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Author Topic:   ID/Creationism - Comparison of Human and Chimp Genomes
Meddle
Member (Idle past 1270 days)
Posts: 179
From: Scotland
Joined: 05-08-2006


Message 1 of 83 (348239)
09-11-2006 9:33 PM


As I said originally my initial post was to understand the other sides point of view, but when you put it like that...
Okay I will go with your suggestion, since I've found this area lacking in Creationist/ID literature. I also find this to be the most compelling evidence in support of evolution.
How would Creationist/ID models be used to interpret artifacts we see in species genomes? For example, looking at the human genome comparing it with chimpanzee's and the other great apes:
(1) In human chromosome 2 there is a telomere sequence and the remnants of a centromere sequence, indicating that this results from the fusion of the chimpanzee chromosomes 2p and 2q.
(2) The presence of endogenous retroviruses at the same position within the genomes of different species.
(3) Both chimp and humans have two 21-hydroxylase genes on their genome - a functional gene and a pseudogene. Both share the same mutation which inactivated the pseudogene.
Finally two questions on how to proceed further in Creationist/ID models:
(4) If humans and chimpanzees are supposed to be entirely separate species, how much value is there in comparing the two genomes?
(5) In terms of ID, at what point would something be declared as 'irreducibly complex'? After such a decision, would study on such an irreducibly complex continue, and if so how? For example Michael Behe's example of the bacterial flagellum.

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Adminnemooseus
Administrator
Posts: 3974
Joined: 09-26-2002


Message 2 of 83 (348241)
09-11-2006 9:37 PM
Reply to: Message 1 by Meddle
09-11-2006 9:33 PM


This was from a lost "Proposed New Topic" from a few months back
New topic from individual message 3 of Can science progress with creationism/ID? "Proposed New Topic". I have chosen to rename the topic to "ID/Creationism - Comparison of Human and Chimp Genomes".
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Damouse
Member (Idle past 4905 days)
Posts: 215
From: Brookfield, Wisconsin
Joined: 12-18-2005


Message 3 of 83 (355471)
10-09-2006 9:03 PM
Reply to: Message 1 by Meddle
09-11-2006 9:33 PM


Pause for effect
Use dumb laguage for those of us who DONT have degrees in genetics!
I think i got the gist of the last two questions, but i stop trying for the others. for (4) you ask the value of comparing the two species' genes. Who decides wether or not they are two species? That we have concluded that they are related proves the original point and comparing for any closer resembalances is futile when we have agreed they are essentially fruits from the same tree (no pun intended)

-I believe in God, I just call it Nature
-One man with an imaginary friend is insane. a Million men with an imaginary friend is a religion.
-People must often be reminded that the bible did not arrive as a fax from heaven; it was written by men.
-Religion is the opiate of the masses

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eggasai
Inactive Member


Message 4 of 83 (357525)
10-19-2006 4:58 PM
Reply to: Message 1 by Meddle
09-11-2006 9:33 PM


