(Undistorted figures are attached.)
Dear Clark,
Thank for your informative comments. My responses to some of them follow:
> On Jul 28, 2014, at 6:24 PM, Sungchul Ji <s...@rci.rutgers.edu> wrote:
>
>> I don't understand what you mean by "holistically" here. I thought
>> there s only one way to understand/interpret thermodynamics --
>> scientifically.
>
> Yes but any scientific model is simplified. You exclude other systems that
> the system under analysis is in connection with. So physicists will
> simplify things as closed systems or drastically limit what systems it is
> in contact with. In the real world what is marginalized in such
> idealizations can have a significance.
>To give a classic example
> Creationists often claim evolution violates the laws of thermodynamics
> because they neglect that the earth and even the solar system is not a
> closed system.
>
They are simply wrong. As you know thermodynamic laws apply to all
material systems that divide into three categories -- isolated (no energy
nor matter is exchanged between the system and its environment), closed
(only energy is exchanged), and open (both energy and matter are
exchanged).
>> I suppose, depending on context, you can interpret thermodynamic
>> concepts and laws "non-scientifically", "non-professionally or
>> "common-sensically.
> No this really is pure physics. So Im not trying to use thermodynamics
> loosely. While Ill be the first to admit its been far too many years
> since I last took thermodynamics (my background is physics) I dont think
> theres anything Ive said that doesnt apply formally. Im using all
> terms in their technical sense except later when I take you to be making a
> broader semiotics point on the basis of thermodynamics as analogy.
I am glad you are making a clear distinction between physics and
semiotics.
>> This statement is true but is missing the point of differentiating
>> between equilibrium structures and dissipative structures: A
>> magnetic tape is an equilibrium structure in contrast to the sound or
>> images it can be induced to generate upon energy input through a tape
>> reader.
>
> Again, at risk of being pedantic, its technically in a quasi-equilibrium
> state due to the temporal issues at play.
>That is a tape left alone decays. My sense is that these temporal issues
are being
> marginalized in your analysis when they are actually quite important. (I
might be
>wrong in that - but it appears a common flaw in these sorts of analysis)
I agree that a tape will decay eventually but not while being read with a
tape reader (to produce sound or visual images that last only very briefly
relative to tape itself).
>> This statement is akin to the claim that there is a continuum between an
>> artificial flower and a real flower, which is true on one level but not
>> true on another level. That is, at the morphological level, both
>> artificial and real flowers can be indistinguishable (or continuous),
>> while at the thermodynamic level, the artificial flower does not
>> dissipative energy and the real flower does. I would not be surprised
>> at all if Peirce discussed something similar in his writings on
>> synechism.
>
> Im not sure that gets at the distinction. It would be better to say an
> idealized flower and a real flower since the artificial flower is still
> dissipative, to use your terminology.
The crucial point to consider is the fact that an artificial flower does
not dissipate any energy to exist but a real flower has to and does. It
is probably for this reason that an artificial flower can last much longer
than a real flower.
> Its this question of idealization which I think is quite key here.
I dont think the terms idealized flower and artificial flower are
synonymous. Viewing them synonymously may lead to undesirable logical
consequences. In Figure 1 below, your idealized flower may correspond
to model and artificial flower to phenomenon.
>Again by way of analogy to thermodynamics the ideal gas law is a very good
> example of what Im getting at. Such idealizations are an important tool
> for physicists and chemists. But it is quite common to assume the
> idealizations are the reality, when they are a model.
I agree. This is made clear in the diagram (Figure 1) for the MPM
category, or what I call the ur-category :
a b
Mechanism --------------> Phenomenon -------------> Model
(Reality) (Idealization)
| ^
| |
| ___________________________________________________|
c
Figure 1. The MPM category as the ur-category or the theory of everything
(TOE). a = natural process; b = mental modeling; c =
validation/experimental proof.
> Now of course we can
> go down the tangent here of discussing scholastic realism and the role of
> such idealisms as laws in science. But my sense is that perhaps gets us
> away from the questions at hand.
