Genetic Code - Frozen Accident?

"TomHendricks474" <[email hidden]> wrote in message
"]news:[email hidden]...

Quoted message said:

Why is the genetic code universal (or virtually universal) The suggestion is that its a frozen
accident. I don't think so. I think this code is the best code for thermally stable chemistry in a
challenging heat cycle environment. Therefore there was only one solution - 1 code that best
adapted to the environment. It did this through the use of energy, replication, and other
adaptation strategies.

Comment?

Hi Tom,

I know next to nothing about the relative (and biologically/biospherically relevant) bond-strength
of different macro-molecules; and much less about any that would or could have existed in the
primordial soup along-side, and that would have been as coding-capable as, RNA/DNA.

However I hope, for your sake, that these 'alternative ancestral' macromolecules did or at least
could have existed; because otherwise there would not be much to hang your hypothesis on. Without
such an assortment of alternatives there would not have been anything for "heat type adversity type"
selection pressures to prune-in our DNA from.

So, as far as I am concerned, you could well be right about what happened in the macro-molecular
stage of (What Is going in respect of our Universe's) our evolution.

And, you might be right for partly the same reason that the anthropic principle (increasingly raised
as something rationally required to fill-in a logical-philosophical gap in fundamental physics)
might have to be enlisted (I don't doubt that it will) to make an approximately all-encompassing
final scientifc "statement" (not just a TOE but a FOOT, flatly put) about (amongst else) the
"Evolutionary Pressure Totality" (or Entire Patterning Tendency) of our Universe.

Now I have to turn my actention modules towards the special task of exposing the AEVASIVE aspect of
everybody - including my perfectly EPTly AEVASIVE self. ;->

Best wishes,

P

<< However I hope, for your sake, that these 'alternative ancestral' macromolecules did or at least
could have existed; because otherwise there would not be much to hang your hypothesis on. Without
such an assortment of alternatives there would not have been anything for "heat type adversity type"
selection pressures to prune-in our DNA from.

Quoted message said:

Quoted message said:

Oh I agree. There was a zoo full. I think complimentary bases were chosen over uncomplimentary
bases for their thermally stable bonding, etc. I think my scenario suggests a world wide
winnowing of alternates which makes it stand apart from most that suggest a single replication
that led to 2 etc. I suggest a planet selection, not a single fluke event. Yes there was a sea
full of variants for sure.

TomHendricks474 <[email hidden]> wrote or quoted:

Quoted message said:

Why is the genetic code universal (or virtually universal) The suggestion is that its a frozen
accident. I don't think so.

There are several explanations for features of the code.

In particular:

* It supports error correction;
* It looks like it could have arisen out of a 2-codon system;
* It has some robustness - in that some point mutations have no effect;
--
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On Wed, 21 Jan 2004 21:19:28 +0000 (UTC), [email hidden]

(TomHendricks474) said:

Why is the genetic code universal (or virtually universal) The suggestion is that its a frozen
accident. I don't think so. I think this code is the best code for thermally stable chemistry in a
challenging heat cycle environment. Therefore there was only one solution - 1 code that best
adapted to the environment. It did this through the use of energy, replication, and other
adaptation strategies.

Comment?

Francis Crick proposed the concept of the genetic code being a "frozen accident" in 1968 when it
appeared that all organisms use the same coding scheme. Crick thought variant codes should be
arising from whatever was the first coding scheme and normal darwinian selection mostly choosing
the "better" codes from these variants. But he felt we should be finding many of these variant
codes and he was really puzzled that they were not found. He understood that at some point when the
genome size got large (meaning many messages were coded for) that all codes would "freeze". He also
understood that a major bottleneck event after all variants were frozen might explain why there is
only one code. He thought these explanations implausible and that if variant codes ever existed we
should be seeing them. Since we don't see them, Crick felt no variants ever existed and natural
selection didn't operate on the genetic code. Crick didn't at all like the "frozen accident" idea
and later took up the idea of panspermia and directed panspermia. The gist of these ideas is that
life arose on another world where you would find many variant genetic codes and then one of these
organisms then "seeded" earth and hense we see only the one code contained in that seeding
organism. I do think that there were variant genetic coding schemes and natural selection did
winnow out the inferior variants. I don't see the problem Crick saw in explaining why all variants
except one have gone extinct. It is not clear to me if you think there were once variant coding
schemes to select from or not? In any case, for 20 amino acids, there are an enormous number of
possible encoding schemes that would all code for the same protein products. The selection process
would be to choose the "best" coding scheme from the variants. The "best" coding scheme should be
seen as the one that minimizes the error in the output messages (the proteins). There is inherent
error generated by the machinery of the ribosome and aminoacylation sites but it can be minimized
by proper choice of an encoding scheme. This is how different encoding schemes should be measured
to determine which is "best". The standard (universal) genetic code is a very very good coding
scheme by all measurements. For many people the problem is explaining why is it so good. But you
shouldn't think this is the "best" possible code. It appears to me to have "design" flaws and
cannot be the "best" possible coding scheme. To put it bluntly, protein products have an
unnecessarily high level error because they are being built using an "inferior" encoding scheme.
Just a point of reference, translation error rates are estimated to be 1 incorrect amino acid in
every 20 proteins. William L Hunt

