Transposons & Shared Endogenous Retrovirus's

I thought I would get some discussion on this topic of genetic evidence for ancestry. Tranquility and Taz I believe are in this type of field, or would know alot about It I would think.Basically the claim for shared Retrovirus's is that because they are only passed on by inheritance. So if two organisms have the exact same ERV, in the exact same place, it's evidence they had a common ancestor. And chimps and people have five of them (or is it seven?).
Some material I have bookmarked on:Retrovirus's - http://www.pnas.org/cgi/content/full/96/18/10254Transposons - http://www.wits.ac.za/myco/html/tn.htm
http://www.ultranet.com/~jkimball/BiologyPages/T/Transposons.html
http://www.bact.wisc.edu/microtextbook/BactGenetics/transtakehome.html------------------

Without getting into the detail one scenario is that the retroviruses insert at specific DNA sequence motifs that are in both man and apes. I'll look into it over the next few days TC.------------------
You are go for TLI

TB: While you're looking up TC's information, you might also want to check out the pseudogenes caused by a single, identical point mutation that are also shared among selected primates but not with other animals or most monkeys. Specifically, there's a point mutation in the RT6 gene and the gene that would code for 1,3 galactosyltransferase, as well as several odorant receptor genes (which I don't remember off hand). A shared point mutation this specific would be hard to attribute to some vulnerability of a particular locus since so many OTHER non-primate mammals have fully functioning genes. TWO or even more identical point mutations between species certainly point to shared ancestry, wouldn't you say?

Camp's refuation of macroevoltuion evidences contains a rebuttal on these issues including retroviral sequences. http://www.arn.org/docs/pbsevolution/camp_all.pdfHe disucsses mainstream literatue that demonstrates that retroviruses have benevolent functions in mammals including gene regulation and also genetic diversification. Hence this opens the possibility that these are created features that have since 'gone tropo' and now mainly have deletrious effects.I do agree that the issue is good evidence for macroevolution, but at the last stand, as a professional molecular biologist, I will side with Camp's creationist angle as a possibility mainly becasue of the host of other evidences against macroevoltuion.

That's some possibility. The notion that retroviruses act like ordinary genes sound plausible. Reminds me of endosymbiosis.BTW, how do one identify ex-viruses lurking within our DNA from all those genes and introns? If we could see a difference, maybe some things would get clear...

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Originally posted by Tranquility Base:

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I do agree that the issue is good evidence for macroevolution, but at the last stand, as a professional molecular biologist, I will side with Camp's creationist angle as a possibility mainly becasue of the host of other evidences against macroevoltuion.

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What host of other evidences against macroevolution?Mark------------------
Occam's razor is not for shaving with.

^ Mark, basically the abrupt appearences of novelty in the fossil record argue against evolution. There is the very occasional example of something that could be a transitional form (eg for whales or the reptile/mammal transition) but what most people forget is that it is the gaps between almost every Linnean family that are unfilled. There are thousands of families of vertebrates. There are not even hypothetical links between pairs of these for the vast majority of family to family transitions. If you pick any two 'related' mammalian families the chances are there will be no transitional forms. It really is dotted lines. Sure, you can call on punctuated equilibrium but it is not a strong point for evolution. And from a molecular point of view I see similar 'abrupt' appearences of new protein families.

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[This message has been edited by Tranquility Base, 05-27-2002]

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Originally posted by Tranquility Base:
^ Mark, basically the abrupt appearences of novelty in the fossil record argue against evolution. There is the very occasional example of something that could be a transitional form (eg for whales or the reptile/mammal transition) but what most people forget is that it is the gaps between almost every Linnean family that are unfilled. There are thousands of families of vertebrates. There are not even hypothetical links between pairs of these for the vast majority of family to family transitions. If you pick any two 'related' mammalian families the chances are there will be no transitional forms. It really is dotted lines. Sure, you can call on punctuated equilibrium but it is not a strong point for evolution. And from a molecular point of view I see similar 'abrupt' appearences of new protein families.

