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Author
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Topic: Darwinian Chance vs. ID Mechanism vs. Robust Physics of Function
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James A. Barham
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Member # 50
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posted 26. April 2002 10:47
The thread on Common Descent has spawned several interesting discussions around the role of chance in evolution that were however off topic for that thread. I thought I would open a new thread to give them a home.
I would like to begin by drawing attention to an important new empirical/theoretical study, which is one of the first fruits of the new Institute for Complex Adaptive Matter:
K.J. Harrington et al., "Balanced Branching in Transcription Termination," PNAS (2001) 98: 5019--5024.
In this study, Harrington et al. challenge the Darwinian explanation for the observed high efficiency with which RNA polymerase reads the stop codon in the procaryotic DNA transcription process (by which the mRNA molecule is produced). (To be more precise, the phenomenon at issue is the "balanced branching ratio" of the termination process. While I think I understand the gist of this article, I freely admit that many of the technical details in it are over my head. Moreover, the branching ratio phenomenon does not appear to be discussed in Alberts et al., so if anyone can explain to me exactly what the branching ratio means, I would be grateful.) According to the standard Darwinian interpretation, this is a "stochastic" phenomenon that is "fine-tuned" by natural selection.
Harrington et al., in contrast, hold that the balanced termination efficiency requires an explanation, and that "The idea that a miracle of evolution causes this phenomenon is quite unsatisfactory because it is too robust" (p. 5019). They go on to note that "There is abundant evidence that large enzymes and proteins often possess 'glasslike' properties of hysteresis, metastability, a broad spectrum of relaxation times, and memory" (p. 5020). From evaluation of the empirical evidence, they conclude that the robust efficiency of the phenomenon at issue can best be explained by positing a small number of metastable states within the RNA polymerase that make the process more nearly deterministic than stochastic.
In conclusion, they write as follows:
"It must be emphasized that our identification of memory as important in termination is based on considerable physics, not phenomenology. The balance in termination is too robust, in our view, to be caused by a delicate balance of stochastic transition rates. A molecule the size of RNA polymerase possesses a spectrum of natural time scales spanning 15 orders of magnitude. Without a physical principle that selects out one of these as preferred, rates should never compete in a balanced way. No microscopic model that can do this has ever been constructed, nor can it be, in our view. However, systems of this size exhibit hysteresis and memory very generally, and indeed only fail to do so if they crystallize with small unit cells. Thus, termination that is partly a deterministic decision based on the state of the polymerase is both physically reasonable and capable of accounting naturally for balance, provided that the number of states is small" (p. 5023).
How does this study relate to the three explanatory frameworks of Darwinism, Intelligent Design, and Self-Organization?
First, granting the validity of the empirical study undertaken by Harrington et al., the "chance" interpretation is definitely defeated. Now, of course, the Darwinian will simply move the "chance" up one level and say that the "mechanism" of the RNA polymerase has simply been harnessed by natural selection. But at least we have here a clear case of a crack in the Darwinian armor. Each and every invocation of "chance" in the Darwinian metaphysics is likely to succumb to exactly the same form of undermining from physics, in my view.
From the ID perspective, I suppose, one could simply say that the RNA polymerase is a fabulously well-designed "machine." But once we admit active matter whose internal dynamics accounts for the robustness of biological phenomena, it seems to me that we have lost the main motivation for invoking external design. Of course, an Occasionalist viewpoint is always open as a fall-back position (just as one can reconcile theism with Darwinism, if one is so inclined). However, it seems more fruitful to me to view the idea that intelligence is being applied externally vs. the idea that intelligence is welling up spontaneously out of the internal dynamics as competing hypotheses.
Finally, for me the fundamental issue is that of robustness. Machines by definition have their functional configuration imposed on them from the outside. Their own matter is quite inert insofar as their functionality is concerned. All such systems are inherently brittle, meaning that the functional configuration tends to degrade over time due to the second law. As Albert Szent-Gyorgyi once remarked: "In a car the screws and bolts are gradually loosened by use while in the living system they are tightened" (The Living State, NY: Academic Press, 1972, p. 41).