quote:
How would Creationist/ID models be used to interpret artifacts we see in species genomes? For example, looking at the human genome comparing it with chimpanzee's and the other great apes:
(1) In human chromosome 2 there is a telomere sequence and the remnants of a centromere sequence, indicating that this results from the fusion of the chimpanzee chromosomes 2p and 2q.
I've seen the supposed fusion site and the TAG seqeunces, it seems pretty convincing. There is just one problem, there is not one but 9 pericentric inversions that total 20 million base pairs (Mb). One of them is 4 Mb long and the shortest is 2 Mb long. What is more there are inversions riddled throughout the two genomes that are not easily explained as naturally occuring.
quote:
(2) The presence of endogenous retroviruses at the same position within the genomes of different species.
Consider this, ERVs (actually LTRs) make up about 8% of the human genome. Do you really expect me to believe that all of this DNA is left over from germline invasions?
http://www.pnas.org/...ontent-nw/full/101/suppl_2/14572/FIG1
I have seen the comparisons and they generally take about half a dozen LTRs and use common alleles as markers. Then they give some convoluted estimate of them arriving independantly in the respective genomes. If we are going to talk about the Transposable Elements the first order of buisness is characterizing them, don't you?
quote:
(3) Both chimp and humans have two 21-hydroxylase genes on their genome - a functional gene and a pseudogene. Both share the same mutation which inactivated the pseudogene.
You see this all of the time and I am wondering if you are serious about this. This is one of those psuedo genes evolutionists want to make such a big deal about. Because there was relaxed functional constraint there was no negative selection acting on the gene so the mutation didn't kill those who had it.
NCBI/eutils201 - WWW Error 404 Diagnostic
quote:
Finally two questions on how to proceed further in Creationist/ID models:
(4) If humans and chimpanzees are supposed to be entirely separate species, how much value is there in comparing the two genomes?
The mutation rate is 2 * 10^-8 which means that 123 germline mutations are getting passed down to the offspring. In comparing the two genomes there are no less then 145 Mb that diverge between the two genomes which leads one to wonder, how did they get there? Random mutation does not account for it so if you have some genetic basis for this I would be glad to hear about it.
quote:
(5) In terms of ID, at what point would something be declared as 'irreducibly complex'? After such a decision, would study on such an irreducibly complex continue, and if so how? For example Michael Behe's example of the bacterial flagellum.
How about the protein coding and regulatory genes involved with neural functions? That seems about as irreducably complex as it gets.
quote:
As I said originally my initial post was to understand the other sides point of view, but when you put it like that...
Okay I will go with your suggestion, since I've found this area lacking in Creationist/ID literature. I also find this to be the most compelling evidence in support of evolution.
If psuedo genes and chromosomal rearrangements are your proof then you really have your work cut out for you. The Chimpanzee Genome is now complete, would you like to share with me how many nucleotides diverge between the two perspecitve genomes? You know creationists can't be trusted to give accurate estimates, perhaps you would like to offer the details from peer reviewed scientific sources.
Edited by eggasai, : Had to format a couple of things
Edited by eggasai, : transcript errors

This message is a reply to:
 Message 1 by Meddle, posted 09-11-2006 9:33 PM Meddle has replied

Replies to this message:
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eggasai
Inactive Member


Message 5 of 83 (357542)
10-19-2006 5:56 PM
Reply to: Message 3 by Damouse
10-09-2006 9:03 PM


Re: Pause for effect
quote:
Who decides wether or not they are two species?
Species has come to mean two species that cannot interbreed. This is just a rule of thumb because the troglogytes and pygmy chimps can still interbreed but they are different enough to be considered seperate species. There is a long list of differnces from head to toe, literally, including vital organs.
quote:
That we have concluded that they are related proves the original point and comparing for any closer resembalances is futile when we have agreed they are essentially fruits from the same tree (no pun intended)
That's the Darwinian tree of life assumption, the problem is that it was concluded we descended from apes before biology was even a seperate discipline in science. The lineage of chimpanzees and humans going back to a common ancestor is far from confirmed. In fact the genetic distance between chimpanzees and humans is growing as we speak. Don't get me wrong, it was allways there but the old saw that the DNA is 99% the same has been proven to be false.
Biological evolution makes assumptions and then makes homology arguments from any simularity. When encountering differences the explanation is allways natural selection. Adaptations are never without costs and they must be outweighed by the affects. Unless scientists have a genetic mechanism for tripling the size of an ape brain then this is all supposition and speculation about what might be an alternative to special creation.

