Transposons & Shared Endogenous Retrovirus's

My main point is that with the cellular/anatomical systems that are well characterised we see, in additon to reused protein families (frequently with unrecognizable sequences mind you), new protein families. Loss of any anatomical feauture could easily be assigned to single point mutations. Every time we get genuine novelty there are genuinely new protein families. Single celled to multicellular, plant/animal differences, immune system proteins etc. Cellular systems, in my experince, have unique protein fmailies in addition to shared ones. I can't tell you that this is the case for every novelty but my professional anecdotally generated suspicion () is that this is the case for the vast majority of well charactersied systems. It does not need to be in every case - the point is that it is generally true and there is no good mainstream theory of where these families came from. I am a creaitonist - so for me they arose in created genomes.PS - I am very interested in molecular developmental biology. It seems to me that this field is still in its infancy. How well do we understand how the genomes dictate body plans and eg, skeletal structure, in particular? I've read anout Hox genes and the basic body axis lessons but I get the feeling the rest is pretty unknown. Most of my comments about protein families I can only say is generally true for biochemical/cellular metabolic processes. I have no idea how well we understand how ribs and legs and inner ear bones are dictated molecularly but have actually tried to find out about this. What do you know?

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[This message has been edited by Tranquility Base, 05-29-2002]

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Originally posted by Tranquility Base:
^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.

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"Almost all" has become "all"?Please answer post 10. That your scenario is the best one is being contested by the fossil record.God creating extant families is supernatural, not natural, surely?Thanks,Mark------------------
Occam's razor is not for shaving with.

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Originally posted by Tranquility Base:
^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.

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"Almost all" has become "all"?Please answer post 10. That your scenario is the best one is being contested by the fossil record.God creating extant families is supernatural, not natural, surely?Thanks,Mark------------------
Occam's razor is not for shaving with.

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Originally posted by Tranquility Base:
^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.

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"Natural"? If you say so...Where - pray tell - is the evidence for the miraculous, 6-day creation event that you arrarently believe to be 'natural'?There may well not be remains for each and every intermediate ancestral stock, but then, where are the bones of every corpse from Adam to you?The 'demands' and the inherent double-standards therein are amazing...

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Originally posted by Tranquility Base:
Every time we get genuine novelty there are genuinely new protein families.

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Perhaps you can provide a reference for this?

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Single celled to multicellular, plant/animal differences, immune system proteins etc. Cellular systems, in my experince, have unique protein fmailies in addition to shared ones.

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And?

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I can't tell you that this is the case for every novelty but my professional anecdotally generated suspicion () is that this is the case for the vast majority of well charactersied systems. It does not need to be in every case - the point is that it is generally true and there is no good mainstream theory of where these families came from. I am a creaitonist - so for me they arose in created genomes.

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"No good" theory. Presumably then there are some bad ones? And they are bad why?

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PS - I am very interested in molecular developmental biology. It seems to me that this field is still in its infancy. How well do we understand how the genomes dictate body plans and eg, skeletal structure, in particular?

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Good question. That is why I asked you. [QUOTE] I've read anout Hox genes and the basic body axis lessons but I get the feeling the rest is pretty unknown. Most of my comments about protein families I can only say is generally true for biochemical/cellular metabolic processes. I have no idea how well we understand how ribs and legs and inner ear bones are dictated molecularly but have actually tried to find out about this. What do you know?

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[This message has been edited by Tranquility Base, 05-29-2002][/B][/QUOTE]Not much. Then, I am not the one claiming that I know enough to state that the best 'natural' answer is a created genome.

Mark, I'm using 'natural' in the sceintific model sense of 'explains the data in the least convoluted way'. Of course the creation of the original genomes themsleves was supernatural for me.Forgive me for dropping the 'almost', that was poor form.

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[This message has been edited by Tranquility Base, 05-30-2002]

Slpx, see the above post for the sense in which I used 'natural'. The evidence for the miraculous, 6-day creation event? We don't expect there to be any evidence other than the distinctness of the genomes and systematic lack of transitions evident in the fossil record.If you think the paleontological data is compatible with the evolution of all families of vertbrates feel free. We find the paleontologuical data is consistent with the burial of contemporaneous life, not withstanding certain dificulties that we would prefer did not exist. I don't think I have double standards. I personally think there are aspects of the data which are more compatible with one side or the other. In general I find the gross data and details are more consistent with creaiton/flood.

