Clark wrote (072814-1), (- 2), (-3), (-4), (-5), (-6), (-12) and (-13): "The implications of this are quite important and demand (072814-1) we consider the thermodynamics far more holistically."
I don't understand what you mean by "holistically" here. I thought there is only one way to understand/interpret thermodynamics -- scientifically. I suppose, depending on context, you can interpret thermodynamic concepts and laws "non-scientifically", "non-professionally" or "common-sensically". Even then, it would be necessary for effective communication to define what one means by certain thermodynamic terms and clearly understand the difference between "scientific" vs. "non-scientific" uses of such terms, including "equilibrium state", "steady state", and "dissipative state". Whenever we talk about equilibrium we are always really (072814-2) talking about equilibrium in a particular context and period. What you say is fine for that. But when we move from these more artificial chemical examples to the broader examples of writing and speech that context matters and matters a lot. Context matters in both thermodynamics and semiotics, since both deal with system and environment and their mutual roles in determining functions and meanings. In other words, functions and meanings are determined not by systems alone (as often believed) but by the combination of a system and its environment (for which I introduced a neologism, systome, in [biosemiotics:4003] attached below for your convenience). The obvious example is the equilibrium of magnetic tape. (072814-3) In practice we always end up with semi-permanent equilibrium. 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. Hopefully I clarified why there is at best a continuum (072814-4) between these two categories. And indeed Id question whether true equilibrium of the sort you specify is truly possible except as a regulative theoretical concept. (Much like the ideal gas law ends up being an idealization) 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. Semiotically this is very important because contamination (072814-5) is always going on. As in physics and chemistry we can do theoretical or empirical perturbation analysis to see how well a system can withstand noise and maintain its equilibrium. However these are often statistical and there usually is a point of external energy where the system starts to break down. This energy can be external or internal (say the very stability of particular chemicals over time). I agree with what you say here if I can replace equilibrium with steady state. Equilibrium systems can maintain their state against noise without any help from outside, whereas steady-state systems cannot maintain their equilibrium (or better homeostasis or no-change state) without receiving energy from external sources and can breakdown with aging, but equilibrium systems do not breakdown, because they have already done so to reach their equilibrium state. When one moves from physics and chemistry to more broad (072814-6) semiotics this principle becomes quite important since equilibrium is maintained by a kind of replication of the sign system as it undergoes semiotic process. 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 disagree, because no sign system can exist in an equilibrium state and still carry out semiosis. 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. Thermodynamic principles universally apply to all (072814-10) physicochemical processes in nature, including those underlying life and semiosis. The statement that equilibrium is maintained by a (072814-11) kind of replication of the sign system as it undergoes semiotic process is invalid since no sign system at thermodynamic equilibrium can perform semiosis without violating the First Principle of Semiotics. 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]. I think a major theme of semiotics in the second half (072814-13) of the 20th century, regardless of jargon, is the denial of such a transcendental sign. Effectively this is the denial, in your terminology, of a pure equilibrium structure. I wonder if our views can be reconciled if we agree (i) that a pure equilibrium is a macroscopic concept which consists of myriads of Brownian motions of molecules at the microscopic level and (ii) that motions divide into random motions (obeying the Gaussian distribution function) and directed/rectified motions obeying the Planckian distribution functions (as exemplified in Figures 5 through 12 in [1]). If you have any questions or comments, please let me know. 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. (2014). Experimental and Theoretical Evidence for the Energy Quantization in Molecular Machines and Living Cells, and the Generalize Planck Equation (GPE). A poster presented at the EMBO/EMBL Symposium on Molecular Machines, Heidelberg, May 18-21. Poster available at conformon.net under Posters and Abstracts. [2] Ji, S. (2014). Planckian Distributions in Molecular Machines and Living Cells: Evidence for Free Energy Quantization in Biology. Computational and Structural Biotechnology Journal (to appear). [3] Deco, G., Rolls, E. T., Albantakis, L., and Romo, R. (2013). Brain mechanisms for perceptual and reward-related decision-making. Progr. Neurobiol. 103: 194213. ----------------------Attachment--------------------------------------- Subject: [biosemiotics:4003] SYSTOME as the complementary union of SYSTEM nad ENVIRONMENT From: "Sungchul Ji" <[email protected]> Date: Mon, December 2, 2013 9:30 am To: [email protected] Priority: Normal Mailing List: Help | Subscribe | Unsubscribe | Post to List | Reply to List | Contact Listowner | List Archives Options: View Full Header | View Printable Version | Download this as a file | View Message details | Bounce Hi, The terms system and environment have been widely used in many fields of natural, engineering, and social sciences for over a half century. Most discussions on systems, e.g., 'systems biology', systems physiology, etc. tend to focus on the structure and workings of a system and its components rather than on the systems' environment and its effects on the system . A paradigm example of system-biased approach to science is provided by the protein folding experiment of Anfinsen carried out in the 1950s focuses on the changes in the conformational structure of a protein, ribonuclease A. His experiments viewed this enzyme as a system and downplayed the role of the environment of the protein on its conformations. To be more specific, when he denatured ribonuclease molecules by adding 2-mercaptoethanol (2ME) and urea and are allowed the denatured protein to refold under two different environmental conditions, i.e., A (removing urea before 2ME) and B (removing 2ME before urea), the enzyme refolds into native the conformation under the condition of A but not