Tim Tyler <[email hidden]> wrote in message news:<[email hidden]>...

Quoted message said:

TomHendricks474 <[email hidden]> wrote or quoted:

Quoted message said:

Why is the genetic code universal (or virtually universal) The suggestion is that its a frozen
accident. I don't think so.

There are several explanations for features of the code.

In particular:

* It supports error correction;
* It looks like it could have arisen out of a 2-codon system;
* It has some robustness - in that some point mutations have no effect;

There is another "pattern" in the code which makes sense on the assumption that in the RNA world,
amino acids were synthesized in place on tRNAs. That is, assume that four or five different
precursor carboxylic acids could be attached to the terminal 3' ribose of a tRNA - PEP, OA, 2KG,
PYR, and perhaps Gly. Ribozymes existed to convert these precursors to the twenty standard amino
acids - without disconnecting the precursor or any intermediate from the tRNA. Assume that OA and
2KG are double-attached - that is, assume that the other carboxylic acid group is also activated by
attachment to some RNA species. Now, list the amino acids that are plausibly derived from each of
the precursors - Phe, Tyr, Ser, Cys, and Trp from PEP. Pro, Gln, Arg, and possibly His from
activated 2KG. Lys, Asn, Met, Ile, and Thr from activated OA. Ala and Val from Pyr. Ser from Gly.
Notice the pattern? This pattern was noted by Nirenberg when the code was first discovered. Wong has
written many papers on it. It seems inconceivable to me that it can be a coincidence.

<< There are several explanations for features of the code.

In particular:

* It supports error correction;
* It looks like it could have arisen out of a 2-codon system;

TH This one needs some support. I have not seen any plausible case for a 2 codon system - unless you
mean that of the 3 the middle, later the middle and first were the key to coding.

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TomHendricks474 <[email hidden]> wrote - or quoted me as saying:

Quoted message said:

Quoted message said:

In particular:

* It supports error correction;
* It looks like it could have arisen out of a 2-codon system;

Quoted message said:

This one needs some support. I have not seen any plausible case for a 2 codon system - [...]

E.g. see:

``Speculations on the evolution of the genetic code.''

- calorierestriction.orgpmidOpen ↗

...and...

``This likely means that the 20 coded amino acids were the ones with secured places in a primitive
code that became frozen it time in the past. An alternate view is that a universal genetic code
arose from a simpler code comprised of 16 codons and 10 amino acids or possibly a four amino acids
system (Ikehara 2002).''

- bayes.colorado.edurewiring.pdfOpen ↗

``The very genetic code suggests an earlier two codon system.
The degeneracy of major amino acids implies as much.'' ;-)
--
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[email hidden] (TomHendricks474) wrote in message news:<[email hidden]>...

Quoted message said:

<< There is another "pattern" in the code which makes sense on the assumption that in the RNA
world, amino acids were synthesized in place on tRNAs. That is, assume that four or five different
precursor carboxylic acids could be attached to the terminal 3' ribose of a tRNA - PEP, OA, 2KG,
PYR, and perhaps Gly. Ribozymes existed to convert these precursors to the twenty standard amino
acids - without disconnecting the precursor or any intermediate from the tRNA. Assume that OA and
2KG are double-attached - that is, assume that the other carboxylic acid group is also activated
by attachment to some RNA species. Now, list the amino acids that are plausibly derived from each
of the precursors - Phe, Tyr, Ser, Cys, and Trp from PEP. Pro, Gln, Arg, and possibly His from
activated 2KG. Lys, Asn, Met, Ile, and Thr from activated OA. Ala and Val from Pyr. Ser from Gly.
Notice the pattern? This pattern was noted by Nirenberg when the code was first discovered. Wong
has written many papers on it. It seems inconceivable to me that it can be a coincidence. >>

Would you go through this a little slower. I'm a bit lost as to its meaning.

