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  1. #81
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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by Mindtrap
    This objection has been brought up already. It has also been addressed.
    First, there is no law or rule governing amino acids that necessarily or "tend to" bring about proteins.
    Unfortunately, there's absolutely no way for you to make this claim. Remember how I said that in chemistry, there are important things like the pressure, temperature, proximity, ph levels, etc? Geology and astronomy give us a loose picture of what the early earth was like. Using similar conditions, it's been a unanimous fact that you can create highly complex protein-like structures:

    Sidney W. Fox also experimented with abiogenesis and the primordial soup theory. In one of his experiments, he allowed amino acids to dry out as if puddled in a warm, dry spot in prebiotic conditions. He found that, as they dried, the amino acids formed long, often cross-linked, thread-like, submicroscopic molecules now named "proteinoids".

    In another experiment using a similar method to set suitable conditions for life to form, Fox collected volcanic material from a cinder cone in Hawaii. He discovered that the temperature was over 100 C (212 F) just 4 inches (100 mm) beneath the surface of the cinder cone, and suggested that this might have been the environment in which life was created—molecules could have formed and then been washed through the loose volcanic ash and into the sea. He placed lumps of lava over amino acids derived from methane, ammonia and water, sterilized all materials, and baked the lava over the amino acids for a few hours in a glass oven. A brown, sticky substance formed over the surface and when the lava was drenched in sterilized water a thick, brown liquid leached out. It turned out that the amino acids had combined to form proteinoids, and the proteinoids had combined to form small, cell-like spheres. Fox called these "microspheres", a name that subsequently was displaced by the more informative term protobionts. His protobionts were not cells, although they formed clumps and chains reminiscent of cyanobacteria. They contained no functional nucleic acids, but split asexually and formed within double membranes that had some attributes suggestive of cell membranes. Professor Colin S. Pittendrigh stated in December 1967 that "laboratories will be creating a living cell within ten years," a remark that reflected the typical contemporary levels of innocence of the complexity of cell structures.[17]

    http://en.wikipedia.org/wiki/Abiogenesis


    This is to say, when you create similar conditions to the early Earth, you create very complex organic compounds that very plausibly would combine chemically to create proteins. While we don't have a million years to do an experiment seeing how proteinoids precisely interact to generate the usual proteins, it's not precisely a stretch of the imagination to see that this how it very likely works. It also demonstrated that it's not particularly hard under the right conditions to create replicating organic polymers. Given it had several hundred million years to continue creating new complex organic compounds with splitting abilities, it's not surprising that at some point, one of these interactions hit the right combination.


    Moreover, the fact that it's not entirely certain how all the details of this work --although the evidence is heavily, as shown, in favor of what I'm saying-- there's exactly no intellectually honest way for you to say what you just did.

    Quote Originally Posted by Mindtrap
    The OP does in fact ignore some rules of chemistry to figure the Odds, but the rules it ignores actually hurts, hinders, or otherwise prevent the formation of proteins naturally.
    Again, it's not known the conditions of how you create proteins in terms of the early phase of the Earth during what was presumably abiogenesis. So, again, there's not a chance what you're saying is intellectually honest.


    Quote Originally Posted by Mindtrap
    Basically, the laws that govern chemical reactions do not help in the formation or have not shown to help.
    Again, this is a condition dependent thing. If I stick them in a freezer, then the interactions are not going to help proteins form from organic compounds. But if you stick it in environments like the early Earth had, what you're saying is, again, simply unproven, and at best conjecture and at worst a straight-up fabrication.

    Quote Originally Posted by MT
    So, if you reject the OP because it presents an unreasonable and unrealistic conditions, you are right to do so.
    But it doesn't address the point being made.
    Done, as above.
    "Those who can make you believe absurdities, can make you commit atrocities." --Voltaire

  2. #82
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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by MindTrap028 View Post
    I was asking for the justification for the belief. Why the conditions that bring them into being would not exist at the same time as the more advanced version.
    Why the more advanced versions would necessarily co-exist with all instances of the first kind of replication.

    If the replication is so "simple" and so regularly forms when the conditions exist, then I don't think it is a safe assumption to say they would not co-exist.
    This is not to say necessarily in the same environmental location, but in the same time frame.

    As though there were no possibility for separation. Thus, I don't think it is a safe assumption that they cannot, would not co-exist.
    In fact we should expect it to exist today wherever the conditions are meet.
    No, we shouldn't and I've already explained why several times - because a protocell wouldn't even have the time to form before it would have been consumed by the bacteria. Separation also seems highly unlikely. Any environment that could have supported the formation of protocells would also have been inhabitable by bacteria. They are much sturdier and less dependent on the environment so they would have been much better travelers. According to the hypothesis, they also evolved from the protocells so it's unclear how this separation would have occurred.

    So your saying that no geological evidence is even possible? I don't know enough about it to challenge that Idea.
    my guess is arrangement. They are different then the building blocks as they must be arranged in specific ways we can recognize. (I would think).
    If not, then how can we tell them apart in a test-tube today?
    A lipid vesicle (which would basically be the structure of a protocell) can certainly be observed in a test tube but I have never heard of such a structure being observed in fossil form.

    In the end, if you claim that the lack of geological or geochemical evidence conclusively excludes self-replicating RNA as a possible origin of life, the onus is on you to support that claim. Pointing to a mere possibility (which I believe to be slim to non-existant) that such evidence could exist is clearly not enough to save your argument. You must conclusively demonstrate that such evidence should be there for us to find. Can you do that?

