From: Robert J. Bradbury (bradbury@aeiveos.com)
Date: Mon Aug 11 2003 - 15:56:12 MDT
On Mon, 11 Aug 2003, Anders Sandberg wrote:
> I think you can deal with it in the standard way, it is just that
> you have to calculate information across the entire gene and not
> just single bases ...[snip]
Anders, if you happen to have a standard reference on this I'd
like to know what it is. (Don't go to any trouble with it, I
can probably Google it.) Its been a number of years (probably
decades) since I've looked at the core of "information theory"
so I'm a bit rusty.
> The question is how the mutual information between the DNA and the
> finished protein differs from the mutual information calculated
> purely from codons; this is the real measure of how much information
> "sneaks in". It should be quite observable.
The RNA modifications may not be too different from post-translational
modifications such as glycosylation or perhaps modifications performed
by kinases or other enzymes that add additional atoms or molecules.
But it seems like there is a "multiplier effect" in that a single enzyme
could enhance the information content of a number of different proteins.
I also am not sure that a simple information content analysis based
on base probability will work because the "multiplier effect" probably
often works on the 3D structure and that *isn't* obvious from a
simple analysis of the DNA/RNA. One would need a much higher level
analysis of what 3D "words" mean. There are protein structure and
protein motif databases with some of this information but I don't
believe we are anywhere near understanding the complete "language".
Robert
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