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[This message has been edited by Tranquility Base, 05-30-2002]

Slpx,I will see what I can find on protein families and association with cellular novelty. There is one fantastic paper (in JMB I think) that studies the distribution of protein families throughout the biochemical pathways of M. genitalium (the simplest free living genome done - about 450 genes). It suports a 'mosaic' origin for protein families. Almost no pathways are duplicated. Almost no consecutive enymes in a pathway are duplicated. New protein families are continually used as one goes from pathway to pathway. The rest of my impression is anecdotal. I'll track down this paper. As a genomic structural biologist I find it to be the best written work on this subject I have come across yet.Is there a 'bad', ie exisitng origin for protein families? I would call duplication/drift/selection a bad (but sensible) one. There was a good creationist study published in CEN TJ earlier this year showing that this mechanism is much, much too slow. I can't say I've professionally reviewed it yet but on casual rading it makes a lot of sense. I have searched Medline in vain for mainstream studies on this. I'm sure they are there but it's not my particular line of research.I am basing my statements on protein families on the hundreds of cellular metabolic pathways (as well as cellular systems like the immune system). I honestly can't comment on molecular developmental biology becasue I have not read enough and both you and I are agreed that it is early days yet. If dev biol is anything like metabolism molecularly then my statement will stand there too.EDIT: I can't seem to track down that paper, but this more general paper, even in its abstract, supports the idea that protein families are linked to cellular novelty: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_ uids=8706840&dopt=Abstract

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"Using the presence of the protein families as taxonomic traits, and linking them to biochemical pathways . . ."

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OK, I found it: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list _uids=11518524&dopt=Abstractdescibes the small molecule metabolic pathways (of E coli not M genitalium) - ie the 700 or so enzyme domains that can be classified into 213 protein families used to make small molecules in this single celled organism. Very good paper covering a specific line of research that I no longer need to bother doing!

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[This message has been edited by Tranquility Base, 05-30-2002]

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Originally posted by Tranquility Base:
Slpx, see the above post for the sense in which I used 'natural'. The evidence for the miraculous, 6-day creation event? We don't expect there to be any evidence other than the distinctness of the genomes and systematic lack of transitions evident in the fossil record.

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What is the 'distinctness' of the genomes within, say, the mammalia? What is it that you would consider a 'transition'?

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If you think the paleontological data is compatible with the evolution of all families of vertbrates feel free.

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I don't expect there to be a nice, complete string of fossils for every 'transition' throughout evolutionary history, and anyone with a passing knowledge of geological and biological processes shopuld not either. The evidence that does exist, however, fits nicely within the evolutionary framework.

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We find the paleontologuical data is consistent with the burial of contemporaneous life, not withstanding certain dificulties that we would prefer did not exist.

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You mean like the obvious progression in the fossil record? Yeah, that must be a bummer - too obvious to ignore, too difficult to explain...

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I don't think I have double standards. I personally think there are aspects of the data which are more compatible with one side or the other. In general I find the gross data and details are more consistent with creaiton/flood.

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[This message has been edited by Tranquility Base, 05-30-2002]

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It seems that one needs to be a creationist in the first place to come to such a conclusion. Why no modern mammals in, say, Cretaceous strata? Let me guess - modern mammals were so smart that when the flood waters were a-rising, they fled to higher ground, and all those dumb dinosaurs just stood there and drowned...

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Originally posted by Tranquility Base:
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Is there a 'bad', ie exisitng origin for protein families? I would call duplication/drift/selection a bad (but sensible) one. There was a good creationist study published in CEN TJ earlier this year showing that this mechanism is much, much too slow.

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Ref? Of course, one would expect a creationist to come to such a conclusion.

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I am basing my statements on protein families on the hundreds of cellular metabolic pathways (as well as cellular systems like the immune system). I honestly can't comment on molecular developmental biology becasue I have not read enough and both you and I are agreed that it is early days yet. If dev biol is anything like metabolism molecularly then my statement will stand there too.

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EDIT: I can't seem to track down that paper, but this more general paper, even in its abstract, supports the idea that protein families are linked to cellular novelty:

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From the abstract:"The phylogenetic distribution of divergently related protein families into the three domains of life (archaea, bacteria and eukaryotes) can signify the presence or absence of entire cellular processes in these domains and their ancestors. We can thus study the emergence of the major transitions during cellular evolution..."Emphasis mine...

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OK, I found it:

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descibes the small molecule metabolic pathways (of E coli not M genitalium) - ie the 700 or so enzyme domains that can be classified into 213 protein families used to make small molecules in this single celled organism. Very good paper covering a specific line of research that I no longer need to bother doing!

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[This message has been edited by Tranquility Base, 05-30-2002]

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From that abstract:"This information allows us to answer general questions on the structural anatomy of the SMM pathway proteins and to trace family relationships and recruitment events within and across pathways.""Excluding isoenzymes, more than twice as many homologues are distributed across pathways as within pathways.""Most of the domains that form SMM pathways have homologues in non-SMM pathways. Taken together, these results imply a pervasive "mosaic" model for the formation of protein repertoires and pathways..."Emphases mine...I submit that these studies don't imply what you want them to...One of the interesting outcomes of the HGP was the dioscovery that huge portions of the genome are in fact the result of dupications - entire chromosomal segments getting duplicated and incorporated into the genome.I wonder what the evolutionary precursors of M. genitalium might have had in their genomes? Since, as far as I can tell, genomes do not fossilize, the creationisyt will always be able to hide in the unknown and draw their newest line in the sand there. A few decades ago - even a few years - , of course, their lines were much, much further ahead of where they are now. I have always thought thusly: evolution is based on what we know, creationism on what we don't.

