Is the idea of junk DNA finally dead?

I think Ohno coined the term “junk DNA” and certainly it is not true that no one used it (see article link above). At first, I think Ohno had in mind pseudogenes, which certainly appear to be either once functional genes that have become damaged and nonfunctional such as the GULO gene in the vitamin C pathway or “genes” that were reverse transcribed from mRNA back into the genome (processed pseudogenes). The best way to understand the junkiness of junk DNA is to understand what the various components are and do. Much of the “junk” consists of repetitive DNA, LTR type transposon and Non LTR types. LTRs are signature retroviral sequences at each end of the retrovirus. Humans contain endogenous retroviral sequences (HERVs) in their DNA. Lines and Sines are Non-LTR retrotransposon where Lines are autonomously replicating fragments that can copy themselves and Sines are not autonomous. Then we have transposons that hop from one place to another. These moveable genetic elements can do damage. There are a number of examples of human genetic diseases where transposons have inserted themselves into functional genes and disrupted the gene. Endogenous retroviruses have been implicated in cancer – for example breast cancer – although that is controversial. Mostly however people have thought that the ability of these sequences to proliferate has expanded the DNA content of the genome as examples of “selfish DNA”. Recently however, cases have been identified were these repetitive sequences have become inserted in introns or near genes and serve to regulate gene expression. So far these examples are rather sparse and are consistent with an evolutionary scenario.