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Thread: DNA, proteins: Chicken, Egg?

  1. #1 DNA, proteins: Chicken, Egg? 
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    Hi,

    I am not a native English speaker, but I'll try to explain my problem. I have a background of High School Biology and pre-medicine (though pre-medical studies in my country are not so in-depth as I would like).

    See my issue is this: In brief terms, we can say that proteins are translated from RNA which is transcribed from DNA. So, in a way, proteins are the products of DNA. However, the processes of transcription, translation essentially require some enzymes, which are proteins.

    This is similar to that chicken-egg analogy, I guess. Can somebody please explain to me, about these two seemingly dependent entities (DNA and proteins) which can not exist without each other, and how they came to shape the molecular genetics that we know today?

    (Can you understand what I am asking? It is very difficult for me to express into words).

    And please forgive me, I couldn't think of the suitable title for this thread.


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    Because proteins can replicate themselves, DNA can not, proteins must be there first.. However, one does not exclude the other. Not speaking of DNA but rather TNA which was probably there before DNA. A pre TNA form could be a TNA protein construct that can replicate itself. It could preform a various amount of functions like shaping the Pre-cell, binding carbon, nitrogen or amino acids (created by electric fields), reducing sulphate, etc. The protein should then have evolved to a shape where the TNA was no longer inside, this would make a smaller protein, plus it could preform better at its task.

    A nice idea is where the protein actually contains its own code. More like mRNA style, but more longevity.

    Most things are speculative, but proteins were there first, no doubt.


    Growing up, i marveled at star-trek's science, and ignored the perfect society. Now, i try to ignore their science, and marvel at the society.

    Imagine, being able to create matter out of thin air, and not coming up with using drones for boarding hostile ships. Or using drones to defend your own ship. Heck, using drones to block energy attacks, counterattack or for surveillance. Unless, of course, they are nano-machines in your blood, which is a billion times more complex..
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    Quote Originally Posted by Zwolver View Post
    Because proteins can replicate themselves, DNA can not, proteins must be there first.. However, one does not exclude the other. Not speaking of DNA but rather TNA which was probably there before DNA. A pre TNA form could be a TNA protein construct that can replicate itself. It could preform a various amount of functions like shaping the Pre-cell, binding carbon, nitrogen or amino acids (created by electric fields), reducing sulphate, etc. The protein should then have evolved to a shape where the TNA was no longer inside, this would make a smaller protein, plus it could preform better at its task.

    A nice idea is where the protein actually contains its own code. More like mRNA style, but more longevity.

    Most things are speculative, but proteins were there first, no doubt.
    Did you really mean TNA?
    Threose nucleic acid (TNA) is an artificial genetic polymer invented by Albert Eschenmoser. TNA has a backbone structure composed of repeating threose sugars linked together by phosphodiester bonds. Like DNA and RNA, TNA can store genetic information in strings of nucleotide sequences (G, A, C, and T). TNA is not known to occur naturally and is synthesized chemically in the laboratory under controlled conditions.
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    There is a hypothesis that it was RNA that started cellular life and both proteins and DNA evolved later.
    Nobody has figured out a way to test it properly so use caution, it might not be true.

    RNA world hypothesis - Wikipedia, the free encyclopedia
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    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by Zwolver View Post
    Because proteins can replicate themselves, DNA can not, proteins must be there first.. However, one does not exclude the other. Not speaking of DNA but rather TNA which was probably there before DNA. A pre TNA form could be a TNA protein construct that can replicate itself. It could preform a various amount of functions like shaping the Pre-cell, binding carbon, nitrogen or amino acids (created by electric fields), reducing sulphate, etc. The protein should then have evolved to a shape where the TNA was no longer inside, this would make a smaller protein, plus it could preform better at its task.

    A nice idea is where the protein actually contains its own code. More like mRNA style, but more longevity.

    Most things are speculative, but proteins were there first, no doubt.
    Did you really mean TNA?
    Threose nucleic acid (TNA) is an artificial genetic polymer invented by Albert Eschenmoser. TNA has a backbone structure composed of repeating threose sugars linked together by phosphodiester bonds. Like DNA and RNA, TNA can store genetic information in strings of nucleotide sequences (G, A, C, and T). TNA is not known to occur naturally and is synthesized chemically in the laboratory under controlled conditions.
    Nope, i mean this.

    Pre DNA system[edit][/h]John Chaput, a researcher at the Center for Evolutionary Medicine, has theorized that issues concerning the prebiotic synthesis of ribose sugars and the non-enzymatic replication of RNA may provide circumstantial evidence of an earlier genetic system more readily produced under primitive earth conditions. TNA could have been an early genetic system. The research paves the way for more sophisticated manipulation of TNA and other xenonucleic acids and may strengthen the case that TNA or a closely related molecule set the stage for the emergence of RNA and the first earthly life.
    Recent advances in protein engineering have produced a new breed of synthetic polymerases. In the current study, one of these – known as Therminator DNA polymerase, faithfully transcribed a 70 nucleotide DNA sequence into TNA, while another, known as SuperScript II (SSII) performed reverse-transcription back into DNA with impressively high fidelity. Sequences of both 3-letter and 4-letter DNA messages were transcribed and reverse transcribed, both with over 90 percent accuracy.
    http://en.wikipedia.org/wiki/Threose_nucleic_acid
    Growing up, i marveled at star-trek's science, and ignored the perfect society. Now, i try to ignore their science, and marvel at the society.

    Imagine, being able to create matter out of thin air, and not coming up with using drones for boarding hostile ships. Or using drones to defend your own ship. Heck, using drones to block energy attacks, counterattack or for surveillance. Unless, of course, they are nano-machines in your blood, which is a billion times more complex..
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    Quote Originally Posted by dan hunter View Post
    There is a hypothesis that it was RNA that started cellular life and both proteins and DNA evolved later.
    Nobody has figured out a way to test it properly so use caution, it might not be true.

    RNA world hypothesis - Wikipedia, the free encyclopedia
    That would be highly improbable, because simulations have shown RNA could not have survived long enough for this. RNA is like a million times more fragile than DNA, it would simply dissolve in the cell after a few hours.
    Growing up, i marveled at star-trek's science, and ignored the perfect society. Now, i try to ignore their science, and marvel at the society.

    Imagine, being able to create matter out of thin air, and not coming up with using drones for boarding hostile ships. Or using drones to defend your own ship. Heck, using drones to block energy attacks, counterattack or for surveillance. Unless, of course, they are nano-machines in your blood, which is a billion times more complex..
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    Quote Originally Posted by Zwolver View Post
    That would be highly improbable, because simulations have shown RNA could not have survived long enough for this. RNA is like a million times more fragile than DNA, it would simply dissolve in the cell after a few hours.

