Making Biological Theory More Down to Earth (preprint 2012)
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1 Making Biological Theory More Down to Earth Koichiro Matsuno Nagaoka University of Technology Nagaoka 940-2188, Japan Abstract All of the basic functional components of living organisms participating in describing, translating and constructing themselves are described deep within the supporting dynamics itself. A most common material vehicle for implementing this type of self-organization is a material vehicle holding its own identity through the constant exchange of the constituent material elements. The exchange of materials serves as a material means for temporarily ameliorating the infliction of vicious circles being inevitable and latent in the self- referential complications when descriptively approached in the present tense alone, thus dissolving the difficulties in making their predication logically transparent on material terms. Since the exchange of materials is demonstrable experimentally as in the running of the citric acid cycle in the absence of biological enzymes under the conditions simulating the prebiotic environments in the vicinity of hydrothermal vents on the primitive ocean floor, the prior emergence of metabolism could make the subsequent emergence of metabolism-replication complex more likely compared to the cases otherwise. An essence of the occurrence of the material vehicle holding its identity through the exchange of reacting molecules with the new ones recruited from the outside is in the soundness of internalizing the description of the dynamics into the dynamics itself, which is approachable through the constant update of the present perfect tense in the present progressive tense. Keywords; citric acid cycle, description, exchange of materials, metabolism, relative state, self reference 1. Introduction To distinguish biology from physics is getting harder and harder as we approach the problem area related to the origins of life. If one happens to adopt the process-perspective instead of the state-perspective prevailing in physics, biology could be seen as a construct out of elementary processes rather than out of elementary particles (von Neumann, 1966). In essence, processes from the process-perspective are considered to be primary over objects to be specified by their state attributes, the latter of which are seen merely as derivative products of the processes. The issue of the origins of life now comes to address how the process-perspective could have taken over the state-perspective and on what ground. What is unique to the state-perspective is the priority of inexorable dynamical laws that can further be supplemented by the external boundary conditions assuming the auxiliary secondary role at best (Polanyi, 1967). In contrast, the process-perspective is peculiar in
Transcript of Making Biological Theory More Down to Earth (preprint 2012)
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Making Biological Theory More Down to Earth
Koichiro Matsuno
Nagaoka University of Technology Nagaoka 940-2188, Japan
Abstract All of the basic functional components of living organisms participating in describing, translating and constructing themselves are described deep within the supporting dynamics itself. A most common material vehicle for implementing this type of self-organization is a material vehicle holding its own identity through the constant exchange of the constituent material elements. The exchange of materials serves as a material means for temporarily ameliorating the infliction of vicious circles being inevitable and latent in the self-referential complications when descriptively approached in the present tense alone, thus dissolving the difficulties in making their predication logically transparent on material terms. Since the exchange of materials is demonstrable experimentally as in the running of the citric acid cycle in the absence of biological enzymes under the conditions simulating the prebiotic environments in the vicinity of hydrothermal vents on the primitive ocean floor, the prior emergence of metabolism could make the subsequent emergence of metabolism-replication complex more likely compared to the cases otherwise. An essence of the occurrence of the material vehicle holding its identity through the exchange of reacting molecules with the new ones recruited from the outside is in the soundness of internalizing the description of the dynamics into the dynamics itself, which is approachable through the constant update of the present perfect tense in the present progressive tense. Keywords; citric acid cycle, description, exchange of materials, metabolism, relative state, self reference 1. Introduction To distinguish biology from physics is getting harder and harder as we approach the problem area related to the origins of life. If one happens to adopt the process-perspective instead of the state-perspective prevailing in physics, biology could be seen as a construct out of elementary processes rather than out of elementary particles (von Neumann, 1966). In essence, processes from the process-perspective are considered to be primary over objects to be specified by their state attributes, the latter of which are seen merely as derivative products of the processes. The issue of the origins of life now comes to address how the process-perspective could have taken over the state-perspective and on what ground. What is unique to the state-perspective is the priority of inexorable dynamical laws that can further be supplemented by the external boundary conditions assuming the auxiliary secondary role at best (Polanyi, 1967). In contrast, the process-perspective is peculiar in
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internalizing the notion of boundary conditions into the processes themselves (Pattee, 1969). Despite that, conceiving of both dynamical laws and the associated boundary conditions on an equal par would raise a formidable problem of how could it be possible to incorporate the descriptive attributes of the boundary conditions into the dynamical processes themselves. Although the boundary conditions can be taken as a theoretical artifact to arbitrarily be imposed if they are regarded as being external to the dynamics in focus, the situation would be made totally upside down once they are taken to be internal to the dynamics. In fact, the boundary conditions must be internalized into the dynamics unless the anthropocentric intervention is forcibly allowed to participate in. The pressing agenda would now become how the dynamics in the natural setting could come to internalize the descriptive attributes that seem quite anthropocentric at least in their outlook.
In particular, any descriptive attribute appearing in natural dynamics is an abstraction because of its implicit appraisal of the abstraction adopted for addressing the relational activity of predication. Relating something to something else is an activity of abstraction since the underlying relational activity does not assume an exhaustive specification of those material objects in focus. The underlying problem is how one can approach a concrete implication of the natural dynamics as starting from those descriptive attributes that are already an abstraction.
The difficulty rests upon the self-referential complications of how the description of the dynamics could be described within the dynamics itself. Linguistic predication of such self-referential complications, if attempted without seeking the help of material and natural dynamics, would remain necessarily unsatisfactory and eventually end up with vicious circles or what may be called impredicativities (Rosen, 1991; Igamberdiev, 2012). If there is any hope for making an access to the likelihood of the process-perspective, it would be required to re-examine the extent to which the functional capability of each atom and molecule could be made descriptively accessible. At issue here will be how one can meet the material activity that could be assimilated with the act of an abstraction that may be done without the anthropocentric intervention. This will be an agenda to be explored in the present article. One prospective clue to addressing the functional capability of an elementary particle is found in the occurrence of the identity of such particle in isolation. The state-perspective being at home with inexorable dynamical laws takes the identity of an elementary particle for granted. Each elementary particle is taken as a functional unit keeping its own identity intact throughout there. However, this observation does not exclude the possibility of the occurrence of the material body whose identity could not reduce to a mere collection of the identities of elementary atoms and molecules in isolation. Consider, for instance, any of a biological organism. It can maintain its identity for some time even if its component particles are constantly exchanged with the new ones coming from the outside. Biology is full of such organisms maintaining their identities through the exchange of materials. That is a metabolism. This simple observation suggests to us that the process-perspective may establish its legitimate status even if the identity of an elementary particle appreciated
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solely from the state-perspective happens to be replaced by another type of the material identity maintained by the constant exchange of the participating elementary particles.1 The real issue is whether the occurrence of those material bodies or vehicles whose identities may be kept through the exchange of the participating elementary particles could be likely even before the onset of biology. Only when such a takeover of the state-perspective by the process-perspective could be likely prior to the onset of biology, there may be a hope for expecting the occurrence of biology running on the process-perspective. This issue must be settled empirically or experimentally, more than anything else, since the linguistic difficulties intrinsic in predicating the self-referential complications cannot be theoretically settled on the linguistic basis alone. One likely candidate for this type of endeavor could be to experimentally examine in a prebiotic setting the possibility of raising and supporting the material body whose identity may be kept through the exchange of the component material elements. 2. Running the Citric Acid Cycle One of the most ubiquitous material bodies supporting their identities through the exchange of the constituent material elements in biology is the oxidative citric acid cycle found in mitochondria in charge of the downstream part of glycolysis while extracting the energy and releasing carbon dioxide molecules from the participating carboxylic acid molecules. The citric acid cycle in mitochondria extracts the energy ultimately stored in pyruvate for the synthesis of ATP is heavily armored with highly sophisticated enzymes. The carbon atoms in the citric acid cycle are constantly alternated by the new ones supplied from pyruvate CH3-CO-COO- through the vehicle of the acetyl group CH3-CO- and are eventually released from the cycle in the form of carbon dioxide molecules.
