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Thread: Why do we assume the first life form had amino acids?

  1. #1 Why do we assume the first life form had amino acids? 
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    All the first life form needs is the ability to self replicate, mutate, and die. It seems to me like it would be possible for a crystal formation to emerge with that trait, and then evolve into bacteria, or other life as we know it.

    People who give the odds of life emerging on its own at being statistically lottery-esq seem to assume an over constructed form of life. It may not spring into being with eyes, bones, and a brain, but even having it spring into being with a fully developed amino acid seems a bit over assumptive.

    I don't see how there's any justification to assume that it couldn't start without amino acids and then evolve into them, any more than there's a justification to assume it couldn't start without hands and then evolve into having hands.


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    You're seeing it as a reaction starting in minerals (which is fine; not as if I have any evidence), but the way I see it is as a reaction between gases in the atmosphere. The basic function of the first bacteria would be absorbing light to turn carbon dioxide and water vapour into sugars and oxygen. The sugars react in the atmosphere, providing energy which bonds amino acids (present from fairly soon on) into chains. These could, over time and with a lot of luck, become enzymes, which build more proteins. And so on, by randomly combining amino acids, a group of proteins stuck to a rock build something resembling life, with all the enzymes used to make it in place ready to create a replica of itself. And it starts from there...

    All the individual processes are completely possible. Where probability comes into it, is the chance of all of these seperate processes coming together in such a way to allow them to become a single, living organism.

    I know I've described how I see it badly, and I have no sources to back any of this up. Just my insight, for those interested.


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    Quote Originally Posted by drowsy turtle
    The basic function of the first bacteria would be absorbing light to turn carbon dioxide and water vapour into sugars and oxygen. The sugars react in the atmosphere, providing energy which bonds amino acids (present from fairly soon on) into chains. These could, over time and with a lot of luck, become enzymes, which build more proteins. And so on, by randomly combining amino acids, a group of proteins stuck to a rock build something resembling life, with all the enzymes used to make it in place ready to create a replica of itself. And it starts from there....
    I imagine it is the way you have written this, but you seem to be generating the sugars, which you think contribute to the formation of the first proteins and lead on to life, with bacteria. A rather circular arrangement, so what were you atually trying to say?

    Kojax - google Cairns-Smith. He envisages the first life as being clay based, with organic life building off of it.
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  5. #4 Re: Why do we assume the first life form had amino acids? 
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    Quote Originally Posted by kojax
    All the first life form needs is the ability to self replicate, mutate, and die. It seems to me like it would be possible for a crystal formation to emerge with that trait, and then evolve into bacteria, or other life as we know it.

    People who give the odds of life emerging on its own at being statistically lottery-esq seem to assume an over constructed form of life. It may not spring into being with eyes, bones, and a brain, but even having it spring into being with a fully developed amino acid seems a bit over assumptive.

    I don't see how there's any justification to assume that it couldn't start without amino acids and then evolve into them, any more than there's a justification to assume it couldn't start without hands and then evolve into having hands.
    The most prominent idea is that life started not from amino acids but from RNA.
    RNA World Hypothesis
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    Why do we assume the first life form had amino acids?
    We don't. As mentioned by gc, the more popular hypotheses consider nucleic acids, RNA in particular, to be the best candidate first replicators. Investigations into lipids and amino acid synthesis etc. are are more relevant to the later stages of abiogenesis.
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    Quote Originally Posted by John Galt
    Quote Originally Posted by drowsy turtle
    The basic function of the first bacteria would be absorbing light to turn carbon dioxide and water vapour into sugars and oxygen. The sugars react in the atmosphere, providing energy which bonds amino acids (present from fairly soon on) into chains. These could, over time and with a lot of luck, become enzymes, which build more proteins. And so on, by randomly combining amino acids, a group of proteins stuck to a rock build something resembling life, with all the enzymes used to make it in place ready to create a replica of itself. And it starts from there....
    I imagine it is the way you have written this, but you seem to be generating the sugars, which you think contribute to the formation of the first proteins and lead on to life, with bacteria. A rather circular arrangement, so what were you atually trying to say?
    Oh, no, sorry, I didn't mean it like that at all. I meant that all of these things were easily able to form seperately (carbohydrates, proteins, lipids, DNA, etc.), and the only part of abiogenesis which seems unlikely is them all being in the same place at the same time, interacting in such a way as to be able to form cellular life. I have great difficulty explaining things like this, and I may have got myself fairly confused in the process.

