Darwin's Dangerous Idea (36 page)

history of primate evolution!)

In Artificial Intelligence, a prized strategy is to work on deliberately The research of Eigen and hundreds of others has definite practical ap-simplified versions of the phenomena of interest. These are engagingly called plications for all of us. It is fitting to observe, then, that this important work

"toy problems." In the Tinker Toy world of molecular biology, we get to see is an instance of Darwinism triumphant, reductionism triumphant, mecha-the simplest versions of the fundamental Darwinian phenomena in action, but nism triumphant, materialism triumphant. It is also, however, the farthest these are
real
toy problems! We can take advantage of the
relative
simplicity thing from
greedy
reductionism. It is a breathtaking cascade of levels upon and purity of this lowest-level Darwinian theory to introduce and illustrate levels upon levels, with new principles of explanation, new phenomena some of the themes that we will trace through the higher levels of evolution appearing at each level, forever revealing that the fond hope of explaining in later chapters.

"everything" at some one lower level is misguided. Here is Eigen's own Evolutionists have always helped themselves to claims about fitness and summary of what his survey shows; you will note that it is written in terms optimality and the growth of complexity, for instance, and these claims have that should be congenial to the most ardent critic of reductionism: been recognized by claimant and critic alike to be serious oversimplifications at best. In the world of molecular evolution, no such apologies are required.

Selection is more like a particularly subtle demon that has operated on the When Eigen speaks of optimality, he has a crisp definition of what he means, different steps up to life, and operates today at the different levels of life, and experimental measurements to back him up and keep him honest. His with a set of highly original tricks. Above all, it is highly active, driven by fitness landscapes and measures of success are neither subjective nor
ad hoc.

an internal feedback mechanism that searches in a very discriminating Molecular complexity can be measured in several mutually supporting and manner for the best route to optimal performance, not because it possesses objective ways, and there is no poetic license at all in Eigen's use of the term an inherent drive towards any predestined goal, but simply by virtue of its

"algorithm." When we envision a proofreading enzyme, for instance, inherent non-linear mechanism, which gives the appearance of goal-chugging along a pair of DNA strands, checking and fixing and copying and directedness. [Eigen 1992, p. 123]

then moving one step along and repeating the process, we can hardly doubt that we are watching a microscopic automaton at work, and the best simulations match the observed facts so closely that we can be very sure there 3. FUNCTION AND SPECIFICATION

are no magical helper-elves, no skyhooks, lurking in these quarters. In the world of molecules, the application of Darwinian thinking is particularly pure Shape is destiny in the world of macromolecules. A one-dimensional se-and unadulterated. Indeed, when we adopt this vantage point, it can seem quence of amino acids (or of the nucleotide codons that code for them) something of a marvel that Darwinian theory, which works so beautifully on determines the identity of a protein, but the sequence only partially constrains molecules, applies at all to such ungainly—galactic-sized—conglomerations the way this one-dimensional protein string folds itself up. It typically springs of cells as birds and orchids and mammals. (We don't expect the periodic into just one of many possible shapes, an idiosyncratically shaped snarl that table to enlighten us about corporations or nations, so why would we expect its sequence type almost always prefers. This three-dimensional shape is the Darwinian evolutionary theory to work on such complexities as ecosystems source of its power, its capacity as a catalyst—as a builder of structures or a or mammalian lineages!?)

fighter of antigens or a regulator of development, for instance. It is a In macroscopic biology—the biology of everyday-sized organisms such as machine, and what it does is a very strict function of the shape of its parts. Its ants and elephants and redwood trees—everything is untidy. Mutation and overall three-dimensional shape is much more important, functionally, than selection can usually only be indirectly and imperfectly inferred, thanks to a the one-dimensional sequence that is responsible for it. The important protein mind-boggling array of circumstantial complications. In the molecular world, lysozyme, for instance, is a particular-shaped molecular machine that is mutation and selection events can be directly measured and manipulated, and produced in many different versions—more than a hundred different amino-the generation time for viruses is so short that huge Darwinian effects can be acid sequences have been found in nature that fold into the same functional studied. For instance, it is the horrifying capacity of toxic shape—and of course differences in these amino-196 BIOLOGY IS ENGINEERING

Function and Specification
197

acid sequences can be used as "philological" clues in re-creating the evo-terized most generally and abstracdy as information, and only the combi-lutionary history of the production and use of lysozyme.

nation of information from the code and the code-reading environment And here is a puzzle, first noted by Walter Elsasser (1958, 1966), but quite suffices to create an organism.3 As we noted in chapter 5, some critics have conclusively solved by Jacques Monod (1971). Considered very abstractly, fastened on this fact as if it were somehow the refutation of "gene centrism,"

the fact that a one-dimensional code can be "for" a three-dimensional the doctrine that the DNA is the sole information store for inheritance, but structure shows that information is added. Indeed,
value
is added. The that idea was always only a handy oversimplification. Though libraries are individual amino acids have value (by contributing to the functional prowess commonly allowed to be storehouses of information, of course it is really of a protein) not just in virtue of their location in the one-dimensional only
libraies-plus readers
that preserve and store the information. Since sequence that forms the string, but in virtue of their location in three-libraries have not—up till now, at any rate—contained among their volumes dimensional space once the string is folded up.

the information needed to create more readers, their capacity to store information (effectively) has been dependent on there being
another
Thus there is a seeming contradiction between the statement that the information-storage system—the human genetic system, of which DNA is the genome 'entirely defines' the function of a protein and the fact that this principle medium. When we apply the same reasoning to DNA itself, we see function is linked to a three-dimensional structure whose data content is that it, too, requires a continuing supply of "readers" that it does not itself
richer
than the direct contribution made to the structure by the genome.

entirely specify. Where does the rest of the information come from to specify

[Monod 1971, p. 94.]

these readers? The short answer is that it comes from the very continuities of the environment—the persistence in the environment of the necessary raw As Küppers (1990, p. 120) points out, Monod's solution is straightforward: (and partially constructed) materials, and the conditions in which they can be

"The seemingly irreducible, or excess, information is contained in the exploited. Every time you make sure that your dishrag gets properly dry in specific conditions of the protein's environment, and only together with these between uses, you break the chain of environmental continuity (e.g., lots of can the genetic information determine unambiguously the structure and thus moisture) that is part of the informational background presupposed by the the function of the protein molecule." Monod (1971, p. 94) puts it this way: DNA of the bacteria in the dishrag whose demise you seek.