Then, a serious question arises with regard to whether or not the presence of highly sophisticated biological enzymes mediating dehydrogenation and decarboxylation of the participating carboxylic acid molecules is prerequisite to the operation of the citric acid cycle. If these biological enzymes are prerequisite to the operation of the citric acid cycle, the likelihood of the cycle as a material unit processing the constant exchange of carbon atoms may be taken as a derivative of biology. However, if the cycle can run even in the absence of such biological enzymes under the conditions simulating the ones conceivable on the primitive Earth, the likelihood would come up to the surface such that the onset of the reaction cycle whose identity may be kept through the exchange of carbon atoms could have been prior to the onset of biology. This will be an experimental issue to be settled before entering into a theoretical speculation of how to make a descriptive access to the material body whose identity can be maintained through the exchange of materials. A key
1 If we try to associate Rosen’s internal principle of organizational invariance on being closed to efficient causation with the sought-after identity of material origin, it would beg the further question of how the internal principle could be vindicated and on what ground. In fact, the organizational invariance comes with the efficient causation in the form of the constant replacement of the participating elements. The underlying question will be whether the process of replacing the elements could be conceived of independently of the internal principle of organizational invariance as Rosen originally formulated.
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question to be settled experimentally at this point will be whether the occurrence of the exchange of materials could be prior or posterior to the onset of biology.
The oxidative citric acid cycle is a reaction cycle maintained by the carbon flow circulating in the direction as depicted in the scheme: oxaloacetate(4) → citrate(6) → isocitrate(6) → alpha-ketoglutarate(5) → succinate(4) → fumarate(4) → malate(4) → oxaloacetate(4), in which the number in the parenthesis attached to each carboxylic acid molecule is the number of carbon atoms included in that molecule.2 The source of the carbon flow is pyruvate(3) which supplies the acetyl group (2) right in the middle of the pathway of oxaloacetate(4) → citrate(6) from the outside of the cycle. There is also a reaction pathway for synthesizing oxaloacetate(4) from pyruvate(3) and carbon dioxide(1). In addition, carbon dioxide(1) is released from the pathway of isocitrate(6) → alpha-ketoglutarate(5) and also from the pathway of alpha-ketoglutarate(5) → succinate(4) in the second and the fourth round of the reaction cycle one by one. All of the carbon atoms constituting the cycle are alternated by the new ones before completing the fourth round of the cycle.3 The prebiotic likelihood of synthesizing each carboxylic acid molecule could be conceivable in the vicinity of hydrothermal vents on the primitive ocean floor (McCollom et al., 1999; Cody et al., 2000; Saladino et al., 2011).
We then used a flow reactor simulating a hydrothermal environment in the primitive ocean (Matsuno and Nemoto, 2005), and examined how the reaction solution including pyruvate and the member carboxylic acid molecules constituting the citric acid cycle, namely, oxaloacetate, citrate, isocitrate, alpha-ketoglutarate, succinate, fumarate, and malate could react among them through the operation of the reactor in the absence of biological enzymes. The reaction solution including various carboxylic acids was injected at a flow rate of 10 mL/min from a 15 mL heated chamber at 120oC and at 15 MPa. The reactants passed through a thin nozzle of diameter 0.8 mm into a larger and cooler chamber at 0°C and approximately the same pressure. Most of the reaction fluid stayed in the large vessels of about 580 mL altogether in stirring conditions at 0°C. Cycle time of the total volume of fluid (600 mL) was about 60 min, but with stirring the reactants cycled roughly once per minute. A summary of the intended experiments (Matsuno and Nemoto, 2005; Matsuno, 2006; 2012a) will be presented in the following.
Firstly, we circulated in the flow reactor the standard mixture solution of the complete set of eight different kinds of carboxylic acid molecules including 10 mM concentration of pyruvate as the carbon source, and 1.0 mM of each of oxaloacetate, citrate, isocitrate, alpha-ketoglutarate, succinate, fumarate and malate. The result was that the reaction cycle was operative. The amount of citrate, for instance, was found to increase with the reactor operation. In particular, a uniform increase of the pH value of the reaction solution with the
2 Although aconitate(6) may intervene in the middle of the pathway of citrate(6) → isocitrate(6) through dehydration and hydration, it is not explicitly displayed in the scheme because of the relative ease with its synthesis and transformation. 3 Each of the carbon atoms constituting the citric acid cycle is distinguishable at least in the sense that each of the two carbon atoms in the form of the acetyl group CH3-CO- supplied into the cycle initially can eventually leave the cycle as an outgoing carbon dioxide molecule only after it is transformed into a carbon atom in the carboxyl group -COO- before completing the fourth round of going around the cycle.
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elapse of time indicates that the unidirectional oxidative reactions letting the water molecules be the effective electron acceptors are constantly operative. Even if the concentration of oxaloacetate may look stationary, the uniform increase of the pH value with time is consistent with the participation of constant through flow of carbon atoms to and from oxaloacetate as being mediated by the underlying oxidative reactions including dehydrogenation and decarboxylation.
Secondly, we ran the flow reactor for the reaction mixture including the seven different kinds of carboxylic acid molecules differing from the standard solution only in the absence of pyruvate in order to examine the likelihood of the occurrence of the reaction cycle. The result was no occurrence of the reaction cycle as being accompanied by no significant variations of the amount of each carboxylic acid molecule present in the solution. Pyruvate was found to be an important and inevitable ingredient as a provider of the carbon source for running the cycle.
Thirdly, we ran the reactor for the reaction solution differing from the standard one only in lacking alpha-ketoglutarate while all of the others including pyruvate were present. The rationale of this experimental attempt was in the perspective that the initially missing component could eventually emerge if the reaction cycle may really be selective and protective for its own sake while in the presence of pyruvate as the both carbon and energy sources. The result was that the initially missing alpha-ketoglutarate emerged with the reactor operation though only by the trace amount of 0.4 mM in 120 min. The reaction cycle was robust even under adverse conditions to some extent. What should be responsible for the emergence of the initially missing alpha-ketoglutarate were the chemical affinities extended over to the emerging alpha-ketoglutarate to be pulled out of the whole reaction system through an intervening process of transformation.
Fourthly, we ran the reactor for the standard reaction mixture with 2.0 mM sodium carbonate Na2CO3 further added in order to examine how the over-all reactions could proceed when the decarboxylation processes are accelerated. In fact, sodium carbonate can accelerate decarboxylation by absorbing the outgoing carbon dioxide through transforming itself into sodium bicarbonate NaHCO3. Since alpha-ketoglutarate is the decarboxylation product of isocitrate positioned in the immediate upstream and since succinate is the further decarboxylation product of alpha-ketoglutarate, the acceleration of decarboxylation due to the added sodium carbonate certainly enhances the production of succinate if other conditions remain equal. This observation serves as another testimony of the operation of the reaction cycle as focusing upon the decarboxylation processes.
Fifthly, we confirmed the over-all reaction of oxidation through the citric acid cycle by controlling the amount of added oxidants. The effects of ferric ions Fe3+ as an oxidant further added into the standard reaction mixture were examined for both cases of their concentrations 0.1mM and 1.0mM. For further comparison, the case of ferrous ions Fe2+ of their concentration 1.0mM as a far-less competent oxidant or rather even as a reductant was also examined. The results reveal that the increase in the amount of the oxidant Fe3+ enhances the amount of dehydrogenation products such as oxaloacetate from malate, oxaloacetate from pyruvate and carbon dioxide, and citrate from oxaloacetate and pyruvate. This enhancement of dehydrogenation is contrasted to the case of 1.0 mM Fe2+, in the latter
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of which the amount of malate to be dehydrogenated into oxaloacetate would be piled up with time because of the absence of the effective oxidant such as Fe3+. In particular, the production of oxaloacetate from malate, which is the dehydrogenation product from malate, required for climbing up the steepest energy uphill in the cycle by the amount of 29.7 kJ/mol was actually accomplished in the presence of the oxidant Fe3+ in the flow reactor simulating hydrothermal circulation of seawater around hot vents in the ocean.