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Wounded King
Member
Posts: 4149
From: Cincinnati, Ohio, USA
Joined: 04-09-2003


Message 6 of 83 (357757)
10-20-2006 1:23 PM
Reply to: Message 5 by eggasai
10-19-2006 5:56 PM


Re: Pause for effect
Don't get me wrong, it was allways there but the old saw that the DNA is 99% the same has been proven to be false.
It isn't an old saw, it is an old estimate based on a crude technique and one acknowledged to be crude. As better techniques have come along better estimates have followed. There are still a number of different possible metrics to measure such conservation by however, and not all of them will give you 95% as your figure.
Unless scientists have a genetic mechanism for tripling the size of an ape brain then this is all supposition and speculation about what might be an alternative to special creation.
You yourself have referenced research on another thread about the ASPM gene. If mutations in a gene can cause a 70% reduction in the size of a brain why do you think that mutations acting over several genes could not increase the size of the brain?
TTFN,
WK
Edited by Wounded King, : typographical errors

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jar
Member (Idle past 394 days)
Posts: 34026
From: Texas!!
Joined: 04-20-2004


Message 7 of 83 (357759)
10-20-2006 1:54 PM
Reply to: Message 6 by Wounded King
10-20-2006 1:23 PM


on brain size
Looks like there is quite a bit of research going on looking at brain size development.
one such
environment changes
and specifically humans

Aslan is not a Tame Lion

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mick
Member (Idle past 4986 days)
Posts: 913
Joined: 02-17-2005


Message 8 of 83 (357878)
10-20-2006 11:18 PM
Reply to: Message 4 by eggasai
10-19-2006 4:58 PM


number of point mutations is not equal to number of nucleotide differences
Hi eggasai,
eggasai writes:
What is more there are inversions riddled throughout the two genomes that are not easily explained as naturally occuring.
Could you give us an unnatural explanation, then?
eggasai writes:
Consider this, ERVs (actually LTRs) make up about 8% of the human genome. Do you really expect me to believe that all of this DNA is left over from germline invasions?...If we are going to talk about the Transposable Elements the first order of buisness is characterizing them, don't you?
The transposable elements have been perfectly well characterized (review aricle). The interesting question is really a) why you would think that 8% of the human genome is too much, since population genetic models predict extremely high frequency of such elements under conditions such as small population size, and more importantly, b) why should humans and chimps share the SAME transposable elements? Question b is really the key here, one you failed to address.
eggasai writes:
This is one of those psuedo genes evolutionists want to make such a big deal about. Because there was relaxed functional constraint there was no negative selection acting on the gene so the mutation didn't kill those who had it.
You have completely missed the point here - why do chimps and humans BOTH have the same pseudogene with the same deactivating mutation? Sure, pseudogenes degenerate because there is no natural selection keeping them faithful to the original copy. That is obvious. But why would humans and chimps have the SAME pseudogene, if they did not share a common ancestor in which that pseudogene arose and degraded? Do you have an alternative explanation or not?
eggasai writes:
The mutation rate is 2 * 10^-8 which means that 123 germline mutations are getting passed down to the offspring. In comparing the two genomes there are no less then 145 Mb that diverge between the two genomes which leads one to wonder, how did they get there? Random mutation does not account for it so if you have some genetic basis for this I would be glad to hear about it.
Since you appear to read the literature, I have to wonder whether you have done this sleight of hand on purpose. The number of point mutations is not equal to the number of nucleotide differences between two species. There are two classes of point mutation: substitution and indel (the latter is an abbreviation of insertion/deletion). A substitution involves one nucleotide being replaced with another, and results in exactly one nucleotide difference between an individual who has the mutation and an individual who does not have it. An indel, on the other hand, changes every nucleotide downstream of the mutation until a further indel puts an end to the frame shift. For example, consider a sequence, and a variation caused by a single substitution:

original sequence: ACTAGGACT
mutated sequence: ACGAGGACT
ONE MUTATION = ONE NUCLEOTIDE DIFFERENCE
Now imagine that a deletion occurs at the first position, removing letter A:

