While going through various discussions on non-coding DNA, I realized that some of the confusion is possibly caused by dual use of the word ‘coding’. Yan Wong explained it elegantly in the sandwalk blog -
I think the root is a grammatical confusion between “coding” in the sense of computer code, and “coding” in the sense of the 3-letter mapping between DNA and aa (the “genetic code”). It was perhaps an unfortunate choice to call this mapping “the genetic code”, as it implies to the layman that all functionality comes through this route. Perhaps a less leading phrase would be “translated DNA”?
Those coming from computer world may not realize that with the genetics definition of ‘coding’, ‘non-coding’ is not synonymous to non-functional. Many components of non-coding genome are functional and that is known for decades.
Known components of non-coding DNA (from the sandwalk blog) -
ribosomal RNA genes
genes for small RNAs (e.g spliceosome RNAs, P1 RNA, 7SL RNA, linc RNA etc.)
5’ and 3’ UTRs in exons
SARs (scaffold attachment regions)
origins of DNA replication
regulatory regions of DNA
transposons (SINES, noncoding regions of LINES, LTRs)
In fact, those components are so well known that sandwalk blog even includes the relative percentages of various categories of non-coding sequences in the human genome in another post.
When Francis Collins and the ENCODE clowns funded by him make statements like the following, they make complete mockery of the scientific process.
In January, Francis Collins, the director of the National Institutes of Health, made a comment that revealed just how far the consensus has moved. At a health care conference in San Francisco, an audience member asked him about junk DNA. We dont use that term anymore, Collins replied. It was pretty much a case of hubris to imagine that we could dispense with any part of the genome as if we knew enough to say it wasnt functional. Most of the DNA that scientists once thought was just taking up space in the genome, Collins said, turns out to be doing stuff.
The consensus has moved based on ENCODE science or junk science, and not real science. One can easily go through various components in sandwalk’s list and their relative percentages to see whether any of them is shown to be functional unlike before. Transposons, members of the biggest group, are ‘doing stuff’, and that ‘stuff’ is to invade other parts of the genome to grow in number. Has anyone shown any other function for a large percentage of transposons? The scientific evidence is not there, but that does not Collins from making false statements.