🚀 go-pugleaf

Ken Muldrew (kmuldrew@acs.ucalgary.ca) wrote:

: (I seem to be suffering now from the same sort of
: confusion that I get when I think about 'communication' theory and
: 'information' theory--I suppose what I really need is to learn more
: about both rather than dwell on my confusion about the difference).

My understanding is that "communication theory" is the name Shannon originally
used but that it was realized by people that the same mathematics applies to
many systems and so is now called "information theory".  Does anyone else have
an idea about this?  On page 173 of Shannon1993 (as listed in the faq) he seems
to use the two interchangeably.

: First is the structural component. The human genome is *enormous*.
: There is some sophisticated house-keeping required just to pack it
: into the nucleus of a cell, let alone maintain it in perfect
: condition. ...

Good point and nicely put.

: The information as to where to
: cut and splice these sequences has to be coded somewhere and the
: introns just happen to be at the right place at the right time. Since
: RNA is single stranded, it can (and probably does) fold in on itself
: to form hydrogen bonds. The introns probably contain sequences which
: allow for specific tertiary structures to form which are then
: recognized by splicing proteins (look at a picture of a tRNA to get an
: idea of what I'm talking about here).

Although you are right that there are structures, I think that the majority
of the sequence conservation for locating the boundaries between introns
and exons is simple pattern in the sequence.  See:

  http://www-lmmb.ncifcrf.gov/~toms/paper/splice

(especially pages 31 and 32) for a detailed information analysis.

: Another idea is that the DNA replication machinery was built to handle
: genomes which are much smaller than in eukaryotic organisms. Thus the
: error rate which was built into the system (it's the same machinery
: for all living things) was designed to introduce novelty at a rate
: which was consistent with a smaller genome. There will be a certain
: critical size for the genome, beyond which, the errors introduced by
: copying will corrupt the genome too quickly (ie. there will be too
: many errors introduced into the genome to make a viable offspring).
: Thus the non-coding DNA is there to absorb mutations. If a point
: mutation occurs every 10^9 bases (I think the copying errors are about
: 1 in 10^6, but there are proof-reading enzymes which improve this),
: then you spread your gene out so that maybe you only get half the
: mutation rate within the coding region.

Shannon's channel capacity theorem says that the copying error can be made
small enough to be tolerable.  See:

  http://www-lmmb.ncifcrf.gov/~toms/paper/ccmm
  http://www-lmmb.ncifcrf.gov/~toms/paper/nano2

In the famous little book:

@book{Schroedinger1947,
author = "E. Schroedinger",
title = "What is life? the physical aspect of the living cell
\& Mind and matter.",
publisher = "Cambridge University Press",
address = "Cambridge",
year = "1947"}

I seem to recall that Schroedinger did some calculations about the target size
of DNA for radiation.  The point is that you can't "hide" because if you
increase the total genomic size, the important genes are still going to be hit
at the same rate because they still present the same physical cross section to
radiation.  Also, the polymerase won't make fewer mistakes in one place just
because it (or an entirely different molecule) also has to function at another,
as this may be mostly from thermal noise, which is everywhwere.  Further,
increasing the size increases the likelyhood of generating binding sites that
sop up proteins from where they are needed.  (The system can eventually evolve
to get rid of many if not most, but the probability of them coming up randomly
is increased.)  Finally, increased size increases the likelyhood of damage to
the long fragile molecule.

  Tom Schneider
  National Cancer Institute
  Laboratory of Mathematical Biology
  Frederick, Maryland  21702-1201
  toms@ncifcrf.gov
  http://www-lmmb.ncifcrf.gov/~toms/