    An apt way of putting it, would be that my thoughts don't translate into words very well.
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    Quote Originally Posted by drowsy turtle

    An apt way of putting it, would be that my thoughts don't translate into words very well.
    Another way to say it is that your thoughts and just-so stories are more properly classified as philosophy as opposed to natural science.
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    Quote Originally Posted by cypress
    Quote Originally Posted by drowsy turtle

    An apt way of putting it, would be that my thoughts don't translate into words very well.
    Another way to say it is that your thoughts and just-so stories are more properly classified as philosophy as opposed to natural science.
    Cypress, if you have a legitimate point to make about the accuracy and/or falsifiability of drowsy turtle's statements, then make it - don't just insult him and run.
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    OK, sorry. My point is we can wax on about any number of ideas on this point, but they are not useful to understanding the difficulty involved in explaining life from non-life. Since Turtle already admitted he had no evidence, so evidence and falsification seems not to apply. The entire thread seems more like idle speculation.

    On the other hand, researchers have been increasingly successful at making self replicating biomolecules using processes that are not similar to any of the ideas suggested here.
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    Quote Originally Posted by cypress
    On the other hand, researchers have been increasingly successful at making self replicating biomolecules using processes that are not similar to any of the ideas suggested here.
    What thread are you reading? I suggested RNA. The most successful research to date has been into... self replicating RNA. Gerald Joyce, if I recall rightly. Publication in Science this year. Doesn't get much more significant or high impact than Science.
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    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress
    On the other hand, researchers have been increasingly successful at making self replicating biomolecules using processes that are not similar to any of the ideas suggested here.
    What thread are you reading? I suggested RNA. The most successful research to date has been into... self replicating RNA. Gerald Joyce, if I recall rightly. Publication in Science this year. Doesn't get much more significant or high impact than Science.
    I suggest you take a closer look at the research then. The conclusions from that series seems to be that while Ribo-enzymes will indeed replicate, they can only be made to do so with completely goal-driven engineered systems and they will not increase in complexity without more engineering. They all strip away complexity rapidly and migrate to the simplest form that will just the minimal molecule. It seems fairly certain that an RNA pathway requires external support from an genetic engineer.
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    I guess the question I should have asked is: What is the minimum?

    So far, I think it's safe to strip it down to 3 elements: 1)- Self replication, 2)- Mutation 3)-Death.

    I used crystals as my starting point because they're fine example of a process that involves self-replication. But... unfortunately... they do not mutate or die. More generally, what I'm getting at is that some very basic chemical reactions might be life like enough to evolve over time. Some people see fire as a sort of life form unto itself, though probably not sustainable enough to evolve.

    Quote Originally Posted by drowsy turtle
    You're seeing it as a reaction starting in minerals (which is fine; not as if I have any evidence), but the way I see it is as a reaction between gases in the atmosphere. The basic function of the first bacteria would be absorbing light to turn carbon dioxide and water vapour into sugars and oxygen. The sugars react in the atmosphere, providing energy which bonds amino acids (present from fairly soon on) into chains. These could, over time and with a lot of luck, become enzymes, which build more proteins. And so on, by randomly combining amino acids, a group of proteins stuck to a rock build something resembling life, with all the enzymes used to make it in place ready to create a replica of itself. And it starts from there...

    All the individual processes are completely possible. Where probability comes into it, is the chance of all of these seperate processes coming together in such a way to allow them to become a single, living organism.

    I know I've described how I see it badly, and I have no sources to back any of this up. Just my insight, for those interested.
    This is a very good correction to my starting point. Probably the first proto-life form would need to react carbon and oxygen. Not guaranteed, but likely.
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    Quote Originally Posted by cypress
    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress
    On the other hand, researchers have been increasingly successful at making self replicating biomolecules using processes that are not similar to any of the ideas suggested here.
    What thread are you reading? I suggested RNA. The most successful research to date has been into... self replicating RNA. Gerald Joyce, if I recall rightly. Publication in Science this year. Doesn't get much more significant or high impact than Science.
    I suggest you take a closer look at the research then. The conclusions from that series seems to be that while Ribo-enzymes will indeed replicate, they can only be made to do so with completely goal-driven engineered systems and they will not increase in complexity without more engineering. They all strip away complexity rapidly and migrate to the simplest form that will just the minimal molecule. It seems fairly certain that an RNA pathway requires external support from an genetic engineer.
    I'm aware of the limitations of the research to date, but my point was the RNA is promising. Shooting down an attempt to replicate in a lab what took perhaps 1 billion years in a culture vessel the size of the entire ocean because it's not yet displaying full and free Darwinian evolution is mighty short sighted. This work may yet find that RNA is a dead end for abiogenesis, but we're not at the point of making such a conclusion yet.

    What research has been more successful at making self replicating sequences than this? What were you referring to when you wrote the part quoted above?
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    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress

    I suggest you take a closer look at the research then. The conclusions from that series seems to be that while Ribo-enzymes will indeed replicate, they can only be made to do so with completely goal-driven engineered systems and they will not increase in complexity without more engineering. They all strip away complexity rapidly and migrate to the simplest form that will just the minimal molecule. It seems fairly certain that an RNA pathway requires external support from an genetic engineer.
    I'm aware of the limitations of the research to date, but my point was the RNA is promising. Shooting down an attempt to replicate in a lab what took perhaps 1 billion years in a culture vessel the size of the entire ocean because it's not yet displaying full and free Darwinian evolution is mighty short sighted.
    I would think that in order for something to be promising, it has to show some possibility that it might work. It is easy to say something is possible even when it is not. Your challenge is to demonstrate that it is in fact possible. Can you do this?

