RNA/pre-RNA world and open thermodynamic systems

[valich]

Most evolutionists agree to consider that our present RNA/DNA/protein world has originated from a simpler world in which RNA played both the role of catalyst and genetic material. Recent findings from structural studies and comparative genomics now allow to get a clearer picture of this transition. These data suggest that evolution occurred in several steps, first from an RNA to an RNA/protein world (defining two ages of the RNA world) and finally to the present world based on DNA. The DNA world itself probably originated in two steps, first the U-DNA world, following the invention of ribonucleotide reductase, and later on the T-DNA world, with the independent invention of at least two thymidylate synthases. Recently, several authors have suggested that evolution from the RNA world up to the Last Universal Cellular Ancestor (LUCA) could have occurred before the invention of cells...[or]...evolution of the RNA world taken place in a framework of competing cells and viruses.

"The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells," by Patrick Forterre; Biochimie, Vol. 87, Issues 9-10, 2005, pp793-803.

The RNA world (4.2-3.8 bya) led to the DNA/protein world (3.8-3.75 bya), yet evidence of cyanobacteria from fossils uncovered from Western Australia date back to 3.86 bya.

I argue for the existence of a pre-RNA world where nuceleotides were catalyzed into polynucleotides, yielding RNA ribozymes capable of self-replication leading to complementary copies and a growing living population. In other words, the entire diversity of life on Earth descended from replicating polynucleotides that formed during the pre-RNA world on Earth over four billion years ago: a revolutionary transition in evolutionary thought and in the current hypothesized time period for the origin of life on Earth.

 

[CharonZ]

I argue for the existence of a pre-RNA world where nuceleotides were catalyzed into polynucleotides, yielding RNA ribozymes capable of self-replication leading to complementary copies and a growing living population.

I don't get what you are saying. If you argue for ribozymes as early enzymes you are in the RNA world already. How can a world acting on RNA as a basis be a pre-RNA world? A pre-RNA world (of which even less hypotheses are around than for the RNA-world) clearly existed before RNA appeared (wouldn't make much sense otherwise, eh?

The only thing that may be argued (and that was what Forterre was in assuming) is whether cellularisation already occred in the RNA-world or not. At this point I am inclined to follow Forterre's reasoning, however the data is far from conclusive.
But this does not appear to be your main point.
Other than that there are some arguing for instance for a PNA world (peptide-NA) mostly due the inefficiency of prebiotic ribose (and desoxyribose) synthesis and comparative instability of RNA. This might be a precursor to the RNA world.

 

[valich]

This would be the origin of the RNA world. I'm looking at Leslie E. Orgel's theory of self-organizing self-replicating metabolic systems. Did you read my last post in "What is the Origin of Life on Earth"? The pre-RNA world has to involve a programming control mechanism that is not genetic, probably involving mycoplasms or thermoplasms, siimilar to an archaic type of citric acid cycle or reverse citric acid cycle. This theme keeps coming up:

Formaldehyde is one of the most common organic compounds in the universe. It was also present in the atmosphere of primordial Earth. Moreover, it was not only present, but was continuously being produced from atmospheric methane by ultraviolet solar radiation, etc....One molecule of glyco aldehyde is formed from two molecules of formaldehyde, and this reaction, although very slow, does take place [ribose phosphate is also generated in this reaction: Albert Eschenmoser's experiments, cited in "Helvetia Chimica Activa," Muller et al, 73, 1990, pp.1410-68]. The further reactions of glyco aldehyde with formaldehyde are sufficiently fast that it is likely that the formose reaction must have been one of the most frequent chemical processes on primordial Earth....Ribose is also produced in the formose reaction, and is the compound to which the nucleotide base, serving as a letter mark, is coupled in ribonucleic acids.

"The Principles of Life," by Tibor Ganti, 2003, p.28-9.

 

[CharonZ]

Ack that's it. I withdraw myself from your posts also. Just a few last pointers, though.
If you argue for a pre-RNA world you are talking about the road to the RNA/DNA world. Let's take this as basis. In your first post you argue that in a pre-RNA world Ribozymes are the effectors. And that can't be as it requires the occurence of RNA already and can't by definition not be *pre*-RNA.

