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Author Topic:   Does gene reuse and genome plasticity have to indicate common descent?
Tranquility Base
Inactive Member


Message 1 of 12 (26901)
12-16-2002 8:42 PM


We have been discussing this issue in an inapprorpiate thread

www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=6&t=36&m=109#109 -->www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=6&t=36&m=109#109">http://www.evcforum.net/cgi-bin/dm.cgi?action=msg&f=6&t=36&m=109#109

so we'll continue here:

Much of this is again simply assumed.
M: For example? What is assumed?

Well in your abstract

Kruppel-related zinc finger proteins, with 564 members in the human genome, probably constitute the largest individual family of transcription factors in mammals. Approximately 30% of these proteins carry a potent repressor domain called the Kruppel associated box (KRAB). Depending on the structure of the KRAB domain, these proteins have been further divided into three subfamilies (A + B, A + b, and A only). In addition, some KRAB zinc finger proteins contain another conserved motif called SCAN. To study their molecular evolution, an extensive comparative analysis of a large panel of KRAB zinc finger genes was performed. The results show that both the KRAB A + b and the KRAB A subfamilies have their origin in a single member or a few closely related members of the KRAB A + B family. The KRAB A + B family is also the most prevalent among the KRAB zinc finger genes. Furthermore, we show that internal duplications of individual zinc finger motifs or blocks of several zinc finger motifs have occurred quite frequently within this gene family. However, zinc finger motifs are also frequently lost from the open reading frame, either by functional inactivation by point mutations or by the introduction of a stop codon. The introduction of a stop codon causes the exclusion of part of the zinc finger region from the coding region and the formation of graveyards of degenerate zinc finger motifs in the 3'-untranslated region of these genes. Earlier reports have shown that duplications of zinc finger genes commonly occur throughout evolution. We show that there is a relatively low degree of sequence conservation of the zinc finger motifs after these duplications. In many cases this may cause altered binding specificities of the transcription factors encoded by these genes. The repetitive nature of the zinc finger region and the structural flexibility within the zinc finger motif make these proteins highly adaptable. These factors may have been of major importance for their massive expansion in both number and complexity during metazoan evolution.

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.

TB:
On the other hand I agree that genes can duplicate and mutate. Some of the members of this family probably have their origin in duplicaiton. But they are all still transcription factors and the protein folds are still the same.

M: I don't get you point. And didnt you just say in the last point that this was also consistent with your god individually creating each duplicate copy and in the process being so completely incompetent that he littered the genome with pseudogenes, recessive lethal mutations, etc etc.?

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.

TB:
I am quite prepared to agree with you that this sort of 'non-homologous replacement' as it is called has occurred in nature. It's clear that this is simply an example of horizontal transfer and that it does not explain how the gene itself arose.

M: I dealt with that in the last post..HERV's are ancient proviruses..if you want to see a modern one look in the T cells of HIV infected patients and you will find modern versions of HERVs...if any of the HIV proviruses were to infect the germ line they would have a chance at becoming HERVs.

Well, we both agree on this.

TB:
Did it create a novel subsystem? No the system was working nicely.

M: What are you talking about?

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.

M: A completely unrelated gene took over a critical function in a specific group of organisms...and you don't consider this a radical difference? By the way, the envelope gene is not a similarly functioning gene...like hemoglobin in bacteria..it has drastically changed its 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.

M: I still get the impression you are looking for the first gene that ever existed i.e. abiogenesis...but in your debates you constantly shift your creation myth in time to it happened in the primate lineage..it happened after bacteria..it happened whenever it is convenient to the arguement.

Not really Mamuthus. Much of the gene families have arisen since abiogeneisis in your scenario as you well know.

When exactly do YOU think the creation event occurred and what is your evidence for it? Since you on and off accept macroevolution, in some twisted way accept a very odd version of evolution within groups, it is not clear what your position is.

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]


Replies to this message:
 Message 2 by Mammuthus, posted 12-17-2002 5:11 AM Tranquility Base has responded
 Message 3 by Quetzal, posted 12-17-2002 5:24 AM Tranquility Base has responded

  
Mammuthus
Member (Idle past 4585 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 2 of 12 (26947)
12-17-2002 5:11 AM
Reply to: Message 1 by Tranquility Base
12-16-2002 8:42 PM


Hi TB,
See also my last post on the subject in the Faith and Belief thread message 120 responding to your last post on the subject in that thread.

TB:
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.

M: Why paralogs at creation? Why did your god create so many defective copies of the KRAB genes at creation? Considering you can experimentally observe duplication events i.e. recombination, why does one need to postulate a non testable non observable god creating paralogs to explain paralogs as opposed to an actual testable and observable system?

TB:
In our model both occur as I mentioned above. God created multiple paralogs that are specialized for specific purposes (eg the multiple hemoglobins).

