Darwin's Dangerous Idea - Evolution and the Meaning of Life

194 BIOLOGY IS ENGINEERING Function and Specification 195
models of evolution are not only possible but positively required if we are
really to explain what Darwinism has always claimed it can explain. Darwin's
idea that evolution is an algorithmic process is now becoming an ever more
enriched family of hypotheses, undergoing its own population explosion
thanks to the opening up of new environments for it to live in.
In Artificial Intelligence, a prized strategy is to work on deliberately
simplified versions of the phenomena of interest. These are engagingly called
"toy problems." In the Tinker Toy world of molecular biology, we get to see
the simplest versions of the fundamental Darwinian phenomena in action, but
these are real toy problems! We can take advantage of the relative simplicity
and purity of this lowest-level Darwinian theory to introduce and illustrate
some of the themes that we will trace through the higher levels of evolution
in later chapters.
Evolutionists have always helped themselves to claims about fitness and
optimality and the growth of complexity, for instance, and these claims have
been recognized by claimant and critic alike to be serious oversimplifications
at best. In the world of molecular evolution, no such apologies are required.
When Eigen speaks of optimality, he has a crisp definition of what he means,
and experimental measurements to back him up and keep him honest. His
fitness landscapes and measures of success are neither subjective nor ad hoc.
Molecular complexity can be measured in several mutually supporting and
objective ways, and there is no poetic license at all in Eigen's use of the term
"algorithm." When we envision a proofreading enzyme, for instance,
chugging along a pair of DNA strands, checking and fixing and copying and
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
are no magical helper-elves, no skyhooks, lurking in these quarters. In the
world of molecules, the application of Darwinian thinking is particularly pure
and unadulterated. Indeed, when we adopt this vantage point, it can seem
something of a marvel that Darwinian theory, which works so beautifully on
molecules, applies at all to such ungainly—galactic-sized—conglomerations
of cells as birds and orchids and mammals. (We don't expect the periodic
table to enlighten us about corporations or nations, so why would we expect
Darwinian evolutionary theory to work on such complexities as ecosystems
or mammalian lineages!?)
In macroscopic biology—the biology of everyday-sized organisms such as
ants and elephants and redwood trees—everything is untidy. Mutation and
selection can usually only be indirectly and imperfectly inferred, thanks to a
mind-boggling array of circumstantial complications. In the molecular world,
mutation and selection events can be directly measured and manipulated, and
the generation time for viruses is so short that huge Darwinian effects can be
studied. For instance, it is the horrifying capacity of toxic
viruses to mutate in deadly combat with modern medicine that spurs on and
funds much of this research. (The AIDS virus has undergone so much mutation
in the last decade that its history over that period exhibits more genetic
diversity—measured in codon revisions—than is to be found in the entire
history of primate evolution!)
The research of Eigen and hundreds of others has definite practical applications
for all of us. It is fitting to observe, then, that this important work
is an instance of Darwinism triumphant, reductionism triumphant, mechanism
triumphant, materialism triumphant. It is also, however, the farthest
thing from greedy reductionism. It is a breathtaking cascade of levels upon
levels upon levels, with new principles of explanation, new phenomena
appearing at each level, forever revealing that the fond hope of explaining
"everything" at some one lower level is misguided. Here is Eigen's own
summary of what his survey shows; you will note that it is written in terms
that should be congenial to the most ardent critic of reductionism:
Selection is more like a particularly subtle demon that has operated on the
different steps up to life, and operates today at the different levels of life,
with a set of highly original tricks. Above all, it is highly active, driven by
an internal feedback mechanism that searches in a very discriminating
manner for the best route to optimal performance, not because it possesses
an inherent drive towards any predestined goal, but simply by virtue of its
inherent non-linear mechanism, which gives the appearance of goaldirectedness.
[Eigen 1992, p. 123]
3. FUNCTION AND SPECIFICATION
Shape is destiny in the world of macromolecules. A one-dimensional sequence
of amino acids (or of the nucleotide codons that code for them)
determines the identity of a protein, but the sequence only partially constrains
the way this one-dimensional protein string folds itself up. It typically springs
into just one of many possible shapes, an idiosyncratically shaped snarl that
its sequence type almost always prefers. This three-dimensional shape is the
source of its power, its capacity as a catalyst—as a builder of structures or a
fighter of antigens or a regulator of development, for instance. It is a
machine, and what it does is a very strict function of the shape of its parts. Its
overall three-dimensional shape is much more important, functionally, than
the one-dimensional sequence that is responsible for it. The important protein
lysozyme, for instance, is a particular-shaped molecular machine that is
produced in many different versions—more than a hundred different aminoacid
sequences have been found in nature that fold into the same functional
shape—and of course differences in these amino-