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  1. #61
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    Smile Re: Abiogenesis and evolution - The protein dilemma

    “A common sense interpretation of the facts suggests that a superintellect has monkeyed with physics, as well as with chemistry and biology, and that there are no blind forces worth speaking about in nature. The numbers one calculates from the facts seem to me so overwhelming as to put this conclusion almost beyond question.”
    Fred Hoyle

    Siegfried
    While the equivocation is understandable the word random has multiple meanings. You are taking the meaning clearly outlined in the literature on evolution and then using the same word to imply they advocate for a purely statistical meaning of the same word.
    As I have explained earlier, there is a random aspect of evolution and an environmentally directed aspect. The common theory on evolution relies on random mutations to produce a protein which is then either selected or discarded depending on the environment of the organism.
    The production of proteins, of which the OP addresses, clearly falls within this random aspect of the way the theory of evolution is currently taught.

    We can show the generation of amino acids, and we can demonstrate how amino acids can form Proteinoids which while not true proteins have many of the same properties and themselves can form cell like membranes.
    Proteinoids! I am going to give you the benefit of the doubt that you are not purposely being dishonest here. This is the most fallacious and disingenuous piece of misinformation that is put forth by proponents of abiogenesis.
    It has nothing to do with a protein! It is merely a polypeptide. A meaningless collection of amino acids – one of the 10e+300 that we discussed earlier.

    To name this a “proteinoid” and then show it as evidence for abiogenesis was a major deception designed to give the appearance of creating proteins when nothing of the kind had been produced. I am guessing there was grant money involved and results that were expected, or just a desire to give false evidence to bolster failing experiments.
    The original experiment was supposed to create proteins, and they went to great lengths, above and beyond the ridiculous to accomplish this. Heating them to 284 deg. F in a dry environment using pure amino acids from living organisms. Basically, he manufactured worthless polypeptides in a laboratory that wouldn’t even resemble the real world conditions. In other words, he failed miserably even though he cheated.

    Let’s look at what Chemical Engineering had to say about Fox’s experiment:

    Sydney Fox and the other researchers managed to unite the amino acids in the shape of "proteinoids" by using very special heating techniques under conditions which in fact did not exist at all in the primordial stages of Earth. Also, they are not at all similar to the very regular proteins present in living things. They are nothing but useless, irregular chemical stains. It was explained that even if such molecules had formed in the early ages, they would definitely be destroyed.
    S. W. Fox, K. Harada, G. Kramptiz, G. Mueller, "Chemical Origin of Cells," Chemical Engineering News, June 22, 1970, p. 80

    So I am not the only one who thinks that proteinoids are the hemorrhoids of abiogenesis research achievement

    While that is far from demonstrating abiogenesis it is also far from just random assemblies of amino acids that arise in equal probability as your mathematical model would have us contemplate. These molecules are not formed randomly but are formed predictably under the right conditions, conditions that can be reproduced in naturally occurring circumstances.
    In order to overcome the probabilities you have to show a natural attraction that assembles amino acids into proteins. This has been tried for well over 50 years and has failed to show any progress despite the huge amount of attempts and myriad of different ways that extend beyond the boundary of reality. At some point in time you have to say this notion has been falsified if you are looking at it reasonably and not religiously.

    No you have not pointed to any actual scientific laws. You have instead implied that chemistry happens by pure random processes that could have any imaginably outcome rather that following predictable and repeatable patterns which is what we actually observe.
    Round and round we go… I am aware that chemistry does not happen by chance. Are you aware that the realities in chemistry make it infinitely more impossible? If the simplistic odds in the OP were 1 in 2 then we would be discussing those realities and how they would again put us into an improbable state for the occurrence of life.

    They only serve as a tool for disinformation and a means of making a false argument.
    And yet, no one has shown where the specifics of this disinformation and false arguments lie. All I hear is people crying foul, because the odds are not in line with chemical attractions and realities, and they won’t even tell me which amino acids or compounds attract to one another to auto-assemble. I have shown you some of the problems that chemistry gives to long chain amino acids, why don’t you share with me the positives that chemistry helps to establish long chain amino acids?

    No, they don't. As I've outlined many of the steps in abiogenesis can be demonstrated in part or in principle eliminating vast swaths of possibilities from your random odds nonsense. Those principles eliminate huge swaths of your "possible" formations thus ruling them out of the set of outcomes. Those outcomes are in fact not part of the possibilities but the impossibilities.
    Maybe in your mind you have, (unless you are referring to proteinoids). The reality is you haven’t shown 1 piece of data that would make me or any other thinking person believe that the odds are lessened against life happening.
    Do me a favor and use just 1 post to list these out with data, because this is the most relevant part of the debate.

    You don't understand the analogy.
    I understand the analogy very well, because I understand amino acids, proteins, and the way they are utilized in the processes of the cells. I have gone to great lengths to understand them because of my interest in how the mechanisms work on a molecular level. The problem, imo, is that none of the people here arguing the naturalistic cause really understand any of the aforementioned and that is why I have to keep repeating myself on some of the basic notions that are covered in cellular biology and evolution.


    The order of the universe is not mysterious, it is evident by observation. Gravity is not a mystery except that we don't as of yet fully understand its operation.
    You were claiming that “Atheists do not see the world as a place of utterly random events that happen without meaning”, thus your reasoning for the existence of life defying great odds.
    Like a Calvinistic atheistic. If there is no God then by definition everything is random because there is nothing to direct anything. Even the very laws that were established at the onset of the universe would be random.

    Just because you fail to understand it, doesn't make in nonsense. Dismiss reason if you like but it won't be lost on everyone.
    DITTO

    My statement does not counter the OP, it is an incitement of your own model of the origin of life, specific creation by a deity.
    My OP is a counter against the current naturalistic theory. So in essence, we are like dogs chasing each others tails

    There are many serious abiogenesis theories. What we don't have are any good experiments that as of yet have proven any of them out. Many theories have been shown true in time that originally required experimentation to demonstrate. Many others have been shown false upon sufficient testing. You seem to lack a basic understanding of the process of science if you think only theories must be verified to be seriously considered. Since you asked we didn't engage in linkwars I won't point you at the many that exist and are under investigation but some simple research can turn them up.
    Please do put links to sites that have data to back up what they say. If it is propaganda sites with someone’s opinion and nothing to back it up, then don’t bother.
    I actually have looked at a good many of the abiogenesis experiments over the years, but, I would welcome any new good sites that are factual.

    I have shown you the universe is not random, that things happen based on causal properties of matter, that simple origins can express complex patterns, that protein like molecules have been proven to form under natural conditions despite whatever odds there may be in that level of complexity, that it doesn't happen randomly but deterministic. Just because we don't yet know the series of events and elements needed, doesn't mean it is not possible.
    None of the above have been shown, and the reason it is doubtful is because of the amount of time and experimentation put forth with no formation of proteins.
    But, as I mentioned twice before, I am willing to look at any proofs that you might have.

  2. #62
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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by rlms View Post
    To avoid repetition, please refrain from the self replicating RNA argument; it is non-existent now and if it did exist in the past we would have geological proof in the way of chemical signatures in the Pre-Cambrian layers of rock.
    What kind of chemical signatures would you expect self replicating RNA to leave?

  3. #63
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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by MindTrap028 View Post
    Actually gravity doesn't help you out. Because Gravity being the value that it does have isn't a sufficient explanation to explain it having that exact value as opposed to any other.
    You have misunderstood my point, I think.
    Perhaps neither of us understands each-other. The theist world view tends to be one like "gravity distorts space time because without that we couldn't live and if we couldn't live we couldn't worship god in the way he likes" or something to that effect. The assume the world we live in was desired, and so its order is one designed to create the outcome we observe. They view the only alternative as a universe where everything is random and anything is possible and only dumb luck produces what we observe.

    But there is another way of thinking that is neither of those and its very hard to get someone in the theist camp to even see or acknowledge it. They have to either have a reason, or no reason. It is an understandably human perspective. That either an event is planed to go as we desire, or it is entirely random and unpredictable. the third way is hard for our minds to see because of this bias of human prediction and planning.

    So what is it? The best I can seem to muster is to tell you the universe is entirely ordered, but that order does not serve a will or desire, it simply is the order that is and it does not serve any emotional need or purpose. It follows a set path but is not part of a plan. The universe does not desire life, but it is a universe that inevitably did create life and I suspect will has and will continue to create life that has nothing to due with us humans other than it is the product of the same or a similar process. The universe does not require something outside the universe to do this, it is part of the universe's inherent function.

    Your conclusion doesn't follow at all.
    Certainly it does. My observation is that the things we observe are caused by the universe we observe them in, and we can create tests that show this or at least that it operates as if this were true. It is not a leap then to think that some phenomena we know to have happened in that universe was also not a product of that universes operation. People once thought maggots were created magically from nothing, part of the spontaneous generation of life. But we learned in fact they come from the eggs of flies that land on the corpse. Every time we get the chance to actually examine the source of an event, the magic explanation invariably fails. It is not so wild to expect it will fail in this case as well once we have the opportunity to observe the process or reproduce it. Magic as an explanation is a consistently loosing bet.

    The problem is, it doesn't matter how it occurred. Using your logic ANYTHING as long as it occurs in the universe is likely to have occurred because of the natural operating mechanisms.
    I changed words in bold to make this sentence accurate to my views. As of yet no one has ever managed to prove that an event was not a natural one. All they can do is say that we as of yet have not proven the natural mechanism. That does not mean there isn't one, only that we may lack the knowledge. But the last few hundred years have shown that over time and with persistence we can and will find the natural explanation for near any event and that the magical explanations will inevitably fall to the objective investigations of science.

    Certainly it is (arbitrary), because you give preference to what you have seen, while the other explanation is equally as valid.
    No it is not. My source of knowledge is such that anyone can experience if they choose to. Any person can make a test of gravity and any person can make an investigation of the behavior of light and they will get the same results if they follow the same steps. But worshiping gods has no consistency. Different people can worship different gods and get the same result, while many people can worship the same god and get wildly different results. Faith and feeling have a track record of unreliable knowledge while science and experimentation have a track record of ever improving results. It is everything but arbitrary.

    Arbitrary: subject to individual will or judgment without restriction; contingent solely upon one's discretion: an arbitrary decision.

    Faith is arbitrary, science is not.