M: Ok, to what specific function did your god create all the psuedogenes and defective copies of the same genes which are also similar by descent to their functional counterparts? Or what exactly are the non-transcribed HERVs or solo LTRs that are in heterochromatic regions of chromosomes doing via their special creation? And why does a snake have and express a gene like Hoxd13 which is invovled in limb formation (mutations in humans and mice leads to syndactyly) yet does not produce limbs if each paralog had a god given function for the paralog. Hoxd13 in snakes is extremely similar to HOXD13 in humans.

TB:
Does that mean that duplication can't occur naturally? Of course not. Duplicaiton can easily occur natrually as you of course know.

M: How do you distinguish the duplications that your god did and those that occurred naturally?

TBoes 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.

M: As a matter of fact I have presented multiple studies entirely consistent with generation of novel genes, pathways, etc. It is you that have failed to produce a single piece of evidence for your god or his involvement in a mythical genetic creation event.

M: I dealt with that in the last post..HERV's are ancient proviruses..if you want to see a modern one look in the T cells of HIV infected patients and you will find modern versions of HERVs...if any of the HIV proviruses were to infect the germ line they would have a chance at becoming HERVs.[/qs]

TB:
Well, we both agree on this.

M: Ummm then you concede that your previous statement is wrong?

TB:
Did it create a novel subsystem? No the system was working nicely.

M: What are you talking about?

TB:
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.

M: Actually you are wrong. The properties of viral envelope genes are to be fusiogenic so that the viral genome can gain access to the cell nucleus. Fusion of the syncytiotrophoblast is an entirely different functional mechanism but has enough similar properties that the HERV-W envelope was able to replace the gene that was previously responsible. These are not the same biochemical pathways.

TB:
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.

M: You repeat this assertion over and over TB without supporting it. I point out a novel function or an explained large difference between huge taxanomic distances and you just repeat the incorrect mantra that I have no evidence. Of course you never produce evidence yourself for your god or creation but that is another matter.

Since you keep talking about all these huge differences among genomes and taxa, list them...it should be interesting considering how few genomes have been sequenced so I am assuming you have personal access to the broadly sampled genomes across the major phyla? Also funny that the tunicate genome sequence is so consistent with evolution including the generation of novel genes.

M: I still get the impression you are looking for the first gene that ever existed i.e. abiogenesis...but in your debates you constantly shift your creation myth in time to it happened in the primate lineage..it happened after bacteria..it happened whenever it is convenient to the arguement.

Not really Mamuthus. Much of the gene families have arisen since abiogeneisis in your scenario as you well know.

M: I don't understand this response. If single cell life began billions of years ago and complex multicellular life evolved from that later, then clearly all gene families did not arise immediately upon abiogenesis. In fact I know of nobody who proposes the sudden appearance of a genome as abiogenesis...that is the kind of scenario creationists use...not scientists.

TB:
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.

M: Then this is falsified as it would require a mutation rate millions of times higher than ever observed, induced, or even chemically possible, to generate the biodiversity and genetic diversity of life on earth in 6000 years...not to mention that huge numbers of organisms could not survive inundation....and there is no evidence of a genetic bottleneck for all species dating back to 6000 years ago which is an absolute requirement if the coalescence is that young. The geologic argument, I have only looked at from time to time but you already have a thread in the geology forum and I have not seen anybody particularly swayed by your arguments there.

cheers,
M


This message is a reply to:
 Message 1 by Tranquility Base, posted 12-16-2002 8:42 PM Tranquility Base has responded

Replies to this message:
 Message 4 by Tranquility Base, posted 12-17-2002 6:37 AM Mammuthus has responded

  
Quetzal
Member (Idle past 3982 days)
Posts: 3228
Joined: 01-09-2002


Message 3 of 12 (26950)
12-17-2002 5:24 AM
Reply to: Message 1 by Tranquility Base
12-16-2002 8:42 PM


Hi TB:

I'm curious - you have consistently asserted that the original genes arose ex nihilo, and that all subsequent novel genes were simply "re-use" of existing structural components. What I'd like to hear is your reason for rejecting the exon theory, for instance, or the other mainstream explanations for the origin of genes. I'd like to see your arguments against, for instance, Blake et al 1987 hypothesis contained in "Proteins, exons and molecular evolution", (Biosystems 20:181-206), or Gilbert's 1997 Origin of Genes, where he tested Blake's idea. You must be familiar with the work, since you have apparently rejected it. I'd like to see your reasoning. Thanks.

quote:
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.
I'm a tad surprised you bring this up again. The helium retention "evidence" you're banking on was quite significantly refuted in this thread. Do you have any new evidence that Humphrey's was actually accurate? Inquiring minds, and all that...
This message is a reply to:
 Message 1 by Tranquility Base, posted 12-16-2002 8:42 PM Tranquility Base has responded

Replies to this message:
 Message 6 by Tranquility Base, posted 12-17-2002 7:32 AM Quetzal has responded

  
Tranquility Base
Inactive Member


Message 4 of 12 (26952)
12-17-2002 6:37 AM
Reply to: Message 2 by Mammuthus
12-17-2002 5:11 AM


Mammuthus

M: Why paralogs at creation? Why did your god create so many defective copies of the KRAB genes at creation? Considering you can experimentally observe duplication events i.e. recombination, why does one need to postulate a non testable non observable god creating paralogs to explain paralogs as opposed to an actual testable and observable system?

