tag:blogger.com,1999:blog-26682722.post15059400396229936..comments2024-03-27T11:39:00.859-07:00Comments on Stones and Bones: Creationist physicist Nathan AviezerGary S. Hurdhttp://www.blogger.com/profile/08296691454238708856noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-26682722.post-12819780500203693422012-07-30T14:27:37.912-07:002012-07-30T14:27:37.912-07:00Thanks for your remark. I have the next few days f...Thanks for your remark. I have the next few days filled, but I'll try to read your citations as soon as I ca. It is currently a very active time in Origin Of Life research.Gary S. Hurdhttps://www.blogger.com/profile/08296691454238708856noreply@blogger.comtag:blogger.com,1999:blog-26682722.post-4392881206001425882012-07-30T13:35:02.895-07:002012-07-30T13:35:02.895-07:00On the RNA world I would add, as I noted over on T...On the RNA world I would add, as I noted over on The Panda's Thumb, that modern genome/protein methods now reach down through the DNA UCA before domain diversification all the way to the RNA/protein world by way of protein fold families.<br /><br />It turns out that the RNA/protein world is ~ 20 % of a fold clock proxy, the DNA UCA another ~ 20 %, and first after comes diversification into domains. ["The evolution and functional repertoire of translation proteins following the origin of life", Goldman et al, Bio Dir 2010; and similar works.] In other words, ~ 50 % of cell history (by proxy) happened before the ancestors of modern cells evolved.<br /><br />To contribute more references here, the existence of a DNA UCA is itself tested by phylometabolic methods. <br /><br />On a trophic level, a robust and doubled autotrophic CO2 metabolism before diversification tests a common root. The robustness further tests that early cell regulation of metabolism and growth, the latter which would have acted as a parasitic drain on the autocatalytic cores of carbon metabolism, was less evolved as would be expected out of an RNA world and/or chemical evolution. [“The Emergence and Early Evolution of Biological Carbon-Fixation, Braakman et al, PLoS Comp Bio 2012.] <br /><br />Similarly a non-stereosymmetric lipid membrane biosynthesis before diversification tests a common root. [“Ancestral lipid biosynthesis and early membrane evolution”, Peretó et al, TRENDS in Bio Sci 2004.]<br /><br />And on the ribozymes I would add that we now know that the chemical selection promotes catalysts. Which implies that pre- to protobiotic pathways could within reach for testability! Yes, it really seems so, as the following toy model shows:<br /><br />DNA-protein cell machinery, RNA or ATP biosynthesis before the first membranes, the first enzymes are examples of (not fully exclusive) common evolutionary chicken-and-egg problems. Luckily such problems conveniently bottleneck possible pathways to a smaller set.<br /><br />Bottom up, chemical network enzymes are a natural outcome in newer scenarios. High-temperature reactions seems to be much faster than orthodox theory believed from scant data. This temperature dependence gives a self-selection for enthalpic pre-proteinous enzymes. ["Impact of temperature on the time required for the establishment of primordial biochemistry, and for the evolution of enzymes", Stockbridge et al, PNAS, 2010.]<br /><br />Now looking top down, we see that pathways meet. The first modern metabolic networks originated with purine metabolism, and specifically with the gene family of the P-loop-containing ATP hydrolase fold. ["The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture", Caetano-Anollés et al. PNAS, 2007; "Rapid evolutionary innovation during an Archaean genetic expansion", David et al, Nature, 2010.]<br /><br />That is, ATP sits at the intersection between a cooling and/or hydrothermal vent active Earth premetabolism and nucleotide protometabolism. (Which compound seems to later have been exaptated by modern proteinous metabolic genes as coenzyme/energy currency.) Minimum change of traits picks ATP use before RNA evolution<br /><br />Note that this is an (informal) test of a phylogenetic pathway. Abiogenesis is actually slightly testable today as far as I can see.