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  1. #1
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    Abiogenesis and evolution - The protein dilemma

    Because of the complex nature of the very basis of life, proteins, how is a purely naturalistic approach possible when faced with such overwhelming odds?

    I would ask that you respond with reasonable, sensible answers that have scientific merit.
    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.
    Also, God of the gaps does not apply here because our current knowledge of proteins excludes the atheistic evolutionary model from explaining the beginning of life over 3.5 bya and the further diversity over the last 500+ million years.

    I hope to spark a scientific and thoughtful debate, not regurgitated sayings from your favorite websites. So please put things in your own words so we donít have people referring to books or websites to support your arguments. If you canít understand them enough to condense them to a post then they are probably not valid points.

    Abiogenesis

    Proteins are essential for life, as they make up most of the structure of the cell and perform the majority of the chemical processes, without them life is impossible. Protein molecules are made of amino acids, there are 20 different types of amino acids that make up proteins.
    These amino acids connect to form a chain that varies not only
    in sequence, but also at what angle the molecules attach to each other.
    As of Sept. 4th 2012 there were 78,110 proteins recorded in the
    Protein Data Bank. Of these proteins, PloS One estimates there
    are only 4,000 protein to protein interactions. This is a result of the
    protein docking that requires a precise shape to interact with
    each other.
    The true figure for proteins is estimated to be in the 200,000 range,
    with up to 10,000 protein to protein interactions.
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    The average protein in a cell is made up of 288 amino acids. Protein Molecule
    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.

    Now letís try to get a protein using all of the bacteria in the world and the mutations they generate. The current estimate by the University of Georgia puts the bacterial number at 5e+30. Using generous assumptions of 30 minutes per generation and 4 billion years, we can say there have been a total of 3.5e+44 bacteria on earth. Now, letís give them an average mutational rate of 1 per generation(which is 5,000 to 10,000 times higher than reality). With these figures we get a total mutational figure of 3.5e+44.
    Now we only need to keep this up for 1.62e+253 times the age of the universe in order to get our 1 protein. So again, we have an impossible situation.

    Explaining the approximately 200,000 proteins that exist, with a process that cannot even produce 1 protein, shows the intrinsic failure of the system.

    I have used simplified equations here for ease of understanding, the reality is much more complex and even more impossible. Even in the simplified form, they clearly show that random mutations can not be the mechanism that drives the diversity or life.


    Links
    First-ever estimate of total bacteria on earth provided by University of Georgia
    http://www.sdearthtimes.com/et0998/et0998s8.html William B. Whitman

    Plos one, June 13 2012, How Many Protein-Protein Interactions Exist in Nature?
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3374795/

    How Many Proteins in PDB?
    http://en.wikipedia.org/wiki/Protein_Data_Bank

    0ver 6,000 genetic diseases, US Dept. of Health and Human Services
    http://report.nih.gov/nihfactsheets/...t.aspx?csid=80 or
    http://webcache.googleusercontent.co...&ct=clnk&gl=us

    256 minimum proteins for life
    http://www.pnas.org/content/103/2/425.full

    1 - Proteins for Cyanobacteria
    http://www.biomedcentral.com/1471-2148/11/187

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

    Interesting post. Chad is our resident, professional scientist, I'd be curious what he thinks about this (but his activity level is on and off lately).
    -=]Apokalupsis[=-
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  4. #3
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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by rlms View Post
    Because of the complex nature of the very basis of life, proteins, how is a purely naturalistic approach possible when faced with such overwhelming odds?

    I would ask that you respond with reasonable, sensible answers that have scientific merit.
    There's not much scientific response required to this, let's instead look at statistical probability.

    Firstly, to cut a long story short, probability is only a useful tool if applied BEFORE an event happens. Consider the following scenarios.

    Scenario A (an analogy of what you just tried to argue in your OP)

    - you thoroughly shuffle a complete deck of cards, minus the jokers
    - you lay out the cards side by side
    - you observe the order you've just laid out
    - you calculate that the odds of you getting that exact order were 1 in 8x10^67
    - you conclude it could not have happened naturally, by chance, without intentional intervention, etc.

    Your mistake here is applying probability post-event to determine whether it happened via chance, when the probability after an event is 1, regardless of how it happened.

    Not that it's too much of a factor but just to cover the base, as well as to make a vastly bigger demonstration of how you've erroneously applied probability in this instance, let's remove the fact that you were always going to get some order of 52 cards in scenario A.