original sequence: ACTAGGACT
mutated sequence: CTAGGACT
ONE MUTATION = SEVEN NUCLEOTIDE DIFFERENCES
Now let's look at your numbers.
Phylogenetic and palaeontological studies suggest that humans and chimps share a most recent common ancestor around six million years ago. Generation time for chimpanzees is around 20 years. Assuming that that generation time is a reasonable approximation for the intervening primate species, and given your rate of 123 mutations per generation, we would have nearly 37 million mutations in each of the human and chimpanzee lineages in that time, i.e. a total of 74 million mutations (since there are two lineages, protochimp and protohuman, which both accumulate mutations).
So it seems that we are missing 70 megabases of mutations? Well, only if ALL mutations are substitutions. That's the implicit assumption of your argument that the mutation rate is too small. In reality, the researchers who published the new analyses of chimp versus human DNA found that around three times more nucleotide differences were caused by indels than were caused by substitutions. Indeed, from a Science Editorial it is reported:
quote:
as suggested by earlier work on portions
of the chimp genome, other kinds of
genomic variation turn out to be at least as
important as single nucleotide base changes.
Insertions and deletions have dramatically
changed the landscape of the human and
chimp lineages since they diverged. Duplications
of sequence “contribute more genetic difference
between the two species”70 megabases
of material”than do single base pair
substitutions,” notes Evan Eichler, also of UW,
Seattle, who led a team analyzing the duplications.
“It was a shocker, even to us.”
Could that be your missing 70 megabases?
It would help to know where the 145 megabase number comes from, so we can examine your source more carefully. Could you give a reference? The results reported in the Science editorial were: 35 million single nucleotide substitions, and 5 million indels. We know that the indels gave rise to 70 megabases of divergent positions, so the authors appear to be reporting a total of 105 megabases, rather than 145, of divergent nucleotide positions caused by point mutation.
More importantly, the total number of point mutations reported is 40 million, well within the bounds of the number of possible mutations according to your own figures.
Mick
Edited by M, : No reason given.
Edited by M, : No reason given.
Edited by M, : No reason given.
Edited by M, : Sorry for editing so many times
Edited by M, : okay that's the last edit, i promise

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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 9 of 83 (357934)
10-21-2006 10:24 AM
Reply to: Message 5 by eggasai
10-19-2006 5:56 PM


Re: Pause for effect
That's the Darwinian tree of life assumption, the problem is that it was concluded we descended from apes before biology was even a seperate discipline in science.
In fact, the word "biology" originated in the early nineteenth century (don't you people ever check your facts? --- it took me fifteen seconds to look that up) and unlike creationism, our common descent from apes has survived, and, indeed, been confirmed by, the rise of the biological sciences, increased knowledge of the fossil record, et cetera.

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eggasai
Inactive Member


Message 10 of 83 (358171)
10-22-2006 5:22 PM
Reply to: Message 6 by Wounded King
10-20-2006 1:23 PM


Re: Pause for effect
It is an old saw, it's wrong and evolutionists know it and keep saying that 98%-99% of the Chimpanzee and human DNA is the same:
"Scientists figured out decades ago that chimps are our nearest evolutionary cousins, roughly 98% to 99% identical to humans at the genetic level...But that's rapidly changing. Just a year ago, geneticists announced that they had sequenced a rough draft of the chimpanzee genome, allowing the first side-by-side comparisons of human and chimpanzee DNA."
Page not found | TIME
The paper they are refering to is the Initial Sequence of the Chimpanzee Genome (Nature, Sept 2005 available online). They did not find the DNA to be 98%-99% the same, in fact they found 35 million bases of single nucleotide substitutions, 90 Mb worth of indels and 20 Mb worth of major chromosomal rearrangements. That comes to 145 Mb in two genomes that are less then 3 billion base pairs long. That does not come to 1%-2% and the scientists that have been saying that 'for decades' have been wrong and the Science editor of Time knows that if he read the paper
"Five chimpanzee bacterial artificial chromosome (BAC) sequences (described in GenBank) have been compared with the best matching regions of the human genome sequence to assay the amount and kind of DNA divergence. The conclusion is the old saw that we share 98.5% of our DNA sequence with chimpanzee is probably in error. For this sample, a better estimate would be that 95% of the base pairs are exactly shared between chimpanzee and human DNA. In this sample of 779 kb, the divergence due to base substitution is 1.4%, and there is an additional 3.4% difference due to the presence of indels."
http://cat.inist.fr/?aModele=afficheN&cpsidt=13976594
The ASPM gene results in a defective spindle, which in turn results in a serverly reduced brain size. Bruce Lahn, one of the authors of the paper mentioned, compared hundreds of genes involved in neural functions. He concluded that it would take hundreds if not thousands of mutations in hundreds if not thousands of genes. There is just one major problem with this, mutations affecting neural genes are exclusivly deleterious.