    I suppose he will argue that the RNA world is untenable.
    I'll let someone else defend that, as again.. I will plead ignorance on the topic.
    Suggested reading on it is welcome. As my current objection is that the RNA world model is not a valid alternative by default.
    For an objection, this seems something of a truism. Obviously no hypothesis is valid "by default". As for suggested reading on the RNA world hypothesis, the Wikipedia page is as good a place as any to start:

    http://en.wikipedia.org/wiki/RNA_world_hypothesis

    The repeated reference to "simple" is as far as I can tell an oversimplification of an RNA world model.
    Simplicity is at the heart of the hypothesis. The object is to find the simplest possible structure that has the capacity to self-replicate and evolve.

    I'm going to skip a number of your points as they no longer seem relevant after you've acknowledged that you had confused mutation rate with evolution rate. I'd like to make a couple of points:

    Population genetics is a complicated field of study and the relationship between population size and evolution rate is not as clear-cut as you make it out to be. Here, e.g., is a paper that argues that evolution is more rapid in smaller populations:

    http://link.springer.com/article/10....LI=true#page-1

    Also, the first crucial step - the formation of the first replicator - is not governed by evolution but by chemistry. This process is what is being researched within the field of abiogenesis and we still don't know nearly enough about it to make any predictions about how long it would take.


    Really.. not very encouraging at all, and certainly not evidence that it hasn't been "abandoned".
    Of course here we don't mean "abandoned" as in no one researches it, but only that it isn't presented as a very viable reality.
    which, your link seems to support that everyone working on it readily admit that it has many problems and so far as we know isn't even possible. only that it "may be".
    The sentence following the one you quoted:

    While a complete solution to the problem is not yet in hand, major advances have recently been made in this area, primarily from the Sutherland lab, such that there is now considerable optimism that a robust pathway to the assembly of ribonucleotides and RNA oligomers will eventually be found.
    I'd say that's conclusive evidence that the work continues and that progress is being made. The fact that there are unsolved problems would be a very odd reason to abandon the hypothesis. Using that logic all research projects should be abandoned. Unsolved problems is the reason we do research in the first place and "unsolved" is clearly not the same as "unsolvable". Hypotheses are abandoned when they're proven to be wrong and so far, the RNA world hypothesis has not.

    BTW, can you explain the difference between possible and may be, it's not clear to me?
    Also, by what evidence do you claim the hypothesis is not possible?


    It seems that everyone agrees that there is a 1billion-ish year window for it to work in.
    so, show what Mutation rate would be necessary (bare minimum) then show that it could achieve it.
    My objection is that I don't think it could.

    as to how it would be "calculated". If the RNA world hypothesis hasn't, then it isn't a viable hypothesis to explain what we find. To me that is a half-assed theory which takes some off the wall hypothetical and forwards it as an actual option... without of course ever trying to establish that it IS an option.
    If it is the case that no one who forwards the theory has bothered to even address the time to mutation rate necessary, then there is no need to even address it as a valid objection. You may as well say "fairies could have done it". .. sure .. it COULD if it was possible and the OP doesn't address it either.
    You seem to be confusing a hypothesis with a theory, which is clearly not the same thing. When faced with an unexplained phenomenon - such as the origin of life on earth - you start by formulating a hypothesis, which is basically an educated guess that's consistent with what we presently know. In order to be useful, the hypothesis should make predictions that can be tested against experimental data or other available evidence. If the hypothesis fails this test against reality, it's discarded and you formulate a new one. If, over time, the hypothesis is consistently confirmed by the evidence it may eventually form the basis of a comprehensive theory.

    The RNA world hypothesis is clearly not yet at this point and faulting it for not being what it doesn't claim to be seems rather pointless. If you have conclusive evidence that the hypothesis is wrong, then by all means present it (and save a bunch of scientists from wasting their time) but until you do, the hypothesis will remain a viable explanation.

    The time restraint argument is entirely based on assumptions at this point. I have no idea how long the process from basic building blocks to a bacterium could have taken and I have yet to see anyone make a solid case for any particular time frame.

    Finally, you seem to have missed my question about the conditions used in abiogenesis experiments. How would you know these conditions could not have existed naturally?

  3. #83
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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by radix
    According to the hypothesis, they also evolved from the protocells so it's unclear how this separation would have occurred.
    The same way any other kind of genetic separation would occur. The kind of separation that Evolution depends on in order to have divergence of species.
    The other way is the re-occurrence of the first forms. See the first forms are proposed as a function of the environment, where as the more advanced forms can not come about on their own.

    So, I hope you can see why we should at least suspect separation.

    Quote Originally Posted by RADIX
    A lipid vesicle (which would basically be the structure of a protocell) can certainly be observed in a test tube but I have never heard of such a structure being observed in fossil form.

    In the end, if you claim that the lack of geological or geochemical evidence conclusively excludes self-replicating RNA as a possible origin of life, the onus is on you to support that claim. Pointing to a mere possibility (which I believe to be slim to non-existant) that such evidence could exist is clearly not enough to save your argument. You must conclusively demonstrate that such evidence should be there for us to find. Can you do that?
    It doesn't need to be "conclusive", all it needs to reach is a reasonable level.
    If we should reasonably expect them to exist due to a realistic view of how things work.
    Then, if we do not find them it does not add support to the theory that, that is how it occurred.
    It may not be the nail in the coffin that makes it impossible, or it maybe that it does.