Then the quote in your second post does not refer to self-replicating systems or even metabolism, as you seem to be believe (as for metabolic functions a cellular system is needed, which likely arose much later). What is typical however, is that the quote does not in any way connect with your statements.

The pre-RNA world has to involve a programming control mechanism that is not genetic, probably involving mycoplasms or thermoplasms, siimilar to an archaic type of citric acid cycle or reverse citric acid cycle.

Here you appearently juggle with a lot of words you actually don't understand.
1. programming control mechanisms: actually I don't have an idea what you mean, but early systems are not likely "programmed" or controlled for that manner as necessary elements are most likely lacking (that is proteins for instance). If anything there will be regulation by the effector molecules themselves (e.g. ribozymes, in the RNA-world and later). But clearly not in the pre-RNA world.

2.myco- and thermoplasms are prokaryotes, coming on much much much later in the DNA/Protein world. Looks like you added them just cause you like the sound of the names.

3. TCA-cycle needs enzymes. Proteins that is. It is quite a complex pathway and can only have developed after the DNA/Protein-World and after cellularisation. I suppose you included it cause it was the first thing after you googled "metabolism"?

Listen, while your topics are quite interesting, I can't put up with the random arguements you put up. I have no idea where you scavange them from (scraps from papers, net, whatever), but they are neither coherent, nor correct in any way. I understand that for laymen some concepts are not easy to grasp, but usually I expect them either to ask the right questions, or at least put up a coherent definition of what they think the stuff means and proceed from there. It is simply emberassing if you use terms with no connection whatsoever with the quotes you submit.

 

[valich]

I'm digging into the information and researching it. What are you suggesting? That I just give up and jump in a lake somewhere? I was hoping that you could provide some constructive input? This is a "forum," not an "Ack" chat session. I'm confiding to you where I am at with what I have found. The pre-RNA world consisted of a non-genetic programmed self-replicating metabolic sytem theat produces nucleotides that lead to the RNA-world.

 

[valich]

Perhaps I should have made the title of this thread simpler, but thermodynamics is an important concept regarding the origin of life. It's much more complex than this, bit I quote from the online encyclopedia Wikipidea:

"Biological thermodynamics may be defined as the quantitative study of the energy transductions that occur in and between living organisms, structures, and cells and of the nature and function of the chemical processes underlying these transductions.

Living cells and organisms must perform work to stay alive, to grow, and to reproduce themselves. The ability to harness energy from a variety of metabolic pathways so to channel it into biological work is a fundamental property of all living organisms.

Typical emphasis is on thermodynamic applications in biology includes the first law of thermodynamics, the second law of thermodynamics, Gibbs free energy, statistical thermodynamics, binding equilibria, reaction kinetics, and on hypotheses of the origin of life. Presently, biological thermodynamics concerns itself with the study of internal biochemical dynamics as: ATP hydrolysis, protein stability, DNA binding, membrane diffusion, enzyme kinetics, and other such essential energy controlled pathways."

 

[valich]

(that is proteins for instance). If anything there will be regulation by the effector molecules themselves (e.g. ribozymes, in the RNA-world and later). But clearly not in the pre-RNA world.

TCA-cycle needs enzymes. Proteins that is. It is quite a complex pathway and can only have developed after the DNA/Protein-World and after cellularisation.

You're counterdicting yourself: "Proteins that is. It is quite a complex pathway and can only have developed after the DNA/Protein-World."

Proteins do not need DNA! And self-replication metabolic pathways do not need cellurasation!

And we are talking abount unconventional TCA or reverse TCA-cycles. And the origin of enzymes? Not needed in a self-programmed self-replicating pre-RNA system.

You're just throwing out contradictory arguments without providing any intelligent constructive progressive leads, and I emphasize the intellectual theme: be progressive and add to the progressive nature of the thread, rather than just being "deconstructive"!