    So, we haven't observed proteins forming in a natural environment, and have only observed them being constructed from scratch by intelligent forces.
    No, unless you consider an Amoeba to be intelligent or the process of cell operation to be willed by human beings, there is no observation of proteins constructed from scratch by intelligent forces. Everything that happens in your cell obeys the laws of chemistry and physics and is not the product of some desire or will. Whatever you might want your cells to do they do what they must do and cannot do anything else. They are natural processes. Living things do not follow different rules than non living things. We have not observed proteins forming spontaneously because we have not yet figured out what circumstances are required. The earth has changed in the billions of years its been around and whatever circumstances were needed clearly aren't in place today nor have we yet figured out what they are. That does not mean they could not have happened. It is not likely a limit on what nature can do, its a limit of what we know about nature.

    No, we just so happen to live in a universe where the milk spontaneously disappeared.
    We do not live in such a universe. If we did, then the event would be expected and consistent provided there were not arbitrary magical agents at work. We often suspect such agents in our world, but when push comes to shove those ideas give way to proven and testable natural explanations.

    As we live in a universe, and the milk diapered, then we are free to conclude that in our universe it is only natural for that milk to have disappeared.
    Sure, but then if you want to understand how that happens, you investigate when it happens and devise experiments to isolate the possible causes. If we never tested any supposition, well we could believe anything, and in times gone past that is exactly how we did it. but as time has gone on, we have learned a process that lets us make much more reliable and effective explanations that prove themselves out.

    If you want me to accept that God created life, you need to give me a test for it or a means to observe it. Or you need to set up a pattern of observable and testable circumstances that are similar enough to set up a likely precedent and while that is not proof it is at least strongly suggestive. If we could demonstrably prove God does anything at all, then we could extrapolate he does other things too. But we don't have hard testable objective evidence of god doing anything at all to extrapolate from.

    All you have is "we don't know how it could have happened yet so god must have done it" And that is not in the least convincing to anyone with a critical mind.

    After all, it is completely possible for milk to disappear (or dematerialize).
    Is it really? Has it every happened? Is there a principle of nature we have observed that makes things dematerialize? I'm not aware of any. Just because you can imagine a thing doesn't mean the thing is actually possible. I can imagine a wizard riding a dragon but that doesn't mean it is truly possible.

    O, well if your bias is not a problem, then by all means just base all of your arguments on your own personal bias, and appeal to it as the validation of your arguments.
    That seems very logical.
    It is logical despite your sarcasm. To dismiss such bias bars any and all of us from using our minds since we can only think based on what we know and we can only know by virtue of experience. The bias of our experience is inescapable it is the limit of human thought.

    If you are willing to accept that an event as unlikely as one with over 100 zeroes behind it, actually did occur.
    Then the odds of letters being eroded into a rock through natural processes are insignificant.
    Any time you are addressing such "odds" you are utterly misunderstanding my position. I do not think anything happens by chance of that sort. Every lottery on earth happens in a precisely deterministic way and has an inevitable outcome, it just so happens no human being is capable of predicting that outcome due to our limited knowledge. There are no odds in the universe, however humans must use probability to make useful predictions because we have limited knowledge.

    I will ignore any further mention of "odds." as a strawman.

    The very reason you "suspect" and thus assert by testing that an intelligent cause should be investigated and given preference so as to justify investigating THAT vs investigating erosion patterns, is because all other explanations are so unlikely as to cause such investigation and suspicion to be unreasonable.
    Investigating likely odds is far more effective than investigating likely ones. If you want to look for an object in an unknown location, you will find it more often by looking int he places it is more often found. If you always start with the least likely places, you are less likely to find it. If you do not find it in likely places then you must look in less likely ones despite the long odds (that is if you wish to find it). To do otherwise is foolish with respect to your goal.

    That is the case of the OP. The idea that it occurred naturally is so absurdly unlikely, that one should not even suspect it as being the cause. Yet you do, and the reasoning you offered applies to EVERY absurd yet physically possible outcome.
    The OP however is simply factually inaccurate. It not only doesn't take into account the way the universe operates, it makes false claims about the nature and composition of proteins. Furthermore it strawmans the opposing view. It is flawed in nearly every respect from the get go. It only succeeds in knocking down its own strawman argument.

    You have asserted that because it occurred in nature, then it must have been the result of nature.
    I have not. I have said if it occurs in nature it is likely the result of nature and that we as yet have never found conclusive evidence that anything in nature is the result of something supernatural. The word "must" is not part of my argument.

    All I have done is assert that natural causes are to be blamed for lettering in Rock....
    Imaginary lettering in an imaginary rock. you can assert anything you like about them. Real lettering in real Rock we can do real investigation to determine where it came from. Imaginary lettering in imaginary rock... well you can imagine any imaginary god you like put it there.

    Your protest shows your standard to be lacking, as it is YOUR standard and your reasoning that I am using.
    My standard has led to the curing of a great many diseases, landing men on the moon, producing enough food for billions of people, identifying the underlying mechanisms of the human body, splitting the atom, and a great many other amazing accomplishments. What amazing things has religious faith brought us that never existed before it?
    Feed me some debate pellets!

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  5. #64
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    Re: Abiogenesis and evolution - The protein dilemma

    "I now believe that the universe was brought into existence by an infinite Intelligence. I believe that this universe’s intricate laws manifest what scientists have called the Mind of God. I believe that life and reproduction originate in a divine Source. Why do I believe this, given that I expounded and defended atheism for more than a half century? The short answer is this: this is the world picture, as I see it, that has emerged from modern science."
    Antony Flew

    Torpex
    Fear not, this "objection" to proteins being formed through chance was dealt with almost 30 years ago, it's just that not all the evolution deniers update their websites to reflect it.
    http://ncse.com/cej/5/2/new-proteins-without-gods-help
    Finally, I commend you on finding something relevant to this debate.
    I heard about this bacteria back in the 90’s in one of my science magazines. At the time I didn’t think much about it, but, since you brought it up I have gone back and researched it.

    First of all you must realize that when bacteria are starved or stressed the transposase enzymes on the pOAD2 plasmid are activated. This mechanism allows them to digest other materials.
    So it is possible this is simply part of the design of the bacteria. Don’t forget that nylon is an oil based material made of carbon, even though it is arranged differently it is still made of the basic components of life, so digestion of it is not a stretch.

    It is also possible, that, like Ohno claims, it is a frameshift mutation and therefore new information.
    The first problem you must overcome with this theory is that frameshift mutation moves all nucleotides one space in the codons. That normally gives you a lot of stop codons in the sequence. Stop codons are made of UGA, UAG, and UAA, so if we have a sequence of UAA-GUA-AUG-UAU-GAU and we delete the first U to shift it we get AAG-UAA-UGU-AUG-AU*. As you can see we lost a stop codon and gained one.

    The real problem is that this particular sequence has 1535 base with no stop codon. That is highly unlikely and points to the first explanation as being the most logical.

    If it is a new protein of sorts, the problem with it is the 2 to 3% efficiency. Kind of reminiscent of the sickle cell anemia, because it creates an extremely weak organism when compared to the non mutant variety. Even though it has some positive due to the mutation, the overall effect is to weaken the organism in a drastic way. Imagine your body only being able to digest 2 to 3% of what you would normally digest.

    You can claim this as proof positive that new proteins can be created, but, I think it is fairly sketchy and imo more likely to prove design.
    Still, I think it is a substantial argument and worthy of bringing into the debate.

    No, please be honest - in your OP you used the average size of a modern protein to argue that "chance is not even a remote possibility to have been the vehicle by which the first life forms came about."
    Because the same basic requirements are needed to drive the mechanisms of life. If you wish to lower the average size that is fine, just give me a figure and your reasoning. The probabilities will still be dismally small.

    The following peptide:
    arg-met-lys-gln-lys-glu-glu-lys-val-tyr-glu-lys-lys-ser-lys-val-ala-cys-leu-glu-tyr-glu-val-ala-arg-leu-lys-lys-leu-val-gly-glu
    is able to self replicate itself, albeit given two specific source peptides.
    This is unbelievably fallacious. I am hoping you are giving this example out of ignorance and that you really don’t understand it, because otherwise it means you are being intentionally deceptive.
    To use the words “self replicating” to describe this process is what assures me that proponents of abiogenesis are devoid of any real self replicating examples.

    First of all we have to have a polypeptide that is 17 amino acids long and then another that is 15 amino acids long. Then we have to align these with the 32 amino acid peptide and 1 bond occurs that puts them together. You would call that self replicating?
    You need to stay away from your propaganda websites, they are making a fool out of you.

    You are never going to get a self replicating system that is simple. The reason for that is you must have energy to replicate and a simple system cannot create or utilize energy to replicate. The problem you end up with is similar to a perpetual motion machine, which the laws of physics simply do not allow.

    This is why people who understand the mechanics of life will tell you that the smallest system that will self replicate will need to have at least 256 proteins. Here is a paper that outlines a discussion of between 206 to 387 proteins and why they came to their conclusions.
    http://www.pnas.org/content/103/2/425.full

    Yet again, this STILL assumes numerous things, for instance that the first ever cell in existence was as complicated as the simplest modern cell, and more importantly, that each of the many amino acid positions in a protein must be filled by the one particular amino acid suitable for that position.
    This comes from the FACT that a 3.5 billion year old fossil prokaryote was found in the western Australia, Warrawoona Group that is similar if not identical to its modern counterparts.
    This means that we must have a similar amount of proteins and complexity. Even if you disagree with that, reduce it to a tenth of the proteins and it is still overwhelmingly impossible because you have to produce these in the short span of 500 million years.

    And as far as substituting one amino acid for another, you proved that with your example of sickle cell anemia. That is only one amino acid different and produces a debilitating, painful condition that shortens the life span of the person afflicted. In 1973 the average lifespan sickle cell anemia was 14, now they have raised it to the 30’s – 40’s. To use this as a positive example, as they did in our science textbooks, is foolishness.

    In reality, the latter is false, and many proteins show in their structure that they were built of smaller subunit sequences of amino acids.
    I am sure in your mind this makes sense somehow, but, you still have to put the units together, then the subunits together, so you still have the exact same amount of complexity.
    “The Edge of Evolution” explains this in much more in depth than I can on a post.

    And I've demonstrated numerous times and in numerous ways why your application of math doesn't make any sense.
    It just doesn't seem to sink in - you need to know precisely how something happened or will happen, before applying probability in any useful way.
    And I’ve responded that numerous times as to why I used simplifications that favor your point of view in every way.
    It doesn’t seem to sink in with you – that when I do show you the chemical realities it will just make it more impossible. But, since that is what you want, that is what I will do when I get the time.

    Since you've failed to understand any of the previous thought experiments I tried to teach you this with, I'll try one last one.
    What you don’t seem to understand is that you are trying to push your philosophical view off on me.
    Basically, you are trying to say if it is here then there are 1 to 1 odds of it happening, and since there is no God then it had to happen naturally, so there is a 1 to 1 odds of it happening naturally.
    It is circular narrow minded reasoning, that is why I don’t even respond. If I said, I am always right, therefore I am right because I just said I was, then you probably would ignore such reasoning because of its irrationality.

