How bad have things gotten for the ID side? Completely unable to make good on their promise to generate any ID based research, they have now taken to outright lying about the work done by real scientists. Okay, so maybe they’ve been doing that for quite some time. Still, William Dembski’s latest blog entry strikes me as even more brazen than usual.
Here is an ID research paper published in PNAS. Note that some important principles of evolutionary theory are criticized in the abstract. This research shows how ID is capable of being applied in biology.
PNAS refers to the Proceedings of the National Academy of Sciences, a prestigious journal indeed. If they ever did publish an ID research paper, that would be big news. Happily, one only has to read a few sentences of the actual paper mentioned here to realize just how silly Dembski is being.
The paper in question is entitled, The regulatory utilization of genetic redundancy through responsive backup circuits. The remainder of Dembski’s post merely reprints the abstract of the paper, and I will now do likewise. The bold face in the final sentence is Dembski’s:
Functional redundancies, generated by gene duplications, are highly widespread throughout all known genomes. One consequence of these redundancies is a tremendous increase to the robustness of organisms to mutations and other stresses. Yet, this very robustness also renders redundancy evolutionarily unstable, and it is, thus, predicted to have only a transient lifetime. In contrast, numerous reports describe instances of functional overlaps that have been conserved throughout extended evolutionary periods. More interestingly, many such backed-up genes were shown to be transcriptionally responsive to the intactness of their redundant partner and are up-regulated if the latter is mutationally inactivated. By manual inspection of the literature, we have compiled a list of such “responsive backup circuits” in a diverse list of species. Reviewing these responsive backup circuits, we extract recurring principles characterizing their regulation. We then apply modeling approaches to explore further their dynamic properties. Our results demonstrate that responsive backup circuits may function as ideal devices for filtering nongenetic noise from transcriptional pathways and obtaining regulatory precision. We thus challenge the view that such redundancies are simply leftovers of ancient duplications and suggest they are an additional component to the sophisticated machinery of cellular regulation. In this respect, we suggest that compensation for gene loss is merely a side effect of sophisticated design principles using functional redundancy.
Now merely using a phrase like “sophisticated design principles” is enough to make the ID folks claim you as one of theirs.
Let’s begin by scouring that abstract for the important principles of evolutionary theory Dembski’s says are criticized.
It’s been known for some time that gene duplication and divergence is an important mechanism for generating novelty in the course of evolution. The duplication of a gene leads to functional redundancy. One of the copies can then mutate, thereby possibly acquiring a new function, without leading to catastrophic damage to the organism. Indeed, gene duplications can be viewed as golden opportunities for functional innovation, and consequently would generally not be expected to remain for long in a population. (This is what the authors of the paper have in mind in describing these redundancies as “evolutionarily unstable.”).
This has been perfectly mainstream evolutionary theory for quite a long time. See, for example, Susumu Ohno’s 1970 book Evolution by Gene Duplication. And it will remain perfectly mainstream after this article. That’s because the remarkable discovery made by the authors of the paper is that, while usually redundant genes behave in accordance with expectations, there are instances where it can actually be selectively advantageous to preserve the duplicated gene.
They explain this clearly in the first two paragraphs of the paper:
Duplicate genes and paralogous gene families long have been perceived as genomic sources of genetics robustness (1-5). The assumption is that a functional overlap of these genes acts to compensate against mutations. Yet, this very fact also renders redundancy evolutionarily instable (5, 6), and functional overlaps,
typically, are rapidly lost because of divergence (7).
Nevertheless, numerous examples of paralogs retaining their functional overlap for extended evolutionary periods (for examples, see refs. 6 and 8-12) suggest that, at least for a fraction of gene pairs, redundancies are conserved throughout evolution despite their predicted instability.
A little later we come to this:
In fact, although retention of redundancy is much less frequent than its loss, its widespread existence is nontrivial and cannot (6) be dismissed as leftovers of recent duplication events.
And later still:
In this work, we wish to adapt the view that, at least in some pathways, redundancies are selected for based on some evolutionary advantage that they confer to the wild-type organism. In particular, we suggest the existence of regulatory designs that exploit redundancy to achieve functionalities such as control of noise in gene expression
or extreme flexibility in gene regulation.
So what have we learned? Most of the time things proceed exactly the way you would naively expect them to. Duplication leads to redundancy, which quickly leads to divergence and new functionalities. But sometimes there is a heretofore unsuspected selective advantage to maintaining both copies of the duplicated gene. Describing some of those advantages is the primary purpose of the paper.
I’d say that paper fits very comfortably indeed within evolutionary theory. That there is so much heretofore unsuspected complexity in the mechanisms of genetics is one of the reasons biology is such a hot science these days.
So, even in the shadow world of ID fanatics, how could this paper be construed as helpful to the cause? Well, you need to realize that ID folks take it as axiomatic that evolutionists are desperate to dismiss large quantities of animals’ genotypes as useless leftovers. So any time something previously dismissed as evolutionary junk is found to have any function at all, they are happy to claim it as a victory.
Never mind that the paper states clearly that most of the time things play out precisely as conventional theory predicts. Never mind that in the handful of cases where redundancy persists it is because natural selection actively works to preserve it. Never mind that the opening paragraph of the paper confirms one of the main scenarios for explaining how structures fitting the ID defintion of “irreducible complexity” can evolve gradually. Never mind that this work was done by biologists working firmly within an evolutionary paradigm and that the ID folks, in their decade plus of bloviating about the great discoveries to be found from ID research, never said a word anticipating the results in this paper. And never mind that ID folks have nothing specific to say about the relationship between design and functional efficiency in organisms. Those considerations only matter if your goal is to say something truthful about an important piece of current scientific research.
If, instead, your goal is to chum the waters for the small cadre of drooling lickspittles who increasingly are the only ones who take you seriously (be sure to note the comments to Dembski’s post), then you can ignore such petty concerns. Instead you merely say, “Look! The word “design” in a real science paper. Another triumph for our side!”
Still, I do get the feeling that every time I think I’ve seen the most ridiculous ID claim imaginable, they struggle hard to prove me wrong.