(I am still in China with disrupted internet. This may have to come to the list 
indirectly. In this reply, I take advantage of the amazing corpus of FIS emails 
over 14 years. This is an important resource and from time to time I use it in 
my work. Thank you, Pedro for sustaining this.)

Koichiro --

As you know, I think you see something important. That it both sounds true and 
also does not fit old models makes it even more appealing.

The model of our project is based on two-sorts, meaning one "logic" apparently 
native to the activity and another synthesized for introspection or external 
observation. As others have remarked, these are different but related concerns. 
Rather than trying to grow a single conceptual framework as most do, we bite 
the bullet on the formal challenge of two integrated logics. So my remarks here 
are framed as questions that can help us implement your insights as fully as we 
can. (While not used here, our test case is an understanding of apoptosis.)

In 1998, you wrote: "once we admit that there is no viewpoint that could 
integrate both that something and something-else, state description, that has 
been a favorite to many physicists, could not be tenable to that complex 
anymore. Information is always about a view from somewhere. It is 
methodologically untenable for the adherent to that view to tell where that 
somewhere is located. By saying this, I see physics loses nothing. Information 
gains something, instead. Information-processing is about a negotiation between 
each view from anywhere.'

In 2002, "A common denominator is serious negotiation between supplier and 
consumer."

In 2003: "(Ted's).. summary reminds... of one recurring theme surrounding the 
sturdy issue on the difference between dynamics in time and dynamics of time."

in 2004: "(Loet) reminds me of the contrast between a unified and a unifying 
theory of anything." And later, "The wide topics covering probability, 
information, entropy, temperature, order, disorder, symmetry and asymmetry 
reminded me of at least one thing. Suppose I am a bacterium. Do I care (about) 
all of them?"

And even later in 2004, "(Eugene Wigner pointed out...) The malaise surrounding 
us is that if we respect both thermodynamics and quantum mechanics on a par, we 
would lose the basis of what has been called probability distributions. Unless 
the notion of probability distribution is available, it would be next to 
impossible to talk about entropy and information in a decent manner.

in 2005: "... a communication system is a matter of a second-person ontology 
instead of a third-person one in the latter of which irreducible fundamentals 
are objectively guaranteed along with an invariant context. Both the sender and 
the receiver of a message conceived in a third-person ontology as with the case 
of the mathematical theory of communication forces us, the externalist, to let 
both be synchronized in sharing the same context. This synchronization is 
exclusively of methodological origin... One crucial issue in this regard may be 
how an asynchronous patchwork of different contexts could come to be integrated 
into a consistent, synchronous one in the effect." 

Throughout, you have discussed this bridging problem in terms of interaction 
(1998), quantum entropy (2004), Maxwell's demon in measurement (2004), Zipf's 
law (2004), consilience (2004), many-worlds (2004), internalism (2005), 
phenomenologism (2005), epistemological synchronization-Dedekind's cut (2005), 
nonlinear quantum coherence (2005), situated logic versus propositional logic 
(2005), Bell's inequity (2006) and quantum electrodynamics (2010). But the most 
compelling metaphors to me have been those of tense, starting with your 1997 
post on the essential difference between the present tense and the progressive 
tense:

"At issue is how to reach the present tense from the present progressive tense. 
Either through the present perfect or through the past progressive tense? If 
one tries to reach the present tense via the present perfect tense, this may 
imply the presence of perfected movement (or progression). And, this may reduce 
to the standard Kantian-Newtonian time."

This always sat well with me. As computer scientists, we routinely consider the 
logic used to reason about a system in the context of the natural language 
members of that system use. And as practical scientists, we constantly question 
the uneasy relationship between logic and science and how logic simply has to 
evolve to capture dynamics of the world. The notions of tense, cause and 
triggering imperative are at the root of this, in a useful way both intuitively 
and formally.

Though attempts to find some sort of a universal grammar to accommodate these 
two views promote some interesting exchanges, my proposal to you is that we 
take the clean approach and consider two related grammars. The formal 
properties of each of these are rather straightforward when considered by 
themselves, coming directly from the respective domains. Let us choose two 
example domains: one being the model and supporting calculus of a 
microbiologist working to create useful models of cell behavior and the other 
the "model" the cell and its constituents use in the conduct of their processes.

