Thank you Dr. Swamidass,
Sorry for the slow response. I read the Cancer and Evolution article carefully and found it interesting (I still want to read your personal story but haven’t had a chance yet). For what it’s worth, I agree that perhaps ID proponents spend too much time debunking Darwinism. I think this tendency is in response to wildly out-of-date popular science education and public-school curriculum, which gives many laypersons the impression that science has proven Darwinian Evolution beyond any reasonable doubt, and that there is no controversy. I myself believed this.
Perhaps we might have different understandings as to what ID theory is and isn’t claiming. Could summarize your understanding of ID? To summarize my position: I am skeptical that naturalistic mechanisms are in principle capable of constructing new body plans (phyla), new complex systems within multi-cellular organisms (for example a digestive system), or the origin of life. I do not deny evolution in the sense of change over time, this is undeniable. I believe intelligent design is a more plausible explanation for such complexity. I also suspect that variability within a type (phyla) was intentionally pre-programmed into archetypal forms, which will then vary (into species) based on various factors typically associated with evolution, such as climate, competition, predators, etc. I think the fossil record also supports this hypothesis.
To be clear, I think that some of your critiques of ID are valid, but I suspect others are simply the result of misunderstandings. Of course, there are varying views within ID theory as well. As always, a prescriptive set of beliefs packaged within generic labels can muddy the waters. I am sure that some claims of ID proponents are mistaken and am happy to see them corrected when they are. I suspect other claims may be more robust to criticism.
Going back to the article, I wish there was more detail on the specifics of what those novel functions are and how they work. From the article alone, it is not clear to me that truly novel functions were generated. How do we know these features weren’t present, but dormant? I don’t follow how neutral evolution explains novel functions. Are you arguing that the accumulation of neutral mutations eventually can generate new functions? If so, why are there drivers and passengers? It sounds like the driver mutations are the ones really imparting novel function, not passengers. Perhaps I am simply misunderstanding.
We’re going from a cell that is part of a harmonious multicellular organism to a homogenous parasite which I presume kills its host (if left untreated). This isn’t exactly the building up of complexity that I think ID theory calls into question. If you could show that truly novel functions are being generated which were not there to begin with (perhaps in some dormant state), then yes, I would agree that this could be evidence against some claims made by ID proponents. But I think the article lacks sufficient detail to demonstrate this.