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Author Topic:   Genetic evidence of primate evolution
lbhandli
Inactive Member


Message 1 of 29 (3224)
01-31-2002 4:27 PM


Since genetic evidence is JP's standard, I thought I'd add an abstract to another article in the Aug 31, 1999 Proceedings of the National Academy of Science. Perhaps JP would like to get the article and discuss it in detail?

Constructing primate phylogenies from ancient retrovirus sequences
Welkin E. Johnson and John M. Coffin
The genomes of modern humans are riddled with thousands of endogenous retroviruses (HERVs), the proviral remnants of ancient viral infections of the primate lineage. Most HERVs are nonfunctional, selectively neutral loci. This fact, coupled with their sheer abundance in primate genomes, makes HERVs ideal for exploitation as phylogenetic markers. Endogenous retroviruses (ERVs) provide phylogenetic information in two ways: (i) by comparison of integration site polymorphism and (ii) by orthologous comparison of evolving, proviral, nucleotide sequence. In this study, trees are constructed with the noncoding long terminal repeats (LTRs) of several ERV loci. Because the two LTRs of an ERV are identical at the time of integration but evolve independently, each ERV locus can provide two estimates of species phylogeny based on molecular evolution of the same ancestral sequence. Moreover, tree topology is highly sensitive to conversion events, allowing for easy detection of sequences involved in recombination as well as correction for such events. Although other animal species are rich in ERV sequences, the specific use of HERVs in this study allows comparison of trees to a well established phylogenetic standard, that of the Old World primates. HERVs, and by extension the ERVs of other species, constitute a unique and plentiful resource for studying the evolutionary history of the Retroviridae and their animal hosts.

Since I have university access I've already downloaded the paper. When do you think you can get a copy and comment JP?

Cheers,
Larry


Replies to this message:
 Message 2 by mark24, posted 01-31-2002 7:34 PM lbhandli has not yet responded
 Message 3 by John Paul, posted 02-01-2002 2:51 PM lbhandli has responded

  
mark24
Member (Idle past 3056 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 2 of 29 (3228)
01-31-2002 7:34 PM
Reply to: Message 1 by lbhandli
01-31-2002 4:27 PM


Larry,

I'd be very interested in the paper,

On a similar note, I've posted this question before, & not got an answer, but it is relevant.

Creationists tell me that humans & chimps are unrelated. But that the genetic sequence similarity is explained away by similar phenotypes needing similar genotypes. At least, this is what they think is required. So, if similar phenotypes are requiring similar genotypes, why do non-phenotypic genes, such as that that makes cytocrome c, itself a molecule used in Krebs cycle, so match the morphological phylogenies?

Mark

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

[This message has been edited by mark24, 01-31-2002]


This message is a reply to:
 Message 1 by lbhandli, posted 01-31-2002 4:27 PM lbhandli has not yet responded

    
John Paul
Inactive Member


Message 3 of 29 (3264)
02-01-2002 2:51 PM
Reply to: Message 1 by lbhandli
01-31-2002 4:27 PM


quote:
Originally posted by lbhandli:
Since genetic evidence is JP's standard, I thought I'd add an abstract to another article in the Aug 31, 1999 Proceedings of the National Academy of Science. Perhaps JP would like to get the article and discuss it in detail?

The genomes of modern humans are riddled with thousands of endogenous retroviruses (HERVs), the proviral remnants of ancient viral infections of the primate lineage. Most HERVs are nonfunctional, selectively neutral loci. This fact, coupled with their sheer abundance in primate genomes, makes HERVs ideal for exploitation as Constructing primate phylogenies from ancient retrovirus sequences
Welkin E. Johnson and John M. Coffin
phylogenetic markers. Endogenous retroviruses (ERVs) provide phylogenetic information in two ways: (i) by comparison of integration site polymorphism and (ii) by orthologous comparison of evolving, proviral, nucleotide sequence. In this study, trees are constructed with the noncoding long terminal repeats (LTRs) of several ERV loci. Because the two LTRs of an ERV are identical at the time of integration but evolve independently, each ERV locus can provide two estimates of species phylogeny based on molecular evolution of the same ancestral sequence. Moreover, tree topology is highly sensitive to conversion events, allowing for easy detection of sequences involved in recombination as well as correction for such events. Although other animal species are rich in ERV sequences, the specific use of HERVs in this study allows comparison of trees to a well established phylogenetic standard, that of the Old World primates. HERVs, and by extension the ERVs of other species, constitute a unique and plentiful resource for studying the evolutionary history of the Retroviridae and their animal hosts.

