scrappy

If scientists ever discover biological traits encoded on molecules other than nucleic acids, especially on alphabetti spaghetti, this discovery would reset the calendar! It would be the biggest WOW! you ever heard of. Well, yes, I can conceived of a lot of things. Give me something worth conceiving. Merged post follows: Consecutive posts merged I don't dispute your claim that "life" can happen without the genetic code. I'm only arguing that biological life can't happen without the genetic code. There could be no natural selection for uncoded "life," no way to propagate heritable generations. This is true and supported, for example, by A. G. Cairns-Smith in his book Seven Clues to the Origin of Life (1985, p. 114): "Genetic information is the only thing that can evolve through natural selection because it is the only thing that passes between generations over the long term." (That is his "First Clue," btw)

Then I don’t suppose you rule out pink unicorns, either. What is truly remarkable here are not these rare exceptions to the universal genetic code, but the fact that there is such a code. I’d say the universal genetic code is about as universal as you can get in biology. Well, maybe something like that. But I would see it more as stereochemistry starting the process and the frozen accident responsible for “distilling” the genetic language—in other words, abiogenesis happened when the genetic code kicked in. Check out A. G. Cairns-Smith’ s Genetic Takeover (1982).

...but all kingdoms are of the same life form. In truth, there is only one kind of life: life that encodes its genetic information on nucleic acids. Show me a life form, present or past, that uses or used different molecules to encode a different genetic information. I don't care how "dramatic" those variations appear to you, they are merely variations off the same theme. Prokaryotes and eukaryotes are of the same life form and they use a universal genetic code.

To me, at least, the emergence of the genetic code was the necessary trick nature had to pull off to make abiogenesis happen. My driving question has been: Why is the genetic code universal? Why is there only one kind of life? The answer, I think, must connected somehow to abiogenesis (and not to the capricious idea that the first life form ate up all of its competitors.). So, it seems relevant here in this discussion on the various theories on abiogensis to differentiate “The Stereochemical Theory” from “The Frozen Accident Theory,” and do this with respect to the evolution of the genetic code. I rather like the way Francis Crick did this in his 1968 paper The Origin of the Genetic Code (J. Mol. Biol. 38, pp. 369-370): Since then there has been a lot of interesting discussion on the molecular aspects of abiogensis, but, IMO, not enough on the digitally coded aspects of it.

Sure, if they had genes just about anything was possible (read Dawkins’ Unweaving the Rainbow). What would be impossible is for your fishes with scissor-like jaws to exist without genes. But you’re confusing “alive” with biological life. Even a virus would not be alive by your wiki definition, but it still has genes. I still maintain that biological life didn’t start until the genes showed up. If you know of any existing or historical forms of biological life that lacked genes please post you evidence. But remember that genes require a digital code with an alphabet as a format for their information storage system. As far as biological life on Earth is concerned there is only one life form. If you think there were other biological life forms before abiogenesis you need to support your hypothesis with something more than a statement like “you cannot simply assume that what exists today is the only possibility.” You want me to prove a negative when you can’t even prove a positive? We’ve been all over this. If you want to call a prebiont a biological life form then go ahead and be wrong. Show me a peer-reviewed paper that claims that a single molecule can be a biological organism.

Are you saying that were organisms in the past that didn’t require genes? If so, what support do you have for this? We’re talking about living organisms. I can’t imagine a living organism without genes, digital genes. But I might agree that dead organisms don’t have any. Such as? And how would you know? You’re going to have come up with something pretty good here to convince me that there ever were any living organisms that lacked genes. Merged post follows: Consecutive posts merged "AA" is a common abbreviation for "amino acid."

Would it be fair to say that digital a "message" requires a code for storing the information, while an analog "message" does not? Well, extant life, as we know it, requires codons, comprising 3 bits of information (a 4^3 coding geometry). This structure enables a genetic alphabet, and thus a language. If you are saying that this coding geometry evolved from a simpler one that engaged stereochemistry instead of digit code I can go along with this, partly. But I'm puzzled about how any early coding geometry could have worked if it was entirely stereochemical. I could see maybe a 2-bit "codon" at first that functioned stereochemically to inform the union of two AAs to make a primitive polypeptide. What I can't see, though, is how that "codon" carries any digital information in the form of a code with a geometric alphabet. Where did that come from?