    Scenario B

    - stand up.
    - take 10 steps in any random direction you like.
    - consider every molecule on the bottom of your feet/socks/shoes and the molecules they each interacted with on your floor, over the entirety of those 10 steps
    - the improbability that all those molecules on your feet/socks/shoes would each interact with the exact ones on your floor that they did, for the duration of just those 10 steps, far, far surpass the kind of supposed improbabilities that your OP describes.

    Are we to conclude therefore, that it did not happen by chance?
    No, we instead rightly conclude that it's a mistake to ever try and use probability in determining whether something that's already happened, did so or did not by chance.

    Secondly, pretending for a second that what I've just mentioned hadn't already negated any usefulness to your OP, please do remember that evolution is not a chance process in the first place, life today did not get here by random permutations of atoms and molecules as your OP fully relies upon insisting. Evolution is a process which effectively builds on what already works and often discards what doesn't, over countless billions of generations.

    To make this point clearer:

    Picture a padlock with 20 tumblers numbered 0-9 that make a pin number 20 digits long.
    So there are 100,000,000,000,000,000,000 permutations.
    if we must try all permutations at random, sure, you could possibly have 100,000,000,000,000,000,000-1 attempts before getting it right. however, random permutations is not how life has come to be as it now is.

    If instead each 0-9 tumbler that we get right, stops moving on successive attempts, you can guarantee getting the correct pin within just 10 attempts by rolling all the tumblers the same way at the same time.
    While this is certainly not an entirely accurate analogy of how life evolves, it should still help explain why your OP (which uses maths based on totally random permutations like the above) is not in any way applicable to life on earth.

    Quote Originally Posted by rlms View Post
    I hope to spark a scientific and thoughtful debate
    I do hope to engage in one but it is, in this instance, entirely unnecessary.

    Quote Originally Posted by rlms View Post
    The same impossibility that plagues the creation of life destroys any possibility of random mutations being the mechanism for creating differing forms of life
    But you just said it's not impossible, just improbable, a statistical phenomenon which (I hope you can now see) only has any meaning, application or usefulness BEFORE an event. Remember your unfathomably improbable 10 steps, purely by chance.

  5. #4
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    Re: Abiogenesis and evolution - The protein dilemma

    So let me get your points straight:

    #1 - Life already exists, therefore we are not allowed to discount your theory despite the impossibility shown because there is no God.
    Let's look at the presumptive circular reasoning here:
    There is no God -> There is Life -> Life is a Naturalistic Miracle despite all odds against it -> Therefore there is no God
    Now let's start this reasoning at another point
    There is Life -> Life is too complex for Naturalistic explanation -> A Supernatural Source built life

    #2 - Evolution doesn't work by chance
    That would be true if we could come up with a protein for the organism to either use or discard, but, before that we are relying on random mutations to get to that protein. This tells me that you do not truly understand evolution based on the arguments you are giving. Here is an excerpt from evolution 101 from the University of Berkely:
    Mutations are Random
    The mechanisms of evolution—like natural selection and genetic drift—work with the random variation generated by mutation.
    http://evolution.berkeley.edu/evosit...1aRandom.shtml

    #3 - You are criticizing my interchangeable use of the words impossible and improbable.
    The odds that are given are impossible by anyone's standard, picking at my use of impossible and improbable isn't going to change that, nor prove your point.

    I find that none of your scenarios disprove the point of what I am saying nor address it in any way. You are shifting the argument instead of proving that it is possible to produce life with a purely naturalistic scenario.
    I also find the argument, life exists therefore it just happened despite the mathematical, scientific objections, especially hypocritical considering that if a religious person gave you the same response you would ridicule them. Your arguments resemble a person with strong religious beliefs that will not waiver no matter what facts there are to the contrary. So, just say,"I am an atheist and choose to believe this no matter what science says", and quit trying to pretend you are arguing at a factual level.

    How about this, an ancient Greek evolutionist believed that arms, hands, feet body, head, and legs crawled out of the ocean and assembled themselves on the beach to make the first man. This is highly improbable, but since man is here, it has to have happened no matter how impossible it is. Kind of silly to ignore the base premise of the mechanism and jump to the conclusion and then proclaim yourself right.

