Is Abiogenesis a fact?

Hello, this is my first post on these boards. I'm a retired biologist who is excessively bothered by this question: Why is life so difficult to explain? For all we know life was sneezed into the universe through the nostrils of God, because we simply do not know where it came from. And for that reason we do not know what life is. Most biologists seem to dwell on the material structures of life and blithely assume it originated here on Earth. I think differently, even to the extent that life may not have originated in this universe. Biologists love to see their universe organized as hierarchies, as do chemists and physicists, but I am suspicious that something non-hierarchical brought life into our universe”something parallel perhaps that allows pure information to exploit certain physical analogs of "our univere" for the sake of its own extra-universal immortality.Magic and spirituality don't do much for me. But the mystery of life remains unsloved. Why? We ought to be making it from scratch by now in our labs.So, regarding this origin-of-life problem, I would like to know if anyone here makes as much fuss as I do about the origin of the genetic code. The genes themselves are "pure digital information," according to Richard Dawkins, and they exist in nature ONLY as linear arrangements of a few kinds of nucleotides on long strings of ephemeral nucleic acids. Yet the gene itself is a very durable structure in nature”we carry around hox genes that are >500 miilion years old”even though it endures as "pure information" on short-lived molecules. This non-analogous requirement of genes for the emergence of life seems especially odd to me; it shifts our attention from the material analogs of life to its digital script.Any thoughts?”HootEdited by Hoot, : common pypos

Thanks for the greeting, Matt. You wrote: Yes, you could say that. Or maybe we see more than we used to. Does it not strike you as strange that computer viruses and biological viruses operate on very simpliar principles? Or it it just popular to think so? To clarify, my frustration is over this question: Why is biological life so difficult to explain? Biologists simply do not know what it is or where it came from. So, I'm ready to take an alternative path away from the analogs and toward the digits. Warm, soupy ponds filled with bio-friendly materials are not enough to explain (to me, at least) how life took hold. I also need to know how a digital genetic language took hold. Hence I am assuming for now that my analog-digital differentiation is not just "pop culture." The way you frame is OK with me, and I may be regarded as a replication-first guy. But isn't it really more than that? Maybe what I'm after is a "replication-system-first" principle”the principle that makes a digitally "symbolic" language fall into place for biological use. I say "symbolic" because a gene configured on a DNA molecule is not stereochemical with the protein it is coded for. I would like to know how that original transmogrification took place.The chemists continue to run with ball, but something more than chemistry is going on with life. Molecules and cells come and go in relatively short order, but genes endure with a tenacity that makes them seem immortal by comparison. I count that as something important.”Hoot Mon

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The most incomprehensible thing about nature is that it is comprehensible. ”A. Einstein

Matt, you wrote: Every time I go back to Schrdinger's "What Is Life" I get the feeling that much more has been added to what he said about it in 1942. I've read several of Dyson's books, but not yet any of Hazen's. So far, for me, the best tentative explanation comes from A. G. Cairns-Smith in his argument for "genetic takeover." This involve silicon crystals acting as sticky templates for nucleotide construction, and thus for building RNA. But he has nothing to say about the origin of the coded genetic language. Not many do. Yet it seems awfully important to me.”Hoot Mon Edited by Hoot Mon, : general corrections

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The most incomprehensible thing about nature is that it is comprehensible. ”A. Einstein

Ringo, you ask: I'm unclear as to why you reject the notion of "language." Perhaps I should use "code" instead, but I doubt if you'll like that any better. If you reject the fact that genes are digital codes with a clearly decipherable "language" for building proteins, then you need to explain why tRNA is necessary to translate those coded messages into the proper selection of amino acids. Bear in mind that the codons on DNA are not stereochemical with the amino acids they select or the proteins they buiild. This lifts genes out of the mechanical role of being "blueprints" for proteins and places them in a role of codified prescriptions. To me, and to a lot of geneticists (e.g. Hartl) and evolutionary biologists (e.g., Dawkin), genes are "pure digital information."”Hoot Mon

Ringo, you ask: What I'm saying is that the molecular bonding sites of codons (triplets of digital nucleotides) on coded DNA are not stereochemical with the proteins they specify, meaning that they don't line up in any mechanical way that allows a protein to be built directly from its gene. Instead, messenger RNA (mRNA) must translate the genetic code and deliver it to transfer RNA (tRNA) to inform it on how to make a stereochemical configuration that will capture the right amino acids and put them in the right order. Ribosomes host of this process in eukaryotes.”Hoot Mon

Ringo, you asked: No, it's not a case of a tool building a tool building a tool. There actually are genetic instructions coded on DNA that specify the sequence of amino acids needed to make a specific protein. A language is involved beyond the tools you prefer. That seems clear enough to me.Suppose, if you will, that genes were never discovered because they simply didn't exist and play no part in expaining biological life. Suppose instead that the proteins of life are made entirely by mechanical processes”"a tool building a tool building a tool." Life and its evolution, under this scenario, would have been an enterprise of macromolecules building more macromolecules, all neatly contained inside cells like a Tinker Toy set replicating itself somehow using unknown laws self-organization.Well, life didn't happen that way. Life needs a non-mechanical code with a highly specific language. Obviously, genes exist in nature to inform, not to machine, the proteins of life. Proteins are very difficult to build without genes, No webpage found at provided URL: but it was done recently in the lab, proving that proteins can be built mechanically. Now that's a case of a tool building a tool building a tool. Add to that the prions, which are proteins that can produce more proteins without the need for genes. It is usually quite a destructive process, though”Mad Cow disease demonstrates that. So there are at least two examples of how proteins can be made mechanically.Let the living cell have all the proetins it needs to stay alive, but take away its genes and see how long it lives. Life is more than a box of tools. It comes with an instruction manual that is as easy to read as a comic strip. That's because there are only 64 words in its language.”Hoot Mon

Ringo, you wrote: Communication between the gene on the chromosome and tRNA in the ribosome. And I can make it even more troubling for you. Francis Crick coined the term "central dogma" to insist that a genetic message is communicated only from DNA/RNA to the protein and never in the opposite direction. Yes, this nature of genetic communication does rely on a language. If you care to look at it this way, you could even say that those genetic instructions are "channeled" by messenger RNA.”Hoot Mon

Ringo, re: It certainly is a mechanical process, but it is still carrying genetic information forward.”Hoot Mon

Chiropter, you wrote: Absolutely none, only the exercising of a metaphor.”Hoot Mon

Chiropter, you wrote: Would you go with "operating system"”you know, the software analogy? These metaphors are impossible to avoid. They are as bad to science as they are good.”Hoot Mon