Lambda the Ultimate

NYT obit.

It's been occurring more and more to me lately that one of the astonishing things about being in computing is that most of our intellectual heros are still with us. Of course in theoretical CS that's a bit less true (Alonzo Church, Haskell Curry, and especially tragically, Alan Turing have all passed). But otherwise it's sufficiently true that it's a shock to my system when we lose an Admiral Grace Hopper or an Edsger Dijkstra. It's hard for me to be reminded that the pantheon of my field more closely resemble Norse gods than Greek ones: they're mortal.

So it is that I note the passing of Dr. Crick, certainly one of the most notable members of the larger pantheon of science. Defining what biological life is at its core, and the structure of its most significant constituent, obviously qualifies as one of the greatest scientific achievements of all time. While not being a member of Dr. Crick's field, I can truthfully say that his commitment to the application of the scientific method to the betterment of mankind, and his keenness of insight into his chosen field, will be sorely missed by us all.

A chemistry professor kindly uploaded an outline summary of DNA. The kitty pictures demonstrate that clones are not identical.

Google managed to hunt down the missing junk DNA article cited in the outline.

Contrary to what the headlines say, the genome has not yet been decoded. It might never be, as the genome now does not appear to be a code at all in the conventional sense. It turns out that genes are not simple "strings," each one encoding for one message, but are combinations of separated segments along the genome. Between them lie intervening segments which can be cut out by the cell, as it translates DNA into proteins, and the relevant or coding parts...can be put together in numerous different ways. Gene[s]...send different messages and make a variety of proteins as the occasion demands.

Imagine that an intelligence service were to discover some unintelligible messages being sent by a spy. At first the intelligence agents naturally assume they are looking at a code. They assume the task of decoding will be straightforward. But on closer analysis it turns out that the message means one thing if the signal has been received and acted upon, another thing if it has been received and not acted upon, another thing if the receiving apparatus is not switched on, and so on. Rather than just a code the message is a bit like a set of rules for a rather complex interactive game. There are feedback loops, and circuits within circuits, and a lot of things happening inside the cell but outside the genome, in the unfashionable realm of cytogenetics. NIH-funded geneticists don't even want to think about that, because they thought that by sticking to the four nucleotide bases, they had the problem neatly "digitized." Computers would hum away unaided, 24 hours a day, and unravel the mysteries for them while they slept....

I asked Watson if one gene can give rise to ten proteins. "Some genes can give rise to 50 different proteins," he said. No problem!

This writer seems to have spent much time interviewing DNA experts. A more recent article reports that

HUMAN DNA IS A GREAT STRING of four nucleotides, three billion letters long. Some of these sequences -- the "coding regions" -- are called genes. They control the construction of proteins in the body. But far greater stretches of the same DNA are "non coding regions," and for many years they were called "junk." That was the word scientists used. Junk DNA had no function and could be ignored. These enormous sequences, amounting to 98.5 percent of the whole genome, were dismissed as the accumulated rubbish and detritus left behind by the constant trial and error of evolution.

Now the white-coats are beginning to suspect that they made a mistake.

The Google search spotted another article on sociobiology of more general interest.

None of the above disparages Francis Crick's monumental achievements. LtU readers might just be curious about our current knowledge of DNA as an information coding system.

Tha Salk news release.

Crick wrote an excellent autobiography, What Mad Pursuit, saying quite a bit about what it takes to do good research (though a lot of it's specific to theoretical biology). The style reminded me of Dijkstra's, going for simple clarity. In the last chapter he described why and how he switched his field to visual consciousness -- I'm sad that he didn't live to see more of the answers.