>
>> You seem to assume here that the thermodynamic principles (e.g.,
>> principles differentiating the equilibrium and dissipative systems)
>> obeyed in physics and chemistry are somewhat different from those obeyed
>> in more broad semiotics.
>
> I think there is a difference between idealized signs and the particular
> objects physics and chemistry studies in the real world.
I would think that your particular objects correspond to phenomenon in
Figure 1 above, and idealized signs correspond to model.
>The question of
> the ontology of thermodynamics and thermodynamic law is an interesting
> one. However Ive intentionally avoided that discussion. Ill just say
> that Im discussing thermodynamics as used in physics (and thereby
> chemistry) rather than attempting to connect *formally* thermodynamics and
> semiotics either via information theory or other ontological commitments.
To me, semiotics is the study of signs, and thermodynamics is the study of
heat. Thermodynamics is necessary for semiotics but not sufficient. We
may indicate this idea simply as Semiotics > Thermodynamics, meaning that
semiotics requires more than thermodynamics. One possibility is that
the missing element is informatics (the study of information which is
considered complementary to energy in the sign-as-the-gnergon hypothesis
[1]), leading to the conclusion that
Semiotics = Thermodynamics + Informatics (072914-1)
> Im just nervous enough about making that ontological leap. There may well
> be mathematical similarities between the two but the subject matter within
> physics simply is different. Put another way while it is amazing the
> universe is as mathematical as it is I am not willing to make the leap to
> saying math is the fundamental ontology of the universe. That seems a leap
> too far and in need of considerable argument.
>
How about including mathematics as a part of informatics and viewing
semiotics as the representation (or sign) of the universe, which will
force the equivalence of physics and reality (or mechanisms) ?
Mechanism --------------> Phenomenon -------------> Model
(Physics) (signs) (Mathematics)
| ^
| |
|______________________________________________________|
c
Figure 2. The possible relation among mathematics, physics, and semiotics
suggested by the MPM category hypothesis.
> So yes, Im making a distinction between semiotics and thermodynamics
> within physics conceived either phenomenologically (in the physics not
> philosophical sense) or in terms of statistical mechanics. I think we can
> discuss the latter as a semiotic system. But I think theres a difference
> between semiotics in the abstract and physics just as there is a
> difference between mathematics and physics. The later applies the former
> to physical phenomena.
>
Would Figure 2 be compatible with your ideas expressed here ?
> I recognize in saying this that at least the early Peirce adopts a
> quasi-neo-platonic ontology that would make semiotics a fundamental
> ontology. After once being convinced that was the view of the mature
> Peirce Im not much more skeptical of that idea. In either case even in
> Peirce did believe this I dont think he offers sufficient argument for me
> to adopt such a view. No matter how attractive it might seem.
>
>> I firmly believe that that following statement is true (and hence
>> recommend it to be referred to as the First Principle of Semiotics, in
>> analogy to the First Law of Thermodynamics):
>>
>> No energy dissipation, no semiosis. (072814-7)
>>
>> The following corollaries would result from Statement (072814-7):
>>
>> Sign systems cannot perform semiosis (072814-8)
>> in their equilibrium states.
>>
>> Sign systems can perform semiosis if and (072814-9)
>> only if they are in non-equilibrium states.
>>
>
> I confess I dont see how those are true, depending upon how you specify
> energy dissipation.
Concrete examples of energy dissipation in biology are provided by the
Gibbs free energy decreases accompanying spontaneous living processes
occurring in homeotherms under constant pressure. As you know, there are
other forms of free energies applicable to conditions other than constant
T and P.
>Or, perhaps another way of putting it within a
> physical system is a total lack of energy dissipation possible?
Yes. I would think so, within the limit of Heisenbergs uncertainty
principle.
>(I suspect, given what I said earlier, this quest for something beyond
> absolute zero is perhaps again the quest for the transcendent sign)
>
> I would like you to perhaps break out a little more what you mean by
> equilibrium state.
Equilibrium state to me is the state of a thermodynamic system that
exhibits no measurable/observable changes (again within the limits of
Heisenbergs uncertainty principle). As John pointed out, equilibrium and
dissipative states are mostly scale-dependent. Under this definition,
steady-states are not equilibrium states, since they do produce observable
effect to maintain their homeostasis with respects to some critical
variables such as temperature, pressure or chemical compositions (the
focus of Koichiros recent post in the biosemiotics list).