Finally, the enhanced production of citrate in the reaction cycle, for instance, could not be due to the direct conversions from the immediate neighborhood reactants such as oxaloacetate and isocitrate since there was observed no such build-up of citrate in the absence of pyruvate. Another confirmation of the participation of the reaction cycle for the build-up of citrate could come from no explicit build-up of citrate in the absence of alpha-ketoglutarate initially even if pyruvate as the carbon source is present. A positive confirmation of the occurrence of decarboxylation could be seen in the enhanced production of succinate as the end product of decarboxylation as responding to further addition of sodium carbonate serving as the absorber of carbon dioxide molecules. Also, another confirmation of the participation of dehydrogenation could be seen from the relative increase of the production of oxaloacetate and citrate as responding to further addition of the oxidant such as ferric ions Fe3+ compared to the similar results presented for less Fe3+ and for Fe2+ as a less competent oxidant or rather as a reductant.
The attempted operation of the reaction cycle residing within the citric acid cycle even in the absence of biological enzymes manifests an experimental likelihood for the synthesis of a reaction cycle holding its own identity through the constant exchange of the constituent carbon atoms even prior to the evolutionary emergence of the reaction cycle of a replication-metabolism complex. The laboratory experiments reveal that the occurrence of those material bodies whose identities may be kept through the exchange of the participating elementary atoms could be likely even before the onset of biology. 3. Proto-Metabolism Dissolving Vicious Circles Addressing the built-in dynamics for supporting the material body keeping its own identity through the constant exchange of the constituent material elements would be a thorny issue if it is approached descriptively or theoretically alone. In view of the fact that the standard description adopted for theoretical discourses assumes third person descriptions in the present tense, the descriptive access to the exchange of materials head on would turn out to face an enormous difficulty.
When a carbon atom in the citric acid cycle is exchanged between the two nearest neighbor molecules of citrate and isocitrate at the present moment, there would necessarily appear such an ambiguous situation that it remains indecisive whether the carbon atom at the present moment belongs either to the citrate or to the isocitrate, or to neither as with the case of being just in between. The event to perspicuously be described at the present moment cannot satisfactorily meet the challenge of describing the exchange of material.
When we say that a carbon atom that will be found in the molecule of isocitrate has been found in the molecule of citrate, the characteristics of the future is assimilated to the characteristics of the past, thus dispensing with the act of exchanging on the spot as leaving the interval separating the future from the past tense as small as possible. The present tense
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is marginalized. Nonetheless, the descriptive access to the exchange of materials making it inevitable to refer to the past and the future tenses also takes it for granted that time is further qualified in terms of the past, present and future tense. Thus, a contradiction arises. The exchange of materials is descriptively approachable as referring to the distinction between the past and the future as marginalizing the present, while the present is inevitable and cannot be marginalized for making a distinction between the past and the future (Matsuno, 2012c).
The present malaise is rooted in the adoption of the three tenses of the past, present and future uncritically as maintaining the separations between the past, present and future to be arbitrarily small. In essence, the act of an experience is unique to the present or today, while its anticipation is about the future or tomorrow and its memory is about the past or yesterday. Then, the statement like that yesterday’s tomorrow is today would come to yield an incomprehensible statement such that the memory of anticipation gives rise to an experience in its implication. Qualities of the past, present and future are different, and assimilating any one of the qualities to any other would be unlikely. As facing this contradictory situation, McTaggart (1908) charged time to be qualified further in terms of the three tenses of the past, present and future as being unreal.
McTaggart’s charge of time as being unreal is in fact a short and economical expression of vices latent in the description of self-referential complications attempted in third person descriptions in the present tense. Internalizing the description of the dynamics into the dynamics itself in the present tense may easily be entrapped by a vicious circle as facing the description of a description ad infinitum, as revealed in the clumsy expression of internalizing the description of the former act of internalizing further into the dynamics itself, unless the activity of description is properly qualified. The description of the exchange of materials addressed in the present tense cannot concurrently find the dynamic counterpart of the exchange of materials accessible at the instant of the present moment. The exchange of materials cannot properly be described in the present tense alone since the activity is agential because the material body processing the exchange is competent enough to cross the different grammatical tenses back and forth with ease naturally on its own. If the dynamics is about a duration as in the case of the exchange of materials, its description will be required to go beyond the standard stipulation limited only to third person descriptions in the present tense.
At this point enters the interplay between the present progressive tense and the present perfect tense. What is unique to the interplay between the two tenses in the actual dynamics is found within the fact that the present progressive tense can be punctuated by the occurrence of the present perfect tense. One unique property of the present perfect tense is that it is already an abstraction out of the present progressive tense whether or not the abstraction may be of anthropocentric origin. In addition, the present perfect tense as a discrete mark of punctuation to occur in the empirical world in due course of time is constantly updated by the subsequent occurrence of the present progressive tense. The record registered in the present perfect tense is specific in maintaining a coherent linguistic interface with the present tense in the sense that the record of the actual dynamics registered in the present perfect tense is directly accessible in third person descriptions in the present tense. The integrity of the record includes, for instance, the observation of
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material flow continuity there. In contrast, the carrier of the present progressive tense anchored at the material
substrate suffering from no abstraction is agential both in detecting any inconveniences coming from the neighborhood that may destroy the integrity of the record if left unattended there and in updating the present perfect tense accordingly so as not to freeze the inconveniences into the record. The internal observation of material flow continuity is then associated with the act of updating the present perfect tense so as to fulfill the condition of material flow continuity from within, and the cause for the act upon the carrier of the present progressive tense comes from detecting the effects of the preceding similar acts made by the other carriers in the neighborhood. Since the detection of the need for updating the present perfect tense and the action for the update are not concurrent but are sequential, the detection of the preceding actions by the neighborhood carriers of the present progressive tense constantly serves as a cause for the subsequent actions on the part of the detecting carrier.4
The action for material flow continuity, that is to say, material flow equilibration constantly reverberates in the carriers of the present progressive tense (Matsuno, 1989). Flow disequilibrium driving material flow equilibration can persistently survive in the carriers of the present progressive tense (Mast et al., 2010), while there is no room allowed for flow disequilibrium surviving in the record registered in the present perfect tense.5 Flow disequilibrium is constantly spilling over and migrating among the carriers of the present progressive tense as leaving none of it behind in the record registered in the present perfect tense. Thus, the vicious circles inevitable to the scheme of internalizing the description of the dynamics into the dynamics itself in the present tense can be dissolved once the descriptive 4 If one adopts the scheme of the mass action approximation that is often employed in theoretical reaction kinetics, the detection of the need for updating and the action for the update are completely synchronized. Once the concentrations of the reacting molecules are specified within the framework of the mass action law, the resulting flow rates of the reactants can also be fixed in a concurrent manner thanks to the presence of the reaction rate constants that can remain immune to whatever reactions may take place there. 5 The source of flow disequilibrium is of external origin. The exogenous disequilibrium is then detected internally by the material participants inhabiting in the inside. The detected disequilibrium internally is going to be dissipated in due course of time. A crucial issue raised at this point is whether every forward process of precipitating the internal disequilibrium to be detected could concurrently be counterbalanced with its reversed backward process of dissipation in a synchronized manner. Although it could be theoretically conceivable to imagine the concurrent balancing between the forward process of synthesis and the backward process of decomposition as met in the principle of the detailed balance in reaction kinetics in thermal equilibrium, such detailed balancing is an abstraction at best. In reality, however, it would become a pressing agenda to figure out what would happen if the principle of the detailed balance may not become available. This issue would become most serious when the operation of the source of flow disequilibrium is intermittent and repetitive in such a manner that before the preceding disequilibrium applied previously is completely dissipated, a new disequilibrium is successively applied. If this is the case, an accumulation of some residual remnant of the applied flow disequilibria may be likely in the present. The material embodiment of flow disequilibrium in the form of a memory of a material origin seems quite suggestive to the emergence of a functional matter.