Since biological systems are highly robust, and since robustness can only be accounted for via some form of physical law, then I would claim that there is a strong prima facie case for taking a "vitalist" physics of biological function seriously. It seems to me that Harrington et al. is one of the first solid empirical studies to back up this general metaphysical claim.
[ 26 April 2002, 10:47: Message edited by: James A. Barham ]
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Art
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posted 26. April 2002 18:55
Hi James,
Regarding the study you mentioned by Harrington et al., I thought I’d toss in a few comments (and maybe clarifications – maybe not, depending on how well I can convey these thoughts).
First – donning my molecular biology instructor coat, I think it may be helpful to clear up a bit of confusion. That is, namely, that transcription termination has nothing to do with stop codons (which are relevant to translation, a totally different if equally fascinating subject).
Second – I am a little bit confused as to why you view von Hippel’s model as “the Darwinian explanation”. Surely you are not equating the idea of a stochastic process with some sort of “random, un-directed” one. (Von Hippel’s model is neither, BTW.) I cannot see any other interpretation of your post, though. In any case, von Hippel’s model and the deterministic model that Harrington et al. are advocating seem to me to be equally “Darwinian”. Indeed, the latter model is more so, since it brings a large degree of unity to mechanisms of termination in eukaryotes and prokaryotes (as an extreme degree of common ancestry might presume).
Thirdly, just to have some fun with this particular phenomenon, maybe you could try turning some preconceptions on their head, and thinking about robustness and termination in a different light. Specifically, what if a proclivity for termination were the default or chemically and physically inherent state(s) of RNA polymerase? What if the addition or alteration of function in this case involves a transition to high processivity?
Finally, for now, my own take on this paper. I think that this paper may be of interest, but their conclusions are actually rather unremarkable. The model Harrington et al. advocate is pretty similar to that which is widely accepted for termination in eukaryotes, and has gathered increasing support in prokaryotes as well. Harrington et al. couch their ideas in rather curious (or, for this forum, provocative) terminology, but the metastability and “learning” are actually nothing more than a cycle of RNAP modification (covalent or noncovalent, depending on where we are) that converts RNAP between highly processive and poorly processive forms. The authors make this much fairly clear when they speak of the roles of termination and antitermination factors. (What I guess I am saying is that, IMO, the authors are arguing after the fact that a physical modeling approach reaches the same point, and speaks more clearly in favor of one than another of the mechanisms that have been floated and tested, as does a whole lot of biochemical and genetic experimentation.) In this light, I would not be inclined to read much of a “vitalist” bent into this study. Rather, I see it as an attempt to show how a "first principles" approach can bring us to the same point as those in which biochemists seem to lose themselves in.
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James A. Barham
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posted 27. April 2002 07:45
Art:
Thank you very much for your help. I'm sorry for the confusion, and getting the terminology mixed up. My problem is that Harrington et al. speak only of "termination," whereas Alberts et al. (3rd ed.) speak of "stop signal" (p. 225) as being synonymous with termination. I guess "stop codon" was my own contribution to the terminological confusion.
Can you throw any light on the "balanced branching ratio" issue, for me?
As for my "vitalist" interpretation, I am not saying that Harrington et al. themselves would go that far, although they are certainly pushing their physical model hard, as opposed to the standard biochemical or stochastic model (von Hippel et al.).
The way I see it, the issue is this. According to Darwinism, the functional correlations in the cell are all "accidental" in the first instance, and can only be rationalized by the selection mechanism. Another way of putting it is that you cannot get functional order out of pure biochemistry or pure statistical mechanics.
But along with many others I dispute the idea that the selection mechanism can create order where there was none. Rather, what Darwinism is doing is presupposing the functional order of the cell surreptitously in many of its fundamental concepts ("survival," "fitness," etc.). In my view, order only arises ultimately out of collective or coherent modes of matter, i.e., out of quantum field physics. If we are to understand life, we must try to extend QFT somehow in order to encompass the living state. This means, above all, understanding the functional properties of proteins (see the work of Hans Frauenfelder, Peter Wolynes, and others) and the global properties of the protein-water gel (Gerald H. Pollack, Cells, Gels, and the Engines of Life, Seattle: Ebner & Sons, 2001). Giuseppe Vitiello, Emilio Del Giudice, and others are attempting to tackle this problem directly via QFT, but of course their approach is pioneering and highly speculative. Who knows what the right approach is?