The fiction until Wigner's insight was that these were one and the same: 
natural objects conform to laws; we discover them and that is that. We have 
outgrown that, and you (with Pedro and Michael) believed that a focus on the 
information that flows in each of those two systems can be placed in a single, 
unifying context. I think it is fair to say that this strategy has failed. Now 
if we allow the information flows (which I see as an result of the calculus) to 
live in their respective domains, the problem becomes one of a third sort of 
information flow, that which relates the two worlds. We bridge that today with 
the two paradigms on which we build science: measurement and theories of cause. 
The notion of tense touches on both, one from one world, the other from the 
second. I ask your opinions on this "third flow."

In our example, the calculus used by the microbiologist may be as it is today, 
some amalgam of particle physics, thermodynamics and empirical geometric 
induction. Perhaps someone like Jerry may make this more robust, but let's just 
assume that in our lifetimes, this logic uses existing notions, albeit 
non-specific, of signals and triggers. The notions native to the cell as it 
relates to other cells, between a cell and its soup, and among the proteins and 
the associated information flows may best be modeled in a different way. I can 
only assert for this position that quantum behavior suggests this, several 
successful quantum "logics" have been proposed, and there is no necessity to 
conflate the tools of the scientist with the introspective dynamics of nature. 
(I understand this will be hard for some to take, but here I speak directly to 
you.) To avoid unnecessary controversy, let us say only that this is a 
categoric system that captures non-contact and non-sequential causality.

Now to your recent emails, and taking into account that I am looking for a 
specific insight (the binding of the two information types in a coherent 
two-logic system)...

On May 10, 2011, at 8:09 AM, Koichiro Matsuno wrote:

> ...
> 1.     Being empirical is not necessarily rational (e.g., Galilei’s empirical 
> inertia v.s. Aristotle’s rational telos).

Though we have in theory three systems of information (behavior, observer, 
binding concepts), I believe that we can in most cases combine the last two. In 
effect, this is saying that we force the scientist to use the same system of 
reasoning about biology as she uses to reason about how she reasons. This is 
just a working hypothesis, because it limits the extent of irrationality we 
have to accommodate. 

I assume here that your use of "empirical" is from the biologist's perspective, 
and that we can use the difference between what is observed and what is cleanly 
modeled in that world as a measure of dissonance between the two systems. 
Anything we can measure, even apparently non-rational behavior is information 
of this third type, right? If so, then the nature of this dissonance is 
significant.

> 2.     Linear progression of time, say time (t+1) following time t, is 
> already a consequence of synchronization among the clocks available to us. A 
> point of clarification is that synchronization in the making as a necessary 
> condition for a meaningful integration into whatever context is not sure 
> about whether it could also proceed upon a linear progression of time. 
> Suppose everybody asks the nearest neighbor “what time do you have?”. The 
> outcome might be somewhere in between the two extremes of a successful 
> synchronization in the end among all of them on one hand and a total mess on 
> the other.

This is a distinction you are making between local situations of different 
observers. Since we are working in one reasoning framework on this side, the 
"dissonances" (the information flows) among situations (here, information about 
clocks) have a richer vocabulary that that mentioned above. Since our main 
challenge is understanding the flow from the event (cell behavior) to the 
observer's model, this difference (which I will generalize to the difference 
between scientific perspectives) informs those flows. Or so I believe.

> 3.     Linguistic or theoretical access to synchronization in the making 
> would be hard to imagine when it is prohibited to refer to time as a 
> comprehensible analytical tool in advance. This does not however mean the end 
> of the whole issue. Empirical access to synchronization in the making is 
> totally different. Cyanobacteria as the first photosynthetic bacteria 
> appeared on Earth could have been quite successful in synchronizing their 
> circadian clocks among them without asking the help of our languages.
> 4.     Addressing the theoretical question of what kinds of material means 
> are employed for the job of synchronization and why, goes far beyond our 
> present rational comprehension. Although the cyanobacterial circadian clocks 
> employ three different kinds of protein called KaiA, B and C for the job, we 
> cannot say for sure at this moment why these particular proteins would come 
> to be focused upon. This has been an irrevocable empirical fact.

... and one driving the creation of alternative logical systems since von 
Neumann's challenge. Your perspective on time prompts me to rephrase the 
question that John addressed last month with his nested worlds post. The 
refactoring suggests that some concepts are more useful than others to consider 
as primitive and universal across worlds and the two logics.

I know you would agree that symmetry and cause are intertwined, more 
fundamental than time and entropy. But lets go further because we have to build 
systems. Each concept is paired with its sibling in the observer's world, most 
fundamental first.

Existence/Existence; Symmetry/Cause; Percept/Measurement; Calculus/Logic; 
Non-commutivity/Time; Transformational Functions/Discreteness.