    True.
    If I had to guess, I would state that a stable RNA-precursor (such as TNA or PNA) is a more likely starting point.
    "The only safe rule is to dispute only with those of your acquaintance of whom you know that they possess sufficient intelligence and self-respect not to advance absurdities; to appeal to reason and not to authority, and to listen to reason and yield to it; and, finally, to be willing to accept reason even from an opponent, and to be just enough to bear being proved to be in the wrong."

    ~ Arthur Schopenhauer, The Art of Being Right: 38 Ways to Win an Argument (1831), Stratagem XXXVIII.
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    I'm new here. If I step on your toes or hijack something, please tell me and I will back out quickly.

    What I am proposing here is not a "theory". It is not even a "hypothesis". It is a "W. E. G." -- a Wild Eyed Guess.

    Here goes:

    Amino acids and such are known to form up spontaneously under certain conditions. Random amino acids.

    Amino acids and such are able to stick to each other by ordinary chemical bonds to make proteins. Random, useless, meaningless proteins.

    Given the proverbial warm shallow sea of which hath been spoken, and a large supply of these necessary ingredients, how long would it be before some very short specimen of DNA was assembled? Random, useless, meaningless DNA. (How long a double helix does it take to count as DNA? Do DNA molecules have end-caps?)

    At this point, would not that single, random, useless, meaningless DNA molecule multiply until it filled the sea?

    Could THAT be our starting point?

    With a virtually unlimited supply of those DNA molecules, if there were a mutation (and there WILL be a mutation!) the one variety would be as likely to multiply as the other.

    Then, if there were another mutation (and there WILL be another!) . . .

    Somewhere down the line, one of the descendant molecules is able to organize a protein that will be to its advantage, and take over the world in about six months or maybe six hundred million years -- EVEN THOUGH IT IS NOT ALIVE IN ANY SENSE OF THE WORD!

    Please advise.

    .
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    Quote Originally Posted by Glenn Jacobs View Post
    I'm new here. If I step on your toes or hijack something, please tell me and I will back out quickly.

    What I am proposing here is not a "theory". It is not even a "hypothesis". It is a "W. E. G." -- a Wild Eyed Guess.

    Here goes:

    Amino acids and such are known to form up spontaneously under certain conditions. Random amino acids.

    Amino acids and such are able to stick to each other by ordinary chemical bonds to make proteins. Random, useless, meaningless proteins.

    Given the proverbial warm shallow sea of which hath been spoken, and a large supply of these necessary ingredients, how long would it be before some very short specimen of DNA was assembled? Random, useless, meaningless DNA. (How long a double helix does it take to count as DNA? Do DNA molecules have end-caps?)

    At this point, would not that single, random, useless, meaningless DNA molecule multiply until it filled the sea?

    Could THAT be our starting point?

    With a virtually unlimited supply of those DNA molecules, if there were a mutation (and there WILL be a mutation!) the one variety would be as likely to multiply as the other.

    Then, if there were another mutation (and there WILL be another!) . . .

    Somewhere down the line, one of the descendant molecules is able to organize a protein that will be to its advantage, and take over the world in about six months or maybe six hundred million years -- EVEN THOUGH IT IS NOT ALIVE IN ANY SENSE OF THE WORD!

    Please advise.

    .
    My thoughts:
    RNA forms in interstellar space so it is RNA first. (Up to this time I hadn't heard of TNA or PNA but we need to look into these other types).
    If it was proteins first the proteins would use amino acids covering the full range of naturally form cis and trans types.

    Note correction:
    Above I used the words "cis or trans" this maybe the incorrect terminology and this next part sentence shows it "only the L-isomer is found." It seems that I should have been saying L-isomer. Biological systems only use the L-isomers even though in normal chemical reactions forming AA both the L and D version are formed.
    Last edited by Robittybob1; March 3rd, 2014 at 08:31 PM. Reason: correction added
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    Just more of your nonsense Bob, none of the standard amino acids that form proteins have a C=C double bond so please explain how they form cis- and trans- types...
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    Technical question: If RNA forms spontaneously in interstellar space, it must take centuries to get here. How does it last that long?
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    Bear in mind Bob often makes stuff up (or wildly misinterprets what he reads) unless he backs up his claims (which he never does) he can be safely ignored. I usually do, he's on my ignore list but I occassionally, masochistically read one of his posts hence my comment above.
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    Me again. Same questions as at first

    1. Do DNA molecules have distinct ends so they cannot keep growing longer?

    2. Is a very short molecule with DNA end caps DNA even if it only has a very few amino acid pairs?

    (and 3.) How would RNA form in interstellar space, seeing that there are so few nitrogen atoms laying around out there? (Or was that a sarcastic answer?)
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    P.S. I was making up that Wild Eyed Guess. Since I have very limited scientific background, I start with that sort of thing and hope someone corrects me.
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    I'll leave someone else to answer your questions, I just pointed out Bob's dubious chemistry and advised you to read his posts with caution
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    Quote Originally Posted by PhDemon View Post
    Just more of your nonsense Bob, none of the standard amino acids that form proteins have a C=C double bond so please explain how they form cis- and trans- types...
    As I said it was just my thoughts, and if you say they seem to be wrong I would like to exchange ideas with you so my thoughts are corrected.

    Even I struggle with the concepts and I'm not a chemist, but I was told that natural Amino Acids (AA) form both types but in biological processes only the cis versions are used.
    So you ask me "none of the standard amino acids that form proteins have a C=C double bond so please explain how they form cis- and trans- types?"

    So help me out here for this is important to me, are there AA that are neither cis or trans due to a double C=C bond? This is the first I heard of this. Do you know the name of one of these AA of this type so I can look it up please?

    Note where previously I used the words "cis or trans" this maybe the incorrect terminology and this next part sentence shows it "only the L-isomer is found." It seems that I should have been saying L-isomer. Biological systems only use the L-isomers even though in normal chemical reactions forming AA both the L and D isomers are formed.
    Last edited by Robittybob1; March 2nd, 2014 at 09:16 PM. Reason: correction added
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    Quote Originally Posted by PhDemon View Post
    I'll leave someone else to answer your questions, I just pointed out Bob's dubious chemistry and advised you to read his posts with caution
    Thanks for pointing out my mistake.
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    Quote Originally Posted by Glenn Jacobs View Post
    Me again. Same questions as at first

    1. Do DNA molecules have distinct ends so they cannot keep growing longer?

    2. Is a very short molecule with DNA end caps DNA even if it only has a very few amino acid pairs?

    (and 3.) How would RNA form in interstellar space, seeing that there are so few nitrogen atoms laying around out there? (Or was that a sarcastic answer?)
    About 2 years ago there were reports that organic molecules were forming in the interstellar space (at least they can be detected there) I'll see if the articles can still be found on the internet. In the coldness of space I'd imagine they would last a long time.