    Probability and impossibility are essential to science to establish good theories and discard bad ones. This is an ongoing process to finding the truth instead of acquiescing to the status quo. Now you are telling me to throw them out because your theory is above all of this.
    So, I am supposed to just trust you and forget the math, I am supposed to believe in this super miracle of naturalism? Throw out that silly belief in the supernatural in exchange for something more unbelievable?

    I would invite you to try again, and this time give a scientific answer as to how proteins can be made instead of a lesson on card shufling, sock molecules and padlocks, none of which apply here.
    Last edited by rlms; November 20th, 2012 at 05:01 AM.

  6. #5
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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by TORPEX
    Firstly, to cut a long story short, probability is only a useful tool if applied BEFORE an event happens
    Not really, because here it is being used to evaluate the descriptive power of a theory.
    If you were holding an orange, and I proposed that an asteroid had collided with the earth only moments before, and causing a shock-wave to blow an orchard down, and cause a single orange to fly through the air getting sucked into a jet engine and exit without being harmed, then fall only to be slowed by excessive updrafts, then landing in your hand, for me to observe. Sure it is "possible", but it is so highly unlikely as to make it a very suspect theory for how the orange came to rest in your hand.

    Here the idea of unguided "random" formation of the most basic proteins is shown to require an incomprehensibly more unlikely event. If there is any theory that increases the likelihood of the event, it should be preferred over that. (unless of course you find my orange example perfectly acceptable, and see no reason why one should accept a more likely scenario of you purchasing it at the orange stand behind you.

    Quote Originally Posted by TORPEX
    Are we to conclude therefore, that it did not happen by chance?
    Probably a bad example because there is a specific choice involved.
    Also, your example here lacks a very important factor, in that it doesn't matter what is touching what at the place where you are standing.
    Or at least, there is a vast array of possible alignments that will all produce the same effect.

    In the case of the OP, there is a very specific alignment that produces one result (life/protein) and a vast array of equally possible/probable alignments that produce the same result of non-life/protein.

    Quote Originally Posted by TORPEX
    To make this point clearer:

    Picture a padlock with 20 tumblers numbered 0-9 that make a pin number 20 digits long.
    So there are 100,000,000,000,000,000,000 permutations.
    if we must try all permutations at random, sure, you could possibly have 100,000,000,000,000,000,000-1 attempts before getting it right. however, random permutations is not how life has come to be as it now is.

    If instead each 0-9 tumbler that we get right, stops moving on successive attempts, you can guarantee getting the correct pin within just 10 attempts by rolling all the tumblers the same way at the same time.
    While this is certainly not an entirely accurate analogy of how life evolves, it should still help explain why your OP (which uses maths based on totally random permutations like the above) is not in any way applicable to life on earth.
    At the level the OP is dealing with, there is no "guiding" law or factor that leads to life or protein. If there is I do not know of it and humbly ask that you point it out.

    In fact, as I understand it there are many laws and conditions that act to prohibit the formations and alignments enumerated in the OP.
    Still, I would for go that if you could demonstrate a law that guides the bonding process so as to end in a successful alignment per the OP.
    I apologize to anyone waiting on a response from me. I am experiencing a time warp, suddenly their are not enough hours in a day. As soon as I find a replacement part to my flux capacitor regulator, time should resume it's normal flow.

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  8. #6
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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by rlms View Post
    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.
    Can you be more specific as to this point? I've scanned your links and I don't see where this comes from. I think it's possible that this figure is likely inflated due to poor reasoning.
    ~Zealous

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by zd
    I think it's possible that this figure is likely inflated due to poor reasoning.
    Why do you think that? what poor reasoning do you see?
    I apologize to anyone waiting on a response from me. I am experiencing a time warp, suddenly their are not enough hours in a day. As soon as I find a replacement part to my flux capacitor regulator, time should resume it's normal flow.

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    Re: Abiogenesis and evolution - The protein dilemma

    Zealous Demon:
    It is just simple math

    atoms 1e+80 x billion per second 1e+9 x seconds in year 31536000 = 3.15e+96 interactions per year

    odds of getting a protein based on proteins per possible permutations 1 in 5e+294 divide by interactions 3.15e+96 and you get 1.59e+198 years to get a protein

    divide the years to get a protein 1.59e+198 by the age of the Universe, I used 14 billion years and you get 1.13e+188

    or (5e+294/(1e+80*1e+9*31536000))/1.4e+10 = 1.13e+188

    This is just to put a perspective on how large the chance 1 in 5e+294 really is and how impossible it is even on a universal scale.