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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 11 of 83 (358178)
10-22-2006 6:40 PM
Reply to: Message 10 by eggasai
10-22-2006 5:22 PM


Re: Pause for effect
It is an old saw, it's wrong and evolutionists know it and keep saying that 98%-99% of the Chimpanzee and human DNA is the same...
Well, in fact what Wounded King said was "it is an old estimate based on a crude technique and one acknowledged to be crude".
And we can all see that.
I don't see what you're trying to achieve by pretending otherwise. Whom do you hope to convince?

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eggasai
Inactive Member


Message 12 of 83 (358181)
10-22-2006 7:05 PM
Reply to: Message 8 by mick
10-20-2006 11:18 PM


Re: number of point mutations is not equal to number of nucleotide differences
First of all an unnatural explanation would be mutations. If you apply the commonly held mutation rate (a mean actually) it comes to 2.5 x 10^8 which translated means 173 germline mutations per diploid generation.
quote:
The transposable elements have been perfectly well characterized (review aricle). The interesting question is really a) why you would think that 8% of the human genome is too much, since population genetic models predict extremely high frequency of such elements under conditions such as small population size, and more importantly, b) why should humans and chimps share the SAME transposable elements? Question b is really the key here, one you failed to address.
Notice the ERV class 1 comparisons, notice any of the comparisons. I have been looking at these ERVs for a week and I can't find a lick of substantive reasoning going into the major assumptions.
I couldn't follow the link to the review but I have done some reading on the subject. For instance, the PtERV1 gene is present in Chimpanzees and OWM but is absent in Asian Great Apes and humans.
quote:
This is one of those psuedo genes evolutionists want to make such a big deal about. Because there was relaxed functional constraint there was no negative selection acting on the gene so the mutation didn't kill those who had it.
Relaxed functional constraint in protein coding genes or regulatory genes involved in neural functions? It does not happen, the human brian tissue has the highest physiological costs of an adaptation in the human body. Relaxed functional constraint would be deadly and what is more you are simply assuming there was a selective advantage for it.
quote:
Since you appear to read the literature, I have to wonder whether you have done this sleight of hand on purpose. The number of point mutations is not equal to the number of nucleotide differences between two species. There are two classes of point mutation: substitution and indel (the latter is an abbreviation of insertion/deletion). A substitution involves one nucleotide being replaced with another, and results in exactly one nucleotide difference between an individual who has the mutation and an individual who does not have it. An indel, on the other hand, changes every nucleotide downstream of the mutation until a further indel puts an end to the frame shift.
Thanks for that, it will save me having to explain this again:
1) 35 million base pairs (Mb) due to single nucleotide substitutions.
2) 5 million indels, coming to 90 Mb in the respective genomes or 3%-4%.
3) 9 pericentric inversions from 2 Mb to 4 Mb in lenght, totally 20 Mb.
Now that we have the biology primer out of the way we can talk about the nucleotide divergance.
quote:
Phylogenetic and palaeontological studies suggest that humans and chimps share a most recent common ancestor around six million years ago. Generation time for chimpanzees is around 20 years. Assuming that that generation time is a reasonable approximation for the intervening primate species, and given your rate of 123 mutations per generation, we would have nearly 37 million mutations in each of the human and chimpanzee lineages in that time, i.e. a total of 74 million mutations (since there are two lineages, protochimp and protohuman, which both accumulate mutations).
With a population of over 6 billion the human genome diverges by 1/10 of 1%, but you know what, we can get back to that one. Let's say that these are permenantly fixed, this would account for the 35 Mb worth of single nucleotide substitutions. What about the indels?
quote:
as suggested by earlier work on portions of the chimp genome, other kinds of genomic variation turn out to be at least as important as single nucleotide base changes. Insertions and deletions have dramatically changed the landscape of the human and chimp lineages since they diverged. Duplications of sequence “contribute more genetic difference between the two species”70 megabases of material”than do single base pair substitutions,” notes Evan Eichler, also of UW, Seattle, who led a team analyzing the duplications. “It was a shocker, even to us.”
I couldn't get your link to work but yes, these are my indels. The number of them that shocked the scientists you quoted is actually 90 Mb not 70 Mb.
quote:
It would help to know where the 145 megabase number comes from, so we can examine your source more carefully. Could you give a reference? The results reported in the Science editorial were: 35 million single nucleotide substitions, and 5 million indels. We know that the indels gave rise to 70 megabases of divergent positions, so the authors appear to be reporting a total of 105 megabases, rather than 145, of divergent nucleotide positions caused by point mutation.
More importantly, the total number of point mutations reported is 40 million, well within the bounds of the number of possible mutations according to your own figures.
I thought I linked to the Chimpanzee Consortiums paper earlier but maybe not. At any rate, here is the paper and the link:
Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, 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. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.
Initial sequence of the chimpanzee genome and comparison with the human genome - PubMed
The full article is available online at Nature but for some strange reason I can't get it to load. BTW, the Table above is from the same paper. Why don't you take a look and I'll check back to see what you came up with.
Edited by eggasai, : No reason given.