    On a Google search "organic molecules in the interstellar space formation and detection" resulted in many articles to read. Cheers.
    Last edited by Robittybob1; March 3rd, 2014 at 12:18 AM. Reason: clarity
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    Quote Originally Posted by Glenn Jacobs View Post
    Me again. Same questions as at first

    1. Do DNA molecules have distinct ends so they cannot keep growing longer?

    2. Is a very short molecule with DNA end caps DNA even if it only has a very few amino acid pairs?

    (and 3.) How would RNA form in interstellar space, seeing that there are so few nitrogen atoms laying around out there? (Or was that a sarcastic answer?)
    This may be of interest.
    List of organisms by chromosome count - Wikipedia, the free encyclopedia
    "Art is the creation of that which evokes an emotional response, leading to thoughts of the noblest kind" (W4U)
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    Quote Originally Posted by Glenn Jacobs View Post
    Me again. Same questions as at first

    1. Do DNA molecules have distinct ends so they cannot keep growing longer?

    2. Is a very short molecule with DNA end caps DNA even if it only has a very few amino acid pairs?

    (and 3.) How would RNA form in interstellar space, seeing that there are so few nitrogen atoms laying around out there? (Or was that a sarcastic answer?)
    1; No, they can grow, break, anything can happen. But usually not, or slowly, or by external energy, like UV, gamma or beta radiation.

    2; DNA does not consist out of amino acids. Deoxyribonucleonic acid is what it is made up off. RNA is ribonucleonic acid. Which is a sugar. Aminoacids, are what they appear to be, nitrogen based (amides), they make up the proteins.

    Back to your question, a Short strain of nucleotides (DNA or RNA) is still considered DNA. It is still a specific sequence, random maybe, but still specific. It's called DNA because of what it contains (the sugar), not of what it does.

    3; RNA won't form in space, there is not enough cohesion for the energy to be applied to bind anything together. All they can do in space, is break apart.
    Growing up, i marveled at star-trek's science, and ignored the perfect society. Now, i try to ignore their science, and marvel at the society.

    Imagine, being able to create matter out of thin air, and not coming up with using drones for boarding hostile ships. Or using drones to defend your own ship. Heck, using drones to block energy attacks, counterattack or for surveillance. Unless, of course, they are nano-machines in your blood, which is a billion times more complex..
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    Thank you. That clarifies many things for me.

    Back to my Wild-Eyed Guess: I guess that out of all the possibilities, a short, useless, random DNA molecule could "fall together" under the right natural conditions.

    I guess that under the same conditions in which it formed, it would replicate itself until it used up the available ingredients.

    I guess that with such a supply of those useless DNA molecules, now and then a gamma ray or something might mutate one or another.

    I guess that eventually some mutation might give one sort of DNA a slight advantage and it would replicate itself and fill up the sea EVEN THO IT COULD NOT IN ANY SENSE BE CONSIDERED TO BE LIVING.
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    Quote Originally Posted by Zwolver View Post
    .....

    3; RNA won't form in space, there is not enough cohesion for the energy to be applied to bind anything together. All they can do in space, is break apart.
    There were statements like the following that seemed to suggest otherwise.
    List of interstellar and circumstellar molecules - Wikipedia, the free encyclopedia
    In August 2012, astronomers at Copenhagen University reported the detection of a specific sugar molecule, glycolaldehyde, in a distant star system. The molecule was found around theprotostellarbinaryIRAS 16293-2422, which is located 400 light years from Earth.[17][18]Glycolaldehyde is needed to form ribonucleic acid, or RNA, which is similar in function to DNA. This finding suggests that complex organic molecules may form in stellar systems prior to the formation of planets, eventually arriving on young planets early in their formation.[19]
    The ingredients seem to be there and there are situations where the pressures could be right, as in the contracting proto-stars.
    So I leave the possibility open that random RNA molecules are preformed in space.
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    Quote Originally Posted by Glenn Jacobs View Post
    Thank you. That clarifies many things for me.

    Back to my Wild-Eyed Guess: I guess that out of all the possibilities, a short, useless, random DNA molecule could "fall together" under the right natural conditions.

    I guess that under the same conditions in which it formed, it would replicate itself until it used up the available ingredients.

    I guess that with such a supply of those useless DNA molecules, now and then a gamma ray or something might mutate one or another.

    I guess that eventually some mutation might give one sort of DNA a slight advantage and it would replicate itself and fill up the sea EVEN THO IT COULD NOT IN ANY SENSE BE CONSIDERED TO BE LIVING.
    Most agree that it was RNA molecules replicating long before DNA developed. So I'd think in terms of RNA and where you wrote DNA I would have inserted RNA. (But there are other types too! TNA and PNA see above)
    Last edited by Robittybob1; March 3rd, 2014 at 08:35 PM.
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    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by Zwolver View Post
    .....

    3; RNA won't form in space, there is not enough cohesion for the energy to be applied to bind anything together. All they can do in space, is break apart.
    There were statements like the following that seemed to suggest otherwise.
    List of interstellar and circumstellar molecules - Wikipedia, the free encyclopedia
    In August 2012, astronomers at Copenhagen University reported the detection of a specific sugar molecule, glycolaldehyde, in a distant star system. The molecule was found around theprotostellarbinaryIRAS 16293-2422, which is located 400 light years from Earth.[17][18]Glycolaldehyde is needed to form ribonucleic acid, or RNA, which is similar in function to DNA. This finding suggests that complex organic molecules may form in stellar systems prior to the formation of planets, eventually arriving on young planets early in their formation.[19]
    The ingredients seem to be there and there are situations where the pressures could be right, as in the contracting proto-stars.
    So I leave the possibility open that random RNA molecules are preformed in space.
    So, what do you think that IRAS 16293-2422 is? It's a star, and however this sugar may form in the gas around the star, so states wikipedia, a gascloud around a star is hardly a place for life to form. I agree this is how some organic molecules may find its way to planets, but glycoaldehyde is one of the most simple sugar forms, while ribose is extremely complex compared to it.
    Growing up, i marveled at star-trek's science, and ignored the perfect society. Now, i try to ignore their science, and marvel at the society.

    Imagine, being able to create matter out of thin air, and not coming up with using drones for boarding hostile ships. Or using drones to defend your own ship. Heck, using drones to block energy attacks, counterattack or for surveillance. Unless, of course, they are nano-machines in your blood, which is a billion times more complex..
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    Quote Originally Posted by Glenn Jacobs View Post
    I guess that eventually some mutation might give one sort of DNA a slight advantage and it would replicate itself and fill up the sea EVEN THO IT COULD NOT IN ANY SENSE BE CONSIDERED TO BE LIVING.
    Hardly, as i said, DNA can not replicate itself from scratch. In a sea made of nucleotides, oligonucleotides, polymerase, and thermal shafts, there may be some random construction going on. But seas like that will not exist.
    Growing up, i marveled at star-trek's science, and ignored the perfect society. Now, i try to ignore their science, and marvel at the society.

