Definition of created kind!

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[This message has been edited by SLPx, 06-27-2002]

[QUOTE]Originally posted by Tranquility Base:Actually, all you did was cite one creationist paper from a creationist magazine.
The other citations, as I showed, didn't exactly demonstrate what you wanted them to.

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Originally posted by Tranquility Base:
We need to discuss the origin of novel protein fold families, biochemical pathways, macromolecualr machines and systems. That is the issue. We don't even have to wait for all the genomes to be reeled into discuss that. We already know that novel protein fold families are correlated with cellular novelty. There is almost no mainstream literature on the origin of protein fold families (which may also be called gene families).

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Hmmm... I punched in "evolution of gene families" at Pubmed and got 1776 returns. "Evolution of protein familiaes" got 1672, including this one which was first on the list:Harrison PM, Gerstein M.Studying genomes through the aeons: protein families, pseudogenes and proteome evolution.
J Mol Biol. 2002 May 17;318(5):1155-74."Evolution opf protein folds" got a mere 176."origin of protein fold families" got 28."origin of protein families" 901.Granted, many of these will not be directly related to the topic at hand, but it should be obvious that this is much more than "almost no mainstream literature".

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The human/chimp discusion will have to await the chimp genome I'm afraid.

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Why is that?

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Originally posted by Tranquility Base:
SLPx, you never responded to (at least the second) of the quotes I dug out from the mainstream FEBBs Lett paper later:

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

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and

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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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[This message has been edited by Tranquility Base, 06-27-2002]

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Whats to reply to? I am aware of no criterion that says that all creatures must be in possession of all protein families. I did my graduate work on the molecular systematics of primates using two unlinked loci, one of which was the gamma1 and gamma2 globin genes. Not all mammals have all of the genes in the cluster. Not all Primates have all of the genes (at least not all of the same genes) in the cluster. What IS present, however, is an interesting phylogenetic history laid out by the very presence or absense of the various genes and the changes within them. They match - gasp! - evolutionary hypotheses of descent.My reply was implicit in my other responses - you are making mountains out of molehills.

Oh - and you did not reply to my question re: chimp genomes.

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Originally posted by Tranquility Base:

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Protein fold families, among other things, do help define created kinds IMO, yes, and this is very well supported by studies of the association of fold families with cellular novelties. I also see it as a micro/macro-evolution differentiation which we equate to the kind distinguishment anyway.

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Then you must be able to easily identify the 'protein fold familiaes' that separate the human-kind from the ape-kind... Or, for that matter, ANY one-kind from another.

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There is a surprising complete silence in the mainstream lit on the issue so I will take that as a sign that the creationists are, at the very least, not stretching the point.

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There is an unsurprising lack of coherent positive evidence for any brand of creationism IN the creationist literature. That should be taken as a sign that the creationist position is an undefensible one.

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Originally posted by Tranquility Base:
SLPx - I said the human/chimp issue will have to await the chimp genome because it is only then that we will find to what extent we (humans) are diferentiated from chimps via

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(i) SNPs (single point mutations)

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SNPs are single nucleotide POLYMORPHISMS - that is, point mutations WITHIN a species. This would have no bearing on the human-chimp issue whatsoever.

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(ii) Regulatory sequences

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Exactly. Indeed, many evoloutionary biolists think that small changes in regulatory sequence are of great import in macroevolution.

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(iii) Paralogs (extra new funtion copies of genes)

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Such as the beta globin cluster.[/quote](iv) New gene families (protein folds)[/quote]If, as you wrote, "99.999% of random proteins" 'do not fold' ( a claim I find fantastic), it stands to reason that selection would weed such sequyences out. Since you admit paralogous duplication, I wonder what the rationale is for the implicit suggestion that such genes could not substantially mutate to produce novel proteins?[/quote]One non-creationist discussion I read recently points out that the 98% similarity experiments (determined by annealing rates) will definitely give an overestimate of similarity (because the non-similar parts wont combine!) and doesn't say much about the presence of new gene families.[/quote]You are referring to DNA-DNA hybridization, I assume. Funny thing about those 'overestimates: they have been borne out by direct sequence comparisons.Chimpanzee Fetal G-gamma and A-gamma Globin Gene Nucleotide Sequences Provide Further Evidence of Gene Conversions in Hominine Evolution
: Slightom et al., 1985
: Mol Biol Evol 2(5):370-389.
: 1.4-2.25% nucleotide difference, depending on which sets of alleles are compared.Primate Eta-Globin DNA and Man's Place Among the Great Apes.
: Koop et al., 1986.
: Nature 319:234-238.
: 1.7% distance measured by direct comparison of aligned nucleotide sequences (2.2 kilobases)Mol Phylogenet Evol 2001 Jan;18(1):14-25
Catarrhine phylogeny: noncoding DNA evidence for a diphyletic origin of the mangabeys and for a human-chimpanzee clade.
Page SL, Goodman M.1.7% difference, 10 kb, serum albumin introns and non-coding globin sequenceI wonder how many creationist 'hypotheses' have actually been borne out by subsequent analyses...

