JM
And then there is this passage:
> I think [the adapter] later split into two versions: tRNA,
> and mRNA - but that is much later and outside of
> this discussion.

A lapse from the clarity of the remainder of the post, but more
importantly, I don't see how it can remain outside the scope of
the discussion.  If your goal is to take a step toward explaining
the genetic code, you have to show that your proposal is actually
a step in the right direction.  How do we get from your time frame,
with amino acids weakly bonded to rna adapters, to a later time
frame, with amino acids covalently bonded to tRNA?  Without at least
a sketch of this transformation, your weakly bonded adapter seems to
me to be moving in the wrong direction.

TH
I'll ink in the first step as I see it.
IF everytime we have this adaptor molecule with
this situation - both sides with the same thermal
bonding strength - then every time that bond is broken on one end, it will also
be broken on the other.
Ex. if 70C breaks up one end - and the other end has
the same type and number of h-bonds - then it will denature at 70C.
Lets' say another set denatures at 60C.
Now we have two worlds. The world of 70c denature molecules - and the world of
60 C denatured molecules.
And everything that happens in the prebiotic chemsitry at 70 C will pedictably
happen when these 70C molocules are denatured or released.
So we have one chemistry at one temp and another at another temp.
This would help this scenario immensely if one of these sets was hydrophobic
the other hydrophilic.
For ex. let's say the 70C denaturing group was all molecules that supported
phobic reactions and 
the 50 C group philic.
See how temperature would set up two chemistries.

Now most of the time the two ends will NOT match.
but so what - nothing will come of the adverse molecules. Gradually the
prebiotic chemistry selection will favor those that are synchronized.

JM
You also don't explain why you want to start work on evolving the
genetic code on "day one".  Given that you have a bunch of RNA sitting
around, I would think that the highest priorities are to evolve 
RNA-directed nucleotide synthesis, RNA-directed energy metabolism, and
RNA-directed RNA replication.

TH
But RNA doesn't have a plan. It has no need for doing any of that. None of that
will help RNA last a day longer.
We can't force a future on these RNA molecules.
All we can do is say they are bumping together - why would that help them last
over those that didn't bump together. We can't suggest prebiotic chemistry
evolution to fit life - life has to fit what kept RNA from burning up on that
day.


JM (continued)
  RNA-directed protein synthesis can wait
for another day, IMO.  Those other things are sufficient to constitute
the origin of life, and hence the origin of natural selection.

But still, the enigma of the code remains - it cannot be explained by
vocalizing the magic words "natural selection" and waving your hands.

TH
There is no magic about it. That is why I favor it.
If you don't have a day to day reason why RNA should
continue to exist - it shouldn't.
We must agree that RNA was not put on earth to start up life! It was there
because it could continue to exist in that environment without being destroyed.
That is its sole purpose for being there then.

JM
Perhaps you feel that the enigma of the code is just as important to
explain as the enigma of the origin of life.  If so, I agree with you.

TH
I really don't see it as an enigma.
It is just what survived heat.
In every case that fits.
Name something that can live in sun type temperature.
We take it for granted that life must live in a very narrow temp range. That is
a major mistake.
Nothing should be taken for granted. No life can exist when it gets too hot.
All life chemistry is destroyed at just a little over 100C. How can that brick
wall, that unsurpassable boundary - not be considered in every aspect. It is
virtually the only thing that no life can not withstand.

JM (continued)
Perhaps you have the further intuition that the two enigmas must
somehow be related - that one explanation can cover both enigmas.  
If so, I respect your intuition, though I don't share it.

Your theory seems to be that there was an old RNA directed protein
synthesis technology that was based on adapters weakly bonded to
amino acids.  And that, later in evolution, this old technology was
replaced by a new technology based on ribosomes, tRNAs covalently
bonded to amino acids, and a collection of AARSs.
  [I hope that this is your theory, otherwise I am wasting time here
  attacking a straw man.]

TH
With this addition. - all of this is a REACTION to an
environment forcing these chemical changes. Nothing in the process of life at
anywhere near the origin - can in anyway select for something that opposses the
environment.
Nothing.
If it did - it would be destroyed by that environment.

 What chemistry is prebiotically selected is that which reacts to the
sun/environment without being destroyed.
And out of those variants - that which best survives is again chemistry that is
prebiotically selected.

So if you'll add that everything is driven by the heat cycle and the high heat
boundary that which no life chemistry can surmmount - then we're pretty close.

JM (continues)
I would claim that this theory only deepens the enigma.  How can this
new technology replace the old?

TH
Because if it did not - it was destroyed.
There was incredible pressure on this first 
prebiotic chemical system when the sun and earth
began to cool.


JM
  It would seem that all of the pieces
of the new technology would have to work before any of it would be
useful. 

TH
It was working in a way - the sun was forcing every
aspect of it. Only when the sun/earth cooling was there
any reason for evolving or changing.

JM
 Why would this new technology use RNA as the material for the
ribosome and for the tRNA?  Wouldn't it make sense to make the ribosome
from protein?  Wouldn't the tRNAs be better built from protein (except
perhaps for the anti-codon part)?

TH
Good points. I think my h-bond world or purine world
or the general outline of my idea above was first
Perhaps best term of all is 'sun world'
1. Sun world (sun forced prebiotic life
2. RNA world (replaces it as earth/sun cools
3. Rna to DNA, and 
   RNA to protein
further refinement - energy moderation with
modification through descent.

JM
Anyway, other than general comments regarding the plausibility of your
chemical assumptions (which you have heard before) that is my response
to your model.  I hope it was to the point.

[snip]
> TH
> Finally,
> Now where is your response to the
> fact that both RNA and DNA have such high Tm's
> if they did not have selection pressure to force
> that.
> No skipping the tough questions Jim.

I'm glad you re-asked that, because it brings up an important point.
Clearly, the Tm of modern DNA, tRNA and rRNA is an adaptation.  If 
the organism lives in an environment with a temperature even approaching 
the Tm, then the nucleic acid is at increased risk of hydrolysis.  See
the literature on C+G for thermophiles, for example.

TH
Exactly - but  Tm is adapting to what? You suggest
modern day temp highs? I think these archae 
and bacteria that can stand high temps - do so now
because they could do it during the origin of life.
It is that old.  They didn't adapt to it as much as
they were born in it IMO. 
I would suggest that as long back as we've had RNA or
DNA we've had those high temps. 

That suggest to me that the origin
was a temp cycle in a  time of very high - up to 100C. 
That also pushes back the time of the origin to perhaps
a hotter earth of 4. or 4.1 bya.
The greenland rocks seem to suggest thriving life at
3.8? So we almost have to have a very hot environment.

JM
Now here is the important point:  SINCE it can be explained as an 
adaptation to present or recent conditions,

TH
we disagree on that 

JM
 it is THEREFORE incorrect
to draw any inference about conditions at the time of the origin.  This
point is made most clearly by Steven Benner in numerous publications
back in the late 80s.  You (and everyone else) should take a look at 
this literature.  A good place to start is at the end of an exchange
of letters with Weiner and Maizels:
http://www.chem.ufl.edu/groups/benner/Publications/030.pdf
Work forward in time from there.

The most complete exposition is in the first few pages of:
Benner, S. A., Ellington, A. D. Interpreting the behavior of enzymes. 
Purpose or pedigree? CRC Crit. Rev. Biochem. 23, 369-426 (1988).






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