    The lab work I had in mind did not attempt to replicate prebiotic conditions, rather it was an attempt to demonstrate that RNA will self-replicate and can generate increasing complexity which is needed in order to chemicly evolve into DNA based biosystems. The results were that this RNA pathway requires too much goal directed intervention to succeed. See reference below.

    On prebioic conditions, according to Scripps research institute biochemist Gerald Joyce, The material processes that favor the formation of the four nucleotide bases, work against formation of the sugar and phosphate groups, and vise versa. He believes RNA had a role but not at the early stages. His work published this year I believe dealt with generation of two of the four bases under very precise and quite artificial conditions. Interested parties should Google it.

    If you can provide some indication that RNA and its precursors have any ability to remain intact in the ocean, please tell me about it. It makes a great story to speculate such things but this is no different than speculating about some white bearded man in the sky.

    For more information on work with biopolymers based on research by Szostak, Gold, and Joyce independently see S. Klug and M. Famulok, "All You Wanted to Know About SELEX," Molecular Biology Reports" 20."

    What research has been more successful at making self replicating sequences than this? What were you referring to when you wrote the part quoted above?
    The research referenced in the paper above plus several similar ones available and referenced in that paper. The original research notes and papers and analysis provided by others mentioned seem to confirm that engineering was responsible for the functioning systems.
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  16. #15 Re: Why do we assume the first life form had amino acids? 
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    Quote Originally Posted by kojax
    People who give the odds of life emerging on its own at being statistically lottery-esq seem to assume an over constructed form of life.
    I have never seen any sort of actual explanation on how the various "odds of life arising" numbers that some people like to throw around were derived. There's always just some big number, with zero actual explanation for how it was calculated. Probably because people are just making shit up.
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  17. #16 Re: Why do we assume the first life form had amino acids? 
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    Quote Originally Posted by Scifor Refugee
    Quote Originally Posted by kojax
    People who give the odds of life emerging on its own at being statistically lottery-esq seem to assume an over constructed form of life.
    I have never seen any sort of actual explanation on how the various "odds of life arising" numbers that some people like to throw around were derived. There's always just some big number, with zero actual explanation for how it was calculated. Probably because people are just making shit up.
    I've seen several explanations of the estimates. Some are better than others, but I don't find any of them overly persuasive. Would you care to walk through one of them?

    To kojax's point, people use "over constructed" forms of life because there is at present no direct evidence for any simpler forms. Since they are attempting to follow defined scientific processes, it would not due to speculate about what life might have been like as the results would be equally speculative and therefore unimpressive.
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  18. #17 Re: Why do we assume the first life form had amino acids? 
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    Quote Originally Posted by cypress
    I've seen several explanations of the estimates. Some are better than others, but I don't find any of them overly persuasive. Would you care to walk through one of them?
    Well as I said, I've never actually seen an explanation for any of them, so I can't list any that I would like to "walk through." If you know of any that actually make sense, I would be interested to read them.
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    Quote Originally Posted by cypress
    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress
    I suggest you take a closer look at the research then. The conclusions from that series seems to be that while Ribo-enzymes will indeed replicate, they can only be made to do so with completely goal-driven engineered systems and they will not increase in complexity without more engineering. They all strip away complexity rapidly and migrate to the simplest form that will just the minimal molecule. It seems fairly certain that an RNA pathway requires external support from an genetic engineer.
    I'm aware of the limitations of the research to date, but my point was the RNA is promising. Shooting down an attempt to replicate in a lab what took perhaps 1 billion years in a culture vessel the size of the entire ocean because it's not yet displaying full and free Darwinian evolution is mighty short sighted.
    I would think that in order for something to be promising, it has to show some possibility that it might work. It is easy to say something is possible even when it is not. Your challenge is to demonstrate that it is in fact possible. Can you do this?
    Joyce's ribozyme work demonstrates that self replicating RNA structures are possible. Can they go further and have full polymerase style activity and undergo natural selection? That's not clear yet. But there's possibility, as you've asked. And by your logic there is therefore promise.

    Quote Originally Posted by cypress
    On prebioic conditions, according to Scripps research institute biochemist Gerald Joyce, The material processes that favor the formation of the four nucleotide bases, work against formation of the sugar and phosphate groups, and vise versa. He believes RNA had a role but not at the early stages. His work published this year I believe dealt with generation of two of the four bases under very precise and quite artificial conditions. Interested parties should Google it.
    When did he say that and where? Must have been a while back. Also an odd claim since the phosphate group and a sugar are the nucleotide, so to say that the conditions favour the formation of the four nucleotides but not the only components of the nucleotides... is pretty confusing. Did you mean that the conditions for nucleoside formation differ from those needed for phosphate group addition? Either way, rather irrelevant since Sutherland's group produced two of the four nucleotides under plausible pre-biotic conditions this year. Nature 459: 239–242.