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[This message has been edited by Tranquility Base, 05-27-2002]

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Camp is the creationist lawyer turned minister, right?From a molecular perspective:Say a point mutation occurs in a gamete that leads to a defective receptor for FGF-3.A possible outcome of this is achondroplasia.'Normal' parents can thus give birth to dwarfs. Would you consider that 'abrupt'?Also, again from a molecular perspective, what happens when there is a change in the timing of development or changes in the genes or regulatory regions controlling genes that influence morphology?

SLPx, I would classify these sorts of changes as microevolutionary changes - abrupt, or not abrupt. The real question is the origin of genuine novelty. It is clearest from the genomic perspective. We know when we go from genome to genome that anatomical/cellualr novelty is not charaterised by point mutaitons or simple duplciations! We get entirely new gene families that are unalignable with existing sequences and often code for proteins of different '3D folds'.It is not as if you can look in the genome and guess where the genes in general came from! Yes, you can cluster a whole series of genes as belonging to some family but you can't guess where each of the 1000s of families came from.So I can already tell you that in going from any organism type to another the origin of novelty involves new protein families that definitley didn't arise through the mechanism you are talking about. So I don't find the sudden appearece of gross anatomical shpe to be a real example of macroevoltuion. If it was then every deformed baby would be hailed as macroevoltuion. Macroevoltuion first has to explain where all of the cellular and atomical systems first arose. Then you can polish it by using single point mutations if you wish. As creationists we have no problem with mutaitons, deletions and duplicaitons allowing for both adaptaiton and genetic decay.

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[This message has been edited by Tranquility Base, 05-27-2002]

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Originally posted by Tranquility Base:
^ Mark, basically the abrupt appearences of novelty in the fossil record argue against evolution.

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And not arguing for an incomplete fossil record?Even if you take a creationist/noachian flood view of the world, & assume the fossil record is relatively complete, there should be a lot of fossils that don’t appear to be there. If not, where are those pre-flood sediments chock full of dinosaurs, elephants, & man? Those petrified forests on the pre-flood surface (the ones that you tell me stay rooted under catastrophic conditions of rapid sedimentation, not to mention all that large stuff that should have sunk first. If you take individual sedimentary beds that you tell me was deposited in a surge, we still don't see the big stuff at the bottom, small stuff at the top.Wouldn’t you therefore agree that the fossil record is extremely incomplete? If you think the fossil record doesn't support evolution, because of a paucity of fossils, then it certainly doesn't support the flood scenario. But, if you are prepared to consider that fossilisation is rare, not to mention subsequent deposition/erosion of sedimentary rocks excising millions of years of the record, then the "abruptness" of forms can be explained.In any case, the absence of something can hardly be used as positive evidence of anything, since I could just as easily argue against the flood scenario with exactly the same negative evidential basis.Furthermore, assuming all baramins & "novelties" were created pre-flood, why does the gc show appearances of these "novelties" at all, abrupt or not, rather than them all being fossilised in pre-flood deposits? My point being, there should be no "novelties" at all, everything should have a pre-flood ancestor.

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Originally posted by Tranquility Base:

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There is the very occasional example of something that could be a transitional form (eg for whales or the reptile/mammal transition) but what most people forget is that it is the gaps between almost every Linnean family that are unfilled. There are thousands of families of vertebrates. There are not even hypothetical links between pairs of these for the vast majority of family to family transitions. If you pick any two 'related' mammalian families the chances are there will be no transitional forms. It really is dotted lines. Sure, you can call on punctuated equilibrium but it is not a strong point for evolution. And from a molecular point of view I see similar 'abrupt' appearences of new protein families.

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[This message has been edited by Tranquility Base, 05-27-2002]

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As far as higher-than-family transitionals go, there are fish-amphibian, reptile-bird, reptile-mammal, etc. Although I’m sure you reject these transitions, you cannot argue that they don’t potentially exist, which you have as good as admitted, so how can you use this, along with the paucity of the fossil record, as an argument against higher than family macroevolution?Regarding abrupt appearances of protein families, how can they be abrupt, when you can only work with extant organisms?I asked for evidences against macroevolution, not God-of-the-gaps arguments. Do you have any positive evidence against macroevolution? Or, perhaps, positive evidence that falsifies macroevolution, would be a better way of phrasing the question.Mark------------------
Occam's razor is not for shaving with.