My only claim is that something like this is logically required by the overall problematic we are faced with, mainly because "chance" is simply out of the question as the primary factor (certainly it will remain a secondary factor). If that is right---if there are intrinsic physical reasons why functional order arises in the cell---then we are looking at a fundamentally different type of explanation of the intelligent agency of life, one that is not mechanistic and reductionist, but rather dynamical and emergentist.
I realize that I am out on a limb here, with respect to what most physicists themselves are willing to say (but see Laughlin's PNAS manifestoes, and his book outline). As a philosopher, though, I am interested in looking at the larger picture---trying to understand how the intelligent agency of life is possible in the light of everything else we know. Looking at the limitations of the conventional biochemical and Darwinian approahces, I have become convinced that a physical approach is the only one that makes sense. Of course, whether the Harrington et al. article actually supports my view is another question. I think it does, but since I admittedly am no expert in molecular biology, I certainly could be wrong.
Anyway, thanks again for your help! I appreciate it very much.
[ 27 April 2002, 07:48: Message edited by: James A. Barham ]
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Art
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posted 29. April 2002 08:50
Hi James,
Getting back to this subject: You asked about “balanced branching ratios” - as far as I can tell, the branching ratio is the ratio of terminating and non-terminating polymerases in any population, and that it is balanced means that the ratio is decidedly different from either zero or one. Harrington et al. are of the opinion that the physical properties of macromolecules as large as RNAP do not permit such a balance to be struck in a stochastic manner.
I’m still not clear as to your train of thought vis-à-vis the Darwinian implications of this process. Probably, the confusion arises out of my own (mis?)conceptions about quantum ideas, statistical mechanics, self-organization, and the like. I am of the mind that there is no distinction to be made between quantum mechanical concepts and statistical mechanics; indeed, I usually rationalize the former in terms of the latter when it comes to the macroscopic. More importantly, I think that living things can easily, and instructively, be described in statistical terms, in terms of large arrays of macromolecules that interact differentially in time and space. In this light, I would argue that the intrinsic reasons that order arises in nature are eminently mechanistic and reductionist - to the point that they flow naturally, inevitably out of the fundamental fabric of nature. (I rather suspect that my naivete regarding “quantum” ideas needs some redressing here ![[Smile]](smile.gif) .)
Another interesting matter here is the idea of selection as it relates to transcription termination. I suspect (but would gladly accept a rebuke) that the focus of selection in the case of the Harrington et al. paper is usually taken as the formation of the 3’ end of the RNA. This view seems to demand an exactness or precision that indeed may seem difficult to rationalize in a Darwinian manner. However, once we remember that 3’ ends are generally not formed by termination, but rather by RNA processing, then the “need” for this precision disappears. Of course, it may seem that the “need” for termination also does, but this misses what is, IMO, the real “niche” for termination in the scheme of things - namely the need to recycle RNAP so that new rounds of transcription can be initiated. Precision is not needed for this purpose, which is satisfied by either the stochastic or deterministic modes under discussion here.
Finally (for now), I would reiterate an idea I clumsily put forth in my earlier post - that, when it comes to the evolution of transcription termination, it may be useful (and it is fun, if nothing else) to think in terms of processivity as being the “added” function or derived state. This is as much an exercise of casting off preconceptions as anything else, but it sheds real insight into the process.
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James A. Barham
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posted 29. April 2002 15:45
Art:
If anyone is naive, I am sure it is me, but let me at least try to clarify what I mean (and what I take Harrington et al. to mean---perhaps wrongly) by the distinction between a "stochastic" or purely "biochemical" process, on the one hand, and a "physical" or "quantum mechanical" one, on the other.
