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The difference between mathematics and biology …


Earlier, I called attention to this longish but very informative article by Carl Zimmer, “Now: The Rest of the Genome” (The New York Times, November 11, 2008). It pretty much blows the genetic reductionism I grew up with out of the water. The “gene” – that little coil of sugar that ran our lives back then – is a dead idea.

Now here’s an exchange that caught my attention:

“The way biology works is different from mathematics,” said Mark Gerstein, a bioinformatician at Yale. “If you find one counterexample in mathematics, you go back and rethink the definitions. Biology is not like that. One or two counterexamples — people are willing to deal with that.”

More complications emerged in the 1980s and 1990s, though. Scientists discovered that when a cell produces an RNA transcript, it cuts out huge chunks and saves only a few small remnants. (The parts of DNA that the cell copies are called exons; the parts cast aside are introns.)

Actually, the biologists flatter themselves. They underbussed vast discrepancies between their belief system and the evidence – along with lots of people who insisted on discussing their implications – until finally, the system is collapsing in the gene’s “identity crisis” (Zimmer’s phrase).

Thomas Kuhn was right. Old paradigms don’t get disproven; they collapse from their own unworkability.

One thing about this article, it is mercifully free of rubbish about evolution.

We actually don’t know what most of the stuff in the genome does. So why not wait until we do know before we begin to describe its history? That will save a lot of rewrites down the road, maybe inconvenient ones.

(Note: Re the business about cutting out huge chunks and saving only a few small remnants … Brings back memories. We textbook editors used to do that when we were racing a deadline. We would copy a whole chapter from the master copy of the manuscript to date, and then select only a few pages for which final revisions had been ordered. Then we just recycled the rest of the pages of the chapter. Wasteful? Yes, of paper. But not of time. Under deadline panic, the most important quantity was time, not paper. And we knew from experience that our method was slightly faster. So I would recommend caution to anyone making claims that such methods show that the system cannot be the product of design.  When we editos did it, that’s precisely what it was – design.)

O'Leary, That makes a lot of sense! Thanks for the explanation. :) On the idea of languages within genetic coding: I find it funny that SETI proponents would suggest that if they found a language or code from outer space it's a sign of intelligence. But we find a code inside DNA (one way more advances than any we've ever devised) and it's explained as the process of natural selection and random mutation. Talk about double standards! Domoman
Denyse: about cutting out huge chunks: the role of introns in eukaryotes is really puzzling. They represent about 37% of the whole human genome, vs 1,3% represented by the protein coding genes. Each protein coding gene is fragmented in exons, a mean of 8-9 per gene, and up to 145 for a single gene. That's really amazing. It is rather certain that introns are functional, and that they have a regulatory role. The real problem with noncoding dna is that nobody really understands how it works. While we can interpret protein coding genes, because we know the symbolic code, we understand practically nothing of how the "noncoding" code is written. We have just glimpses of some regulation effects, and nothing else. Maybe non coding DNA, including introns, contains the "procedures", but how are they written? At present, we just understand the gross code of the gross effectors, the proteins, but almost nothing about the procedure code. gpuccio
For years I've been thinking of the gene as a template that can be instantiated in various forms when combined with other information. Or perhaps an information holder for interlocking data. I also believe that many aspects of the resulting physiology are not exactly specified like a blueprint. Instead it's a combination of semi-static information and dynamic functions. Personally I think the idea of the gene is fine as a conceptual working model that must be adjusted over time as research continues. The problem comes about if people begin thinking the model trumps reality. This holds true for the ID community as well. Quite frankly we only are making very rough estimates when it comes to calculating information content. Patrick
Hi, Domoman, Maybe the problem with genes is this: If we assume that the genome is a language that utters living beings, we can possibly compare it to a word in a human language. Some might insist that a word must have only one meaning. The dogmatist feels safe with that, for sure. It has the unvarying certainty of bricks in a building. But consider words like "way" or "right" or "down" ... The dogmatist is little help to people trying to interpret a string of text. My own view is that the idea of the "gene" won't die out but will come to be understood as more similar to a "word" in a language. That is, its function depends on what it is doing where it is. And, of course, languages arise all the time without any design or intelligence at all, right? O'Leary
O'Leary, why were so many scientists obsessed with keeping genes alive? I don't see the problem with just letting the idea of genes die out. Perhaps this is because I'm in favor of ID though. Domoman

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