    Quote Originally Posted by cypress
    If you can provide some indication that RNA and its precursors have any ability to remain intact in the ocean, please tell me about it.
    We routinely store RNA samples in water in my lab. Now it's not a very long lived molecule, but it certainly sticks around in reasonable concentrations on the scale of several days.

    Quote Originally Posted by cypress
    It makes a great story to speculate such things but this is no different than speculating about some white bearded man in the sky.
    That's nonsense. We know RNA exists, that it can form many complex tertiary structures and that it can mediate a variety of enzyme-like functions due to that capacity. We know the ocean exists and that it shares many properties (such as density and pH) with the bodily fluids of life forms that use RNA as well as conditions known to facilitate nucleotide synthesis (UV light) and RNA polymer replication (catalytic clays). So whilst there's a lot we don't know, and certainly much hypothesis and even speculation, none of this is even vaguely comparable to speculating about a bearded man in the sky with no defined or testable properties.

    Quote Originally Posted by cypress
    For more information on work with biopolymers based on research by Szostak, Gold, and Joyce independently see S. Klug and M. Famulok, "All You Wanted to Know About SELEX," Molecular Biology Reports" 20."
    I think you're a little confused. SELEX is not an attempt to model preobiotic conditions or to replicate abiogenesis. It's a lab technique used to generate libraries of target specific oligonucleotides. It's a tool, like phage display or the like, used for other research. In short, an application of what we know about selection and evolution rather than an experiment that investigates it (or abiogenesis) in itself.

    Quote Originally Posted by cypress
    Quote Originally Posted by TheBiologista
    What research has been more successful at making self replicating sequences than this? What were you referring to when you wrote the part quoted above?
    The research referenced in the paper above plus several similar ones available and referenced in that paper. The original research notes and papers and analysis provided by others mentioned seem to confirm that engineering was responsible for the functioning systems.
    Well of course... from what I know of SELEX it was always meant to be so. It's not at all comparable to the ribozyme work, either in the intention of the work, the methods used, or the outcome. I mean, the generation of the oligonucleotide library uses conventional synthesis techniques, not a simulation of pre-biotic conditions.

    Am I missing something here? I mean this seems to me almost like pointing at PCR and claiming it's an attempt to study abiogenesis...
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    I don't want to judge for you what makes sense, since I am not particularly satisfied with any of the ones I read. To help you decide I offer the following:

    Most of the articles follows a protein to life hypothesis and recognizes the observation of a minimal subset of proteins required for functional cells. The objections raised against this hypothesis and quantified in these calculations have most researchers looking for other pathways.

    Others that I recall seeing calculations are in the area of emergence of biochemisty by way of self-ordering systems. One is through establishment of metabolic processes first then ever increasing complex systems to drive them. Another is through self-catalyzing reactions and yet another is lipids to vesicles and on to life.

    Or better still Google some, I bet there will be a paper or two.
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    Quote Originally Posted by cypress
    I don't want to judge for you what makes sense, since I am not particularly satisfied with any of the ones I read. To help you decide I offer the following:

    Most of the articles follows a protein to life hypothesis and recognizes the observation of a minimal subset of proteins required for functional cells. The objections raised against this hypothesis and quantified in these calculations have most researchers looking for other pathways.
    What articles are you talking about? The concept of a minimal subset of proteins assumes a multi protein system and thus the existence some sort of protocell. That's not considered a plausible first step in abiogenesis at all, in fact I would go so far as to say that it would be pretty much the last step.

    Quote Originally Posted by cypress
    Others that I recall seeing calculations are in the area of emergence of biochemisty by way of self-ordering systems. One is through establishment of metabolic processes first then ever increasing complex systems to drive them. Another is through self-catalyzing reactions and yet another is lipids to vesicles and on to life.
    Again, that's kinda jumping to the end. Far more plausible that life started as self-replicating polymers, be they oligonucleotides or something else, that were initially selected for nothing more than replication efficiency and stability.

    Quote Originally Posted by cypress
    Or better still Google some, I bet there will be a paper or two.
    Rather than have us search for evidence to support your claims, why not direct us to it more specifically?
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    I would suggest scifor do the research. I don't find it compelling enough to look it up. I simply offered to discuss it a bit. He seems to prefer to read about it and I am ok leaving it there.
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    Quote Originally Posted by TheBiologista

    Joyce's ribozyme work demonstrates that self replicating RNA structures are possible. Can they go further and have full polymerase style activity and undergo natural selection? That's not clear yet. But there's possibility, as you've asked. And by your logic there is therefore promise.
    Joyce demonstrated that highly engineered biopolymers are possible. It does not follow that non-goal driven processes can do the same.