> Again there are temporal issues at play. For instance
> even a system that, when perturbed, returns to its original state can be
> said to be in a kind of equilibrium yet when analyzed carefully along a
> temporal analysis there are places where actions are taking place. (In
> particular the perturbation) It seems like you are considering a start
> state and end state but neglecting what happens in the middle.
>
Of course there are two ways of describing a thermodynamic system
macroscopically (also called phenomenologically) and microscopically
(also called statistical mechanically). The distinction between
equilibrium and dissipative structures are valid on both scales.
Again, macroscopically an artificial flower is an equilibrium structure
and a real flower is a dissipative structure, because the former does not
dissipate energy (and hence does not produce any heat) whereas the latter
does. Microscopically, the molecules in an artificial flower undergo
symmetric Brownian motions whereas the molecules in a real flower undergo
both symmetric Brownian motions and asymmetric or symmetry-broken
Planckian motions (obeying the generalized Planckian equation discovered
in 2008; see Eq. 2 in [2].
> Now of course for some sorts of physics (say within Feynman diagrams for
> the quantum mechanical analogy of Lagrangian mechanics interactions) we
> can talk about virtual particles and cant say whether such virtual
> particles are really modifying or not. Mathematically they are the same as
> if they were undergoing all sorts of changes. However in terms of the
> thermodynamic analysis in which you are making of course theres all the
> difference in the world.
>
>> Yet (and this is key for Peirces semiotics) there is (072814-12)
>> always a gap between object and interpretant in this
>> process. For Peirce this is best conceived by way of
>> the Epicurean notion of swerve.
>>
>> This statement is interesting to me because it seems to bring together
>> semiotics and thermodynamics in an imaginative manner. If I am right in
>> interpreting the Epircurean swerve as analogous to Brownian motions in
>> statistical mechanics, i.e., the microscopic version of thermodynamics,
>> just as Democritus atom is analogous to the quantum mechanical atom, I
>> can see how Epicurean swerve may be implicated in semiosis. Brownian
>> motions are random, whereas semiosis is non-random, but these two may be
>> fundamentally linked if we can assume that semiosis implicates selecting
>> one out of all possible choices made available by random motions. This
>> picture of semiosis is suggested by my recent findings (i) that the
>> decision-time histograms fit the Planckian distribution function (PDF),
>> also called GPE, the generalized Planck equation (see Eq. (2) in [1])
>> and (ii) that PDF can be derived from the Gaussian distribution function
>> based on the drift-diffusion model of decision making [2, 3].
>
> While Epicurus swerve has some parallel to statistical mechanics I think
> he meant it in a far more fundamental ontological fashion. Peirces
> adoption of this notion also was a fundamental ontology. One can of course
> disagree with Peirce but it is quite interesting that he did adopt such a
> notion during an era of physics when determinism ruled. Decades before
> quantum mechanics was discovered let alone accepted uncontroversially.
>
> I think one should be careful here or at least make explicit ones
> assumptions. (Peirce is quite good about that) I think Peirces point
> though is that semiosis unavoidedly has this random element to it. This
> can be conceived along two different axes. First the semiotic evolution as
> the object determines its interpretant. (It is key for Peirces semiotics
> that one starts with object not the interpreter as in so many others
> conceptions - in modern philosophical parlance I think this means that
> Peirce is an Externalist. At least epistemologically and semantically and
> most likely in other ways as well.)
>There is an element of swerve in this
> process from object via sign to interpretant. Indeed this gap is key to
> Peirces conception of sign. (He makes this quite explicit in his mature
> thought such as in his Letter to Lady Welby)
If the MPM category depicted in Figure 1 is applied to semiosis, Figure 3
would result, which suggests that Steps a and b may be subject to
Epicurean swerve leading to the sign gap.
a b
Object -------------------> Sign ----------------> Interpretant
(Mechanism) (Phenomenon) (Model)
| ^
| |
|___________________________________________________|
c
Figure 1. The MPM category as applied to semiosis. a = natural
process; b = mental modeling; c = validation/grounding.
