The YEC's most common error?

"I take issue with that definition. Any mutational event is no more micro or macro than any other."
--I see what you mean, however, what I was addressing is the quantitative accumulation of mutations rather than a single genetic alteration (a macro-mutation & micro-mutation). Without considering this on a numerical basis, a single to few mutations over a number of generations resulting in very little morphologic change would be considered micro, this is not a majorly marked main event in the evolutionary history of life. We see these macro events, assuming geologic time, throughout the geologic column. The latter part of your post:

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The original speciation event that ultimately separated reptiles & mammals was no more "macro" than the events that separated grey & red squirrels. The individual mutations that led to a single mammal jaw bone were no more macro than any other point mutation, it is the collective, accumulated effect, relative to other organisms. Macroevolution is the sum of mutations that lead to larger scale morphological & chemical differences between clades.

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--[Continued] does seem to reflect my differentiation.------------------[This message has been edited by TrueCreation, 10-03-2002][This message has been edited by TrueCreation, 10-03-2002]

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Originally posted by TrueCreation:

Macroevolution is evolution which marks the main events in the evolutionary history of life.

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TC,It's a small point, I confess, but "main events" are often only discernable retrospectively. Like I say, the speciation event of one species from another, when one goes on to propogate a major clade can be considered a "main event". I'm thinking the speciation event that gave rise to a species that ultimately gave rise to mammals. But could you say the same of red & grey squirrels? Maybe one will go on to become a major group of mammal, or even a new taxanomic classification equal to mammals. My point is, this sort of event begins as a "micro" event, whether it goes on to lead to a major clade isn't known at that time.------------------
Occam's razor is not for shaving with.

AndyaMy claims are neither proven or flipant (I know you didn't accuse it of the latter). They are however more than anecdotal. They come simply from having read dozens of genome papers. I do protein folding simulation research but am branching out into genomics proper. I currenlty have one genomics project going (my students have written software which properly crosslinks the 3D structure database (PDB) with the biochemical pathway database (KEGG) and allows joint querying and data-mining. I am in the process of adding Swissprot/Pfam to this - the protein family database. My major aim at this point is studying differnetial enzyme substrate binding within pathways and across folds. However, as a side issue I will do some work that could be construed as 'E vs C motivated' (totally unbiased of course ) that will make my statements here less anecdotal.Here's how my taxonomy would work. It may not become the 'be all and end all' and is already implicitly done by comparative genomics people anyway. Basically when one compares two closely realted genomes (eg two bacteria in the same genus) one finds a large core genome and a surprisingly large (although smaller than the core) 'species specific' genome (as far as that genus is concerned). As we all know this is basically due to the taxonomy being determined from phenotype. But generally the organisms are probably closely evoltuionary related - even for creationists. Even the evoltuionists propose that the differnet sub-genomes are due to differential losses via different histories. So not even evoltuionists propose that the sub-genomes evolved seperately in each organism. How can this be proven? Easily for most of the genes. Many of the sub-genome genes an be found in lower organisms or in 'off-lineage' organisms strongly suggesting at being losses. Creationists interpret this only slightly differently - we hold to the idea tha tthe 'core' genome had originally contained the other genes and lost them. Other evidence for loss is of course pseudo-genes.All I'm saying is that analyses like this may eventually allow 'original stock' genomes to be recontructed irrespective of E vs C bias. The creationist will without apology interperet this as created 'kinds' and the evolutionist might say this supports PE and demonmstrates that batches of new genes evolved suddenly 'in samll populations'. It wont necessarily resolve the E vs C debate but will clarify what it is that both sides are arguing.The current genomes support what I have said. However, it will be in the extent that this is unravellable that its relevance to E vs C will be determined.[This message has been edited by Tranquility Base, 10-03-2002]

QuetzalRead my post to Andya above. I really am not proposing something different to what mainstream comparative genomics people are already doing. The 'original stock' idea of evolutionists will be able to be genomically reconstructed to some extent and probably will correspond pretty close to our 'kind' idea. It may not prove anything but so far it is suggestive of creation IMO.

SLPxI've posted stuff here before showing that in addition to paralogs cellular systems are characterizable by distinct protein families.No one denies that gene regulation also distinguishes organisms.

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Originally posted by Tranquility Base:
Quetzal

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Read my post to Andya above. I really am not proposing something different to what mainstream comparative genomics people are already doing. The 'original stock' idea of evolutionists will be able to be genomically reconstructed to some extent and probably will correspond pretty close to our 'kind' idea. It may not prove anything but so far it is suggestive of creation IMO.

