Lenski et al., "The Evolution of Biological Complexity, " Nature, 423:139-144 (May 8, 2003)
by Casey Luskin (with a little help from my friends) (Updated November, 2006)
On May 8, 2003, Nature published an article, "The Evolutionary Origin of Complex Features" (by Richard E. Lenski, Charles Ofria, Robert T. Pennock, and Christoph Adami, Nature, 423:139-144; herein the "Lenski article," or "Lenski paper"), which uses computer simulations of evolution via a program called Avida, to purport to "demonstrate 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). Not only does the paper (and some of its subsequent evolutionist commentators) vastly overstate the implications for the creative power of Darwin's mechanism, it also unwittingly gives credibility to the intelligent design hypothesis.
A. Some insightful comments from William Dembski:
The Lenski paper has been cited by some evolutionists as providing a refutation of the claims of ID proponents. William Dembski recounts that biologist Andrea Bottaro cites to the Lenski paper as one example of a refutation of the claims of ID. Below is an excerpt of Dembski's response to the Lenski article:
"Unfortunately the simulation presupposes the very point at issue. It therefore begs the question and doesn't prove a thing about real-life biological evolution. The Lenski simulation requires that complex systems exhibiting complex functions can always be built up from (or decomposed into) simpler system exhibiting simpler function. This is a much stronger assumption than merely allowing that complex systems may include functioning subsystems. Just because a complex system can include functioning subsystems doesn't mean that it decomposes into a collection of subsystems each of which is presently functional or vestigial of past function and thus amenable to shaping by natural selection.
"The simulation by Lenski et al. assumes that all functioning biological systems are evolutionary kludges of subsystems that presently have function or previously had function. But there's no evidence that real-life irreducibly complex biological machines, for instance, can be decomposed in this way. If there were, the Lenski et al. computer simulation would be unnecessary. Without it, their demonstration is an exercise in irrelevance. Bottaro's 'fatal blow' against irreducible complexity is nothing of the sort."
(William Dembski, Introduction to Uncommon Dissent, pg. xxv, xxix (ISI Books, 2004).)
When I originally read the Lenski paper a couple years ago, I felt that they did make a good faith effort to model some aspects of biological reality. For example, the simulations began with a population of "computer programs" or "digital organisms" which could reproduce but occasionally made mistakes (mutations) when copying their code. Fitness was also increased by having a mutation which added a "logic operation" to its code. I recommend reading the original paper to see how the logic operations can build upon one another to produce the target logic operation, called "EQU."
I break my criticisms into the following categories:
As Dembski notes, the simulation did indeed "stack the deck" in favor of evolution. The subsystems in the Lenski article were guaranteed to be capable of producing the target function from the very beginning. In fact, the authors were able to hand-code (i.e. intelligently find) a solution to create the target system ("EQU") from the simpler functions which required only 5 of the logic operations. This means that the target system is, logically speaking, just a combination of a few subsystems! It is not clear this models biological reality because the authors knew the subsystems were eminently capable of capable of creating the target system completely apart from running the simulations. The evolution seems to be guaranteed to be possible--which does not test Darwin's theory--it assumes it.
D. Too Much Selective Advantage
A selective advantage was granted with the "evolution" (i.e. addition) of any additional logic operations. These logic operations were the very tools by which the target function could be built. It thus seems unsurprising and inevitable that the target function evolved with such stepwise selection pressure in a population. This is like evolution which has been pre-programmed by intelligent design. Darwinian processes are just the vehicle to achieve the inevitable simple "evolution" of the easily-evolvable target system (EQU). Whether or not this is the biological reality was not tested. In the real world biological function is much more difficult to come across. For example, a paper in Journal of Molecular Biology calculates that the "prevalence of sequences performing a specific function by any domain-sized fold may be as low as 1 in 1077, adding to the body of evidence that functional folds require highly extraordinary sequences." (Axe, JMB, 341:1295-1315 (2004).) Every mutation had meaning within the environment, distancing the simulation from biological reality.