>When we reverse this process
> in order to interpret signs in order to understand their object we have to
> bridge this gap with a guess.
Followed by Step c, namely, validation or experimental proof, I suppose.
>This is the place of abduction. The gap can
> never be eliminated which is why such regulatory concepts as Peirces in
> the long run and the community of inquirers play such an important
> role.
>
> The problem of treating this gap as random can be dangerous as one must
> then unpack what one means by random.
According to Figure 3, the sign gap is bridged by two steps, a and b. I
am of the opinion that the source of Step a is associated with random or
quasi-random variations obeying the Gaussian distribution and Step b
involves an environment-induced selection leading to functions obeying the
Planckian distribution [3].
>I confess this is an area of Peirce
> I just havent read much on. So perhaps others can chime in. My sense is
> that random as used in gaussian distributions or the like assumes a
> particular distribution that the gap in a sign doesnt assume. That is
> randomness of the sort we typically worry about in physics or statistics
> is actually well defined. (Thus our focus on gaussian or poisson
> distributions for example).
> What Peirce wants is something far more
> fundamental in its indeterminism. How far he wishes to go, whether merely
> epistemological or ontological I cant say. Certainly in his early
> neoPlatonic period it seems quite deep indeed. (See Peirce as a
> NeoPlatonist: The Ascent of the Soul to Nous by Kelly Parker for an
> excellent treatment although in one key place in his argument the evidence
> isnt quite as strong as one would wish)
Can we say that there are two types of randomnesses (i) the
epistemological randomness that is due to our ignorance and hence in
principle can be accounted for deterministically when enough becomes known
about the system under consideration, and (ii) the ontological that is due
to the unknowability of the ultimate reality, which can only be reached
asymptotically with progress in our knowledge.
It seems to me that the MPM category can work with both types of
randomnesses.
With all the best.
Sung
___________________________________________________
Sungchul Ji, Ph.D.
Associate Professor of Pharmacology and Toxicology
Department of Pharmacology and Toxicology
Ernest Mario School of Pharmacy
Rutgers University
Piscataway, N.J. 08855
732-445-4701
www.conformon.net
References:
[1] Ji, S. (2012). Peircean Signs as Gnergons. In: Molecular theory
of the Living Cell: concepts, Molecular Mechanisms, and biomedical
Applications. Springer, New York. Section 6.2.3, pp. 176-182. PDF at
http://eee.conformon.net under Publications > Book Chapters.
[2] Ji, S. (2014). The poster entitled Experimental and Theoretical
Evidence for Energy Quantization in Molecular Machines and Living
Cells, and Generalized Planck Equation (GPE), available at
http://www.conformon.net under Publications> Posters and Seminars.
[3] Ji, S. (20214). Planckian Distributions in Molecular Machines and
Living Cells: Evidence for Free Energy Quantization in Biology.
Computational and Structural Biotechnology Journal (to appear
>
> On Jul 28, 2014, at 6:24 PM, Sungchul Ji <s...@rci.rutgers.edu> wrote:
>
>> I don't understand what you mean by "holistically" here. I thought
>> there
>> is only one way to understand/interpret thermodynamics --
>> scientifically.
>
> Yes but any scientific model is simplified. You exclude other systems that
> the system under analysis is in connection with. So physicists will
> simplify things as closed systems or drastically limit what systems it is
> in contact with. In the real world what is marginalized in such
> idealizations can have a significance. To give a classic example
> Creationists often claim evolution violates the laws of thermodynamics
> because they neglect that the earth and even the solar system is not a
> closed system.
>
>> I suppose, depending on context, you can interpret thermodynamic
>> concepts and laws "non-scientifically", "non-professionally or
>> "common-sensically.
>
> No this really is pure physics. So Im not trying to use thermodynamics
> loosely. While Ill be the first to admit its been far too many years
> since I last took thermodynamics (my background is physics) I dont think
> theres anything Ive said that doesnt apply formally. Im using all
> terms in their technical sense except later when I take you to be making a
> broader semiotics point on the basis of thermodynamics as analogy.
