Dear FISers:
Posted below are the closure post and responses by Karl and John. H.
Apparently my views of bionetworks gave karl indigestion. I hope you
have recovered your usual good - humor by now.
I must say in advance, karl, that you risk further indigestion by
reading the remainder of this post!
As I continue my exploration of the interrelations between
bionetworks, mathematics, information and philosophy, I am enjoying
creating innovative positions based on syllogisms connected to the
atomic numbers. Recognition that this symbol system developed its
own unique form of grammatical sentences and syllogisms opens new
opportunities. Karl's responses gave me a hearty laugh.
At the root of this activity is a simple fact, Karl.
Atomic numbers were created by the chemists for logical descriptions
of empirical material observations of networks of relations, both
biological and non-biological relations. Our understanding of these
numbers lead directly to our understanding of DNA as the genetic
material and as a source of genesis of life itself.
In order to understand the usage of these numbers, one must recognize
that chemists also developed and perfected proof methods; methods
that are syllogistic and parallel to the proof methods of mathematics.
My closure comments emerged from consideration of these facts, as
stated in various forms during the discussion.
Karl. if you wish to disagree with these facts, please state your
reasons.
Merely posting negative comments may relieve your indigestion, but
fails to contribute to the growth of the community.
Merely modifying my grammar to fit your personal philosophy does not
communicate anything to me except the absence of capacity to follow
rational arguments.
Firstly, I view all chemical processes as electrical flows.
Apparently you view electrical flows as something connected solely
with the central nervous system. I suggest you talk to an electro-
chemist and learn about the intimate relationships between the
historical development of electrical concepts concomitantly with
chemical concepts. Have you not heard of batteries?
Secondly, the language of chemistry was developed by the chemical
community to express empirical observations. If you wish to
subscribe tot he narrative of physics and mathematics, then you
should show - or, are obligated to show, that the the information of
DNA can be calculated using Shannon information, or, that you can
calculate the number of isomers of organic molecules or that
biological species are distinguishable in such language.
In other words, the absence of correspondence between arithmetic
operations of mathematics and the operations of valence and covalent
bond re-arrangements are well known. Or, have you solved these
problems, Karl?
With regard to the third issue raised by Karl, you ignored the word,
"typically". Please read more carefully.
With regard to the fourth issue, Karl, please give us your methods of
calculating the information content of DNA as a molecule
participating in the genesis of a biomolecular network.
Karl, while I think that you express a philosophy held by many, if
you wish to disagree with my closure, then the appropriate way to do
so is to develop your arguments such that they are persuasive. Give
us your reasoning, not your bouts of indigestion!
----------
John:
You raise questions about consciousness, a very difficult problem
indeed.
In recent years, numerous philosophers have attempted to explicate
conscious phenomenon, using the languages that they understand or at
least, know the nouns.
In order to have a concrete abstraction about consciousness, one must
be able to do calculations, not merely use nouns in sentences.
This topic is far beyond the scope of biomolecular networks.
Consciousness is just one of the many emergent properties of certain
(not all!) bionetworks. I have little to say except that for eight
years I worked in the NIH Neurology Institute developing drugs for
brain diseases and for the past ten years I have been affiliated with
the Krasnow Institute for the study of Consciousness. I recommend a
healthy attitude of skepticism!
One example suffices.
If the nature of consciousness is a superposition of quantum states,
why does think normally during an MRI scan?
The reasoning is simple. The extremely strong magnetic field of the
MRI re-aligns the atomic nuclei. New quantum states are formed and
differences measured. If consciousness depends on quantum states,
why no noticeable differences in thinking?
(Does anyone have a plausible explication for this disappointment?)
Finally, fundamental questions are inherent in your questions as to
the issue of the nature of information.
Is information a unitary concept? If so, why? If not, why not?
Is information a concrete abstraction? Or, merely a conscious
abstraction?
Is information individual? Or. is it a universal?
Is information a symbolic logical system? Or, merely a collation of
symbols?
Once again, I bid adieu.
Cheers to all.
Jerry
On Feb 23, 2006, at 2:15 AM, fis-request@listas.unizar.es wrote:
>
> From: Jerry LR Chandler <Jerry.LR.Chandler@Cox.net>
> Date: February 21, 2006 1:02:40 PM EST
> To: fis@listas.unizar.es
> Subject: [Fis] Closing Out the Molecular Bionetworks Session
>
>
> Dear Colleagues:
>
> Pedro asks that we post some closing remarks.
>
> My comments will be very sparse.
>
> It appears to me that the concepts of molecular bionetworks remain
> as an esoteric language that are outside the traditional language
> and philosophy of science. The vocabulary is so specialized that
> high entry criteria must be met before one can enter the discussion.