If an enzyme is fundamentally no different from an inorganic catalyst, then the fact that it is present in a given time and place in the cell can only be attributable to chance. That is, there is no intrinsic tendency (at least that I am aware of) for ordinary catalysts to partcipate in particular reactions in a biased way. That is, although a catalyst can bias which way a reaction goes, there is no higher level principle or force or constraint that is biasing the catalyst itself so that it is precisely in the place where it is needed by the functional logic of the cell, at the time when it is needed. In short, all there is, on the standard view, is biochemistry, and the only way the biochemistry can cohere together is through random collisions. Darwinians believe this is okay because once the "right" reaction happens by chance, then it is "selected" and we don't have to worry our heads any more about that one, and we can go on to the next one.
From the point of view of physics, I submit, none of this makes any sense. Nothing in the cell is really happeneing at random. It is all a vast "conspiracy" to make everything come out just right. And furthermore, it is responsive and adaptive to external conditions moment by moment. Chance simply cannot be a major factor in any of this.
What is the alternative view? That there is some sort of higher-level order that is constraining things to happen in a rational, goal-directed way. What might this order consist of? Of course, I don't know, although I have speculated that it might have something to do with the fact the phase space of protein vibrations defined by all of the isoenergetic substates possible has been empirically observed to be "condensed." That is, a protein seems to be obeying some sort of conservation law that is constraining its motions from within. This has been called by Hans Frauenfelder and colleagues the "minimum frustration principle" ("frustration" being the technical term used in condensed-matter physics to describe the inability of very large molecules with very many self-interactions to relax into a minimum-energy state).
Now, obviously, you don't get the overall functional coherence of the cell out of minimum frustration alone, although I think that we must absolutely find some sort of inherent tendency toward functional order at the macromolecular level in order to give a satisfactory account of the functional organization of the cell. No doubt, there is order at multiple levels, including that of the cell as a whole. But there is not even any speculative scheme I am aware of to explain global functional coherence. At least the protein minimum frustration idea is something to work with.
As far as quantum mechanics is concerned, we are talking here about macroscopic quantum coherence (like in lasers, superconductors, crystals, etc.), not atomic-level quantum processes. So the appeal to QFT is an appeal to a lawlike process, not to an acausal process.
Actually, I believe that we must eventually learn to think in terms of 3 separate "causal" regimes: purely indeterministic (acausal), quasi-deterministic (I do not believe that strict determinism exists), and goal-directed or teleological (basically, a low-energy trigger-dependent nonlinear oscillator). That is, I do not believe that funtionality (intelligent agency) can be reduced to either deterministic causes or to indeterministic deviations from strict causation. There must be a sui generis form of "causation" (for lack of a better word), if the cell is to make any sense. (Walter Thirring and other physicists talk about the "evolution of the laws of nature" over the course of cosmic evolution---what I am saying is that this sui generis form of final causation is emergent with the origin of life.)
At any rate, if there is anything to any of these ideas, and proteins spontaneously seek out their functional states, and even perhaps spontaneously aggregate into functional units, then that is very different from the standard view of biochemistry, where everything is supposed to happen "by chance", is it not?
Now, as I acknowledged in my original post, the Darwinian can always co-opt any form of physical order at a higher level (the proteins could be "selected for" their minimum frustration capabilities), but I view that as a retreat that will inevitably turn into a rout.
It is another question yet again whether I have interpreted Harrington et al. correctly, but it seems to me that the whole point of their article is to say that the RNA polymerase molecule has an intrinsic tendency to fulfill its function, and so we are no longer obliged to invoke a purely random, purely biochemical process.
That is the way I understand it, but if I am wrong, I am very willing to be set straight!
[ 29 April 2002, 15:53: Message edited by: James A. Barham ]
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kyle7
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Member # 191
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posted 02. May 2002 07:21
James,
Thanks again for so many lucid posts. I enjoy reading them.
I am not an expert in QM but I have a general understanding of the topic (not real deep though), so feel free to point out any errors that you may see.
First, let me address the issue of "random" versus "stochastic". Neo-Darwinists seem to dislike the term random when speaking of mutations. A definition of the term random from Webster's New World Dictionary is the following:
"3. Statistics with each in a set or group having an equal opportunity of occurring or of occurring with a particular frequency."
