Hypotheses Evolve Too

Discussion in 'Health and medical' started by TomHendricks474, Feb 3, 2004.

  1. In my origin scenario I suggested that a single RNA strand folded upon itself with two ends loose.
    This was one of the first and earliest key developments in the origin.

    Now I think a more reasonable scenario for this early period, is short complimentary strands base
    paired together with 4 ends sticking out. This lets each end have a loose 3' end that is stacked but
    not base paired.

    Its on these two ends that I think other prebiotic material h-bonded to. And remember though h-bonds
    are slight there is no reason to think that these 'loose ends' are limited to h-bonding to just one
    aa, or one other rna. They could be quite long and have many h-bond partners. Enough so that for
    every 3 (allowing a protected middle spot) there could be h-bonding to either an aa or other rna.
    (Later this would lead to the tRNA system with aa at one end and mRNA at the other)

    This set the stage for the adaptor molecule to connect up the two worlds of aa's and rna's. The h-
    bonding is possible between aa and proto-tRNA yet is very weak. But because it is possible it
    probably happened, and would be hard to stop from happening.

    This building on the loose 3' ends of a paired proto RNA was thermally stable and helped all survive
    in a type of chemical symbiosis.

    Notes: Whether this means anything or not, I find it strange that in the anticodon loop, there is a
    2nd loop cleaved. It has this coding uuu - ACCA (as in the acceptor stem) -cuacg - aaa. Base 76 is
    not stacked. That leaves a 3 base stacked but unpaired row of 73 (discriminator base) 74, 75. I
    wonder if these 3 didn't once act as the codon does or vice versa. I think the anticodon loop was
    first a loose end that later evolved to a closed loop. The process of making a tRNA seems to suggest
    that possibility. Thus it looks like that on earliest times, we had an RNA molecule with two 3'
    loose ends.

    Note in both ends there is the 3rd base in least stacked or naked end territory. That would seem to
    suggest wobble in that position. Also note how important shape is for the 3rd wobble position. it
    seems that for every codon either pyrimidine can code and is interchangeable in 3rd and almost in
    every case, either purine can code in 3rd.

    Comment?

    Tom Hendricks

    The main points of my hypothesis are:
    1. How life began as a reaction to the sun/UV and the thermal cycle of hot-dry-sun/cold-wet-night.
    Then continued as an energy moderator with modification through descent.
    2. The Four Options and how they relate to thermodynamics, biological classification, the first
    cell, modification on all levels, psychological behavior of individuals and groups, inner
    conflicts and a therapy of resolving them, etc.
    3. Model showing relationship between adaptation fitness and natural selection. How it supports
    punctuated equilibrium and the 'slope and plateau' model etc.

    For a reader friendly summary see my arts/media website url for Musea issue#122
    http://musea.digitalchainsaw.com/122Musea1.html

    Tom Hendricks, Hendricks Health Theory text files at <A
    HREF="http://www.ediacara.org/~josh/hendricks.html">http://www.ediacara.or
    g/~josh/hendricks.html (text #10 has a not-too-out of date summary)

    Remember YOUR chemistry can't hide from MY sun.
     
    Tags:


  2. Dan Bolser

    Dan Bolser Guest

    On Tue, 3 Feb 2004 [email protected] wrote:

    >
    > In my origin scenario I suggested that a single RNA strand folded upon itself with two ends loose.
    > This was one of the first and earliest key developments in the origin.

    As far as I know (an I may be way off) but the *big* callenge to rna world is how the hell you get a
    rna multimer in the first place. You may hapily create all kinds of monomers in the whats-its-name
    aperatus, but hydrolysis of monomers to form peptid or whats-is bonds (between ribonucleotides?) is
    hard. As far as I know there is no satisfactory explaination of how strings of rna could have ever
    formed. I am quite sure that given strings of rna and some method of hydrolysis, you can dream up
    any synario you like - some more mathematically founded than others.

    > Now I think a more reasonable scenario for this early period, is short complimentary strands base
    > paired together with 4 ends sticking out. This lets each end have a loose 3' end that is stacked
    > but not base paired.
    >
    > Its on these two ends that I think other prebiotic material h-bonded to. And remember though h-
    > bonds are slight there is no reason to think that these 'loose ends' are limited to h-bonding to
    > just one aa, or one other rna. They could be quite long and have many h-bond partners. Enough so
    > that for every 3 (allowing a protected middle spot) there could be h-bonding to either an aa or
    > other rna. (Later this would lead to the tRNA system with aa at one end and mRNA at the other)

    Show me an atomic coordinate file of this structure, run it through some basic md tests, and I will
    tell you if the above is plausabe or not.

    > This set the stage for the adaptor molecule to connect up the two worlds of aa's and rna's. The
    > h-bonding is possible between aa and proto-tRNA yet is very weak. But because it is possible it
    > probably happened, and would be hard to stop from happening.

