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> The usual explanation is that the "first copy" arose randomly, and then kept going. Do you believe that? I believe a variation of that. I believe that the f

by Cogito 6y ago

> The usual explanation is that the "first copy" arose randomly, and then kept going. Do you believe that? I believe a variation of that. I believe that the first copy arose through physical processes. Evoking 'randomness' is unnecessary and misleading. Do you not believe this? To my knowledge, we don't yet have a mechanism for how such a molecule came in to being (though there are ideas). We also don't have any reason to think that it must be some random single choice from a large possibility space, and we don't have any evidence at all that it could have arisen from non-physical processes (what would that even look like?).

erichocean 6y ago
This is what I mean by random: no DNA sequence is privileged over any other, and no (known) physical process produces anything but random DNA sequences (excluding, of course, copying already useful DNA sequences). DNA has about as much structure as bits on a disk (with coding for one of 20 amino acids as the "bits"). No DNA sequence is more likely than any other to exist. I think that means we need to identify strong physical processes that produce useful DNA strands; you, apparently, aren't as concerned about it. Maybe you're right, but from where I'm sitting, it's hard to imagine what those physical processes might be since the strands they must produce are extremely, unimaginably rare in practice. DNA is basically information[0], and we literally have no example of a chemical process producing valid DNA information, nor is it all obvious how such a process might work in practice. In the past, large amounts of time + equal likelihood of producing random DNA was considered sufficient to think "well, useful DNA stands could appear randomly." We now know that's extremely unlikely to the point of being effectively impossible, statistically-speaking. [0] https://www.nature.com/scitable/topicpage/dna-is-a-structure-that-encodes-biological-6493050/ https://www.nature.com/scitable/topicpage/dna-is-a-structure...
- Cogito 6y ago
  But some DNA sequences are privileged over others! The mechanisms for producing new DNA sequences involves copying existing DNA sequences. Thus, the ones that exist are privileged over the ones that do not exist (yet), and the adjacent sequences are privileged over a random sequence. > No DNA sequence is more likely than any other to exist. It is far more likely for a DNA sequence very similar to my own to exist than a random sequence. > we need to identify strong physical processes that produce useful DNA strands We have already identified those processes! We know quite well how the machinery of DNA replication works. If we care about the first DNA molecule to ever exist it's a very different question. We don't need to find a physical process that produces a modern DNA molecule from 'raw parts', rather one that takes not-quite-DNA and converts it into DNA. > it's hard to imagine what those physical processes might be since the strands they must produce are extremely, unimaginably rare in practice. Can you imagine slightly simpler DNA? Say just a bit shorter? What's the simplest molecule we might still call DNA, that is reproducing? Can we imagine machinery that would produce that? I think it's very reasonable to think such machinery could exist, even if we don't know the exact mechanisms involved. We know that RNA can self-reproduce, and also produce proteins, so it's reasonable to think that machinery to produce RNA strands could evolve to produce DNA strands (for example). The only involvement randomness has in this whole process are (relatively) rare and infrequent changes to self-replicating molecules, and (potentially) the initial formation of a self-replicating molecule. It is irrelevant how many possible DNA sequences there are, or how much information is stored within them, as we know new sequences are derived from previous ones.
  - erichocean 6y ago
    > If we care about the first DNA molecule to ever exist it's a very different question. We don't need to find a physical process that produces a modern DNA molecule from 'raw parts', rather one that takes not-quite-DNA and converts it into DNA. We haven't found that, and apparently aren't even close. We don't even have any idea what something like that might look like, or even more critically: given all the incredibly, insanely, unbelievably rare DNA sequences that exist in the world today, why is such a fundamental process capable of producing them not abundant as fuck already? Where'd it go? Why is this process even a mystery in 2020? It should be ubiquitous; in fact, all of the primordial soup mechanisms should be. Certainly that's what we expected when the theory was developed, and it hasn't panned out. Anyway, I think we've exhausted this topic. Thanks for commenting.
    - Cogito 6y ago
      > We haven't found that, and apparently aren't even close. We do have ideas! Specifically, within the RNA world hypothesis, the transition period is called the virus world [0] > given all the incredibly, insanely, unbelievably rare DNA sequences that exist in the world today, We have a good understanding of where diversity comes from, I'm not sure what point you're making here. > why is such a fundamental process not abundant as fuck already. Where'd it go? Why is this even a mystery? I don't think anyone thinks this process need be 'fundemental', though it definitely is pivotal. It only really needed to happen once, and then DNA was off reproducing and spreading by itself. That said, it looks like viruses converting RNA to DNA could still be happening today. In general, we don't expect novel self-reproducing molecules to arise today, because they are out-competed by existing self-replicating molecules. In a world where nothing is replicating the first replicator is king. In today's world a brand new replicator is food for something else. > Maybe it's possible that your romantic view of how this all happens (pseudo-Darwinian circa 2020) isn't telling the whole story? I don't think I, or anyone else really, is claiming to tell the whole story - just that we have good reason to believe this came about through physical processes, and no evidence to believe... well I'm not sure what else there could be. What are you proposing? [0] https://en.wikipedia.org/wiki/RNA_world#Evolution_of_DNA https://en.wikipedia.org/wiki/RNA_world#Evolution_of_DNA

