ABOUT DNA FOLDING

A comment on this item in the TED blog: http://blog.ted.com/2008/09/the_immense_pro.php

What speaker Paul Rothemund says is utterly absurd and flies in the face of the bulk of discoveries and developments in genetics and genomics of the last 20-25 years and completely ignores all we know now of the risks and faulty scientific assumptions of genetic engineering.

Especially sad and embarassing is his analogy of genetics to computer programming. Such an analogy would have been fine 30 years ago, as it parts from some very simplistic and obsolete assumptions about biology.

Rothemund is blissfully unaware that genes are not independent, context-free units of information. DNA strands are folded in chromosomes in very particular ways, and these are not arbitrary. Changes in the folding can have dramatic effects on transcription, and can therefore result in a cascade of unwanted and unforeseen effects.

To say that it does not matter how DNA is folded is just as absurd as saying that it does not matter how proteins fold. We know now that how a protein is folded matters an awful lot. The best example of this is CJD/mad cow disease. The prion protein responsible for this disease is pathogenic because of the way it is folded. A mere reading of its aminoacid sequence would not reveal anything unusual or dangerous about it.

In few words: when it comes to DNA and proteins, position and shape do matter an awful lot.

A biologist friend of mine commented:

I've only watched a portion of the video, but DNA folding isn't 'magic.' It turns out that many of the regulatory functions of DNA are not controlled at the level of the sequence, but by the 3 dimensional orientation of the nucleotides in space. The folding of DNA into its 3D structure is not random, but mediated by a host of regulatory proteins and structures that are just beginning to be understood. Nanotech scientists are interested in finding ways to control and manipulate this process to, in the words of the blog post, "create tiny machines that assemble themselves from a set of instructions." This is still a rather speculative proposition. This lecturer's approach is mechanistic and reductionist to the extreme; honest biologists have rarely taken this "life as computation" paradigm seriously, but it's still very fashionable among software engineers and researchers.

The most accessible article on the role of DNA folding in biology, and how it defies the mechanistic outlook of biotechnology, is still Barry Commoner's classic piece in Harper's Magazine from Feb. 2002.
(http://www.saynotogmos.org/dna_myth.html)

May I also suggest "Blinded by the Gene" by GRAIN: http://www.grain.org/seedling/?id=239