Evolution Easily Refuted

Hi TB:Actually, there are quite a few papers on the subject. Look up sdic, jingwei, etc. There are novel genes - and the pathways that lead to them - being discovered all the time. I agree that there hasn't been huge amounts of papers published on the evolution of protein families, but there have been a few. One example: Saier MH Jr, Eng BH, Fard S, Garg J, Haggerty DA, Hutchinson WJ, Jack DL, Lai EC, Liu HJ, Nusinew DP et al. (1999): Phylogenetic characterization of novel transport protein families revealed by genome analyses. Biochim Biophys Acta, 1422:1-56. Here's one on line for you: A conserved domain is present in different families of vesicular fusion proteins: A new superfamily. Finally, you’ll enjoy this one, being a structural guy — it discusses improvements in delineating families of paralogs in completely sequenced genomes. Includes a table showing examples of protein superfamilies recently expanded as a result of improved techniques and additional data: Koonin EV, Tatusov RL, Galperin MY (1998): Beyond complete genomes: from sequence to structure and function. Curr Opin Struct Biol, 8:355-363.And that taxic barrier was what, again?

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Originally posted by Quetzal:
Uhh, Philip? Reread your definitions. Enzymes are proteins acting as catalysts. Because proteins are pretty ubiquitous, we often change the name to signify their specific actions or use within the organism. For example, contractile proteins are called "muscles" (myofibrils, the bulk of muscle fiber, are composed of the proteins actin and myosin, with a dash of the proteins troponim and tropomyosin for flavor), cell membranes are made of proteins called "collagens" (mostly glycoproteins), "transcription factors" that turn genes on and off are proteins, etc. Back to your basic biology text, there, Philip. The only one twisting definitions is you.

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Now, would you care to address any of the rest of the post?

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--Appeal to your formalized yet fatal nondistinction of enzymes vs. proteins? No way!
--Back to basic biology? Resorting to scornful ploys are you, Quetzel?
--Yes, back to the rest of the post: Demonstrate my original question without APRIORI reasoning just how any enzyme could have evolved under any ToE (micro- or mega-).

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--Appeal to your formalized yet fatal nondistinction of enzymes vs. proteins? No way!

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Well, I guess you're free to change the definition any way you want - you've done it before. Doesn't make your misunderstanding correct.

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--Back to basic biology? Resorting to scornful ploys are you, Quetzel?

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Nope. Just pointing out your basic lack of knowledge of biology - again. 'Course, this is much milder than your insistance that evolutionary biology is worse than Haitian devil worship...

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--Yes, back to the rest of the post: Demonstrate my original question without APRIORI reasoning just how any enzyme could have evolved under any ToE (micro- or mega-).

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Okay. Try this on for size:Nurminsky DI, Nurminskaya MV, De Aguiar D, Hartl DL (1998), "Selective sweep of a newly evolved sperm-specific gene in Drosophila", Nature 396:572-5

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The pattern of genetic variation across the genome of Drosophila melanogaster is consistent with the occurrence of frequent 'selective sweeps', in which new favourable mutations become incorporated into the species so quickly that linked alleles can 'hitchhike' and also become fixed. Because of the hitchhiking of linked genes, it is generally difficult to identify the target of any putative selective sweep. Here, however, we identify a new gene in D. melanogaster that codes for a sperm-specific axonemal dynein subunit. The gene has a new testes-specific promoter derived from a protein-coding region in a gene encoding the cell-adhesion protein annexin X (AnnX), and it contains a new protein-coding exon derived from an intron in a gene encoding a cytoplasmic dynein intermediate chain (Cdic). The new transcription unit, designated Sdic (for sperm-specific dynein intermediate chain), has been duplicated about tenfold in a tandem array. Consistent with the selective sweep of this gene, the level of genetic polymorphism near Sdic is unusually low. The discovery of this gene supports other results that point to the rapid molecular evolution of male reproductive functions.

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There you go Philip - the evolutionary pathway of a new gene that evolved by the duplication, fusion, and modification of two genes that are now on each side of Sdic on the chromosome. Answer your question?