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.

M: Ok, to what specific function did your god create all the psuedogenes and defective copies of the same genes which are also similar by descent to their functional counterparts? Or what exactly are the non-transcribed HERVs or solo LTRs that are in heterochromatic regions of chromosomes doing via their special creation?

I think you can see from the above that I agree with you about the reality of duplication and horizontal transfer.

And why does a snake have and express a gene like Hoxd13 which is invovled in limb formation (mutations in humans and mice leads to syndactyly) yet does not produce limbs if each paralog had a god given function for the paralog. Hoxd13 in snakes is extremely similar to HOXD13 in humans.

Haven't you read that God cursed the serpent with 'and forever shall you crawl on your belly'.

TB: 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.

M: As a matter of fact I have presented multiple studies entirely consistent with generation of novel genes, pathways, etc. It is you that have failed to produce a single piece of evidence for your god or his involvement in a mythical genetic creation event.

All you have shown is reuse of genes in differnt pathways. Such evidence simply does not distinguish evolution from creation.

M: I dealt with that in the last post..HERV's are ancient proviruses..if you want to see a modern one look in the T cells of HIV infected patients and you will find modern versions of HERVs...if any of the HIV proviruses were to infect the germ line they would have a chance at becoming HERVs.

TB:
Well, we both agree on this.

M: Ummm then you concede that your previous statement is wrong?

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.

TB:
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.

M: Actually you are wrong. The properties of viral envelope genes are to be fusiogenic so that the viral genome can gain access to the cell nucleus. Fusion of the syncytiotrophoblast is an entirely different functional mechanism but has enough similar properties that the HERV-W envelope was able to replace the gene that was previously responsible. These are not the same biochemical pathways.

I'd like to hear more on this. Is the celluar funciton or the biochemical funtion altered?

TB:
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.

M: You repeat this assertion over and over TB without supporting it. I point out a novel function or an explained large difference between huge taxanomic distances and you just repeat the incorrect mantra that I have no evidence. Of course you never produce evidence yourself for your god or creation but that is another matter.

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.

Since you keep talking about all these huge differences among genomes and taxa, list them...it should be interesting considering how few genomes have been sequenced so I am assuming you have personal access to the broadly sampled genomes across the major phyla? Also funny that the tunicate genome sequence is so consistent with evolution including the generation of novel genes.

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.

TB: Much of the gene families have arisen since abiogeneisis in your scenario as you well know.

M: I don't understand this response. If single cell life began billions of years ago and complex multicellular life evolved from that later, then clearly all gene families did not arise immediately upon abiogenesis. In fact I know of nobody who proposes the sudden appearance of a genome as abiogenesis...that is the kind of scenario creationists use...not scientists.

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.

TB: 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.

M: Then this is falsified as it would require a mutation rate millions of times higher than ever observed, induced, or even chemically possible, to generate the biodiversity and genetic diversity of life on earth in 6000 years...not to mention that huge numbers of organisms could not survive inundation....and there is no evidence of a genetic bottleneck for all species dating back to 6000 years ago which is an absolute requirement if the coalescence is that young.

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]


This message is a reply to:
 Message 2 by Mammuthus, posted 12-17-2002 5:11 AM Mammuthus has responded

Replies to this message:
 Message 5 by Mammuthus, posted 12-17-2002 7:18 AM Tranquility Base has responded

  
Mammuthus
Member (Idle past 4585 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 5 of 12 (26955)
12-17-2002 7:18 AM
Reply to: Message 4 by Tranquility Base
12-17-2002 6:37 AM


Hi TB:
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.

M: Actually, redundancy and the next paragraph you write are in conflict as you make some overly broad claims about paralogs. In any case, there is no support for the YEC timespan.

TB:
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.

M: Actually this is not entirely correct either. In many cases the paralogs perform exactly the same function and are not specialized for different functions i.e. red and green color vision genes on the X chromosome or the salivary amylase genes. However, multiple independent lines of evidence argue that we inherit our genes from our parents who inherited theirs from their parents etc etc and thus we have a common ancestor. The fact that you can trace duplicated genes to an original copy is much more supportive of identity by descent than of an unobservable god creation event unless you have evidence otherwise.

TB:
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.

M: I never suggested that they drift to new functions. Redundancy provides a substrate for generation of novel traits i.e. bacterial adaptation to new sources of energy etc. In most cases I would think it is selection that drives the development of a novel function and not drift....