by Cogito 6y ago

erichocean 6y ago

This is what I mean by random: no DNA sequence is privileged over any other, and no (known) physical process produces anything but random DNA sequences (excluding, of course, copying already useful DNA sequences). DNA has about as much structure as bits on a disk (with coding for one of 20 amino acids as the "bits"). No DNA sequence is more likely than any other to exist. I think that means we need to identify strong physical processes that produce useful DNA strands; you, apparently, aren't as concerned about it. Maybe you're right, but from where I'm sitting, it's hard to imagine what those physical processes might be since the strands they must produce are extremely, unimaginably rare in practice. DNA is basically information[0], and we literally have no example of a chemical process producing valid DNA information, nor is it all obvious how such a process might work in practice. In the past, large amounts of time + equal likelihood of producing random DNA was considered sufficient to think "well, useful DNA stands could appear randomly." We now know that's extremely unlikely to the point of being effectively impossible, statistically-speaking. [0] https://www.nature.com/scitable/topicpage/dna-is-a-structure-that-encodes-biological-6493050/ https://www.nature.com/scitable/topicpage/dna-is-a-structure...

Cogito 6y ago
But some DNA sequences are privileged over others! The mechanisms for producing new DNA sequences involves copying existing DNA sequences. Thus, the ones that exist are privileged over the ones that do not exist (yet), and the adjacent sequences are privileged over a random sequence. > No DNA sequence is more likely than any other to exist. It is far more likely for a DNA sequence very similar to my own to exist than a random sequence. > we need to identify strong physical processes that produce useful DNA strands We have already identified those processes! We know quite well how the machinery of DNA replication works. If we care about the first DNA molecule to ever exist it's a very different question. We don't need to find a physical process that produces a modern DNA molecule from 'raw parts', rather one that takes not-quite-DNA and converts it into DNA. > it's hard to imagine what those physical processes might be since the strands they must produce are extremely, unimaginably rare in practice. Can you imagine slightly simpler DNA? Say just a bit shorter? What's the simplest molecule we might still call DNA, that is reproducing? Can we imagine machinery that would produce that? I think it's very reasonable to think such machinery could exist, even if we don't know the exact mechanisms involved. We know that RNA can self-reproduce, and also produce proteins, so it's reasonable to think that machinery to produce RNA strands could evolve to produce DNA strands (for example). The only involvement randomness has in this whole process are (relatively) rare and infrequent changes to self-replicating molecules, and (potentially) the initial formation of a self-replicating molecule. It is irrelevant how many possible DNA sequences there are, or how much information is stored within them, as we know new sequences are derived from previous ones.
- erichocean 6y ago
  > If we care about the first DNA molecule to ever exist it's a very different question. We don't need to find a physical process that produces a modern DNA molecule from 'raw parts', rather one that takes not-quite-DNA and converts it into DNA. We haven't found that, and apparently aren't even close. We don't even have any idea what something like that might look like, or even more critically: given all the incredibly, insanely, unbelievably rare DNA sequences that exist in the world today, why is such a fundamental process capable of producing them not abundant as fuck already? Where'd it go? Why is this process even a mystery in 2020? It should be ubiquitous; in fact, all of the primordial soup mechanisms should be. Certainly that's what we expected when the theory was developed, and it hasn't panned out. Anyway, I think we've exhausted this topic. Thanks for commenting.
  - Cogito 6y ago
    > We haven't found that, and apparently aren't even close. We do have ideas! Specifically, within the RNA world hypothesis, the transition period is called the virus world [0] > given all the incredibly, insanely, unbelievably rare DNA sequences that exist in the world today, We have a good understanding of where diversity comes from, I'm not sure what point you're making here. > why is such a fundamental process not abundant as fuck already. Where'd it go? Why is this even a mystery? I don't think anyone thinks this process need be 'fundemental', though it definitely is pivotal. It only really needed to happen once, and then DNA was off reproducing and spreading by itself. That said, it looks like viruses converting RNA to DNA could still be happening today. In general, we don't expect novel self-reproducing molecules to arise today, because they are out-competed by existing self-replicating molecules. In a world where nothing is replicating the first replicator is king. In today's world a brand new replicator is food for something else. > Maybe it's possible that your romantic view of how this all happens (pseudo-Darwinian circa 2020) isn't telling the whole story? I don't think I, or anyone else really, is claiming to tell the whole story - just that we have good reason to believe this came about through physical processes, and no evidence to believe... well I'm not sure what else there could be. What are you proposing? [0] https://en.wikipedia.org/wiki/RNA_world#Evolution_of_DNA https://en.wikipedia.org/wiki/RNA_world#Evolution_of_DNA