This is from creationist Slevesque, who started the thread:
I haven't followed the whole thread so I don't really know where this fits in, but just to answer what is written here, it seems to me this supposed discovery that some junk DNA is "functional" simply reflects the fact that some of it hasn't TOTALLY lost its function, it's just been crippled, not killed.
What I was saying was: The % of functioning genome has been ever increasing in the past few years, as I'm sure you know. Right now, anyone can safely say that at least 30% of the genome is functional.
What I said concerning ENCODE was simply that it ''opened up the possibility'' that the entire genome had a function. I'm not saying it proved anything, and I certainly know the difference between functional and transcribed.
Therefore, all I'm saying is that when seeing how genetics has been unravelling the secrets of previously thought ''junk DNA'', and how more evidence comes to open the possibility that maybe the whole genome is functional, I think it is the idea that any part of the genome is junk that should be regarder with great skepticism, not the other way around.
An accumulation of mutational disruptions of the code along the length of a gene over generations eventually has to render it less and less functional although it may retain SOME function, and this is most likely all that has been discovered.
Of course the whole genome was once completely and perfectly functional, but the processes of disease and death have been rendering it less and less functional down the generations.
I think slevesque is making a very common mistake that creationists, especially Intelligent Design creationists, often make, that is, not to recognize that dead DNA reflects the Biblical Fall. The whole genome is not NOW functional and it shouldn't be if the Fall is true. The Fall is still operating, at all levels of life, still accumulating death and disease from generation to generation.
It's testimony to the immense vitality of the original Creation that there's still a lot of life left in God's created world, but no matter how much life they discover remaining in the junk DNA it isn't going to be the original life that it was created to have, but something like haphazard spasms of its original life.
ALSO, the idea that deleterious mutations will be wiped out of the population by natural selection is no doubt true -- another notion that always comes up in these discussions, and on this thread as well -- as long as there are viable genes in the population at large that survive and get passed on. However, what is not being taken into account in this cheery scenario is that ALL death in a population contributes to the gradual reduction of genetic diversity over time, just as all the selection processes do, just as anything that isolates a portion of a population does.
ALSO, there is no reason for "neutral" mutations to be selected out so they continue in the population even though they represent a segment of dead DNA that means SOME function or other has been destroyed or crippled. As genes accumulate more mutational assaults down the generations, eventually they contribute to the DNA cemetery or junk DNA although the organisms go on apparently functioning, and there is simply no way to know what was lost. A whole population eventually comes to carry these cemeteries in their DNA although they apparently continue to function without them, though no doubt in an increasingly disease-prone condition.
Since we don't know what the original Creation was like we can't appreciate what has been lost, but it would certainly help if science weren't addicted to this idea of evolution and could get focused on the reality of gradual degeneration over time or the reality is going to rise up and bite them in the end (in both senses of the word). Reality is always a nice thing for science to keep in mind.