During the discussion in the comment to my posting, I challenged Nils to answer a number of questions. He has responded on his blog SciPhu with Hey junk people, I accept your challenge (part I).
Here are the first four questions with my personal summary of his answers.
Q: Why do pseudogenes and most of the transposon-related sequences look so much like broken genes?
A: They may look like broken genes but they probably have some function.
Q: Why is the DNA sequence in most of our DNA not conserved?
A: It's not conserved because it's a reservoir for evolution. In addition, it probably contains genes for small RNAs and, as we all know, those predicted small RNA genes are not conserved.
Q: Why can we delete large segments of mammalian DNA with no observable effect?
A: There is an effect. We just haven't found it yet.
Q: Why is there so much variations in repetitive DNA within a species? Some people have segments that are ten times longer than segments found in other people. Are all of the nucleotides in the longer segments functional?
A: There are some examples of differences in repeats that do make a difference. Therefore, it is wrong to conclude that most of the variation has no effect. Furthermore, the discovery of copy number variation is a new phenomenon and it may turn out the have profound effects.
Nils concludes Part 1 by repeating his earlier complaint ..
This belief that there’s hidden function to be found, treasures to unearth if you will, is the difference between those advocating these parts of DNA as “junk” and me. In my opinion, It’s not the details of what is junk and what isn’t, ..- and how much, that bothers me…..This is nonsense but I already covered that complaint in my previous posting.
It’s the attitude. To dismiss something as junk is contrary to my idea of science being driven out of curiosity and the need to explore. Curiosity may kill a cat every now and then, but I’ll take that risk and continue to praise the scientist who recognize possibilities in the junk rather than dismissing it.
Nils seems to think that the adaptationist program is the only way to remain curious and excited about science. This is in direct contrast to the original Spandrels paper by Gould and Lewontin. They argued that strict application of the adaptationist program prevents people from seeing other possibilities. It's a science stopper.
Gould and Lewontin argued that a pluralist worldview was far superior because it considers a wider range of possible explanations.
Personally, I'm as excited about the possibility that our genome could be 95% junk as I am about the possibility that there may be strange new features that we don't know about. At least the tentative conclusion that much of it is junk has the advantage of being a superior explanation of the data.
The conclusion that most of the DNA has some unknown function in spite of much evidence to the contrary strikes me as non-scientific. To justify it on the ground that such a belief is required in order to maintain an interest in the subject is almost unbelievable.
Incidentally, despite some initial skepticism1, Richard Dawkins—not usually thought of as the best example of a pluralist—has now resorted to using junk DNA as one of his arguments against Intelligent Design Creationism.
Gene duplications have occurred from time to time throughout the genomes. It is by these, and similar means, that genome size can increase in evolution. But remember the distinction between the total capacity of the whole genome, and the capacity of the proportion that is actually used. Recall that not all the globin genes are actually used. Some of them, like theta in the alpha cluster of globin genes, are pseudogenes, recognizably kin to functional genes in the same genomes, but never actually translated into the action language of protein. Genomes are littered with with nonfunctional pseudogenes, faulty duplicates of functional genes that do nothing, while their functional cousins (the word doesn't even need scare quotes) get on with their business in a different part of the same genome. And there's lots more DNA that doesn't even deserve the name pseudogene. It, too, is derived by duplication, but not duplication of functional genes. It consists of multiple copies of junk, "tandem repeats," and other nonsense that may be useful for forensic detectives but which doesn't seem to be useful in the body itself.
Richard Dawkins in "The "Information Challenge",
The Skeptic magazine, 1998
1. The Extended Phenotype p. 157