Darwin's Dangerous Idea (29 page)

"messenger" system during "expression"). If we follow standard practice and 2. For just this reason, Richard Dawkins also presents a discussion and elaboration of reserve the term
virus
for a parasitic macromolecule, we need a name for Cairns-Smith's ideas in
TheBlind Watchmaker
(1986a, pp. 148-58). Since Cairns-Smith's 1985 account and Dawkins' elaboration are such good reading for nonexperts, I will refer these earliest ancestors. Computer programmers call a cobbled-together you to them for the delicious details, and provide just enough summary here to whet fragment of coded instructions that performs a particular task a "macro," so I your appetite, adding the warning that there are problems with Cairns-Smith's hypothe-propose to call these pioneers
macros,
to stress that although they are "just"

ses, and balancing the warning with the reassurance that even if his hypotheses are all huge macromolecules, they are also bits of
program
or ultimately rejected—an open question—there are other, less readily understandable, alternatives to take seriously next.

158 PRIMING DARWIN'S PUMP

Molecular Evolution
159

replicator that could somehow serve as a temporary scaffolding to hold the One of the leading researchers on this period of evolutionary history is protein parts or nucleotide bases in place until the whole protein or macro Manfred Eigen. In his elegant little book,
Steps Towards Life
(1992)—a good could get assembled. Wondrous to say, there is a candidate with just the right place to continue your exploration of these ideas—he shows how the macros properties, and more wondrous still,
it
is just what the Bible ordered: clay!

gradually built up what he calls the "molecular tool-kit" that living cells use Cairns-Smith shows that in addition to the carbon-based self-replicating to re-create themselves, while also building around themselves the sorts of crystals of DNA and RNA, there are also much simpler (he calls them "low-structures that became, in due course, the protective membranes of the first tech") silicon-based self-replicating crystals, and these silicates, as they are prokaryotic cells. This long period of precellular evolution has left no fossil called, could themselves be the product of an evolutionary process. They traces, but it has left plenty of clues of its history in the "texts" that have been form the ultra-fine particles of clay, of the sort that builds up just outside the transmitted to us through its descendants, including, of course, the viruses strong currents and turbulent eddies in streams, and the individual crystals that swarm around us today. By studying the actual surviving texts, the differ subtly at the level of molecular structure in ways that they pass on specific sequences of A, C, G, and T in the DNA of higher organisms and the when they "seed" the processes of crystallization that achieve their self-A, C, G, and U of their RNA counterparts, researchers can deduce a great replication.

deal about the actual identity of the earliest self-replicating texts, using Cairns-Smith develops intricate arguments to show how fragments of refined versions of the same techniques the philologists used to reconstruct protein and RNA, which would be naturally attracted to the surfaces of these the words that Plato actually wrote. Some sequences in our own DNA are crystals like so many fleas, could eventually come to be used by the silicate truly ancient, even traceable (via translation back into the earlier RNA crystals as "tools" in furthering their own replication processes. According to language) to sequences that were composed in the earliest days of macro this hypothesis (which, like all really fertile ideas, has many neighboring evolution!

variations, any one of which might prove to be the eventual winner), the Let's go back to the time when the nucleotide bases (A, C, G, T, and U) building blocks of life began their careers as quasi-parasites of sorts, clinging were occasionally present here and there in varying amounts, possibly con-to replicating clay particles and growing in complexity in the furtherance of gregated around some of Cairns-Smith's clay crystals. The twenty different the "needs" of the clay particles until they reached a point where they could amino acids, the building blocks for all proteins, also occur with some fend for themselves. No skyhook—just a ladder that could be thrown away, frequency under a wide range of nonbiotic conditions, so we can help as Wittgenstein once said in another context, once it had been climbed.