Interestingly you claim you cannot test for a creation event i.e. untestable hypothesis and thus it is not science.

TB:
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.

M: Unlike you I can get experimental backup for random processes including generation of paralogs. I can also demonstrate identity by descent. This leads to the principles of phylogenetics which are far more explanatory in tracing the relatedness of duplicated genes then an untestable and unobservable poof bang goddidit scenario. Each part of what I am proposing is testable and predictions can be made that either re-enforce the theory or cause portions of it to be re-evaluated. You cannot make that claim so in principle no..you cannot ask me the same question because I can give an answer..unless you are witholding some evidence of your specific god creating anything ex nihilo?

TB:
Are you aware that paraloggs within human are more differnt to each other than homologs of genes between species?

M: And are you aware that selection varies from gene to gene?

TB:
In other words, many paralogs of kinases in yeast are matchable to significantly differnt sequences in human, on a 1-1 basis, wihtout ambuiguity.

M: I doubt there are any genes in yeast and humans that have 100 percent identity. On the other hand, since kinases are often involved in cell cycle control in humans and yeast I would not expect them to tolerate much mutation...why is this surprising?

TB:
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.

M: Your example makes very little sense and still does not provide evidence of creation. The fact that genes are transmitted from parent to offspring, means that mutations are as well, which means that duplications and paralogs are as well which means you get the genome you have from events that have transpired since your last common ancestor. I would not expect to see any of this from ex nihilo creation i.e. why should we have anything to do with yeast i.e. lots of genomic similarity if we were supposedly created in your gods image? And how can you claim the paralogs are related to each other on one hand but claim independent creation on the other?

M: Ok, to what specific function did your god create all the psuedogenes and defective copies of the same genes which are also similar by descent to their functional counterparts? Or what exactly are the non-transcribed HERVs or solo LTRs that are in heterochromatic regions of chromosomes doing via their special creation?

TB:
I think you can see from the above that I agree with you about the reality of duplication and horizontal transfer.

M: Clearly you do not agree because you have both denied the possiblity of its occurrence and accepted it both within your post.

And why does a snake have and express a gene like Hoxd13 which is invovled in limb formation (mutations in humans and mice leads to syndactyly) yet does not produce limbs if each paralog had a god given function for the paralog. Hoxd13 in snakes is extremely similar to HOXD13 in humans.

Haven't you rad that God cursed the serpent with 'and you shall

M: Your irony aside, this was just one example of many...and you did not answer the question. And actually snakes are highly variable, adaptable, and successful animals in nature regardless of the silly superstitions and "immoral" properties attributed to them.

M: Ummm then you concede that your previous statement is wrong?

TB:
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.

M: LOL! Not qualitatively relevant that Aribidopsis has 18 percent of the genome composed of cyanobacterial genes horizonatlly transferred? Or that adzuki beetles have a huge chunk of the bacterial Wollbachia genome transposed into their sex chromosomes? I am not jumping the gun when the data is consistent with evolution and there is no data for your position or any other i.e. Lamarkian mechanisms, panspermia, etc.

M: Actually you are wrong. The properties of viral envelope genes are to be fusiogenic so that the viral genome can gain access to the cell nucleus. Fusion of the syncytiotrophoblast is an entirely different functional mechanism but has enough similar properties that the HERV-W envelope was able to replace the gene that was previously responsible. These are not the same biochemical pathways.

I'd like to hear more on this. Is the celluar funciton or the biochemical funtion altered?

M: Both since the envolope protein no longer functions as an envelope and is specifically expressed in the placenta.

Yu C, Shen K, Lin M, Chen P, Lin C, Chang GD, Chen H.
GCMa Regulates the Syncytin-mediated Trophoblastic Fusion.
J Biol Chem. 2002 Dec 20;277(51):50062-50068.

Keith JC Jr, Pijnenborg R, Van Assche FA.
Placental syncytin expression in normal and preeclamptic pregnancies.
Am J Obstet Gynecol. 2002 Oct;187(4):1122-3; discussion 1123-4.

Kudo Y, Boyd CA.
Changes in expression and function of syncytin and its receptor, amino acid transport system B(0) (ASCT2), in human placental choriocarcinoma BeWo cells during syncytialization.
Placenta. 2002 Aug;23(7):536-41.

Knerr I, Beinder E, Rascher W. Related Articles, Links
Syncytin, a novel human endogenous retroviral gene in human placenta: evidence for its dysregulation in preeclampsia and HELLP syndrome.
Am J Obstet Gynecol. 2002 Feb;186(2):210-3.

Lee X, Keith JC Jr, Stumm N, Moutsatsos I, McCoy JM, Crum CP, Genest D, Chin D, Ehrenfels C, Pijnenborg R, van Assche FA, Mi S.
Downregulation of placental syncytin expression and abnormal protein localization in pre-eclampsia.
Placenta. 2001 Nov;22(10):808-12.

