Joining the Conversation: Perspectives on the Discussion with James Shapiro
I have followed with interest the discussion ("Is James Shapiro a Design Theorist?") initiated by Bill Dembski and now involving James Shapiro, Ann Gauger and Douglas Axe. The nub of the issue seems to relate to conflicting conceptions about what constitutes a legitimate scientific explanation (what philosophers call the "demarcation problem").
For Shapiro, scientific enquiry is strictly limited to the material realm. This likely reflects a skepticism on the part of many scientists about whether a non-material causal explanation may carry significant heuristic value. Conversely, those of us who support ID take the view that science can and does detect the activity of non-material causes. Many of us also think that the paradigm of ID provides an innovative way of understanding biology that can be used to guide future research. Indeed, Doug Axe recently indicated his intent to conduct research elucidating design principles that operate in nature.
The line between science and philosophy can sometimes be a fine one, however, presumably because science often validates particular premises of a philosophical syllogism that in turn may provide support for the supernatural (e.g. the Kalam argument). As a substance dualist, for instance, I maintain that consciousness itself -- though it intimately interacts with the brain -- is not entirely reducible to the material constituents thereof. Evidence for this claim lies in phenomena such as the placebo effect (see O'Leary and Beauregard, 2007) and the existence of existential freedom of the will (which I take to be a properly basic belief).
There is also an important distinction to be made between the terms "natural" and "material." Conscious deliberative activity is certainly a natural cause, and one that we are accustomed to dealing with -- but I would argue that it is not a material cause. Some forms of intelligent agency may indeed be of a supernatural nature -- but that question is beyond the realm of scientific inquiry. Intelligent design does not logically require that its proponents embrace theism, or even the supernatural. Regardless of whether an agent is natural or supernatural, we have uniform and repeated experience of the kinds of effects that intelligent causes produce and that non-intelligent causes do not. The secondary question of the identity and nature of the designer may well be philosophical; but the primary question of whether intelligence was involved is inherently scientific.
Shapiro takes the view that what many of us would regard as a teleological process -- he calls it "natural genetic engineering" -- has played a key role in the evolution of life on earth. There has been some interesting discussion in the ID community regarding so-called front-loaded evolution (e.g. see Mike Gene's book The Design Matrix and the Telic Thoughts blog).
When Axe and Gauger brought up their published work regarding the non-evolvability of protein folds as a consequence of their rarity and isolation in sequence space, Shapiro responded,
Proteins evolve largely by shuffling and accreting functional subregions called "domains," not through the Darwinian modifications of individual amino acids (Doolittle and Bork 1993). Domain accretion and shuffling are inherently natural genetic engineering processes (i.e. non-Darwnian) because they involve the rearrangement of extended DNA segments that encode the different domains. As my book details, we have many examples of this process mediated by mobile genetic elements in nature as well as its replication in living cells in the laboratory. Moreover, we know a great deal about the roles of mobile genetic elements as sources for completely novel domain coding sequences through the process currently known as "exoneration."It appears, then, that we are in agreement that the findings of Axe and Gauger (as well as other scientists such as Robert Sauer and Sean Taylor) do not bode well for the Darwinian story that protein domains evolve by virtue of "modifications of individual amino acids." If this scenario is not adequate to account for novel protein domains, what does Shapiro suggest? He proposes the processes of "domain accretion and shuffling" which "involve the rearrangement of extended DNA elements that encode the different domains" and are "mediated by mobile genetic elements."
As Douglas Axe explained in his reply, much of what is hypothesized about protein origins is inferred by comparing genome sequences, with little regard given for estimation of the available probabilistic resources and experimental evaluation of the difficulty of the innovation in question.
Some ID proponents would be quite happy to entertain the idea of some sort of front-loaded evolution (that is, as Mike Gene has defined it, where "the original front-loaded state had sufficient information that would bias evolutionary trajectories needed to evolve complex, multi-cellular organisms"). Such a scenario may well involve mobile elements or insertion sequences that have preferences for certain integration sites. For example, Lönnig and Saedler (2001) suggest that preferences for transposon insertion imply "preestablished rather than accidental chromosome rearrangements for nonhomologous recombination of host DNA" and "the possibility of a partly predetermined generation of biodiversity and new species."
One interesting paper, by Zhang and Saier (2009), documents the phenomenon whereby, in the presence of glycerol, an insertion sequence (IS5) is incorporated into the glpFK operon's promoter region. The glpFK operon contains genes encoding for proteins GlpF and GlpK. The former of those is a glycerol facilitator, while the latter is involved in glycerol metabolism (it converts it to glycerol-3-phosphate). When the IS5 element inserts into the promoter, it induces the expression of the pertinent genes. What's remarkable is that it does this only in the presence of glycerol.
It turns out that the presence of glycerol causes a repressor protein (which is ordinarily bound to the promoter, thus covering the insertion target for IS5) to be removed. What's more, the sequence of the IS5 element is essential to this process -- integration of other insertion elements won't work. Perhaps it is possible that, at some level, evolution proceeds in a manner similar to this. However, the original front-loaded system(s) would still require the input of an intelligent designer. I am skeptical of whether such genome re-arrangements, under the assumption that they were not guided (at least by pre-existing information), would possess the power to account for novel protein domains. Somebody has to do the hard work of determining whether adequate probabilistic resources were available.
Further work needs to be done to determine the extent to which the various mechanisms that Shapiro proposes really are efficacious in accounting for the significant innovations in form and function that have occurred throughout the history of life. Processes such as genome rearrangements and duplications, chromosomal breakage and fusion, cross-species hybridization, and stress-induced wide-scale mobile element activation are known to occur.
However, these processes have a high propensity towards being harmful to an organism's fitness. Genomic analysis does reveal the past occurrence of entire genome duplications in vertebrates, but the interesting question is whether such events were guided by pre-existing information. The current evidence would seem to suggest so.