The 20th anniversary of the human genome sequence: 5. 90% of our genome is junk

This is the fifth (and last) post in celebration of the 20th anniversary of publishing the draft sequence. The first four posts dealt with: (1) the way Science chose to commemorate the occasion [Access to the data]; (2) finishing the sequence; (3) the number of genes; and (4) the amount of functional DNA in the genome.

Back in 2001, knowledgeable scientists knew that most of the human genome is junk and the sequence confirmed that knowledge. Subsequent work on the human genome over the past 20 years has provided additional evidence of junk DNA so that we can now be confident that something like 90% of our genome is junk DNA. Here's a list of data and arguments that support that claim.

• Evolutionary theory; Modern evolutionary theory includes Nearly-Neutral Theory and the importance of random genetic drift. This accommodates the presence of large amounts of junk DNA and removes the old objection that natural selection would have removed non-functional DNA.
• The C-value paradox: The fact that different related species can have very different genome sizes was a paradox 50 years ago but it is easily explained by junk DNA. The Onion Test is now a powerful tool in refuting most claims of function in our genome.
• Transposons: The human genome sequence is littered with fragments of defective transposons that take up as much as two-thirds of the genome. These fragments are obvioulsy mutated versions of once-active transposons that became established millions of years ago and subsequently degenerated. They are junk.
• Introns: About 25% of our genome is located in introns and introns are almost entirely junk DNA.
• Sequence conservation: No more than 12% of the genome is conserved and the best current estimate is about 8%. Since sequence conservation is our best measure of function, this means that less than 10% of the genome is functioal.
• Genetic load: Our species cannot survive if the number of deleterious/lethal mutations per generation is too high. The resulting genetic load (mutation load) would soon lead to extinction if there were more than a few deleterious mutations per individual per generation. Geneticists have known for more than 70 years that, given the best estimates of mutation rate, the human genome is too large if all of the genome is functional and that led to predictions that we only have about 30,000 genes and much of our genome is non-functional so that mutations in that fraction do not contribute to mutation load. These predictions turned out to be correct; our species is viable because most of our genome is junk.

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