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anglagard
Member (Idle past 836 days)
Posts: 2339
From: Socorro, New Mexico USA
Joined: 03-18-2006


Message 13 of 83 (358183)
10-22-2006 7:22 PM
Reply to: Message 12 by eggasai
10-22-2006 7:05 PM


Re: number of point mutations is not equal to number of nucleotide differences
The full article is available online at Nature but for some strange reason I can't get it to load. BTW, the Table above is from the same paper. Why don't you take a look and I'll check back to see what you came up with.
Try this link instead: Initial sequence of the chimpanzee genome and comparison with the human genome | Nature

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eggasai
Inactive Member


Message 14 of 83 (358184)
10-22-2006 7:23 PM
Reply to: Message 9 by Dr Adequate
10-21-2006 10:24 AM


Re: Pause for effect
I'm not taling about the word, I am talking about Biology as a specialized discipline. In Darwin's day they simply refered to it as naturalists. What is more I was talking about the Darwinian tree of life diagram, the only diagram in his book On the Origin of Species. Don't you people read the posts you respond to?

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Dr Adequate
Member (Idle past 284 days)
Posts: 16113
Joined: 07-20-2006


Message 15 of 83 (358187)
10-22-2006 7:59 PM
Reply to: Message 14 by eggasai
10-22-2006 7:23 PM


Re: Pause for effect
I'm not taling about the word, I am talking about Biology as a specialized discipline.
So you claim that the word existed but the discipline did not ... ?
In Darwin's day they simply refered to it as naturalists.
... or you're claiming that the discipline existed but people called its practitioners "naturalists"?
What is more I was talking about the Darwinian tree of life diagram, the only diagram in his book On the Origin of Species. Don't you people read the posts you respond to?
Not only did I read it, I quoted it. You wrote: "the problem is that it was concluded we descended from apes before biology was even a seperate discipline in science."
Don't you read your own posts?

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 Message 14 by eggasai, posted 10-22-2006 7:23 PM eggasai has not replied

  
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