By Richard B. Hoppe
Posted October 1, 2005
Writing for the Discovery Institute, Casey Luskin has dissed evolutionary research
performed using the Avida research platform. (Luskin is a new
"program officer" for the DI.) As I wrote last year, computer models employing
evolutionary mechanisms are a thorn (or maybe a dagger?) in the side of ID
creationists. The models allow testing evolutionary hypotheses that in "real"
life would take decades to accomplish or are impractical to run in wet lab or
field. They also allow close control of relevant variables -- mutation rates,
kinds of mutations, the topography of the fitness landscape, and a number of
others, enabling parametric studies of the effects of those variables on
evolutionary dynamics. A number of publications using Avida (see also
here) have established that it is a valuable
complement to wet lab and field studies in doing research on evolutionary
In his testimony at the Dover trial on September 28, Rob Pennock described a
study that has particularly irritated ID creationsts, The
evolutionary origin of complex features, published in
Nature in 2003. In that paper Lenski, Ofria, Pennock and Adami showed
that there are circumstances under which structures that meet Behe's operational
criterion for irreducible complexity (IC) -- loss of function due to knockout --
can evolve by random mutations and selection. Since IC is the core negative
argument of ID -- IC structures and processes allegedly cannot evolve by
incremental "Darwinian" processes -- the demonstration that they can
evolve by Darwinian processes knocks out IC as a marker of intelligent design.
And since IC is a special case of Dembski's Specified
Complexity, it also weakens Dembski's core argument.
Various ID creationists have criticized the Lenski, et al., study on a
variety of specious grounds, and I've discussed those critiques in several
places, including an extended discussion here. Luskin's critique is shallower and less
informed than some I've read. I'll hit a few low points in his critique.
Pennock and his other co-authors claim the paper "demonstrate[s] the
validity of the hypothesis, first articulated by Darwin and supported today by
comparative and experimental evidence, that complex features generally evolve
by modifying existing structures and functions" (internal citations removed).
Today in court, Pennock discussed the paper today asserting that it was a
"direct refutation" of irreducible complexity and a "general test" of
I do not have access to Pennock's testimony at the moment, but that's about
what I'd have said. Co-option and modification of existing structures is a
ubiquitous phenomenon in evolution at levels ranging from molecular mechanisms
to high-level structures like wings. And in the Lenski, et al., study, sure
enough, those same phenomena were observed occurring under the Darwinian
mechanisms -- reproduction, heritable variation, competition, and mutation.
Luskin spent a good deal of space exploring the conjecture that Pennock's
co-authorship of the Lenski, et al., paper was a conspiracy to get an expert on
Behe's irreducible complexity involved without directly citing Behe. He
I can think of no reason why a philosopher, who otherwise never authors
technical papers in scientific journals, whose career specializes in rebutting
ID, should be a co-author a [sic] technical research paper in a top technical
science journal on the evolutionary origin of biological complexity, a claim
which ID challenges, unless that paper somehow required some expertise on ID.
Indeed, this paper now appears strategically arranged: is it mere coincidence
that this paper appeared as a primary exhibit in the first trial against
teaching ID? The reality is that Avida study, in which Pennock was third
author, has much to do with strategically rebutting ID.
Looks more to me like it empirically rebuts irreducible
In his conspiracy theorizing Luskin neglected to mention that in addition to
his appointment in philosophy, Pennock is also a Member of the Digital Life
Laboratory at Michigan State, along with two of the other authors,
Charles Ofria and Richard Lenski. Chris Adami is also associated with the
Devolab as a collaborator. The work published in the Lenski, et al., paper is
well within Pennock's professional purview: it's by four colleagues associated
with the same lab. It wouldn't surprise me at all to find that Pennock suggested
the study's main outlines to his co-authors, since IDists use the notion of
irreducible complexity as their primary weapon in their culture war against
evolutionary theory and Pennock is interested in that effort. Knowing something
about Avida, I have no problem imagining that Pennock saw the Avida platform, a
main tool in the Devolab, as an excellent tool to do some research on the
question of the evolvability of IC structures.
That they didn't mention intelligent design isn't amazing. As far back as
Darwin the question of how those kinds of structures could evolve has been
raised, so Behe contributed no new issue to address. Lenski, et al., anchored
their paper directly to Darwin in the first paragraph. Since the ID creationists
have not published anything in the professional literature of biology to which
to refer in the context of the Lenski, et al., paper, it seems strange to
complain that they didn't reference ID. If ID had some actual professional
literature to cite one might sympathize, but it doesn't. Luskin's conspiracy
theory is more than a little incongruous coming from the socio-political
movement that didn't bat an eyelash when the ID-sympathetic editor of an obscure
taxonomic journal slid around the publishing society's editorial guidelines to
get Meyer's Hopeless Monster published. Do I
detect projection here?
Then Luskin repeated a common ID creationist criticism by writing
Pennock asserted on the witness stand that this study accurately modeled
biological reality. Well, if biological reality was pre-programmed by an
intelligence to evolve certain simple logic functions, then he's right. Avida
programmers knew that EQU was easily evolvable from the proper combination of
only 5 primitive logic operations before the simulation even began. This is
called "evolution by intelligent design," because the environment seems
literally pre-programmed to evolve the desired phenotype.
In fact, Avida programmers had no idea whether digital critters capable of
performing input-output mappings corresponding to EQU could evolve in Avida.