B. (http://sandwalk.blogspot.com/2007/02/anfinsen-experiment-in-protein-folding.html). Thus, it is logical to conclude that The Anfinsen dogma is upheld when the refolding (1201-1) experiment is performed under the experimental condition A and disproved when it is carried out under the experimental condition of B. In other words, The Anfinsen dogma can be experimentally proven or (1201-2) disproven, depending on which of the two possible environmental conditions of the experiment is chosen. One corollary of Statements (1201-1) and (1201-2) is that The native folding of proteins is determined not (1201-3) only by the amino acid sequence of the protein but also by the environmental condition under which proteins fold. The concept of the environment of a system is synonymous with the term boundary condition of a system. There are two kinds of boundary conditions stationary boundary condition (SBC) and moving boundary condition (MBC). A boundary condition of a system can move or change in space, in time, or in both space and time. An example of a system with a boundary condition (this combination may be conveniently referred to as a systome; see below) that moves is the combination of a surfer who maintains his/her upright position and moving waves (see the picture attached). Another example of the systome with MBC is the beating heart (see http://vimeo.com/8321006) where the muscle cells are the system and the blood vessels and nerves providing oxygen and electrical impulses to muscle cells constitute the boundaries that are constantly in periodic motion. Thus, when what is observed is the result of the interaction between a system and its environment, it would be useful to have a term that combines the system and its environment. Since there seems to be no English word for such an entity, to the best of my knowledge, I elected to coin one: Systome, a neologism derived from system with a minimal alteration: Systome = System + Environment (1201-4) The following characteristics of a systome come to mind: A systome is characterized by a set of internal (1201-5) states, each with discrete (or quantized) enegy levels. Energy is defined as the systomes ability (1201-6) to do work, is in turn defined as the product of force and displacement. Depending on the properties of the boundary (1201-7) condition, the the energy of a systome can be internal energy, E, or Gibbs free energy, G = E + PV - TS, where P is pressure, V is volume, T is temperature and S is entropy. A systome can undergo state transitions (1201-8) from one energy level to another, leading to experimentally observable changes or observables of the systome, just as electronic transitions in atoms lead to emission or absorption of photons. I suggest that all of the Statements (1201-5) through (1201-8) presuppose the QUANTIZATION of ENERGY of a systome, without which no organization of any kind is possible. Since biological systomes are ORGANIZED in space and time, it would follow that their energies must be QUANTIZED, as directly demonstrated by the fitting of biological data from many systomes (e.g., proteins, enzymes, RNA metabolic network in cells, T-cell receptors, and human breast cancer tissues) to the blackbody radiation-like equation, BRE (see attached) -- the gold standard for the existence of ENERGY QUANTIZATION in physics. 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 > > On Jul 28, 2014, at 10:47 AM, Sungchul Ji <[email protected]> wrote: > >> Conversely, anything that remains unchanged when energy supply is >> removed >> would be equilibrium structures, such as an artificial candle or flower, >> the photograph of a computer screen with images, words written down on a >> piece of paper (which lasts a much longer time than a spoken word can >> after it leaves the vocal cord of the speaker), melodies encoded in >> sheet >> music, etc. > > Im not trying to be pedantic in what follows because I think it a key > issue. We have to qualify this with when a particular energy supply is > removed. This is key since of course we arent dealing with a closed > system except in very artificial thought experiments. The implications of > this are quite important and demand we consider the thermodynamics far > more holistically. This then leads to the points I raised earlier. > > Whenever we talk about equilibrium we are always really talking about > equilibrium in a particular context and period. What you say is fine for > that. But when we move from these more artificial chemical examples to the > broader examples of writing and speech that context matters and matters a > lot. The obvious example is the equilibrium of magnetic tape. > > In practice we always end up with semi-permanent equilibrium. > > >> By denying the distinction between equilibrium and dissipative >> structures >> in semiotics or philosophical discourse in general, one is denying the >> fundamental role that energy plays in these disciplines and hence the >> fundamental neurobiological mechanisms (or underpinnings) supporting >> such >> mental activities. > > Hopefully I clarified why there is at best a continuum between these two > categories. And indeed Id question whether true equilibrium of the sort > you specify is truly possible except as a regulative theoretical concept. > (Much like the ideal gas law ends up being an idealization) > > Semiotically this is very important because contamination is always going > on. As in physics and chemistry we can do theoretical or empirical > perturbation analysis to see how well a system can withstand noise and > maintain its equilibrium. However these are often statistical and there > usually is a point of external energy where the system starts to break > down. This energy can be external or internal (say the very stability of > particular chemicals over time) > > When one moves from physics and chemistry to more broad semiotics this > principle becomes quite important since equilibrium is maintained by a > kind of replication of the sign system as it undergoes semiotic process. > Yet (and this is key for Peirces semiotics) there is always a gap between > object and interpretant in this process. For Peirce this is best conceived > by way of the Epicurean notion of swerve. Peirce uses this by way of > analogy I think. (Others might disagree) However regardless of how one > takes Peirces ontology, I think the notion of this sign gap is a > tremendously significant in semiotics. > > Effectively to deny this gap is to claim the legendary transcendental sign > which is key to certain philosophies - especially many Platonic ones. I > think a major theme of semiotics in the second half of the 20th century, > regardless of jargon, is the denial of such a transcendental sign. > Effectively this is the denial, in your terminology, of a pure equilibrium > structure.
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