    Here, I'm not debating the later, only the former. That we should expect to find them if they existed at all to be co-existant.

    Quote Originally Posted by RADIX
    For an objection, this seems something of a truism.
    Yes, because you offer as an objection to the OP that the RNA world is a plausible alternative.
    You have not shown that it is realistic as a possibility on it's own. In effect expecting the OP and defenders of it
    to "prove" that it is not. Which of course only needs to be done in a case where it is accepted as a valid alternative.

    Quote Originally Posted by RADIX
    Also, the first crucial step - the formation of the first replicator - is not governed by evolution but by chemistry. This process is what is being researched within the field of abiogenesis and we still don't know nearly enough about it to make any predictions about how long it would take.
    No the objection is that GIVEN the RNA world start of a first replicator, that IT can not produce enough mutations to become what we find in the fossil record 1billion years later.

    It's like saying of all the vehicles that can start the race of life, RNA is too slow to reach the check point known in the fossil record.
    The RNA world is based on something that is "too" simple and has too far to go.

    Quote Originally Posted by radix
    I'd say that's conclusive evidence that the work continues and that progress is being made.
    The claim was not that no research goes on, or that no-one thinks it could happen.
    It is that the general feeling is that it is not the vehicle that is responsible.

    It is nice to know that the people getting paid to research it, think that one day they will find something to justify it. That while they haven't solved any of the problems, they HOPE to one day do so, and are encouraged by their current work.

    Really, there are so many negative qualifiers I don't see how you can take it seriously. It is a long drawn out way of saying "as far as we know it is still not possible".

    Here it is important to note that the "unsolved" things are all reasons to not believe that RNA world is NOT possible in early earth. They are trying to show it possible, but the current state is that it is NOT possible or even reasonable.

    It is not simply to say "there is no known way" it is to say "Given what we know it can not be expected UNLESS we discover something new to change this".

    You are pointing to a brick wall, and saying "If we can get through that, then the OP fails".
    What response is even necessary? There is no "theory" to attack, because there is no theory only an "idea".

    Quote Originally Posted by RADIX
    The RNA world hypothesis is clearly not yet at this point and faulting it for not being what it doesn't claim to be seems rather pointless. If you have conclusive evidence that the hypothesis is wrong, then by all means present it (and save a bunch of scientists from wasting their time) but until you do, the hypothesis will remain a viable explanation.
    No, that is not quite how a debate works.
    See, your saying that the OP is flawed because there is another alternative.
    But you are not really offering an "alternative" you are just throwing out an idea.
    An alternative would be a valid explanation, yet the RNA world has not reached that point.

    All you are really doing is appealing to ignorance in an attempt to object to the OP. Sure we don't "Know" that it is not an RNA based start, but there is a lot of good evidence to think that it is not. Firstly because the RNA world fails to produce a theory to even address.

    Quote Originally Posted by RADIX
    The time restraint argument is entirely based on assumptions at this point. I have no idea how long the process from basic building blocks to a bacterium could have taken and I have yet to see anyone make a solid case for any particular time frame.
    Right, but you have the burden to show that the idea you bring up is a VALID objection.
    I don't have to DISPROVE it, you need to support it. if you do not offer reason why it should be accepted as valid, and if no one has bothered to establish that it is a valid vehicle,
    then there is no reason to accept it as a valid alternative, and it is thus not a response to the OP. Nor can you fault the OP for not addressing that which is not a valid vehicle to start with.

    Quote Originally Posted by RADIX
    Finally, you seem to have missed my question about the conditions used in abiogenesis experiments. How would you know these conditions could not have existed naturally?
    I can't speak to all of them, I'll try to answer this soon.
    To serve man.

  4. #84
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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by MindTrap028 View Post
    The same way any other kind of genetic separation would occur. The kind of separation that Evolution depends on in order to have divergence of species.
    The other way is the re-occurrence of the first forms. See the first forms are proposed as a function of the environment, where as the more advanced forms can not come about on their own.

    So, I hope you can see why we should at least suspect separation.
    Anywhere a protocell can go, a bacterium can go - and wherever the twain shall meet, the bacterium will eat the protocell and be on its merry way. There's no way for them to co-exist. Really. However, I'm fine with agreeing to disagree on this as it's not really the main point anyway.


    It doesn't need to be "conclusive", all it needs to reach is a reasonable level.
    If we should reasonably expect them to exist due to a realistic view of how things work.
    Then, if we do not find them it does not add support to the theory that, that is how it occurred.
    It may not be the nail in the coffin that makes it impossible, or it maybe that it does.
    Of course it needs to be conclusive. If the OP can't conclusively demonstrate that we should see evidence of self-replicating RNA, he can't use the lack of evidence as conclusive proof that the self-replicating RNA didn't exist. It's as simple as that.

    Yes, because you offer as an objection to the OP that the RNA world is a plausible alternative.
    You have not shown that it is realistic as a possibility on it's own. In effect expecting the OP and defenders of it
    to "prove" that it is not. Which of course only needs to be done in a case where it is accepted as a valid alternative.
    I'm expecting the OP to justify his claim that self-replicating RNA didn't exist. So far he hasn't.

    No the objection is that GIVEN the RNA world start of a first replicator, that IT can not produce enough mutations to become what we find in the fossil record 1billion years later.
    I'm aware of the objection - I just haven't seen any justification for it.