Mi S, Lee X, Li X, Veldman GM, Finnerty H, Racie L, LaVallie E, Tang XY, Edouard P, Howes S, Keith JC Jr, McCoy JM.
Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis.
Nature. 2000 Feb 17;403(6771):785-9.

TB:
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.

M: I will keep providing evidence. But you did not do it or did not agree to provide evidence for your assertions...can you and will you?

TB:
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.

M: However, even cursory examination of the tunicate genome (or any of the genomes) sequenced to date only re-enforce evolutionary theory and absolutely refute a 6000 year before present ex nihilo creation event. The only thing that will become more precise with the more sequenced genomes is the evolutionary mechanisms driving genomic evolution. I don't see any huge creation research projects testing...tell me again what the testable hypothesis is? I seem to have forgotten?

TB:
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.

M: Actually, you almost always claim any example I give was a sudden creation and not evolution. You also stated that your god created all genomes 6Kya. Thus, you do imply it all was created once. But given your question, why would you expect bacteria to have the same genes as a multicellular organism? What would be the selective advantege to E. coli of having a hox gene when it is never going to have a segmented morphology? You harp on the genes that are absent in bacteria versus humans rather often but there is no expectation that all organisms should have the same genes or adaptations.

M: Then this is falsified as it would require a mutation rate millions of times higher than ever observed, induced, or even chemically possible, to generate the biodiversity and genetic diversity of life on earth in 6000 years...not to mention that huge numbers of organisms could not survive inundation....and there is no evidence of a genetic bottleneck for all species dating back to 6000 years ago which is an absolute requirement if the coalescence is that young.

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.

M: This still does not help with the argument that the genetic diversity, much less morphological diversity, could not have occurred in 6K years and there is no evidence of the requisite bottleneck in any species which thus, falsifies your assertion.

(post edited by Mammuthus since half of TB's message was cut off and I thought he had not answered..sorry TB!)

[This message has been edited by Mammuthus, 12-17-2002]


This message is a reply to:
 Message 4 by Tranquility Base, posted 12-17-2002 6:37 AM Tranquility Base has responded

Replies to this message:
 Message 9 by Tranquility Base, posted 12-17-2002 7:07 PM Mammuthus has responded

  
Tranquility Base
Inactive Member


Message 6 of 12 (26957)
12-17-2002 7:32 AM
Reply to: Message 3 by Quetzal
12-17-2002 5:24 AM


Quetzal

Exon 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]


This message is a reply to:
 Message 3 by Quetzal, posted 12-17-2002 5:24 AM Quetzal has responded

Replies to this message:
 Message 7 by Quetzal, posted 12-17-2002 8:44 AM Tranquility Base has responded

  
Quetzal
Member (Idle past 3982 days)
Posts: 3228
Joined: 01-09-2002


Message 7 of 12 (26962)
12-17-2002 8:44 AM
Reply to: Message 6 by Tranquility Base
12-17-2002 7:32 AM


Hi TB:

quote:
Exon 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.
Actually the exon theory isn't all that controversial. What is controversial is the introns early/introns late question. However, it seems the dust has mostly settled. About the only person still holding to the introns late idea is Ayala's group. Here are a couple of recent papers concerning this:

Large-scale comparison of intron positions among animal, plant, and fungal genes
Toward a resolution of the introns earlyylate debate: Only phase zero introns are correlated with the structure of ancient proteins
Intron distribution difference for 276 ancient and 131 modern genes suggests the existence of ancient introns

Anyway, that's not really important to what I was asking. I was curious as to your take on the PNA exon shuffling as producer of the first proto-gene and why you consider that to be an unacceptable answer.

On the biotite - I didn't say "you" were getting trashed. I said that Humphreys was shown to be in error. Hence, you must have additional/new data available that shows he wasn't.


This message is a reply to:
 Message 6 by Tranquility Base, posted 12-17-2002 7:32 AM Tranquility Base has responded

Replies to this message:
 Message 8 by Tranquility Base, posted 12-17-2002 5:47 PM Quetzal has responded

  
Tranquility Base
Inactive Member


Message 8 of 12 (27073)
12-17-2002 5:47 PM
Reply to: Message 7 by Quetzal
12-17-2002 8:44 AM


Quetzal

Exons. 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.

On the biotite - I didn't say "you" were getting trashed. I said that Humphreys was shown to be in error. Hence, you must have additional/new data available that shows he wasn't.

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.


This message is a reply to:
 Message 7 by Quetzal, posted 12-17-2002 8:44 AM Quetzal has responded

Replies to this message:
 Message 11 by Quetzal, posted 12-18-2002 5:46 AM Tranquility Base has not yet responded

  
Tranquility Base
Inactive Member


Message 9 of 12 (27087)
12-17-2002 7:07 PM
Reply to: Message 5 by Mammuthus
12-17-2002 7:18 AM


Mammuthus

M: Actually this is not entirely correct either. In many cases the paralogs perform exactly the same function and are not specialized for different functions i.e. red and green color vision genes on the X chromosome or the salivary amylase genes.