[QUOTE]Originally posted by Quetzal:
Nurminsky DI, Nurminskaya MV, De Aguiar D, Hartl DL (1998), "Selective sweep of a newly evolved sperm-specific gene in Drosophila", Nature 396:572-5

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The pattern of genetic variation across the genome of Drosophila melanogaster is consistent with the occurrence of frequent 'selective sweeps', in which new favourable mutations become incorporated into the species so quickly that linked alleles can 'hitchhike' and also become fixed. Because of the hitchhiking of linked genes, it is generally difficult to identify the target of any putative selective sweep. Here, however, we identify a new gene in D. melanogaster that codes for a sperm-specific axonemal dynein subunit. The gene has a new testes-specific promoter derived from a protein-coding region in a gene encoding the cell-adhesion protein annexin X (AnnX), and it contains a new protein-coding exon derived from an intron in a gene encoding a cytoplasmic dynein intermediate chain (Cdic). The new transcription unit, designated Sdic (for sperm-specific dynein intermediate chain), has been duplicated about tenfold in a tandem array. Consistent with the selective sweep of this gene, the level of genetic polymorphism near Sdic is unusually low. The discovery of this gene supports other results that point to the rapid molecular evolution of male reproductive functions.

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There you go Philip - the evolutionary pathway of a new gene that evolved by the duplication, fusion, and modification of two genes that are now on each side of Sdic on the chromosome. Answer your question?[/B][/QUOTE]I hand it to you, Quetzel, you don't give up with your formalistic yet arbitrary bio-babble. Your hitchhiking genes continue to smell strongly of APRIORI cascades, APRIORI mutation spots, and APRIORI higher-level gene functions of which you and I have minimal knowledge of. This injudicious conclusion that you just demonstrated enzymatic evolution (micro or mega) with such an oversimplified example is thus another rhetorical not-so-cleverly-twisted lie. Bold and subtle lies like these (and like your equating enzymes with proteins) have no place in our making empirical generalizations of any ToE. These lies (as well as mine) need to stop.Respectfully,
Philip

Lies? Whatever, Philip. You asked for the evolutionary pathway of a novel gene. I provided one from the literature. You claim it's a lie. Here's another: Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates.

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An improved understanding of the evolution of gene function at the molecular level may provide significant insights into the origin of biological novelty and adaptation. With the approach of ancestral protein reconstruction, we here address the question of how a dramatically enhanced ribonucleolytic activity and the related antiviral activity evolved in a recently duplicated ribonuclease (eosinophil-derived neurotoxin) gene of higher primates. We show that the mother gene of the duplicated genes had already possessed a weak antiviral activity before duplication. After duplication, substitutions at two interacting sites (Arg-643Ser and Thr-1323Arg) resulted in a 13-fold enhancement of the ribonucleolytic activity of eosinophil-derived neurotoxin. These substitutions are also necessary for the potent antiviral activity, with contributions from additional amino acid changes at interacting sites. Our observation that a change in eosinophil-derived neurotoxin function occurs only when both interacting sites are altered indicates the importance of complementary substitutions in protein evolution. Thus, neutral substitutions are not simply ‘‘noises’’ in protein evolution, as many have thought. They may play constructive roles by setting the intramolecular microenvironment for further complementary advantageous substitutions, which can lead to improved or altered function. Overall, our study illustrates the power of the ‘‘paleomolecular biochemistry’’ approach in delineating the complex interplays of amino acid substitutions in evolution and in identifying the molecular basis of biological innovation.

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Of course, you can always claim that one's a lie, as well. Feel free to argue with yourself. Your assertion stands refuted.

I thought enzymes were proteins ... is that wrong?

Enzymes are indeed proteins. Not all proteins are, however, enzymes.

Yep. Philip doesn't believe that enzymes are proteins, however. It's all just an evilutionist devil-worshipping conspiracy to bring good Christians to sin. Just ask him.

[QUOTE]Originally posted by Quetzal:
[B]Here's another: Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates. [quote]An improved understanding of the evolution of gene function at the molecular level may provide significant insights into the origin of biological novelty and adaptation. With the approach of ancestral protein reconstruction, we here address the question of how a dramatically enhanced ribonucleolytic activity and the related antiviral activity evolved in a recently duplicated ribonuclease (eosinophil-derived neurotoxin) gene of higher primates. We show that the mother gene of the duplicated genes had already possessed a weak antiviral activity before duplication. After duplication, substitutions at two interacting sites (Arg-643Ser and Thr-1323Arg) resulted in a 13-fold enhancement of the ribonucleolytic activity of eosinophil-derived neurotoxin. These substitutions are also necessary for the potent antiviral activity, with contributions from additional amino acid changes at interacting sites. Our observation that a change in eosinophil-derived neurotoxin function occurs only when both interacting sites are altered indicates the importance of complementary substitutions in protein evolution. Thus, neutral substitutions are not simply ‘‘noises’’ in protein evolution, as many have thought. They may play constructive roles by setting the intramolecular microenvironment for further complementary advantageous substitutions, which can lead to improved or altered function. Overall, our study illustrates the power of the ‘‘paleomolecular biochemistry’’ approach in delineating the complex interplays of amino acid substitutions in evolution and in identifying the molecular basis of biological innovation.[/B][/QUOTE]--In honesty, I admit evolutionary adaptations like the above, seem, superficially, powerfully complex -- extremely so. Yet, the forceful evo-mechanism here still requires far more complex APRIORI mechanisms that you and I don't understand.Quetzel, I propose that these APRIORI mechanisms (that you and I don't understand) are mechanisms that both of us must realize by faith.Now your empirical faith can never grasp these mechanisms: i.e., APRIORI protein factors with synchronous and harmonious cascading events that somehow interact by and for transcriptional and translational events within exhaustively complex APRIORI biochemical and biophysical parameters.Likewise, my metaphysical faith, while skipping many details, goes right to the redemptive-ID and works in reverse, i.e., from the beginning of the creation as an APRIORI APRIORI mechanism.You, in essence, are not seeing the forest from the trees when it comes to ToE mechanisms. I, on the other hand, am seeing more of the forest SANS the trees. Yet, from each of our points of view, I suppose an argument could be stated that both of us are honest ... Deluded but honest ... Compulsively ignorant, but honest ... Liars and yet true.This seems a big problem with empirical faith vs. metaphysical faith. Yet God forbid that I should deride either faith.Philip

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Originally posted by Peter:
I thought enzymes were proteins ... is that wrong?

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--Karls reply is right.
--The wrongness of Quetzel's response(s) lay in subtly equating the two, presumably with the motive to oversimplify a mega-protein evolution model. Most proteins in humans do not behave as enzymes, whose exquisitely sensitive (catalytic) active sites indeed seem strong evidence of APRIORI ID mechanism(s).--In sum, we might hypothesize that enzymes basically beget enzymes that are ultimately more complex and more beneficial than the APRIORI ones, and that somehow re-code the APRIORI ones in the process, via strong natural selection pressures.
I strongly refute this ToE concept because:
1) Irreducibly complex APRIORI events, force-vectors, exquisite harmonization of molecules, etc. in the genome(s) would become detrimentally broken.
2) Resultant beneficial mutations themselves (if there really be such a thing) would always abide within fixed APRIORI parameters of the genome, forcing a 'kinds' taxonomy to exist within any adaptive radiation, e.g., of any evolving new species.
3) That hitchhiking genes, mutation spots, etc. might punctuate greater harmonious complexity during (micro)evolution always begs a god-of-the-gaps fallacy, for I see that increased harmonious synchronizations and orchestrations of molecules would quickly destroy the APRIORI catalytic force vectors that were formerly operative. Such is the problem with successive mutations per se.Philip

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Originally posted by Philip:

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Originally posted by Peter:
I thought enzymes were proteins ... is that wrong?