>
>> This statement is true but is missing the point of differentiating
>> between equilibrium structures and dissipative structures: A
>> magnetic tape is an equilibrium structure in contrast to the sound or
>> images it can be induced to generate upon energy input through a tape
>> reader.
>
> Again, at risk of being pedantic, its technically in a quasi-equilibrium
> state due to the temporal issues at play. That is a tape left alone
> decays. My sense is that these temporal issues are being marginalized in
> your analysis when they are actually quite important. (I might be wrong in
> that - but it appears a common flaw in these sorts of analysis)
>
>> This statement is akin to the claim that there is a continuum between an
>> artificial flower and a real flower, which is true on one level but not
>> true on another level. That is, at the morphological level, both
>> artificial and real flowers can be indistinguishable (or continuous),
>> while at the thermodynamic level, the artificial flower does not
>> dissipative energy and the real flower does. I would not be surprised
>> at all if Peirce discussed something similar in his writings on
>> synechism.
>
> Im not sure that gets at the distinction. It would be better to say an
> idealized flower and a real flower since the artificial flower is still
> dissipative, to use your terminology.
>
> Its this question of idealization which I think is quite key here. Again,
> by way of analogy to thermodynamics the ideal gas law is a very good
> example of what Im getting at. Such idealizations are an important tool
> for physicists and chemists. But it is quite common to assume the
> idealizations are the reality, when they are a model. Now of course we can
> go down the tangent here of discussing scholastic realism and the role of
> such idealisms as laws in science. But my sense is that perhaps gets us
> away from the questions at hand.
>
>> You seem to assume here that the thermodynamic principles (e.g.,
>> principles differentiating the equilibrium and dissipative systems)
>> obeyed in physics and chemistry are somewhat different from those obeyed
>> in more broad semiotics.
>
> I think there is a difference between idealized signs and the particular
> objects physics and chemistry studies in the real world. The question of
> the ontology of thermodynamics and thermodynamic law is an interesting
> one. However Ive intentionally avoided that discussion. Ill just say
> that Im discussing thermodynamics as used in physics (and thereby
> chemistry) rather than attempting to connect *formally* thermodynamics and
> semiotics either via information theory or other ontological commitments.
> Im just nervous enough about making that ontological leap. There may well
> be mathematical similarities between the two but the subject matter within
> physics simply is different. Put an other way while it is amazing the
> universe is as mathematical as it is I am not willing to make the leap to
> saying math is the fundamental ontology of the universe. That seems a leap
> too far and in need of considerable argument.
>
> So yes, Im making a distinction between semiotics and thermodynamics
> within physics conceived either phenomenologically (in the physics not
> philosophical sense) or in terms of statistical mechanics. I think we can
> discuss the latter as a semiotic system. But I think theres a difference
> between semiotics in the abstract and physics just as there is a
> difference between mathematics and physics. The later applies the former
> to physical phenomena.
>
> I recognize in saying this that at least the early Peirce adopts a
> quasi-neo-platonic ontology that would make semiotics a fundamental
> ontology. After once being convinced that was the view of the mature
> Peirce Im not much more skeptical of that idea. In either case even in
> Peirce did believe this I dont think he offers sufficient argument for me
> to adopt such a view. No matter how attractive it might seem.
>
>> I firmly believe that that following statement is true (and hence
>> recommend it to be referred to as the First Principle of Semiotics, in
>> analogy to the First Law of
>> Thermodynamics):
>>
>> No energy dissipation, no semiosis. (072814-7)
>>
>> The following corollaries would result from Statement (072814-7):
>>
>> Sign systems cannot perform semiosis (072814-8)
>> in their equilibrium states.
>>
>> Sign systems can perform semiosis if and (072814-9)
>> only if they are in non-equilibrium states.