Regarding biological reality, one critique of Avida published in a biology journal recognized the unrealistic ease by which Avida allowed evolution to proceed:
(Nick Barton and Willem Zuidema, "Evolution: The Erratic Path Towards Complexity," Current Biology, Vol. 13, R649–R651, August 19, 2003)
By allowing for a selective advantage every time a new logic operator was formed, their fitness function may look something like this:
It should be noted that the Lenski study found that sometimes fitness would decrease (i.e. they might lose some key logic functions after a mutation), only to then later increase by a subsequent mutation. Thus, they might claim their fitness function looks something like this:
E. Modeling Irreducible Complexity
The paper made one profound finding when it accurately modeled true irreducible complexity (first full paragraph, pg. 143). Michael Behe has defined irreducible complexity as:
The Lenski article makes a bold claim: "Our experiments demonstrate 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." But it seems clear that this claim is based upon an inadequate test of the model. Furthermore, this claim seems to contradict the finding of the Lenski paper that when no selective advantage exists until the target function is achieved, evolution cannot produce that final function. If anything, this paper confirms a prediction made by Charles Darwin in 1859:
Part 2: How Lenski et al. Lends Credibility to Intelligent Design
The Lenski paper can only be seen as a scientific response to the claims of ID proponents, published in a high profile journal such as Nature. Despite the fact that the authors of the Lenski paper would likely deny this fact, there are many clues which show that the article is intended as a rebuttal to the claims of ID proponents. Not only does this validate the work of ID proponents as posing a legitimate challenge to Darwin's theory, but it also indicates that the claims of ID proponents are eminently testable, falsifiable (though as discussed above, not yet falsified), and therefore also scientific in nature.
Exhibit A: A notable co-author of the Lenski paper is philosopher Robert T. Pennock. Pennock is the author / editor of two books critiquing intelligent design (Tower of Babel [author] and Intelligent Design Creationism and its Critics [editor]) and is also a public activist, having testified in favor of evolution before the Texas State Board of Education. While Pennock is surely an accomplished academic, his co-authoring of a Nature article on evolving complexity is very odd for someone who teaches nothing but courses in philosophy, humanities, and history at Michigan State University. Pennock is surely a qualified academic, but he is not trained in the fields from which one should be publishing science articles in Nature? This odd fact turns out to have a simple explanation.
Given the odd presence of a an anti-ID co-author such as Pennock, the Lenski paper can be viewed as nothing other than a response to the claims of intelligent design proponents. While the Lenski article is careful to avoid legitimization of intelligent design by avoiding any direct citations to ID proponents, the article is couched as nothing less than a rebuttal to the claims of ID proponents. This brings us to Exhibit B: the abstract of the paper begins "A long-standing challenge to evolutionary theory has been whether it can explain the origin of complex organismal features" and ends "These findings show how complex functions can originate by random mutation and natural selection." Thus the article is framed as a rebuttal to those who "challenge" evolutionary theory.
The article even attempts to address irreducible complexity without using the term. "Thus, although more than two dozen mutations were used to build EQU, undoing any one of them destroyed this function." They are stating that EQU was irreducibly complex, but yet it evolved. Thus, Exhibit C is as follows: the article directly purports to test the evolution of irreducible complexity but yet never uses the phrase. (Note: It is arguable that their stated conclusions about the evolution of irreducible complexity do not match the findings of their simulations. When EQU evolved, the study did not truly model irreducible complexity because it employed a "reward-all" environment where some function could be gained by adding parts which could also contribute to the final function. When the article properly modeled irreducible complexity, where only EQU was rewarded, EQU never evolved!)
Exhibit D: To ice this cake, consider this statement from the February, 2005 of Discover Magazine (where references to the true point of the article were apparently not censored):
The publication of this paper presented a dilemma to the authors because they wanted to simultaneously refute ID, and validate the faith of the scientific community in Darwin's magic mechanism, but yet not validate ID in the process through any references to proponents of ID-concepts. This strategic tactic has been employed numerous times in the Darwinist community, as NCSE Director Barbara Forrest has implied that Darwinists should not share the stage with ID proponents at conferences because it "lends [ID proponents] an undeserved academic legitimacy" (see "Barbara Forrest's Letter to Simon Blackburn"). Perhaps she gave similar advice to Pennock. (Pennock and Forrest think alike and have worked together against ID: After she encourages academics to avoid ID proponents, Forrest recommends Pennock's book in the very next paragraph of her Letter to Simon Blackburn; Pennock has returned such favors as he contributed reviews of the pre-print manuscript of Forrest's book against ID [see pg. viii].) In the case of the Lenski paper, the careful balancing act failed in its attempt to refute ID without legitimizing ID literature.
All in all, it is a great thing that a study in a journal like Nature took the challenges of ID proponents seriously and tried to test them through a computer simulation. ID proponents should laud any scientist who tests and critique the claims of ID, regardless of the outcome of the study. However, it is unfortunate that here, the study was done published in such a manner which avoided acknowledgment that it was actually testing the claims of ID proponents. This covert "refutation without citation" does not do service to unbiased scientists who want to really investigate and understand the challenges posed to Darwin's mechanism by ID proponents.
In the future, when scientific journals want to attempt to publish scientific refutations of intelligent design, but walk-the-tightrope and in-doing-so, avoid legitimizing the claims of intelligent design proponents, they may want to consider doing the following: