No, not a tale, rather a reflection.
Our physics commentator Rob Sheldon writes to reflect on the many meanings of the word “function” in biology:
If I recall correctly, the original definition of “functional” was whether that piece of DNA was turned into a protein, which depended on finding a “start” and a “stop” codon. The Human Genome Project reported that some 90% of the human genome didn’t have these “start/stop” features, and hence was “non-functional”.
a) However, there was extensive editing of RNA in the “spliceosome” with the removal of introns and customization of proteins such that one “start/stop” strand of DNA could make 100 distinct proteins. So the first piece of news is that the mapping is “one to many”.
b) Since the function of start/stop was to tell the DNA polymerase where to start/stop reading, then the fact that the “spliceosome” is spitting out chunks of RNA totally indiscriminately of start/stop codons, means that start/stop is not a good way to characterize functional DNA. Some pieces were still being transcribed into protein without these markers.
So that led to the second method of defining “functional”. Let’s cut out that piece of DNA using CRISPR (or more likely, blocking it with a small anti-sense RNA fragment). Is the edited critter still viable after that DNA is rendered inoperable?
c) Again, a person is “still viable” without legs, just not very competitive. So what exactly does viable mean? If a bacterium lives for 2 weeks but doesn’t reproduce, is it viable? If a bacterium lives indefinitely in a Petri dish but dies when injected into a host, is that viable? If a bacterium lives in a host but dies when the host runs a fever, is that viable?
So we are back to not really knowing when something is functional or not.
So that led to a third method of defining “functional”. Let’s see if there are any protein strands in the organism that are derived from that piece of DNA.
d) But then we discovered that RNA does a million other things — it builds the ribosome, it brings in marked amino acids, it regulates transcription, it carries information outside the cell. Just because a piece of DNA isn’t converted to protein doesn’t mean that it has no function.
So we are up to our fourth method of defining “functional”. If that DNA is turned into RNA then it is functional.
e) That’s where ENCODE comes in and says that 80% and more of the DNA is converted to RNA, which is where Dan Graur loses it and starts ranting about creationists and TV sets. He builds a toy population genetics model and says that 80% destroys his model, and therefore the data is wrong. (No, he isn’t unique, all theorists harbor dark thoughts about experimentalists.)
f) But as experimentalists showed all the new things RNA does, Dan’s model gets less and less compelling. For one example, a piece of “junk DNA” was found to regulate cancer. When that junk DNA was removed, the organism died early of cancer. It was viable, just not competitive.
My analogy is that DNA is like a tool box. Just because we don’t have a hammer in our hand all day, doesn’t mean that the hammer is junk. When you need a hammer, a screwdriver just won’t do. I’ve used pipe wrenches as a hammer in a pinch, but I’ll tell you, it was ugly. My brother spent ten years as a truck mechanic, and as he would gladly tell you, he was often hired because of his toolbox.
So why should the genome be any different? Shouldn’t the default be that if some item is found in his toolbox, it has a function? Why is Dan Graur so adamant to tell my brother that his toolbox is full of junk? Whose reputation is he spitting on anyway?
Dan Graur had announced in 2014 that he didn’t “do politeness” on this topic so maybe forewarned is forearmed.