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--Karls reply is right.
--The wrongness of Quetzel's response(s) lay in subtly equating the two, presumably with the motive to oversimplify a mega-protein evolution model. Most proteins in humans do not behave as enzymes, whose exquisitely sensitive (catalytic) active sites indeed seem strong evidence of APRIORI ID mechanism(s).

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So are you saying that Quetzal said that all proteins were
enzymes? Was that the error you were pointing out? [B][QUOTE] --In sum, we might hypothesize that enzymes basically beget enzymes that are ultimately more complex and more beneficial than the APRIORI ones, and that somehow re-code the APRIORI ones in the process, via strong natural selection pressures.
I strongly refute this ToE concept because:
1) Irreducibly complex APRIORI events, force-vectors, exquisite harmonization of molecules, etc. in the genome(s) would become detrimentally broken.
2) Resultant beneficial mutations themselves (if there really be such a thing) would always abide within fixed APRIORI parameters of the genome, forcing a 'kinds' taxonomy to exist within any adaptive radiation, e.g., of any evolving new species.
3) That hitchhiking genes, mutation spots, etc. might punctuate greater harmonious complexity during (micro)evolution always begs a god-of-the-gaps fallacy, for I see that increased harmonious synchronizations and orchestrations of molecules would quickly destroy the APRIORI catalytic force vectors that were formerly operative. Such is the problem with successive mutations per se.Philip [/B][/QUOTE]So if there was a mechanism within the gene repair functions
that could effectively mask-out some mutations, perhaps to
later release them all at once ... would that alter your objections?

Philip,

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Originally posted by Peter:
I thought enzymes were proteins ... is that wrong?

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--The wrongness of Quetzel's response(s) lay in subtly equating the two, presumably with the motive to oversimplify a mega-protein evolution model. Most proteins in humans do not behave as enzymes, whose exquisitely sensitive (catalytic) active sites indeed seem strong evidence of APRIORI ID mechanism(s).

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There is no subtle equating. Quetzal & John are correct. Enzymes ARE proteins. No one said all proteins are enzymes.And WHAT is a "mega protein evolution model?????Mark------------------
Occam's razor is not for shaving with.

So if there was a mechanism within the gene repair functions
that could effectively mask-out some mutations, perhaps to
later release them all at once ... would that alter your objections.
--Thank you for this excellent mechanism to rebut.
--This mechanism has been reported, hypothesize, purported, purpetrated, etc. in various guises.
--It is a powerful mechanism that would support a ToE, until you go back in time to the pre-existing elements that made such a DNA-repairase/repairase complex (if you will) subsist to begin with.
--Recalling these repairase enzymes as the most complex enzymes on the planet, with millions of precisely arranged atoms somehow interacting to make this awesome function possible. Could they have evolved from even a slightly different pre-existent repairase protein?
Methinks not.
Thus I'd continue to object on these APRIORI grounds.Sincerely,
Philip

[QUOTE]Originally posted by mark24:
Philip,
There is no subtle equating. Quetzal & John are correct. Enzymes ARE proteins. No one said all proteins are enzymes.
--Mark, he called them "synomonous" and proceded to snowball his own psuedo-scientific definition of all proteins actually being enzymes. He did this and many lurkers did witness. Then, he told me to go back to basic biology, even after I gave him the dictionary defs.And WHAT is a "mega protein evolution model?????
--Essentially, the model of a ToE that is used to explain the development of organelle/organ proteins and enzymes from aa's and proteins, in a genetic manner. (Please rebut any grammatical onslaughts here)Sincerely,
Philip

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And WHAT is a "mega protein evolution model?????

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It's yet another made-up term that Philip likes to spout about.If he uses his own terms instead of those boring old well-defined and generally-used standard scientific terms, he doesn't ever have to be very specific about what the hell he is talking about.It is an evasive debate tactic; "baffle them with bullshit". You spend so much time trying to nail him down on what he means by these invented terms of his, because they are nearly always fuzzy, vague definitions at best, that often his original points and claims are left behind.[This message has been edited by schrafinator, 11-16-2002]