Since I have university access I've already downloaded the paper. When do you think you can get a copy and comment JP?

Cheers,
Larry


John Paul:
I would like to know why this can't be used as evidence for a Common Creator with the Common Mechanism Brown talks about here:

Pseudogenes

Of course the difference being that Brown can test his hypothesis in a lab whereas Father Time and someunknown natural process prevent that with the alleged evolutionary scenario.

So I take it I should look for this paper- Constructing primate phylogenies from ancient retrovirus sequences
Welkin E. Johnson and John M. Coffin NAS 8-31-99.

Just so we understand each other- phylogeny, as conducted by the so called 'mainstream', assumes the ToE is indicative of reality and its conclusions are biased accordingly.

Do we even know what was the common ancestor of primates?

------------------
John Paul


This message is a reply to:
 Message 1 by lbhandli, posted 01-31-2002 4:27 PM lbhandli has responded

Replies to this message:
 Message 4 by Quetzal, posted 02-01-2002 3:18 PM John Paul has responded
 Message 5 by mark24, posted 02-01-2002 3:40 PM John Paul has responded
 Message 6 by lbhandli, posted 02-01-2002 9:23 PM John Paul has not yet responded
 Message 15 by derwood, posted 02-19-2002 11:51 AM John Paul has responded

  
Quetzal
Member (Idle past 3733 days)
Posts: 3228
Joined: 01-09-2002


Message 4 of 29 (3265)
02-01-2002 3:18 PM
Reply to: Message 3 by John Paul
02-01-2002 2:51 PM


JP: A point of correction, the article discusses retroviral insertions, not pseudogenes. You really should take a peek inside a biology textbook at some point in your refutations of biology. Just a suggestion.

Ilbhandi: Interesting reference. It goes nicely with my last post (message 221) on the "Why creation "science" isn't science" thread. Thanks.


This message is a reply to:
 Message 3 by John Paul, posted 02-01-2002 2:51 PM John Paul has responded

Replies to this message:
 Message 7 by John Paul, posted 02-04-2002 3:40 PM Quetzal has not yet responded

  
mark24
Member (Idle past 3056 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 5 of 29 (3266)
02-01-2002 3:40 PM
Reply to: Message 3 by John Paul
02-01-2002 2:51 PM


quote:
Originally posted by John Paul:

Just so we understand each other- phylogeny, as conducted by the so called 'mainstream', assumes the ToE is indicative of reality and its conclusions are biased accordingly.


The old complaint that ToE is assumed & everything is bent to fit. Did it occur to you that it actually provides evidence of the ToE without assuming it. If not, explain what retroviral gene insertion hereditability does provide evidence for........

Mark

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

[This message has been edited by mark24, 02-01-2002]


This message is a reply to:
 Message 3 by John Paul, posted 02-01-2002 2:51 PM John Paul has responded

Replies to this message:
 Message 8 by John Paul, posted 02-04-2002 3:51 PM mark24 has responded

    
lbhandli
Inactive Member


Message 6 of 29 (3283)
02-01-2002 9:23 PM
Reply to: Message 3 by John Paul
02-01-2002 2:51 PM


Just so you know, science is designed to test hypotheses and thus provide an answer to questions. It isn't a post modern exercise in whining as you have attempted to portray it. Now, either you address the specific evidence or stop your whining about bias. A hypothesis is a test and it is dependent on objective evidence. Whining that such a test produces a bias is one of the most inane arguments available given a test should result in a bias towards the correct answer.

Cheers,
Larry


This message is a reply to:
 Message 3 by John Paul, posted 02-01-2002 2:51 PM John Paul has not yet responded

  
John Paul
Inactive Member


Message 7 of 29 (3388)
02-04-2002 3:40 PM
Reply to: Message 4 by Quetzal
02-01-2002 3:18 PM


quote:
Originally posted by Quetzal:
JP: A point of correction, the article discusses retroviral insertions, not pseudogenes. You really should take a peek inside a biology textbook at some point in your refutations of biology. Just a suggestion.

