SF Matheson, on his fascinating Quintessence of Dust blog, provides some useful clarification regarding the significance of the genetic evidence for common descent (see previous post), in a passionate, take-no-prisoners post entitled “Talking trash about ‘junk DNA'”.
In particular, Matheson emphasises that arguments for common ancestry based on non-coding DNA do not depend on assumptions as to the functionality of non-coding DNA, either in general or as regards the specific elements used as evidence for common ancestry:
To be brief: biologists make neither of those suppositions when they use non-coding DNA elements to establish common ancestry and particular evolutionary relationships. Whether or not a certain DNA element is “functional” doesn’t make it any less an indication of common descent, nor have biologists ever assumed universal non-function of non-coding DNA in the first place.
Pseudogenes and mobile elements constitute overwhelming evidence for common ancestry, not because of “presumptions” regarding their function, but because they exhibit patterns of inheritance and location (within the genome) that are best explained by common descent.
Indeed, in some cases these “mobile elements” (such as SINEs) acquire functionality, without this undermining their usefulness as indicators of common descent:
Even if a particular mobile genetic element has been put to work by the genome in which it is embedded, its conserved location in particular lineages (and not in others) presents an observation that is readily explained by common ancestry. In other words, even when it’s true that a particular piece of non-coding DNA has a biological function, it’s not true that this falsifies the basic explanation of common descent.
Hence I remain persuaded by the evidence for common descent of humans and other primates as set out in my previous post.