Cytosine

Discussion in 'Biology & Genetics' started by chinglu, Jun 12, 2014.

  1. chinglu Valued Senior Member

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    Can anyone provide a viable stable source of cytosine for RNA replication with prebiotic life?

    Thanks.
     
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  3. chinglu Valued Senior Member

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    Well cytosine is required to implement RNA replication. So, if there is no viable source of cytosine, then life could have never got off the ground on this planet.

    I would assume those in this thread would know this.
     
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  5. origin Heading towards oblivion Valued Senior Member

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    I don't think that there is a stable source of cytosine in isolation. I guess that proves that life does not exist on earth.
     
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  7. chinglu Valued Senior Member

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    I guess that proves the RNA pathway is not valid.
     
  8. wellwisher Banned Banned

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    The lack of a stable source of cytosine suggests that protein based pre-life came before RNA.

    from Wikipedia; (cytosine)

    Before the repair enzymes were available, back in the day, cytosine deamination into uracil, would have caused all the genes on the RNA, with cytosine, to become richer in uracil and lighter in cytosine over time. This makes it harder for any genes on the RNA to be permanent.

    Does anyone know the gene composition for the repair enzyme, uracil glycosylase, to see if these genes contains cytosine. If so, how does the cytosine in these genes remain stable to make repair enzymes, before there are repair enzymes?

    The conceptual problem with pre-repair enzyme RNA replicators, is that the deamination drift of cytosine to uracil could result in useful gene for one replication cycle. But the next time the RNA divides, continuing drift makes the same genes different, causing loss of what had been gained. What that would do is add more protein variety to the cytoplasm through a spontaneous deamination version of epi-genetics.
     
  9. chinglu Valued Senior Member

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    How nice. How do you get from here to there given the fact that the lack of cytosine refutes any RNA replication?
     
  10. wellwisher Banned Banned

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    The analysis I presented is more appropriate, further down the time-line of life, after pre-cells become viable, but before repair enzymes. The genes will spontaneously drift from being richer in cytosine to richer uracil, adding protein variety to the cytoplasm; deamination epi-genetics. Since the chemical reaction is consistent, the protein drift will have a reflected goal in mind; higher and higher uracil mRNA.

    Your original question is occurs much earlier in the time-line of life. This does create a problem for the replicator theory. This is not the only problem with the replicator theory. The replicator theory also causes entropy to get lower (nature of a template), whereas nature requires the entropy to increase. The deamination moves in the direction of higher entropy so this is expected as an offset. To fight this, the enzymes have to fight entropy. Starting with only replicators has a second law problem, with deamination reflecting the need for more entropy.

    This entropy problem, implicit of bare bone replicators, can be resolved if there is an entropy off-set. This could be done with protein scaffolding appearing first, that supports decomposition or crude metabolic reactions. This will add high levels of entropy to compensate. This consideration would suggest cytosine coming from protein, with the needed protein entropy off-set also leading to synthesis reactions for cytosine.
     
  11. chinglu Valued Senior Member

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    Interesting post. However, you suggest a protein scaffolding somehow generates cytosine.

    However, that would indicates this protein contains either cyanoacetaldehyde or cyanoacetylene.

    This paper indicates how these 2 can be used to generate cytosine.
    http://issuu.com/hosomichi/docs/chemistry_menor-salvan

    This paper demonstrates this construction in a prebiotic earth is extremely unlikely.
    http://www.pnas.org/content/96/8/4396.full

    But, I am curious how you are going to construct a protein containing cyanoacetaldehyde or cyanoacetylene.

    Can you explain that?
     
  12. wellwisher Banned Banned

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    My best guess is cytosine will appear from protein decomposition reactions, instead of protein template reactions. In the second (very large) figure, notice uracil has the atoms from two peptide links in the ring.