Basically, I'm saying that there is a correlation between the first base of the codon and the
pathway for biosynthesis of the amino acid. This is independent of the better known correlation
between the second base and the chemical properties of the amino acid's R group.

The correlation of the code with a biosynthetic pathway makes absolutely no sense if you assume that
the pathway developed after the code. But, if you assume that RNA world organisms made amino acids
themselves, rather than somehow finding and recognizing them in the soup, then it suggests something
interesting about the nature of metabolism in the RNA world.

Quoted message said:

Also it all seems like we're starting out at step one, but step ones highly evolved chemistry.
What came before step one? What is the en Zvironment like during this phase?

I am talking about a clue to the origin of the genetic code in the RNA world. I have no idea what
the phrase "highly evolved chemistry" might mean, but the RNA world (or at least the later stages of
it when the code arose) certainly involved fairly evolved biology and biochemistry - probably tens
of millions of years of evolution since the origin of life.

Tom, EVERYONE EXCEPT YOU believes that the origin of the code and the origin of life are completely
different problems, taking place in completely different eras and completely different environments.
Please, when other people are talking about the code, don't complain that they are not
simultaneously talking about the origin of life.

<< It is not clear to me if you think there were once variant coding schemes to select from or not?

TH I do, but we differ as to what the selection pressure was. I think you suggest it was to get to a
better code. I think the code was there to get to a more thermally stable molecule. Then , later,
once there are 2 coding systems that both have similar thermal stability - then, but only then, is
there selection on the other aspects of the code. For me, no matter what the code did, it still must
survive that day's heat cycle. And the only molecules that wil survive are those most stable.
Inherent in all this is the idea that the earth was very hot and its temp range was such that it
completely denatured and annealed h-bonded variants on a cyclic basis. If any of that is wrong, my
scenario is wrong.

In any case, for 20 amino acids, there are an enormous number of possible encoding schemes that
would all code for the same protein products. The selection process would be to choose the "best"
coding scheme from the variants. The "best" coding scheme should be seen as the one that minimizes
the error in the output messages (the proteins).

TH For me this 'best' comes much later as competing codes have selection presure - but all have
similar thermal stability - or more likely the earth has simply cooled and thermal stability is no
longer such a factor as it was at the origin.

There is inherent error generated by the machinery of the ribosome and aminoacylation sites but it
can be minimized by proper choice of an encoding scheme. This is how different encoding schemes
should be measured to determine which is "best". The standard (universal) genetic code is a very
very good coding scheme by all measurements. For many people the problem is explaining why is it so
good. But you shouldn't think this is the "best" possible code. It appears to me to have "design"
flaws and cannot be the "best" possible coding scheme. To put it bluntly, protein products have an
unnecessarily high level error because they are being built using an "inferior" encoding scheme.
Just a point of reference, translation error rates are estimated to be 1 incorrect amino acid in
every 20 proteins. William L Hunt

[email hidden] (TomHendricks474) wrote in message news:<[email hidden]>...

Quoted message said:

<< Basically, I'm saying that there is a correlation between the first base of the codon and the
pathway for biosynthesis of the amino acid. This is independent of the better known correlation
between the second base and the chemical properties of the amino acid's R group. >>

Now this (upon rereading) I find very interesting.

What can you tell me about the 2nd base and chemical properties of the aa's R group's
carboxyl group?

What the hell do you mean by "chemical properties of the aa's R group's carboxyl group"? Don't you
reread what you have written before hitting Post?

My theory says almost nothing about the second base. "Almost nothing" means that it DOES suggest
that Asn and Gln will agree on 2nd base, and that Val and Ile agree. But nothing else.

Quoted message said:

Such as in glutamic acid, and aspartic acid.

It turns out that Glu and Asp are the two amino acids which this theory says the least about! In a
sense, the theory suggests that these two were latecomers to the code (though not latecomers to
metabolism). What the theory does suggest is that amino acids derived from Glu all have the same 1st
base, and that amino acids derived from Asp also share a 1st base.