    Imagine, being able to create matter out of thin air, and not coming up with using drones for boarding hostile ships. Or using drones to defend your own ship. Heck, using drones to block energy attacks, counterattack or for surveillance. Unless, of course, they are nano-machines in your blood, which is a billion times more complex..
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    It's just Bob making stuff up/wildly misinterprating what he reads again
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    Quote Originally Posted by Glenn Jacobs View Post
    Me again. Same questions as at first

    1. Do DNA molecules have distinct ends so they cannot keep growing longer?

    2. Is a very short molecule with DNA end caps DNA even if it only has a very few amino acid pairs?
    DNA molecules do indeed have distinct ends - they are said to have a polarity or directionality. One end is designated as the 3' ("three prime") end, the other as the 5' end. The 3' end is characterised by a free hydroxyl group (-OH) on carbon no. 3 of the deoxyribose sugar of the DNA backbone; the 5' end is characterised by a phosphate group on carbon no. 5 of the termimal deoxyribose sugar.

    One strand of a double-stranded DNA is orientated 5' -> 3', the other 3' -> 5', like so:

    5' ----------- 3'
    3' ----------- 5'

    DNA molecules can only extend in the 5' -> 3' direction. The process does not occur spontaneously; instead, it is carried out by a stupendously complex set of enzymatic reactions. ALL nucleic acids are replicated in the 5' -> 3' direction, without exception. DNA replication requires a template strand to serve as substrate. The ends can't just keep getting longer by themselves.

    In the diagram below, the bottom strand is extending to the right. The process will stop when the top strand is fully copied.

    3' ----------- 5'
    5' -------> 3'

    RNA molecules are often capped by additional structures. These are to prevent degradation by cellulareno nucleases, rather than to prevent elongation.

    Not really sure what your asking in the second question... there are no amino acids in DNA.
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    Quote Originally Posted by PhDemon View Post
    It's just Bob making stuff up/wildly misinterprating what he reads again
    Glycolaldehyde is needed to form ribonucleic acid, or RNA, which is similar in function to DNA. This finding suggests that complex organic molecules may form in stellar systems prior to the formation of planets, eventually arriving on young planets early in their formation.
    Can you read that in any other way?
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    Thank you.

    Well, again I have led myself on a wild ride over the mountain!

    TECHNICAL QUESTION: What sorts of thingies pair up to connect one strand to the other?

    (Someone told me there are just four varieties, and THIS only pairs up with THAT and so on, to make the genetic code.)
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    Quote Originally Posted by Zwolver View Post
    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by Zwolver View Post
    .....

    3; RNA won't form in space, there is not enough cohesion for the energy to be applied to bind anything together. All they can do in space, is break apart.
    There were statements like the following that seemed to suggest otherwise.
    List of interstellar and circumstellar molecules - Wikipedia, the free encyclopedia
    In August 2012, astronomers at Copenhagen University reported the detection of a specific sugar molecule, glycolaldehyde, in a distant star system. The molecule was found around theprotostellarbinaryIRAS 16293-2422, which is located 400 light years from Earth.[17][18]Glycolaldehyde is needed to form ribonucleic acid, or RNA, which is similar in function to DNA. This finding suggests that complex organic molecules may form in stellar systems prior to the formation of planets, eventually arriving on young planets early in their formation.[19]
    The ingredients seem to be there and there are situations where the pressures could be right, as in the contracting proto-stars.
    So I leave the possibility open that random RNA molecules are preformed in space.
    So, what do you think that IRAS 16293-2422 is? It's a star, and however this sugar may form in the gas around the star, so states wikipedia, a gas cloud around a star is hardly a place for life to form. I agree this is how some organic molecules may find its way to planets, but glycoaldehyde is one of the most simple sugar forms, while ribose is extremely complex compared to it.
    I'm not suggesting replicating life forms in interstellar space but the possibility that RNA molecules form as the planets form doesn't seem impossible if the molecules needed to produce RNA are there in the medium to begin with.
    How ribose is formed I'm not sure , but I was just saying it seems to be possible.
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    Quote Originally Posted by Glenn Jacobs
    What sorts of thingies pair up to connect one strand to the other?


    Those are single and double-ringed molecules called bases or nitrogenous bases or nucleobases. There are four common ones and a bunch of exotic ones that you don't really need to know about. The common four are adenine (A), thymine (T), cytosine (C) and guanine (G).

    They pair like so: A-T and C-G through hydrogen bonding and some other fancy stuff.

    So the diagrams above could look like this:

    5'...G C T C C A G A G C..........G C T C T G G A G C...3'
    3'...C G A G G T C T C G..........C G A G A C C T C G...5'
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    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by PhDemon View Post
    It's just Bob making stuff up/wildly misinterprating what he reads again
    Glycolaldehyde is needed to form ribonucleic acid, or RNA, which is similar in function to DNA. This finding suggests that complex organic molecules may form in stellar systems prior to the formation of planets, eventually arriving on young planets early in their formation.
    Can you read that in any other way?

    Obviously, just because a precursor (glycolaldehyde) is present does not automatically mean the product (RNA) will form. If I tried to pull that shit in a paper on a chemical mechanism I would be laughed out of the building. The link actually only says "complex organic molecules may form" not RNA which AFAIK would require a hell of a lot more than the just the presence of glycolaldehyde.
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    Quote Originally Posted by Robittybob1 View Post
    I'm not suggesting replicating life forms in interstellar space but the possibility that RNA molecules form as the planets form doesn't seem impossible if the molecules needed to produce RNA are there in the medium to begin with.
    How ribose is formed I'm not sure , but I was just saying it seems to be possible.
    There is the Murchison meteorite. It contains quite a few amino acid and RNA precursor molecules that appear to be interstellar in origin due to their isotope numbers.
    Murchison meteorite - Wikipedia, the free encyclopedia
    Last edited by dan hunter; March 3rd, 2014 at 06:07 PM.
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    Quote Originally Posted by PhDemon View Post
    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by PhDemon View Post
    It's just Bob making stuff up/wildly misinterprating what he reads again
    Glycolaldehyde is needed to form ribonucleic acid, or RNA, which is similar in function to DNA. This finding suggests that complex organic molecules may form in stellar systems prior to the formation of planets, eventually arriving on young planets early in their formation.
    Can you read that in any other way?

    Obviously, just because a precursor (glycolaldehyde) is present does not automatically mean the product (RNA) will form. If I tried to pull that shit in a paper on a chemical mechanism I would be laughed out of the building. The link actually only says "complex organic molecules may form" not RNA which AFAIK would require a hell of a lot more than the just the presence of glycolaldehyde.
    On the page List of interstellar and circumstellar molecules - Wikipedia, the free encyclopedia there must be close to 180 organic molecules mentioned. Would a combination of those be enough.? I'm not pretending to be a chemist, but they might just do the trick. And I'm only saying "may" as well just like the article but instead of just saying complex molecules I have taken that to read short chain RNA (a complex molecule for sure).
    No one knows for certain so it will always be ideas with varying degrees of possibility. What alternative do you propose?
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    I don't propose an alternative as a) there is no evidence that RNA is present in space (and every bit of chemical intuition I have about it would tell me it cannot form in space) and b) I am not an expert in astrochemistry so even if it could form in space even with my chemistry background the chances of me coming up with a plausible mechanism would be slim. But then again I acknowledge this and don't try to build a fantasy world picture that backs up my imaginings from a position of utter cluelessness. That's where our approaches differ.
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    Quote Originally Posted by Robittybob1 View Post
    What alternative do you propose?