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TB: I don't consider your arguments to be spurious. However, I do take exception to your continually using the "original stock" idea and "unique protein family" arguments as a basis for your assertions as if they had ANY evidentiary basis. THERE IS NOTHING IN ANY GENOME SO FAR SEQUENCED THAT LEADS TO THIS CONCLUSION!!! Sorry for shouting, but I'm getting a tad frustrated that you continually use a mere, unsupported guess as "evidence".No one argues that there aren't specific genetic differences between even closely-related species. In fact, karyotyping of subpopulations of various organisms have shown that even subspecies differences within inter-breeding populations can have genetic bases (c.f., Mus musculus domesticus in the Alps: 24 distinct, cross-fertile populations with genetic differences caused by recent Robertsonian fusions - no apparent reproductive barriers). Over time, the idea is that genetic differences like this accumulate (as you're well aware from your own work). It'll probably be even more obvious when they actually get around to sequencing the full genomes at the subspecies level (so far all I've seen is chromosome-level comparisons). Your bacterial genome example in the post to Andya is pure NDS - not creation.As to this bit in your post to Andya:

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Even the evoltuionists propose that the differnet sub-genomes are due to differential losses via different histories. So not even evoltuionists propose that the sub-genomes evolved seperately in each organism. How can this be proven? Easily for most of the genes. Many of the sub-genome genes an be found in lower organisms or in 'off-lineage' organisms strongly suggesting at being losses.

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This is somewhat inaccurate. The different genomes are mostly due to different mutations at certain loci after the populations diverged. Nobody (except creationists, apparently) say that changes in the genomes between species - or between genera, for that matter - are always "losses". Even at the protein level there are a lot of genes for which evidence exists that they are either homologous or paralogous with genes coding for completely different functions between vastly different organisms. For example, the nucleotide-binding subunits of F-ATPase in mammals (and actually across entire kingdoms) are homologous not only to the nucleotide-binding subunits of other ion-translocating ATPases, they also are homologous to an ATPase involved in the assembly of bacterial flagella (Vogler AP, Homma M, Irikura VM, Macnab RM: Salmonella typhimurium mutants defective in flagellar filament regrowth and sequence similarity of FliI to F0F1, vacuolar, and archaebacterial ATPase subunits. J Bacteriol 1991, 173:3564-3572) and to a bacterial transcription termination factor (Opperman T, Richardson JP: Phylogenetic analysis of sequences from diverse bacteria with homology to the Escherichia coli rho gene. J Bacteriol 1994, 176:5033-5043). We can't (yet, and possibly ever) trace the exact evolutionary ancestry of every single gene in every single organism. However, we CAN and HAVE traced enough of them to show that there is no gene-family based taxic discontinuity.I'll grant you a caveat to that last sentence: "yet uncovered". However, this means that you cannot use the existence of novel gene families as evidence for your assertion - anymore than I can say they don't exist.Sorry TB, I honestly think you're going to have to find a new argument - or at least a new basis for your assertions - until the question is answered one way or the other.

Same diff since Scopes is not a mouth wash and dentene has not been iced for a long toxic time.

I would like to know if the actual difference of splitting vs multiplication is not an artifact of different science training but I do not yet know how to implement Wolfram's view to marshall such a conflict that would likely still seperate Fisher and Wright for any pond in which the emprics is derivable (from).

QuetzalWe don't need all the genomes to know that (i) protein families fall into distinct families that at some point, are not unambiguously inter-relatable. This is a fact. It doens't destroy evolution theory - you can claim the connections have been washed away by time but it is consistent with our viewpoint.The idea of an 'original stock' genome per major taxonoic step is something that clearly transceneds the E vs C debate. We already know that novel protein familes characterize cellular subsystems. We know what the genome of Mycoplasma, yeast, worm etc have. We know what 'got added' in between these stages. This transcends the E vs C debate.It almost seems as if you want to bring every protein family back to the abiogeneiss of an original cell and claim losses and allelic mutation since even though there is not a single genomics researcher who suggests this! ( Or perhaps that every gene family is a paralog of the original genes. This is simply impossible. New gene families have arisen throughout the tree of life).So I completely disagree with your first paragraph. It is not true to say 'there is no evidence in genomes' for what I am saying. The genomes very well support what I am saying.Do you read the genome papers?
Do you read the section describing the Pfam/Interdom protein family presences or do you just look out for the SNP or repetive DNA sections?
Do you read the detailed comparative genomics papers?The point in genomic comparisons as far as E vs C goes is whether differnces were allelic, gains or losses.You say "The different genomes are mostly due to different mutations at certain loci after the populations diverged." I just read a genomic comaprison of two Baccilus genomes. There are thousands (yes, thousands) of novel genes that distinguish these members of the same Genus. The paper unambiguously puts it down to horizontal transfer and differential genetic losses.I am not debating that paralogs of genes exist. But they get put into families. I am talking about the origin of the first member of each family. Resuse of proteins as paralogs does not distinguish C vs E.You clearly focus on similarities to determine relationship (very logical) but you ignore the differneces that suggest that that relationship is not evolutionary but created.[This message has been edited by Tranquility Base, 10-06-2002]

TB, of course I am very interested with the suggestion that novel gene families can be a useful yardstick in higher-level taxonomy. That will end most (but not all) controversy and subjectivity arguments in taxonomy, like Mayr's Biological Species Concept rids many confusion in taxonomy (and adds some minor problems such as ring species and sibling species).Btw, I am not impressed by your bacteria example, too. Bacteria can be helpful in most evolutionary studies but not in taxonomy. They're a taxonomical mess. The two Bacillus you mention could have been two different genus! Ask any microbiologist and s/he would say that bacteria are classified morphologically, not biologically. Any bacteria with a rodlike appearance can be named Bacillus. Have you any eukaryote examples?

