Re: DNA carries information


"Friar Broccoli" <EliasRK@xxxxxxxxx> wrote in message news:1156098296.075392.240620@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Perplexed in Peoria wrote:
"Friar Broccoli" <EliasRK@xxxxxxxxx> wrote in message news:1156088418.946849.215670@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
[snip]
For me, only something which is possibly substantive can
have properties, I simply could not imagine what you were
describing without its being explicitly spelled out.

My future intentions:

That said, I BELIEVE (and will (sooner or later) have a shot at
proving (probably in a vague handwaving sort of way)) that
information is a physical property of matter via its connection
with entropy/eXergy. This in the same way that elements (like
hydrogen and aluminum) are properties of matter due entirely to
their physical organisation of elementary particles.

Some things to think about as you set off down this path:

Answering quickly, something I rarely do, and almost always
regret:


John's paper begins with an epigraph from Weiner: "Information
is information, not matter or energy. No materialism which
does not admit this can survive at the present day." This is
true, of course, but it doesn't go far enough. Not only is
information different from mass, and extension, and Gibbs free
energy, and thermodynamic entropy, and other properties of
objects; it is 'contained in' objects in a completely different
way from those other kinds of properties. So, it seems to me
that the first step is to disentangle just how a claim that
a particular DNA molecule contains a certain amound of information
is different in kind from a claim that the DNA molecule has a
particular mass.

On its face this seems easy (at least indirectly).
I don't know about mass, but I would compare information as a
property with colour as a property. Although it is possible to
confuse the issue A LOT, something I frequently do, red has
well defined measurable physical parameters.

On a butterfly wing, the colour property is changed from red to
yellow to blue etc by simply changing the arrangement and/or
spacing of the molecules on the surface, thus a "property" is
changed by the mere fact of molecular reoganisation (or even
viewing angle). Not a lot different from reorganising words in
a sentence to achieve a new meaning.

Finally, your example of Mass is (I believe) highly
uninformative because no one has the slightest idea how to
account for mass as a fundamental property. Thus for the
purposes of analysis it is like invoking magic. We just cannot
say anything about it.


Another epigraph could probably be found to the effect that
observations and measurements are 'theory laden'. [Anyone
know a good original source for this epigraph?] And, from
relativity theory and other sources, we are aware that the
results of a measurement of even the most fundamental and
'physical' properties of an object may depend upon the
reference frame of the observer. Well, that is enough for
me to claim that there simply are no simple concrete properties
of objects. All properties are, in John's unfortunate words,
"in the head".

The fact that measurements are reference dependent does not
mean the measurements are meaningless, or that we cannot figure
out what the measurements would be in a different frame of
reference.

Right. And by the same mode of reasoning, carried just a bit
farther, I would suggest that John's denigration of information
as "in the head" misses the point. Things which make sense
only in the context of a model are no less objective and no
less useful than things which are less model-dependent. In
fact, if you want to be purist about it, nothing is completely
model-independent.

But information is even more "in the head" than is mass or
Gibbs free energy. Consider that to quantify information,
one first assigns a set of a priori probabilities, and then
computes a summation over an ensemble of 'alternate worlds'.
An information-theoretic quantity is not just dependent upon
our model of this reality, it is dependent upon a model of
a system of alternate realities.

I'm not sure but I think that all you're saying here is that
information is not the same information in a different frame of
reference or within a different Information Processing Unit
(IPU). So for example information in an old Apple would (most
likely) be garbage in an IBM and vice-versa.

No, my point was different. It was more like if you only have
one Apple, then quantifying its "information content" is impossible.
But if you have an ensemble of Apples, then you can quantify
the information in any one of them by looking at the things that
are different between them. Aspects of an Apple that are the
same in all Apples (for example, the memory patterns that implement
the bios) are not to be counted as information, by some definitions
of 'information'.

This was the point of proposing "efficiency" as a test/measure
of information content, because information is only efficient
within the context of the appropriate IPU. So (begging the
question) if DNA is information then the
cell/organism/species/ecosystem is(are) the IPU. A mess, I
agree, but that doesn't mean it's false.


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.

For an analogy to a different concrete metric - volume - I
would invite you to consider the 0.5 liter pickle jar in my
refrigerator, which is currently half full, of used cooking
oil. What is the volume?

Of what, the jar, the oil, or the remaining air.
I have no idea what your point might be here.

My point is that you seem to be focusing on one of several
possible meanings of information. If you wish to talk about
the volume of the contents, then you will have to make clear
that you are not talking about the volume of the container.
And if you seek to explain qualities of the contents - if
you want to talk about how the information in a genetic
sequence TATAUUCG is different information than that in
GCATGGCA, then you need to make that clear to someone who
wants to think that both sequences contain the same amount
of information - 16 bits.


.

Loading