    The alternative that RNA could have been formed in the prebiotic conditions on Earth from its components, delivered by (but not limited to) comets and/or asteroids. The hypothetical formation of RNA must have taken place under mild conditions due to its instability, presumably in the deep sea (and thus independent of the primordial atmosphere). The mild conditions might have been present under the form of primitive proto-cells, already felt with peptides.

    It could have been that RNA was formed in and originated from interstellar space, but we do not have (as member PhDemon pointed out) evidence that RNA is present in space, nor do we have evidence that RNA is stable enough to survive the harsh conditions of interstellar space travel.
    Last edited by Cogito Ergo Sum; March 4th, 2014 at 08:08 AM.
    "The only safe rule is to dispute only with those of your acquaintance of whom you know that they possess sufficient intelligence and self-respect not to advance absurdities; to appeal to reason and not to authority, and to listen to reason and yield to it; and, finally, to be willing to accept reason even from an opponent, and to be just enough to bear being proved to be in the wrong."

    ~ Arthur Schopenhauer, The Art of Being Right: 38 Ways to Win an Argument (1831), Stratagem XXXVIII.
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    Quote Originally Posted by Cogito Ergo Sum View Post
    The hypothetical formation of RNA must have taken place under mild conditions due to its instability, presumably in the deep sea (and thus independent of the primordial atmosphere).
    i.e. not in space (take note Bob).
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    Quote Originally Posted by PhDemon View Post
    I don't propose an alternative as a) there is no evidence that RNA is present in space (and every bit of chemical intuition I have about it would tell me it cannot form in space) and b) I am not an expert in astrochemistry so even if it could form in space even with my chemistry background the chances of me coming up with a plausible mechanism would be slim. But then again I acknowledge this and don't try to build a fantasy world picture that backs up my imaginings from a position of utter cluelessness. That's where our approaches differ.
    Did I really say RNA formed "in space"? No, as I recall my hypothesis was that the RNA molecules formed in the pressure of the collapsing protostars. So that is not technically interstellar space any more, but who knows and you guys could be right, it doesn't matter that much. Could be in the oceans could be elsewhere, but I struggled to see how one would get the right number of chances and the high enough concentration without some mechanism to condense these organic molecules together. So that is what I have been looking for.

    I have spent 20 years looking for clues as to how life formed so it is a bit harsh to say my ideas are "from a position of utter cluelessness".
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    I have spent 20 years looking for clues as to how life formed so it is a bit harsh to say my ideas are "from a position of utter cluelessness".
    A wasted 20 years, but then I suspect that whatever you do is wasted time.
    Its the way nature is!
    If you dont like it, go somewhere else....
    To another universe, where the rules are simpler
    Philosophically more pleasing, more psychologically easy
    Prof Richard Feynman (1979) .....

    Das ist nicht nur nicht richtig, es ist nicht einmal falsch!"
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    Quote Originally Posted by AlexG View Post
    I have spent 20 years looking for clues as to how life formed so it is a bit harsh to say my ideas are "from a position of utter cluelessness".
    A wasted 20 years, but then I suspect that whatever you do is wasted time.
    Where have you come from? Life has been a struggle. True mate.
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    Quote Originally Posted by Robittybob1 View Post
    I have spent 20 years looking for clues as to how life formed so it is a bit harsh to say my ideas are "from a position of utter cluelessness".

    Where have you searched for clues?
    "The only safe rule is to dispute only with those of your acquaintance of whom you know that they possess sufficient intelligence and self-respect not to advance absurdities; to appeal to reason and not to authority, and to listen to reason and yield to it; and, finally, to be willing to accept reason even from an opponent, and to be just enough to bear being proved to be in the wrong."

    ~ Arthur Schopenhauer, The Art of Being Right: 38 Ways to Win an Argument (1831), Stratagem XXXVIII.
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    So collapsing proto-stars are not "technically" in space now? OK even if I give you that one, what temperatures and densities are prevalent in these areas? What are the mixing ratios of organic precursors present? What is the collision frequency of these molecules and what are their collision cross sections for the reactions required to make RNA compared to those to make other products via reaction with other things? Does heterogeneous chemistry play a role? Are they barrierless reactions or is there a kinetic limitation? If there is an activation barrier is the temperature adequate to overcome this? As a chemist these are just some of the basic questions I would be asking myself before spouting off a half-assed idea. I'm guessing you haven't thought about any of them (or even know what some of them mean) yet you are pontificating. This is why I suggested "utter cluelessness".

    If it's taken you 20 years to get to the level you are at now you must be a very slow learner. You are still at the stage where your understanding of the chemistry and biology involved is so poor you did not know the difference between types of isomerism and you think making stuff up is a substitute for knowledge, most people grow out of this before high school.

    That's it, I'm out.
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    Quote Originally Posted by PhDemon View Post
    So collapsing proto-stars are not "technically" in space now? OK even if I give you that one, what temperatures and densities are prevalent in these areas? What are the mixing ratios of organic precursors present? What is the collision frequency of these molecules and what are their collision cross sections for the reactions required to make RNA compared to those to make other products via reaction with other things? Does heterogeneous chemistry play a role? Are they barrierless reactions or is there a kinetic limitation? If there is an activation barrier is the temperature adequate to overcome this? As a chemist these are just some of the basic questions I would be asking myself before spouting off a half-assed idea. I'm guessing you haven't thought about any of them (or even know what some of them mean) yet you are pontificating. This is why I suggested "utter cluelessness".

    If it's taken you 20 years to get to the level you are at now you must be a very slow learner. You are still at the stage where your understanding of the chemistry and biology involved is so poor you did not know the difference between types of isomerism and you think making stuff up is a substitute for knowledge, most people grow out of this before high school.

    That's it, I'm out.
    There are lots of unanswered questions for sure, but same goes for where ever you favor the process to occur. But would anyone have thought of organic molecules forming in interstellar space 20 years ago? But certainly today it can't be denied.
    Learning from the news, science news, etc and then looking it up on Google. That sort of continual focused interest with the goal of trying to work out how life formed. OK it wasn't from University, but just from interest.
    I corrected myself regarding the isomerism issue. No one is perfect, but I admitted my error and I'm moving on.
    I'm listening to all objections but truly your criticism is so personally directed it does nothing to improve my knowledge. Raving on about how slow a learner I am does not help me at all. I really don't know why you bother. Cogito is far more helpful in that regard.
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    Quote Originally Posted by Robittybob1 View Post
    I really don't know why you bother.
    Because I have no patience for bullshit merchants posting in the real science areas. You want us to help you? You have shown in other threads it's a waste of time. JG said it better than I could here. But fair enough I'll just put you back on ignore and let others point out your nonsense.

