PM


quote:
Originally posted by peter borger:
Dear Dr Page,
It is hard to make links, isn't it?
In a previous mail you admitted that neutral positions are able to change over time more rapidly than non-neutral position. Kim et al demonstrate that the ZFX region doesn't change at all over 20 million years or so, not even on neutral positions. I find this a bit suspicious. What kind of evolution is this? Non-random evolution? Maybe you can help out?
Best wishes,
Peter

***************************
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.

This message is a reply to:
 Message 202 by peter borger, posted 10-15-2002 7:31 PM peter borger has replied

Replies to this message:
 Message 204 by peter borger, posted 10-16-2002 8:06 PM Mammuthus has replied

peter borger
Member (Idle past 7752 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 204 of 274 (20044)
10-16-2002 8:06 PM
Reply to: Message 203 by Mammuthus
10-16-2002 4:21 AM


dear mammuthus,
You wrote:
quote:
--------------------------------------------------------------------------------
Originally posted by peter borger:
Dear Dr Page,
It is hard to make links, isn't it?
In a previous mail you admitted that neutral positions are able to change over time more rapidly than non-neutral position. Kim et al demonstrate that the ZFX region doesn't change at all over 20 million years or so, not even on neutral positions. I find this a bit suspicious. What kind of evolution is this? Non-random evolution? Maybe you can help out?
Best wishes,
Peter
--------------------------------------------------------------------------------
***************************
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

This message is a reply to:
 Message 203 by Mammuthus, posted 10-16-2002 4:21 AM Mammuthus has replied

Replies to this message:
 Message 207 by Mammuthus, posted 10-17-2002 5:00 AM peter borger has not replied
 Message 210 by derwood, posted 10-18-2002 11:03 AM peter borger has replied

monkenstick
Inactive Member


Message 205 of 274 (20052)
10-16-2002 9:21 PM


borger, you're an arrogant fool

Replies to this message:
 Message 206 by peter borger, posted 10-16-2002 10:39 PM monkenstick has not replied

peter borger
Member (Idle past 7752 days)
Posts: 965
From: australia
Joined: 07-05-2002


Message 206 of 274 (20058)
10-16-2002 10:39 PM
Reply to: Message 205 by monkenstick
10-16-2002 9:21 PM


dear Monkenstick,
There will be a day that YOU have to apologize.
best wishes,
Peter

This message is a reply to:
 Message 205 by monkenstick, posted 10-16-2002 9:21 PM monkenstick has not replied

Replies to this message:
 Message 211 by derwood, posted 10-18-2002 11:06 AM peter borger has not replied

Mammuthus
Member (Idle past 6562 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 207 of 274 (20084)
10-17-2002 5:00 AM
Reply to: Message 204 by peter borger
10-16-2002 8:06 PM


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 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.

This message is a reply to:
 Message 204 by peter borger, posted 10-16-2002 8:06 PM peter borger has not replied

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 Message 213 by Mammuthus, posted 10-22-2002 5:48 AM Mammuthus has not replied

monkenstick
Inactive Member


Message 208 of 274 (20113)
10-17-2002 10:17 AM


I don't think i'd ever apologise, even if your crackpot multipurpose genome idea turned out to be true - you're still an arrogant fool

derwood
Member (Idle past 1963 days)
Posts: 1457
Joined: 12-27-2001


Message 209 of 274 (20170)
10-18-2002 10:56 AM
Reply to: Message 202 by peter borger
10-15-2002 7:31 PM


quote:
Originally posted by peter borger:
Dear Dr Page,
It is hard to make links, isn't it?
In a previous mail you admitted that neutral positions are able to change over time more rapidly than non-neutral position. Kim et al demonstrate that the ZFX region doesn't change at all over 20 million years or so, not even on neutral positions. I find this a bit suspicious. What kind of evolution is this? Non-random evolution? Maybe you can help out?
Best wishes,
Peter

Lets watch out word choice, shall we? I "admitted" nothing - I knew this all along and never said otherwise.
the region Kim et al. analyzed was a little over 300 bp in length. Is it a little odd that no changes occurred? Perhaps. Then, there is no requirement that any changes - neutral or otherwise - should have occurred.
Unless you have some documentable 'rules' that state as much?

This message is a reply to:
 Message 202 by peter borger, posted 10-15-2002 7:31 PM peter borger has not replied

derwood
Member (Idle past 1963 days)
Posts: 1457
Joined: 12-27-2001


Message 210 of 274 (20173)
10-18-2002 11:03 AM
Reply to: Message 204 by peter borger
10-16-2002 8:06 PM


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.
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?
Not that it matters, really.
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...
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).

This message is a reply to:
 Message 204 by peter borger, posted 10-16-2002 8:06 PM peter borger has replied

Replies to this message:
 Message 212 by peter borger, posted 10-22-2002 12:20 AM derwood has not replied

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