  11. #9
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    Re: Abiogenesis and evolution - The protein dilemma

    There is absolutely no way that proteins and multicellular life forms developed entirely randomly. A complex scientific understanding is not necessary to realize this, but rather some basic knowledge of statistics, and biology. Time alone is not a biological mechanism of increasing complexity. Evolution has been solidly demonstrated on a certain scale, but the uncaused genesis of life has not, and will not be shown to have any evidence.

  12. #10
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    Re: Abiogenesis and evolution - The protein dilemma

    The only problem with considering such odds is that your domain is limited to one planet (Earth), one universe (our own), and one time cycle (Big Bang to present).

    The odds shift if you account for every planet in the universe on which proteins might form, shift again if you consider the possibility of there being any number of multiverses in which this could happen, and shift yet again if you allow for the possibility that the birth and death of universes is cyclical and might even occur an infinite amount of times.

    You can't ever really rely on probability to support how possible or impossible something is, just as you can't rely on it to suggest a deeper significance than what it means at face value.

    Consider this--out of all the atoms in the universe and all the possible combinations of putting them together, what are the odds that you'd be exactly who you are right now, this exact amalgam of individual atoms pieced together? Now do the same thing for all the atoms that comprise the keyboard you're using to write in this thread. What are the odds of that exact combination being used by the combination of atoms that make you you? Now do the same thing for the computer itself and all its constituent parts--the case, the hard drive, the RAM, the monitor. Keep going as you take stock of every physical object in your house. And that's all without stepping outside! How long would it possibly take for this precise arrangement of atoms to fall into place as they are right this moment? And yet there you are, reading this.
    "Today a young man on acid realized that all matter is merely energy condensed to a slow vibration, that we are all one consciousness experiencing itself subjectively. There is no such thing as death, life is only a dream, and we're the imagination of ourselves." --Bill Hicks

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by thrashee View Post
    The odds shift if you account for every planet in the universe on which proteins might form, shift again if you consider the possibility of there being any number of multiverses in which this could happen, and shift yet again if you allow for the possibility that the birth and death of universes is cyclical and might even occur an infinite amount of times.
    Even theoretically, an infinite number of locations, over an infinite amount of time still would not produce complex protein chains and eventually living organisms, without some external input (cause). Time + chance =\= functional (and almost certainly designed) complexity.

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by KevinBrowning View Post
    Even theoretically, an infinite number of locations, over an infinite amount of time still would not produce complex protein chains and eventually living organisms, without some external input (cause). Time + chance =\= functional (and almost certainly designed) complexity.
    The external inputs are as varied as the possible worlds/universes, if by external inputs you mean environmental catalysts.
    "Today a young man on acid realized that all matter is merely energy condensed to a slow vibration, that we are all one consciousness experiencing itself subjectively. There is no such thing as death, life is only a dream, and we're the imagination of ourselves." --Bill Hicks

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by MindTrap028 View Post
    Why do you think that? what poor reasoning do you see?
    I didn't see any reasoning, just a claim. I was skeptical of the claim and asked for more information.

    Quote Originally Posted by rlms View Post
    Zealous Demon:
    It is just simple math

    atoms 1e+80 x billion per second 1e+9 x seconds in year 31536000 = 3.15e+96 interactions per year

    odds of getting a protein based on proteins per possible permutations 1 in 5e+294 divide by interactions 3.15e+96 and you get 1.59e+198 years to get a protein

    divide the years to get a protein 1.59e+198 by the age of the Universe, I used 14 billion years and you get 1.13e+188

    or (5e+294/(1e+80*1e+9*31536000))/1.4e+10 = 1.13e+188

    This is just to put a perspective on how large the chance 1 in 5e+294 really is and how impossible it is even on a universal scale.
    If I understand your argument, you seem to be making the assumption that abiogenesis/evolution requires that proteins must have appeared randomly in a fully-formed state with no intermediate steps. In other words, that a protein is built by randomly combining individual atoms and not by "trial-and-error" chemistry of smaller component molecules.

    Am I correct in my understanding? And if I am correct, do you really feel that you're making a safe assumption?

