This paper provides an extensive critique of the Encyclopedia of DNA Elements (ENCODE) project and explores the question of whether the data it provides implies the dismissal of the concept of junk DNA.

Doolittle attempts to uphold the notion of junk DNA by reviewing the evidence and literature which construct the theory and by defending its existence and significance in light of the work done by ENCODE. A large part of the author’s argument also grapples with the changing definition of the word “function,” which he argues should be upheld to its traditional understanding in its application to genetics.

At the center of the issue of junk DNA is what is known as the “C-value paradox,” which is the notion that quantity and intricacy of genetic information do not correlate to the complexity or “advancement” of an organism. The C-value refers to the content of haploid nuclear DNA, a quantity which can be applied to the comparison of organismal genomes.

Junk DNA comes into play here in providing an explanation for the lack of proportionality between an organism’s complexity and its genome size – large amounts of this genome were thought to have little to do with reproduction or survival. The author maintains that, despite ENCODE’s work claiming the majority of the human genome to have some sort of biochemical “function”, the junk DNA concept is still applicable and should be upheld based on our understanding of genetics and definition of “function”, and that ENCODE’s interpretation of their data is problematically anthropocentric and applies an inaccurate ontology allowing for the sensationalist claims that the idea of junk DNA has been debunked.