Quoted message said:

This would fit in with my scenario perhaps. I suggest that these acids may have been very early on
and helped start the symbiosis between rna and aa's.

Please do not use the word symbiosis incorrectly. PLEASE.

[email hidden] (TomHendricks474) wrote in message news:<[email hidden]>...

Quoted message said:

What does PEP, OA, 2KG, PYR stand for?

PEP = Phospho-enol-pyruvate OA = Oxaloacetate 2KG = 2-ketoglutarate PYR = Pyruvate.

[email hidden] (TomHendricks474) wrote in message news:<[email hidden]>...

Quoted message said:

TH There is some confusion here. I think the origin of 'life' is chemicals ability to survive high
heat. And in that sense , long before any RNA world there were certain chemical reactions that
were chemically selected. The coding was one of many strategies of THERMAL SURVIVAL (if we are to
capitalize key comments to each other) Perhaps you are right to note that I standout in that
opinion. But no other scenario makes sense to me. I encourage you to present any that does. I have
yet to find one.

Tom, if I come across another scenario that makes sense to you, I'll be sure to let you know.

[email hidden] (TomHendricks474) wrote in message news:<[email hidden]>...

Quoted message said:

I notice you skipped over the tough questions I asked you. How about some replies to those?

Questions, in sbe, seem to fit into one of three categories:
1. Requests for technical information.
2. Requests for clarification.
3. Challenges.

I try to answer all questions in categories 1 and 2. Sometimes I ignore challenges.

As I look back in this thread, I think that I have responded to every group of words terminated by a
question mark, except one. It was:

Quoted message said:

TH But why would RNA need protein? Or as Moore put it, "Why would a device for making polypeptides
evolve in an organism that had no use for protein?"

That is indeed a challenge. In a sense, it is THE challenge faced by any theory of an RNA world
without polypeptides. I don't have an answer. But I will note that variants of this challenge are
common in evolutionary theory. An attempt to sketch a portion of a general answer to this challenge
may be found in Gould and Lewontin "The Spandrels of San Marco".

TomHendricks474 said:

Why is the genetic code universal (or virtually universal) The suggestion is that its a frozen
accident. I don't think so. I think this code is the best code for thermally stable chemistry in a
challenging heat cycle environment. Therefore there was only one solution - 1 code that best
adapted to the environment. It did this through the use of energy, replication, and other
adaptation strategies.

Comment?

Wow, lots of ideas... I don't think I can remember all the points made in this thread, although I
didn't think too much of some of the problems people put forward.

Anyway, what do I know.

One interesting theory of the origin of coding and language in general is 'semio-genesis' the
cultrual formation of 'meaning'. This theory was developed by a Japanese group (sorry I forget
names) working on genetic code.

It postulates a 'community' of ribo-organisms, with basic functions - which form some kind of
hypercycle, and in the process of chance associations between them and amino acids form a protein
which catalyses ribonucleotide linkage.

It is a nice idea, and it adresses the central philosophical problem of 'where did meaning
come from?'.

I have actually been subjected to this as a 'proof' of god - god provides language, whithout which
everything is meaningless.

I dont buy this argument, as systems of meaning can evolve.

This reminds me of my own prejudice on the subject (lacking a foundation in the details of
the GC)...

Assumption I make: 'meaning' comes from networks of associations. I think networks make up the
'context' without which there is no such thing as meaning.

Evolution of networks of interactions (physical or associative) slows down the possible pace of
evolution (acording to Kaufmann), - Things do get 'locked in', but not without evolution first.
Major refinements can come, but at higher levels of evolution.

An anser to Crick dilema (which doesn't invoke spacelife) is the lipid theory of the origin of life
- If lipids ruled the early earth, genetic systems (viruses) would spread like wild fire...

not sure if this is theoretically sound, but this brings me to my second problem,

science acording to popper must make testable predictions (not just explain the extant data better
and better), something which many early-lifers struggle with (IMHO).

Any comments Tom? Although your theory of heat survival sounds nice - It sounds a bit too much like
a fary tale to me ... (sorry for being confruntational... I am sure you can explain all your
predictions given sufficient space...)

I guess it would be good if people could post up some 'major event' timelines for the different
theories, Should be very informative.

Thanks for reading this far, Dan.