    I was going to post this link...

    http://www.origin-life.gr.jp/3103/3103161/3103161.html

    but I am not that cleaver...

    Hear is a nice short paper...

    http://www.jsbi.org/journal/GIW99/GIW99P64.pdf

    And extended version...

    http://www.jsbi.org/journal/GIW02/GIW02F008.pdf

    > This building on the loose 3' ends of a paired proto RNA was thermally stable and helped all
    > survive in a type of chemical symbiosis.
    >
    > Notes: Whether this means anything or not, I find it strange that in the anticodon loop, there is
    > a 2nd loop cleaved. It has this coding uuu - ACCA (as in the acceptor stem) -cuacg - aaa. Base 76
    > is not stacked. That leaves a 3 base stacked but unpaired row of 73 (discriminator base) 74, 75. I
    > wonder if these 3 didn't once act as the codon does or vice versa. I think the anticodon loop was
    > first a loose end that later evolved to a closed loop. The process of making a tRNA seems to
    > suggest that possibility. Thus it looks like that on earliest times, we had an RNA molecule with
    > two 3' loose ends.
    >
    > Note in both ends there is the 3rd base in least stacked or naked end territory. That would seem
    > to suggest wobble in that position. Also note how important shape is for the 3rd wobble position.
    > it seems that for every codon either pyrimidine can code and is interchangeable in 3rd and almost
    > in every case, either purine can code in 3rd.

    Yup, sounds right.

    >
    > Comment?
    >
    > Tom Hendricks
    >
    > The main points of my hypothesis are:
    > 1. How life began as a reaction to the sun/UV and the thermal cycle of hot-dry-sun/cold-wet-night.
    > Then continued as an energy moderator with modification through descent.
    > 2. The Four Options and how they relate to thermodynamics, biological classification, the first
    > cell, modification on all levels, psychological behavior of individuals and groups, inner
    > conflicts and a therapy of resolving them, etc.
    > 3. Model showing relationship between adaptation fitness and natural selection. How it supports
    > punctuated equilibrium and the 'slope and plateau' model etc.
    >
    > For a reader friendly summary see my arts/media website url for Musea issue#122
    > http://musea.digitalchainsaw.com/122Musea1.html
    >
    > Tom Hendricks, Hendricks Health Theory text files at <A
    > HREF="http://www.ediacara.org/~josh/hendricks.html">http://www.ediacara.or
    > g/~josh/hendricks.html (text #10 has a not-too-out of date summary)
    >
    > Remember YOUR chemistry can't hide from MY sun.
     
  3. << > In my origin scenario I suggested that a single RNA strand
    > folded upon itself with two ends loose. This was one of the first and earliest key developments in
    > the origin.

    As far as I know (an I may be way off) but the *big* callenge to rna world is how the hell you get a
    rna multimer in the first place. You may hapily create all kinds of monomers in the whats-its-name
    aperatus, but hydrolysis of monomers to form peptid or whats-is bonds (between ribonucleotides?) is
    hard. As far as I know there is no satisfactory explaination of how strings of rna could have ever
    formed. I am quite sure that given strings of rna and some method of hydrolysis, you can dream up
    any synario you like - some more mathematically founded than others.

    TH I think some type of hot/dry then cool/wet cycle is necessary for all the polymerization type
    steps in prebiotic chem whether its putting aa's together, or building nucleotides or cell
    membranes or etc.

    You are correct in saying that rna is scarce in prebiotic experiments. I tend to think that somehow
    the chem symbiosis between the more prevalent aa's latching on to the ends of short RNA stretches,
    helped support the building of nucleotides and set up the basics for life.

    Comment?
     
  4. Dan Bolser

    Dan Bolser Guest

    On Fri, 6 Feb 2004, TomHendricks474 wrote:

    > << > In my origin scenario I suggested that a single RNA strand
    > > folded upon itself with two ends loose. This was one of the first and earliest key developments
    > > in the origin.
    >
    > As far as I know (an I may be way off) but the *big* callenge to rna world is how the hell you get
    > a rna multimer in the first place. You may hapily create all kinds of monomers in the whats-its-
    > name aperatus, but hydrolysis of monomers to form peptid or whats-is bonds (between
    > ribonucleotides?) is hard. As far as I know there is no satisfactory explaination of how strings
    > of rna could have ever formed. I am quite sure that given strings of rna and some method of
    > hydrolysis, you can dream up any synario you like - some more mathematically founded than others.
    >
    > TH I think some type of hot/dry then cool/wet cycle is necessary for all the polymerization type
    > steps in prebiotic chem whether its putting aa's together, or building nucleotides or cell
    > membranes or etc.

    Possibly ;)

    >
    > You are correct in saying that rna is scarce in prebiotic experiments. I tend to think that
    > somehow the chem symbiosis between the more prevalent aa's latching on to the ends of short RNA
    > stretches, helped support the building of nucleotides and set up the basics for life.
    >
    > Comment?
    >
    >
     
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