GunnerJ

What's the story with crystal abiogenesis? I've been reading about Vernor Vinge's technological singularity (which I may post about later) and he mentions in an article that someone named Cairns-Smith hypothesized that carbon-based life arose by piggybacking on simpler crystalline life forms. I can't seem to find much on the Net about it, but I'm not asking for links. I want to know what people think about this. Is it feasible?

Christopher Lord

Without seeing the proposed method, I would have to say it doesn't seem the best candidate. Crystals are far too uniform for simple replicators to ride on. Perhaps as molds for protiens?

I would hold that a quick-and-dirty protien that just happened to replicate (more or less) started the Great Loop.

lpetrich

I think that Cairns-Smith is partially correct. Clay does not have very dynamic chemistry; for the most part, it simply sits there. However, clay can provide convient meeting places for prebiotic molecules and catalytic ability to enable them to react with each other. In fact, some enzymes continue to have metal ions, which are a part of clay and most other rocky materials.

However, what is the first self-reproducing molecule is an unsolved problem. One way to solve that problem is to extrapolate backwards from existing biochemistry, but the most plausible candidate from that is RNA. And although the bases are not difficult to form with prebiotic chemistry, the ribose in it is much more difficult, requiring relatively unusual conditions.

This backwards extrapolation has produced the hypothesis of the "RNA world"; it is done with the help of classic evolutionary-biology reasoning: looking for vestigial features in present-day biochemistry. And such features are indeed found:

• Several coenzymes and cofactors use RNA nucleotides, despite often having functions completely unrelated to the usual nucleic-acid functions.
• Adenosine triphosphate (ATP) is an energy intermediate; the energy is in the phosphate-phosphate bonds and the adenosine part is a "handle"; why a RNA-nucleotide handle and not some other handle?
• RNA is used in both transient molecules (messenger RNA) and persistent ones (transfer RNA and ribosomal RNA); its relative DNA is only used for persistent molecules.
• The RNA in ribosomes (protein-assembly sites) is the really essential part; the protein in them is a helper part.
• RNA molecules can act as enzymes, making proteins unnecessary.

Here's a possible sequence:

• Some unknown pre-RNA system?
• Some sort of "RNA takeover", where RNA takes over the functions of the pre-RNA molecules?
• The "RNA world", where RNA is both information carrier and catalyst.
• RNA often gets modified for catalytic purposes, sometimes with extra molecules (cofactors) added on.
• A master-copy variant of RNA emerges: DNA
• A RNA-cofactor-assembly system emerges, producing many cofactors from amino acids.
• The amino-acid cofactors grow in importance and bulk, as a result of their superior efficiency, with the result that many of the original RNA enzymes are phased out.

The result is our present-day world of DNA -> RNA -> protein.

Gurdur

Cairns-Smith does in fact provide detailed hypotheses how clay layers could provide sem-dynamic frame-works for organic molecules.
Impurities in clay, and crytal differences between micro-layers, add up to a fair bit of smi-dynamism.

Quetzal

Cairns-Smith's hypothesis is interesting, although as Christopher Lord points out, the real problem with it is clay doesn't necessarily form a lattice/matrix that is perfectly designed for the arrangement of biologically significant molecules. Since there are a rather large number of potential arrangements, getting the precise arrrangement necessary to act as a catalyst for a specific molecule is pretty problematic.

I like to call his theory the "Magic Crystal Hypothesis". The fundamental problem he was trying to address is the requirement that the first "life" (using the term very loosely) had to have been self-replicating. Cairns-Smith speculated that the earliest replicators were not organic at all, but rather were self-replicating crystals that were later superseded by the rise of the far-more-efficient organic replicators. In this view, the first replicators were crystals of the type that exist in clay or mud along riverbanks; they transmitted their "genetic" information through the natural tendency of these types of molecules to fit together into a geometric pattern.

The fundamental characteristic of crystals as replicators must be hereditary variation, or inheritance. Fortunately, crystals in nature display this pattern: they may be perfectly aligned until a specific point is reached, in which a flaw has accumulated (these are quite common in natural crystals). This flaw has a tendency to percolate down the subsequent layers of crystal, setting up a rudimentary system of heredity. Furthermore, atoms of the crystal's substance may be more attracted to certain geometric patterns than they are to others. This sets up a kind of "differential reproduction" which then leads logically to a form of natural selection.

The hypothetical crystals described above may very well begin a basic process of cumulative selection. Certain crystals may have the property of altering streams or other water sources for their own "benefit", such as by increasing the likelihood of more of the same material being deposited in the same location. Crystals may also encourage the formation of "spores" by breaking easily into subsequent "generations" Those crystals that broke into generations most easily would be selected for; these generations would invariably contain mutations on occasion and would intensify the competition between rival variants.

In time, the crystals could evolve a sort of "phenotype" by altering other materials in their environment. These materials could be used to further the crystal's replication by inhibiting rival crystals from forming or promoting the parent crystal's reproduction. Cairns-Smith's hypothesis is that these materials used by the crystals for self-replication later turned out to be even more efficient replicators in their own right. This process of replacement might repeat for several cycles, or the first products used by the crystals may have been the ancestors of modern replicators - i.e., RNA and eventually DNA. Magic crystals, indeed.

