He thinks I am rationalising junk DNA with a pile of ‘what-ifs’. But the fact is that most of my ‘what-ifs’ are already known to have some basis in reality. I am not denying any obvious reality. Indeed, the basic machinery of life looks like design, far more than when Paley was around. Yes, there could also be a great deal of junk. That’s why I have said a number of times that ID is not committed to the idea that there is no junk.
Yet, from my point of view, I see a whole pile of Darwinian/post-Darwinian materialists who have only partly explored the genome, working from an assumption that the genome was not designed, and thus are jumping the gun on the evidence. For example, Larry still seems to think that pseudogenes are of themselves ‘solid evidence’ of broken genes despite the fact that we know that at least some pseudogenes influence the rate of translation of real genes by competing with them; a simple design reason why there should be ‘false genes’ = pseudogenes. Who has explored the rest of them?
From his emotive response to my perfectly valid, albeit speculative suggestions (though they were not plucked out of the air either), I don’t trust this guy to think clearly and calmly about the possibility of design. That’s the real problem.
Edit 12 May 2013:
Larry’s insistence that pseudogene = ‘broken gene’ comes from a particular way of thinking about biology: thinking of it in terms of a historical narrative rather than simply reporting the facts of what we see now. This affects much of what he talks about, but here I am choosing to focus on pseudogenes. The best way to talk science is to first state facts and provide an explanation, and then let the observer make up his mind, having been educated, and then let the observer attempt his own explanation of the facts. Being clear about what are facts, and what are interpretations, aids this, but Larry does not practice this when dealing with ID.
The facts are that we have many false genes (pseudogenes) that look like strikingly like particular real genes, and that some of them are known to be functional, and some of those are known to operate by regulating their corresponding real genes by generating competing transcripts. One possible history that would arrive at these observations is if a real gene was duplicated and then one copy was broken to make the pseudogene, and that some subsequently ‘discovered’ a function by chance. Larry believes this is the only possible explanation. He asserts ‘pseudogenes are broken genes’, as if true by definition. However, it is not the only explanation if one considers design. A designer might well make a false gene to regulate a real gene in this way. Why not? But Larry doesn’t consider design. He doesn’t even look at the possibility. That’s why he doesn’t understand that pseudogenes are not necessarily broken genes, and thus are not evidence for junk.
Larry was rather snide about computer scientists, as if they don’t understand the fundamentals of biology. Hmmm. I am more of a mathematical physicist than a computer scientist, and it seems to me that Larry doesn’t understand that stories/narratives about genes breaking and then discovering new function, are not enough for those looking for a natural (physical) explanation. I want to see hard probabilities. It seems that biologists are too happy with narrative and don’t realise the importance of probabilities. If you don’t know how to estimate probabilities, I am sure people like Doug Axe and the Biologic Institute could help you.