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That's an interesting point, thanks. Please pardon some ignorant questioning. How far down does this apply? E.g., do amino acids come basically for free in the

That's an interesting point, thanks. Please pardon some ignorant questioning. How far down does this apply? E.g., do amino acids come basically for free in the same way? If not, what's the bootstrapping process like, and how random is it? How many steps do you have to take from self replication to functional cells? That chemical reactions are quite deterministic makes sense to me, but I don't quite understand how one gets from chemistry to biology.

yamrzou 5y ago
Good question, I wonder the same. If I may add, how far does this apply when getting from biology to consciousness, i.e from functional cells to general intelligence, as seen in living organisms and humans?
carbonguy 5y ago
I'm not the parent commenter, but I studied biochemistry and find abiogenesis to be a particularly fascinating topic, so I'll take a crack at answering your questions: > How far down does this apply? E.g., do amino acids come basically for free in the same way? Broadly, I think it is fair to say that many molecules that we associate with biological processes (e.g. amino acids, nucleotides, simple alcohols, etc.) do come "for free" in the sense that there are known pathways for these molecules to be produced in the absence of living organisms. The Miller-Urey experiment is probably the most well-known proof of concept of this idea, though it's debated how well the experimental conditions correspond with "the real world." > ... [W]hat's the bootstrapping process like, and how random is it? If I understand you correctly, here you're asking "what does it take to get from prebiotic organic molecules to living organisms?" And that is a fascinating question that has, to my mind, several possible answers, though ultimately I think the answer is "we don't know." One very suggestive paper I read describes the bootstrapping process as a "surface metabolism" [1] that succeeds through several epochs before eventually producing free-floating lipid-membrane-enclosed micelles containing complex organic molecules and a rudimentary metabolism - i.e. protocells. However, the IIRC paper falls short of explaining how these protocells can then start to independently reproduce. One hypothesis I recall from David Deamer is that hydration/dehydration cycles in shallow pools promote complex organization of simpler protomolecules into structures we typically associate with living organisms [2]; in other words, given the protobiomolecules mentioned above, certain environmental conditions encourage [proto]cell formation. So, to answer your question (I think), there are many good candidates for the "bootstrapping process" and while there is randomness involved, it turns out that certain environmental conditions that were present on the early Earth (as well as currently!) tended to promote complex molecular formation. > How many steps do you have to take from self replication to functional cells? Not many; I would say that if you have something that looks like a cell and reproduces itself, it's a "functional cell." Personally, I think from that point we are at an, if not the, "origin of life," and understand in broad strokes "what happens next" - ever-more-refined single-celled organisms, multi-cell aggregates becoming "true" multi-celled organisms, and so on. Let me know if you're curious about any other aspect of this topic and I'll try to provide more info! [1] https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC373159/ https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC373159/ [2] https://www.liebertpub.com/doi/10.1089/ast.2019.2045 https://www.liebertpub.com/doi/10.1089/ast.2019.2045
- bediger4000 5y ago
  I read a paper somewhere along the line that claimed that DNA itself shows evidence of having evolved - the 3-pair codons that have some error-correcting capacity evolved from single-pair codons. When I write that down it seems wrong, but that's what I remember. Can't recover the paper, however so you don't need to believe me.
  - memling 5y ago
    > I read a paper somewhere along the line that claimed that DNA itself shows evidence of having evolved - the 3-pair codons that have some error-correcting capacity evolved from single-pair codons. When I write that down it seems wrong, but that's what I remember. Can't recover the paper, however so you don't need to believe me. Thinking about this a little bit, what are likely traces that we could even identify in the evolution of these building blocks? If, hypothetically, single-codon DNA went "extinct," is it possible we could even find evidence of it?
- memling 5y ago
  These are good comments and resources; thanks! I'm a bit out of my depth in the papers, but reading through them gradually and trying to absorb them. Again, please bear with me--this is not an area in which I have much experience. A couple quick follow-ups on your thoughts, though: > Broadly, I think it is fair to say that many molecules that we associate with biological processes (e.g. amino acids, nucleotides, simple alcohols, etc.) do come "for free" in the sense that there are known pathways for these molecules to be produced in the absence of living organisms. How likely are the conditions for such pathways to obtain? At a minimum it seems like you need the constituent elements to be collocated and for appropriate environmental conditions to occur. In order- or structure-sensitive reactions, is it true that further conditions need to be met? (Unless the argument advanced is that these challenges are addressed by a (somewhat?) deterministic process that results in appropriate chirality of molecules?) Is there a substrate or solvent in which these reactions are postulated to have occurred? The challenges with the primordial soup hypothesis, as described in the first paper, are fairly well known to me...but the reactions have to take place in some kind of an environment. The obvious solvent is water, or you could imagine some other viscous substrate (like clay?); are there other candidates? Or are these questions just terribly ignorant? > > How many steps do you have to take from self replication to functional cells? > Not many; I would say that if you have something that looks like a cell and reproduces itself, it's a "functional cell." How would we measure what "looks like" means? Through functional analysis (like metabolic action?) or constituent parts (e.g., we differentiate eukaryotes and prokaryotes but consider both cells--is there something distinct from prokaryotes that we would also consider a cell?)? > Let me know if you're curious about any other aspect of this topic and I'll try to provide more info! I'm super interested. Do you have a set of base references that are your go-to sources for reacquainting yourself with these things? I'd love to keep reading.
bediger4000 5y ago
I'm not an expert - I just follow this as an amateur, and I don't know those answers. Amino acids seem to form fairly often - they find (spectroscopic) evidence of them in deep space: https://www.newscientist.com/article/dn2558-amino-acid-found-in-deep-space/ https://www.newscientist.com/article/dn2558-amino-acid-found... and in the clouds of Venus: https://www.sciencealert.com/astronomers-report-they-ve-detected-an-amino-acid-found-in-dna-in-venus-atmosphere https://www.sciencealert.com/astronomers-report-they-ve-dete... There's also the famed Mill-Urey experiments. There's quite a bit of thought and argument about that "bootstrapping". Little cell-sized bags of lipids form pretty readily, but the problem is how to get the information (DNA) and metabolism into the cell-sized bags. You can google for "metabolism first hypothesis" and "rna world" for 2 different ideas about how that might have happened. PBS Eons has a video about the "Last Universal Common Ancestor" that might be of help: https://www.youtube.com/watch?v=pk213XSSktQ&t=0s https://www.youtube.com/watch?v=pk213XSSktQ&t=0s