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tense is switched over from the present tense alone to the interplay between the present progressive and the present perfect tense. The advantage of this switchover is in the elimination of the vicious circles inflicting the description limited only to the present tense by way of looking at the record maintaining a coherent interface between the present tense and the present perfect tense, while the price to pay for it is the acceptance of some inconveniences such as flow disequilibrium to be tolerated by the material carriers of the present progressive tense. Appreciation of the present perfect tense by way of the present tense now provides a descriptive scheme of making it possible to refer to an object being in conformity with the operation of the exchange of materials that is referable in the present progressive tense. The object identified in the present perfect tense as the material body holding its own identity through the exchange of materials in fact turns out to be a derivative of the process in the present progressive tense. The process-perspective letting objects be derivatives of processes holds itself upon the priority of the present progressive tense over the present tense in description, while the process-perspective to supposedly be addressed exclusively in the present tense alone is self-defeating and cannot claim for its priority over the state-perspective because of letting both processes and objects be coextensive in the same present tense. Experimental confirmation of the citric acid cycle keeping its own identity through the constant exchange of the constituent carbon atoms as a form of proto-metabolism even without being accompanied by cellular structures reveals that proto-metabolism is a material means for dissolving vicious circles of descriptive origin that might emerge if only the present tense is allowed for. Shedding light on the material unit whose identity is kept through the constant exchange of the constituent material elements is in fact a way of appreciating the positive aspect of the scheme of internalizing the description of the dynamics into the dynamics itself while relieving the negative drawback of being entrapped by vicious circles. The competency of the present progressive tense is both linguistic and dynamic. It can carry some dynamic attributes that remain linguistically inaccessible in the present tense alone such as flow disequilibrium to be deciphered as a momentary violation of material flow continuity in a manner of not being registered in the record. The present progressive tense holds its regulative linguistic capacity of maintaining a congruent interface with the occurrence of the present perfect tense. This observation suggests to us the likelihood of a new type of cohesion between the present progressive and the present perfect tense as letting none of dynamic inconveniences remaining linguistically inaccessible in the present tense be left behind. Punctuating the present progressive tense by the present perfect tense, that is not accessible to the dynamics framed in the present tense alone, is cohesive in inducing the present progressive tense to further be punctuated. Its consequence is the constant update of the present perfect tense the latter of which is duly accessible linguistically in the present tense. 4. The Relative State Formulation Punctuating the present progressive tense by the present perfect tense, which is neither accessible to nor conceivable in the present tense alone, is quite dynamic in addition to
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being linguistic. Consider, for instance, a system of reacting chemicals like those constituting the citric acid cycle. When we say there is a chemical molecule X in the reaction system, it also implies that the system itself can detect the presence of X internally. The system’s detection of reactant X is in a process of duration occurring in the present progressive tense, and the detection completed is punctuated by the present perfect tense. Similarly, reactant X is also involved in detecting the system itself from the inside, and the detection completed is also punctuated by the present perfect tense on the part of reactant X. However, if both the detections are not completely synchronized with each other, it would become inevitable for each of the detecting parties to update the present perfect tense in the succeeding present progressive tense because of the punctuated interventions by one party before completing the punctuation by the other party.
One consequence of the frequent update of the present perfect tense may be a transformation of reactant X into Y which could differ from the original X. While there would be no likelihood of transforming reactant X into Y if both the detections of reactant X by the system and of the system by X are completely synchronized with each other as is the case with the mass action approximation, such a complete synchronization would be unlikely because of the absence of the material means for the purpose. The production of reactant X is due to making, breaking, or transforming chemical bonds of a limited local extension. Because of this local characteristic, the produced reactant X would subsequently come to face a new opportunity of transforming X into, say, reactant Y as experiencing and detecting the immediate neighborhood emerging towards X through non-local interactions such as electrostatic or van der Waals attractions. Each reactant in the reaction system can be cohesive in inducing its transformation, and the induced reactant can again be cohesive in inducing the further transformation down the road ad infinitum. A linguistic vehicle for making it possible to address the cohesive induction of chemical transformation is the frequent update of the present perfect tense in the present progressive tense. This scheme is also upheld on the ground of quantum mechanics when viewed from the relative state formulation, as will be seen in the following (Matsuno, 2012b).
For simplicity, suppose a quantum system S allows for only two distinct states |A>and |B> like in the case of an atom of a spin one-half. Here we will follow the conventional notation available to quantum mechanics such that each state is represented as an orthogonal unit vector in the corresponding Hilbert space H. The initial state of S denoted as |init> can be expressed generally as a linear superposition of the two states in the form of
|init> = α|A> + β|B> with |α|2 + |β|2 = 1, in which α and β are complex numbers specifying the nature of the superposition. This specification comes from the theoretical premise on the part of external measurement which has not yet been committed to the actual measurement. Furthermore, when the observer Oint as another quantum mechanical system is introduced into the scheme, it can decisively identify the initial state as either |A> or |B> internally. The internal observer Oint can thus hold its quantum state |OintA> as being relative to |A> when it observes |A>, while it can hold its quantum state |OintB> as being relative to |B> when it observes |B>. The quantum states |A> and |OintA> are correlated with each other in the sense that Oint measures the quantum state |A> internally as such. That implies that the occurrence of the quautum state
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|A> relative to another quantum state |OintA> is equated to the measurement of |A> by the internal observer Oint. A similar correlation also applies to the pair |B> and |OintB>. Rather, the participation of the internal observer Oint is a necessary precondition for the occurrence of the relative states |A> and |B>.
In contrast, the external observer Oext, who pays its attention to the composite complex of the system S and the internal observer Oint, comes to regard the quantum state of the complex to be in the superposition
α|A>|OintA> + β|B>|OintB> even prior to being committed to the actual measurement externally without specifying the explicit values of the complex amplitudes α and β (Everett, 1957). 6
The role of the internal observer to be appreciated by the external observer is such that the identification of the relative state, say, |A>, by the internal observer Oint proceeds only through as referring to the representation |A> rather than directly to identifying the material object itself to eventually be represented as the state vector |A>. This is in fact a concrete case demonstrating the distinction between de re and de dicto. Consequently, the identity of the state |A> is relative only to the internal observer whereas it is not absolute to the external observer. The relative nature of the identity of the relative state is in fact equated to the identity of the class property applied to and perceived by the internal observer in the sense that the relative identity of the state can be maintained in the eyes of the internal observer. The class identity of a material body whose relative identity is applied to the internal observer can be maintained even if the individual material components of the body are exchanged with the new different individuals belonging to the same kind in the eyes of the external observer.
What is unique to the relative state formulation of quantum mechanics is that the act of representing |A> in reference to |OintA>, though in the form of an abstraction, is internalized into the natural dynamics. The naturalization of the act of representation can provide us 6 Latent in the relative state formulation is the interaction between the relative states belonging to different Hilbert spaces as embodied in the distinction between a system and the corresponding internal observer. The effect of the internal measurement between the two is summarized in the magnitude of the complex amplitude of each branching relative state of the system. The interaction between different Hilbert spaces is a type of signaling interaction in the sense that it can serve as a means for letting one system belonging to one Hilbert space detect another system belonging to another Hilbert space. The signaling interaction is thus local in that the signal propagation cannot be instantaneous globally. Nonetheless, this does not contradict nonlocality entertained in quantum mechanics. Nonlocality in quantum mechanics applies only to the simultaneous propagation of interaction within a single definite Hilbert space. In particular, signal propagation in chemical reactions is local and heterogeneous because of the participation of chemical bonds strictly of a local nature. The speed of communication between reactants and its type depend upon the intervening chemical bonds of a local character. Detection of a reactant and the consequential bond making or breaking are sequential, but are not concurrent. Although the mass action approximation letting both the detection of a reactant and the resulting production be concurrent has often been attempted in theoretical reaction kinetics, such a concurrency would be no more than an abstraction in theory. Because of this absence of concurrency, the indefinite reshuffling of the bond making and its transformation would become inevitable in a reverberating manner unless the prohibitive means may be imposed externally. Detection of the detected can indefinitely survive through the bond making and transformation as constantly acting upon the detected.