>>
>
> I confess I dont see how those are true, depending upon how you specify
> energy dissipation. Or, perhaps an other way of putting it within a
> physical system is a total lack of energy dissipation possible? (I
> suspect, given what I said earlier, this quest for something beyond
> absolute zero is perhaps again the quest for the transcendent sign)
>
> I would like you to perhaps break out a little more what you mean by
> equilibrium state. Again there are temporal issues at play. For instance
> even a system that, when perturbed, returns to its original state can be
> said to be in a kind of equilibrium yet when analyzed carefully along a
> temporal analysis there are places where actions are taking place. (In
> particular the purtebation) It seems like you are considering a start
> state and end state but neglecting what happens in the middle.
>
> Now of course for some sorts of physics (say within Feynman diagrams for
> the quantum mechanical analogy of Lagrangian mechanics interactions) we
> can talk about virtual particles and cant say whether such virtual
> particles are really modifying or not. Mathematically they are the same as
> if they were undergoing all sorts of changes. However in terms of the
> thermodynamic analysis in which you are making of course theres all the
> difference in the world.
>
>> Yet (and this is key for Peirces semiotics) there is (072814-12)
>> always a gap between object and interpretant in this
>> process. For Peirce this is best conceived by way of
>> the Epicurean notion of swerve.
>>
>> This statement is interesting to me because it seems to bring together
>> semiotics and thermodynamics in an imaginative manner. If I am right in
>> interpreting the Epircurean swerve as analogous to Brownian motions in
>> statistical mechanics, i.e., the microscopic version of thermodynamics,
>> just as Democritus atom is analogous to the quantum mechanical atom, I
>> can see how Epicurean swerve may be implicated in semiosis. Brownian
>> motions are random, whereas semiosis is non-random, but these two may be
>> fundamentally linked if we can assume that semiosis implicates selecting
>> one out of all possible choices made available by random motions. This
>> picture of semiosis is suggested by my recent findings (i) that the
>> decision-time histograms fit the Plackian distribution function (PDF),
>> also called GPE, the generalized Planck equation (see Eq. (2) in [1])
>> and
>> (ii) that PDF can be derived from the Gaussian distribution function
>> based on the drift-diffusion model of decision making [2, 3].
>
> While Epicurus swerve has some parallel to statistical mechanics I think
> he meant it in a far more fundamental ontological fashion. Peirces
> adoption of this notion also was a fundamental ontology. One can of course
> disagree with Peirce but it is quite interesting that he did adopt such a
> notion during an era of physics when determinism ruled. Decades before
> quantum mechanics was discovered let alone accepted uncontroversially.
>
> I think one should be careful here or at least make explicit ones
> assumptions. (Peirce is quite good about that) I think Peirces point
> though is that semiosis unavoidedly has this random element to it. This
> can be conceived along two different axes. First the semiotic evolution as
> the object determines its interpretant. (It is key for Peirces semiotics
> that one starts with object not the interpreter as in so many others
> conceptions - in modern philosophical parlance I think this means that
> Peirce is an Externalist. At least epistemologically and semantically and
> most likely in other ways as well.) There is an element of swerve in this
> process from object via sign to interpretant. Indeed this gap is key to
> Peirces conception of sign. (He makes this quite explicit in his mature
> thought such as in his Letter to Lady Webly) When we reverse this process
> in order to interpret signs in order to understand their object we have to
> bridge this gap with a guess. This is the place of abduction. The gap can
> never be eliminated which is why such regulatory concepts as Peirces in
> the long run and the community of inquirers play such an important
> role.
>
> The problem of treating this gap as random can be dangerous as one must
> then unpack what one means by random. I confess this is an area of Peirce
> I just havent read much on. So perhaps others can chime in. My sense is
> that random as used in gaussian distributions or the like assumes a
> particular distribution that the gap in a sign doesnt assume. That is
> randomness of the sort we typically worry about in physics or statistics
> is actually well defined. (Thus our focus on gaussian or poisson
> distributions for example) What Peirce wants is something far more
> fundamental in its indeterminism. How far he wishes to go, whether merely
> epistemological or ontological I cant say. Certainly in his early
> neoPlatonic period it seems quite deep indeed. (See Peirce as a
> NeoPlatonist: The Ascent of the Soul to Nous by Kelly Parker for an
> excellent treatment although in one key place in his argument the evidence
> isnt quite as strong as one would wish)
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