yamrzou 5y ago

Good question, I wonder the same. If I may add, how far does this apply when getting from biology to consciousness, i.e from functional cells to general intelligence, as seen in living organisms and humans?

carbonguy 5y ago

I'm not the parent commenter, but I studied biochemistry and find abiogenesis to be a particularly fascinating topic, so I'll take a crack at answering your questions: > How far down does this apply? E.g., do amino acids come basically for free in the same way? Broadly, I think it is fair to say that many molecules that we associate with biological processes (e.g. amino acids, nucleotides, simple alcohols, etc.) do come "for free" in the sense that there are known pathways for these molecules to be produced in the absence of living organisms. The Miller-Urey experiment is probably the most well-known proof of concept of this idea, though it's debated how well the experimental conditions correspond with "the real world." > ... [W]hat's the bootstrapping process like, and how random is it? If I understand you correctly, here you're asking "what does it take to get from prebiotic organic molecules to living organisms?" And that is a fascinating question that has, to my mind, several possible answers, though ultimately I think the answer is "we don't know." One very suggestive paper I read describes the bootstrapping process as a "surface metabolism" [1] that succeeds through several epochs before eventually producing free-floating lipid-membrane-enclosed micelles containing complex organic molecules and a rudimentary metabolism - i.e. protocells. However, the IIRC paper falls short of explaining how these protocells can then start to independently reproduce. One hypothesis I recall from David Deamer is that hydration/dehydration cycles in shallow pools promote complex organization of simpler protomolecules into structures we typically associate with living organisms [2]; in other words, given the protobiomolecules mentioned above, certain environmental conditions encourage [proto]cell formation. So, to answer your question (I think), there are many good candidates for the "bootstrapping process" and while there is randomness involved, it turns out that certain environmental conditions that were present on the early Earth (as well as currently!) tended to promote complex molecular formation. > How many steps do you have to take from self replication to functional cells? Not many; I would say that if you have something that looks like a cell and reproduces itself, it's a "functional cell." Personally, I think from that point we are at an, if not the, "origin of life," and understand in broad strokes "what happens next" - ever-more-refined single-celled organisms, multi-cell aggregates becoming "true" multi-celled organisms, and so on. Let me know if you're curious about any other aspect of this topic and I'll try to provide more info! [1] https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC373159/ https://www.ncbi.nlm.nih.gov/labs/pmc/articles/PMC373159/ [2] https://www.liebertpub.com/doi/10.1089/ast.2019.2045 https://www.liebertpub.com/doi/10.1089/ast.2019.2045