    I've never seen any current theory which reflects the theory your OP objects to.
    Then post links to a clearly defined theory that I can look at.

    "This, much like your OP, merely assumes that the evolution of complex proteins is a process that necessarily goes on in organisms"
    when clearly every naturalistic hypothesis of abiogenesis suggests that complex proteins existed long before the first thing that might be called an "organism" did.
    Wrong on both counts. I assume that you can’t produce complex proteins in organisms. Reread the post.
    And I strongly oppose the theory that you have complex proteins before an organism. The only place you are going to find such pseudoscience is on your propaganda websites. Even if it was possible to produce them how do you imagine they would have kept from unraveling as fast as they were put together.

    It really is - the odds of you winning the lottery are slightly different if, instead of one ticket, you have 50 billion.
    I gave you 10e+80 tickets and you still couldn’t win the lottery.

    However, stochastic self-assembly mechanisms, the self organizing patterns predicted by the late Alan Turing, have been observed in cultures of E Coli.
    I will look at these when I get time. Please put a link for this.

    but in the same breath, to claim that because we've done lots of experiments, haven't found any, therefore:
    a) they don't exist
    There is a time and amount of experimentation that each person will consider an idea falsified. That will vary per person, imo, the auto assembly of proteins has been falsified. I am sure that in your opinion and people of your faith, it will never be falsified.

    and I say again; many proteins show in their structure that they were built of smaller subunit sequences of amino acids.
    And the odds against those assembly of substructures weigh in the same as if it was done at one time, because, there is no attraction or auto assembly shown in an amount that would make a difference. In fact, just the opposite is shown to be true, there are natural chemical forces that make a lot of the proteins almost impossible to put together.
    I will try to condense that information and put it into a post so you can see what I am talking about.

    I can only imagine why you'd be looking at modern life forms and viruses to argue anything about how life originated - that's like looking at a cruise missile and arguing the first weapons could not have been made by cavemen.
    Because the same basic systems are needed to accomplish these goals and life is using the same basic mechanics. In fact, the first cells we find that are 3.5 billion years old can be categorized with their modern day counterparts.

    aah yes, what chemical signature would you expect and why? You already know that proteins easily denature, organic compounds can be found everywhere, regardless of whether life ever did, what would you expect to see?
    Organic compounds can be found everywhere? I think that geologists missed that memo. Study the Hadeon Eon - 4.5 to 3.8 bya to find the error in what you are saying.

    Rocks that have been made when there is life are distinguishable even if there are no fossils because of the chemical signatures.
    There should be large amounts of inorganic carbon, which would be distinguishable from carbon produced from life and there should be a "tar" layer that is very deep based on the current theories.

    Not realized - concluded.
    OK – got me there

    The flat earthers out there say the exact same thing.
    You mean people that stubbornly ignore overwhelming odds and cling to their illogical beliefs…

    I expected a better argument than:
    - strawman
    This is not a strawman argument. In order for it to be a strawman argument I would have to make up the base for the argument, but, I didn’t. I used an assumption that was based on the smallest number of proteins that was set by evolutionary authors( http://www.pnas.org/content/103/2/425.full ) for abiogenesis and I used what I had been taught that evolution was and have backed that up with what is still being taught by the major universities today.
    I have tried to be as factual as possible and as fair as possible in reflecting the traditional thought on evolution and abiogenesis.

    And I'm still disappointed that every attempt to draw your attention to these things has fallen on deaf or non-understanding ears.
    Neither deaf, nor non-understanding; I understand perfectly what you are saying and most of it is totally irrelevant because of your lack of understanding of the basic mechanisms of the cell.
    I feel exactly the same way about your disregard for mountains of evidence while holding on to faulty and inconsequential arguments to prove your point.

    [quote] Since I'm not supposed to post links and just expect you to read through it, I'll quote from the following link:
    http://ncse.com/cej/5/2/new-proteins-without-gods-help
    Since there are twenty different amino acids available for each position, the chance of randomly getting a string of 200 amino acids all in the right order is (1/20)200

    Your “expert” at your propaganda site doesn’t even know how to do basic math (1/20)200 = 6.22e-261. Also, he doesn’t know that proteins are folded and can be construed at a multiple amount of angles in relation to each other affecting the basic equation exponentially.

    These calculations almost always involve the erroneous assumption that each of the many amino acid positions in a protein must be filled by the one particular amino acid suitable for that position… But proteins, even modern highly evolved specialized proteins, are not built with that degree of specificity.
    I would like to see proof of this, because every thing that I have seen concerning genetic diseases says just the opposite. If you can show a large amount of proteins that have amino acid variances with no effect then I will be happy to take that into consideration .
    Last edited by rlms; December 3rd, 2012 at 06:18 PM.

  6. #65
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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by SIG
    The assume the world we live in was desired, and so its order is one designed to create the outcome we observe. They view the only alternative as a universe where everything is random and anything is possible and only dumb luck produces what we observe.
    That is because "purposed" or "random" is the exhaustive list of possibilities.


    Quote Originally Posted by SIG
    The best I can seem to muster is to tell you the universe is entirely ordered, but that order does not serve a will or desire, it simply is the order that is and it does not serve any emotional need or purpose.
    Look the universe is based on some basic values, and there is nothing that makes those values "necessary".
    Such as the value of gravity. That means that the value of gravity is either ordered to be such that it is in order to achieve a result Or The value is random and the result is the natural effect of it.

    In other words, if gravity were stronger, then naturally the uni would have collapsed into a black hole or the "big crunch" much sooner.

    What you seem to be holding is that because gravity IS what it is then we can not nor should not derive any meaning from it.
    If a universe with life in it is impossibly unlikely and falls within a precise range, then you say .. 'well that is just how it is."
    Of course, you don't or refuse to do this in regards to anything else on much smaller orders. (such as the 10 commandments etched in a wall). For some reason then you gladly appeal to your human bias.

    IMO your application of your belief is inconsistent and thus unpersuasive and unreasonable.

    Quote Originally Posted by SIG
    My observation is that the things we observe are caused by the universe we observe them in,
    Right.. like this response. It just occured in the universe.. so clearly it was caused by the universe.

    You are either ignoring intellegence/will or counting it as the "universe". both are Flawed understandings IMO.

    Quote Originally Posted by SIG
    It is not so wild to expect it will fail in this case as well once we have the opportunity to observe the process or reproduce it. Magic as an explanation is a consistently loosing bet.
    If your official response is to rely on your "faith", then state it clearly.
    That you have no response but you have faith the case made in the OP will one day be responded too.

    Your objections to the OP are not sustained as all you are doing is asserting a blind faith.
    Quote Originally Posted by SIG
    I changed words in bold to make this sentence accurate to my views. As of yet no one has ever managed to prove that an event was not a natural one. All they can do is say that we as of yet have not proven the natural mechanism. That does not mean there isn't one, only that we may lack the knowledge. But the last few hundred years have shown that over time and with persistence we can and will find the natural explanation for near any event and that the magical explanations will inevitably fall to the objective investigations of science.
    So your faith is what gives you comfort in the face of irrationally high odds or in the face of as close to can be estimated an event that should not be expected to be a result of random natural processes.

    ------

    .. Honestly. I'm not going any further into your post. Consider the rest of it your last word.
    You have just stated your belief, you have not offered a rebuttal or reasoning against the OP. You have every right to your faith. I'm sorry the OP contradicts your faith... good luck with that.
    To serve man.

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by rlms View Post
    To avoid repetition, please refrain from the self replicating RNA argument; it is non-existent now and if it did exist in the past we would have geological proof in the way of chemical signatures in the Pre-Cambrian layers of rock.
    I would still like to know what chemical signatures of self replicating RNA we could expect to find - not to mention where we would look for them. It seems vaguely important as you're apparently dismissing the "RNA world" hypothesis based on this evidence.

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by MindTrap028 View Post
    That is because "purposed" or "random" is the exhaustive list of possibilities.
    That is a misconception. I covered what Random means in a reply to the OP but let me review. It can have two primary meanings, which are similar but distinct in use.

    The OP uses Random in the sense that there is no possible predictive causality and thus every imaginable amino acid combination has equal probability. This is what you might call a pure idea of randomization. Pure probability. My critique of this is that there is no such thing as pure probability in the universe. Gravity is not as likely to push mass away as to pull mass to it. While you could imagine that, the nature of the universe makes it impossible so it is neither realistic nor equally probable. In fact it only has one way it operates. The cells of our body are no different, they follow the same kinds of laws, they are just more complicated for us to describe.

    The OP considers all formations of amino acids equally probably but makes no support for that. Science has shown that in fact amino acids behave in some rather predictable ways under given conditions, not in random ways. Furthermore proteins to not require absolute precision, there is what you might call a margin of error in positioning and orientation for proteins that makes a whole set of combinations functionally equivalent so even if you allow randomness (for no good reason) it is not 1 to X. Nor are the proprieties he is using as an example expected to be the sort that was part of early life. Expectations are that the proteins would be far more simple and cells far more primitive. The odds he provides are commonly known as Hoyle's Fallacy http://en.wikipedia.org/wiki/Hoyle%27s_fallacy Perhaps the article there can explain better than I can but it is using more technical terms to make the same argument undermining the OP's probability claims. Hoyle BTW was an atheist and astronomer, not a biologist or theist.

    Analogy time. Lets say you are having a foot race with 100 runners. Hoyle would argue the odds of any given runner winning the race is 1 in 100. You could imagine that any of them could win. But in reality the winner of the race is the one who has the best training and runs into the least difficulties in the process of running the race. The more you bother to learn about the runners and the race course the better you could figure out which of them will win. If you had the foresight to see things like which one would sprain an ankle due to where they will put their feet during the race and which one might get a call the night before about a divorce and how his personality will react to that and so forth to the point of infinite knowledge, then you could simply state for fact which one will win. It is not random. Amino acids are not random, nor are proteins. Just because you can imagine them doing something they didn't do, doesn't mean they actually might do that. Just like you might imagine fat jimmy winning the foot race, it may well be he has 0 chance of winning that race.

    The second use of Random is used to distinguish between what we intend and can control as human beings, and what we did not intend and cannot control. So we might say the path of a river is random, or the roll of a dice is random because we don't control those things and thus they don't follow our will. This kind of randomness is rightly referenced when talking about nature. Nature does not obey our will nor do we observe it directly obeying the will of any other entity that we are aware of. Evolution does not appear to have any single direction or purpose nor serves any entities direct interest including the living organisms themselves. It is in that sense random rather than directed. But this sense of random does not lead to 1 in X type odds which is the basis of the OPs argument.