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.

However, multiple independent lines of evidence argue that we inherit our genes from our parents who inherited theirs from their parents etc etc and thus we have a common ancestor.

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!

The fact that you can trace duplicated genes to an original copy is much more supportive of identity by descent than of an unobservable god creation event unless you have evidence otherwise.

Like I said I distinguish between the paralogs that have significantly different sequnces and have got niche activities vs the near identical copies.

M: I never suggested that they drift to new functions. Redundancy provides a substrate for generation of novel traits i.e. bacterial adaptation to new sources of energy etc. In most cases I would think it is selection that drives the development of a novel function and not drift....

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.

Interestingly you claim you cannot test for a creation event i.e. untestable hypothesis and thus it is not science.

Where did I say that? We can certainly check for the effects of creation. Cosmologists can't rerun the Big Bang either.

M: Unlike you I can get experimental backup for random processes including generation of paralogs.

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.

TB:
Are you aware that paraloggs within human are more differnt to each other than homologs of genes between species?

M: And are you aware that selection varies from gene to gene?

What are you getting at?

TB:
In other words, many paralogs of kinases in yeast are matchable to significantly differnt sequences in human, on a 1-1 basis, wihtout ambuiguity.

M: I doubt there are any genes in yeast and humans that have 100 percent identity. On the other hand, since kinases are often involved in cell cycle control in humans and yeast I would not expect them to tolerate much mutation...why is this surprising?

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).

TB:
For you the paralog variation that supposedly occurred in many duplication events is considerably greater than the 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.

M: Your example makes very little sense and still does not provide evidence of creation. The fact that genes are transmitted from parent to offspring, means that mutations are as well, which means that duplications and paralogs are as well which means you get the genome you have from events that have transpired since your last common ancestor. I would not expect to see any of this from ex nihilo creation i.e. why should we have anything to do with yeast i.e. lots of genomic similarity if we were supposedly created in your gods image? And how can you claim the paralogs are related to each other on one hand but claim independent creation on the other?

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.

TB:
I think you can see from the above that I agree with you about the reality of duplication and horizontal transfer.

M: Clearly you do not agree because you have both denied the possiblity of its occurrence and accepted it both within your post.

I nowhere deny this. I just don't think that specialized paralogs arrived the way you think they did.

TB:
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.

M: LOL! Not qualitatively relevant that Aribidopsis has 18 percent of the genome composed of cyanobacterial genes horizonatlly transferred? Or that adzuki beetles have a huge chunk of the bacterial Wollbachia genome transposed into their sex chromosomes? I am not jumping the gun when the data is consistent with evolution and there is no data for your position or any other i.e. Lamarkian mechanisms, panspermia, etc.

Yes, genomic plasticity does not explain the origin of gene families.

M: Both since the envolope protein no longer functions as an envelope and is specifically expressed in the placenta.

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?

M: I will keep providing evidence. But you did not do it or did not agree to provide evidence for your assertions...can you and will you?

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.

M: However, even cursory examination of the tunicate genome (or any of the genomes) sequenced to date only re-enforce evolutionary theory and absolutely refute a 6000 year before present ex nihilo creation event.

How?

The only thing that will become more precise with the more sequenced genomes is the evolutionary mechanisms driving genomic evolution.

Even if the idea of kinds comes out?

I don't see any huge creation research projects testing...tell me again what the testable hypothesis is? I seem to have forgotten?

Genomes categorizable into kinds, distinguished by non-allelic gains and distinguished within by allelic and differential losses.

M: Actually, you almost always claim any example I give was a sudden creation and not evolution. You also stated that your god created all genomes 6Kya.

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.

Thus, you do imply it all was created once. But given your question, why would you expect bacteria to have the same genes as a multicellular organism?

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.

What would be the selective advantege to E. coli of having a hox gene when it is never going to have a segmented morphology?

That's a very good point. What is the role of the Hox gene in E. coli?

M: This still does not help with the argument that the genetic diversity, much less morphological diversity, could not have occurred in 6K years and there is no evidence of the requisite bottleneck in any species which thus, falsifies your assertion.

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.

(post edited by Mammuthus since half of TB's message was cut off and I thought he had not answered..sorry TB!)

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]


This message is a reply to:
 Message 5 by Mammuthus, posted 12-17-2002 7:18 AM Mammuthus has responded

Replies to this message:
 Message 10 by Mammuthus, posted 12-18-2002 4:37 AM Tranquility Base has not yet responded

  
Mammuthus
Member (Idle past 4585 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 10 of 12 (27148)
12-18-2002 4:37 AM
Reply to: Message 9 by Tranquility Base
12-17-2002 7:07 PM


TB:
I don't think I stated that all paralogs perform different functions.