bediger4000 5y ago
I read a paper somewhere along the line that claimed that DNA itself shows evidence of having evolved - the 3-pair codons that have some error-correcting capacity evolved from single-pair codons. When I write that down it seems wrong, but that's what I remember. Can't recover the paper, however so you don't need to believe me.
- memling 5y ago
  > I read a paper somewhere along the line that claimed that DNA itself shows evidence of having evolved - the 3-pair codons that have some error-correcting capacity evolved from single-pair codons. When I write that down it seems wrong, but that's what I remember. Can't recover the paper, however so you don't need to believe me. Thinking about this a little bit, what are likely traces that we could even identify in the evolution of these building blocks? If, hypothetically, single-codon DNA went "extinct," is it possible we could even find evidence of it?
memling 5y ago
These are good comments and resources; thanks! I'm a bit out of my depth in the papers, but reading through them gradually and trying to absorb them. Again, please bear with me--this is not an area in which I have much experience. A couple quick follow-ups on your thoughts, though: > Broadly, I think it is fair to say that many molecules that we associate with biological processes (e.g. amino acids, nucleotides, simple alcohols, etc.) do come "for free" in the sense that there are known pathways for these molecules to be produced in the absence of living organisms. How likely are the conditions for such pathways to obtain? At a minimum it seems like you need the constituent elements to be collocated and for appropriate environmental conditions to occur. In order- or structure-sensitive reactions, is it true that further conditions need to be met? (Unless the argument advanced is that these challenges are addressed by a (somewhat?) deterministic process that results in appropriate chirality of molecules?) Is there a substrate or solvent in which these reactions are postulated to have occurred? The challenges with the primordial soup hypothesis, as described in the first paper, are fairly well known to me...but the reactions have to take place in some kind of an environment. The obvious solvent is water, or you could imagine some other viscous substrate (like clay?); are there other candidates? Or are these questions just terribly ignorant? > > How many steps do you have to take from self replication to functional cells? > Not many; I would say that if you have something that looks like a cell and reproduces itself, it's a "functional cell." How would we measure what "looks like" means? Through functional analysis (like metabolic action?) or constituent parts (e.g., we differentiate eukaryotes and prokaryotes but consider both cells--is there something distinct from prokaryotes that we would also consider a cell?)? > Let me know if you're curious about any other aspect of this topic and I'll try to provide more info! I'm super interested. Do you have a set of base references that are your go-to sources for reacquainting yourself with these things? I'd love to keep reading.

bediger4000 5y ago

I'm not an expert - I just follow this as an amateur, and I don't know those answers. Amino acids seem to form fairly often - they find (spectroscopic) evidence of them in deep space: https://www.newscientist.com/article/dn2558-amino-acid-found-in-deep-space/ https://www.newscientist.com/article/dn2558-amino-acid-found... and in the clouds of Venus: https://www.sciencealert.com/astronomers-report-they-ve-detected-an-amino-acid-found-in-dna-in-venus-atmosphere https://www.sciencealert.com/astronomers-report-they-ve-dete... There's also the famed Mill-Urey experiments. There's quite a bit of thought and argument about that "bootstrapping". Little cell-sized bags of lipids form pretty readily, but the problem is how to get the information (DNA) and metabolism into the cell-sized bags. You can google for "metabolism first hypothesis" and "rna world" for 2 different ideas about how that might have happened. PBS Eons has a video about the "Last Universal Common Ancestor" that might be of help: https://www.youtube.com/watch?v=pk213XSSktQ&t=0s https://www.youtube.com/watch?v=pk213XSSktQ&t=0s