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with a physical means of referring to the class identity in the realm of material dynamics even without introducing the anthropocentric intervention. The class identity is taken as an identity kept in relation or in relating any member of the class to the contextual regulation of material origin, rather than that kept in isolation, while physics has been so far quite competent in coping with the material identity kept in isolation. It is thus unique to the relative state formulation even within the framework of physics to explicitly thematize the issue of how the class identity of the participating material elements could be addressed. Focused upon here is how the class identity could be reached as starting from those material elements whose individual identities are supposedly available when they are kept in isolation. In short, the relative state formulation is a physical scheme of appreciating the class identity of the participating material element of whatever type as letting each element be a member of the identifiable class internally.
The present scheme of relating the external observer to the composite complex of the system and the internal observer can further be explicated as referring to a chain of the chemical reactions R1→R2→・・・→Rn, where Ri ( i = 1,2,…) denotes each intervening reactant. The presence of reactant R1 is supported and identified by the whole reaction system except for the targeted reactant R1, which is denoted as the internal observer O1, as expressed in the conventional quantum-mechanical form of the state representation: |R1>|O1R1>. However, this representation still remains incomplete in leaving intact another internal observer supporting and identifying the internal observer O1 as such. Exactly at this point enters the reaction R1→R2, in which the newly emerging reactant R2 assumes the role of supporting and identifying O1 internally. That is to say, the internal observer O1 synthesizes R2 as a consequence of identifying R1. Alternatively, the internal observer O1 comes to exercise the agential capacity of feeding upon R1 located in the immediate upstream so as to transform it into R2.
Unique to the relative state formulation is the appraisal of the cohesive and agential capacity for searching for and figuring out the reactant that can be relative to each participating reactant from within. Each reactant looks for the close relative partner of its own. If the sought-after relative partner is not directly available, on the other hand, the reaction system as a whole comes to exercise on its own the synthetic capacity of synthesizing the missing relative partner from the resources then available nearby. The reaction R1→R2 is in fact a summary expression of the agential activity that the material support O1 demonstrates a chemical affinity toward R1 for transforming it into another reactant R2. The occurrence of chemical affinities between the reactants is evidently a scheme of implementing the relative states in chemical reactions. Detection of a reactant and its further transformation acting upon the detection are not concurrent, but are sequential. Accordingly, the relative state formulation comes to yield the on-going process such that detection of the detected may induce the further transformation of the detected product that can also be subsequently detected by others unless the sequence of detection of the detected is forcibly truncated.
In a similar vein, the reactant R2 requires another internal observer O2 which can support and identify R2 as such internally, in which the internal observer O2 is the whole reaction system except for the targeted reactant R2. The internal observer O2 can thus be regarded as
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a transformation product from reshuffling the preceding support O1. Basic to the reaction R1
→R2 is the observation that the reaction is the operation of projecting the state vector |R1> belonging to one Hilbert space onto another state vector |R2> belonging to another Hilbert space.
A formal expression of the contribution of internal measurement for precipitating both the emerging reactant R2 and the internal observer O2 can be expressed as a mapping:
M2 |R1>|O1R1> = α2|R2>|O2R2> with |α2|<1. Here the mapping operator M2 represents a contribution of internal measurement required for supporting and identifying O1 by the emerging reactant R2, and a complex number α2 represents the complex amplitude of the branching state |R2>. Since the conservation of probability is maintained between before and after each branching, the squared absolute value of the amplitude will be unity only in the case that the outcome consists exclusively of a single branch, otherwise it would be less than unity. The transference sequence from |R1>|O1R1> to |R2>|O2R2> is due actually to the sequential nature of the internal measurement involved for making the intervening states relative to each other, whereas such a transference could totally be dismissed if only external measurement is allowed to intervene. It is internal measurement that is responsible for making a new synthesis out of the repeated sequence from the detected to detection of the detected proceeding in the manner ad infinitum. The relative state formulation thus renders internal measurement into a synthetic factor or agency that underlies the physical qualification of the mapping that is operating between reactants and the internal observer.
This sequence of internal measurement further proceeds in a similar fashion as Mi+1 |Ri>|OiRi> = αi+1|Ri+1>|Oi+1Ri+1> with |αi+1| < 1 (i=1,2,…)
Here the mapping Mi+1 represents a contribution of internal measurement acting upon the internal observer Oi for precipitating both the emerging reactant Ri+1 and the internal observer Oi+1.
A significance of the present sequence of internal measurement will be found when the reaction sequence happens to form a reaction cycle R1→・・・→Rn→R1 as supplemented by the further scheme of M1 |Rn>|OnRn> = α1 |R1>|O1R1> with |α1| < 1. The integration of internal measurement round the cycle now amounts to
M |R1>|O1R1>=α |R1>|O1R1> with M = M1 Mn Mn-1 … M2; α = α2・・・αnα1; |α| < 1.
The identity of the state |R1> in the cycle is relative to the reference state |O1R1>. The identity in the relative state formulation is relative to the internalist, rather than being absolute to the externalist like the physicist looking into from the outside. The identity is thus not restricted to the sort of absolute type kept in isolation that does not allow for the exchange of the components elements with those of the same kinds coming from the outside. This is because the relative identity of the state perceived by the internal observer is about a representation of some object, rather than about the object itself in the absolute sense. That is a distinction between de re and de dicto. Consequently, the relative identity can be kept even though the component elements constituting the state |R1> are replaced by
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the new ones of the same kinds as going round the cycle if the reference state remains indifferent to the replacement.7
In particular, the relative state formulation is most significant in providing a physical scheme of guaranteeing the identity of a material body whose components can constantly be exchanged with those of the similar kinds from the outside. The identity held upon being relative and through the constant exchange of the component elements is in fact cohesive in making those elements relatively interchangeable with each other in the manner that could not be conceivable if each element is supposed to hold the absolute identity kept in isolation. Of course, the likelihood of such a relative identity has to be examined empirically or, if ever possible, even experimentally.
Once the reaction cycle is focused upon, the two of the relative identity of the cycle as an organizational invariance and the process of replacing the elements constituting the cycle remain inseparable, as being contrary to Rosen’s distinction between the efficient causation of replacement and the internal principle of organizational invariance on being closed to efficient causation (also, see footnote 1).
The complex amplitude α of the composite mapping M in the above can thus be equated to the probability amplitude for holding the reaction cycle through internal measurement according to Born’s probability rule. The most durable event as being subject to frequent internal measurement turns out to be the one that can make the absolute value of the probability amplitude to be unity as depicted as |α| = 1. And, the internal dynamics being responsible for varying the complex amplitude α eventually toward |α| = 1 from within is through varying the extent of quantum interferences internally without destroying the
7 Emergence of a class identity of a material body made out of the component material elements is grounded upon the degree and the extent of the reference state of a relative nature being indifferent to the exchange of the those component elements of the similar kinds occurring in the corresponding state relative to it. The relative state formulation of quantum mechanics is unique in relegating the capacity of detecting the identity of a representation to each relative state. Detection of the identity of a representation serves as a scaffolding of forming a class identity out of the participating material elements. Sustenance of the class identity is sought within the dynamic scheme of abstracting and representing a common property out of the participating material elements at the expense of tracing out each individual identity to be kept when isolated. For instance, the dynamic nature underlying the sustenance of a class identity can be made explicit by comparing the ribosomal protein synthesis with the artificial solid-phase peptide synthesis. The identity of a protein molecule made by the ribosomal synthesis that is initiated from the N-terminus is about the class property of the participating each amino acid molecule since the identity can be kept even as suffering from the inevitable degradation if the constituent amino acid molecules are exchanged with the different molecules of the similar kinds. In contrast, the identity of a peptide molecule made by the artificial solid-phase synthesis that is initiated from the C-terminus can go along with the identity of each individual amino acid molecule within the peptide. The artificially synthesized peptide molecule does not incorporate into itself the dynamic scheme of compensating for its degradation, and does not naturalize by itself the scheme for distinguishing the production of each individual peptide to be synthesized from another type of production for supporting the class property necessary for making the synthesis possible. In the artificial synthesis, the class property of the products is controlled exclusively by the experimenter concerned sitting outside.
