From: lip@s1.gov (Loren I. Petrich)
Subject: Was There Once an RNA World of Life?
Organization: LLNL
Date: Mon, 17 Aug 1992 13:23:42 GMT


	In a previous post, I described some research that suggests
what the youngest common ancestor of all currently existing life was
like:

	It was a thermoacidophile, inhabiting hot springs with high
concentrations of sulfuric acid, it was almost certainly autotrophic,
it was possibly photosynthetic, and it had full-fledged biosynthesis
and DNA -> RNA -> protein information transfer systems, including
ribosomes and transfer RNA's.

	This does not look like the result of spotaneous generation,
unless one allows for extreme improbabilities, so it is presumed that
there has been a lot of evolution behind it, evolution that may have
left some vestiges, in the fashion of the numerous vestigial features
generated by later evolution (I wonder if anyone has compiled a
reasonably comprehensive list).

	A system where there are two kinds of nucleic acids and where
nucleic acids and proteins function together is rather complex, and it
may be asked if there is any simpler kind of system.

	For the nucleic acids, the answer seems to be straightforward.
RNA was the original molecule, with DNA a specialization for long-term
information storage. This is from several reasons, one being that it
is RNA in transfer and ribosomal nucleic acids, when DNA could do just
as well (has the experment of making transfer and ribosomal DNA's ever
been tried?), and also the biosynthesis of DNA nucleotides, which is
generally from RNA nucleotides.

	We are left with two of our original three, any more to go?
Yes, as hinted by the recent discovery of self-splicing RNA. According
to the "RNA world" hypothesis, there were once organisms in which
there were no proteins, but which had RNA's doing all their functions,
such as serving as enzymes. Proteins were invented later, as a way of
making more efficient enzymes and other useful molecules.
Relationships among the transfer RNA's may well give clues as to how
translation evolved; there is some work that suggests that the tRNA's
fall into two big families, with the present-day precision a
refinement of the original imprecise translation.

	Of course, this leads to the question of where the original
RNA came from, but I will deal with that later.

	There is an interesting paper, ["Modern metabolism as a
palimpsest of the RNA world", Steven A. Benner, Andrew D. Ellington,
and Andreas Tauer, Proc. Natl. Acad. Sci. USA, vol. 86, pp. 7054,
September 1989] which suggests that the RNA organisms may have gotten
to be rather sophisticated before they learned how to make proteins.
The authors point out that RNA groups appear in several cofactors,
such as NAD (contains niacin) and Coenzyme A, that are ubiquitous; the
RNA is not directly connected to the functioning of these cofactors,
and is presumably a vestigial feature of the RNA world. Synthesis of
other molecules, such as the tetrapyrrole ring (a ring of rings that
appears in heme, chlorophyll, vitamin B12, and other important
molecules), terpenes, and even DNA, is traced back to the RNA world.
Fatty acids probably came after proteins were invented, as did the
cofactor biotin.

	As mentioned earlier, we are stuck with the question of where
the RNA come from. From prebiotic synthesis experiments, it is
possible to make amino acids, both biological and non-biological, in
quantity; it is much more difficult to make nucleotides, though it can
be done by rather contrived experiments. I have seen serious
speculation that RNA was a "takeover" from another self-replicating
molecule that was probably simpler.


	Now that we have gotten so close to the question of the origin
of life, we must consider what the early Earth was like and what could
have been synthesized. Organic synthesis experiments of the
Urey-Miller type work well in reducing (hydrogen-rich) environments;
they produce an abundance of various organic molecules. Doing such
experiments in neutral environments (with carbon dioxide and nitrogen)
generally does not go much past formaldehyde. Naturally, our current
atmosphere, which is oxidizing, is the worst kind of atmosphere for
such syntheses -- it tends to undo already existing syntheses.

	The early Earth's atmosphere was thought to be reducing
earlier in this century; it fitted well with the Urey-Miller picture
and it seemed to fit well with the expected geochemistry. But more
recent work suggests that the early Earth's atmosphere was neutral,
with an abundance of carbon dioxide and nitrogen. Organic synthesis
cannot proceed very far. But there is one kind of micro-environment
that can serve as a much better candidate for Darwin's warm little
pond. It is the hot spring, preferably underwater oceanic. It produces
a wide range of temperatures, it offers a variety of inorganic
chemical species to react with, and nearby soil can offer an abundance
of catalytic surface. As the water comes out, it will be out of
thermal equilibrium as it cools, allowing interesting chemical
reactions. Furthermore, it may be out of reduction equilibrium, being
more reducing than the bulk of the ocean. Here again, we have some
interesting disequilibria.

	It might be possible to test this hypothesis of
organic-chemical synthesis by looking for varieties that are not
metabolized by most organisms. These might include mirror images of
asymmetric biological molecules, for example.


	I am not sure if anyone else has noticed this, but there is an
interesting convergence between work on possible prebiotic
environments and work backwards to find what the common ancestor was
like. They both seem to agree that the original organism was a
thermoacidophile that lived in an oceanic hot spring.

	Any comments?