I think that’s possible, as I said in post #46: Your hypothetical scenario doesn’t seem too far-fetched to me; it’s reasonable to assume that the extant digital genetic code had stereochemical precursors. But I still don’t see how you can call any of those stereochemical precursors “genes” unless there was a digital genetic language for encoding the genetic information. What we are talking about here, IMO, is the key aspect of abiogenesis: genetic digitization. I'm saying that abiogenesis cannot be effectively understood until we know more about how a genetic language evolved. There are several good hypotheses, and all of them are of interest to me. As one astute poster here already said: understanding abiogenesis is more challenging than understanding the Big Bang. This is why I'm still suspicious of a "frozen accident." In truth, we still don't know for sure that abiogenesis was NOT a "one off." And we still don't even know if it happened here on Earth.

Ribonucleic acid (RNA) is a type of molecule that consists of a long chain of nucleotide units. it is the exact sequence of nucleotides that give the ribozyme its properties. I’m fine with that. But you haven’t yet explained how a prebiotic RNA’s nucleotides could assemble as genetic information before there was a genetic code.

Are you saying that ribozymes had genes? Even before a genetic language was invented? Wow! I'd be very interested in learning about them. Merged post follows: Consecutive posts merged This is crazy! Either you haven't been pay attention or you don't know what you're talking about.

What a shallow accusation! So, what meaning do you think it has? I'm talking about biological life. Perhaps prebiotic life forms managed their structural/informational tasks thru stereochemistry. I don't reject that. But when abiogenesis managed to whelp a living organism it had to have a genetic code. I know of no organism, present or past, that existed without genes. This is purely true belief on your part. What do you have, other than hopeful speculation, to back it up. No one here ever said it was. Who said anything about a computer? I didn't. But nobody at least not me, claimed any such thing.

Ah, you're not serious are you? If so, you don't understand what an organisms is. What genetic information? No, not with a coded language. I'm going to leave it here. Good luck with your metaphors. As Schrödinger pointed out in his famous essay What Is Life?: "The price of a metaphor is constant vigilance."

I think that’s possible. But before anything digital could have worked there had to be a genetic language with a digital alphabet. Otherwise there would be nothing but stereochemistry to propagate information. I certainly don’t rule that out. Yes, from stereochemistry to digital information. I agree. Most of what you say here seems reasonable. Still, I don’t see biological life emerging without the code. No, not if you include evolution as a criterion for an organism. Organisms do not evolve; only populations of organisms evolve. But a motor doesn’t need to be an internal cumbistion engine. Oxford Dict., for example, includes this definition of a motor: “a source of power, energy, or motive force : hormones are the motor of the sexual functions.”

Don't you usually need an organism to have biological life? Yes, and it's important. No person educated in biology should equate a gene with a blueprint. This is a serious misrepresentation. A gene is digital code; it's pure information, just as Dawkins said.

There was? Please explain how. Now you're catching on, with one critical exception: there was no digital code without a digital alphabet. Of course. I'm asking how it evolved from stereochemistry to digital code. And why you call the RNA world "biological life" is beyond me. How do you define "biological life"?

Well, OK, if you have to be clinical about it, but it looked like more fun than the Swine Flu.

Is dancing contagious? This pandemic happened at The Gorge in WA state:

But is it digital information? For that to be the case there had to be a digital language with a digital alphabet. What I'm talking about is the way proteins are informed. My only point here is the need to take notice that nature did a very remarkable thing when it stored the structural information to make a protein on a nucleic acid molecule using a digital language. That's all I'm saying. Biological life didn't show up until that happened. Yes, maybe there were protogenes in the RNA world that acted stereochemically to make proteins. Maybe is was a gradual process, as some have argued, or maybe it was a frozen accident, a mysterious emergent property that still defies understanding. But we wouldn't be here talking about it if nature didn't allow such a magnificent emergent property as biological life. There was no magic in it, no godly activities. It's just that we don't know enough yet about biological life to figure out abiogenesis. I still think the RNA world is our best theory for abiogenesis. To me, it came with the emergence of a digital genetic language, something that is not entirely stereochemical. Instead, it has a geometric logic with a 4^3 structure that ushered in a whole new venue for molecular affairs.