    Did you mean that the conditions for nucleoside formation differ from those needed for phosphate group addition? Either way, rather irrelevant since Sutherland's group produced two of the four nucleotides under plausible pre-biotic conditions this year. Nature 459: 239–242.
    I don't think beginning with non-racemic reactants, purification of intermediate results and precise heating and uvradiation at key points is a good model of pre-biotic conditions. It is good lab work to be sure.

    Quote Originally Posted by cypress
    If you can provide some indication that RNA and its precursors have any ability to remain intact in the ocean, please tell me about it.
    We routinely store RNA samples in water in my lab. Now it's not a very long lived molecule, but it certainly sticks around in reasonable concentrations on the scale of several days.
    Is that sea water you are using?

    Am I missing something here? I mean this seems to me almost like pointing at PCR and claiming it's an attempt to study abiogenesis...
    I think so, I took your comment to be about self-replicating RNA structures given the existence of RNA when you were referring to generation of RNA in the first place. So we missed each other.
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    Quote Originally Posted by cypress
    Quote Originally Posted by TheBiologista

    Joyce's ribozyme work demonstrates that self replicating RNA structures are possible. Can they go further and have full polymerase style activity and undergo natural selection? That's not clear yet. But there's possibility, as you've asked. And by your logic there is therefore promise.
    Joyce demonstrated that highly engineered biopolymers are possible. It does not follow that non-goal driven processes can do the same.
    Not as a certainty, but as a possibility.

    Quote Originally Posted by cypress
    Did you mean that the conditions for nucleoside formation differ from those needed for phosphate group addition? Either way, rather irrelevant since Sutherland's group produced two of the four nucleotides under plausible pre-biotic conditions this year. Nature 459: 239–242.
    I don't think beginning with non-racemic reactants, purification of intermediate results and precise heating and uvradiation at key points is a good model of pre-biotic conditions.
    Oh come on. Nor is failing to let the lot stew in a wide variety of conditions over an entire planet for 1 billion years, but we're doing science here. We're trying to establish what conditions do allow for nucleotide synthesis. So the question becomes whether the conditions that do allow this to occur could plausibly have come about on the early Earth. The use of non-racemic mixtures shouldn't really enter into the matter as we'd merely expect this to reduce the efficiency of the reaction. That life preferentially uses L-enantiomers doesn't mean that the existence of D-enantiomers is a problem in the pre-biotic environment. They'll compete, and the yield of each reaction will be reduced. That's hardly a show stopper. Similarly, the purification steps serve only to make the experiment that bit more controlled, to make the results easier to interpret, the roles of each reagent and the steps involved the clearer. Timing on the heating, temperatures and UV, again just to control conditions but all within plausible limits. We're not zapping them with UV intensities beyond those the sun could produce, nor heating the mixture to implausible levels.

    Simplification, that's why it's called modelling or simulating rather than replicating.

    Once the simple, clear story is established we can by all means set about trying to complicate the mixture, the conditions etc. to see what allows the reaction occur at a reasonable rate and with good frequency and what does not.

    Quote Originally Posted by cypress
    Quote Originally Posted by cypress
    If you can provide some indication that RNA and its precursors have any ability to remain intact in the ocean, please tell me about it.
    We routinely store RNA samples in water in my lab. Now it's not a very long lived molecule, but it certainly sticks around in reasonable concentrations on the scale of several days.
    Is that sea water you are using?
    Nope, as it's not ideal, but RNA is stable in sea water for at least 2 days (1) and some sources show persistence beyond 10 days if the RNA is associated with sand (2). I'm sure there are plenty of other sources on this.

    1. Appl Environ Microbiol. 1995 January; 61(1): 363–366.
    2. Appl Environ Microbiol. 1986 September; 52(3): 504-509

    Quote Originally Posted by cypress
    Am I missing something here? I mean this seems to me almost like pointing at PCR and claiming it's an attempt to study abiogenesis...
    I think so, I took your comment to be about self-replicating RNA structures given the existence of RNA when you were referring to generation of RNA in the first place. So we missed each other.
    No, we've been talking about both topics and SELEX is relevant to neither. SELEX involves the generation of an oligo library by means that have squat to do with abiogenesis and then the selection of sequences with desired ligand activity which resembles natural selection (sort of) and then finally the amplification (or replication) of those sequences by means that have squat to do with abiogenesis.
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    Quote Originally Posted by cypress

    The lab work I had in mind did not attempt to replicate prebiotic conditions, rather it was an attempt to demonstrate that RNA will self-replicate and can generate increasing complexity which is needed in order to chemicly evolve into DNA based biosystems. The results were that this RNA pathway requires too much goal directed intervention to succeed. See reference below.
    I don't see how increasing complexity would be possible without a highly complex environment to drive the selection process.