If we could repetitively perform cell fusion on the same two cells, over time we could develop a distribution over the length of the DNA that would specify the probability for mutation. Integration over the length of the genome would result in one. Now, the probability would vary over the length of the DNA, but the general trend would not vary significantly. Using the definition of "Random", as specified above, would apply to the mutations. The frequency of mutation could be specified over length segments of the genome. This point may seem insignificant, but I voice it because some Neo-Darwinists present an illusion that "stochastic" mutations are somehow significantly different than random mutations in relation to the probability of macroevolution. Even taking the stricter definition of "random" (mutations being equally probable over the genome) does not necessarily make it more probable. This can be seen in cases where the mutations need to occur at low probability points along the genome.
You speculate how phase space of protein vibrations may hold an answer to evolutionary biological development. You say:
"I have speculated that it <higher-level ordering> might have something to do with the fact the phase space of protein vibrations defined by all of the isoenergetic substates possible has been empirically observed to be 'condensed'. That is, a protein seems to be obeying some sort of conservation law that is constraining its motions from within. This has been called by Hans Frauenfelder and colleagues the 'minimum frustration principle' ('frustration' being a technical term used in condensed-matter physics to describe the inability of very large molecules with very many self-interactions to relax into a minimum-energy state.)"
First, I would like to point out that we can use statistical thermodynamics derived from a quantum mechanics perspective to analyze systems. For example, we can analyze isolated polymer molecules in dilute solutions. The canonical ensemble partition function uses a sum of energy levels and not states as used by the classical method. I believe the same methods are being applied to DNA and RNA structures - though in a limited way. The point of this discussion is that Quantum Mechanics applied to statistical thermodynamics is not shedding light on how complex specified mutations occur in biological systems.
You mentioned the phase space of protein vibrations as being a possible reason for biological ordering. I think this argument is similar to the dissipative structures argument for self-ordering. There are simple systems found in nature that act as thermodynamic mechanisms (or devices), which allow complex ordering. I hardly dare call the systems complex, because really they don't even compare to life, which not only has complexity of form but function. One example of a dissipative system is the water action on the beach. The waves of water wash up on the shore and order the sand, sometimes in ripple patterns. Now if we walked along the beach and found an ordering of the sand into the words "I am here", we would not explain away the event due to natural causes - at least most would not. I am sure that some ingenious person could analyze wave patterns using Monte Carlo methods and fluids analysis and come up with a theory how the words naturally came into being. Most people would see that an intelligent agent wrote the words in the sand, given that the ordering of the sand is complex and specified. The probability of natural phenomena explaining the words is too small.
Another example of ordering occurs in the waves of a rope. For example, we could take a long rope and tie it to a wall and pull the rope tight. Next, we could vibrate the rope and try to create a mode of vibration that spells words. For example, I may try to spell my name by alternating the amplitude and frequency of the vibration. You may be able "write" the letter "n" but you would find it very difficult to write your name! The constraints imposed by nature can be limiting. A mathematical way to analyze this problem, investigating if a wave form is designed by an ID agent or not, would be to use Fourier Analysis. The Fourier series is of the form:
Y(x) = <summation sign, n = 1-infinity> An Sin(w1n*x) + Bn Cos(w2n*x)
This infinite series can be used to describe any function f(x) exactly. An approximate solution can be found if you take the solution to less than infinity, assuming the function is not a "simple" sinusoidal function. The more complex the function you are seeking to duplicate (e.g. the more letters you are trying to spell out) the more Fourier coefficients are needed to describe your function, such that your letters are readable. Although my example is not exactly precise, I think that anyone with a mathematical background will understand what I am saying. The number of required Fourier coefficients can therefore be a measure of the specification of the CSI, though one has to keep in mind what are the relevant phenomenological factors. This wave discussion applies to QFT. I don't think answers concerning Neo-Darwinian theory will come from QFT, though further investigation is warranted. Again, the issue of CSI comes into play. It may help to coin the phrase "complex specified dynamics" (CSD). Maybe we could start a discussion on this topic.