I couldn't agree more. This statement by lucaspa astonishes me: I think he must have been using the term "purpose" metaphorically, which of course is teleological. Perhaps the word "function" would have been a better coice.

I’m still waiting to learn how (from your post #31): “the rna world came first and rna is clearly digital.” Yes, I think it came first, but I'm not at all sure how it was digital. I'll try to answer your question anyway. For the RNA world to be digital it would need to have a digital genetic alphabet, comprising nucleotides (A,G,C and T/U) as bits and codons as bytes. From there an RNA analog could carry the digital information necessary to make a protein to a ribozyme or ribosome, if there had been a genetic language to transcribe and translate. Nascent biological life, as we know, required a digital language to synthesize proteins, which was not present in the RNA world, so far as we know. As such, the real biological fun didn't start until the digits showed up.

Sorry, but a gene is not a "blueprint" of a protein, not literally, not metaphorically, not even allegorically. The analog world. It is? How? But you're the one who brought it up. ...and Hamlet said: "There are more things in heaven and earth, Horatio, than are dreamt of in your philosophy."

I’ll be very interested in learning how prebiotic chemicals in the RNA world were “definitely digital.” To say that a gene is a “blueprint” of a protein is a huge misnomer. A blueprint: bears an analog representation of the structure to be built. A blueprint is nothing like what a gene is; indeed it’s even a very poor metaphor for a gene. Instead, a gene is purely digital information. To wit: From R. Dawkins’ River Out Of Eden (1995, p. 19): This is a legitimate scientific debate. Just calling your opponent a troll doesn’t win you any points. I could make the same claim about you and be just as wrong.

lucaspa, Thanks for that ref. by Wolf and Koonin. They come mighty close to addressing the issue of “poof,” but they call it a “frozen accident.” I think they are asking the very same question I’m asking: How do get from stereochemistry to digital code, especially one with a 4^3 geometry, in a natural system? Maybe it was built up slowly and there was no frozen accident. Maybe it was an emergent property that came on incrementally. That seems to be the prevailing opinion in the field of abiogenesis hypotheses. I’m certainly not against it. I just think it assumes too much, at least without challenge, to count on such an extraordinary emergent property so blithely. My biggest problem is trying to understand how nature can reduce its physical analogues to digital information, which involved inventing a genetic alphabet with an elegant geometry. It must have happened somehow, of course, and maybe slowly rather than in a poof. But I know of no other occasion in natural history where such an incredible thing occurred. From Wolf and Koonin: This gets things going in the right direction, I think. Thanks for helping to educate me on what’s happening. “Selection for ribozymes” definitely interests me. Not bad! Well, I like this all right. "Families of codons"? (I would have guessed adenine instead.) Where do you think the stereochemistry ended and the digital alphabet began? There was a huge emergent property in there somewhere. Good luck with your work; it looks quite interesting. We’re both in the business of predicting emergent properties, and that’s a very risky business indeed.

Thank you for that explanation, iNow. I do understand what you are saying. But the issue, as it is being resolved, ultimately concerns the constitutionality of "gay marriage." That's really all that's important here. There rest is politics and whose biases prevail in the end. I'm sure glad science doesn't work that way. (Or does it?)

Watching the news coverage on this issue leaves me in a quandary. Those who argue for “gay marriage” do so on the grounds that such a marriage is protected by the CA constitution. And then when the SCOCA rules that Prop. 8 is not unconstitutional those who oppose it are all pissed off. But why? Don’t they now have their legal answer after their day in court? Are they interested in constitutional law? Or are they interested in self-serving politics? The matter has been rightfully settled: Prop. 8 prevailed and if gays want to get “married’ they can go to Iowa. Sorry, but that’s just the way constitutional governments work.