    Quote Originally Posted by cypress

    To kojax's point, people use "over constructed" forms of life because there is at present no direct evidence for any simpler forms. Since they are attempting to follow defined scientific processes, it would not due to speculate about what life might have been like as the results would be equally speculative and therefore unimpressive.
    It's ok to blindly speculate at the hypothesis level, so long as you don't convert anything into an actual theory until you've run tests to confirm that what you're looking for does actually happen. Without a working (if highly speculative) hypothesis, there's no way to know what tests to run, nor what evidence to look for in the natural world.

    What if it turns out that the first proto-life form was a single molecule, or just a handful of molecules working together ? Without a speculative hypothesis, we'd never look for it. Sometimes, when you're having trouble coming up with a functional theory, it's because you weren't considering a wide enough range of possibilities.
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  26. #25  
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    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress
    Quote Originally Posted by TheBiologista

    Joyce's ribozyme work demonstrates that self replicating RNA structures are possible. Can they go further and have full polymerase style activity and undergo natural selection? That's not clear yet. But there's possibility, as you've asked. And by your logic there is therefore promise.
    Joyce demonstrated that highly engineered biopolymers are possible. It does not follow that non-goal driven processes can do the same.
    Not as a certainty, but as a possibility.
    No, I'm sorry, I disagree. Just because engineers are able to design and construct a system capable of carrying a human to the moon and back it does not follow that non-goal driven processes can possibly accomplish the same. It is a logical fallacy. No you must demonstrate that something is possible before we should accept it as so.

    We're trying to establish what conditions do allow for nucleotide synthesis. So the question becomes whether the conditions that do allow this to occur could plausibly have come about on the early Earth.
    Fair point. Let's see if the conditions used are really plausible as the article claims.

    The use of non-racemic mixtures shouldn't really enter into the matter as we'd merely expect this to reduce the efficiency of the reaction. That life preferentially uses L-enantiomers doesn't mean that the existence of D-enantiomers is a problem in the pre-biotic environment. They'll compete, and the yield of each reaction will be reduced. That's hardly a show stopper. Similarly, the purification steps serve only to make the experiment that bit more controlled, to make the results easier to interpret, the roles of each reagent and the steps involved the clearer.
    It is not always true that mixtures just reduce reaction frequency. Many times they cause competing side reactions that so over-compete with the desired reaction that it effectively ceases to happen. If you doubt this I am certain with a little research I can provide examples of this even in racemic mixtures. I didn't see in the paper where these situations were tested to confirm that purification served only to aid the research process and not the outcome.

    Timing on the heating, temperatures and UV, again just to control conditions but all within plausible limits. We're not zapping them with UV intensities beyond those the sun could produce, nor heating the mixture to implausible levels.
    OK, I accept this to a point. However plausibility means something more than that the conditions were in the same range as you would find on the earth. It means there is an actual set of natural conditions that does produce the same conditions.


    Quote Originally Posted by cypress

    Is that sea water you are using?
    Nope, as it's not ideal, but RNA is stable in sea water for at least 2 days (1) and some sources show persistence beyond 10 days if the RNA is associated with sand (2). I'm sure there are plenty of other sources on this.

    1. Appl Environ Microbiol. 1995 January; 61(1): 363–366.
    2. Appl Environ Microbiol. 1986 September; 52(3): 504-509
    Two days in solution and 10 more stabilized by sand but now largely immobile, doesn't provide much time for appreciable concentrations to accumulate to a point where polymers would form. See D. P. Bartel and J. W. Szostak, "Isolation of New Ribozymes from a Large Pool of Random Sequences, " Science 261 for an indication of the concentrations and related conditions required to form RNA polymers.

    Quote Originally Posted by cypress
    Am I missing something here? I mean this seems to me almost like pointing at PCR and claiming it's an attempt to study abiogenesis...
    I think so, I took your comment to be about self-replicating RNA structures given the existence of RNA when you were referring to generation of RNA in the first place. So we missed each other.
    No, we've been talking about both topics and SELEX is relevant to neither. SELEX involves the generation of an oligo library by means that have squat to do with abiogenesis and then the selection of sequences with desired ligand activity which resembles natural selection (sort of) and then finally the amplification (or replication) of those sequences by means that have squat to do with abiogenesis.
    Now I see what you were getting at here. Sorry, my mistake. I was looking at a number of loosely related articles on Rybozyme engineering and copied one I had not intended. You are correct, SELEX is not the topic I intended to reference.

    This is the reference I meant to have provided.

    R. Green and J Szostak, "Selection of a Ribozyme That Functions as a Superior Template in a Self-Copying Reaction," Science 258
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  27. #26  
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    Quote Originally Posted by cypress
    Quote Originally Posted by TheBiologista
    Quote Originally Posted by cypress
    Quote Originally Posted by TheBiologista

    Joyce's ribozyme work demonstrates that self replicating RNA structures are possible. Can they go further and have full polymerase style activity and undergo natural selection? That's not clear yet. But there's possibility, as you've asked. And by your logic there is therefore promise.
    Joyce demonstrated that highly engineered biopolymers are possible. It does not follow that non-goal driven processes can do the same.
    Not as a certainty, but as a possibility.
    No, I'm sorry, I disagree. Just because engineers are able to design and construct a system capable of carrying a human to the moon and back it does not follow that non-goal driven processes can possibly accomplish the same.
    What? When phenomenon A and phenomenon B share some process X that its required for either to be possible, the full demonstration of A including X demonstrates that B is possible. It does not make B probable, nor does it demonstrate that B ever happened, but it certainly gives us valid reason to hypothesise that B is plausible and worthy of investigation.