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[This message has been edited by mark24, 05-28-2002]

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[This message has been edited by mark24, 05-28-2002]

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Originally posted by Tranquility Base:
SLPx, I would classify these sorts of changes as microevolutionary changes - abrupt, or not abrupt. The real question is the origin of genuine novelty. It is clearest from the genomic perspective. We know when we go from genome to genome that anatomical/cellualr novelty is not charaterised by point mutaitons or simple duplciations! We get entirely new gene families that are unalignable with existing sequences and often code for proteins of different '3D folds'.

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We DO know this? I have been looking for some time for genes that control anatomical traits, and it seems that you know what they are, since you can say that 'novelty' is not influenced by point mutations and such. Could you tell me where I can read about them? Where do you think gene families come from?

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It is not as if you can look in the genome and guess where the genes in general came from! Yes, you can cluster a whole series of genes as belonging to some family but you can't guess where each of the 1000s of families came from.

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Why guess?

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So I can already tell you that in going from any organism type to another the origin of novelty involves new protein families that definitley didn't arise through the mechanism you are talking about.

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What did I talk about? Oh - altering morphology via minor genetic changes. Which can and does occur. What protein family arose to account for the loss of abdominal ribs? Did one need to?

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So I don't find the sudden appearece of gross anatomical shpe to be a real example of macroevoltuion. If it was then every deformed baby would be hailed as macroevoltuion.

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That, clearly, was not my point.

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Macroevoltuion first has to explain where all of the cellular and atomical systems first arose.

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It does? And what is your preferred scientific explanation?

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Then you can polish it by using single point mutations if you wish. As creationists we have no problem with mutaitons, deletions and duplicaitons allowing for both adaptaiton and genetic decay.

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[This message has been edited by Tranquility Base, 05-27-2002]

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Well, thats good to know...

What I find interesting is the reverse, can one have gene changes by behvior adpated morphology (meaning morphology changed by behavior (behavior is INside not out in this sense that goes either way)) Needs more than point for mutation to constrain the answer to this question. Difficulty I was closed out from access professionally to the same that others could out of the blue come to cricize my geneis creating in time with what I have to work with. keep talking.

Yeah, Brad, you can have morphology change through behavior - happens all the time. However, it wouldn't be inheritable - at least in the first generation, so has no effect on evolution. There's that teleology/directed evolution of yours slipping in again.OTOH, behavioral changes CAN lead to morphological changes if the behaviors are maintained over many generations (I'm thinking niche selection in Lake Victoria cichlids, f'rinstance). Also, Muller pretty conclusively showed non-random mate selection can provide impetus for morphological change over many generations. Somehow, I don't think that's what you were referring to, however.Damn, I need to check my meds. I actually understood Brad...

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Originally posted by Tranquility Base:
...but what most people forget is that it is the gaps between almost every Linnean family that are unfilled. There are thousands of families of vertebrates. There are not even hypothetical links between pairs of these for the vast majority of family to family transitions. If you pick any two 'related' mammalian families the chances are there will be no transitional forms.

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After re-reading this, I almost chuckled out loud.I am alive. I have a cousin that is also alive. Yet there are no intermediates between us. If I were to draw a geneaology chart, there would be a huge gap between us. Clearly, therefore, we cannot be related via shared (recent) ancestry; there are no transitional forms!Say I have two baseballs. One I throw to the north-east. The other I throw to the north-west. They both travel about 100 yards away from me, and end up about 150 yards apart. It should be obvious that I could not have thrown both balls,as they are so far apart with nothing between them...Well, you get the picture. I hope...

^Thanks for those simple analogies . If you want to believe that all of these families of vertebrates evolved without leaving a trace of evidence feel free. I think our scenario is the more natual one.