    The claim was not that no research goes on, or that no-one thinks it could happen.
    It is that the general feeling is that it is not the vehicle that is responsible.
    The "general feeling" (how would you gauge that, BTW?) is irrelevant. What matters is if the hypothesis is fruitful - which it clearly is.

    It is nice to know that the people getting paid to research it, think that one day they will find something to justify it. That while they haven't solved any of the problems, they HOPE to one day do so, and are encouraged by their current work.

    Really, there are so many negative qualifiers I don't see how you can take it seriously. It is a long drawn out way of saying "as far as we know it is still not possible".
    I don't know what your point is here. Are you saying that we shouldn't do basic research unless we absolutely know we'll get the desired results and when we'll get them?

    Here it is important to note that the "unsolved" things are all reasons to not believe that RNA world is NOT possible in early earth.
    I'm pretty sure you put a "not" too many in there. Either that or you seem to be arguing against yourself.

    They are trying to show it possible, but the current state is that it is NOT possible or even reasonable.
    To say that "the current state is that it is not possible" is meaningless. Claiming that something can never happen because it hasn't happened yet would be an argument from ignorance.

    It is not simply to say "there is no known way" it is to say "Given what we know it can not be expected UNLESS we discover something new to change this".

    You are pointing to a brick wall, and saying "If we can get through that, then the OP fails".
    What response is even necessary? There is no "theory" to attack, because there is no theory only an "idea".
    Any research project is going to be stuck unless it finds something new so that would be another truism. As new discoveries have recently been made and there are testable solutions to the problems as outlined in Szostak's paper, your brick wall analogy is obviously flawed.

    No, that is not quite how a debate works.
    See, your saying that the OP is flawed because there is another alternative.
    But you are not really offering an "alternative" you are just throwing out an idea.
    An alternative would be a valid explanation, yet the RNA world has not reached that point.
    An alternative to what? The OP hasn't presented anything for me to offer an alternative to. He's made the specific claim that self-replicating RNA is not a possibility so clearly the onus is on him to justify that claim - that's how all the debates I've been in have worked.

    All you are really doing is appealing to ignorance in an attempt to object to the OP. Sure we don't "Know" that it is not an RNA based start, but there is a lot of good evidence to think that it is not. Firstly because the RNA world fails to produce a theory to even address.
    Im asking the OP to justify his claim, how is that an appeal to ignorance? Since you admit that we don't know (why the quotation marks?) that RNA wasn't the start, you obviously agree that he so far hasn't sufficiently supported his assertion. What good evidence are you referring to?

    Again, you're faulting a hypothesis for not being a theory. This is nonsensical. The RNA world hypothesis will remain a possibility until it's been proven wrong - that's how hypotheses work.

    Right, but you have the burden to show that the idea you bring up is a VALID objection.
    I don't have to DISPROVE it, you need to support it.
    No, sorry, I don't. All I have to do is point to the fact that the OP has made a claim that he hasn't substantiated. Trying to shift the burden of proof onto me isn't going to work.

    if you do not offer reason why it should be accepted as valid, and if no one has bothered to establish that it is a valid vehicle,
    then there is no reason to accept it as a valid alternative, and it is thus not a response to the OP. Nor can you fault the OP for not addressing that which is not a valid vehicle to start with.
    The RNA world hypothesis has been around since the 80's and has since that time gathered quite a bit of supporting evidence: the fact that RNA can both store genetic information and work as an enzyme (thus solving the chicken/egg conundrum of what came first - DNA or proteins), the fact that plausible chemical pathways to the building blocks of a protocell (activated nucleotides and lipids) have been presented, the fact that activated nucleotides can spontaneously form RNA strands, the fact that lipids in water will spontaneously form bilayer vesicles (which is basically what a cell membrane is), the fact that these vesicles can grow and divide by purely mechanical means etc.

    The hypothesis has definitely earned the right to be considered a viable explanation and dismissing it off hand is baseless. Not only is it not being abandoned - it's currently the best-supported abiogenesis hypothesis presented (and still the only explanation offered in this thread). You think it's impossible? Prove it.


    I can't speak to all of them, I'll try to answer this soon.
    I'll settle for any one of them.

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    Re: Abiogenesis and evolution - The protein dilemma

    I am deep in the middle of a project that is taking up every spare moment of my time. As soon as I get freed I will go over the threads and answer the questions.
    Sorry for the delay.

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by RADIX
    Anywhere a protocell can go, a bacterium can go - and wherever the twain shall meet, the bacterium will eat the protocell and be on its merry way. There's no way for them to co-exist. Really. However, I'm fine with agreeing to disagree on this as it's not really the main point anyway.
    I don't mean co-exist in the same place at the same time. I mean co-exist geologically because of repeated occurrence (of what is said to be a naturally forming self replicating photocell) and the fact that the re-occurrence will not necessarily evolve into higher forms every time.

    Quote Originally Posted by RADIX
    Of course it needs to be conclusive. If the OP can't conclusively demonstrate that we should see evidence of self-replicating RNA, he can't use the lack of evidence as conclusive proof that the self-replicating RNA didn't exist. It's as simple as that.
    I will gladly concede the point. IF you agree that you must CONCLUSIVELY show that RNA world can occur in your use of it to contradict the OP in saying that it CAN be an explanation.

    See, the entire debate revolves around what we should reasonably accept. If the most reasonable way in which we should expect an RNA world idea to be the cause of bio-genesis, is such a way that also causes certain other observations to be expected reasonable predictions based on that model, then when we see the lack of fulfillment of those predictions it counts as a reason to discount the idea.

