Passage A:

For decades, the vast stretches of the human genome that do not encode proteins were dismissed as junk - evolutionary detritus tolerated because it exacts no appreciable cost. That verdict now looks premature. Comprehensive biochemical surveys have assigned reproducible activity to the overwhelming majority of the genome: segments are transcribed into RNA, bound by regulatory proteins, or marked by chemical modifications associated with the control of nearby genes. If activity is the signature of function, then function, not junk, is the rule. The inference is bolstered by a developmental argument. What distinguishes a human from a nematode is not a dramatically larger repertoire of protein-coding genes - the counts are broadly comparable - but the intricacy with which those genes are deployed across tissues and across time. That intricacy demands an elaborate regulatory apparatus, and the noncoding genome is precisely where such an apparatus would reside. Enhancers, insulators, and the templates for regulatory RNAs are exactly the sort of elements that leave biochemical footprints without themselves coding for proteins. Skeptics reply that biochemical activity is cheap and therefore uninformative: a polymerase may transcribe a sequence adventitiously, without the cell making any use of the product. But the burden of proof runs the other way. When a sequence is reproducibly transcribed in particular cell types, bound by particular factors, and modified in patterned ways, the parsimonious reading is that the cell is doing something with it. To presume otherwise - to treat pervasive, patterned activity as systematic accident - multiplies improbabilities needlessly. The genome should be read as an instrument most of whose parts are in use, until a positive case for silence is made for a given stretch.

Passage B:

That a stretch of DNA is transcribed, or bound by a protein, tells us what it does biochemically; it does not tell us whether the organism needs it. Function, in the sense that matters to biology, is defined by selection: a sequence is functional if its specific composition is maintained because the alternatives are weeded out. By that criterion the evidence is unambiguous. Cross-species comparison shows that only roughly a tenth of the human genome is conserved - protected from the steady drift of mutation - while the remainder diverges at the rate expected of sequence under no constraint at all. The appeal to biochemical activity mistakes a byproduct for a purpose. Transcription is leaky; regulatory proteins bind degenerate motifs that occur by chance millions of times over. A genome need not be an efficient instrument. Consider that the onion carries a genome five times larger than a human's, and that closely related plant species can differ severalfold in genome size with no corresponding difference in complexity. If every transcribed base were functional, such variation would be inexplicable; under the view that most noncoding DNA is tolerated rather than used, it is exactly what one expects. None of this denies that important regulatory elements lie outside the coding regions - they plainly do, and identifying them is real work. The claim is narrower and firmer: pervasive activity is not pervasive function, and the fraction of the genome that selection actively maintains remains small. A sequence earns the title functional by being defended against mutation over evolutionary time, not by being chemically busy in the present.