    Quote Originally Posted by cypress
    It is a logical fallacy.
    No it isn't, as outlined above. At most it's a semantic argument in the making, and seeing as how you seem to be some sort of quasi-creationist I'm quite certain you'll be only to happy to go down that road.

    Quote Originally Posted by cypress
    No you must demonstrate that something is possible before we should accept it as so.
    Well of course. That's what we have done. Demonstrated that some limited element X of hypothesised phenomenon B is possible. And we've dared to go so far as to say that B shows promise now. But I don't see anyone leaping to conclude that B, the RNA world hypothesis in this case, is now theory. Do you?

    Quote Originally Posted by cypress
    We're trying to establish what conditions do allow for nucleotide synthesis. So the question becomes whether the conditions that do allow this to occur could plausibly have come about on the early Earth.
    Fair point. Let's see if the conditions used are really plausible as the article claims.
    Then do it. With some specifics if you don't mind.

    Quote Originally Posted by cypress
    The use of non-racemic mixtures shouldn't really enter into the matter as we'd merely expect this to reduce the efficiency of the reaction. That life preferentially uses L-enantiomers doesn't mean that the existence of D-enantiomers is a problem in the pre-biotic environment. They'll compete, and the yield of each reaction will be reduced. That's hardly a show stopper. Similarly, the purification steps serve only to make the experiment that bit more controlled, to make the results easier to interpret, the roles of each reagent and the steps involved the clearer.
    It is not always true that mixtures just reduce reaction frequency. Many times they cause competing side reactions that so over-compete with the desired reaction that it effectively ceases to happen.
    I don't doubt that at all. But when dissecting a complex process, we have to start with the simplest, most stripped-down system possible and build up the complexity from there. There's far more that needs to go in there than enantiomers and unintended products. For all we know, a racemic mixture may indeed break the process, but another side product, common impurity or other plausible environmental fact may then rescue it. We've a long way to go before we can have confidence in this, but we've had a good start.

    Now, is there some specific evidence that the presence of enantiomers is going to sink this one?

    Quote Originally Posted by cypress
    If you doubt this I am certain with a little research I can provide examples of this even in racemic mixtures. I didn't see in the paper where these situations were tested to confirm that purification served only to aid the research process and not the outcome.
    There's a great many things they surely did not test, but a PhD student can only do so much, a paper has a word limit and all projects come to a point when someone has to say "that's enough for now". If purification is considered to be a potential confounding factor here, that can now be investigated. But if that happens it'll surely be done on firmer ground than your vague hand-waving. So again I'll ask whether there's evidence to warrant your concern?

    Quote Originally Posted by cypress
    Timing on the heating, temperatures and UV, again just to control conditions but all within plausible limits. We're not zapping them with UV intensities beyond those the sun could produce, nor heating the mixture to implausible levels.
    OK, I accept this to a point. However plausibility means something more than that the conditions were in the same range as you would find on the earth. It means there is an actual set of natural conditions that does produce the same conditions.
    What, like an ocean and millions of rock pools with plenty of organics, and a star that produces heat and UV radiation? Am I missing your point here? What exactly was implausible about the conditions used? Or the conditions producing the conditions or wherever the goalposts are now?

    Quote Originally Posted by cypress
    Quote Originally Posted by cypress

    Is that sea water you are using?
    Nope, as it's not ideal, but RNA is stable in sea water for at least 2 days (1) and some sources show persistence beyond 10 days if the RNA is associated with sand (2). I'm sure there are plenty of other sources on this.

    1. Appl Environ Microbiol. 1995 January; 61(1): 363–366.
    2. Appl Environ Microbiol. 1986 September; 52(3): 504-509
    Two days in solution and 10 more stabilized by sand but now largely immobile, doesn't provide much time for appreciable concentrations to accumulate to a point where polymers would form.
    With an enzyme or ribozyme catalyst, polymer formation takes minutes. Should it take more than two days with an inorganic catalyst? Since it's thought that certain clays might be good catalysts for polymerisation, we might even be getting the association with sand and thus a stability more like 10 days. As long as replication is happening faster than degradation anywhere at all, we're sorted. None of this is a done deal of course, but would you now be happy to concede that this claim

    "It makes a great story to speculate such things but this is no different than speculating about some white bearded man in the sky"

    which started our whole sea water investigation, is in fact an unfair comparison?