    So the level is not "conclusive" it is only what is "reasonable". The basis for any theory of an RNA world is not simply a weaving around the observed world evidence we have, but to establish what the initial conditions were and what effect we should reasonably expect.

    You are IMO setting an unrealistic level of expectation of evidence. That is how one saves hopeless theories.



    Quote Originally Posted by RADIX
    I'm expecting the OP to justify his claim that self-replicating RNA didn't exist. So far he hasn't.
    I think all of your links have have shown why it didn't. It is currently impossible according to what we know of RNA.

    Quote Originally Posted by RADIX
    I'm aware of the objection - I just haven't seen any justification for it.
    One justification of it is the lack of evidence provided by the theory to show that it CAN do it.

    The default position is not to simply assume that RNA world is capable, that is the burden of those who say it is a
    serious consideration. I have simply pointed out that without any reason to think that RNA can produce enough mutations, then it is not established, and can not be used as evidence.

    IE, your shifting the burden of proof by waiting for the idea to be proven wrong. If you forward it, you have to prove it right.

    Quote Originally Posted by RADIX
    The "general feeling" (how would you gauge that, BTW?) is irrelevant. What matters is if the hypothesis is fruitful - which it clearly is.
    Fruitful in that there are numerous problems which currently make the idea impossible. That the only progress is that some HOPE that one day they will be able to figure it out?
    That is not "fruitful" it is wishful thinking.

    Quote Originally Posted by RADIX
    I don't know what your point is here. Are you saying that we shouldn't do basic research unless we absolutely know we'll get the desired results and when we'll get them?
    No, I'm saying that you have to argue from where the evidence is now. Which in the case of RNA world seems to be that of impossibility. You are arguing from hope.

    Quote Originally Posted by RADIX
    I'm pretty sure you put a "not" too many in there. Either that or you seem to be arguing against yourself.
    Excessive use of the negative.

    Quote Originally Posted by MT CORRECTED
    Here it is important to note that the "unsolved"
    things are all reasons to believe that RNA world is NOT possible in early earth.
    Quote Originally Posted by RADIX
    To say that "the current state is that it is not possible" is meaningless. Claiming that something can never happen because it hasn't happened yet would be an argument from ignorance.
    No. We know of specific problems that cause RNA to fail to produce a protocell.
    To argue that it CAN produce a protocell, is to argue that we simply don't know the answer.. but it certainly must exist.

    You are appealing to our ignorance.

    Quote Originally Posted by RADIX
    Any research project is going to be stuck unless it finds something new so that would be another truism. As new discoveries have recently been made and there are testable solutions to the problems as outlined in Szostak's paper, your brick wall analogy is obviously flawed.
    Not really. The brick wall is that there are specific walls that prevent RNA from being the cause. The research hasn't removed them, it has only given the scientists hope that one day they will remove them.
    You can not mistake HOPE for facts.

    Furthermore, you are side stepping my point. My point is not the truism, it is that you are pointing to that truism and basically assuming what you are trying prove.
    Your response would be "valid" (if it were accepted as such) to any theory no matter how bad.

    Theor - earth is flat
    Evidence = earth is round.
    Response (according to you).. Any research project is going to be stuck until something new is found.

    Quote Originally Posted by RADIX
    An alternative to what? The OP hasn't presented anything for me to offer an alternative to. He's made the specific claim that self-replicating RNA is not a possibility so clearly the onus is on him to justify that claim - that's how all the debates I've been in have worked.
    Not so. The op presents a world where amino acids self assemble into a protein.
    You then objected that the OP ignores RNA world model.

    It is your job to establish that the RNA model is more than simply an idea, but an actual alternative.

    Quote Originally Posted by RADIX
    Im asking the OP to justify his claim, how is that an appeal to ignorance? Since you admit that we don't know (why the quotation marks?) that RNA wasn't the start, you obviously agree that he so far hasn't sufficiently supported his assertion. What good evidence are you referring to?

    Again, you're faulting a hypothesis for not being a theory. This is nonsensical. The RNA world hypothesis will remain a possibility until it's been proven wrong - that's how hypotheses work.
    It will never be proven wrong as long as you see all the things that make it impossible to be simply "roadblocks" and reduce them to "signs that more research is needed".

    Instead, the OP is simply recognizing that there is no reason to account for that idea, because it isn't viable.

    Quote Originally Posted by RADIX
    No, sorry, I don't. All I have to do is point to the fact that the OP has made a claim that he hasn't substantiated. Trying to shift the burden of proof onto me isn't going to work.
    So you don't have to support that your objection is valid? It could be that the objection named regarding RNA world is wrong. That does not mean that your objection defaults to valid, you still need to support it.


    Quote Originally Posted by RADIX
    The RNA world hypothesis has been around since the 80's and has since that time gathered quite a bit of supporting evidence: the fact that RNA can both store genetic information and work as an enzyme (thus solving the chicken/egg conundrum of what came first - DNA or proteins), the fact that plausible chemical pathways to the building blocks of a protocell (activated nucleotides and lipids) have been presented, the fact that activated nucleotides can spontaneously form RNA strands, the fact that lipids in water will spontaneously form bilayer vesicles (which is basically what a cell membrane is), the fact that these vesicles can grow and divide by purely mechanical means etc.
    Again, all things that are convenient to respond to the OP, but not enough to show that it is a working solution.
    It is not what the idea does account for that discounts it as an option. There are many ideas that explain things, but are discounted for it's problems.

