Interleaving comments in Bob's introduction --
-snip-
>We next review the work of Propagating Organization: An Enquiry (POE)
>(Kauffman, Logan et al. 2007) in which it is shown that Shannon
>information cannot describe a biotic system. The core argument of POE was
>that Shannon information "does not apply to the evolution of the
>biosphere" because Darwinian preadaptations cannot be predicted and as a
>consequence "the ensemble of possibilities and their entropy cannot be
>calculated. Instead of Shannon information we defined a new form of
>information, which we called instructional or biotic information, not with
>Shannon, but with constraints or boundary conditions. The amount of
>information will be related to the diversity of constraints and the
>diversity of processes that they can partially cause to occur.
S: I have previously suggested that there are three aspects of
information that have appeared in discourse about it: (1) A reduction in
possibilities, (2) functioning as a constraint on entropy production, (3),
which makes a difference to the informed system.
(1) Is perfectly general outside of information theory. It is always the
case that whatever appears was only one of several to many possibilities,
but, as Bob notes with biology, it is almost never possible in complex
material systems to assess the prior possibilities (and/or probabiliities)
to get a measure. (Incidentally, preadaptations are not particularly
'Darwinian', but belong to organic evolution discourse more generally than
just in neoDarwinian theory, where I'd be surprised to see it mentioned
ever)
(2) I use entropy production as the general key here because whatever
happens produces entropy, and all configurations will constrain this
production to less than that which would be produced in an explosion of the
same energy gradient. Thus, any reduction in informational entropy in a
given system has the effect of reducing the rate of physical entropy
production by that system relative to what would be the case if the
constraints had not appeared. However, the maximum entropy production
princple (MEP) suggests that constraints will tend to apear that will allow
the greatest physical entropy production consistent with the integrity of
the system.
(3) Focuses on particular systems as those informed and/or affected by the
information in place.
>The Relativity of Information
>
>In POE we associated biotic or instructional information with the
>organization that a biotic agent is able to propagate. This contradicts
>Shannon's definition of information and the notion that a random set or
>soup of organic chemicals has more Shannon information than a structured
>and organized set of organic chemicals found in a living organism.
S: This 'notion' would be valid IF the comparison was strictly between
a soup of subatomic particles and the arrangement of subatomic particles
entrained by a biotic organization.
>This argument completely contradicts the notion of information of a system
>biologist who would argue that a biological organism contains information.
S: That is true because the systems biologist talks about
macromolecules and the cellular configurations constrainig them.
>This argument contradicts the notion that information is an invariant like
>the speed of light, the same in all frames of reference.
S: As above, a material system exists at several scales, and
information at one scale can have no meaning, as such, at another scale.
>Shannon information and biotic or instructional information are quite
>different. Information is a tool and as such it comes in different forms
>just as screwdrivers are not all the same. They come in different forms,
>slot, square, and Philips---depending in what screw environment they are
>to operate. The same may be said of information.
>
>Another distinction between Shannon information and biotic or
>instructional information as defined in POE is that with Shannon there is
>no explanation as to where information comes from and how it came into
>being. Information in Shannon's theory arrives deus ex machina, whereas
>biotic information as described in POE arises from the constraints that
>allow a living organism to harness free energy and turn it into work so
>that it can carry out its metabolism and replicate its organization.
>Kauffman (2000) has described how this organization emerges through
>autocatalysis as an emergent phenomenon with properties that cannot be
>derived from, predicted from or reduced to the properties of the
>biomolecules of which the living organism is composed and hence provides
>an explanation of where biotic information comes from.
>
>
>Information and Its Relationship to Materiality
>
>"Shannon's theory defines information as a probability function with no
>dimension, no materiality, and no necessary connection with meaning. It is
>a pattern not a presence (Hayles 1999a, p. 18)." The lack of a necessary
>connection to meaning of Shannon information is what distinguishes it from
>biotic information. Biotic information obviously has meaning, which is the
>propagation of the organism's organization.
S: This is why I have suggested that the meaning of information is
related to final causation. The 'propagation' referred to by Bob is the
final cause regarding biological reproductive actvities.
>I would interpret the signals transmitted between Shannon's sender and
>receiver as data, Consistent with MacKay and Bateson's position
>information makes a difference when it is contextualized and significant.
>Knowledge and wisdom represent higher order applications of information
>beyond the scope of this study. The contextualization of data so that it
>has meaning and significance and hence operates as information is an
>emergent phenomenon. The communication of information cannot be explained
>solely in terms of the components of the Shannon system consisting of the
>sender, the receiver and the signal or message. It is a much more complex
>process than the simplified system that Shannon considered for the
>purposes of mathematizing and engineering the transmission of signals.
>First of all it entails the knowledge of the sender and the receiver, the
>intentions or objectives of the sender and the receiver in participating
>in the process and finally the effects of the channel of communication
>itself as in McLuhan's notion that "the medium is the message". The
>knowledge and intention of the sender and the receiver as well as the
>effects of the channel all effect the message that is transmitted by the
>signal in addition to its content.
