Caledonian2 comments on Natural Selection's Speed Limit and Complexity Bound - Less Wrong
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Excluding the complex and subtle regulatory functions that non-coding DNA can possess strikes me as being extremely unwise.
There is no DNA in the maize genome that codes for striped kernels, because that color pattern is the result of transposons modulating gene expression. The behavior of one transposon is intricately linked to the total behavior of all transposons, and the genetic shifts they result in defy the simple mathematical rules of Mendelian inheritance. But more importantly, the behavior of transposons is deeply linked to the physical structure of the encoding regions they're associated with.
Roughly half the genome of corn is made up of transposons. Is this 'junk' or not?