    Also, as I read your link more (in small bits because of time..sorry) all of it is solution oriented without ever connecting it to real world conditions. It notes how many conditions are specifically ignored and they present problems that must be addressed (eventually). Certainly it may be a promising idea, but that doesn't make it reasonable to accept as possible, or even probable. As such, using it as an objection to the OP is not a valid objection.

    Quote Originally Posted by RADIX
    The hypothesis has definitely earned the right to be considered a viable explanation and dismissing it off hand is baseless. Not only is it not being abandoned - it's currently the best-supported abiogenesis hypothesis presented (and still the only explanation offered in this thread). You think it's impossible? Prove it.
    Go read your link. http://www.jsystchem.com/content/3/1/2

    Look, basically the objection to the OP goes like this.
    IF RNA world is possible, THEN the OP is mistaken in it's assumption.

    One can not simply gloss over the challenges to RNA world in asserting that it IS possible.
    The burden is not to prove that it is impossible, but to prove that it is. Yes they are working on it, when they have it worked out then you will have a valid objection. Until then, all you have is a hope that the idea of RNA world can work in reality. As such, there is no reason for the OP to account for it in it's case.


    Quote Originally Posted by RADIX
    I'll settle for any one of them.
    Punting this point to the next post... or when I have more time (again).
    To serve man.

  7. #87
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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by MindTrap028 View Post
    I don't mean co-exist in the same place at the same time. I mean co-exist geologically because of repeated occurrence (of what is said to be a naturally forming self replicating photocell) and the fact that the re-occurrence will not necessarily evolve into higher forms every time.
    This still does nothing to save the OP's argument. He has to either demonstrate conclusively that self-replicating RNA must necessarily leave evidence for us to find or concede that the lack of such evidence does not constitute proof that self-replicating RNA did not exist.

    I will gladly concede the point. IF you agree that you must CONCLUSIVELY show that RNA world can occur in your use of it to contradict the OP in saying that it CAN be an explanation.
    I need to show no such thing, since I haven't made the claim that the RNA world did occur. The OP on the other hand has made the absolute claim that it didn't occur (since we would otherwise see evidence of self-replicating RNA) so the burden of proof obviously rests solely with him. The idea that I have to prove the possibility of self-replicating RNA is in itself nonsensical. A hypothesis is by definition possible until it's been proven wrong.

    See, the entire debate revolves around what we should reasonably accept. If the most reasonable way in which we should expect an RNA world idea to be the cause of bio-genesis, is such a way that also causes certain other observations to be expected reasonable predictions based on that model, then when we see the lack of fulfillment of those predictions it counts as a reason to discount the idea.
    No, that's not what the debate revolves around. It may have been the case, had the OP said that it's reasonable to believe that self-replicating RNA didn't exist but that's not what he posted. He explicitly excluded the possibility of self-replicating RNA on the basis of a lack of evidence, thereby acquiring a burden of proof that he has still to meet. This is what the debate is about: the OP's justification for excluding the possibility of self-replicating RNA. He has referred to a theory which would predict that self-replicating RNA would somehow lead to large deposits of tar. I have never heard of such a theory so I asked the OP to provide some references to study but this has not yet happened.

    So the level is not "conclusive" it is only what is "reasonable". The basis for any theory of an RNA world is not simply a weaving around the observed world evidence we have, but to establish what the initial conditions were and what effect we should reasonably expect.
    Obviously, for a hypothesis to be viable (and possibly graduate to a theory) it has to be consistent with the observed evidence. Has this ever been contested in this thread? Certainly not by me.

    You are IMO setting an unrealistic level of expectation of evidence. That is how one saves hopeless theories.
    Not at all. I'm just expecting people to substantiate their claims, i.e. meeting the burden of proof. It's a basic tenet of human discourse. The OP has not sufficiently demonstrated that we should expect to see evidence of self-replicating RNA and you have provided no evidence suggesting that the RNA world hypotheis is hopeless.

    I think all of your links have have shown why it didn't. It is currently impossible according to what we know of RNA.
    To say that "it is currently impossible according to what we know of RNA" is still a meaningless statement. If you claim that it's impossible, please present your evidence for this. Until you do, the hypothesis remains a possibility.

    One justification of it is the lack of evidence provided by the theory to show that it CAN do it.
    On the contrary, there's plenty of evidence that support the hypothesis as I 've already posted.

    The default position is not to simply assume that RNA world is capable, that is the burden of those who say it is a
    serious consideration. I have simply pointed out that without any reason to think that RNA can produce enough mutations, then it is not established, and can not be used as evidence.
    These are straw man arguments as no-one has "assumed that the RNA world is capable" or tried to use it as evidence.

    IE, your shifting the burden of proof by waiting for the idea to be proven wrong. If you forward it, you have to prove it right.
    The only one trying to shift the burden of proof here is you. It will remain with the person who made the claim, i.e. the OP.

    Fruitful in that there are numerous problems which currently make the idea impossible. That the only progress is that some HOPE that one day they will be able to figure it out?
    That is not "fruitful" it is wishful thinking.
    Argument from ignorance. Unsolved problems are clearly not the same as unsolvable problems. Again, if unsolved problems make a hypothesis impossible, then all hypotheses are impossible. This is obviously nonsense - unsolved problems is the very reason we put forward a hypothesis.