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interferences altogether as revealed in the occurrence of weak measurements (Vaidman, 1996; Aharonov et al., 1998).
What is specific to the occurrence of weak measurement is that it can proceed under the context of regulating and preserving some extent of the quantum interference without destroying it altogether even if the act of measurement, though which must be weak, is involved. Thus, it would become likely to conceive of the probability amplitude of the context of quantum interference in the sense that the probability amplitude assigned to each relative state constituting the reaction cycle just happens to be an instance of such a concrete measure. The internal regulation of the probability amplitude through weak measurement certainly proceeds in such a manner that its consequence will have been observed externally in accordance with the global conservation of probability to unity to be registered in the record. That is Bayesian in the sense that the internal regulation of the probability amplitude of an event precedes the external measurement of the probability value as such. In essence, implementation of the reaction cycle is a consequence of the internal regulation for the conservation of probability to unity from within.
As a matter of fact, the intervention of Born’s probability rule upon the internal regulation of weak measurement operating with Everett’s relative states makes the probability of interest a Bayesian type rather than a frequentist’s type. In contrast to the standard interpretation of quantum mechanics separating the presence of the state and its measurement, the relative state interpretation integrates both the presence of the states that are relative and the internal measurement of their probability amplitudes so as to let the measurement regulate and constantly update the probability amplitudes in accordance with the conservation of probability from within. This is Bayesian in assigning a probability to an event, though paraphrased only in terms of the relative states alone without introducing any subjective observer of an external origin. Weak measurement regulating the quantum interference without destroying or collapsing it comes to eventually imply that the changes in the interference, that could induce the associated changes in the probability of the occurrence of an event when measured externally, can actually be likely. It certainly remains legitimate even prior to the actual external measurement going with the collapse of the wavefunction after the event as perceived within the standard interpretation.
One relevant consequence from this observation is that if some context of quantum interference can eventually survive, it must be the one that can let the absolute value of the probability amplitude of the context itself to approach to unity. Although the relative state formulation has often been denounced as lacking the standard in reference to which the claimed relative states could be objectified, under the proclaimed charge of the lack of the clear definition of the pointer-basis problem, the appraisal of the reaction cycle is exempted from the present charge as appealing to the objective standard of the Bayesian probability of occurrence approaching unity. Once the Bayesian scheme is adopted, the most likely event must be the one whose probability of occurrence could approach unity if ever possible. The likely occurrence of the reaction cycle is objectively associated with the Bayesian probability of its occurrence to be unity. Rather, the relative state formulation of quantum mechanics provides a wide-covering mold for figuring out whatever event whose probability of occurrence in the empirical world would eventually approach unity.
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The factual robustness of the resultant reaction cycle as a concrete case comes to rest upon the chemical affinities that the reaction system would exhibit altogether (Matsuno, 2012b).8 The reaction cycle lets each reactant in the cycle be fed upon by the emerging reactant located in the immediate downstream. The probability amplitude of the reaction cycle that can approach unity is consistent with both conserving the probability to be unity and actualizing an event with its probability of occurrence to be unity. The relative state formulation is agential by itself in acting for and fulfilling the conservation of probability to unity from within when it is aided by weak measurements. The occurrence of a reaction cycle and the fulfillment of the conservation of probability to unity are coextensive with each other and mutually supportive in that the occurrence of the cycle connected through single branches meets both the conditions at the same time. More specifically, the reaction system detecting a reactant then can transform it into another reactant so as to make it relative to the system itself. The synthesized reactant now comes to appear on a single branch as dismissing all of the other alternatives on the basis of first come, first served.
In short, both classical physics upon Bayesian probabilities registered in the present perfect tense and quantum physics in terms of Bayesian probabilities surviving in the present progressive tense go hand in hand when the holding of the material identities in the form of a reaction cycle to be kept through constant exchanges of the constituent material elements is the case.
A significance of Bayesian probability eventually approaching unity is found in the physical anchoring of the operation of the components in accord with their context on the
8 The factor driving the implementation of the actual chemical affinities is the absolute value of the complex amplitude of each relative state belonging to the burgeoning reaction cycle. The relative state formulation of quantum mechanics has the natural tendency toward fixing the probability amplitude of the participating relative state approaching unity. The present natural tendency latent in the probability amplitude comes to tailor the actual chemical affinities to accordingly be implemented. The functional origin of the cohesiveness for implementing reaction cycles including the activities of feeding upon the resources available from their outside is thus sought in the occurrence of relative states in quantum mechanics. The probabilistic nature latent in the relative state formulation is Bayesian in that it enables us to perceive that the event occurring with probability unity comes to dominate the dynamics proceeding there even prior to the actual measurement. One advantage of referring to a Bayesian probability is that it could be possible to estimate its value even prior to the actual act of its measurement externally, while Born’s probability rule alone limits the external quantification of the probability value only after the events statistically. The relative state formulation of quantum mechanics can in fact assign the a priori probability of unity to the occurrence of a reaction cycle connected through only single branches, since the reaction cycle carrying the reaction pathway whose probability amplitude is less than unity in its absolute value is less robust because of its probability of occurrence less than unity. However, the present dominance of the reaction cycle with no branching off, except for those for importing the necessary resources and exporting the excretions, does not exclude the possibility such that one cycle to appear later may feed upon the pre-existing other cycles as its own resource of a de novo type. This is due to the empirical nature of the Bayesian characteristic distinguishing between the a priori and a posteriori probabilities. The underlying distinction is certainly irreversible and asymmetric in time. The event carrying its probability of occurrence of unity when viewed from the present towards the past does not necessarily imply that the probability of the occurrence of the same event may also remain unity when viewed from the present towards the future.
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firm empirical ground. Even a philosophical doctrine of autopoiesis emphasizing a relational totality of the components with no direct reference to the totality on the part of the components themselves (Maturana, 2011) could be anchored at the act of internalizing the description of dynamics into the dynamics itself. Thus, the origin of autopoiesis that could be made empirically accessible must be sought within something other than autopoiesis itself since the origin is definitely an empirical, rather than a merely philosophical, issue like the origins of life on the planet Earth. That is downward causation (Noble, 2008). Downward causation may become explicit once the distinction between the identity of a systemic organization and the identity of each component element is clearly made. In fact, whatever material body to be maintained by constant exchanges of the component elements can hold its systemic identity even though the residence time of each component holding its individual identity inside the body is definitely limited. Autopoiesis is simply a consequence of downward causation, rather than the other way around. Although the causation over a short time scale less than each residence time may be microscopic and efficient in the upward direction, the causation running over a much longer time scale in a coherent manner is downward from the top of the context holding the systemic identity instead of the individual identity of each participating component. There should be no likelihood of mixing both upward and downward causations in an undisciplined manner once a material body holding its own systemic identity comes on the scene. Prerequisite to the operation of downward causation are frequent exchanges of the component elements participating in the holding of a systemic identity.