    Who is raving? You brought up the fact that you've been at this for 20 years, I just pointed out that you don't seem to have learned much. No raving involved.
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    Quote Originally Posted by PhDemon View Post
    Quote Originally Posted by Robittybob1 View Post
    I really don't know why you bother.
    Because I have no patience for bullshit merchants posting in the real science areas. You want us to help you? You have shown in other threads it's a waste of time. JG said it better than I could here. But fair enough I'll just put you back on ignore and let others point out your nonsense.
    If I said something in error I'll admit that and correct myself, but all the rest is just from possibilities introduced from ideas that have come up.
    Why call me a bullshit merchant? If you think I'm wrong tell me where I'm going wrong, don't just say I'm wrong. That is the help you could have given me, and you'd be teaching the other 100 or so of others who are reading the thread as well. This debate is not just between you and me but the others as well.
    Have I actually said anything else wrong?
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    I confess. I'm with Bob. I take a wild guess and it sounds good to me because I don't know any better.

    Then someone points out my cluelessness.

    Back to the drawing board!

    Let me generalize my W.E.G. (Wild-Eyed Guess):

    In the warm shallow sea of which hath been spoken, with lots of atoms of all kinds available at hand, many kazillions of different combinations turned up, at random.

    Something (Which I guessed was DNA, made up from amino acid sub-assemblies) formed up a random molecule which was capable of replicating itself as it happened upon the necessary spare parts.

    An absolutely meaningless, random, lifeless molecule.

    This filled the sea with duplicates of itself.

    Random mutations made slightly different versions.

    When some version turned out to have a slight advantage, it replaced all the others.

    This in spite of having NO ATTRIBUTES OF LIFE EXCEPT THE REPLICATION THING.

    - - - - - -

    The only alternative I can see to this is that Fred, the Head Technician, went to a lot of trouble to set things up to bring this to pass.

    Much later, when the process was well under way, Fred was promoted to Deity and given the new name, El Shadai (God Almighty).
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    There is also the idea of autocatalyzing reactions where complex molecules are able to bootstrap themselves into being.
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    Quote Originally Posted by Glenn Jacobs View Post
    I confess. I'm with Bob. I take a wild guess and it sounds good to me because I don't know any better.

    Then someone points out my cluelessness.

    Back to the drawing board!

    Let me generalize my W.E.G. (Wild-Eyed Guess):

    In the warm shallow sea of which hath been spoken, with lots of atoms of all kinds available at hand, many kazillions of different combinations turned up, at random.

    Something (Which I guessed was DNA, made up from amino acid sub-assemblies) formed up a random molecule which was capable of replicating itself as it happened upon the necessary spare parts.

    An absolutely meaningless, random, lifeless molecule.

    This filled the sea with duplicates of itself.

    Random mutations made slightly different versions.

    When some version turned out to have a slight advantage, it replaced all the others.

    This in spite of having NO ATTRIBUTES OF LIFE EXCEPT THE REPLICATION THING.
    It is generally accepted the RNA world preceded the DNA world.
    Please use the word RNA rather than DNA for RNA is single stranded and some combinations are capable of folding into a shape that MAY have enzymatic activity. Hypothetically it would be possible to have one RNA type that could replicate itself but itself was an enzyme that promoted that replication, or two RNA molecules working as a pair one doing the replication and the other the storage of the information.

    I like your idea and even though it is purely hypothetical, it might still be possible to get such a sequence of nucleotide bases that do this.
    The RNA nucleotides are guanine, adenine, uracil and cytosine.
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    RNA. RiboNucleicAcid. Guanine. Adenine. Uracil. Cytosine. Nucleotides.

    If RNA is a single strand, how does it replicate itself?

    Do the nucleotides just stick out into space?

    When DNA unzips, does it turn into two RNA molecules?

    Are there organisms that use RNA?
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    Quote Originally Posted by Glenn Jacobs View Post
    RNA. RiboNucleicAcid. Guanine. Adenine. Uracil. Cytosine. Nucleotides.

    If RNA is a single strand, how does it replicate itself?

    Do the nucleotides just stick out into space?

    When DNA unzips, does it turn into two RNA molecules?

    Are there organisms that use RNA?
    They are all good questions and I'm sure they could be answered.

    "If RNA is a single strand, how does it replicate itself?"
    It could be via an alternating process of producing a complimentary strand as well. We would be talking of processes that have become evolutionary extinct. So cells today may not have the same processes.
    So even the description of the process might have to be hypothetical. (In other words I don't know!)

    "Do the nucleotides just stick out into space?" Yes I think they do in places but there can be sections along the RNA molecules that compliment each other so you get these folded shapes. Look up Google images "RNA folded shapes" Plenty of examples.

    "When DNA unzips, does it turn into two RNA molecules?" DNA and RNA use different molecules in their formation so they are different and hence splitting DNA does not make two RNA.

    "Are there organisms that use RNA?" Some viruses still use RNA as their genetic carrier. RNA virus - Wikipedia, the free encyclopedia
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    "Art is the creation of that which evokes an emotional response, leading to thoughts of the noblest kind" (W4U)
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    Quote Originally Posted by Glenn Jacobs View Post
    RNA. RiboNucleicAcid. Guanine. Adenine. Uracil. Cytosine. Nucleotides.

    If RNA is a single strand, how does it replicate itself?

    Do the nucleotides just stick out into space?

    When DNA unzips, does it turn into two RNA molecules?

    Are there organisms that use RNA?
    You may find this interesting.

    Drew Berry: Animations of unseeable biology | Video on TED.com
    "Art is the creation of that which evokes an emotional response, leading to thoughts of the noblest kind" (W4U)
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    Quote Originally Posted by Robittybob1 View Post
    Quote Originally Posted by Glenn Jacobs View Post
    RNA. RiboNucleicAcid. Guanine. Adenine. Uracil. Cytosine. Nucleotides.

    If RNA is a single strand, how does it replicate itself?

    Do the nucleotides just stick out into space?

    When DNA unzips, does it turn into two RNA molecules?

    Are there organisms that use RNA?
    They are all good questions and I'm sure they could be answered.

    "If RNA is a single strand, how does it replicate itself?"
    It could be via an alternating process of producing a complimentary strand as well. We would be talking of processes that have become evolutionary extinct. So cells today may not have the same processes.
    So even the description of the process might have to be hypothetical. (In other words I don't know!)
    I find the university courses on YouTube pretty effective starting points to finding the answers to issues. This lecture covers RNA viruses that don't use a DNA phase (as the Retroviruses do), and they behave differently if it is a positive sense RNA or a negative sense RNA strand in the virion package.
    3.7. RNA Virus Replication Strategies-I - Medical Microbiology - YouTube
    It was interesting to learn that since animal cells don't use RNA in this way these viruses had to either code for a RNA polymerase or to have an RNA polymerase packaged along with the RNA strand to replicate.
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    Quote Originally Posted by Write4U View Post
    It'd probably be best if you ignored almost everything written in that article. I've not seen so much wrongness masquerading as science in a long, long time. A shameful and irresponsible piece of science writing.
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    Quote Originally Posted by Glenn Jacobs View Post
    RNA. RiboNucleicAcid. Guanine. Adenine. Uracil. Cytosine. Nucleotides.