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[This message has been edited by SLPx, 05-31-2002]

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Originally posted by Tranquility Base:

If you think the paleontological data is compatible with the evolution of all families of vertbrates feel free. We find the paleontologuical data is consistent with the burial of contemporaneous life, not withstanding certain dificulties that we would prefer did not exist.

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[This message has been edited by Tranquility Base, 05-30-2002]

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How is paleontological data compatible with the burial of contemporaneous life? You can’t wave your hand & make it so.If it were compatible, you could substantively answer the points in post 10. You seem to be saying the fossil record is compatible with creation science, but at the same time, it isn’t really.Either creation science can sufficiently explain the pattern of fossils or it can’t. If it can’t, then you are unable to claim we find the paleontological data is compatible with the burial of contemporaneous life.Mark------------------
Occam's razor is not for shaving with.

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[This message has been edited by mark24, 06-01-2002]

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[This message has been edited by mark24, 06-01-2002]

[QUOTE]Originally posted by Tranquility Base:
If you think the paleontological data is compatible with the evolution of all families of vertbrates feel free. We find the paleontologuical data is consistent with the burial of contemporaneous life, not withstanding certain dificulties that we would prefer did not exist. [This message has been edited by Tranquility Base, 05-30-2002][/B][/QUOTE]Please explain to me or give me a reference how a global flood could deposit the species in a temporal fashion, ie no trilobites with sabertooth tigers; OK, bad example but I think you know what I mean. How about giant sloths and corytheosaurus, or mastadons and Allosaurus, ect.------------------
"Chance favors the prepared mind." L. Pasteur
Taz

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Originally posted by Dr_Tazimus_maximus:
Please explain to me or give me a reference how a global flood could deposit the species in a temporal fashion, ie no trilobites with sabertooth tigers; OK, bad example but I think you know what I mean. How about giant sloths and corytheosaurus, or mastadons and Allosaurus, ect.

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Or man with non-avian dinosaurs.

SLPx, here's the pdf of the creationist study of pre-selction statistical bariers to protein family evoltuion (I plan to semi-profesionally review it in the near future):

Answers in Genesis: Protein Families Paper

[Edited too long link. --Percy]In the FEBBS Lett paper I cited I read the 'divergently related protein families' as the members of the family being (potentialy) divergent. The full pdf of this paper I think clarifies that that is what was meant although it doesn't use the same language. Many protein families defined by their sequence/structural similarity can be pronounced (by evoltuionists) as 'divergent' (within the family) without debate.In addition the pdf makes clear that distict protein families can be good indicators of cellular novelty:

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The mere presence or absence of a protein family can be indicative of the existence of an entire cellular process

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I don't deny that there might be systems that don't involve novel protein families but the evidence seems to be that the norm is to expect new protein families amongst the reused ones in novel systems.I agree that the JMB paper (my 2nd ref) studies reuse of protein families and that that is what the evolutionist can try to use to work out what happened. So, yes, reuse is one message of the paper. The other message is that 200 distinct proteins families, the origin of which are not explained, are distributed throughout the SMM pathways. If you read the entire paper it is also explained that the pattern found does not support that expected by well known models of pathway evoltuion, namely that one might expect serial recruitment of a protein family within pathways because the first, or last, member of the pathway protein will already have favourable binding affinity.I certianly am very aware of the idea of core genomes throughout life but am also very aware of the large number of distinct protein families used to achieve this and that a good proportion of families are not represented in lower life. I find all of this very consistent with the supernatural creation of genomes.Creationists, at least myself, are excitedly awaiting the publication of vast numbers of genomes. Our model predicts the 'kind' concept and the flood constrains us to not have too many of them. We will see to what extent the data backs up this concept of distinct genomes, presumably characterised by novel protein families and pathways, but diversified through microevoltuionary phenomena. I for one am not scared of the data - I say bring it on.

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[This message has been edited by Tranquility Base, 06-05-2002]

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[This message has been edited by Percipient, 06-05-2002]

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Originally posted by Tranquility Base:
SLPx, here's the pdf of the creationist study of pre-selction statistical bariers to protein family evoltuion (I plan to semi-profesionally review it in the near future):

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Thanks for the link. I will review when I have time.

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Creationists, at least myself, are excitedly awaiting the publication of vast numbers of genomes. Our model predicts the 'kind' concept and the flood constrains us to not have too many of them. We will see to what extent the data backs up this concept of distinct genomes, presumably characterised by novel protein families and pathways, but diversified through microevoltuionary phenomena. I for one am not scared of the data - I say bring it on

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What is to be scared of? A creationist (Barry Setterfield's wife) once claimed on another board that she would find evidence of a 'smooth distance transition between species' very troubling for creationism. I presented just such a smooth transition (see http://www.gate.net/~rwms/EvoEvidence.html, the Genetic distance link). Did she find it troubling? not at all. I got the standard "I'll wait until the entire genome of all those species have been sequenced" and "I don't understand gene sequencing, so I can't comment on it" schtick.Are you familiar with the CRSQ baraminology papers by Robinson and Cavanaugh? They weren't scared of the data, either...