M: Your statement was fairly general and I was not sure if you meant all or some.

TB:
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!

M: First off, there is no evidence of a genetic bottleneck which would be required for humans to have originated 6kya from a single human couple. Second, Noah would also have a non-human animal common ancestor Procreation is evidence against poof bang creation. It is a requried mechanism for genetics and evolution but is the antithesis of creationism. There is evidence for 1) procreation (usually in the back of video stores 2) tranmission of genes from parents to offspring. Where is the evidence for creation ex nihilo?

TB:
Like I said I distinguish between the paralogs that have significantly different sequnces and have got niche activities vs the near identical copies.

M: And this is evidence for creation how?

TB:
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.

M:This is not consistent..you understand how evolutoin works and believe in it yet don't understand or believe in evolution of gene families and paralogs with divergent function?...that is like saying thank god I'm and atheist

TB:
Where did I say that? We can certainly check for the effects of creation. Cosmologists can't rerun the Big Bang either.

M: However, there are both testable hypothesis and predictions that can be tested for both evolution and the Big Bang but not for creation unless you can come up with a testable hypothesis?

TB:
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.

M: However, you have no evidence and frankly, no way of finding evidence for an intervention from a creator as it is a non-falsifiable hypothesis. I could assert that a galactic monkey created the genome of every living thing on earth 5 minutes ago and it would be just as non-falsifiable and non-testable as your creator assertion.

TB:
And your random processes haven't shown where the gene families and systems came from since abiogenesis anyway.

M: They actually explain the observations very well.

M: And are you aware that selection varies from gene to gene?[/qs]

TB:
What are you getting at?

M: What I am getting at is the degree of paralog divergence will be highly variable among paralogs dependent on the selective pressures. The three copies of the salivary amylase genes may or may not be more divergent within and among species as say the HLA genes dependent on the selective pressures involved.

TB:
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).

M: I lost track of where this part of the debate was going since we both agree on this.

TB:
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.

M: However, many paralogs start out that way. You can find duplication events rather frequently among species or at higher taxanomic levels. Whether they gain a new function will depend on selection and chance.

TB:
I nowhere deny this. I just don't think that specialized paralogs arrived the way you think they did.

M: You claimed you agreed with me and then say you disagree with me was my point.

M: LOL! Not qualitatively relevant that Aribidopsis has 18 percent of the genome composed of cyanobacterial genes horizonatlly transferred? Or that adzuki beetles have a huge chunk of the bacterial Wollbachia genome transposed into their sex chromosomes? I am not jumping the gun when the data is consistent with evolution and there is no data for your position or any other i.e. Lamarkian mechanisms, panspermia, etc.[/qs]

TB:
Yes, genomic plasticity does not explain the origin of gene families.

M: Um, this was a non answer.

TB:
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?

M: It causes syncytiotrophoblasts to fuse together. When this does not happen, placental development is perturbed i.e. pre-eclampsia.

TB:
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.

M: However, you do not show how your novel gene families demonstrate creation ex nihilo. Whereas evolutionary explanations (based on experimental evidence) can demonstrate the production of novel gene familes.

The only thing that will become more precise with the more sequenced genomes is the evolutionary mechanisms driving genomic evolution.

Even if the idea of kinds comes out?

M: There is no idea of kinds...it is a completely fuzzy definition.

I don't see any huge creation research projects testing...tell me again what the testable hypothesis is? I seem to have forgotten?

Genomes categorizable into kinds, distinguished by non-allelic gains and distinguished within by allelic and differential losses.

M: How is this supportive evidence of ex nihilo creation? How do you distinguish the data with or without a creator involved and test it? Which creator was it? Was it multiple creation events? A single event?
How do you falsify the hypothesis?

TB:
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.

M: The contradiction is that you constantly shift your placement of the creation events i.e. some genes in chimps were created since the divergence from humans..sometimes between bacteria and humans. But I am interested in how the genetic data is consistent with a 6Kya creation event.

Thus, you do imply it all was created once. But given your question, why would you expect bacteria to have the same genes as a multicellular organism?

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.

M: What is the evidence that a creator had to be involved? If it is an all powerful creator then why are there "biochemical processes required"? Why the ploy by this creator to make the genome appear to be similar among species by common descent? Seems like this creator had very limited capabilities.

What would be the selective advantege to E. coli of having a hox gene when it is never going to have a segmented morphology?

That's a very good point. What is the role of the Hox gene in E. coli?

M: None, they don't have hox gene clusters.

TB:
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.

M: Sorry, no dice, every single species on the planet would have to show a genetic bottleneck coalescing to the same time point for your flood scenario to be true. This is not the case and this research has been done contrary to your claim. Human genetic diversity does not coalesce to 6Kya either.

(post edited by Mammuthus since half of TB's message was cut off and I thought he had not answered..sorry TB!)

That was me. I used the submit button as a 'save' function while I had to attend to something.