The present observation of the uniqueness of downward causation comes to imply that the underlying computational process is also under the influence of downward causation. Computation upon logical operations processing abstract truth-values of possible virtual worlds is however not entitled to dismissing the occurrence of a situated internal observer adaptively modifying any inconvenience, or any flow-disequilibrium in a less colorful term in the light of invincible flow-continuity law (Matsuno, 1989), inflicted upon it from the neighborhood. Even the internal observer is not necessarily put under the burden of examining the abstract truth-values of the possible-world scenarios every time it meets any inconvenience. Even if a many-world interpretation of quantum mechanics is arguably invoked, it could be conceivable to imagine a particular observer or the inhabitant within a particular world inside of which no splitting of the worlds could be experienced, as correctly noticed in the note added in proof of Everett (1957). This comes to remind us the distinction between a statement and its proof in computation.
First-order logic reveals that even if the Gödel number of a statement is determinate, there may be a case such that the Gödel number of its proof remains indeterminate, as implying that no proof is available to the statement. If proof is not available or equivalently if no truth-value is evaluated, a computational simulation is no more than a mere simulation. In fact, downward causation is not necessarily computable within the framework of first-order logic since it is hard to implement the implication of downward causation in the initial setup of both the axioms and the rules of inference to start with. Downward causation is an instance of measurement. Rather, the computability of downward causation must be figured out as facing the issue of how the logical conjunction between measurement and computation could be addressed and then evaluated.
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5. Synthesis From an Abstraction The relative state formulation of quantum mechanics as revealed in the concrete example of the reaction cycle includes a descriptive component in addition to material components as reflecting the built-in stipulation of internalizing the description of the dynamics into the dynamics itself, though the latter would eventually be entrapped by vicious circles if addressed in the present tense alone. In particular, the activity of relating something to something else or predicating something in terms of something else is descriptive-origin because of the capacity of applying constraints through the action of an abstraction. Applying constraints upon matter is equivalent to its further qualification.
The material origin of description is thus sought in the qualifying action of matter by itself. That is an abstraction. Accordingly, the descriptive component of material origin is required to maintain the descriptive identity while it is also required to carry out the activity of relating something to something else at the same time. Unless such an identity is guaranteed, there would be no chance of referring to it as a descriptive component carrying its identity. In addition, even if the descriptive agents like us who can identify whatever descriptive object with ease are not present, the descriptive component, if it is appropriate in any case, would require its descriptive identity from the verge of the origins of life onward at least on our Earth. A serious issue at this point will be how the descriptive component could come to maintain its identity even in the absence of the descriptive agents like us.
What the relative state formulation suggests to us will be in its essence to look for a material vehicle carrying a descriptive component holding its own identity. That will be about a possibility of a material vehicle possessing a new type of the identity of descriptive origin to be kept in relation, which cannot simply be reduced to those identities of the elementary material components kept in isolation constituting the lifeless matter. At the same time, the living matter also consists of the same types of the material components as the lifeless does. A significant subtlety then comes to appear in the difference between the reducibility of a material vehicle into the material components and the irreducibility of the descriptive identity.
In particular, one concrete example of the material vehicle carrying its own identity differing from those individual identities of the components is a reaction cycle processing the constant exchange of the component atomic elements. The residence time of each carbon atom inside the citric acid cycle is limited. Accordingly, the individual identity of each carbon atom is kept only over a limited time interval inside the citric acid cycle, while the identity of the material vehicle holding the cycle can be maintained far beyond the limited residence time of each carbon atom in the cycle. The identity of the reaction cycle, which is certainly kept in relation, is thus descriptive in remaining indifferent to the vicissitude of the component elements carrying their own individual identities. An advantage of paying attention to the descriptive identity resides within the room available for accepting a certain extent of abstraction, such as dismissing the distinction between the individual identities of the material elements of the same type, compared to the case of addressing and identifying what the component material element kept in isolation is all about.
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Since the descriptive identity is about a descriptive object that is durable in the empirical domain, the reaction cycle maintained through the exchange of the component atomic elements can assume the descriptive identity much more durable and reliable than the individual identity of the component element whose residence time in the cycle is necessarily limited. This observation comes to gain its unique significance in the origins of life and the subsequent biological evolution compared to those cases surrounding physical sciences at large. Biology is distinctive in synthesizing the organic matter that can maintain its irreducible descriptive identity despite the intervention of the exchange of the component elements whose residence time in the organic matter is limited, while physics is competent in reducing both the living and the lifeless matter into the individual material elements carrying their irreducible material identities.
Although Darwinian natural selection is legitimate in focusing upon the selective and analytical aspect being vital to clarifying the descriptive identity of the organic matter, the synthetic and generative aspect of the matter is sought in the capacity of holding the material bodies whose identities may be kept by themselves through constant exchanges of the constituent material elements. What remains prerequisite to the operation of natural selection is the occurrence of the durable material bodies holding their own identities, rather than the other way around. The likelihood for the occurrence of such durable material bodies prior to the onset of natural selection must have been a decisive factor on the verge of the origins of life. Those durable material bodies are already organized in their robust and heterogeneous makeup out of the component atomic and molecular elements in the manner of being able to distinguish, from within, each element from all of the others residing in the same material bodies. In particular, each carbon atom involved in the citric acid cycle distinguishes itself from all of the other carbon atoms in the cycle as revealing how the atom is going to come around as itinerating on the various carboxylic acid molecules in the cycle in a specifically sequential manner until leaving it in the end before completing the fourth round of the cycle. The significance of the descriptive identity of a system of chemical reactions would become most acute when the onset of self-replicating molecules such as self-catalyzing RNA molecules may be approached prebiotically. What is decisive for the onset is the descriptive identity of the system that could facilitate the synthesis of self-replicating molecules, rather than the molecules themselves. It is a descriptive scheme of predicating the relational activity on the material ground that is necessary for the onset of self-replicating molecules. Since a reaction cycle is a form of the descriptive object that is durable through chemical reactions, the emergence of durable self-replicating molecules can be taken as a specific case of the likelihood of reaction cycles that may be conceivable in a much wider context. A sine qua non for the evolutionary emergence of self-replicating molecules is sought within the class identity, rather than the individual identity, of those molecules to be synthesized by the constant exchange and reshuffling of the constituent atoms and molecules.
More specifically, the constituent atoms and molecules to constantly be exchanged remain in the cycle for the time being as the heterogeneous elements, which are mutually distinguishable from each other, while upholding the class identity of the supporting reaction cycle. A carbon atom going to leave the citric acid cycle, for instance, certainly
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differs from all of the other carbon atoms still remaining in the cycle in a distinguishable manner in identifying a specific carboxylic acid molecule, either isocitrate or alpha-ketoglutarate, from which a carbon dioxide molecule is going to be excreted toward the outside. Accordingly, the evolutionary appearance of a reaction cycle can be seen as a prebiotic precursor or harbinger to the emergence of self-replicating molecules amenable to the operation of natural selection.
In essence, the reaction cycle grounded upon the relative-state formulation of quantum mechanics can serve as a cradle for giving the potential birth to and further nurturing of self-replicating molecules. The role of the cradle is sought in the concrete characteristic that the reaction cycle perceived from the relative state formulation sets the context that can exert the synthetic chemical affinities from within onto each participating chemical reactant for the own sake of sustaining the identity of the cycle, while it is involved in constant exchanges of the constituent atoms and small molecules at the same time.
Chemical evolution takes full advantage of the agency of maneuvering relativity in such a manner that each state in the relative-state formulation may require its close partner, whether or not available directly on the spot, in order to make it relative to something other than itself.9 Each state comes to synthesize the state relative to it for its own sake from within unless the relative state is available in a ready-made manner.