    If RNA is a single strand, how does it replicate itself?

    Do the nucleotides just stick out into space?

    When DNA unzips, does it turn into two RNA molecules?

    Are there organisms that use RNA?
    I will just answer it because i think above answer was not correct enough, i hate flaming so i will just say bob is on the right path, but has some studying to do to fully be able to understand the questions.

    RNA is a single strand, only virusses can replicate their RNA directly. First they make proteins that can do this, who can then copy the RNA. A normal cell can not replicate RNA, only recycle it into nucleotides. (to prevent excess errors)

    RNA does not simply stick into space, proteins bind to it to keep it from connecting to their complementary nucleotides again, ribosomes can remove the proteins.

    When DNA unzips, it turns into two single strands of DNA.

    All organisms use RNA, but you mean instead of DNA, only virusses, which are not really organisms.

    Quote Originally Posted by Zwirko View Post
    Quote Originally Posted by Write4U View Post
    It'd probably be best if you ignored almost everything written in that article. I've not seen so much wrongness masquerading as science in a long, long time. A shameful and irresponsible piece of science writing.
    Junk DNA is required to quickly and easily respond to environmental changes and to have better odds at positive random mutations. An organism like a carnivorous plant, that hasn't changed, or needed to change for a billion years has only little junk DNA, because it works.
    Growing up, i marveled at star-trek's science, and ignored the perfect society. Now, i try to ignore their science, and marvel at the society.

    Imagine, being able to create matter out of thin air, and not coming up with using drones for boarding hostile ships. Or using drones to defend your own ship. Heck, using drones to block energy attacks, counterattack or for surveillance. Unless, of course, they are nano-machines in your blood, which is a billion times more complex..
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    Quote Originally Posted by Zwolver View Post

    Junk DNA is required to quickly and easily respond to environmental changes and to have better odds at positive random mutations.

    Nope.

    Evolution is a blind process and can't plan for future changes in climate.
    Last edited by Zwirko; March 4th, 2014 at 07:15 AM.
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    Quote Originally Posted by Zwirko View Post
    Quote Originally Posted by Write4U View Post
    It'd probably be best if you ignored almost everything written in that article. I've not seen so much wrongness masquerading as science in a long, long time. A shameful and irresponsible piece of science writing.
    Thanks for the "heads up".


    Did you like the Drew Berry link about "unseeable biology"?
    "Art is the creation of that which evokes an emotional response, leading to thoughts of the noblest kind" (W4U)
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    Quote Originally Posted by Write4U View Post

    Did you like the Drew Berry link about "unseeable biology"?
    I did. Some nice animations.
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    I watched the Drew Berry animation twice.

    I am less and less inclined to believe that this system just fell together by the random motion of naturally-occurring molecules.
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    Quote Originally Posted by Zwirko View Post
    Quote Originally Posted by Zwolver View Post

    Junk DNA is required to quickly and easily respond to environmental changes and to have better odds at positive random mutations.

    Nope.

    Evolution is a blind process and can't plan for future changes in climate.
    Nope, mutations are not totally random.

    You have, inversions, deletions, duplications, moving of introns, exons, start codon, and stop codon. Don't tell me that junk dna does not become a part of seemingly random mutations. It was also proven that the occurence of many T=A or G=C around a gene either promotes, or prevents environmental damage. Because it positions the gene on a susceptible spot, or somewhere deep in the genome.
    Growing up, i marveled at star-trek's science, and ignored the perfect society. Now, i try to ignore their science, and marvel at the society.

    Imagine, being able to create matter out of thin air, and not coming up with using drones for boarding hostile ships. Or using drones to defend your own ship. Heck, using drones to block energy attacks, counterattack or for surveillance. Unless, of course, they are nano-machines in your blood, which is a billion times more complex..
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    Mutations are totally random with respect to future outcomes. Do different areas of a genome mutate are different rates? Sure, but that's not what I disputed.


    You're suggesting that junk DNA has a sequence-independent function, either as a sink or false target for mutations or as a resevoir of nucleotides awaiting mutation. There's no good evidence in support of these ideas, and much against.
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    Quote Originally Posted by Zwolver View Post
    Quote Originally Posted by Glenn Jacobs View Post
    RNA. RiboNucleicAcid. Guanine. Adenine. Uracil. Cytosine. Nucleotides.

    If RNA is a single strand, how does it replicate itself?

    Do the nucleotides just stick out into space?

    When DNA unzips, does it turn into two RNA molecules?

    Are there organisms that use RNA?
    I will just answer it because i think above answer was not correct enough, i hate flaming so i will just say bob is on the right path, but has some studying to do to fully be able to understand the questions.

    RNA is a single strand, only virusses can replicate their RNA directly. First they make proteins that can do this, who can then copy the RNA. A normal cell can not replicate RNA, only recycle it into nucleotides. (to prevent excess errors)

    RNA does not simply stick into space, proteins bind to it to keep it from connecting to their complementary nucleotides again, ribosomes can remove the proteins.

    When DNA unzips, it turns into two single strands of DNA.

    All organisms use RNA, but you mean instead of DNA, only virusses, which are not really organisms.

    Quote Originally Posted by Zwirko View Post
    Quote Originally Posted by Write4U View Post
    It'd probably be best if you ignored almost everything written in that article. I've not seen so much wrongness masquerading as science in a long, long time. A shameful and irresponsible piece of science writing.
    Junk DNA is required to quickly and easily respond to environmental changes and to have better odds at positive random mutations. An organism like a carnivorous plant, that hasn't changed, or needed to change for a billion years has only little junk DNA, because it works.
    I accept what you say here except that the point of the thread was to look at life starting off, and we were considering a time before proteins and even ribosomes. What was the RNA world like? Were there proteins or just peptides at this time?
    I imagine RNA Viruses or their progenitors are replicators just like RNA would have been at this time too, we are trying to imagine the world prior to cellular life.
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    Quote Originally Posted by Robittybob1 View Post
    I accept what you say here except that the point of the thread was to look at life starting off, and we were considering a time before proteins and even ribosomes. What was the RNA world like? Were there proteins or just peptides at this time?

    I have described in post #36 how the RNA World might have looked like.
    Nevertheless, it is odd that you ask such questions, because I assume your knowledge concerning abiogenesis vastly exceeds mine because you stated that you "have spent 20 years looking for clues as to how life formed (...)".