    Quote Originally Posted by KevinBrowning View Post
    There is absolutely no way that proteins and multicellular life forms developed entirely randomly.
    Do evolutionary biologists actually make that claim? I'm pretty sure that the scientific understanding of evolution is that favorable traits tend to get passed on and that unfavorable traits tend not to.
    ~Zealous

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by THRASHEE
    The only problem with considering such odds is that your domain is limited to one planet (Earth), one universe (our own), and one time cycle (Big Bang to present).
    No, the Odds are not limited to one earth. The odds are made based on all the possible interactions. I don't see any account being taken for the universe inherent limiting elements so as to suppose how many combinations are tried.

    Quote Originally Posted by THRASHEE
    The odds shift if you account for every planet in the universe on which proteins might form, shift again if you consider the possibility of there being any number of multiverses in which this could happen, and shift yet again if you allow for the possibility that the birth and death of universes is cyclical and might even occur an infinite amount of times.
    And again if there is some law which makes the interaction necessary in our universe.

    But there is no reason to believe such are actual factors.

    Quote Originally Posted by THRASHEE
    You can't ever really rely on probability to support how possible or impossible something is, just as you can't rely on it to suggest a deeper significance than what it means at face value.
    But we can use it as a tool to evaluate the sufficiency of a given theory.

    Quote Originally Posted by THRASHEE
    Consider this--out of all the atoms in the universe and all the possible combinations of putting them together, what are the odds that you'd be exactly who you are right now, this exact amalgam of individual atoms pieced together? Now do the same thing for all the atoms that comprise the keyboard you're using to write in this thread. What are the odds of that exact combination being used by the combination of atoms that make you you? Now do the same thing for the computer itself and all its constituent parts--the case, the hard drive, the RAM, the monitor. Keep going as you take stock of every physical object in your house. And that's all without stepping outside! How long would it possibly take for this precise arrangement of atoms to fall into place as they are right this moment? And yet there you are, reading this.
    Those odds would apply to or stack onto the ones given. Because they are not specific element to anything.
    I apologize to anyone waiting on a response from me. I am experiencing a time warp, suddenly their are not enough hours in a day. As soon as I find a replacement part to my flux capacitor regulator, time should resume it's normal flow.

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by MindTrap028 View Post
    No, the Odds are not limited to one earth. The odds are made based on all the possible interactions. I don't see any account being taken for the universe inherent limiting elements so as to suppose how many combinations are tried.
    Both the age of the Earth and the age of the Universe were mentioned in the OP within the context of how impossible it would be for such combinations to come about by chance. And the reason other planets and other universes matter is because the more "test beds" you have to play with, the greater the odds of some improbable thing happening.

    And again if there is some law which makes the interaction necessary in our universe.

    But there is no reason to believe such are actual factors.
    Not sure what you're referring to here?

    But we can use it as a tool to evaluate the sufficiency of a given theory.
    Perhaps, but I question the usefulness of looking at such odds if you don't even know the proper context in which they belong. Something that happens within even a 14 billion year time frame may seem miraculous to us, but if time is in fact infinite, the miraculous becomes the mundane.

    Those odds would apply to or stack onto the ones given. Because they are not specific element to anything.
    That's my point, though. They're just meaningless odds. Any isolated event or arbitrary arrangement of things in any particular point in space-time can be thought to be miraculous if you just consider the odds of it being just so, but of course the whole universe is made up of such "miraculous" occurrences all the time, so that rather than being exceptional, it's actually pretty mundane.
    "Today a young man on acid realized that all matter is merely energy condensed to a slow vibration, that we are all one consciousness experiencing itself subjectively. There is no such thing as death, life is only a dream, and we're the imagination of ourselves." --Bill Hicks

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by thrashee View Post
    The only problem with considering such odds is that your domain is limited to one planet (Earth), one universe (our own), and one time cycle (Big Bang to present).
    The odds shift if you account for every planet in the universe on which proteins might form,
    I made a ridiculous assumption, every atom in the universe being an amino acid, just to show the impossibility of making one protein. Now you have to have a minimum of 256 just such extreme miracles happening all at the same time in the exact same place and then interacting together in a way to create energy, create more proteins, procreate, etc... The odds of the proteins interacting in such a manner even if they were together in the same time and space, are so far out there they are not calculable.

    and shift yet again if you allow for the possibility that the birth and death of universes is cyclical and might even occur an infinite amount of times.
    The laws of thermodynamics as we know them do not allow for this. Basically, the law of entropy would reduce the energy to a useless state with enough cycles. I am not saying there may be forces we are not familiar with that would supercede this law, but, most scientists no longer subscribe to the eternal cycle model because of this.