That human programmers could write an Avida instruction string that performed
the EQU mapping is irrelevant to the question of whether it could
evolve via Darwinian mechanisms. Programmers writing code is ID's
position, not evolution's. (Incidentally, Luskin misrepresents what actually
evolved in the Lenski, et al., experiments. "EQU" didn't evolve any more than
flight evolved in animals like birds and bats. Morphological structures that
enable flight evolved; flight didn't. Similarly, assembly language programs that
performed the input-output mapping corresponding to EQU evolved, not EQU itself.
That's not a trivial distinction. A given function can be performed by a number
of different structures.)
Further, while human programmers could write an Avidian critter to perform
the input-output mapping corresponding to EQU using 5 "primitive" logic
functions, the 23 lineages that evolved in the main condition in the Lenski, et
al., study did so in 23 different ways. The 23 lineages that evolved to
perform the mapping were all different, and in addition to EQU they performed 17
different combinations of the "primitive" functions, ranging from four to eight.
None of them evolved the 'EQU' program the human programmers wrote. That
phenomenon extends to other aspects of the Avida critters. For example, running
Avida with no fitness landscape, so selection is on replication efficiency
alone, evolves critters that perform self-replication in fewer instructions than
any human-written program. Recall Leslie Orgel's Second Law: Evolution is
smarter than [programmers] are.
Luskin then wrote a particularly error-filled paragraph.
Pennock seemed impressed that the digital organisms "invented" many
creative ways of performing EQU. But the flaw of the simulation lies therein:
EQU was destined to evolve because the addition of each logic function greatly
improved the fitness of the digital organism. Pre-programmed into the Avida
environment were functionally advantageous digital mutations which were
guaranteed to keep the digital organisms alive and doing interesting things.
Thus, if one assumes that anything more than extremely minor cases of
irreducible complexity never exist, then Pennock's program show evolution can
There are four main problems with Luskin's representation in those four
sentences. First, "functionally advantageous mutations" were not
"pre-programmed" into the Avida environment. Random mutations occurred,
some of which were deleterious (in the sense of decreasing reproductive fitness)
or even lethal, some were neutral, and some were advantageous. Gee. That's just
what a slew of biological research teaches us: mutations come in three basic
Second, Luskin claimed that those mutations were "... guaranteed to keep the
digital organisms alive ...". That's flatly false. Tens of thousands of digital
organisms die in the course of an Avida run under the conditions Lenski, et al.,
used. Some die because they fail to replicate due to lethal mutations in their
replication code, and some die because they're killed -- over-written -- by a
reproducing neighbor regardless of their advantageous mutations. Thousands of
species emerge, flourish for a while, and then go extinct, and thousands of
lineages go extinct. There are no guarantees at all.
Third, it is not necessary that "...the addition of each logic
function greatly improve[s] the fitness ...". While the fitness landscape defined
by the values assigned to the various logic functions in the Lenski, et al.,
study was fairly steep from simple to complex logic functions, a number of Avida
runs I have done with a flatter topography produce lineages that also perform
the most complex logic functions. It just takes longer because the dynamics of
lineages evolving on flatter landscapes are slower. So long as there is at least
some net selective advantage for performing a more complex function, more
complex functions can evolve.
Finally, do we now have a distinction between micro-IC and macro-IC? Luskin's
reference to "extremely minor cases of irreducible complexity" suggests that we
have to make that distinction, but where the boundary might be is not clear. Do
I hear echoes of "microevolution is fine, but not macroevolution"?
I'll note here that what one might reasonably believe to be cases of
irreducible complexity, like a three-legged stool which cannot function if any
of the three legs or the seat is 'knocked out', are no longer IC. William
Dembski has recently added two new operational tests for ICness. In
addition to Behe's original knockout operational criterion, now Dembski tells us
we must also determine (1) that a simpler structure cannot perform the same
function, and (2) after a successful knockout one must show that no adaptation
and/or rearrangement of the remaining parts can perform the original function.
As Dembski tells us, that means that a three-legged stool is not IC since a
solid block of wood can keep one's butt off the ground. I have argued elsewhere
that Dembski's additional operational criteria mean the Death of Irreducible Complexity (see also here and Mark Perakh's post here). On Dembski's new and
improved definition, not even Behe's mousetrap is IC.
Finally, Luskin claimed that a control condition in the Lenski, et al., paper
that employed a fitness landscape that was flat across logic functions except
for EQU showed that
... when there is no selective advantage until you get the final function,
the final function never evolved! This accurate modeling of irreducible
complexity, for there is no functional advantage until you get some to some
minimal level of complexity—that's IC in a nutshell. Yet the study found that
the evolution of such a structure was impossible.
Of course they claim this is what they "expected," but without using the
words "irreducible complexity," they just demonstrated that high levels of
irreducible complexity are unevolvable.
I'll be darned. Luskin is back to If it can evolve
incrementally by indirect routes involving intermediates that are themselves
functional, it ain't IC. If it can't evolve, it is IC, and by
the way, IC shows that it can't evolve. In other words, we're back to the
"We don't know how it could have, so it couldn't have and therefore ID" style of
argument. And there's that "high levels of irreducible complexity" phrase --
we've got to deal with microIC and macroIC again, too. Stuff that's got just a
little bit of IC can evolve, but stuff that's got a whole lot of IC can't. When
did irreducible complexity become a scalar variable? Luskin must be resurrecting
Behe's even more question-begging "evolutionary" definition of irreducible
complexity. I guess it's handy to have a series of alternative definitions of a
core concept ready to hand.
In a way I feel sorry for Luskin. It can't be easy writing about genuine
research when you have no clue what it did and what it means. On the other hand,
he has plenty of role models for that behavior at the Discovery Institute, and I
have no doubt that he'll learn fast.
Originally posted to The Panda's Thumb.