M: Ah, that is what happened. It was really strange as suddenly there was nothing left except my previous text from the previous post. But then when it appeared on the screen I saw that your post continued.

cheers,
M


This message is a reply to:
 Message 9 by Tranquility Base, posted 12-17-2002 7:07 PM Tranquility Base has not yet responded

Replies to this message:
 Message 12 by Mammuthus, posted 12-18-2002 10:00 AM Mammuthus has not yet responded

  
Quetzal
Member (Idle past 3982 days)
Posts: 3228
Joined: 01-09-2002


Message 11 of 12 (27154)
12-18-2002 5:46 AM
Reply to: Message 8 by Tranquility Base
12-17-2002 5:47 PM


Hi TB:

quote:
Exons. 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.
That's nice (see below), but that wasn't the question I asked. For reference, I asked for your take on the exon theory of the origin of genes, and why you felt that it was inaccurate. Just to remind you what the theory states, it's the idea that the first genes were short strands with an intron-exon structure whose products were short polypeptides (like, 15-20 amino acids long). The intron sequences served as structural frameworks for exon shuffling, and helped with some elements of protein folding. The first shuffled exons were later fused by reverse transcription (retrotransposition) into more complicated exons. There's a growing amount of support for the "introns early" argument - some of which I posted above. There is support also for the creation of complex exons by retrotransposition (like the jingwei gene). So what's your argument against it?

As for the protein folding bit, I do appreciate the opportunity to look up some new information afforded by this discussion that I wouldn't normally have bothered with. Are you aware that there have been lab experiments that show what appears to be novel protein domains formed from disassociated exons precisely by the method predicted in the exon theory? One recent example is Riechmann L, Winter G, 2000, "Novel folded protein domains generated by combinatorial shuffling of polypeptide segments", PNAS 97:10068-10073

quote:
It has been proposed that the architecture of protein domains has evolved by the combinatorial assembly and/or exchange of smaller polypeptide segments. To investigate this proposal, we fused DNA encoding the N-terminal half of a beta-barrel domain (from cold shock protein CspA) with fragmented genomic Escherichia coli DNA and cloned the repertoire of chimeric polypeptides for display on filamentous bacteriophage. Phage displaying folded polypeptides were selected by proteolysis; in most cases the protease-resistant chimeric polypeptides comprised genomic segments in their natural reading frames. Although the genomic segments appeared to have no sequence homologies with CspA, one of the originating proteins had the same fold as CspA, but another had a different fold. Four of the chimeric proteins were expressed as soluble polypeptides; they formed monomers and exhibited cooperative unfolding. Indeed, one of the chimeric proteins contained a set of very slowly exchanging amides and proved more stable than CspA itself. These results indicate that native-like proteins can be generated directly by combinatorial segment assembly from nonhomologous proteins, with implications for theories of the evolution of new protein folds, as well as providing a means of creating novel domains and architectures in vitro.
Sure appears to me to indicate that exon shuffling as proposed in the exon theory has some experimental support. What does this do to your domaine creation ex nihilo theory?

[This message has been edited by Quetzal, 12-18-2002]


This message is a reply to:
 Message 8 by Tranquility Base, posted 12-17-2002 5:47 PM Tranquility Base has not yet responded

  
Mammuthus
Member (Idle past 4585 days)
Posts: 3085
From: Munich, Germany
Joined: 08-09-2002


Message 12 of 12 (27202)
12-18-2002 10:00 AM
Reply to: Message 10 by Mammuthus
12-18-2002 4:37 AM


Hi TB,
Here is another article I just found on the subject of mechanisms for the origin of genes.

Genome Research Vol. 12, Issue 12, 1854-1859, December 2002

LETTER
Retroposed New Genes Out of the X in Drosophila
Esther Betrán,1 Kevin Thornton,2 and Manyuan Long1,2,3
1 Department of Ecology and Evolution; 2 Committee on Genetics, The University of Chicago, Chicago, Illinois 60637, USA

New genes that originated by various molecular mechanisms are an essential component in understanding the evolution of genetic systems. We investigated the pattern of origin of the genes created by retroposition in Drosophila. We surveyed the whole Drosophila melanogaster genome for such new retrogenes and experimentally analyzed their functionality and evolutionary process. These retrogenes, functional as revealed by the analysis of expression, substitution, and population genetics, show a surprisingly asymmetric pattern in their origin. There is a significant excess of retrogenes that originate from the X chromosome and retropose to autosomes; new genes retroposed from autosomes are scarce. Further, we found that most of these X-derived autosomal retrogenes had evolved a testis expression pattern. These observations may be explained by natural selection favoring those new retrogenes that moved to autosomes and avoided the spermatogenesis X inactivation, and suggest the important role of genome position for the origin of new genes.


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 Message 10 by Mammuthus, posted 12-18-2002 4:37 AM Mammuthus has not yet responded

  
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