    You can't ever really rely on probability to support how possible or impossible something is, just as you can't rely on it to suggest a deeper significance than what it means at face value.
    All true science relies on probability and impossibility to determine the most plausible theories to qualify as fit. This is part of the scientific method, we make predictions based on logical assumptions(what is probable), and we discard theories based on falsification(impossible). Anything else is just pseudoscience, born of prejudice to a preconceived notion.

    ---------- Post added at 05:55 AM ---------- Previous post was at 04:26 AM ----------

    Quote Originally Posted by ZealousDemon View Post
    If I understand your argument, you seem to be making the assumption that abiogenesis/evolution requires that proteins must have appeared randomly in a fully-formed state with no intermediate steps. In other words, that a protein is built by randomly combining individual atoms and not by "trial-and-error" chemistry of smaller component molecules.
    Am I correct in my understanding? And if I am correct, do you really feel that you're making a safe assumption?
    A string of amino acids is known as a polypeptide. A protein is a polypeptide that has a function in living cells. The reason a protein is so rare is that it has to have an exact chemical makeup and shape as to interact with other proteins to do its job. Hence the 1 in 5e+294 chance of getting a protein out of the possibilities of permutations of the polypeptide. Go to the link from Plos one and it will explain the even more restrictive "protein on protein" interactions, that might give you a feel for what we are dealing with here.
    In answer to your question on "trial and error", no, there is no trial and error. It is either a protein or it is not. We have over 6,000 genetic diseases because the protein is changed, many are the result of just one wrong fold or one wrong amino acid. Like sickle cell anemia, one wrong amino acid and the ability of the red blood cell is so hampered as to produce a debilitating disease. Proteins are very specific, that is why mutations are so harmful and "trial and error" to create new proteins is just mathematically impossible.



    Do evolutionary biologists actually make that claim? I'm pretty sure that the scientific understanding of evolution is that favorable traits tend to get passed on and that unfavorable traits tend not to.
    Don't forget, we have to have a new viable protein to get a favorable trait.
    Evolution teaches that we have "random mutations" http://evolution.berkeley.edu/evosit...1aRandom.shtml
    That is random at the codon level(1 codon = 1 amino acid), then evolution claims that once a new protein has been produced it is either kept or discarded through natural selection.
    This is the whole premise of what I am saying, that we will never produce a new protein to try out because it is statistically impossible to create one based on random mutations to the codon.
    If proteins weren't so scarce and every mutation created a new protein then it might be feasible that you would get lucky at some point and get a better protein for the job. But, with the new knowledge that we are gaining of protein interactions, this is simply not the case.
    There are many other factors that I did not bring up on the original post that make it much harder to get a new protein through mutations, but that gets a bit complicated and would require many more posts.
    Last edited by rlms; November 21st, 2012 at 06:49 AM.

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    Re: Abiogenesis and evolution - The protein dilemma

    I admit that I'm not versed enough in this topic to be able to evaluate your argument on an equal footing. However, I do find it hard to believe that the entirety of abiogenesis and evolutionary research could be shut down by "simple math". If that was the case, scientists would have stopped looking many, many years ago.

    There is a page on Talk Origins concerning probabilities of abiogenesis that might be relevant to the conversation, but I know this forum frowns upon including outside links to do the debating for us. Thus, being a laymen with only so much free time (and honestly, an unwillingness to do exhaustive research into molecular biology), I will simply state that potential refutations of your argument exist, even if nobody here could adequately do so.
    ~Zealous

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by THRASHEE
    Both the age of the Earth and the age of the Universe were mentioned in the OP within the context of how impossible it would be for such combinations to come about by chance. And the reason other planets and other universes matter is because the more "test beds" you have to play with, the greater the odds of some improbable thing happening.
    You missed this line in the OP then
    Quote Originally Posted by OP
    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
    This is far beyond their considering multiple earths in the uni.

    In fact the OP is so generous with it's calculations as to make it an unreasonably favorable conditions. It is thus reasonable to argue that there is NO POSSIBLE WORLD which reflects it if we assume purely natural processes in that world. So even given infinite time would not make it more reasonable to accept. Because it is not reasonable to expect it to occur in any possible world through purely natural processes.