Ilbhandi: Interesting reference. It goes nicely with my last post (message 221) on the "Why creation "science" isn't science" thread. Thanks.


John Paul:
I know what the article discusses, thank you. The link I posted also discusses retroviral insertions. If you would have read the link you would have known that. You should really read the links if you are going to comment on them. Just a suggestion.

------------------
John Paul


This message is a reply to:
 Message 4 by Quetzal, posted 02-01-2002 3:18 PM Quetzal has not yet responded

Replies to this message:
 Message 9 by lbhandli, posted 02-04-2002 5:49 PM John Paul has responded

  
John Paul
Inactive Member


Message 8 of 29 (3389)
02-04-2002 3:51 PM
Reply to: Message 5 by mark24
02-01-2002 3:40 PM


quote:
Originally posted by mark24:
The old complaint that ToE is assumed & everything is bent to fit. Did it occur to you that it actually provides evidence of the ToE without assuming it. If not, explain what retroviral gene insertion hereditability does provide evidence for........

Mark


John Paul:
It's not a complaint, just an observation. Materialistic naturalism is the prevailing bias. That is just the way it is.

Science, fundamentally, is a game. It is a game with one overriding and defining rule:

Rule No. 1: Let us see how far and to what extent we can explain the behavior of the physical and material world in terms of purely physical and material causes, without invoking the supernatural.

So according to Richard Dickerson, it doesn't matter if what we call the supernatural is responsible for reality, it ain't science. However, I could not find any supporting literature for his rule. I am surely glad that Newton, Kepler, Mendell, Pasteur et al. didn't have to listen to that silliness. They might have pursued different venues of study.
The point is you can't take this stuff into a lab and verify it.

And as my link states- This evidence can be viewed as Common Creator with Common Mechanism.

------------------
John Paul


This message is a reply to:
 Message 5 by mark24, posted 02-01-2002 3:40 PM mark24 has responded

Replies to this message:
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lbhandli
Inactive Member


Message 9 of 29 (3398)
02-04-2002 5:49 PM
Reply to: Message 7 by John Paul
02-04-2002 3:40 PM


I have a suggestion. Why don't you read the articles cited to you? You have not bothered to read either the whale article or this one. How do you make assertions about them if you don't read?

I expect you to either respond in detail to the articles, or admit you have no response. You "article" simply asserts that such things are consistent with creationism without ever explaining how such non-functional evidence would occur in identical locations in the genome in different populations over a 6000 year history which is necessary given they are caused by retroviruses. Provide how creationism accounts for this.

A retrovirus wouldn't be placed in the same portion for any rational reason. The assertion is ludicrous and baseless.. Or can you provide a specific example of how this would happen--not a similar mechanism as is so often cited, but NEVER identified.

Just curious,
Larry

[This message has been edited by lbhandli, 02-04-2002]


This message is a reply to:
 Message 7 by John Paul, posted 02-04-2002 3:40 PM John Paul has responded

Replies to this message:
 Message 10 by John Paul, posted 02-04-2002 6:47 PM lbhandli has responded

  
John Paul
Inactive Member


Message 10 of 29 (3401)
02-04-2002 6:47 PM
Reply to: Message 9 by lbhandli
02-04-2002 5:49 PM


quote:
Originally posted by lbhandli:
I have a suggestion. Why don't you read the articles cited to you? You have not bothered to read either the whale article or this one. How do you make assertions about them if you don't read?

I expect you to either respond in detail to the articles, or admit you have no response. You "article" simply asserts that such things are consistent with creationism without ever explaining how such non-functional evidence would occur in identical locations in the genome in different populations over a 6000 year history which is necessary given they are caused by retroviruses. Provide how creationism accounts for this.

A retrovirus wouldn't be placed in the same portion for any rational reason. The assertion is ludicrous and baseless.. Or can you provide a specific example of how this would happen--not a similar mechanism as is so often cited, but NEVER identified.

Just curious,
Larry

[This message has been edited by lbhandli, 02-04-2002]


John Paul:
Um, I read the article you cited- I found it here:

Constructing primate phylogenies from ancient retrovirus sequences

That should take care of that silly accusation.