This theory has been well-publicised by Dawkins in <a href="http://www.world-of-dawkins.com/Dawkins/Work/Books/blind.htm" target="_blank"> The Blind Watchmaker </a>. AG Cairns-Smith’s theory can be read in his book, <a href="http://www.chem.gla.ac.uk/~bobh/agcs1.gif" target="_blank"> Seven Clues to the Origin of Life,</a> a very readable expose.

As lpetrich mentioned, it really appears that Cairns-Smith's idea is better understood as only partial. John Corliss in "Dynamics of Creation" states that Cairns-Smith's magic crystals could have assisted, but were not required, for his theory (using the geothermal and chemical energy in submarine hot springs as the life engine). IOW, the crystal lattice could have helped a more dynamic process. You can read a very good synopsis of Corliss on <a href="http://www.syslab.ceu.hu/corliss/Nature.html" target="_blank">this site.</a> Corliss ALSO has a problem, in that he sort of throws in a "miraculous membrane" about half-way through the process. Adding Russell's iron sulfide "biomorphic" boundary solves that problem.

OOL is complicated by the fact that researchers have, in the main, focused on one hypothesis sort of in limbo. I think the final result will be a synthesis of several different theories.

lpetrich

Morpho's description of "magic crystals" is interesting. And it suggests something that can be tested with observations and laboratory experiments, though there is the problem that the Earth's atmosphere has changed enough to make a difference in the clay chemistry.

I've also tracked down some RNA-world sites, and I've found that some RNA-like molecules have been studied as possible RNA precursors. These include pyranosyl RNA and Peptide Nucleic Acids (PNA); PNA especially avoids the ribose problem by using some building blocks more easily formed in prebiotic conditions.

I personally think that demonstrations of the catalytic abilities of certain RNA molecules ("ribozymes") does not demonstrate a RNA world -- such demonstrations only indicate that a RNA world is possible.

But it is significant that it's been much easier to get nucleic acids to be catalysts than to get proteins to replicate themselves; only some unusual proteins may be able to do that, while it's a no-brainer for nucleic acids, as Watson and Crick had discovered when they worked out DNA's "Double Helix" structure.

And what I consider "real" evidence is the stray RNA that appears in various places; such stray RNA is reasonably interpreted as vestigial RNA from long-gone ribozymes. It is significant that there is no corresponding stray DNA known to exist in such places. I've mentioned ribosomal and transfer RNA and ATP; here are some RNA-containing coenzymes:

• NAD (niacin adenine dinucleotide) (vitamin B3)
• FAD (flavin adenine dinucleotide) (vitamin B2)
• Coenzyme A (pantothenate; vitamin B5)
• Cyanocobalamin (vitamin B12)

all from <a href="http://www.math.auckland.ac.nz/~king/Preprints/Elechem.htm" target="_blank">http://www.math.auckland.ac.nz/~king/Preprints/Elechem.htm</a>

Although an adenosine is an add-on for all of these, in NAD, the niacin takes the place of a RNA base! (top left molecule in that URL's first image)

I close by noting that there may be other such early-biochemistry vestigial features, but recognizing them may be difficult without a better understanding of early-life biochemistry.

Quetzal

lpetrich: You might find <a href="http://www.science.siu.edu/microbiology/micr425/425Notes/14-OriginLife.html" target="_blank"> this site</a> interesting (hold on to your chemistry!). Although the author is apparently a protein-worlder, he discusses a great deal of the possible chemistry behind the formation and polymerization of early biomolecules. IMO, many of the same reactions could lead to an RNA world. Note especially the description of the creation of adenine from HCN, and the subsequent polymerization to polypeptides and rybose.

CodeMason

Morpho: Thanks for the exceptional link!

GunnerJ

Thanks for the great replies, guys. Some of it was a little over my head, not being well-versed in chemistry, but all was interesting.

BTW, something strange happened after I posted this: I thought, for some reason, that the CS hypothesis had something to do with clays, although I had no idea why, as I knew nothing about this theory before. And then LP started off his post about the properties of clay... very weird.

Anyway, I'm going to look into all these links, as my knowledge of the current trends in abiogenesis is severely limited. Thanks once again.

Coragyps

Ipetrich- I seriously doubt that clays have changed much since the good old atmosphere of the late Hadean, with the possible exception of those rare ones that contain ferric iron. The only place that I, with only a petroleum-related knowledge of clays, am aware of ferric-containing clays is in surface soils. They certainly wouldn't be present in "black smokers" and in early reducing atmospheres. IOW, nearly any "modern" clay should be a candidate for primordial catalytic clays, and there are about a blue zillion different ones known, each with its own scaffolding potentially capable of providing sites for different reactions.
This whole area sounds like a good playground for a chemist, like me, who never took enough biology in school. To the library!