We see here a special case of a very general principle: any
functioning

... of all the structures possible only one is actually realized. Initial con-structure carries
implicit
information about the environment in which its ditions hence enter among the items of information finally enclosed within function "works." The wings of a seagull magnificently embody principles of the ... structure. Without specifying it, they contribute to the realization aerodynamic design, and thereby also imply that the creature whose wings of a unique shape by eliminating all alternative structures, in this way these are is excellently adapted for flight in a medium having the specific proposing—or rather imposing—an unequivocal interpretation of a poten-density and viscosity of the atmosphere within a thousand meters or so of the tially equivocal message.2

surface of the Earth. Recall the example in chapter 5 of sending the score of Beethoven's Fifth Symphony to "Martians." Suppose we carefully preserved What does this mean? It means—not surprisingly—that the language of the body of a seagull and sent it off into space (without any accompanying DNA and the "readers" of that language have to evolve together; neither can explanation), to be discovered by these Martians. If they work on its own. When the deconstructionists say that the reader brings something to the text, they are saying something that applies just as surely to DNA as to poetry; the something that the reader brings can be charac-3. David Haig (personal communication) has drawn my attention to a fascinating new wrinkle in this unfolding story about folding proteins: molecular chaperones. "Chaperones are molecular cranes
par excellence.
They are proteins with which an amino acid 2. Philosophers will recognize, I trust, that Monod thus both posed and solved chain associates while it is folding that allows the chain to adopt a conformation that Putnam's (1975) problem of Twin Earth, at least in the context of the "toy problem" of would be unavailable in the absence of the chaperone. The chaperone is then discarded molecular evolution. Meaning "ain't in the head," as Putnam famously observed, and it by the folded protein. Chaperones are highly conserved.... Molecular chaperones were ain't (all) in the DNA either. Twin Earth, otherwise known as the problem of broad named by analogy to the functions of chaperones at a debutante ball: their role was to versus narrow content, will get exhumed briefly in chapter 14, so I can give it its proper encourage some interactions and to discourage others." For recent details, see Martin et Darwinian funeral.

al. 1993, Ellis and van der Vies 1991.

198 BIOLOGY IS ENGINEERING

Function and Specification
199

made the fundamental assumption that the wings were functional, and that selection competition; this was not, however, because symmetry is—
a priori
—an their function was flight (which might not be as obvious to them as we, who indispensable requirement for the fulfillment of a functional purpose." [Küppers have seen them do it, think), they could use this assumption to "read off' the 1990, p. 119, incorporating a quotation from Eigen and Winkler-Oswatitsch implicit information about an environment for which these wings would be 1975.]

well designed. Suppose they then asked themselves how all this aerodynamic theory came to be implicit in the structure, or, in other words: How did all But what about the asymmetric or chiral shapes? Is there a reason why this information get into these wings? The answer
must
be: By an interaction they should be one way—left-handed, say—rather than the other? No, prob-between the environment and the seagull's ancestors. ( Dawkins 1983a ably not, but: "Even if there is no
a priori
physical explanation for the explores these issues in more detail.)

decision, even if it was just a brief fluctuation that gave one or the other The same principle applies at the most basic level, where the function is equivalent possibility a momentary advantage, the self-reinforcing character specification itself,
the function on which all other functions depend.
When of selection would turn the random decision into a major and permanent we wonder, with Monod, how the three-dimensional shape of the proteins breach of symmetry. The cause would be a purely 'historical' one" (Eigen gets fixed, given that the information in the genome must underspecify them, 1992, p. 35 ).5

we see that only a pruning of the nonfunctional (or less functional) could The shared chirality of organic molecules (in our part of the universe ) was explain it. So the acquisition of a
particular
shape by a molecule involves a thus probably another pure QWERTY phenomenon, or what Crick (1968) has mixture of historical accident on the one hand and the "discovery" of called a "frozen accident." But even in the case of such a QWERTY

important truths on the other.

phenomenon, if the conditions are just right and the opportunities and hence From the outset, the process of the design of molecular "machines" ex-pressures are great enough, the tables might be turned and a new standard hibits these two features of human engineering. Eigen (1992, p. 34) provides established. This is apparently just what happened when the DNA language a good instance of this in his reflections on the structure of the DNA code.

displaced the RNA language as the
lingua franca
of encoding for complex

"One might well ask why Nature has used four symbols, when she might just organisms. The
reasons
for its preferability are clear: by being double-as well have made do with two." Why indeed? Notice how naturally and stranded, the DNA language permitted a system of error-correcting or inevitably a "why" question arises at this point, and notice that it calls for an proofreading enzymes, which could repair copying errors in one strand by

"engineering" answer. Either the answer is that there is no reason—it is reference to its mate. This made the creation of longer, more complicated historical accident, pure and simple—or there
is
a reason: a condition was or genomes feasible (Eigen 1992, p. 36).