    Look the universe is based on some basic values, and there is nothing that makes those values "necessary".
    Such as the value of gravity. That means that the value of gravity is either ordered to be such that it is in order to achieve a result Or The value is random and the result is the natural effect of it.
    In other words, if gravity were stronger, then naturally the uni would have collapsed into a black hole or the "big crunch" much sooner.
    Indeed, but it isn't, it never will be, it never has been and you have no reason to think that such a universe is equally likely as the one we have. In fact there is no probability, because we have no good reason to think that other universe actually is possible just because you can imagine it.

    There is a further challenge. Even if you allow for god, you have the same dilemma. God could have made your big crunch universe just as much as he could have made our universe or any number of other "possible" infinite universes. So the "odds" of us having a god that makes a universe like the one we have is just as remote as the "odds" of us naturally having the universe we have without a god. God does not narrow down the odds in any way.

    You can say God doesn't play odds, that is the point, but I can and do simply say the universe doesn't play odds either. On all these cases the positions are exactly equal. What makes the theist view inferior is it invents an agent for which there is no president or objective evidence, while evidence for the universe itself is literally self evident.

    The OP is dependent on the idea that in the atheist view literally anything is possible. But no atheist I have ever met holds such a view.

    What you seem to be holding is that because gravity IS what it is then we can not nor should not derive any meaning from it.
    It is its own meaning. The kind of meaning you are thinking of is human. You might like gravity or dislike it for one reason or another. But gravity does not serve our will. What it does is have a causal effect on us, part of the constraining web of universal causality.

    If a universe with life in it is impossibly unlikely and falls within a precise range, then you say .. 'well that is just how it is."
    No, I don't. I say that given the universe we have, life is inevitable. In a different universe perhaps it is not, but there are no other universes but the one we exist in so far as we can tell. Just because you imagine it could happen, doesn't mean it actually can.

    Right.. like this response. It just occured in the universe.. so clearly it was caused by the universe.
    Correct, it was.

    You are either ignoring intellegence/will or counting it as the "universe". both are Flawed understandings IMO.
    You at least follow my reasoning. Intelligence is indeed part of the universe, specifically our intelligence is part of the universe. Without the universe our intelligence cannot exist. Your brain is a fundamental component of the universe as is mine. No universe, no will. If you can show me a will in action that is not part of the universe... well I'll be quite impressed. If you can show me a single decision that is made without a physical manifestation to make it, go for it. If you can show me a single uncased event, I'll be quite impressed.

    In the end you want there to be magic, so you believe in it. And that too is part of the function of the universe in action.

    If your official response is to rely on your "faith", then state it clearly.
    As hard as it may be to imagine, philosophically I have no faith, I could always be wrong. The only respect in which I have faith is there are some questions as a practical matter I don't bother asking. I don't question if gravity will apply to me in the next 10 seconds, I have a practical faith it will be there. But philosophically, perhaps it won't.

    That you have no response but you have faith the case made in the OP will one day be responded too.
    Your objections to the OP are not sustained as all you are doing is asserting a blind faith.
    Incorrect. The OP asserts that all possible amino acid combinations are equally probably. I have argued from a number of points that this is not true. None of that has been refuted. The OP simply keeps demanding I demonstrate exactly without any doubt, how it happens. I don't have that knowledge to share, but the OP is about odds, not about whether or not we have made a given discovery.

    So your faith is what gives you comfort in the face of irrationally high odds or in the face of as close to can be estimated an event that should not be expected to be a result of random natural processes.
    No MT. My mind tells me the universe doesn't have odds, that there is only ever one possibility but that my limited mind is not capable of knowing it in full and thus I use probability as a tool for making predictions of the unknown, not as an accurate description of the nature of reality.

    Time and time again you and the OP keep telling me what I think, and you keep getting it wrong. Its no surprise you can't rebut my points if you can't comprehend them. (Though to your credit you are at least batting about 50% in this most recent rebuttal.
    Feed me some debate pellets!

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by sig
    The OP uses Random in the sense that there is no possible predictive causality and thus every imaginable amino acid combination has equal probability. This is what you might call a pure idea of randomization. Pure probability. My critique of this is that there is no such thing as pure probability in the universe.
    That is not an actual counter to the OP though. Your right, IF it is possible for amino acids to form naturally into proteins, then there is a given set of conditions which will CAUSE proteins to form.

    In fact, that is exactly what the OP argues from. We know the given conditions, and we can see that we should not expect them to exist anywhere in the universe naturally. Further, there is nothing in nature that causes those conditions to occur naturally.

    Quote Originally Posted by SIG
    Gravity is not as likely to push mass away as to pull mass to it. While you could imagine that, the nature of the universe makes it impossible so it is neither realistic nor equally probable. In fact it only has one way it operates. The cells of our body are no different, they follow the same kinds of laws, they are just more complicated for us to describe.
    Right, but the laws governing amino acids and proteins etc.. make any idea of natural formation even more unlikely (here used as unreasonable to accept as a naturally occurring event). Because there are forces which actively destroy/prohibit and hinder the process. (see the bottom of post to see some context regarding "natural event).

    The OP is being vastly generous in it's "conditions". You are not adequately defending that we should reject it on the basis of not being generous enough.
    See there is no "law" by which all amino acids MUST interact, further there are laws that cause the interactions to be unstable. The fact that the OP causes all amino acids to interact and hold together is far more than we OUGHT to consider reasonable. Thus if such conditions can not reasonable be held to produce a protein, then the ACTUAL conditions are even more unreasonable to accept as being capable of producing a protein naturally.

    So your objections if we do take them into account only cause the problem to be even more remote.
    Appealing to the "laws of nature" only assumes that they CAN make proteins from scratch. .. which as I understand it has never been demonstrated using natural processes.

    Quote Originally Posted by SIG
    Analogy time. Lets say you are having a foot race with 100 runners. Hoyle would argue the odds of any given runner winning the race is 1 in 100. You could imagine that any of them could win. But in reality the winner of the race is the one who has the best training and runs into the least difficulties in the process of running the race. The more you bother to learn about the runners and the race course the better you could figure out which of them will win. If you had the foresight to see things like which one would sprain an ankle due to where they will put their feet during the race and which one might get a call the night before about a divorce and how his personality will react to that and so forth to the point of infinite knowledge, then you could simply state for fact which one will win. It is not random. Amino acids are not random, nor are proteins. Just because you can imagine them doing something they didn't do, doesn't mean they actually might do that. Just like you might imagine fat jimmy winning the foot race, it may well be he has 0 chance of winning that race.
    That is why the OP makes unreasonable and unrealistic assumptions in order to INCREASE THE ODDS of a naturally forming protein.

    The fact is, Abiogenises is the blind/def/dumb/legless, armless torso boy in a race with 99 Usain Bolt clones.

    Quote Originally Posted by SIG
    Indeed, but it isn't, it never will be, it never has been and you have no reason to think that such a universe is equally likely as the one we have. In fact there is no probability, because we have no good reason to think that other universe actually is possible just because you can imagine it.
    How do you know it isn't? The multi-verse theorist require it to exist.
    Second, we know it is possible because our universe had a beginning and there is NOTHING that makes the current values necessary. You are making a faith claim not one that is born out by the evidence.

    If you did the big bang over, the universe we currently have is not "necessary", thus all the "possible" values it could have had are not simply "hypothetical" but ACTUAL possibilities. There is a reason our uni is as it is, but the evidence doesn't suggest that the "reason" is because this version is "necessary".


    Quote Originally Posted by SIG
    There is a further challenge. Even if you allow for god, you have the same dilemma. God could have made your big crunch universe just as much as he could have made our universe or any number of other "possible" infinite universes. So the "odds" of us having a god that makes a universe like the one we have is just as remote as the "odds" of us naturally having the universe we have without a god. God does not narrow down the odds in any way.
    Please see your runner example, because you just made the same fallacy you accused the OP of.

    Quote Originally Posted by SIG
    You can say God doesn't play odds, that is the point, but I can and do simply say the universe doesn't play odds either. On all these cases the positions are exactly equal. What makes the theist view inferior is it invents an agent for which there is no president or objective evidence, while evidence for the universe itself is literally self evident.
    Then your argument is completely circular.. and thus rejected.
    You are arguing that the universe is the cause, because it occurs in nature.

    I have already addressed this and shown how this applies to ALL possible events, thus if you are consistent you will be unable to justifiably and consistently differentiate between events. You can not reject the claim that Jesus Walked on water, because it is only natural that he should as it occurred in nature.
    (see? you couldn't even argue against such a statement by the reasoning you have used here.)

    Quote Originally Posted by SIG
    No, I don't. I say that given the universe we have, life is inevitable.
    That is a great way to assume what is being discussed, without actually addressing the arguments against it.
    All you are forwarding is a truism.

    Quote Originally Posted by SIG
    In a different universe perhaps it is not, but there are no other universes but the one we exist in so far as we can tell. Just because you imagine it could happen, doesn't mean it actually can.
    addressed above.

    Quote Originally Posted by SIG
    Correct, it was.
    Consider your circular argument rejected as meaningless.

    Quote Originally Posted by SIG
    In the end you want there to be magic, so you believe in it.
    Nope, just following the evidence.

    Quote Originally Posted by SIG
    Incorrect. The OP asserts that all possible amino acid combinations are equally probably. I have argued from a number of points that this is not true. None of that has been refuted. The OP simply keeps demanding I demonstrate exactly without any doubt, how it happens. I don't have that knowledge to share, but the OP is about odds, not about whether or not we have made a given discovery.
    No sig, the OP is showing what nature MUST overcome in order to produce an effect.
    Whatever "law" (if one exists) that actually causes proteins to form it must select from the possible combinations. It must show preference (not the intelligent kind) or a built in per-disposition that can be repeated. (otherwise called a law)

    It has been further argued that given the tests done, we can conclude that no such law or predisposition exists.

    Quote Originally Posted by SIG
    No MT. My mind tells me the universe doesn't have odds, that there is only ever one possibility but that my limited mind is not capable of knowing it in full and thus I use probability as a tool for making predictions of the unknown, not as an accurate description of the nature of reality.
    Right, now we are talking about what that one reality entails. It is logically possible that God/s caused life to occur in this uni.
    It is also logically possible that it occurred naturally. We are making arguments for which one should be accepted.


    Quote Originally Posted by SIG
    Time and time again you and the OP keep telling me what I think, and you keep getting it wrong. Its no surprise you can't rebut my points if you can't comprehend them. (Though to your credit you are at least batting about 50% in this most recent rebuttal.
    I'm trying

    As I see it, the basic disagreement is this.
    You hold that because it exists in nature, then nature is it's cause. This you hold to be "self evident".