As for the article I linked to, this snippet is relevant:

"So I think there is a mechanistic process that has produced many of the Pseudogenes that we have, rather than a random process. If the Pseudogene is truly defective and if the mutations are truly found in patterns (not random), then the idea that it's a common mechanism is possible. Viruses have enzymes that, under the same conditions, do repeatable reactions.

If the DNA in Humans, Chimps, Monkeys, etc., are very similar, then if they are all infected by the same virus, would we expect the virus to do the same thing in the different species? I think so.

The "dreaded endogenous retroviral sequence common to both chimp and human DNA" is probably the major example of Common Mechanism. Viral enzymes (proteins) react with specific DNA sequences. If both chimp and human DNA have the same active sites, I would expect the viral proteins to react in the same exact way to both human and chimp.

Common descent or common Ancestor is not the only answer."

That should take care of silly accusation 2.

Like I said before- this hypothesis can be tested in a lab by taking 2 different (but similar) species and infecting them with the same virus. The evolutionary hypothesis has no such test.

------------------
John Paul


This message is a reply to:
 Message 9 by lbhandli, posted 02-04-2002 5:49 PM lbhandli has responded

Replies to this message:
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mark24
Member (Idle past 3056 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 11 of 29 (3402)
02-04-2002 6:51 PM
Reply to: Message 8 by John Paul
02-04-2002 3:51 PM


quote:
Originally posted by John Paul:
John Paul:
It's not a complaint, just an observation. Materialistic naturalism is the prevailing bias. That is just the way it is.

Science, fundamentally, is a game. It is a game with one overriding and defining rule:

Rule No. 1: Let us see how far and to what extent we can explain the behavior of the physical and material world in terms of purely physical and material causes, without invoking the supernatural.


Rule no.1 is spot on & with good reason. The supernatural has never been observed. Natural mechanisms have. What would you go with?

Unless you can give good reason to the question :

"Why is it reasonable to infer the supernatural mechanisms above natural mechanisms, when:

1/ Every known process is a natural mechanistic one, bar none. DNA replication, radioactive decay, nuclear fission, nuclear fusion, etc. ad infinitum.

2/ Supernatural mechanisms are entirely unobserved.

Obviously your answer is one of inferrence. But why chuck what is POSSIBLE for an entire frame of reference that has never been observed? There are natural phenomena that make the likes of abiogenesis possible, & give evidence of the big bang, so why go elsewhere? Not just elsewhere, but to somewhere that has NEVER been, or has any reason, for being inferred over a natural mechanism.

Mark

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


This message is a reply to:
 Message 8 by John Paul, posted 02-04-2002 3:51 PM John Paul has not yet responded

Replies to this message:
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lbhandli
Inactive Member


Message 12 of 29 (3414)
02-04-2002 8:57 PM
Reply to: Message 10 by John Paul
02-04-2002 6:47 PM


quote:
Originally posted by John Paul:
John Paul:
Um, I read the article you cited- I found it here:

That should take care of that silly accusation.


Given that you can't respond substantively I'm not sure what linking to it proves. However, from you later comments it is clear you didn't read it.

[QUOTE]
As for the article I linked to, this snippet is relevant:

"So I think there is a mechanistic process that has produced many of the Pseudogenes that we have, rather than a random process. If the Pseudogene is truly defective and if the mutations are truly found in patterns (not random), then the idea that it's a common mechanism is possible. Viruses have enzymes that, under the same conditions, do repeatable reactions.

If the DNA in Humans, Chimps, Monkeys, etc., are very similar, then if they are all infected by the same virus, would we expect the virus to do the same thing in the different species? I think so.

The "dreaded endogenous retroviral sequence common to both chimp and human DNA" is probably the major example of Common Mechanism. Viral enzymes (proteins) react with specific DNA sequences. If both chimp and human DNA have the same active sites, I would expect the viral proteins to react in the same exact way to both human and chimp.

Common descent or common Ancestor is not the only answer."

That should take care of silly accusation 2.

Like I said before- this hypothesis can be tested in a lab by taking 2 different (but similar) species and infecting them with the same virus. The evolutionary hypothesis has no such test.