    Quote Originally Posted by cypress
    See D. P. Bartel and J. W. Szostak, "Isolation of New Ribozymes from a Large Pool of Random Sequences, " Science 261 for an indication of the concentrations and related conditions required to form RNA polymers.
    I see it. What part of that paper is relevant to our discussion here? Can you quote the part and explain to me what your point is in reference to it?

    Quote Originally Posted by cypress
    Quote Originally Posted by cypress
    Am I missing something here? I mean this seems to me almost like pointing at PCR and claiming it's an attempt to study abiogenesis...
    I think so, I took your comment to be about self-replicating RNA structures given the existence of RNA when you were referring to generation of RNA in the first place. So we missed each other.
    No, we've been talking about both topics and SELEX is relevant to neither. SELEX involves the generation of an oligo library by means that have squat to do with abiogenesis and then the selection of sequences with desired ligand activity which resembles natural selection (sort of) and then finally the amplification (or replication) of those sequences by means that have squat to do with abiogenesis.
    Now I see what you were getting at here. Sorry, my mistake. I was looking at a number of loosely related articles on Rybozyme engineering and copied one I had not intended. You are correct, SELEX is not the topic I intended to reference.

    This is the reference I meant to have provided.

    R. Green and J Szostak, "Selection of a Ribozyme That Functions as a Superior Template in a Self-Copying Reaction," Science 258
    So this is the research that you reckon is "more successful at making self replicating sequences than this" where by "this" I was referring to was Joyce's 2009 work on self-replicating RNA ribozymes...

    Step back through this thread. I claim that work with self replicating RNA is promising. You then mention research on the far superior "self replicating biomolecules using processes that are not similar to any of the ideas suggested here." I provide my reference which is Gerald Joyce's 2009 paper on self-replicating ribozymes. You say my source no good. I press you for your source and after a false start, you reference a 1993 paper on non-self-replicating... ribozymes. So you're claiming that a 1993 work regarding ribozymes as catalysts for the polymerisation of unassociated RNA oligos is somehow more successful at demonstrating the use of self replicating ribozymes than a 2009 paper demonstrating the use of actual self-replicating ribozymes, which itself was a development of the ideas in the 1993 paper?

    Did you quote the wrong paper again or are you just having a laugh?
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    Now we are are just going in circles. If we relax our standards for critical analysis, in our minds, I suppose anything becomes possible, the unrealistic becomes plausible and most any scenario becomes promising.

    My point was that RNA pathways are unrealistic because self-replicating RNA polymers require too much engineering input to form and then shed complexity without more intervention.

    We will just have to disagree.
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  29. #28  
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    Quote Originally Posted by cypress
    Now we are are just going in circles. If we relax our standards for critical analysis, in our minds, I suppose anything becomes possible, the unrealistic becomes plausible and most any scenario becomes promising.
    You pretty much took four posts to say "self-replicating ribozymes are a dead end, not like self-replicating ribozymes", before giving me two references neither of which referred to self replicating ribozymes. So if we're going in circles it might just be because you're contradicting yourself.

    Quote Originally Posted by cypress
    My point was that RNA pathways are unrealistic because self-replicating RNA polymers require too much engineering input to form and then shed complexity without more intervention.
    And again, nobody is disputing the shortcomings of the current research nor downplaying the gaps in our knowledge. It's early days and there's a long way to go before we can emulate abiogenesis in the lab. And yes, RNA-first hypotheses may even be a total dead end. But we won't know until we look, and the first step has worked, so we need to look further. You seem to be crying "impossible" simply because we haven't got there yet.

    Quote Originally Posted by cypress
    We will just have to disagree.
    Well that was inevitable. You've demonstrated here that your conclusion came first and the evidence, in the form of papers you clearly either have not fully read or do not understand, came second. Try starting with "I don't know" and go from there.
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    As I said previously (and will now elaborate about what I meant), if you read the actual article published in the Journal of Science near the beginning of this year, (the one that you mentioned), you will note that they began with a designed molecule, make engineered revisions to it to improve replication capability and then allowed it to compete with the variants created by the mutations.

    They designed the molecules because we have been unable to get them to form by non-goal directed processes.

    The more robust mutations out-competed less robust ones. What they didn’t state directly but what appears to be true was that simpler variants were the ones that outperformed the more complex ones. While improved in some ways, this is consistent with the earlier research going back to the early 90's.

    I think this is excellent research, but it does not follow that it applies to chemic evolution the way you seem to think it does.

    I am not saying that it is impossible that chemic processes generated life from non-life through RNA based processes. I am saying that while engineered systems demonstrates it is possible that an unexplained event could have an engineered cause, it is not proper to infer that it is likewise possible for a material only process to cause the event.

    You disagree with me. I see no further reason to continue to discuss it.
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    Quote Originally Posted by kojax
    I guess the question I should have asked is: What is the minimum?
    Chirality? Then your minimum drops to known subatomic particles and beyond. So the fabric of the universe, if not alive, is fertile in one way or the other.
    A pong by any other name is still a pong. -williampinn
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