    The OP and I hold that we commonly separate things into naturally occurring events, and non-naturally occurring events. We know of the second because we can see the effect that our intelligence has on the world, and that it is different from all other occurrences.

    IE we can distinguish between the pyramids and the grand canyon because while rocks are naturally occurring, the arrangement in the pyramids is not a "naturally occurring" arrangement.

    The assertion is that we can apply this principle beyond only human activities. When we do we are justified in concluding a non-natural source for life, because it just as the pyramids
    are not naturally occurring events, even though they occur in nature.

    I reject your position, because it is incapable of distinguishing the Pyramids with the Grand Canyon.


    ***Note****
    Hoyle's Fallacy, is not an actual logical fallacy. It is claimed to be fallacious and simply "labeled" a fallacy.
    It is not nor should we accept it to be an actual fallacy. .. you will have to support the assertion yourself
    To serve man.

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by radix View Post
    I would still like to know what chemical signatures of self replicating RNA we could expect to find - not to mention where we would look for them. It seems vaguely important as you're apparently dismissing the "RNA world" hypothesis based on this evidence.
    Sorry for the delay in answering, I have been struggling to get time to answer all the posts.

    That would be a secondary dismissal for the self-replicating RNA.
    The main reason for RNA not being able to self-replicate requires an understanding of life and how it operates.
    You have to have the basic components including:
    • Instructions
    • Gathering of Molecules(exterior)
    • Transport of Molecules(interior)
    • Removal of Waste Molecules
    • Conversion of Energy

    If you remove any one of these you cannot have a serious reproducing organism. It might happen by chance, but it would be rare to never.

    Modern life pushes the limit of simplicity at the expense of reproductive capabilities.
    We can see that in obligate intracellular parasites, which consist of certain bacteria, protozoa and fungi. They are unable to reproduce without a host cell because one or more of these elements are missing. They are far more complex than the supposed self-replicating RNA and yet still incapable of reproduction on their own.

    The experiments that claimed to have accomplished the self-replicating RNA have been basically “manufactured” in the lab by methods that are not even remotely realistic or possible in real life.

    But, let’s say the impossible did happen, we have RNA-peptide interactions made by amyloid and nanotube-forming peptides.
    That is the most plausible and widely accepted theory because of its introduction of energy to the equation.
    Both amyloid-forming motifs and nanotube-forming peptides have aromatic residues.
    The aromatic stacking interactions theoretically would supply the energy that would be missing without the cells mechanisms.

    The aromatic resins would have created large amounts of tar. One website had predicted 1 to 10 meters, which I am not sure how they calculated that, but, it would be significant nonetheless. To have none would prove there was no activity of this kind, which is exactly how much is in the earliest pre-biotic(pre-life) rocks from the Hadean Eon, zero.

    Also, you would have inorganic carbon in large amounts that would be very detectable in these rocks, and again you have none in the Hadean Eon formations. Inorganic carbon is distinguishable from organic carbon so when we find it later in the Archean Eon we can tell it comes from cells.
    Last edited by rlms; December 5th, 2012 at 07:19 AM.

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by rlms View Post
    The main reason for RNA not being able to self-replicate requires an understanding of life and how it operates.
    You have to have the basic components including:
    • Instructions
    • Gathering of Molecules(exterior)
    • Transport of Molecules(interior)
    • Removal of Waste Molecules
    • Conversion of Energy

    If you remove any one of these you cannot have a serious reproducing organism. It might happen by chance, but it would be rare to never.
    How do you define a "serious reproducing organism"? Your list of requirements would certainly apply to living cells we can observe today but why would you assume this would also be the case for their early ancestors? After all, modern cells have had something like 4 billion years to evolve. The protocell model that Szostak and others are working on only has two components: a replicator (RNA or some chemical equivalent) and a lipid bilayer membrane. That's it. No instructions are needed, just the capacity to self-replicate. Gathering of molecules (in this case nucleotides and lipids) would rely on diffusion and convection. The protocell wouldn't be considered to be "alive" by any commonly used definition but it would still be able to serve as a starting point for life through its ability to self-replicate and evolve.


    But, letís say the impossible did happen, we have RNA-peptide interactions made by amyloid and nanotube-forming peptides.
    That is the most plausible and widely accepted theory because of its introduction of energy to the equation.
    Both amyloid-forming motifs and nanotube-forming peptides have aromatic residues.
    The aromatic stacking interactions theoretically would supply the energy that would be missing without the cells mechanisms.
    The most plausible and widely accepted theory of what? Abiogenesis? I've read quite a bit on this subject but I must admit I've never come across this theory. Got any references I could check out? As for energy, there would have been external sources (mainly solar and volcanic) that would have been able to provide the energy needed.


    The aromatic resins would have created large amounts of tar. One website had predicted 1 to 10 meters, which I am not sure how they calculated that, but, it would be significant nonetheless. To have none would prove there was no activity of this kind, which is exactly how much is in the earliest pre-biotic(pre-life) rocks from the Hadean Eon, zero.

    Also, you would have inorganic carbon in large amounts that would be very detectable in these rocks, and again you have none in the Hadean Eon formations. Inorganic carbon is distinguishable from organic carbon so when we find it later in the Archean Eon we can tell it comes from cells.
    The lack of detectable amounts of tar doesn't strike me as a very convincing piece of evidence against the RNA world hypothesis. I'm actually at a loss to understand why anyone would think large amounts of tar would be a necessary byproduct of abiogenesis. Even if the proposed RNA world inhabitants would have left some geologic traces behind, you have to remember just how old those rocks would have to be. The oldest fossilized organisms I'm aware of are about 3.5 billion years old. They are believed to be sulphur compound-metabolizing bacteria so they would most certainly have been DNA/RNA/protein organisms. Traces of a possible RNA-only world would have to be found in even older rocks. I'm not a geologist but it's my understanding that rocks that are older than 3.5 billion years and that can still be examined in their original state are very rare. If the RNA world ever existed, it may well have been a very localized phenomenon limited to one or a few favourable microenvironments so in this case I would say that the absence of evidence is certainly not evidence of absence.

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by RADIX
    Even if the proposed RNA world inhabitants would have left some geologic traces behind, you have to remember just how old those rocks would have to be. The oldest fossilized organisms I'm aware of are about 3.5 billion years old. They are believed to be sulphur compound-metabolizing bacteria so they would most certainly have been DNA/RNA/protein organisms. Traces of a possible RNA-only world would have to be found in even older rocks. I'm not a geologist but it's my understanding that rocks that are older than 3.5 billion years and that can still be examined in their original state are very rare. If the RNA world ever existed, it may well have been a very localized phenomenon limited to one or a few favourable microenvironments so in this case I would say that the absence of evidence is certainly not evidence of absence.
    Why would the rock have to be older than 3.5 by? Why do you expect them to disappear from existence 3.5 by ago?
    The first extinction event didn't occur until 2.4by ago when micro life is said to introduce free oxygen, according to the BBC. If there is no reason why they couldn't have existed from 3.5-2.4 by ago, then a lack of their existence may indeed indicate that they never did exist.
    It seems to me that there is about 1billion years of recorded history in which we should expect to find the side effects of these things.
    I am a little fuzzy as to what the early earth looked like and what the first hints of life is said to have converted to what.
    But if it was plentiful, then we shouldn't expect it to be "localized" as you say. And considering the problems with it forming at all to begin with, we would expect the conditions that it could form to be abundant.
    To serve man.

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by MindTrap028 View Post
    Why would the rock have to be older than 3.5 by? Why do you expect them to disappear from existence 3.5 by ago?
    Because DNA/RNA/protein organisms are much more efficient in accessing the available resources than an RNA-only organism. By the time bacteria like the ones in the 3.5 billion year old fossils had appeared, the RNA-only organisms would have been long gone. There would simply have been no way for them to compete.

    I am a little fuzzy as to what the early earth looked like and what the first hints of life is said to have converted to what.
    But if it was plentiful, then we shouldn't expect it to be "localized" as you say. And considering the problems with it forming at all to begin with, we would expect the conditions that it could form to be abundant.
    I don't think we can assume that the first protocells were plentiful. Compared to a bacterium, they would have been very flimsy structures that most likely didn't travel well. They would also have been dependant on passive transport of nutrients and probably needed rather specific temperature conditions to replicate. All of this would point to a pretty limited geographic propagation.

    My biggest problem with the "lack of geological evidence" line of reasoning, however, is how would you distinguish between traces of RNA-only organisms and DNA/RNA/protein organisms? I would want to see something a bit more solid on this tar business before I'm ready to buy it as evidence one way or another.

    The Hadean/Archean boundary isn't set in stone (if you pardon the pun) but it's somewhere around 4 billion years ago, which would be right around the time when conditions on Earth would have first allowed life to develop. The fact that we can't find any evidence of life (RNA- or DNA-based) before that is entirely consistent with the proposed hypotheses.

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by radix
    Because DNA/RNA/protein organisms are much more efficient in accessing the available resources than an RNA-only organism. By the time bacteria like the ones in the 3.5 billion year old fossils had appeared, the RNA-only organisms would have been long gone. There would simply have been no way for them to compete.
    That is an assumption I have never understood. Specifically that survival is a zero sum game.
    A more efficient organism doesn't equate to the automatic destruction of a less efficient organism.
    Especially if the difference is minimal. There are also a lot of timing assumptions that are simply not safe ones to make. Specifically, how long from the first instance of replication, to the current fossilized record.

    Basically, you don't know when the first one appeared, you don't know how much of it their was, you don't know how much more efficient the various evolved forms were (so as to wipe out the occurrence of the first). Another consideration is that IF the first one occurred naturally, and the conditions were abundant, then some chemical law would be in-effect (and discoverable) that would make multiple occurrence very probable. In other words if it is the case, exactly as has been hoped in this thread, that there is a force of chemistry which causes it, then it would have continued to occur naturally. Meaning, that it would be impossible or unreasonable to think it eradicated by the evolved forms. I mean, if you have a pool of food that continues to produce the base form, then no evolved form which also converts the same food source ,only faster/better, can wipe it out.

    So, I do not share your assumption that it would be "long gone", nor do I feel that it is very well founded.

    Quote Originally Posted by radix
    I don't think we can assume that the first protocells were plentiful. Compared to a bacterium, they would have been very flimsy structures that most likely didn't travel well. They would also have been dependant on passive transport of nutrients and probably needed rather specific temperature conditions to replicate. All of this would point to a pretty limited geographic propagation.
    If we take this line, thus taking a different line of argument from above, then it becomes very unlikely indeed that such an event would have occurred.
    So far, as I understand it, the tests that have produced anything close to what is proposed prove that the conditions are NOT natural, nor can be expected to exist anywhere on an early earth.
    So if we hold that the conditions are special and limited to scant few locations. The evidence points to there being 1) no such locations 2) That the chances of it occurring in a universe FULL of amino acids is ridiculous, to then narrow the field to a single specific location on earth is beyond comprehension.

