Commenter DK asks:
What is the official ID position on junk DNA? Has anyone proposed that it might be a mechanism to cause wholesale change in other parts of the DNA?
I thought this subject might be good for its own discusson thread so here it is. I don’t believe ID has any more “official” position on it than NDE does. It is largely regions of DNA with no known function and that isn’t to say it has no function at all. IDists tend to say there is a lot of function waiting to be discovered in it under the rubric that design is less wasteful than chance processes. The NDE position tends more toward much of it being detritus of an evolution driven by chance processes.
Clearly some of it is detritus, at least in sequence information. A good example is the remnants of retrovirus gene insertions. Absent selection pressure the useless DNA would first be peppered by point random mutations over time (it is) then discarded wholesale by larger random deletion events over larger timespans.
It seems to me that there is a larger accumulation of junk DNA than NDE would predict. Given the large amount of it in the human genome (some 98% if memory serves) natural selection should really favor larger deletion events that clean it out from the genome. In computer programming we call this “garbage collection” and go to great lengths to eliminate code and data that is no longer required. In a living cell, as in computer programs, useless code consumes resources and returns no value for it. Replication of DNA takes up time, energy, and raw materials. If it could be done faster, using less energy, and fewer raw materials that should be a strong selection factor in getting rid of stuff that isn’t used. Yet there’s a ton of it there.
When I’ve made this argument in the past the counter argument was that it’s really not that much extra burden in eukaryote cells because they are so big and have such slow reproductive rates to begin with regardless of how much DNA they have to replicate in the process of making a new cell. Prokayrotes have virtually no junk DNA in comparison and their reproductive success is largely due to how rapidly they can reproduce in great numbers. It’s a good counter argument but I’m not sure I buy it.
What really raises a red flag about how much junk is really in all our junk DNA is a how much information is required to build an organism as complex as a human. If every single bit of information in all 3 billion bases was being used for some purpose I still find it incredible that the schematics (or recipe) for a human can be contained in a gigabyte (a gigabyte is roughly how much information is in 3B bases). To posit that it can be contained in 20 megabytes (2% of one gigabyte) stretches the limit of credulity far beyond the breaking point.
So the idea that natural selection should work hard at eliminating useless DNA combined with the incredulity of a human organism being able to be specified in so little storage space makes me strongly suspect that just about every shred of it is being put to some use and then some. The “then some” is the structure of the rest of the cell or epigenetic information. Because we can see some of the junk getting peppered with point mutations it’s obvious that the specific sequence information isn’t important in some of it. To explain this I have proposed that useful information is also encoded into the 3 dimensional structure of the DNA molecule. Thus an apparently useless remant of a viral insertion would serve to subtly (or maybe not very subtly) change the shape of the molecule and thus have an effect on the organism it describes. This handily explains why so much junk is still hanging around in the human genome and where at least some extra storage space beyond codified sequence information is contained.
On the other hand maybe it is mostly junk and the answer is that there is far more epigenetic information than is known about or widely postulated.