[/B][/QUOTE]

But your test has been disproven and the evidence of this is cited in the article you supposedly read:

22. Varmus, H. E. & Swanstrom, R. (1984) in RNA Tumor Viruses, eds. Weiss, R., Teich, N. M., Varmus, H. E. & Coffin, J. M. (Cold Spring Harbor Lab. Press, Plainview, NY), pp. 369-512.
23. Brown, P. O. (1997) in Retroviruses, eds. Coffin, J. M., Hughes, S. H. & Varmus, H. E. (Cold Spring Harbor Laboratory Press, Plainview, NY).
24. Withers-Ward, E. S., Kitamura, Y., Barnes, J. P. & Coffin, J. M. (1994) Genes Dev. 8, 1473-1487 [Abstract].

quote:

Endogenous retrovirus loci provide no less than three sources of phylogenetic signal, which can be used in complementary fashion to obtain much more information than simple distance estimates of homologous sequences. First, the distribution of provirus-containing loci among taxa dates the insertion. Given the size of vertebrate genomes (>1 109 bp) and the random nature of retroviral integration (22, 23), multiple integrations (and subsequent fixation) of ERV loci at precisely the same location are highly unlikely (24). Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place (14). Furthermore, integrated proviruses are extremely stable: there is no mechanism for removing proviruses precisely from the genome, without leaving behind a solo LTR or deleting chromosomal DNA. The distribution of an ERV among related species also reflects the age of the provirus: older loci are found among widely divergent species, whereas younger proviruses are limited to more closely related species. In theory, the species distribution of a set of known integration sites can be used to construct phylogenetic trees in a manner similar to restriction fragment length polymorphism (RFLP) analysis.

So you read it, huh? Not very well apparently. Retroviral insertions do occur within the genome randomly. Thus, the argument you makes fail. Additionally, retroviral insertions occur in a pattern that is nested hierarchy that fits evolutionary predictions.

Would you care to explain that too?

Of course, to add problems to your claim, the different lineages match based upon their expected rates of insertions with the expected timeline of evolution. All just coincidence?

http://www3.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=94285820&form=6&db=m&Dopt=r

It is bad enough to not to read, but lying about reading is just bad form.

Cheers,
Larry


This message is a reply to:
 Message 10 by John Paul, posted 02-04-2002 6:47 PM John Paul has not yet responded

Replies to this message:
 Message 13 by lbhandli, posted 02-18-2002 5:04 PM lbhandli has not yet responded

  
lbhandli
Inactive Member


Message 13 of 29 (4965)
02-18-2002 5:04 PM
Reply to: Message 12 by lbhandli
02-04-2002 8:57 PM


I'd like for some creationists to respond to where this thread stopped since John Paul has left us.
This message is a reply to:
 Message 12 by lbhandli, posted 02-04-2002 8:57 PM lbhandli has not yet responded

Replies to this message:
 Message 14 by mark24, posted 02-19-2002 9:37 AM lbhandli has not yet responded

  
mark24
Member (Idle past 3056 days)
Posts: 3857
From: UK
Joined: 12-01-2001


Message 14 of 29 (5069)
02-19-2002 9:37 AM
Reply to: Message 13 by lbhandli
02-18-2002 5:04 PM


I want to bump this back to the top again.

I have heard a lot of creationists tell me that the evidence of evolution is guesswork, or "it's how you interpret the evidence". So, by all means, interpret away.

Mark

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

[This message has been edited by mark24, 02-19-2002]


This message is a reply to:
 Message 13 by lbhandli, posted 02-18-2002 5:04 PM lbhandli has not yet responded

    
derwood
Member (Idle past 229 days)
Posts: 1455
Joined: 12-27-2001


Message 15 of 29 (5077)
02-19-2002 11:51 AM
Reply to: Message 3 by John Paul
02-01-2002 2:51 PM


quote:
Originally posted by John Paul:
John Paul:
I would like to know why this can't be used as evidence for a Common Creator with the Common Mechanism Brown talks about here:

Pseudogenes

Of course the difference being that Brown can test his hypothesis in a lab whereas Father Time and someunknown natural process prevent that with the alleged evolutionary scenario.


Ahh, how soon they resort to denial and selective memory....


This message is a reply to:
 Message 3 by John Paul, posted 02-01-2002 2:51 PM John Paul has responded

Replies to this message:
 Message 16 by John Paul, posted 05-24-2002 2:08 PM derwood has responded

    
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