>
> Although the concepts of molecular bionetworks were grounded in the
> early 20 th century, they remained within the specialized discourse
> of the biomedical community. During the last 3 decades of the 20
> th Century, the gradual transfer of the technical terms into common
> language accelerated. With the sequencing of genomes, new
> terminology was introduced and the implications of biochemistry for
> ethical and economic systems became widely discussed in the public
> and in government.
>
> The language of mathematics and physics ground the abstraction of
> electrical networks. Certainly, life itself is an electrical
> network. But, the language of mathematics and physics seem very
> remote from life itself and the network relations that sustain it.
> Shannon information theory works very effectively for mechanically
> encoding messages into transferable forms and transferring them
> from place to place. But, Shannon's theory, after more than fifty
> years, has not been shown to be representative of biological
> information and certainly not representative of the geno-dynamics
> of molecular bionetworks (Examples: reproduction, consciousness.)
>
> The language of bionetworks, the language of individuals and
> species, is remote from the typical language of philosophy and
> logic. Consequently one finds little guidance from such sources.
> Stan is one of the rare individuals whose attempts are to be
> acknowledged and applauded. But, it seems to me, his attempts just
> miss the whole point.
>
> So, we have a informational conundrum.
> 1. Aristotelian categories provide a rational basis for
> classification of chemical and biological networks.
> 2. The empirical sciences of biochemistry, neurology, physiology,
> pharmacology, toxicology and therapeutics, provide a rich source of
> dynamic data that is certainly informative and carries practical
> meaning to the skilled practitioners of these arts.
> 3. But, we lack a consistent means of quantitatively expressing the
> information content of molecular bionetworks.
>
> The depth of this conundrum appears to ensure the longevity of our
> FIS discussion.
>
> Thanks to all who contributed to the discussions.
>
> Cheers
>
> Jerry
>
>
>
>
> From: <kj04@chello.at>
> Date: February 21, 2006 1:59:05 PM EST
> To: Jerry LR Chandler <Jerry.LR.Chandler@Cox.net>,
> <fis@listas.unizar.es>
> Subject: Re: [Fis] Closing CORRECTLY the Molecular Bionetworks Session
> Reply-To: kj04@chello.at
>
>
> Please let me take issue with Jerry's following assertions:
>
> a) Certainly, life itself is an electrical network
> This statement is false.
> Correctly, it would read:
> "Life itself is a continuous mapping between representations as an
> electrical network and as a physiological melee."
>
> b) the language of mathematics and physics seem very remote from
> life itself
> This statement is false.
> Correctly, it would read:
> "The language of mathematics and physics is depicting life itself
> quite correctly."
>
> c) The language of bionetworks, the language of individuals and
> species, is remote from the typical language of philosophy and logic.
> This statement is false.
> Correctly, it would read:
> "The language of philosophy and logic is not at all remote from the
> language of bionetworks, of individuals and of species"
>
>
> d) we lack a consistent means of quantitatively expressing the
> information content of molecular bionetworks.
> This statement is false.
> Correctly, it would read:
> "We do possess a consistent means of quantitavely expressing the
> information content of molecular bionetworks.
>
> Otherwise, a fine closing piece.
> Karl
>
>
>
>
On Feb 23, 2006, at 6:03 AM, fis-request@listas.unizar.es wrote:
> -----Original Message-----
> From: John Holgate
>
> Sent: Wednesday, 22 February 2006 14:13
> To: 'Jerry LR Chandler'; fis@listas.unizar.es
> Subject: RE: [Fis] Closing Out the Molecular Bionetworks Session
>
>
> Hi Jerry,
>
> Thanks for your excellent moderation.
>
> <we lack a consistent means of quantitatively expressing the
>
> <information content of molecular bionetworks.
>
> Do you have any comments on the function of 'information' at the
> level of microtubule networks in the brain?
>
> We might consider Michael Conrad's hierarchical approach and more
> recently the Stuart Hameroff/Ronald Penrose quantum view of
> 'information' as an entity 'leaking'
> from microtubules (and in a sense more primary than consciousness
> particularly
> in Near Death Experiences - can a brain-dead person still have
> information?).
>
>
> http://www.quantumconsciousness.org/penrose-hameroff/
> quantumcomputation.html
>
> But what is actually 'leaked' and how do we measure it? Perhaps
> information itself is in
>
> a perpetual state of superposition with present progressive mean-
> ing but no perfect sense.
>
> It seems that information at the chemical level is not only
> transferred
> but also 'flows in' from the environment - molecules (and
> individuals) don't
>
> just actively 'recognise' - they are continually bombarded by
> thermal noise.
>
> Maybe Pedro or John Collier could comment too since it is an
> important debate within consciousness studies and neurobiology.
>
>
> I don't wish to extend the session so possibly we could chat
> privately during the
> virtual postconference drinks...
>
> John H
>
>
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Received on Sat Feb 25 17:21:59 2006
