I ended up with a much longer comment (to my own post) dealing with a newer view about ENCODE than I’d expected and really the comment is more like a post, so here’s a way to find it. One of the “insights” I included in my comments I then also found in PZ’s criticism in a more pithy and humorous way:
The ENCODE group could only declare function for a sequence by ignoring all other context than the local and immediate effect of a chemical interaction — it was the work of short-sighted chemists who grind the organism into slime, or worse yet, only see it as a set of bits in a highly reduced form in a computer database.
I hope to get back to this subject since it’s so much more interesting than all the fake crisis politics and brutally selfish partisan politics that I am so sick of I hope I can tune it all out and spend my time on more interesting subjects.
OH! I do want to mention one idea that my hero Nate Silver managed to miss. The critical paper discusses what ‘functional’ means by getting at the distinction:
In biology, there are two main concepts of function: the “selected effect” and “causal role” concepts of function.
The initial explanation of this (sorta like one of those dry philosopher papers) was unhelpful so instead I’ll just use the example which is much easier to follow:
For example, while the selected effect function of the heart can be stated unambiguously to be the pumping of blood, the heart may be assigned many additional causal role functions, such as adding 300 grams to body weight, producing sounds, and preventing the pericardium from deflating onto itself.
So instead of just dealing with Nate’s distinctions of association, correlation, and causation, here we have “causation” that is effectively irrelevant, given that biology looks function far differently than just what a bunch of molecules do (physics (or big data), for instance, would be equally convinced of all these “causes”).
So this is an interesting debate and I hope I can get back to it.