14. Hooptedoodle 3: The Seductive Gene

“Scientists crack ‘entire genetic code’ of cancer

So, in the much simpler programming terms: the scientists now just have to determine which of the 23,000 identified errors, or combination of some subset of the 23,000, causes the undesired system behaviour. There are more candidate subsets than atoms in the Universe (even if we assume the simplification that the temporal order of occurrence of the accumulated errors is not a significant factor). In addition, we note that this is the DNA of one individual, and therefore there is no general problem (such as which errors, in general, trigger lung cancer) until many more lung-cancerous genomes have been sequenced and the common errors among the 23,000 have been identified. This strategy for homing in on the likely suspects further assumes that there is a general lung-cancer disease whose genetic causes are being sought. Each example may be individual, or any intermediate option between totally general and totally individual. If this is not daunting enough, we might also note that significant causal factors may be external to the genome itself.

L. D. Stein’s Nature article (see note 9, below) begins by explaining the ‘unfinished’ nature of the human genome sequence work.

The research, published in the Journal Stem Cells and Development, was conducted by scientists at Newcastle University and the North East England Stem Cell Institute.

N. Dillon, Nature 425, 2 Oct. 2003, p. 457.

The information coded into the body of the computer can with reasonable assumptions be ignored, and is easy to discover at any rate. We know, after all, what wires are. But the information encoded by the body of an organism can NEVER be ignored, there’s a lot more of it than there is information encoded by the genome, and we have very little idea how to specify any of it. We can’t predict protein folding. We can’t model metabolism. In any really interesting case, we can’t even measure a metabolic state, at least not without perturbing it so badly we have no idea what the next state would have been. We do not know, and cannot find out, the biochemical history of any given organism, so there is no sense in which we can predict the current biochemical state of any organism’s body, or even any one its cells, from some hypothetical initial state. So even if the genome was TRIVIAL, we’d still be totally in the soup.

The issue of ‘junk’ DNA is constantly under review. In 2004, M. Peplow (Nature, 21 October, p. 923) stated that “More than one-third of the human genome, previously thought to be non-functional [i.e., junk], may in fact help to regulate gene expression …”.

D. Bentley writing in Nature in 2004 (27 May, p. 440) suggests that it was perhaps “premature to write noncoding DNA off as ‘junk’, and so it has proved” for among other things, “it maintains short-range and long-range spatial organization of sequences”.

In his article “The End of the Beginning” (Nature, 21 October, 2004, pp. 915–916) L. D. Stein begins to acknowledge the enormity of the new task of decoding the genome; he wrote:

In sequencing the human genome, researchers have already climbed mountains and travelled a long and winding road. But we are only at the end of the beginning: ahead lies another mountain range that we will need to map out and explore as we seek to understand how all the parts revealed by the genome sequence work together to make life.

S. Bottomly, Bioinformatics: smartest software is just a tool, Correspondence, Nature 429, 20 May 2004, p. 241.