<br /><br />To solve the new chicken-and-egg problem between RNA and coenzymes in metabolism, it turns out ATP, CoA et cetera coenzyme's synthesis can be easily RNA-catalyzed by polyphosphate activation. ["RNA-Catalyzed CoA, NAD and FAD Synthesis from Phosphopantetheine, NMN, and FMN", Huang et al, Biochem 2000.] Finally there is also recent implications of selection of RNA in its enhanced enzymatic capability in the presence of iron under anoxic conditions, as on the primeval Earth.Torbjörn Larssonhttps://www.blogger.com/profile/13304729731231255545noreply@blogger.comtag:blogger.com,1999:blog-26682722.post-22265215033711633112012-07-30T13:25:51.649-07:002012-07-30T13:25:51.649-07:00On the RNA world I would add, as I noted over on T...On the RNA world I would add, as I noted over on The Panda's Thumb, that modern genome/protein methods now reach down through the DNA UCA before domain diversification all the way to the RNA/protein world by way of protein fold families.<br /><br />It turns out that the RNA/protein world is ~ 20 % of a fold clock proxy, the DNA UCA another ~ 20 %, and first after comes diversification into domains. ["The evolution and functional repertoire of translation proteins following the origin of life", Goldman et al, Bio Dir 2010; and similar works.] In other words, ~ 50 % of cell history (by proxy) happened before the ancestors of modern cells evolved.<br /><br />To contribute more references here, the existence of a DNA UCA is itself tested by phylometabolic methods. <br /><br />On a trophic level, a robust and doubled autotrophic CO2 metabolism before diversification tests a common root. The robustness further tests that early cell regulation of metabolism and growth, the latter which would have acted as a parasitic drain on the autocatalytic cores of carbon metabolism, was less evolved as would be expected out of an RNA world and/or chemical evolution. [“The Emergence and Early Evolution of Biological Carbon-Fixation, Braakman et al, PLoS Comp Bio 2012.] <br /><br />Similarly a non-stereosymmetric lipid membrane biosynthesis before diversification tests a common root. [“Ancestral lipid biosynthesis and early membrane evolution”, Peretó et al, TRENDS in Bio Sci 2004.]<br /><br />And on the ribozymes I would add that we now know that the chemical selection promotes catalysts. Which implies that pre- to protobiotic pathways could within reach for testability! Yes, it really seems so, as the following toy model shows:<br /><br />DNA-protein cell machinery, RNA or ATP biosynthesis before the first membranes, the first enzymes are examples of (not fully exclusive) common evolutionary chicken-and-egg problems. Luckily such problems conveniently bottleneck possible pathways to a smaller set.<br /><br />Bottom up, chemical network enzymes are a natural outcome in newer scenarios. High-temperature reactions seems to be much faster than orthodox theory believed from scant data. This temperature dependence gives a self-selection for enthalpic pre-proteinous enzymes. ["Impact of temperature on the time required for the establishment of primordial biochemistry, and for the evolution of enzymes", Stockbridge et al, PNAS, 2010.]<br /><br />Now looking top down, we see that pathways meet. The first modern metabolic networks originated with purine metabolism, and specifically with the gene family of the P-loop-containing ATP hydrolase fold. ["The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture", Caetano-Anollés et al. PNAS, 2007; "Rapid evolutionary innovation during an Archaean genetic expansion", David et al, Nature, 2010.]<br /><br />That is, ATP sits at the intersection between a cooling and/or hydrothermal vent active Earth premetabolism and nucleotide protometabolism. (Which compound seems to later have been exaptated by modern proteinous metabolic genes as coenzyme/energy currency.) Minimum change of traits picks ATP use before RNA evolution<br /><br />Note that this is an (informal) test of a phylogenetic pathway. Abiogenesis is actually slightly testable today as far as I can see.<br /><br />To solve the new chicken-and-egg problem between RNA and coenzymes in metabolism, it turns out ATP, CoA et cetera coenzyme's synthesis can be easily RNA-catalyzed by polyphosphate activation. ["RNA-Catalyzed CoA, NAD and FAD Synthesis from Phosphopantetheine, NMN, and FMN", Huang et al, Biochem 2000.] Finally there is also recent implications of selection of RNA in its enhanced enzymatic capability in the presence of iron under anoxic conditions, as on the primeval Earth.Torbjörn Larssonhttps://www.blogger.com/profile/13304729731231255545noreply@blogger.com