Here is an interesting take on junk DNA by Scientific American
Extract:
As a summary then, we should be surprised to find someone who says they are surprised by junk DNA. Even someone like me who is not an expert can think of at least three simple reasons to like junk DNA:
1. The understanding that evolution is an inherently messy and inefficient process that often produces junk. This junk may be retained if it’s not causing trouble.
2. The realization that the vast differences in genome sizes are much better explained by junk DNA than by assuming that most DNA is truly functional.
3. The understanding that mutational loads would be prohibitive had most of our DNA not been junk.
Also
The reason why most of these useless pieces have not been weeded out is simply because there was no need to. We should remember that evolution does not work toward a best possible outcome, it can only do the best with what it already has.
This can really only be understood under a evolutionary model rather than a model based on ID.
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