    I picture, protein driven decomposition of other protein, increasing the pre-cell entropy, by cleaving bonds. This is not being done in the most efficient way leading toward any goal but higher entropy. The atoms in the active peptide links recombine in new ways. If the cleaved fragments have radicals, they can combine in reverse peptide fashion, with side by side nitrogen. As long as the ring closes this will remain.

    The enthalpy of formation of cytosine is about 60 k.joules/mole so this is a favorable reaction.

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  13. origin Heading towards oblivion Valued Senior Member

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    Here is one avenue. Maybe there is life on earth after all!

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  14. chinglu Valued Senior Member

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    I am not following you. Your bottom diagram is the natural evolution of cytosine into uracil because cytosine is so unstable.

    I want to see your proposed protein as I said before and show that evolution into cytosine.
     
  15. chinglu Valued Senior Member

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    No. This paper cuts off the RNA pathway. I have no idea why you think it supports it. If you really think it supports the RNA pathway, prove it.
     
  16. origin Heading towards oblivion Valued Senior Member

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    Nah, I don't feel like it. Let's just assume there is no life on earth.
     
  17. Aqueous Id flat Earth skeptic Valued Senior Member

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    Aw, gee, some folks just won't feed the troll(s).

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  18. chinglu Valued Senior Member

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    Cool. Can you provide a viable stable source of cytosine for RNA replication with prebiotic life?
     
  19. Aqueous Id flat Earth skeptic Valued Senior Member

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    Define "stable". Then define "provide".
     
  20. chinglu Valued Senior Member

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  21. Walter L. Wagner Cosmic Truth Seeker Valued Senior Member

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    It seems a mystery, does it not?

    Pre-biotic means there wouldn't be complex biotic proteins to decay; so one needs to look for a formation method from simpler materials. A good graduate student problem to do a thesis on.
     
  22. Aqueous Id flat Earth skeptic Valued Senior Member

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    Ah so we don't get to ask you what your OP means without being insulted?

    This is a paper I've read before, and it doesn't answer what I asked you, so I'm not going to waste my time trying to sort out what the hell you expect posters to say to you.

    You didn't define "produce", so I'll refer you to the calderas of Yellowstone for all the cytosine needed to keep living cells healthy and prosperous at boiling temperatures. I guess you're the wise guy so you can figure out how to harvest it.

    Thermus aquaticus.

    You'll need to work with it indirectly anyway when you get to the step of proving life does not exist on Earth as claimed by mad scientists who are out to bring New World Order in to subjugate the religions. That kind of proof will at least leave you doing PCR analysis, hence the above microbe kills two birdbrains with one stone.

    In the mean time you can tell your creationist buddies who are quote mining science to try to shore up religious pseudoscience that no one has any idea of the abundance of prebiotic cytosine so it doesn't matter how fast it degenerates. If it only lasted one nanosecond and there were 100 yotta moles per nanosecond being manufactured near some thermal vent at one of the poles, where they are instantly chilled and preserved for a 100 million years each, who cares? Your point is to make some lame excuse for propping up superstition, isn't it? Just lace up and try to be candid for once in you propagandizing life. Tell it, but at least TRY to be honest. Or at least put the face on if you can't bear the indignity of being reminded how badly you fared in school. That will take a lot more than finally learning Tex and copying a bunch of meaningless formulas into another irrelevant diatribe against relativity. But you'll feel better when it's over. And readers will be elated.

    :spank:
     
    Last edited: Jun 20, 2014
  23. wellwisher Banned Banned

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    Animo acids can form relatively easy, like with the Miller experiment. There are also methods for polymerization into proteins like dehydration with clays. If you start with complex macro-molecules, before life, like protein and run enzymatic or other decomposition reactions, you can end up with a variety of fragments. The cyclic and resonance natures of nucleic acids are stable and self limiting (seal themselves off). We do not need a cell for pseudo-enzymes or for other methods to grind down prebiotic protein, into active fragments, that combine into stable resonance rings, based on free energy.
     

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