    No, I'm saying that you have to argue from where the evidence is now. Which in the case of RNA world seems to be that of impossibility. You are arguing from hope.
    No, I'm arguing from a simple point of intellectual rigour: if you make a claim, you need to back it up. I'm not the one making claims here (if you can't see the difference between a claim and a hypothesis I really can't help you), the OP is.

    No. We know of specific problems that cause RNA to fail to produce a protocell.
    To argue that it CAN produce a protocell, is to argue that we simply don't know the answer.. but it certainly must exist.
    Specific problems such as...?

    You are appealing to our ignorance.
    Actually, it's the other way round. You're asking me to accept the OP's claim (that self-replicating RNA can be excluded based on the lack of evidence) as true unless I can prove it to be untrue. This is the very definition of an appeal to ignorance.

    Not really. The brick wall is that there are specific walls that prevent RNA from being the cause. The research hasn't removed them, it has only given the scientists hope that one day they will remove them.
    You can not mistake HOPE for facts.
    Another unsubstantiated claim. What are these brick walls?

    Furthermore, you are side stepping my point. My point is not the truism, it is that you are pointing to that truism and basically assuming what you are trying prove.
    Your response would be "valid" (if it were accepted as such) to any theory no matter how bad.

    Theor - earth is flat
    Evidence = earth is round.
    Response (according to you).. Any research project is going to be stuck until something new is found.
    I'm not assuming anything. The only test of whether a hypothesis is good or bad that I'm aware of is the test against the observed evidence. If you have information of the RNA world hypothesis failing such a test, please present it.

    Not so. The op presents a world where amino acids self assemble into a protein.
    You then objected that the OP ignores RNA world model.

    It is your job to establish that the RNA model is more than simply an idea, but an actual alternative.
    Incorrect. I didn't introduce the idea of self-replicating RNA into the thread, the OP did. He is also the one who found it necessary to provide a reason to exclude it. I'm simply asking him to qualify this reason. Your continued attempts to reverse the burden of proof are duly noted, though.

    It will never be proven wrong as long as you see all the things that make it impossible to be simply "roadblocks" and reduce them to "signs that more research is needed".
    The hypothesis will remain valid as long as it passes the test against observed evidence, that's how a hypothesis works.

    Instead, the OP is simply recognizing that there is no reason to account for that idea, because it isn't viable.
    Incorrect, the OP found it necessary to explain why he excluded the possiblity. I'm asking him to justify this exclusion.

    So you don't have to support that your objection is valid? It could be that the objection named regarding RNA world is wrong. That does not mean that your objection defaults to valid, you still need to support it.
    My objection is that the OP hasn't fully explained why we should see evidence of self-replicating RNA. Do you think he has? If so - great! Then would you mind explaining to me what this evidence supposedly would consist of, what its origin was, how it was deposited, where we should expect to find it, what methodology we should use to examine it, if someone has actually looked for it and what conclusions they drew and - most importantly - where has this information been published so that the rest of us can examine it? Unless you can provide this, I stand by my objection.

    Again, all things that are convenient to respond to the OP, but not enough to show that it is a working solution.
    It is not what the idea does account for that discounts it as an option. There are many ideas that explain things, but are discounted for it's problems.
    Not in science. A scientific idea is discarded if it's proven to be wrong, not because of its "problems".

    Also, as I read your link more (in small bits because of time..sorry) all of it is solution oriented without ever connecting it to real world conditions. It notes how many conditions are specifically ignored and they present problems that must be addressed (eventually). Certainly it may be a promising idea, but that doesn't make it reasonable to accept as possible, or even probable. As such, using it as an objection to the OP is not a valid objection.
    I'm not using it as an objection as I just explained. My objection is that the OP has so far failed to justify his claim that we should expect to see evidence of self-replicating RNA.

    Go read your link. http://www.jsystchem.com/content/3/1/2

    Look, basically the objection to the OP goes like this.
    IF RNA world is possible, THEN the OP is mistaken in it's assumption.
    No, that's not my objection. See above, I don't think I need to repeat it a 3rd time.

    One can not simply gloss over the challenges to RNA world in asserting that it IS possible.
    The burden is not to prove that it is impossible, but to prove that it is. Yes they are working on it, when they have it worked out then you will have a valid objection. Until then, all you have is a hope that the idea of RNA world can work in reality. As such, there is no reason for the OP to account for it in it's case.
    Your argument makes no sense as the OP has already acknowledged the need to explain why he excludes the possiblity of self-replicating RNA. He brought it up, not me. His claim that we should see evidence of this self-replicating RNA still needs substantiation. Until the OP returns to provide it, we seem to be stuck.

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by radix View Post
    Actually, it's the other way round. You're asking me to accept the OP's claim (that self-replicating RNA can be excluded based on the lack of evidence) as true unless I can prove it to be untrue. This is the very definition of an appeal to ignorance.
    I pointed out precisely that on more than one occasion in this thread, similarly the favourite defender of the OP bizarrely said "I" was appealing to ignorance.

    The lack of intellectual honesty in a debate makes debating pointless, although I still look forward to any response from the OP - there may yet be more sophistry and outright fallacies cunningly disguised as science that we have to find and point out.

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    Re: Abiogenesis and evolution - The protein dilemma

    The OP is misleading.