    Quote Originally Posted by radix
    My biggest problem with the "lack of geological evidence" line of reasoning, however, is how would you distinguish between traces of RNA-only organisms and DNA/RNA/protein organisms? I would want to see something a bit more solid on this tar business before I'm ready to buy it as evidence one way or another.
    A fine question.. but one that is beyond my ability to answer.
    I shall continue to pine for the days of Chad ,our resident micro biologist and all round good guy, who would regularly make my head explode with his extensive knowledge of technical biology inter-workings. ... ahh .. good times. ... You guys are great too

    Quote Originally Posted by radix
    The Hadean/Archean boundary isn't set in stone (if you pardon the pun) but it's somewhere around 4 billion years ago, which would be right around the time when conditions on Earth would have first allowed life to develop. The fact that we can't find any evidence of life (RNA- or DNA-based) before that is entirely consistent with the proposed hypotheses.
    It would potentially be in line with ALL hypothesis. If aliens seeded the planet, then they would have done so AFTER it was no longer being bombarded by meteorites.
    So, that it is consistent doesn't really tell us very much IMO.
    Second, the challenge presented is that what we do have access to is not consistent with what we would expect.
    Namely, if we are to expect it to occur, then the conditions would have had to be plentiful. Given plentiful conditions the bi-product would have also been plentiful and present in the geology we have access to (or potential access to).



    I think you are sort of stuck in a catch 22. If the conditions were abundant, then the geology doesn't/or may not (pending that argument) support it's existence (not to be confused with disproves).
    If the conditions were not abundant, but very specific and localized, then you have a very limited base from which to "evolve". From which I suspect that reasonable projections would not favor a evolution speed that would
    give us the results we see.

    In other words, as you said it doesn't travel well, the conditions were specific. Well, how big of a ball of these first things could we expect to exist? If the conditions were not replenishing, how long would it take to convert all of the energy to an unusable form and is that enough time to expect an evolution?

    IE, suppose we had a swimming pool filled with whatever it takes to feed the first replicating thingy. How long would it take to convert it all into,apparently, tar?


    Then of course... how does the evolved forms get out of the tar ball produced by it's parents? Is it possible that the existence of one, would make it unreasonable to expect the survival of a sufficiently different version (so as to assimilate new food)?
    To serve man.

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by rlms
    The average protein in a cell is made up of 288 amino acids.

    There are 1e+300 (1 with 300 zeros behind it) different variations to
    construct these amino acids because of the order and the degree at which they are connected.
    Any variation in degree or sequence will render the amino acids useless or toxic to life. So, we have a very limited chance of getting a protein when we consider there are only 200,000 proteins while there are over 1e+300 possibilities to arrange the amino acids. That gives us 1 in 5e+294 odds of getting a protein by chance.

    If we were to convert every atom in the universe(1e+80 atoms) to an amino acid, then try 1 billion different combinations per second, it would take 1.59e+198 years to produce our first protein. That is 1.13e+188 times the age of the universe.
    This shows that even if we have a huge planet, with oceans teaming with amino acids, we are still incapapable of producing life as we know it.

    The first life form, Cyanobacteria, ďhad a genome size of approx. 4.5 Mbp and 1678 to 3291 protein-coding genesĒ.1 This is a fairly complex life form that used photosynthesis. This all happened within 500 million years from the formation of the earth. We could have 1e+500,000,000 years and never attain this miracle.

    Letís back up and assume that there was a simpler start. In an article in Pnas.org it was suggested that life can exist with only 256 proteins. With 1 protein in 1.13e+188 years we will need 255 more that will need to be produced at the same time so they can interact. Not only that, but we have to arrange them in an order so complex that it is impossible to figure the odds.

    Because of the use of proteins as a basis for life, and the complexity and precision of the structures necessary to build even the most rudimentary organism, chance is not even a remote possibility to have been the vehicle by which the first life forms came about.


    Evolution

    Now we come to the issue of mutations that create new proteins.
    The same impossibility that plagues the creation of life destroys any possibility of random mutations being the mechanism for creating differing forms of life.

    A protein has to be chemically correct and folded perfectly to work for its specific purpose, just like a key in a lock, when it comes to turning chemical processes on or off, or transporting molecules. That is why we have over 6,000 identified genetic disorders, one mistake in the coding or folding of a protein and it will not work properly.

    We will use the number 5e+294 to stand for our probability of producing a protein, even though it is much higher than this due to several factors.

    The human mutation rate is 176 mutations per generation. At 20 years per generation and 7 billion people it will take us 8.12e+283 years to get that new protein.
    I'm surprised that no one seems to have caught this yet. What you don't seem to understand is that biochemical interactions aren't modeled by some tremendous slot machine, where you pull the lever once to get one configuration of atoms, and then you pull the lever again to get another mixture of atoms in a new arbitrary configuration. You see, atoms interact in a way based on rules. These rules make up the subject of chemistry. Things matter, like temperature, pressure, and proximity, that dictate how often the interactions will take place. Moreover, you don't need to hit a compound of 10^60 atoms in a single go. It's not a zero sum game. You can build up a 10 carbon compound, then the next round get a 1000 carbon compound, etc. Also, many combinations of matter are not possible, the Vander Waal forces will cause atoms to come together to form molecules in specific ways, because molecules

    I think I can best explain why this reasoning is wrong with another complex mixture of atoms --galaxies. Galaxies are objects that are made out of about 10^70 atoms. You might then ask how galaxies got here from clumps of hydrogen we know were around in the early Universe? If we used your reasoning, we could pretend like the Universe had to pull the slot machine's lever 10^N number of times until it interacted correctly to create the galaxy.

    Or you could properly realize that the forces present at the size of galaxies, which is gravity, will cause galaxies to have the structure that they do because that's the structure that gravity will most often create.

    Likewise, proteins are a simple thing that the intermolecular forces will create (In fact the maths & simulations of molecules and of galaxies are actually essentially the same, the only real differences is the forces, which accounts for the different structures seen).



    If there's a thing that I should stress strongly about science, it's the statement that not all things are equally probable or possible. Not all things are possible and few things are equally probable. The point of science is to understand the patterns of the Universe, to understand why things are more probable than others. It is not to say that "things just randomly happen" and then to point out that since there's order to the Universe, this order must come from a higher power. It doesn't. The orders comes from physical principles, and it's the job of the scientist to uncover them.
    "Those who can make you believe absurdities, can make you commit atrocities." --Voltaire

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  19. #75
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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by MindTrap028 View Post
    That is an assumption I have never understood. Specifically that survival is a zero sum game.
    A more efficient organism doesn't equate to the automatic destruction of a less efficient organism.
    It most certainly does if the organisms are competing for the same limited resources. The only way a less efficient organism would be able to survive is if it was able to fit into a niche which is not occupied by the more efficient organism. I don't see how that would apply here.

    Especially if the difference is minimal.
    It wouldn't have been. The transition from an RNA world to a DNA/RNA/protein world would have been a major step in the evolution of life. For one thing, proteins have 20 different building blocks instead of 4 and have a vastly larger array of possibilities to build 3-dimensional structures.

    There are also a lot of timing assumptions that are simply not safe ones to make. Specifically, how long from the first instance of replication, to the current fossilized record.

    Basically, you don't know when the first one appeared, you don't know how much of it their was, you don't know how much more efficient the various evolved forms were (so as to wipe out the occurrence of the first). Another consideration is that IF the first one occurred naturally, and the conditions were abundant, then some chemical law would be in-effect (and discoverable) that would make multiple occurrence very probable.
    Why would you think the conditions were abundant?

    In other words if it is the case, exactly as has been hoped in this thread, that there is a force of chemistry which causes it, then it would have continued to occur naturally. Meaning, that it would be impossible or unreasonable to think it eradicated by the evolved forms. I mean, if you have a pool of food that continues to produce the base form, then no evolved form which also converts the same food source ,only faster/better, can wipe it out.
    If by base form you mean the first protocells they wouldn't even have had the time to form before they had been devoured by more evolved life-forms. You just can't compare organisms with an enzymatic metabolism with a protocell that has to rely on simple diffusion and non-catalyzed chemistry. They exist on different time-scales.

    If we take this line, thus taking a different line of argument from above, then it becomes very unlikely indeed that such an event would have occurred.
    So far, as I understand it, the tests that have produced anything close to what is proposed prove that the conditions are NOT natural, nor can be expected to exist anywhere on an early earth.
    What specific tests are you referring to?

    So if we hold that the conditions are special and limited to scant few locations. The evidence points to there being 1) no such locations
    Again, what do you base this on?

    2) That the chances of it occurring in a universe FULL of amino acids is ridiculous, to then narrow the field to a single specific location on earth is beyond comprehension.
    Not sure what your point is here, I thought we were discussing the possibility of life starting with self-replicating RNA?


    It would potentially be in line with ALL hypothesis. If aliens seeded the planet, then they would have done so AFTER it was no longer being bombarded by meteorites.
    So, that it is consistent doesn't really tell us very much IMO.
    Indeed- but thatís not really relevant to my point, which is that the OP has excluded the possibility of self-replicating RNA without any solid justification (at least until we get this tar thing sorted out).

    Second, the challenge presented is that what we do have access to is not consistent with what we would expect.
    Namely, if we are to expect it to occur, then the conditions would have had to be plentiful. Given plentiful conditions the bi-product would have also been plentiful and present in the geology we have access to (or potential access to).
    I realize that Iím repeating myself here but why would you expect the conditions to be plentiful?

    I think you are sort of stuck in a catch 22. If the conditions were abundant, then the geology doesn't/or may not (pending that argument) support it's existence (not to be confused with disproves).
    If the conditions were not abundant, but very specific and localized, then you have a very limited base from which to "evolve". From which I suspect that reasonable projections would not favor a evolution speed that would
    give us the results we see.
    I donít see any catch 22 (one of my favourite novels of all time, btw). I find no compelling reason to believe conditions were abundant and I would very much like to see what you would base your ďreasonable projectionsĒ on.

    In other words, as you said it doesn't travel well, the conditions were specific. Well, how big of a ball of these first things could we expect to exist? If the conditions were not replenishing, how long would it take to convert all of the energy to an unusable form and is that enough time to expect an evolution?
    We donít know that conditions were not replenishing. There are possible chemical pathways for abiotic synthesis of activated nucleotides and lipids which is basically all the first protocells would need.

