Re: DNA carries information
- From: r norman <r_s_norman@xxxxxxxxxxxx>
- Date: Mon, 04 Sep 2006 17:41:08 -0400
On 4 Sep 2006 13:37:47 -0700, "Friar Broccoli" <EliasRK@xxxxxxxxx>
wrote:
Perplexed in Peoria wrote:
[extensive snipping]
And, as a final caution, I would urge you to be clear on
the distinction between three things, all of which are
sometimes called 'information'. One is information as
capacity, one is information as quantity of contents, one
as information as distinctive quality of contents.
The information (I am speculatively asserting) is the degree to
which a user (an IPU) can act efficiently based on the
measurement in whatever form presented. Thus there should be
no need to account for such distinctions.
Well, then it seems that you are maybe defining "fitness" rather
than information. Take a look at this paper:
The Fitness Value of Information
Carl Bergstrom and Michael Lachmann
http://arxiv.org/PS_cache/q-bio/pdf/0510/0510007.pdf
which shows how fitness and information can be related.
Right now, I am feeling particularly uninspired by this topic,
but I absolutely wanted to get back to you on this.
During the last 2 weeks I have swung back and forth on the
question of whether their "fitness value" of information is the
same thing that I mean by "efficiency value" but I now think it
is.
I think I was confused because they treat an IPS (apparently
always a complete organism) as a black box, and never ask
anything about the internal workings. Since we were focussed
on a detail (DNA), it took me some time to develop a coherent
model.
I was disturbed to notice that "fitness value" highlights a
weakness, I had hoped "efficiency" would overcome. If someone
is a good liar, then he can be very fit if the measure of
fitness is making money, or self-replication. Thus, false
information is information.
Although it remains possible to distinguish a Ray Martinez
sentence (which is either unconvincing or just incoherent) from
an rnorman one, the inability to get rid of false info
is annoying.
I am also not too sure what the authors have actually done. Dr
Norman has been arguing that entropy and information are not
necessarily the same thing (or in the same class), just because
they follow the same mathematical rules.
So what does showing that some fitness values follow Shannon
information logic really show?
Is a mathematical model like an analogy? Things are the same
only when the entire model can be overlain from one system to a
second?
On the other hand, I don't think that asking if two different
(even identical things) are the same is a meaningful question.
On that confusing note:
So you made me read the Bergstrom+Lagstrom paper, too. It is an
interesting ecology-type analysis of fitness, but there is essentially
zero in it which might be appropriate to whether DNA carries
information. The information they consider deals with gaining
information about the environment, and is completely abstract,
completely conceptual. There is no notion of looking at, smelling,
tasting, making any measurement on the environment, nothing at all
like that. Only the fact that "knowledge" of the environment given
that the environment is variable, helps evolution select an
appropriate strategy for selecting phenotypes to deal with that
environment.
The paper's introduction opens with a paean to information: "Living
organisms acquire, store, process, and transmit information and as
such, information is a central organizing principle in biological
systems at every scale from the digital coding in DNA to the
long-range calls of cetaceans" citing John Maynard Smith. The idea of
information in biology. Quart Rev Biol, 74(4):395-400, 1999.
Unfortunately, it really doesn't say anything. This is the kind of
talk that seems to drive John Wilkins crazy. I accept it since I
believe in the 'information processing' ability of higher level
complex systems even though the molecular processes run perfectly
fine with the notion.
However the true state of the paper is represented by its closing
argument in the conclusion section: "... we should take
a closer look at the concept of information: information is the
reduction of uncertainty, where uncertainty measures the number of
states a system might be in. Thus mutual information between the world
and a cue is the fold reduction in uncertainly about the world after
the cue is received." Given this definition, it is not surprising
that Shannon information and the entropy measure emerges because that
is exactly what those computations evaluate. Then, later, "We can
now see why the concept of information is the same across different
disciplines. In biology, fitness refers to the fold increase in the
number of surviving lineages. In communication theory, information
refers to the fold increase in the number of messages to encode. In
physics, entropy refers to the fold increase in the number of possible
states in phase space."
In this context, the information "encoded" by DNA is the reduction in
uncertainty in the type of organism produced by the expression of that
DNA. If two sequences result in the same phenotype, the differences
between them carry no information And you must look at the actual
final organism in toto, not merely at the amino acid sequence of a
single peptide if you want information in an evolutionary sense. If
two sequences produce essentially the same "kind" of organism (i.e.
with the same fitness in identical environments), then the differences
in their genome carry no information. The problem is that there is an
enormous set of sequences all of which produce essential the same
living product and at this time we have no real way of cataloging
these. We can only identify specific changes that result in
distinctly different phenotypes, but without the complete set of
possibilities, without knowing the "phase space" under consideration I
don't see how to quantify the "information content" that we can
identify.
.
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