    You do not solve mysteries with deductive reasoning. It simply is too cumbersome and inflexible. You solve mysteries with abductive logic. What the OP has done is to make a blanket generalization that it knows all conditions of all environments and that it knows all possibilities within all possible environments from the formation of amino acids until today. This is impossible. It would mean that the author knows everything about all possibilities. Not likely.

    But then the OP goes on to suggest that a more probable answer is that some supreme being created life. As if the origin of that being is certain. I think the probability of that is impossible to calculate, as there is zero evidence to support the concept. So even if the OP was using right assumptions, which it is not, it would still need to show that the other answer is more likely using mathematics. To say "I can use math to show it can't be the way you say, so I am right." is bogus. You must go on to apply the same mathematics to your own reasoning to show that it is more likely. Good luck with that.

    Let me introduce you to a common sense axiom:

    "Anything that can happen will happen, given ample time and opportunity."

    The OP basically says: As far as we know, all things being equal to our expectations, there is no way that amino acids can bond into proteins randomly within the time allotted.

    Or written with a more humble hand: We do not understand the mechanism by which amino acids first became proteins, but we know it could not have happened randomly.

    All completely assumptive. Anyone familiar with abductive reasoning will simply reason out that there must be some environments where the likelihood of amino acids bonding into proteins is highly increased, and that those environments existed for long enough to allow for their development. That is the most reasonable and probable explanation. Much more reasonable and probable than a supreme being that needs no creation itself.



    Researchers analyzing meteorite fragments that fell on a frozen lake in Canada have developed an explanation for the origin of life's handedness – why living things only use molecules with specific orientations. The work also gave the strongest evidence to date that liquid water inside an asteroid leads to a strong preference of left-handed over right-handed forms of some common protein amino acids in meteorites. The result makes the search for extraterrestrial life more challenging.

    "Our analysis of the amino acids in meteorite fragments from Tagish Lake gave us one possible explanation for why all known life uses only left-handed versions of amino acids to build proteins," said Dr. Daniel Glavin of NASA's Goddard Space Flight Center in Greenbelt, Md. Glavin is lead author of a paper on this research to be published in the journal Meteoritics and Planetary Science.

    http://www.nasa.gov/topics/solarsyst...rned-left.html


    The reasonable mind does not assume that because something looks statistically impossible that it actually is. That would assume we knew of all possible conditions and that we know which ones actually occurred. We do not. The fact remains life does exist. The fact remains that the most reasonable explanation is found within the realm of science. To simply attempt to create impossible scenarios to disprove science is to assume there is enough known to accurately deduce such mathematical models. As shown by the recent discovery posted above; we have many, many more pieces of knowledge which will become available to reduce the odds and fill in the gaps which were glossed over with assumptions in the OP.

    ---------- Post added at 02:51 PM ---------- Previous post was at 01:13 PM ----------

    Quote Originally Posted by rims
    I also find the argument, life exists therefore it just happened despite the mathematical, scientific objections, especially hypocritical considering that if a religious person gave you the same response you would ridicule them. Your arguments resemble a person with strong religious beliefs that will not waiver no matter what facts there are to the contrary. So, just say,"I am an atheist and choose to believe this no matter what science says", and quit trying to pretend you are arguing at a factual level.
    Life does exist. We all agree upon that.

    The question is, "how?" You are failing to see that the most persuasive argument is that life does exist. The mathematics about how it could not possibly exist naturally are overcome by the evidence that it does occur naturally. Your "theory" about the impossibility of the mathematical likelihood is based upon what we know about amino acids and proteins. Your opponents argument is based upon the fact we exist. A much stronger argument.

    Your argument did not poof us out of existence. So the far more reasonable argument would be to say that we simply have a void in our understanding yet to fill. I do not find this outrageous, do you?

    Yet you would prefer to jump to a supernatural answer as if our current knowledge is airtight and complete. Really? You honestly believe that is the more probable answer? That would be blind belief in science! Let me write it out for you in simplified form.

    We do not know how amino acids could randomly form into proteins, therefore:

    1.We have work to do to learn how it happened

    or

    2. This proves there is a God.

    I fail to see how any sane person could not choose option 1 as a reasonable option. It certainly does not prove there is a God. The fact we do not know the answer to a question is no proof of anything except we do not know.

    Science is still in its infancy. What we know is infantessimal compared to what we will know. It only makes perfect sense to say that our gaps of knowledge will fill in over time. That is not "choose[ing] to believe this no matter what science says." This is exactly what science says.

    Abduction is a form of logical inference that goes from data description of something to a hypothesis that accounts for the reliable data and seeks to explain relevant evidence.

    For example, the lawn is wet. But if it rained last night, then it would be unsurprising that the lawn is wet. Therefore, by abductive reasoning, the possibility that it rained last night is reasonable.

    http://en.wikipedia.org/wiki/Abductive_reasoning
    We do exist. Amino acids occur naturally. Proteins are made from amino acids. Let's look at the logic you offer.

    1. Based upon what we know randomly appearing proteins are impossible, will always be impossible no matter what we learn, therefore, there is a God.

    Or

    2. We must be missing key information to make an accurate determination because we do exist

    Any human being that reasons can see that the logic of postulate two is far superior to postulate 1. Number 1 supposes we know all we need to know without going to the effort to prove this. That is never logical. Then it claims a supernatural being exists without the slightest empirical evidence. That's not logical either.

    Your claim about your opponent is hereby debunked. They did not blindly believe, they made the most reasonable choice of those presented. That's what scientists do.
    Last edited by Joe Friday; March 26th, 2013 at 11:08 AM.

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