    Would you also be so kind to answer my question in post #41?
    Last edited by Cogito Ergo Sum; March 4th, 2014 at 02:10 PM.
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    "The only safe rule is to dispute only with those of your acquaintance of whom you know that they possess sufficient intelligence and self-respect not to advance absurdities; to appeal to reason and not to authority, and to listen to reason and yield to it; and, finally, to be willing to accept reason even from an opponent, and to be just enough to bear being proved to be in the wrong."

    ~ Arthur Schopenhauer, The Art of Being Right: 38 Ways to Win an Argument (1831), Stratagem XXXVIII.
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    Quote Originally Posted by Cogito Ergo Sum View Post
    Quote Originally Posted by Robittybob1 View Post
    I accept what you say here except that the point of the thread was to look at life starting off, and we were considering a time before proteins and even ribosomes. What was the RNA world like? Were there proteins or just peptides at this time?

    I have described in post #36 how the RNA World might have looked like.
    Nevertheless, it is odd that you ask such questions, because I assume your knowledge concerning abiogenesis vastly exceeds mine because you stated that you "have spent 20 years looking for clues as to how life formed (...)".


    Would you also be so kind to answer my question in post #41?
    I know you know more than I do. I have spent those years on the project but not really in the right environment.
    I had answered you in #43
    Learning from the news, science news, etc and then looking it up on Google. That sort of continual focused interest with the goal of trying to work out how life formed. OK it wasn't from University, but just from interest.
    So don't worry.

    I did read your post #36
    The alternative that RNA could have been formed in the prebiotic conditions on Earth from its components, delivered by (but not limited to) comets and/or asteroids. The hypothetical formation of RNA must have taken place under mild conditions due to its instability, presumably in the deep sea (and thus independent of the primordial atmosphere). The mild conditions might have been present under the form of primitive proto-cells, already felt with peptides.

    It could have been that RNA was formed in and originated from interstellar space, but we do not have (as memberPhDemon pointed out) evidence that RNA is present in space, nor do we have evidence that RNA is stable enough to survive the harsh conditions of interstellar space travel.
    I have been on a different path for some years, which I have covered from time to time on the forums but it generates animosity, so I'll say no more.
    But I'm going to look into the TNA and PNA concepts, things I hadn't heard of before. Thanks.
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    Quote Originally Posted by Zwirko View Post
    Mutations are totally random with respect to future outcomes. Do different areas of a genome mutate are different rates? Sure, but that's not what I disputed.


    You're suggesting that junk DNA has a sequence-independent function, either as a sink or false target for mutations or as a resevoir of nucleotides awaiting mutation. There's no good evidence in support of these ideas, and much against.
    Not exactly what i meant to say, rather that Junk DNA holds many of the leftovers from previous mutations, and also hold partly functioning sequences that could be mutated in already existing genes, or to mutate a code into a start codon. But this is evolutionary relevant, not relevant to the issue of the mutation itself.

    I am just saying that mutation is not totally random. Neither is the effect this mutation has. Otherwise explain the large amount of sudden mutations of a specific gene. Yes some are hereditary but some mutations will occur, spontaneously, and mostly on the same spot. Out of trillions of nucleotides, the mutation occurs a million times more frequently on a single nucleotide. That is no longer a coincidence. This nucleotide must be marked somehow, or affected by surrounding junk DNA to be easier to mutate.

    This marking could also be simply the type of gene it codes for, that if this gene is damaged, the cell's repair mechanism is damaged as well. But then again, why so few spots in this gene that mutate?
    Growing up, i marveled at star-trek's science, and ignored the perfect society. Now, i try to ignore their science, and marvel at the society.

    Imagine, being able to create matter out of thin air, and not coming up with using drones for boarding hostile ships. Or using drones to defend your own ship. Heck, using drones to block energy attacks, counterattack or for surveillance. Unless, of course, they are nano-machines in your blood, which is a billion times more complex..
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    Quote Originally Posted by Zwolver View Post
    Quote Originally Posted by Zwirko View Post
    Mutations are totally random with respect to future outcomes. Do different areas of a genome mutate are different rates? Sure, but that's not what I disputed.


    You're suggesting that junk DNA has a sequence-independent function, either as a sink or false target for mutations or as a resevoir of nucleotides awaiting mutation. There's no good evidence in support of these ideas, and much against.
    Not exactly what i meant to say, rather that Junk DNA holds many of the leftovers from previous mutations, and also hold partly functioning sequences that could be mutated in already existing genes, or to mutate a code into a start codon. But this is evolutionary relevant, not relevant to the issue of the mutation itself.

    I am just saying that mutation is not totally random. Neither is the effect this mutation has. Otherwise explain the large amount of sudden mutations of a specific gene. Yes some are hereditary but some mutations will occur, spontaneously, and mostly on the same spot. Out of trillions of nucleotides, the mutation occurs a million times more frequently on a single nucleotide. That is no longer a coincidence. This nucleotide must be marked somehow, or affected by surrounding junk DNA to be easier to mutate.

    This marking could also be simply the type of gene it codes for, that if this gene is damaged, the cell's repair mechanism is damaged as well. But then again, why so few spots in this gene that mutate?
    I was a bit confused by what you're saying here when talking about a single nucleotide mutating rapidly, for isn't there only 4 variations any 1 place can have? Places where it is important not to change the order of the nucleotides, these regions remain stable, for mutations on these sites could be fatal (hence mutations are selected against). Other sites that doesn't affect the functionality of a protein (or whatever is being coded for or even in a non coding portion) it doesn't matter what happens so mutations occur rapidly without consequence in these places.
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    Even tho mutations are random, they might be thought to be targeted at particular areas because of their effects.

    PLAN A: A given mutation is fatal.

    PLAN B: A given mutation is somewhat disadvantageous to an organism -- which in the long run is the same thing.

    PLAN C: A given mutation neither hurts nor favors an organism.

    PLAN D: A given organism is somehow marginally favorable to an organism -- which means Darwin wins this round.

    The organism which receives the favorable mutation will multiply more successfully, and further mutations on it will seem to be targeted just because suddenly there are more of them.
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    Quote Originally Posted by Glenn Jacobs View Post
    Even tho mutations are random, they might be thought to be targeted at particular areas because of their effects.

    PLAN A: A given mutation is fatal.

    PLAN B: A given mutation is somewhat disadvantageous to an organism -- which in the long run is the same thing.

    PLAN C: A given mutation neither hurts nor favors an organism.

    PLAN D: A given organism is somehow marginally favorable to an organism -- which means Darwin wins this round.

    The organism which receives the favorable mutation will multiply more successfully, and further mutations on it will seem to be targeted just because suddenly there are more of them.
    ".... more of them.." More of what? Mutations or organisms with the mutation?
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    Oops. Sorry.

    The subject was if mutations were "targeted" at certain genes.

    Because a successful mutation will allow its possessor to multiply more, a subsequent mutation will be more likely to affect it than the runner-up -- because there are more "chickens with lips" or whatever.
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