    IE, suppose we had a swimming pool filled with whatever it takes to feed the first replicating thingy. How long would it take to convert it all into,apparently, tar?


    Then of course... how does the evolved forms get out of the tar ball produced by it's parents? Is it possible that the existence of one, would make it unreasonable to expect the survival of a sufficiently different version (so as to assimilate new food)?
    I donít really want to comment on this tar thing until I see some more solid reason to assume that it would be a necessary biproduct of self-replicating RNA. At this point it looks very much like a red herring.

  20. #76
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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by GP
    I'm surprised that no one seems to have caught this yet. What you don't seem to understand is that biochemical interactions aren't modeled by some tremendous slot machine, where you pull the lever once to get one configuration of atoms, and then you pull the lever again to get another mixture of atoms in a new arbitrary configuration. You see, atoms interact in a way based on rules. These rules make up the subject of chemistry.
    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.

    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.

    Basically, the laws that govern chemical reactions do not help in the formation or have not shown to help.

    By pointing out this specific and purposeful omission in the OP, first assumes that the laws are not hindrances, which has not been shown. Second assumes that there is some law which will cause proteins to form
    in a generally mixed environment. (IE that there is some preference for the bonding of protein forming combinations among non-protein forming combinations), which has also not been shown.
    or thirdly, that an environment under which protein forming combinations will necessarily occur CAN exist naturally.


    I am all for the objection being sustained and proving a real problem in the OP, but the objection is not valid until it's assumptions are supported.
    Without it, the OP represents an unreasonably favorable conditions for the creation of protein forming amino acid combinations.
    It creates the conditions for interactions on a scale which is unreasonable to accept.
    It creates bonding rates that are unreasonable to accept
    and it creates interactions of each one with all others in existence.. which is unreasonable to accept.


    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.

    Quote Originally Posted by RADIX
    It most certainly does if the organisms are competing for the same limited resources. The only way a less efficient organism would be able to survive is if it was able to fit into a niche which is not occupied by the more efficient organism. I don't see how that would apply here.
    Well, was it a "limited" resource? What was it?
    What you say may be true, but you have not established that we should think it.


    Quote Originally Posted by RADIX
    It wouldn't have been. The transition from an RNA world to a DNA/RNA/protein world would have been a major step in the evolution of life. For one thing, proteins have 20 different building blocks instead of 4 and have a vastly larger array of possibilities to build 3-dimensional structures.
    Well, I was referring to the step immediately following the first instance.
    My point is that if the first instance existed for 1billion years UN-opposed or without significantly better competition, then when the transition you point to does occur it doesn't whip out the first instance over night. Thus, we could find them together. We may be crossing our communications a bit.

    Quote Originally Posted by RADIX
    Why would you think the conditions were abundant?
    Because if the massively abundant conditions of the OP can not reasonably be thought to produce it, then an extremely limited conditions
    on earth, even more limited by confinement to a specific and small geographic area appears to be an unreasonable assumption compared to abundant conditions on earth.

    Quote Originally Posted by RADIX
    If by base form you mean the first protocells they wouldn't even have had the time to form before they had been devoured by more evolved life-forms. You just can't compare organisms with an enzymatic metabolism with a protocell that has to rely on simple diffusion and non-catalyzed chemistry. They exist on different time-scales
    Maybe, I think there is far to much speculation down this line to follow.

    Quote Originally Posted by RADIX
    What specific tests are you referring to?
    All that produce from scratch what is said to be building blocks of life.

    Quote Originally Posted by RADIX
    I would very much like to see what you would base your ďreasonable projectionsĒ on.
    This is not an official assertion. More of me just voicing an opinion. That being, time frame and evolution rate matter.
    Limited resources mean limited evolution rate. My suspicion is that the evolution rate (whatever it is) is going to point to a larger resource pool rather than a limited one.

    Also, this is apparently a serious objection
    http://science.howstuffworks.com/lif...-on-earth5.htm

    Quote Originally Posted by LINK
    . But there is one criticism that any abiogenesis hypothesis has difficulty overcoming: time. DNA-based life is thought to have developed on Earth beginning around 3.8 billion years ago, giving pre-cellular life forms about 1 billion years to carry out random processes of encoding useful proteins and assembling them into the precursors of cellular life [source: Discovery News]. Critics of abiogenesis say that simply isn't enough time for inorganic matter to become the theorized precellular life.
    Quote Originally Posted by RADIX
    I donít really want to comment on this tar thing until I see some more solid reason to assume that it would be a necessary biproduct of self-replicating RNA. At this point it looks very much like a red herring.
    I'm a bit out of my element, and there is so much speculation that this general line is not very useful IMO.

    It seems to be argued that RNA can start it off, but that it produces toxic tar.
    To serve man.

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    Re: Abiogenesis and evolution - The protein dilemma

    Well, was it a "limited" resource? What was it?
    What you say may be true, but you have not established that we should think it.
    In the case of the first proposed protocells, the resources would be activated nucleotides and lipid molecules. Of course, to a DNA creature like a bacterium, a protocell wouldn't be a competitor for food - it would be the food, a nice little agglomerate of goodies. Obviously the hypothesis is that the protocells evolved into more complex systems that could use other types of nutrients long before bacteria emerged. The problem for the OP's argument is that the more sophisticated the RNA world organisms get, the more they resemble the DNA/RNA/protein organisms.

    Let's for the sake of argument assume that the RNA-only organisms were able to stand up to the DNA/RNA/protein organisms long enough to survive into a geological time frame where we should be able to see traces of them. Again I would have to ask, how would you be able to tell if these traces were from an RNA-only organism or a DNA/RNA/protein organism? Exactly what traces are we talking about? Carbon? How would the carbon from one type of organism differ from the other? Tar? Where is it coming from and why would it be a necessary biproduct of an RNA organism? Enquiring minds want to know (well, at least this enquiring mind).*

    Well, I was referring to the step immediately following the first instance.
    My point is that if the first instance existed for 1billion years UN-opposed or without significantly better competition, then when the transition you point to does occur it doesn't whip out the first instance over night. Thus, we could find them together. We may be crossing our communications a bit.
    Well, I maintain that the advantage of having access to a whole new world of protein chemistry is so huge it wouldn't even be a fair fight. I'm talking bazookas against bows and arrows. If you think otherwise you're still left with the problem of interpreting the evidence (see above).

    Because if the massively abundant conditions of the OP can not reasonably be thought to produce it, then an extremely limited conditions
    on earth, even more limited by confinement to a specific and small geographic area appears to be an unreasonable assumption compared to abundant conditions on earth.
    That's if you accept the OP's calculations. Well, I'm contesting the OP's calculations - that's my whole point. The numbers he presents may be correct if proteins are the result of chemistry alone but if proteins emerged as a result of an evolutionary process that math is out the window.

    All that produce from scratch what is said to be building blocks of life.
    You're saying that all attempts to produce the building blocks of life have proven that the conditions could not have existed on an early earth? How did they do that?

    This is not an official assertion. More of me just voicing an opinion. That being, time frame and evolution rate matter.
    I'm sure they do - I just don't see how we can reliably calculate or even reasonably estimate the required time for life to emerge.

    Limited resources mean limited evolution rate.
    Limited resources may mean limited abundance of life (or protolife) but not necessarily limited evolution rate. If anything, I would say the opposite would be closer to the truth. Limited resources is a strong selection pressure that can increase evolution rate.

    Also, this is apparently a serious objection
    http://science.howstuffworks.com/lif...-on-earth5.htm
    The article uses similar numbers as the OP and I contest them for the exact same reason: the numbers are only valid if proteins are the result of a random process which they're clearly not if they evolved. BTW, that short piece at howstuffworks manages to get a lot of things wrong about the RNA world hypothesis but I won't burden this thread with that.

    I'm a bit out of my element, and there is so much speculation that this general line is not very useful IMO.

    It seems to be argued that RNA can start it off, but that it produces toxic tar.
    Hopefully the OP will come back and solve this mystery.

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by radix
    In the case of the first proposed protocells, the resources would be activated nucleotides and lipid molecules. Of course, to a DNA creature like a bacterium, a protocell wouldn't be a competitor for food - it would be the food, a nice little agglomerate of goodies. Obviously the hypothesis is that the protocells evolved into more complex systems that could use other types of nutrients long before bacteria emerged. The problem for the OP's argument is that the more sophisticated the RNA world organisms get, the more they resemble the DNA/RNA/protein organisms.
    Well, you are jumping light years into the future of evolution. When the topic is the first and early instances.

    Quote Originally Posted by radix
    Let's for the sake of argument assume that the RNA-only organisms were able to stand up to the DNA/RNA/protein organisms long enough to survive into a geological time frame where we should be able to see traces of them. Again I would have to ask, how would you be able to tell if these traces were from an RNA-only organism or a DNA/RNA/protein organism? Exactly what traces are we talking about? Carbon? How would the carbon from one type of organism differ from the other? Tar? Where is it coming from and why would it be a necessary biproduct of an RNA organism? Enquiring minds want to know (well, at least this enquiring mind).*
    Good questions.. I don't know.

    Quote Originally Posted by RADIX
    Well, I maintain that the advantage of having access to a whole new world of protein chemistry is so huge it wouldn't even be a fair fight. I'm talking bazookas against bows and arrows. If you think otherwise you're still left with the problem of interpreting the evidence (see above).
    Not sure what you mean.

    Quote Originally Posted by RADIX
    That's if you accept the OP's calculations. Well, I'm contesting the OP's calculations - that's my whole point. The numbers he presents may be correct if proteins are the result of chemistry alone but if proteins emerged as a result of an evolutionary process that math is out the window.
    Well, it isn't the calculations you argue against, it is the assumption of the result of chemistry alone.
    In fact, all you are doing is trying to change the approach to reflect a different formation. You are appealing to a very similar but "less complex" start.
    For it is the start that is necessary.

    But you can't simply throw out the OP without constructing a reasonable and realistic alternative.
    By appealing to RNA, it may be "more likely" than the OP, but that doesn't make it reasonable or even likely in itself.

    Quote Originally Posted by RADIX
    You're saying that all attempts to produce the building blocks of life have proven that the conditions could not have existed on an early earth? How did they do that?
    By using conditions that can not exist in nature.


    Quote Originally Posted by RADIX
    Limited resources may mean limited abundance of life (or protolife) but not necessarily limited evolution rate. If anything, I would say the opposite would be closer to the truth. Limited resources is a strong selection pressure that can increase evolution rate.
    That is wishful thinking and backwards.
    10billion units will produce more variations than 100.
    That is the reason why it requires millions &/or billions of generations to see significant evolution in anything.