I would suggest that there are useful definitions of information flow at each 
level.

> 5.     Neuronal dynamics is full of synchronization in the making by means of 
> exchanging an extremely wide variety of chemical messengers, including for 
> instance acetylcholine, available empirically. 
> 6.     Even if we take a pause for a while for addressing the grandiose 
> why-questions, there may still remain some room for tailoring time for a 
> comprehensible analytical tool. Time is further qualified in terms of its 
> tense. There remains a likelihood of addressing how the actual dynamics would 
> proceed through the interplay between the different tenses, especially 
> between the present progressive and the present perfect tense.

Would you suppose that this analytical tool can leverage a distinction of cause 
from temporal sequence? 

> 7.     Put it bluntly, information synthesizes the flow of time from scratch.

And as you have said elsewhere, it may do so dynamically and different each 
"time."

On May 24, 2011, at 7:18 AM, Koichiro Matsuno wrote:

> Dear Joseph,
>  
> > I feel that in point 3. of your note you describe a key to time but you do 
> > not use it!
>  
> Right. The last time, I skipped over something. The issue is how to 
> descriptively approach phenomenological time via the interplay between real, 
> physical systems without prior reference to the flow of time on the global 
> scale. My intended entry for this endeavor has been to pay attention to some 
> physical body remaining invariant while being constantly involved in 
> exchanging its constituent subunits. That is to say, once a molecular 
> aggregate happens to appear whose class identity is kept intact while the 
> constituent subunits constantly come and go, the through-flow maintaining the 
> class identity of the aggregate can superficially be associated with the flow 
> of time as we know of it in the contradictory sense that while passing away 
> constantly, time remains as time as keeping its identity. The flow of time 
> here is only taken as “a representation”, or an anthropocentric metaphor at 
> best, of the material through-flow as a decisive factor for keeping the class 
> identity of a physical body at the cost of the vicissitude of the individual 
> identities of the constituent subunits. The cyanobacterial circadian clocks 
> are just an empirical example of keeping the class identity of a KaiC hexamer 
> while constantly exchanging or shuffling the monomeric KaiC subunits.

Would this work as a description?

The issue is how to relate the internal "logic-of-effect" of a cell regarding 
its temporal identity to the causal logic of the scientist. The "time" of the 
scientist (I hesitate to say "global") is relentlessly linear, the cell appears 
invariant and can be modeled as an invariant, discrete agent.

Yet, supposing we can put ourselves in the world of the biological system, a 
cell is a fiction. We have only extremely primitive elements (let's say quarks) 
that interact in ways in which no event is complete, few things linear or 
discrete in the human sense and everything reactively coupled. And yet, though 
the couplings are partially unknown, there is an organizational imperative and 
supporting calculus (that is profoundly non-thermodynamic). Though it does not 
lend itself well to concepts of forces, fields and Aristotelian logic, there 
surely is some match among: the information within the system, the information 
among the agents we model, and the information we get from the first (as 
measurements) that color the second.

Time is not central to the relationships among these three types of information.

>  >The objective, as you have written well earlier, is to better understand 
> the interplay of what we call the tenses in language.
>  
>    The underlying issue is how can we construct the flow of time from the 
> tenses. When the constant update of the present perfect tense in the present 
> progressive tense is referred to in the finished record,  we can perceive the 
> flow of time as driven by the transitive verb “update” in the present tense, 
> though only in retrospect. This updated version of the flow of time in 
> retrospect exhibits a marked contrast to the flow of time riding on the 
> intransitive verb “flow” in the present tense unconditionally, the latter of 
> which is common to the standard practice of physical sciences even including 
> relativity.  The occurrence of the perfect tense is due to the act of 
> measurement of material origin distinguishing between the before and after 
> its own act, while its frequent update in the progressive tense will be 
> necessitated so as to meet various conservation laws such as  material or 
> energy flow continuity to be registered in the record, e. g., not to leave 
> the failure in meeting the flow continuity behind. The KaiC hexamers of 
> cyanobacteria are involved in the constant update of the prefect tense in the 
> progressive tense.

This point is not one essential to my program. If we can usefully model the 
times and dynamics of the two worlds in integrated fashion, that is enough. We 
don't have to go further with the philosophical exercise of generating one from 
the other. Moreover, I question the wisdom of this because it assumes a 
priority.

--Ted



_____
Ted Goranson
tedgoran...@mac.com
http://www.sirius-beta.com






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