Does gene reuse and genome plasticity have to indicate common descent?

We have been discussing this issue in an inapprorpiate threadhttp://EvC Forum: What I have noticed about these debates... -->EvC Forum: What I have noticed about these debates...so we'll continue here: Well in your abstract it is assumed that simply because there is sequence similarity there were dupliction events. In our scenario it may be duplication events or multiple paralogs at creation. In our model both occur as I mentioned above. God created multiple paralogs that are specialized for specific purposes (eg the multiple hemoglobins). Does that mean that duplication can't occur naturally? Of course not. Duplicaiton can easily occur natrually as you of course know. Does duplication generate genes that go to contruct completely novel pathways? No, you have not shown that at all. You have assumed that. God could have created most of the paralogs for specific purposes. Well, we both agree on this. The non-homologous replacement of the gene by the viral gene did not generate a novel subsystem. It used an existing gene which already performed the required existing biochemical function. I do consider this a radical differnce. I find it fascinating just as you do. We can agree on it. However, it does not represent the origin of a new biochemical funciton, gene or system. Genomes are littered with novel functions, genes and systems as one looks across taxa. It's there that you have no evidence. Not really Mamuthus. Much of the gene families have arisen since abiogeneisis in your scenario as you well know. Creation occurred arond 6000 years ago. Evidence? Helium retention in biotites suggests the geo-col is only 4000 to 14,000 years old. Only the flood could do this of course. Genomes could be only this old too if God created them as kinds that have since diversified.[This message has been edited by Tranquility Base, 12-16-2002]

Mammuthus These are very logical quesitons Mamuthus but I do have very good reasons for making these assertions.Firstly, I do not have a problem with there being many duplications becasue, as you know, I understand that that is a process that occurs as a part of genomic plasticity and perhaps occasionally benefits oranisms even in the YEC time span but for rather more simple reasons. For example duplication undoubtedly introduces redundancy.Secondly, as you are probably aware, especially in smaller families, each paralog has a specific function in a specific tissue or at a specific stagfe of the cell cycle or development. In addition to being expressed in particualr tissues paralogs, although usually doing the same basic biochemical function, do have specialised secondary binding modes etc. So we would obviously believe that God created these important specializations: eg adult vs. fetal hemoglobin. Of course the seqeunces could have drifted to their current settings but when they perform important functions we would tend to believe they were separately created. We can't prove it and I wont be dogmatic on that in every case. This is very different to seeing near identical cpoies and pseudo-genes that are obviously duplication events.So although one doesnt' need God to get a near duplicate copy why should be need your hopeful random processes to generate highly specialized paralogs, with quite distinct seqeunces, when we already believe God created the genomes? See I can ask you the same question.Are you aware that paraloggs within human are more differnt to each other than homologs of genes between species? In other words, many paralogs of kinases in yeast are matchable to significantly differnt sequences in human, on a 1-1 basis, wihtout ambuiguity. For you the paralog variation that supposedly occurred in many duplication events in considerably greater tha nthe variaiton that occurs in these sequences between yeast and man. My point is that these are highly refined specializations that have been maintained since yeast for dozens of kinases and it is the same in any protein family. So for us these paralogs, although clearly realted to each other by basic biochemical function wer specifically created. Near-identical copies and pseudo-genes? Sure that is duplication and drift. I think you can see from the above that I agree with you about the reality of duplication and horizontal transfer. Haven't you read that God cursed the serpent with 'and forever shall you crawl on your belly'. All you have shown is reuse of genes in differnt pathways. Such evidence simply does not distinguish evolution from creation. I just don't have a problem with horizontal transfer via viruses occurring. This is evidence of genomic plasticity, not that that is how the immune system originated. This is where you jump the gun and keep insisting this is complelling evidence of evulution between kinds. It is simply not qualitatively relevant to what we know distinguishes genomes. I'd like to hear more on this. Is the celluar funciton or the biochemical funtion altered? Keep proiviind evidence. As you can see from the above I may be willing to concede that in some cases you may something interesting. Most examples are allelic or gene-loss or horizontal gain. Obviously I am basing my viewpoint on the genomes we have. There are huge differnces, involving entirely new gene families, systems and organs that distinguish yeast from flies from fish from man as you well know. Of course our conversations will becoem more precise as the genomes continue to roll out. Where do I state that I think you think all the genes arose at once? Doesn't my excerpt up above show that I'm saying that in yuor scenario new gene familis arose throughout evolution? Very puzzled TB. I'm saying that a lot has occurred since abiogenesis (in your scenario) and that is why our discussion is evolutionary, not just abiogenesis. Given that we don't have many genomes yet as you have pointed out I think what you have said is very premature. We can't hoipe to identiy the kinds yet so how can we work out how much mutaitons we have to explain? Of course we can look at the data we have but we need more, as you do.[This message has been edited by Tranquility Base, 12-17-2002]

