Re: [asa] The Multiverse - Physics or Metaphysics?

Paul Mason wrote:

<< Is real science imagining some RNA world that doesn't exist and even if it could it would have to convert to DNA. So we need to deal with the complex DNA code, it's replication and protein synthesis need to all been i place for life to go on. There are not just 2 proteins but doesn't that need to be the right shape just to translate genes into proteins. Without that there is no replication, no life to select.? >>

I actually work with RNA so I think I have put my share of time
on this matter -- though most of my work is in prediction of? RNA
structure.?

The hypothesis is that the RNA was the first
form of "life", and the continued basis for it is the discovery of
various types of ribozymes (a derived word from "enzyme").
The concept is that RNA originally did all the function of
proteins and DNA. Because DNA is more stable than RNA, eventually
DNA replaced RNA for storage of replication.? Likewise, RNA is
very inefficient compared to proteins (that is putting it charitable),
so proteins eventually replaced most RNA for enzymatic function.

The most profound remnant is ribosomal RNA which is contained
in every living organism (other than viruses -- if those are
considered "living").? Ribosomal RNA is coated with proteins, but the
proteins are the scaffolding in this case, not the functional part of the
structure.? The real player is the RNA itself.? But note that proteins are
needed to protect this enormous machine.

Other important remnants are the ribonucleoproteins which involve a
combination of RNA and proteins.? They are involved in the splicosome
which is used to process RNA.? Again, proteins may play a bigger functional
role, but the RNA is very important. The splicosome exists because the
messenger RNA that codes for proteins have RNA inserts known as "introns"
that must be removed before a mature segment of RNA is made.
So of the introns are functional, some of them even contain
coding sequences within themselves.? It is also present to construct
a proper messenger RNA that is transported to cytosol for processing
into a protein.

There are many examples of ribozymes, these are just a few
at the top of my head.

I don't have a firm position on the RNA world.? Frankly, I think
the function of RNA is very weak.? RNA has a comparatively short
"shelf life" -- it is somewhat unstable to metal ion cleavage.
I might still prefer coevolution of these various parts at
this point (if I must chose), though this introduces other difficult
issues of course.
?

At any rate, I think it is not so wise to speculate on what can or cannot happen.
If the RNA world is the true picture (which again I don't insist on), it may have
used an archaic mechanism to replicate that we don't know about now. In other
words, I don't think it is foolish or wrong to speculate that it came that way.? I
simply don't know.? It seems to be a very hard experiment, that I can conclude.?
It also may be difficult to prove even if it was a little less hard.?

Moreover, to some extent, I'm not even sure I agree with Koonin on the improbabilities,
though I can certainly agree with him more than I can agree with people who
seem to think that life is essentially "inevitable".??? It is very difficult to say how easy
or difficult it is for "life" to form.? It is not trivial, that I am sure, but I am still willing
to accept that? it could be far more probably than Koonin proposes.

<<RNA or any replicating molecule has to eventually get to DNA that has the information to make proteins that help it replicate itself and. The odds of getting just two genes that code for two proteins to work together seem to exceed what is possible with just 10 to the 115th rolls of the dice so to speak. To get two protein that fit together or work together - >>

It is not clear how the RNA world came together to recruit proteins and DNA.
Being skeptical of it is fine.? But realize it is also not the case that it is impossible.

<<a protein can be 100 to over 10,000 amino acids long - 2 proteins at 100 each -- there are over 10 to the 200th different ways to arrange those amino acids. Remember there are only 10 to the 115th events in all time - even if every one of them was a different configuration 10 to the 115th only tests a small number of them. It would be hard to get even one protein of 100 that was functional.

It's just like language - it's impossible to get even two lines of sensible text by chance - 100 letters or so exceed the 10 to the 115th = impossible.>>

Actually, with proteins, it is not like mutations are that
big of a deal.? Some are of course, and those you hear about.
But proteins typically have more than one functional group
that is similar, and their codon sequences are organized with
some contingency for putting similar residue types at the
same codon position.? I recall some proteins structures can
be constructed with only about 5 amino acids --- though they
lose a lot of their variation in flexibility that is also
very important.? A protein is a dynamic entity, not a fixed
block.? There is packing in the structure that is very important,
but polymorphism and variation in the human genome mean
that some proteins have more than one coding sequence that
is perfectly functional with no observable difference in selective
advantage. Others have a more gray reputation.

Protein and RNA/DNA interactions are largely context
dependent.? Cytochrome C is somewhat exceptional because
it is used for respiration.? However, even it is part of
a larger context dependent system because it much interact
with other proteins to achieve its function.?

What we have before us is the whole functioning complex.

Exactly how it came together remains a mystery.? If you
don't find the RNA world persuasive, perhaps that is
fine, but the fact is that we don't know exactly how
a lot of this stuff works (if we are honest), and
therefore arguing this or that (at this point in our
level of understanding) seems to me largely pointless
and maybe even possibly dangerous.

by Grace we proceed,
Wayne

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Received on Sun Sep 9 11:39:18 2007