I would say, in terms of junk DNA, we don't use that term any more 'cause I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome as if we knew enough to say it wasn't functional. There will be parts of the genome that are just, you know, random collections of repeats, like Alu's, but most of the genome that we used to think was there for spacer turns out to be doing stuff and most of that stuff is about regulation and that's where the epigenome gets involved, and is teaching us a lot.- Francis Collins
Zimmer talks to a number of scientists who present some pretty convincing evidence about the lack of correlation between genome size and biological complexity, including the plant with the biggest genome. The article presents the tension between those, like T. Ryan Gregory from University of Guelph (one of the stars of Zimmer's article) who see lots of junk, and those, such as John Rinn, who are busy looking for things that non-coding DNA do.
As background for the current dispute, Zimmer goes back to Gould and Lewontin and their view of evolutionary mechanisms. Gould in particular, was frequently represented as "not believing in natural selection" because he believed that it wasn't all of evolution. What Gould (read closely) was saying was that of course, natural selection worked, but it, and evolution didn't make perfection. Exaptation, in his paper with Elizabeth Vrba, succinctly points out that selection often works with what already exists when a new structure evolves. Examples include skull sutures which make significant brain growth possible in mammals exist as joints in ectotherms that have neither large brains nor live birth. The Panglossian concept of perfection, as generated by natural selection, is something that has been argued about for years. The debates about junk DNA are just its current incarnation.
What fascinates me are the folks who object to the concept of junk DNA. Zimmer points out that even if John Rinn finds that "junk genes" have an important purpose, its much more like looking for gold in the sand on the beach. He quotes Alex Palazzo from University of Toronto: “probably what you found is a little bit of noise.” Zimmer, at the end of the article, comes down firmly on the side of some DNA being junk, and in fact not "a sign of evolution’s failure. It is, instead, evidence of its slow and slovenly triumph". As Zimmer implies, part of this defense of the Human Genome Project, but perhaps there is more going on.
The idea that there is junk, or waste, or nonsense in nature is tough for some people. They may or may not be overtly or classically religious, but slovenly nature, to use Zimmer's word, is an anathema to them. Many people who are in awe of nature, be it towering redwoods, or the intricate dance of genes, find stuff that doesn't serve a purpose, well, unsettling. The explanations of the accumulation of junk DNA, just like the accumulations of non-functional bits of anatomy, just happens. Zimmer, as Steve Gould famously did every year, goes back to Darwin for defense of both other forces of evolution beyond natural selection. What is tough is when the data, be it in the natural world, one's laboratory or genome, don't conform to one's preconceptions of the world.