Saturday, February 23, 2013

Fisking ENCODE

A recent slew of ENCODE Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is under 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 – 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these “functional” regions, or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly (1) by employing the seldom used “causal role” definition of biological function and then applying it inconsistently to different biochemical properties, (2) by committing a logical fallacy known as “affirming the consequent,” (3) by failing to appreciate the crucial difference between “junk DNA” and “garbage DNA,” (4) by using analytical methods that yield biased errors and inflate estimates of functionality, (5) by favoring statistical sensitivity over specificity, and (6) by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.

--On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE
by Dan Graur, Yichen Zheng, Nicholas Price, Ricardo B. R. Azevedo, Rebecca A. Zufall, and Eran Elhaik

Saturday, February 16, 2013

The Limits of Natural Law

In abstraction from specific religious or metaphysical traditions, there really is very little that natural law theory can meaningfully say about the relative worthiness of the employments of the will. There are, of course, generally observable facts about the characteristics of our humanity (the desire for life and happiness, the capacity for allegiance and affinity, the spontaneity of affection for one’s family) and about the things that usually conduce to the fulfillment of innate human needs (health, a well-ordered family and polity, sufficient food, aesthetic bliss, a sense of spiritual mystery, leisure, and so forth); and if we all lived in a Platonic or Aristotelian or Christian intellectual world, in which everyone presumed some necessary moral analogy between the teleology of nature and the proper objects of the will, it would be fairly easy to connect these facts to moral prescriptions in ways that our society would find persuasive. We do not live in such a world, however.

--David Bentley Hart, First Things (March 2013 issue).

Friday, February 08, 2013

The Middle Ages ... and Your Latest Laptop

Those rules of argument became increasingly complex. Many, after several centuries, now seem almost banal: it is perhaps a testimony to the effectiveness and importance of the foundations laid down in the twelfth century that stages in argumentative processes which then had to be carefully thought through and elucidated are now taken for granted, with stages in the process being skipped as not needing individual proof.... 
It was on these rules that twelfth-century thinkers like Abelard raised their logical and argumentative edifices, with ramifications way beyond the basics of logic. (It was, perhaps, on the basis of teaching such fundamentals that some of them also earned their livings.) The fluidity of the times and the constant flow of novelties meant that everything was always in flux: all resolutions became provisional, because the questions were constantly changing, and the resources available from which to construct a solution changed as well. This constant and continuing challenge to thought was important: it forced development, made old ideas constantly outdated. Abelard, although the most dynamic thinker of his time, was rapidly overtaken and outmoded. The progress of twelfth-century thought in some ways matches the current succession of computer generations. Individuals had immediate impact, but it was often transient, as new ideas came along to supplant them. Once supplanted, they were rarely recalled. 
R.N. Swanson, The Twelfth-Century Renaissance, pp. 110-111.

Now, there's no way to know for sure, eight centuries later, what St. Thomas Aquinas meant when he stopped working on his Summa, after reportedly experiencing a mystical vision, and declared that everything he had written amounted to only just so much straw.

But Swanson's passage makes me wonder whether (in addition to the sheer intellectual exhaustion at this stage of his short life) Aquinas wasn't acutely aware (as Abelard was not) of how quickly his own work might suffer the fate of Abelard's and others.

It didn't of course, at least in terms of its importance for the Catholic Church. But Swanson's passage does bring home a sense of how dynamic the 'flux' of that age was for those living in the center of it.