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Human gene families that aren't in pan are known and extrapolation suggests about 30 novel gene families might be present in man. We will just have to see.

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What are these 'known' novel gene families? Refs?

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[This message has been edited by SLPx, 07-04-2002]

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Originally posted by Tranquility Base:

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My refed quote The mere presence or absence of a protein family can be indicative of the existence of an entire cellular process" shows what I claimed, that protein folds accompany cellular novelty - at least some of the time (if not most of the time). In other words if you pick almost any cellular cystem you will need new protein folds to constrcut them.

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I fail to see how that indicates creation. Of course, quite disparate cellular systems utilize quite similar proteins - e.g., type III secretory systems and the flagella of some bacteria.
I think that example alone takes the wind out of your sails.

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Your study of globin genes is a study within a gene family - they are all homologs or orthologs of a single gene. These could have arisen by either creation or evolution.

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Yet the products of these genes exhibit distinct characteristics, and not all of the genes in the cluster in humans are found in other creatures. That was my point.

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Originally posted by Tranquility Base:
SLPx

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I recently read about novel protein fmailies in man vs chimp. The researchers extrapolated to predict about 30 novel families but this could be a lower limit. DNA hybridization experiments that say we are 98% similar almost definetely will generate an underestimate. We'll soon see.

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Ref please? I don't understand the sentence on 98% similarity. Could you rephrase?

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Originally posted by Tranquility Base:
SLPx

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SNP may be defined that way

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Of course it is, because that is what it is - a single nucleotide polymorphism.

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but I am simply extending the term to refer to the way of comapring two near identical sequences regardless of where they came from. Just subsitute 'point substitution' for SNP.

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Oh, so you mean you are making up your own definition to suit your needs? You see, what you are really referring to is homoplasy, and believe it or not, we stupid evolutionists have taken that into consideration.

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I agree about small changes in reg sequences and potential macroevolution.

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Selection will weed out non-folding proteins if your random protein also has a (new) function!

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I think I am a bit confused by your use of the term 'fold' - are you saying that only some proteins exhibit secondary and tertiary structure? I suppose I should have asked for a clarification earlier.

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I would generally see paralogous duplication as paralogous creation but I will concede that it is a potential mechanism of evolution. The rationale that duplication has not lead to novel gene families is that (a) there is not enough time and (b) there is very little, if any, sequence evidence that that has occurred.

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But I suppose thgere is sequence evidence of a loss of the unnecessary genes from the original kinds?

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Something that rarely gets talked about is that it is not just the active sites of proteins which are conserved. For many homologous proteins, even though seprated by 100s of millions of years, the entire length of the sequences are similar even though only a handful of residues are really invovled in function.

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I think I weill need some documentation on this. I know, for example, that cytochrome c's differ by as much as 50% in their AA sequence, so forgive me iof I do not take you at your word.

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The rest are there no doubt for issues of folding. Since that is the case I would also expect different protein fold families to share sequence similarities across their lengths since we know that many protein families suppossedly evolved during the last 100 million years. This is rarely, if ever seen except where it is a funtional motif, yet we have non-functional folding motifs conserved across 100s of millions of years. This all fits our scenario superbly. The sequences, though related to each other, were sperately created and have drifted for only 10,000 years or so.

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Hmmm.... So this 10,000 year drift (we will ignore the wholsale slaughter of innocents by Yahweh and the ensuing bottlenecks and such) can explain the 50% divergence in cytochrome c?

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The direct human-chimp sequence comparisons involve a priori similar genes of course. I do not debate at all that human and chimp genes are about 98% similar when comapred. Who knows howmany unique families there are. But I am prepared to concede that we are 98% similar regardless.

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Novel human genes?

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In this set of abstracts

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http://sayer.lab.nig.ac.jp/GEMINI/abstract.html

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it is stated that chorionic gonadotropin beta-chain is unique to anthropoid primates, that 300 human genes are not in mouse and that, by extrapolation, about 30 genes will differ between man and chimp. We'll see.