ourselves to them as well. Moreover, it has been shown by Sidney Fox (Fox But this cannot be close to the whole story, even if it is all true. Suppose and Dose 1972) that individual amino acids can condense into "protein-oids,"

that short self-replicating strings of RNA got created by this low-tech pro-protein-like substances that have a very modest catalytic ability ( Eigen 1992, cess. Cairns-Smith calls these entirely self-involved replicators "naked p. 32). This is a small but important step up, since catalytic ability— the genes," because they aren't
for
anything except their own replication, which capacity to facilitate a chemical reaction—is the fundamental talent of any they do without outside help. We are still left with a major problem: How did protein.

these naked genes ever come to be clothed? How did these solipsistic self-Now suppose some of the bases come to pair up, C with G, and A with U, reproducers ever come to
specify
particular proteins, the tiny enzyme-and make smallish complementary sequences of RNA—less than a hundred machines that build the huge bodies that carry today's genes from generation pairs long—that can replicate, crudely, without enzymatic helpers. In terms to generation? But the problem is worse than that, for these proteins don't just of the Library of Babel, we would now have a printing press and a book-build bodies; they are needed to assist in the very process of self-replication bindery, but the books would be too short to be good for anything except once a string of RNA or DNA gets long. Although short strings of RNA can making more of themselves, with lots of misprints. And they would not be replicate themselves without enzyme assistants, longer strings need a retinue
about
anything. We may seem to be right back where we started—or even of helpers, and specifying
them
requires a very long sequence—longer than worse. When we bottom out at the level of molecular building blocks, we could be replicated with high-enough fidelity until those very enzymes were face a design problem that is more like construction out of Tinker Toy than already present. We seem to face paradox once again, in a vicious circle gradual sculpting in modeling clay. Under the rigid rules of physics, either succinctly described by John Maynard Smith: "One cannot have accurate the atoms jump together into stable patterns or they don't.

replication without a length of RNA of, say, 2000 base pairs, and one cannot Fortunately for us—indeed, fortunately for all living things—scattered in have that much RNA without accurate replication" (Maynard Smith 1979, p.

the Vast space of possible proteins there happen to be protein constructions 445).

that—if found—permit life to go forward. How might they get found? Somehow we have to get those proteins together with the protein-hunters, the 160 PRIMING DARWIN'S PUMP

Molecular Evolution
161

fragments of self-replicating nucleotide strings that will
eventually
come to enough to build plenty of bias into the probability space from the outset.

"specify" them in the macros they compose. Eigen shows how the vicious So some of the possible macros, inevitably, are more probable—more circle can turn friendly if it is expanded into a "hypercycle" with more than likely to be stumbled upon in the Vast space of possibilities—than others.

two elements (Eigen and Schuster 1977). This is a difficult technical concept, Which ones? The "fitter" ones? Not in any nontrivial sense, but just in the but the underlying idea is clear enough: imagine a circumstance in which tautological sense of being identical to (or nearly identical to) previous fragments of type A can enhance the prospects of hunks of B, which in turn

"winners," who in turn tended to be almost identical to still earlier "winners."

promote the well-being of bits of C, which, completing the loop, permit the (In the million-dimension Library of Mendel, sequences that differ at a single replication of more fragments of A, and so forth, in a mutually reinforcing locus are shelved "next to" each other in some dimension; the distance of any community of elements, until the point is reached where the whole process one volume from another is technically known as the Hamming distance.