You also discuss the "minimum frustration principle". You define frustration "as being a technical term used in condensed-matter physics to describe the inability of very large molecules with very many self-interactions to relax into a minimum-energy state". I think there is a common sense explanation for this. The large molecules require activation energy at precise locations to enable the molecule to alter position so that minimum energy is achieved. Without this precise application of energy, a higher energy state is maintained. Another term that I would propose for the ID movement is "complex specified application of energy" (CSAE). For example, to build a house one cannot put the building materials together with a fuel (enough to build the house) and expect the house to be built after the fuel is ignited. One would have to apply the energy very precisely. Nails would have to be pounded into the wood at precise locations. Tile would have to be laid down using precise energy. We could go on and on describing the requirement of precise applications of energy. CSAE as well as CSD are evidence for ID agents.
In conclusion, the natural laws of physics constrain our environment but do not explain systems with CSI, CSD, or CSAE.
[ 02 May 2002, 07:26: Message edited by: kyle7 ]
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James A. Barham
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posted 02. May 2002 23:07
Kyle7:
Thank you very much for your extensive response to some of my ideas. I am much in need of feedback of this sort, and very glad indeed to get it. BTW, I think you probably know a lot more of the science than I do (I am just a poor humanities scholar, turned philosopher, turned amateur compiler of scientific information, all in an effort to understand what I am doing here!).
I don't mean that to be a cop-out, though. I want to get this all as straight as I can. I think I understand what you are saying, and really can't find much of anything in your posting to disagree with, except to try to point out the couple of places where what I am saying goes beyond conventional views of physics. I think one of the basic problems is that among philosophers "physics" usually means high-energy physics, whereas I think it is condensed-matter physics that is most relevant to understanding the problems we deal with here at ISCID.
First, let me ask you if your view of physics is basically reductionist, or emergentist? I am most impressed with people like Philip W. Anderson (author of the famous paper "More Is Different") and Robert Laughlin, who argue that the "Theory of Everything" view of people like Stephen Hawking and Steven Weinberg is fundamentally mistaken. Rather, they view physics as a "tower of effective theories." An "effective theory" is one that has to have order parameters put in by hand for the length and time scales in question (these are the emergent properties of the system), although the general form of the equations may be carried over from higher energy levels (these are the "universality classes," as I understand it). The renormalization group is the crucial mathematical formalism used to rescale theories in this way. This is my fundamental understanding of "emergence" (this is all beautifully laid out in the new book by Robert W. Batterman, "The Devil in the Details").
Now, if you are willing to go along with me this far, then I can answer a couple of your points. The main thing I am saying is that by positing a higher-level conservation principle that may be active in the cell ("minimum frustration," or whatever it may be), we are precisely getting beyond a purely statistical mechanical or thermodynamic approach. We are also going beyond nonequilibrium thermodyamics, which we certainly must do, since a hurricane is not alive! It is not alive precisely because it is entrained willy-nilly by local thermodynamic gradients (even though it is self-organized to a degree). In short, self-organization is necessary but not sufficient for life and for intelligent agency.
What else is necessary? The basic problem of teleology may be stated as follows: The cell is not merely minimizing energy, it is doing work---that is, it is moving things around (by drawing on stored energy) in a purposeful way, namely, in such a way as to maintain itself out of equilibrium with its surround. In short, it is resisting (not violating) the second law.
How does QFT help explain how this is possible? Well, we don't really know that it does, but there are hints. The basic idea is that with each new emergent level you get symmetry breakings; with each symmetry breaking, you get collective, coherent "Goldstone modes" of the quantum field, obeying some conservations laws. The speculation is that the cell somehow forms coherent modes that obey a rational or teleological principle---moving things around in order to preserve itself---instead of a mere action principle (energy minimization).
I realize this is all horribly speculative and hand-waving. But if you interested, do read Giuseppe Vitiello's book, "My Double Unveiled: The Dissipative Quantum Model of Brain." It is the best semi-technical discussion of these basic ideas that I have found. There are some other aspects to my idea (like F.E. Yates's "homeodynamics" and my own low-energy trigger model of intelligent action), but the quantum coherence and the conservation principle based on some higher-level conserved quantity (like minimum frustration) are the foundation upon which everything else rests.
I don't say any of this is right. I merely say that something LIKE this is necessary if we are to explain the manifest intelligent agency of the cell in naturalistic terms.
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