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We don't need all the genomes to know that (i) protein families fall into distinct families that at some point, are not unambiguously inter-relatable. This is a fact. It doens't destroy evolution theory - you can claim the connections have been washed away by time but it is consistent with our viewpoint.

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Actually, I think that you were the one that said the evidence would become obvious once we sequenced more genomes. However, I certainly concur that genes fall into distinct families and superfamilies. That's not in dispute. What is in dispute is your assertion that these distinct families somehow represent the taxic discontinuity between kinds. This assertion is fundamentally no different than the assertion that simply because an organism is classified as belonging to a particular linnean classification that it was separately created. Classification schemes, even at the gene level, are simply convenient labels we use to group related organisms (or proteins, for that matter). Unless you can point to the specific families (not individual genes, remember) that represent this taxic discontinuity, then your assertion is groundless.

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The idea of an 'original stock' genome per major taxonoic step is something that clearly transceneds the E vs C debate. We already know that novel protein familes characterize cellular subsystems. We know what the genome of Mycoplasma, yeast, worm etc have. We know what 'got added' in between these stages. This transcends the E vs C debate.

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I'm not really sure I follow you here. What do you mean "transcends the E vs C debate"? Every one of the organisms you mention here OF COURSE has a distinct genome. If it didn't, they'd be the same organisms. There are, however, shared gene families and superfamilies across these kingdoms. They all have ATPases, for instance. There are other examples. What hasn't been shown are families that distinguish these organisms that cannot unambiguously be shown to be totally unique to the particular organism until you get way up the classification ladder (say, phylum).

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It almost seems as if you want to bring every protein family back to the abiogeneiss of an original cell and claim losses and allelic mutation since even though there is not a single genomics researcher who suggests this! ( Or perhaps that every gene family is a paralog of the original genes. This is simply impossible. New gene families have arisen throughout the tree of life).

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Actually, that's pretty much what the ToE says. Given the vast size of protein sequence space, the observed mechanisms for creation of novel proteins (duplication, mutation, etc, etc), plus the existence of multidomain proteins coupled with horizontal transfer and known homologs and paralogs, lends a lot of credence to the idea. This doesn't even consider the role played by complete genome duplication, interspecies hybridizations, and large-scale genomic rearrangements. Does it prove the evolutionary explanation? No. But all the evidence certainly points to evolution rather than the ex nihilo creation of novel proteins at the base of the stem of a particular protein family.

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So I completely disagree with your first paragraph. It is not true to say 'there is no evidence in genomes' for what I am saying. The genomes very well support what I am saying.

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You have provided no evidence in support of what you are saying. Therefore, I will just say "no it doesn't".

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The point in genomic comparisons as far as E vs C goes is whether differnces were allelic, gains or losses.

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No, it isn't. The points we're arguing are:1. whether there is evidence of the existence of novel protein families in distinct, related genomes that can be used to distinguish species, genera, or families (the creationist "kinds")2. whether genomic comparisons and sequencing provides support to the existence of an "original stock genome".I'd have to say everything I've read to date indicates that neither #1 nor #2 have been supported. I'd be delighted to look at any references to the contrary.

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You say "The different genomes are mostly due to different mutations at certain loci after the populations diverged." I just read a genomic comaprison of two Baccilus genomes. There are thousands (yes, thousands) of novel genes that distinguish these members of the same Genus. The paper unambiguously puts it down to horizontal transfer and differential genetic losses.

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Right. And your point is what? Horizontal gene transfer is a well known mechanism at the bacterial level. Hell, there's quite a bit of evidence showing that gene swapping was a factor between archaea and bacteria - it's the reason rooting the "tree of life" is so difficult - it's more like a mangrove than a tree. This does nothing to support your contention, btw."Thousands of genes" seems a bit excessive - care to provide a reference?

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I am talking about the origin of the first member of each family.

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As am I. See for example, Pebusque MJ, Coulier F, Birnbaum D, Pontarotti P: Ancient large-scale genome duplications: phylogenetic and linkage analyses shed light on chordate genome evolution. Mol Biol Evol 1998, 15:1145-1159. There are a LOT of papers describing this - more and more all the time. Oddly enough, no research shows the de novo creation of new protein families in separate organisms.

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Originally posted by Tranquility Base:
SLPx

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I've posted stuff here before showing that in addition to paralogs cellular systems are characterizable by distinct protein families.

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No one denies that gene regulation also distinguishes organisms.

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Maybe they are, but again, the organs you mentioned all have pretty much the same proteins.