    Pressures do not "cause" evolution, they SELECT mistakes.
    I would like you to support that selection pressure increases evolution rates or withdraw the point.



    Quote Originally Posted by RADIX
    The article uses similar numbers as the OP and I contest them for the exact same reason: the numbers are only valid if proteins are the result of a random process which they're clearly not if they evolved. BTW, that short piece at howstuffworks manages to get a lot of things wrong about the RNA world hypothesis but I won't burden this thread with that.
    I used it for it's claim that the hypothesis is largely abandoned.
    That it was abandoned based on the limited time.

    Which was my exact objection. I was using it to support that I am not out of left field with the objection that time was against such a theory.
    There is a known window of about 1billion years. The RNA hypothesis apparently has a serious problem with that time constraint.

    Quote Originally Posted by RADIX
    Hopefully the OP will come back and solve this mystery.
    I stand by the time objection to that theory. I hope that can be sorted out by RNA proponents.


    *Edit*
    @ Radix
    As I read more about the RNA world angle, I get the feeling that it is more of a solution to the of the OP rather than a merited by the evidence conclusion. In that, in response to the much more simple replicating RNA is pointed to. However, a replicating RNA is not enough, because it would not inherently copy only itself. The point of course is that pointing to a short RNA is not sufficient if it doesn't have real world application.

    It appears to me to look good on paper, but without a real world path to creation.

    The same is true with what is pointed out in the OP. There is no known, and probably no possible real world conditions under which any of the complex chemical reactions could take place. I know it is the subject of great study and interest.

    You have heard of the "frog nog" example? You take a frog, put it in a blender, and turn it on for a few minutes. Now, you have frognog. Everything you need to make a frog is present. But no frog will ever rise up from it. The reason, just because the parts are present doesn't mean that the whole will form or is even reasonably possible. So I wonder, we know what replicating RNA looks like or at least what it is made of. Are their any experiments which reflect real world conditions that bring about SELF replicating RNA (as replicating RNA is not a valid counter)?
    What happens when you mix Phosphoric acid, sugar and Adenine(the building blocks of RNA...I think) in a test tube? Where do these things come from naturally?

    Of course I don't know the answers, they are real questions born of my limited knowledge on RNA. As RNA world is your counter.. I get to pose them to you Cheers.
    Last edited by MindTrap028; December 8th, 2012 at 05:06 AM.
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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by MindTrap028 View Post
    Well, you are jumping light years into the future of evolution. When the topic is the first and early instances.
    Am I understanding you correctly that you're claiming that we should expect the first and early instances (i.e. the proposed protocells) to have survived into a geological time frame which would make them contemporary with early bacteria? This simply isn't possible. A protocell relying on un-catalyzed chemistry wouldn't even have had time to form before it would have been consumed by the bacteria. It would simply be a collection of nutrients for the bacteria to feed on.

    You need to understand how simple these "first instances" were. RNA (or some chemical equivalent) and lipids. That's it. The protocell wouldn't be able to produce these by itself, it had to be available in the environment. Suppose there's a way to find traces of RNA or lipids in a 4 billion year old rock. How are you going to tell if it came from an RNA-only organism or if these molecules were just swimming around by themselves? This "lack of geological evidence" argument simply doesn't work.


    Not sure what you mean.
    I mean the suggestion that protocells could have survived into the same geological period as the early bacteria (which I think is absurd) is still a periferal point to the problem of distinguishing between traces from RNA- only organisms and DNA/RNA/protein organisms.


    Well, it isn't the calculations you argue against, it is the assumption of the result of chemistry alone.
    In fact, all you are doing is trying to change the approach to reflect a different formation. You are appealing to a very similar but "less complex" start.
    For it is the start that is necessary.

    But you can't simply throw out the OP without constructing a reasonable and realistic alternative.
    By appealing to RNA, it may be "more likely" than the OP, but that doesn't make it reasonable or even likely in itself.
    You have that backwards. The only suggestions on the table in this thread are abiogenesis and evolution (they're in the OP's first post). It's the OP that hasn't presented any alternative, he even makes a specific note of this in a later post. What the OP has presented are his objections to abiogenesis and evolution as explanations. Staying with the abiogenesis part, I don't find his objections convincing. They assume a random formation of the first proteins and I think that assumption hasn't been sufficiently justified.


    By using conditions that can not exist in nature.
    And how do you know they cannot exist in nature?

    That is wishful thinking and backwards.
    It's neither wishful thinking nor backwards. Scarcity of resources create competition. The tougher the competition, the bigger the impact of a favourable gene variant. This is the selection pressure.

    10billion units will produce more variations than 100.
    That is the reason why it requires millions &/or billions of generations to see significant evolution in anything.
    This isn't what you said, though, is it? You made the specific claim that "limited resources mean limited evolution rate" which doesn't say anything about the size of the population. You may claim that the less limitation on resources, the bigger the population but then you also have the opposite effect that a growing population will create more competition for resources. Population dynamics will usually tend towards a situation with limited resources.

    Pressures do not "cause" evolution, they SELECT mistakes.
    I would like you to support that selection pressure increases evolution rates or withdraw the point.
    Of course selection pressure causes evolution, that's one of the defining features of the process. It's not a case of selecting mistakes, it's a case of selecting what is functional or not in a specific environment. You're asking me to withdraw the ToE - I don't think I have that mandate. You also haven't provided me with any good reason to do so.


    I used it for it's claim that the hypothesis is largely abandoned.
    That it was abandoned based on the limited time.
    Which is one of several things the article got wrong. There are no signs that the RNA world theory is being abandoned - quite to the contrary, it shows every sign of being a fruitful line of research that's producing a steady stream of peer-reviewed papers. Jack Szostak has a recent summation of the current state of the research here:

    http://www.jsystchem.com/content/3/1/2

    Which was my exact objection. I was using it to support that I am not out of left field with the objection that time was against such a theory.
    There is a known window of about 1billion years. The RNA hypothesis apparently has a serious problem with that time constraint.


    I stand by the time objection to that theory. I hope that can be sorted out by RNA proponents.
    What exactly are you standing by? What would be a reasonable estimate of the required time and how would you calculate it?

  24. #80
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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by RADIX
    Am I understanding you correctly that you're claiming that we should expect the first and early instances (i.e. the proposed protocells) to have survived into a geological time frame which would make them contemporary with early bacteria?
    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.


    Quote Originally Posted by RADIX
    You need to understand how simple these "first instances" were. RNA (or some chemical equivalent) and lipids. That's it. The protocell wouldn't be able to produce these by itself, it had to be available in the environment. Suppose there's a way to find traces of RNA or lipids in a 4 billion year old rock. How are you going to tell if it came from an RNA-only organism or if these molecules were just swimming around by themselves? This "lack of geological evidence" argument simply doesn't work.
    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?

    Quote Originally Posted by RADIX
    I mean the suggestion that protocells could have survived into the same geological period as the early bacteria (which I think is absurd) is still a periferal point to the problem of distinguishing between traces from RNA- only organisms and DNA/RNA/protein organisms.
    Good question, not sure.

    Quote Originally Posted by RADIX
    You have that backwards. The only suggestions on the table in this thread are abiogenesis and evolution (they're in the OP's first post). It's the OP that hasn't presented any alternative, he even makes a specific note of this in a later post. What the OP has presented are his objections to abiogenesis and evolution as explanations. Staying with the abiogenesis part, I don't find his objections convincing. They assume a random formation of the first proteins and I think that assumption hasn't been sufficiently justified.
    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.
    The repeated reference to "simple" is as far as I can tell an oversimplification of an RNA world model.

    Quote Originally Posted by RADIX
    It's neither wishful thinking nor backwards. Scarcity of resources create competition. The tougher the competition, the bigger the impact of a favorable gene variant. This is the selection pressure.
    That does not increase mutation rate, that only increases selection.
    If a force came along and killed everyone with out 3 arms... that would not cause a 3rd arm mutation to OCCUR.
    You said that pressure increases mutation rate.. it does not.

    Quote Originally Posted by RADIX
    This isn't what you said, though, is it? You made the specific claim that "limited resources mean limited evolution rate" which doesn't say anything about the size of the population. You may claim that the less limitation on resources, the bigger the population but then you also have the opposite effect that a growing population will create more competition for resources. Population dynamics will usually tend towards a situation with limited resources.
    You are misunderstanding what I mean by "limited resources". I don't mean "limited" in relation to the size of the population. I mean limited in the sense of it's general scarcity on earth.
    So, a small puddle of resources mean a necessarily small population. An ocean of resources mean a large population. In both instances resources may be "limited" in relation to the individual organisms as each one fights to be among the maximum living the total resources can support.

    So I indeed intended it to be all about population size. Because population size is directly related to the amount of possible mutations and thus the "rate" of mutations.
    Again, see 3rd arm example.

    Quote Originally Posted by RADIX
    Of course selection pressure causes evolution, that's one of the defining features of the process. It's not a case of selecting mistakes, it's a case of selecting what is functional or not in a specific environment. You're asking me to withdraw the ToE - I don't think I have that mandate. You also haven't provided me with any good reason to do so.
    o.. I think I see our problem.
    I made the mistake of equating "evolution rate" with "mutation rate".
    The rate of mutation is what I was talking about. That is why I was arguing for a larger population being necissary to achieve what we find from what you propose was a viable start.
    So "evolution rate" (the rate of mutation + selection), would not be fast enough specifically because the "mutation rate" (number of new mutations due to mistakes in copying and all the other causes of mutations) would be limited by the smaller population size resulting from a "limited resource" (small amount of resource on earth) model.

    ... Let me know if we are on the same page now, and if you maintain your objection. .. maybe we can start over from there.
    Basically you need to support that the evolution rate of a limited resource on earth start of RNA world is reasonably fast enough to achieve what we find some 1 billion years later.
    If not, then there is no reason to accept the RNA world hypothesis as reasonable.

    Quote Originally Posted by RADIX
    Which is one of several things the article got wrong. There are no signs that the RNA world theory is being abandoned - quite to the contrary, it shows every sign of being a fruitful line of research that's producing a steady stream of peer-reviewed papers. Jack Szostak has a recent summation of the current state of the research here:
    Thanks for the link... I read the first paragraph only. Not sure if that really supports your point, as he seems to acknowledge that it appears to be impossible but "may not be"

    Quote Originally Posted by LINK
    As recently as 2004, Leslie Orgel, one of the great founding fathers of the field of prebiotic chemistry, suggested that "the abiotic synthesis of RNA is so difficult that it is unclear that the RNA World could have evolved de novo on the primitive earth
    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".

    Quote Originally Posted by RADIX
    What exactly are you standing by? What would be a reasonable estimate of the required time and how would you calculate it?
    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.
    To serve man.

 

 
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