    Quote Originally Posted by THRASHEE
    Not sure what you're referring to here?
    I'm saying that you can imagine all sorts of factors that would effect the odds in the OP.
    Unless you wish to contend that we should assume the actually exist, then they are not a factor, and thus the OP is the most reasonable understanding we can currently hold on the topic.

    Quote Originally Posted by THRASHEE
    Perhaps, but I question the usefulness of looking at such odds if you don't even know the proper context in which they belong. Something that happens within even a 14 billion year time frame may seem miraculous to us, but if time is in fact infinite, the miraculous becomes the mundane.
    but time is known to have a defined beginning (big bang). So there is no reason to assume otherwise, unless of course you want to make the case. You aren't really positing something meaningful by pointing out that IF conditions were different then the odds would be different.
    It's a truism.

    Quote Originally Posted by THRASHEE
    That's my point, though. They're just meaningless odds. Any isolated event or arbitrary arrangement of things in any particular point in space-time can be thought to be miraculous if you just consider the odds of it being just so, but of course the whole universe is made up of such "miraculous" occurrences all the time, so that rather than being exceptional, it's actually pretty mundane.
    Your point is not really relevant though, BECAUSE it is true for every interaction. It doesn't add a distinction.
    In other words if all the odds you use in your example would simply add to the odds that are described in the OP, then you can not draw a comparison in any way between the odds in the OP and the odds you listed. The odds you point to seems more like a function of existence, as they are true in all cases and produce no difference in outcome, or represent a significant differentiation between events.

    The Op however has the distinction of Life and not life or protein or not protein.

    Odds without a relevant distinction are meaningless.


    Quote Originally Posted by ZD
    I will simply state that potential refutations of your argument exist, even if nobody here could adequately do so.
    Thank you for that. I am comforted that potential refutations to the refutations one may possibly offer to the OP also possibly exist
    I apologize to anyone waiting on a response from me. I am experiencing a time warp, suddenly their are not enough hours in a day. As soon as I find a replacement part to my flux capacitor regulator, time should resume it's normal flow.

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by rlms View Post
    I made a ridiculous assumption, every atom in the universe being an amino acid, just to show the impossibility of making one protein. Now you have to have a minimum of 256 just such extreme miracles happening all at the same time in the exact same place and then interacting together in a way to create energy, create more proteins, procreate, etc... The odds of the proteins interacting in such a manner even if they were together in the same time and space, are so far out there they are not calculable.
    If they're not calculable, then what was the point of your OP? I thought you used calculations to show how "impossibly" long it would take (that is, much longer than the age of the universe).

    The laws of thermodynamics as we know them do not allow for this. Basically, the law of entropy would reduce the energy to a useless state with enough cycles. I am not saying there may be forces we are not familiar with that would supercede this law, but, most scientists no longer subscribe to the eternal cycle model because of this.
    That's no longer the case--there are several cyclic models around today that account for that (check out the Steinhardt-Turok model and the Baum-Frampton model). So a cyclical universe is still very much a possibility.

    Quote Originally Posted by MindTrap028 View Post
    In fact the OP is so generous with it's calculations as to make it an unreasonably favorable conditions. It is thus reasonable to argue that there is NO POSSIBLE WORLD which reflects it if we assume purely natural processes in that world. So even given infinite time would not make it more reasonable to accept. Because it is not reasonable to expect it to occur in any possible world through purely natural processes.
    But this isn't true--the OP himself has given us calculations for how long it could possibly take for such a thing to occur, and ANY odds, no matter how incredibly small, are significant in the face of infinity. Indeed, not just significant, but akin to happening all the time when you have no temporal limit. This is the problem with odds and things like infinity--as humans, what seems utterly impossible to us is mundane, given a wide enough perspective.

    but time is known to have a defined beginning (big bang). So there is no reason to assume otherwise, unless of course you want to make the case. You aren't really positing something meaningful by pointing out that IF conditions were different then the odds would be different.
    It's a truism.
    I meant, of course, the aggregate of time, or whatever you'd like to call it, if the universe is indeed a cyclical phenomenon. Instead of time, let's simply call it the number of chances amino acids have to arrange themselves in the perfect way. And again, we're not discussing just this one universe repeating itself over and over again, but potentially an infinite amount of other universes doing the same. In other words, the sample space of these odds is infinite, so the possibilities are thus infinite as well.

