The most common approach was from commenters who thought that junk DNA was just a term to describe our ignorance of what's in the genome. They believe that scientists know very little about genomes and that's why they came up with the junk DNA concept. Words like "hubris" and "arrogance" are thrown about.
This is a problem because it indicates a mistrust of scientists and a misunderstanding of how science works. But in fairness, there are a good number SCIENTISTS who also think that there's no evidence for junk DNA.
The other common misconception was that evolution (i.e. natural selection) is so powerful that any real junk DNA would have been eliminated by now. This is also a slap at scientists because in order to make this argument you have to claim that Ryan Gregory and other junk DNA proponents know nothing about evolution. The irony is that the proponents of junk DNA seem to be far more knowledgeable about evolution than those who oppose junk DNA.
Here's the article about the comments: Re: Is Most of Our DNA Garbage?.
Is there garbage in our genome? Carl Zimmer’s March 8 article about the debate in the scientific community over junk DNA sparked a conversation that spread to the blogs of half a dozen scientists.It's true that many of us commented on Carl's article but it's also true that Carl's article was, in part, prompted by science blogs. This is a debate that's been taking place on the internet for 25 years.
For the most part, the comment on comments makes reference to supporters of junk DNA. That's good.
The photo below shows Carl Zimmer having lunch with three science bloggers last December [Is most of our DNA garbage?].
Image Credit: The cartoon is by Tom Gauld and it was published online at the The New York Times Magazine website. I hope they will consider it fair use on an educational blog.