S: Of course, none of this INVALIDATES Shannon, but merely states
that in most natural contexts it would be woefully underdetermining even if
it could be calculated.
>The Meaning of Information in Biotic Systems
>
>Biotic or instructional information, defined in POE as the constraints
>that allow an autonomous agent, i.e. a living organism, to convert free
>energy into work so that the living organism is able to propagate its
>organization through growth and replication, is intimately connected with
>meaning. "For Shannon the semantics or meaning of the message does not
>matter, whereas in biology the opposite is true. Biotic agents have
>purpose and hence meaning (Kauffman et al. 2007).
S: This is a bit tricky, insofar as careful consideration suggests
that non-intensional systems cannot have purposes. However, we just need
to note that purpose (teleology) is generalizable in biology to 'function'
(teleonomy), and that this in turn is generalizable to physical tendency or
propensity (teleomaty). Thus, {teleomaty {teleonomy {teleology}}} saves
the idea.
>" One can therefore argue that since the meaning of instructional
>information is propagating organization that we finally understand the
>meaning of life ñ the "meaning of life" is propagating organization. This
>remark is not meant to trivialize the great philosophical quest for the
>meaning of life from a human perspective but there is a sense in which the
>meaning of life including human life is indeed the propagation of
>organization. The purpose of life is the creation or propagation of more
>life.
S: So,possibly, {tendency {survival {meaninfulness}}}.
>In addition to the fact that Shannon information does not necessarily
>entail meaning whereas biotic or instructional information always entails
>meaning there is one other essential difference between the two. Shannon
>information is defined independent of the medium of its instantiation
>whereas biotic information is very much tied to its material instantiation
>in the nucleic acids and proteins of which it is composed. The
>independence of Shannon and cybernetic information from the medium of its
>instantiation is what gives rise to the notion of strong artificial
>intelligence and claims like those of Moravic, Minsky and to a certain
>extent Wiener that human intelligence and the human mind can some how be
>transferred to a silicon-based computer and does not require the wet
>computer of the human brain. Shannon and cybernetic information can be
>transferred from one material environment to another, from one computer to
>another or in the case of Shannon information from one telephone to
>another or from a computer to a hard copy of ink on paper. This is not the
>case with living organisms in the biosphere where information is stored in
>DNA, RNA and proteins.
S: We now know that meaninful bits of genetic material can be
transferred from species to species.
For the rest, I have no further comments.
STAN
---------------
>Shannon information whether on paper, a computer, a DVD or a
>telecommunication device, because it is symbolic, can slide from one
>medium or technology to another and not really change, McLuhan's "the
>medium is the message" aside. This is not true of living things. Identical
>genotypes can produce very different phenotypes depending on the physical
>and chemical environment in which they operate. Consider the fact that
>identical twins are not "identical". The reason identical twins are not
>"identical" is that the environment in which the biochemical interactions
>between biomolecules takes place can alter the outcome.
>
>
>The Materiality of Information in Biotic Systems
>
>Another way to distinguish the difference between biotic or instructional
>information and either Shannon or Kolomogorov information is that the
>latter are symbolic which is not the case for biotic or instructional
>information. The information coded in the chemical alphabet of
>biomolecules that make up living organisms acts through the chemical
>interactions of those biomolecules. "DNA is a molecule interacting with
>other molecules through a complex set of mechanisms. DNA is not just some
>text to be interpreted, and to regard it as such is an inaccurate
>simplification (Sarkar 1996, p. 860)." It is not the symbolic nature of
>DNA that gives rise to messenger RNA and it is not the symbolic nature of
>RNA that gives rise to proteins but rather the chemical properties of DNA
>that produce or catalyze the production of RNA and the chemical properties
>of RNA that produce or catalyze proteins and the chemical properties of
>proteins that carry out the protein's various functions such as:
>
>1. serving as enzymes to catalyze biochemical reactions vital to metabolism,
>
>2. providing structural or mechanical functions, such as building the
>cell's cytoskeleton,
>
>3. playing a role in cell signaling, immune responses, cell adhesion and
>the cell cycle.
>
>
>Organization as Information
>
>What is the relationship of organization and information?
>What we discovered in POE was that the autocatalysis of biomolecules led
>to the organization of a biological living organism whose organization of
>constraints allowed it to convert free energy into work that sustained
>growth and permitted replication. We identified the constraints as
>instructional or biotic information which loops back into the organization
>of the organism. This model of information holds for biotic systems where
>autocatalysis is the organization and the components are the individual
>biomolecules.
>
>The argument seems circular only because a living organism represents a
>self-organizing system. This is still another way that biotic information
>differs from Shannon information which is defined independent of meaning
>or organization. In fact organized information has less Shannon
>information because it does not reduce as much uncertainty as disorganized
>information. It is also the case as we mention above that this model
>provides a mechanism for the creation of information which is not the case
>with the Shannon model of information.
>
>-------------------------------------------------------------------------------
>---------
>
>Thanking your attention, ----Bob
>
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