can take off, creating environments that normally serve to replicate longer This process spreads "winners" out gradually—taking leaps of small and longer strings of genetic material. (Maynard Smith 1979 is a great help in Hamming distances—from any initial starting point in any and all directions understanding the idea of a hypercycle; see also Eigen 1983.) in the Library.) This is the most rudimentary possible case of "the rich get But even if this is possible in principle, how could it get started? If all richer," and since the success of the string has an explanation with no possible proteins and all possible nucleotide "texts" were truly equiproba-ble, reference beyond the string itself and its resemblance as a string to its parent then it would be hard to see how the process could ever get going. Somehow, string, this is a purely
syntactic
definition of fitness, as opposed to a
semantic
the bland, mixed-up confetti of ingredients has to get some structure imposed definition of fitness (Kiippers 1990, p. 141). That is, you don't have to on it, concentrating a few "likely-to-succeed" candidates and thereby making consider what the string
means
in order to determine its fitness. We saw in them
still more
likely to succeed. Remember the coin-tossing tournament in chapter 6 that mere typographical change could never explain the Design that chapter 2? Somebody has to win, but the winner wins in virtue of no virtue, needs explaining, any more than you could explain the difference in quality but simply in virtue of historical accident. The winner is not bigger or between two books by comparing their relative frequencies of alphabetic stronger or better than the other contestants, but is still the winner. It now characters, but before we can have the meaningful self-replicating codes that seems that something similar happens in prebiotic molecular evolution, with make this possible, we have to have self-replicating codes that don't mean a a Darwinian twist: winners get to make extra copies of themselves for the thing; their only "function" is to replicate themselves. As Eigen (1992, p. 15) next round, so that, without any selection "for cause" (as they say when puts it, "The structural stability of the molecule has no bearing upon the dismissing potential jurors), dynasties of sheer replicative prowess begin to semantic information which it carries, and which is not expressed until the emerge. If we start with a purely random assortment of "contestants" drawn product of translation appears."

from the pool of self-replicating fragments, even if they are not initially This is the birth of the ultimate QWERTY phenomenon, but, like the distinguishable in terms of their replicative prowess, those that
happen
to win cultural case that gives it its name, it was not
entirely
without point even in the early rounds will occupy more of the slots in the subsequent rounds, from the outset. Perfect equiprobability could have dissolved into a mo-flooding the space with trails of highly similar (short) texts, but still leaving nopoly by a purely random process, as we have just seen, but perfect vast hypervolumes of the space utterly empty and inaccessible for good. The equiprobability is hard to come by in nature at any point, and at the very initial threads of proto-life can emerge before there is any difference in skill, beginnings of this process of
text
generation, a bias was present. Of the four becoming
the
actuality from which the Tree of Life can then grow, thanks to bases—A, C, G, and T—G and C are the most structurally stable: "Calcula-tournaments of skill. As Eigen's colleague Bernd-Olaf Küppers (1990, p.

tion of the necessary binding energies, along with experiments on binding 150) puts it, "The theory predicts
that
biological structures exist, but not
what
biological structures exist."3 This is

square. Throw the dice again; go to the square they name and check the color of the marble on this square and put a marble of that color on the just-vacated square ( "reproduction" of that marble). Repeat the process, over and over. Eventually, it has the effect 3. Kiippers (1990, pp. 137-46) borrows an example from Eigen (1976) to illustrate the of unrandomizing the initial distribution of colors, so that one color ends up "winning"

underlying idea: a game of "non-Darwinian selection" you can play on a checkerboard but for no reason at all—just historical luck. He calls this "non-Darwinian selection"

with differently colored marbles. Start by randomly placing the marbles on all the squares, because it is selection in the absence of a biasing cause;
selection without adaptation
creating the initial confetti effect. Now throw two (eight-sided!) dice to determine a would be the more familiar term. It is non-Darwinian only in the sense that Darwin didn't square (column 5, row 7, for instance) on which to act. Remove the marble on that see the importance of allowing for it, not in the sense that Darwin ( or Darwinism ) cannot accommodate it. Manifestly it can.

162 PRIMING DARWIN'S PUMP

The Laws of the Game of Life
163

and synthesis, show that sequences rich in G and C are best at self-replication ger, faster, more effective—but also more expensive—self-replicating sys-by template instruction without the help of enzymes" (Eigen 1992, p. 34).

tems. Our pointless coin-tossing tournament of luck has transformed itself This is, you might say, a natural or physical
spelling
bias. In English, "e" and into a tournament of skill. It has a point, for there is now something for the