The occurrence of a reaction cycle of reacting molecules is a natural way of abstracting a class identity from each participating molecule as a member of the cycle at the cost of being indifferent to the maintenance of the individual identity of each participant that could be discernible in isolation. The reaction cycle internalizes the description of its own dynamics by way of abstracting the invariable class property from each participating individual atom and molecule. Furthermore, while it is descriptively abstract, the reaction cycle is materially concrete and synthetic in constantly exchanging the constituent elements in a heterogeneous manner with those of new elements of the similar kind coming from the outside. While it is about an identity of a type, the reaction cycle is a token processor
9 Relativity in the relative state formulation differs from Einstein’s relativity, in the latter of which while time is legitimately taken to be local or relative instead of being absolute, the extent for setting the condition of simultaneity is still global. That condition for Einstein’s relativity is anchored at the hypothesis that the speed of light, which is also interpreted as the speed of signal propagation, is the same in all inertial frames. Einstein’s relativity establishes simultaneity to the global extent in the special theory framed in the present tense thanks to the invariance of the speed of light confirmed on the Michelson-Morley experiments. In contrast, the relative state formulation relativizes the occurrence of global simultaneity only to the record registered in the present perfect tense in the sense that it can also be referred to in the present tense. However, no simultaneity to the global extent is conceivable in action in the making in the present progressive tense because of the absence of the material means for the global synchronization on the spot. This is because the speed of signal propagation is not uniquely determined in the relative state formulation especially when it is applied to chemical reactions. The participation of a wide variety of chemical affinities causes a difficulty in fulfilling the uniformity of the speed of signaling toward the reactants available in the immediate neighborhood. What is present in the relative state formulation and is absent in Einstein’s relativity is the dynamics of constantly updating the present perfect tense in the present progressive tense as a physical scheme for fulfilling the condition of global simultaneity registered in the record in the perfect tense.
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exclusively on the concrete material basis in which each constituent element to be exchanged is taken as a token.
Physical underpinning of a functional matter as revealed in a concrete experimental demonstration of running the citric acid cycle in the absence of biological enzymes comes to shed light on the foundational role that quantum mechanics would play for the occurrence of such a functional matter. One major characteristic of a functional matter is its material organization upheld by the internal coherence or correlation. Quantum coherence or correlation is certainly pivotal in keeping a robust organization as displayed in the functional polymers made of an extremely heterogeneous sequence of the component monomers, though the number of whose kinds is quite limited like only the four different kinds of nucleotide molecule A, T, G, and C for a DNA molecule as a resulting hetero-copolymer.
In particular, one likely physical means for implementing the quantum coherence for securing the linear organization of a hetero-copolymer is to let it contact with an extremely low-temperature heat reservoir, even if locally, just to avoid or mitigate thermal disturbances coming from the ambient at the higher temperatures, say, at 290 K (Matsuno, 1993). One possible scheme for this objective of making a contact with such a low-temperature heat bath while inhabiting on the thin surface of our planet Earth is to dissipate energy by emitting the microwave photons toward outer space, whose frequency is far less than 150 GHz characterizing the cosmic microwave background maintained at 2.725 K. As a matter of fact, the radiation from a coherent condensation of molecular dielectric polarizations in the form of a movable giant dipole meets the requirement for dissipating energy by emitting the microwave photons at the frequency around 10 MHz into outer space just for the sake of upholding the coherent condensation through dissipation (Fröhlich, 1968; Bandyopadhyay, 2010; Sahu et al., 2011). The temperature of the transparent outer space to be read out on the surface of the Earth with use of a radiation thermometer focused on the frequency band over, say, 10-100 MHz must be far below several milli-Kelvin degrees without being disturbed by the cosmic microwave background being influential at the much higher frequencies.
Further, in addition to a physical contact with an extremely low temperature heat reservoir even locally for making indispensible energy dissipation manageable, one more condition required for the occurrence of the quantum coherence is the availability of a specific cohesion of a physical origin that could not directly be perceivable in the standard practice common in the inorganic physical realm. That is the cohesion operating among the constituent material elements, which could eventually play a decisive role for forming a functional matter.
At this point enter the relative states formulated in quantum mechanics. Each state conceived within the relative state formulation is intrinsically cohesive toward another state that comes to be relative to it. The cohesion upon the relative state formulation is due to the sequential nature between detecting a state and implementing another state relative to it, while such cohesion may totally be nullified and dismissed once the two processes of detection and implementation are taken completely synchronized with each other as practiced in physics so far because of the uniquely methodological and idiosyncratic stipulation of synchronization as set in the fixed mold provided externally. If the detection
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were completely synchronized with the consequential action in relation to the detection, there would remain no room left for allowing for the cohesive activity between the two to actually be exercised on the physical basis. The activity of detection is cohesive in inducing the following activity of implementation in a manner of repeating the similar procedure of internal measurement ad infinitum (Matsuno, 1989). Above all, what remains basic to the cohesive coupling latent in a functional matter is the constant exchange of the constituent material elements on the part of the material body processing the sequential activities of detection and implementation indefinitely, without being entrapped by a spontaneous synchronization between the two.
6. Concluding Remarks Conceiving of the boundary conditions applied to an inexorable dynamical law is already agential in allowing the physicist to exercise the agential capacity of controlling the conditions from the outside even if the lifeless matter is a matter of concern. This intervention of external control into the dynamics of concern is however a special case of the scheme of internalizing the description of the dynamics into the dynamics itself. A more inclusive question is whether it could be likely to expect the occurrence of the descriptive self in a much wider context that can internalize the description of the dynamics into the dynamics itself at large even in the absence of the physicist with whose agential capacity we are already quite at home.
What is specific to the descriptive self involved in the relational activity of making predication, including the observing physicist as a special case of course, is the preservation of its own identity while exercising the descriptive specification onto what is to be described. The descriptive self is already agential in that the agency of specification comes from the robust maintenance of the identity of the descriptive self being competent in applying the relational activity of predication. The relative state formulation of quantum mechanics certainly provides a physical means of linguistic predication as focusing upon a physical state being relative to another state. The relativity of a state is in fact a code applied to the physical specification of the state attribute, which is also approachable to us linguistically.10 Thus, raising the question of the likelihood of the descriptive self on a more inclusive ground is quite empirical in admitting that there is no specific metaphysical reasoning for being partial exclusively to the anthropocentric self. Although comprehending the separation between self and everything else must be a notoriously hard problem if one starts from the line along which there is no such separation, this perspective is quite metaphysical in accepting the initial assumption of no separation in the beginning. Once the present undue intrusion of metaphysical overhang is lifted, the chance of paying due attention to empirical facts may be enhanced. The relevant question will be whether the descriptive self or, equivalently, the consequential descriptive identity could be latent in matter itself.
10 The genetic code is indicative of the code of natural origin applied to a functional matter that may be translatable even into the code of natural language for us as the biochemists have collectively demonstrated so far.
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Experimental observation of the running of the citric acid cycle in the absence of biological enzymes comes to reveal that the cycle is a descriptive self in the sense that the cycle is an abstraction when viewed from the perspective of each participating carbon atom as a material element. The descriptive identity upheld by the descriptive self is about the identity of the reaction cycle even though the constituent carbon atoms constantly come and go on the scene. They are constantly exchanged by the new ones recruited from the outside. The identity of the cycle is thus descriptive rather than merely being exclusively materialistic, since the individual material identity specific to each carbon atom is abstracted away in the process of descriptive specification and identification of the cycle.
In contrast to the identity in isolation, the identity in relation can address the class property of a material body whose identity is kept even through the constant exchange of the constituent material elements. If the origin of life presupposes the occurrence of a spontaneous appearance of self-replicating molecules, it must have been supplemented by a scheme of protecting the once appeared self-replicating molecules against the then conceivable hostile environments in prebiotic settings. One likely candidate for the protective means could have been the robust class identity of a reaction cycle to be maintained through the constant exchange of the component atoms and small molecules. Matter can be functional in exchanging the constituent material elements without referring to what life is all about. This observation now suggests an opportunity that the onset of biology can take advantage of metabolism that is already latent in matter itself even before the evolutionary emergence of cellular components. Rather, the emergence of the cellular structures could have been a consequence of taking advantage of the material activity of metabolism. The essence of a functional matter is rooted in the soundness of internalizing the description of the dynamics into the dynamics itself. Synthesis comes from an abstraction. References Aharonov, Y., Albert, D.Z., Vaidman, L., 1998. How the result of a measurement of a
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