QuetzalExon hypothesis. The papers I have read testing the exon hypothesis (recent stuff in the last 4 years) comes out against it. Somewhere down the track I may post you some refs. The early proposals were extrememly speculative. The analysis by structural biologists (ie people like me who understand protein folds) has shown that exons do not systematically correspond to sub-domians or anything like that. But I can't say I've read Blake who obviously comes to the opposite conclusion. The last paper I read on it was very negative and I wasn't looking for a negative one! At the least it is a controversial area.Helium retenion It's amazing how you guys always think you have 'trounced' me in my threads. Wmscott thinks I got trounced in my '3 catch cries of uniformitarinism' thread. I read it again carefully. I did not get trounced! The issue was hardly addressed by the evolutionary posters! My points that gully size, layering and sedimentary envonments are equally-well explained by the flood came thorugh unscathed! All that happened is that the evos bring up the half-dozen problematic issues for us. I can mention a half-dozen issues that are problematic for them! The total data, the bread and butter of the ge0o-col, is explainable by the flood.There will always be enough problematic beds to go around for all of us!The same goes for the helium retenion thread. Wehappy has, to his credit, done a lot of work to try and anticipate what RATE has done. Good for him, truly (and over X-mas I really do intend havign a look at that Wehappy). But that does not mean he has discredited RATE! RATE is presenting this work in its entirety soon and then we will see.If you expect my threads to prove creation or the flood then, yes, I fail everytime. If instead I am simply attempting to show that creation and the flood can naturally and parsimoniously explain genetic and geological data then I consider my threads to be, on the large, successful.[This message has been edited by Tranquility Base, 12-17-2002]

QuetzalExons. I'm actaully referring to the idea that exons correspond to 3D protein structural units becasue that is what is relevant if we are talking evolution between protein familes. Every study I've ever seen done of that has come out pretty negative. Precisely where was Humphreys shown to be in error?! By Joe or Wehappy? Joe was clearly completely mistaken and if you prefer to trust Wehappys calcs in a discussion group than a paper being submitted to a conference then I'll let that speak for itself. I respect what Wehappy has done but he has no major accountability for it except as part of a discussion group. RATE is staking their reputation on it and it is part of a funded 5 year plan that is getting published and presented at conferences.

Mammuthus I don't think I stated that all paralogs perform different functions. Without being an expert, from the seminars I attend, paralogs generally have specialized funcitons. And as I said paralog X in human can usually be matched with paralog X in eg yeast without confusion over whether it should be matched with paralog Y. When you have hundreds of duplicaitons I agree this may not be true and the genes may not have genuine specilized functions. If you want to keep using hat arguement feel free but I has no impact on me whatsoever! Of course we have a common anscestor. For us it is Noah not an non-human animal. Procreation is not evidence for evolution. It is required for it but it is not evidence for it! Like I said I distinguish between the paralogs that have significantly different sequnces and have got niche activities vs the near identical copies. I used 'drift' in a very sloppy manner. I meant 'mutate'. Of course selection is important. Having said that if somehting has to find a completely new funciton it may have to drift for a while before selction comes into play. I completely understand how evolution works (and I believe in it!), I just don't think that means it is necessarily responsible for the distinct gene families or the specialized paralogs. Where did I say that? We can certainly check for the effects of creation. Cosmologists can't rerun the Big Bang either. I'll pay that, but by the very nature of our claim it involves God so if you want to eliminate on that basis feel free, but it wasn't eliminated becasue it didn't explain the facts. We're claiming that random processes after creation generates the current genomes from created genome kinds. So we use the random processes just like you, our starting point is different however. You accept abiogenesis by faith too as a starting point. And your random processes haven't shown where the gene families and systems came from since abiogenesis anyway. What are you getting at? There's no 100% identity. The point is that even though yeast genes are, let's say 40% differnt on average from human, it is still possible to identify which human paralog goes with which yeast paralog (unless it is not there). My main point is that the paralogs are typically specialized and those specilizations have been geernally maintained aross species. I can agree with you that it doesn't particularly differntiate E vs C except to point out that paralogs generally are fine-tuned for a specific cellular function rather than just being 'copies'. They are not just copies. I nowhere deny this. I just don't think that specialized paralogs arrived the way you think they did. Yes, genomic plasticity does not explain the origin of gene families. OK let's carefully go over this. What does it do in the placenta? From your paper titles it seems to be a ligand (??) of an amino acid transport receptor? Our evidence will continue to be the novel gene families and the systems they construct. Your demonstrating non-homologous replacement is interesting but I have no problem with it.Let's keep working your envelope example. How? Even if the idea of kinds comes out? Genomes categorizable into kinds, distinguished by non-allelic gains and distinguished within by allelic and differential losses. You're confusing what I believe with what I am saying about your scenario. I believe the data is consistent with God creating the genomes about 6Kya. But when you try to tell me that we are only arguing abiogenesis then I simply point out that you still have to explain the thousands of novel gene families and thousands of novel systems since abiogeneis. This doesn't mean I suddenly believe your scenario! I'm telling you that your scenario has a lot of non-allelic explaining to do post-abiogenesis. There is no contradiction here. God reused genes as an engineer would. You know that is what we believe. There are a lot of conserved processes between bacteria and multicellular organisms. You interperet it as common descent. We point out that many of the biochemical processes required to do the jobs are the same. If you think every organism needs a different paradigm for data storage you argue that with your creator. I have no problem with DNA, RNA and ribosomal translation being universally used by God. That's a very good point. What is the role of the Hox gene in E. coli? Keep remembering that we don't need to explain your hundreds of milions of years differneces between taxa for homologous proteins. We just have to explain it within kinds. So if we end up defining kinds and find that the diversifcation requires 100,000 years does that rule out our model? On the surace, yes. But (i) that work has not been done and (ii) I'm sure your aware that we explain radiodecay data via acclerated decay during the flood amd possibly shortly afterwards. This undoubtedly increased mutation rates and may have been responsible for the drop in longevity reported in Scripture. That was me. I used the submit button as a 'save' function while I had to attend to something.[This message has been edited by Tranquility Base, 12-17-2002]