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Allow me to remove the ambiguities and implicit spin:Evolutionarily significant genetic differences between Homo and Pan (i.e.,
those contributing to phenotypic differences) can potentially be of several
forms, given our knowledge of comparative data from other species. These
can range in type from single nucleotide changes in coding or regulatory
regions to the acquisition of novel expressed genes. Although changes in
regulatory evolution are considered to be the primary means by which new
phenotypes are created (Carroll, Grenier, and Weatherbee, 2001), the
acquisition of novel genes is also likely to play a role in Homo-Pan
differences. Given that the human genome has 300 genes which the mouse
genome lacks, this is a net additive gain of 4-5 novel genes per million
years, assuming a 65 million year old common primate-rodent ancestor. If
novel genes were acquired at roughly a constant rate (4-5 genes per million
years per lineage), then we would expect to see approximately 27-28 novel
genes unique to humans since the 6 million year divergence from Pan (and
similarly, the same number of novel genes unique to Pan).30 genes is small potatoes. Where is the 'novel gene familiaes' you mentioned before? Novel protein families? Novel protein fold families? Or was that all just hyperbole?

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Originally posted by Tranquility Base:
SLPx

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And how does this issue relate to homoplasy? Homoplasy for you is conincidence (or physi-chemio-bio predisposition), for us it is design.

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Apparently you do not deal with sequence data. An example of Homoplasy in sequence data might be something like a human and a rabbit 'sharing' a unique mutation that neither share with any other taxon. Looking at the entire alignment of, say, 10,000 bps, such synapomorphies might number half a dozen. But the synapomorphies between, say, rhesus monkey and human number in the hundreds. Therefore, the alleged synapomorphy between human and rabbit would be an example of homoplasy.
Is that design? If so, why on earth would it be?

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Only very few random protein sequnces have stable folds with appreicable secondary structure content. Most of the coding genome of course codes for folded proteins.

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I find thathard to believe, frankly. It could be true, of course, it just seems fantastic.

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In mainstream analyses of genomes of closely related bacteria potential gains in one species are often interpreted as losses in the other species. Presumably in some cases there is pseudo-gene evidence for this. A real comparative genomics person would know the answer of the top of their head. I'm moving into this area but am concentrating on structural aspects.

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Of the top of my head ubiquitin is a remarkably conserved protein going a long way back. I plan to come up with documentaiton of this. I have read mainstream comments of surprise on the extent of concervation. I of course am not surprised.

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I am not either. I see no reason to be surprised that certain proteins (via their gene) exhibit a great deal of conservation, just as I am not surprised that some proteins - metabolically important ones, like cytochrome c, for example - vary considerably in their structure yet still perfrom the 'necessary' function.

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The 50% conservation of cytomchrome C is still rather surprising since there is usually zero sequence relationship between folds which are younger than cytochrome C. Active sites usually only involve 3 or 4 residues that must be absolutely conserved. I will document this gradually. To do it propoerly is real work and I have a day time job but I will do it.

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Really? What about the globins? Of course, it really shouldn't that surprising at all. Proteins like cytochrome c are necessary - or close to it - for energy production. Organisms with defective cytocrome cs will not likely survive to pass on their malady. No surprise.

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The 10,000 year drift would explain the small drifts but the sequences are also related via the heirarchy of life (proportional to useage rather than time in our sceanrio) and is hence a designed difference. 10,000 years would be long enough to explain large drifts evident in closely related rapidly reproducing organisms (bacteria etc).

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If you say so...

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I am prepared to concede that genetically there are only 30 gene families between us and chimps.

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But the abstracts you provided mentioned "30 genes", NOT 30 gene families. Were you hiding some?

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Given that there are no sequence hints as to the origin of protein folds it is hard to avoid the implication that these new families came out of thin air.

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Hmmm... It seems to me that protein folds are a byproduct of the coding sequence of the gene that encodes them, no?

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To many without knwoledge of structural biology and protein engineering a new gene family is 'dime a dozen', just a sequence of letters. To me it is an optimized machine different to all of the other machines in the genome.

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And that gives you. above all others, special insight into this matter such that you can see the fingerprints of the Hebrew tribal deity, right?

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More generally I am prepared to concede that macroevolutionary nearby organisms are separated by millions of point mutations, dozens of chromosomal rearrangements and about 20 novel gene families. The hardest part to explain for you guys is the 20 novel gene families.

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And yet you have failed to produce the documentation for these 'protein families' that you are hanging your hat on.
For Fred Williams, it is Haldane's model. For Gish it is the fossil record. For you, it is 'protein fold families' (or is it now gene families'?). A bunch of hedgehogs...

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Why we got latte-drinking primates sitting at computers out of all of this is also a problem but with evoltuion anything is possible of course when you know the answer beforehand.

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Or when some magical superbeing simply wills it to be so, no questions asked, no answers forthcoming...