    Your point is not really relevant though, BECAUSE it is true for every interaction. It doesn't add a distinction.
    In other words if all the odds you use in your example would simply add to the odds that are described in the OP, then you can not draw a comparison in any way between the odds in the OP and the odds you listed. The odds you point to seems more like a function of existence, as they are true in all cases and produce no difference in outcome, or represent a significant differentiation between events.
    Precisely. So the only reason why the odds of amino acids randomly forming proteins seems so remarkable to us is because our perspective is necessarily limited. The distinction is a product of that limited perspective, not of the odds themselves. If you're dealing with either an infinite amount of time (or chances), and/or an infinite amount of universes--in which the laws of physics might be drastically different than our own--then what seems like a great distinction to us might be pretty mundane indeed. In other words, the odds only seem significant because we're only looking at one tiny sliver of the sample space, our own universe in this current cycle of time.
    "Today a young man on acid realized that all matter is merely energy condensed to a slow vibration, that we are all one consciousness experiencing itself subjectively. There is no such thing as death, life is only a dream, and we're the imagination of ourselves." --Bill Hicks

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    Re: Abiogenesis and evolution - The protein dilemma

    Quote Originally Posted by rlms View Post
    Because of the complex nature of the very basis of life, proteins, how is a purely naturalistic approach possible when faced with such overwhelming odds?

    Now we only need to keep this up for 1.62e+253 times the age of the universe in order to get our 1 protein. So again, we have an impossible situation.

    Explaining the approximately 200,000 proteins that exist, with a process that cannot even produce 1 protein, shows the intrinsic failure of the system.
    It seems I spot a few contradictions in your post. You state; "We have an impossible situation...", yet the logical fact remains; "The universe produced all you speak about", and to state it not to be possible of a random system is still no more than mere conjecture, as we do not yet know the possible simplicity of these mammoth figures' possible combinations. Just because science has not yet discovered the proper combination is no indictment or "intrinsic failure of the system" of science, as you "seem" to impute. It's simply the incompleteness of present science, which scientists well-know to be incomplete. Yet, a genius may appear in the bio-physics, electro-chemico-universe tomorrow_I only say; "May..." Yet, you seem to not be recognizing the fact that randomness and dis-order also produces order, just as we logically perceptually witness the universe to exhibit and be, as "A = A", or more simply put; "The universe is the universe" and; "The universe exists as the universe" biology and all, alive and well at the biological level, and with all its trillions, to the trillions, of possible combinations, as you openly admit; but, one can not possibly knowledgeably state that science can not figure out the key combination to all her sequences, as the scientific knowledge is, as I already mentioned, admittedly known to be presently incomplete; iow, we can't know the future, as you seem to be implying, which leaves room for the possibility of humanity discovering the all important key sequence of protein ordering__"Maybe..." Your mathematical assumption of time; "1.62e+253 times the age of the universe" also seems to be far beyond any logically scientific possibility, at least as far as we now understand it, but if we grant the age of the universe to be even larger, then that simply only more-so invalidates your time-logic, as the Earth is securely scientifically known to be approx. 4.5 billion years old through very sound x-ray spectrography and other measuring methods, and bio-organisms surely didn't exist in the stars, which produced the Earth, before the Earth produced bio-organisms. I simply think you are being far too pessimistic about future human and scientific possibilities. Imo, to 'seemingly so' pronounce the "logical death of science" before the future has played out, is a bit pre-mature__No...?

    One should remember; "The odds of scientific discovery have always been stacked in humanity's and science's favor", as we have no contrary information to this fact, so there's yet no evidence to show that science will not continue to discover entirely new processes. Further, science is nothing but a methodological process, over time, and time, "imo", is still in humanity's favor, also__No...?

    And btw, I don't think any "serious" scientists are stating we will discover the total bio-code of producing the protein of everything, as bio-organisms are scientifically admittedly, extremely complex, due to the hyper-fine structures of their near infinitesiml quantum structures. I think it's only the "radical" scientists who claim more than science may be possible of discovering. Anyone who attempts to derive more from science than science is capable of is going beyond what science actually advocates, as all the great scientists I know about, and have studied, have warned about the over-abstracting of information. In this area, science has the same problems that many religions have, and that is the over-abstracting of information into fictitious truths, pseudo-knowledge and pure nominalism...

    On the whole though, I personally agree with the fact that discovering the entire protein code may not be possible, but I simply have problems with your assumptions as presented...

 

 
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