Quantum as a heat engine—the physics of intensities unique to the origins of life

Physics of Life Reviews 2 (2005) 227–250 www.elsevier.com/locate/plrev

Review

Quantum as a heat engine—the physics of intensities unique to the origins of life Koichiro Matsuno ∗ , Atsushi Nemoto Department of BioEngineering, Nagaoka University of Technology, Nagaoka 940-2188, Japan Accepted 30 June 2005 Available online 11 August 2005 Communicated by E. Di Mauro

Abstract Experimental endeavor for addressing the origins of life when viewed from the physical perspective presents a new opportunity of developing physics further for its own sake. A case in point is the issue of intensities. The physics of the origins of life may more readily be approachable by way of the dynamics of intensities or intensive quantities such as temperature and force strengths, compared to the standard dynamics of extensive quantities such as molecule numbers, densities, masses and charges. What is unique to the dynamics of intensities is that it is already contextual in addressing the context under which the intensities in focus are generated and maintained. In particular, because of the contextual nature of temperature grounded upon the material context in which the contextual elements move almost randomly with each other, the occurrence of temperature gradients provides an impetus for transforming the material context. The physical origins of life are just associated with the emergence of the robust material context that can serve as a heat engine. One likely candidate for the material context serving as a heat engine that could emerge in the presence of temperature gradients near hot vents in the primitive ocean on the Earth might have been a citric acid cycle running with no help of enzymes of biological origin. Underlying the emergence of a robust heat engine is the pruning principle of the faster temperature drop going with the greater stored latent heat applied to any reacting molecules crossing the temperature gradients.  2005 Elsevier B.V. All rights reserved.

* Corresponding author. Fax: +81 4 2957 8870.

E-mail address: [email protected] (K. Matsuno). 1571-0645/$ – see front matter  2005 Elsevier B.V. All rights reserved. doi:10.1016/j.plrev.2005.06.002

228

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

Contents 1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2. Evolutionary significance of the presence of temperature gradient 3. Chemical evolution in the cosmological context . . . . . . . . . . . . 4. Chemical evolution in the primitive ocean on the Earth . . . . . . . 5. Planck’s context in the evolutionary perspective . . . . . . . . . . . . 6. Evolutionary quantum as a heat engine . . . . . . . . . . . . . . . . . . 7. Toward igniting a citric acid cycle . . . . . . . . . . . . . . . . . . . . . . 8. Concluding remarks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

. . . . . . . . .

......... ......... ......... ......... ......... ......... ......... ......... .........

228 229 230 232 235 239 241 247 249

1. Introduction Chemical evolution underlying the emergence of what is called the phenomenon of life has been a time-honored subject matter of both chemistry and physics, among others, calling for intensive research endeavors [25,54]. A major focus of interest has been on the possible evolutionary onset of reaction cycles, either of replicating molecules or of metabolic reactions, or both. In particular, the RNA world has been proposed as a neat evolutionary model of both replicating molecules and the associated metabolic cycles, thanks to the two distinctive catalytic capabilities that RNA molecules can assume on self-splicing and on molecular ligation interchangeably [18,19,52]. Chemistry of the RNA world is straightforward in presenting and deciphering the chemical makeup of molecular replication and of processing both the uptake and the disposal of participating nucleotide molecules [4]. Nonetheless, if it could evolutionarily happen to appear by any chance at a certain point on the primitive Earth, the RNA world would have required an additional material support that could have protected and preserved the molecular replication scheme, once emerged, against all possible perturbations and even hostile disturbances coming from the outside environments [1]. Replicating RNA molecules alone would not specify how robust or fragile they would have been as facing these adverse disturbances from the outside. At this point enters the physics of chemical evolution. Evolutionary stability of the molecular replications and the associated metabolisms is about the robustness of the material context in which the constituent material elements could participate. Replicating molecules could not survive unless the supporting network of reaction cycles remain robust in the face of disturbances of whatever kind coming from the outside. The supporting reaction network also cannot come into existence unless replenishing the necessary constituent molecules by whatever means are guaranteed. This issue is about the physics of material dynamics addressing the relationship between the context and the contextual elements both on a par with equal footing with each other. The present view on physics is however somewhat different from the traditional one elevating the context of material origin to the boundary conditions of exogenous origin or of an imposed character [8,30]. Needless to say, the significance of boundary conditions in physics cannot be overemphasized both in classical and quantum mechanics. Despite that, the physics of the evolutionary onset and sustenance of replicating molecules comes to raise one more issue on how what may look like boundary conditions could emerge along with the constituent material elements. The physics of the origins of life, if ever feasible, may address a physical agenda on how boundary conditions could emerge and develop

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

229

along with the material elements bounded accordingly [24]. Explicating evolutionary boundary conditions of endogenous origin will be a main theme of the present article. We shall first review and focus on the evolutionary significance of the contextual dynamics in terms of temperature, since temperature is a representative quantitative figure characterizing the material context after Boltzmann, in which the contextual elements, whatever they may be, may move almost randomly with each other.

2. Evolutionary significance of the presence of temperature gradient At the least, temperature serves as a quantitative figure characterizing a material context in thermal equilibrium with its surroundings. The present stipulation of a theoretical nature, however, does not necessarily imply that temperature should be relevant only to the notion of thermal equilibrium that remains homogeneous both in space and in time. If it is possible to conceive of a thermometer in an operational sense, the temperature it could measure can be heterogeneous both in space and in time insofar as the contact between the thermometer and its local surroundings operationally guarantees an attainment of thermal equilibrium even locally. For instance, any contrast between a hot and a cold locale within the same shared space like a hot spring from the seafloor spewed into the cold surrounding ocean on the Earth, once taken legitimate, is an empirical testimony to the fact that temperature can be heterogeneous both in space and in time [3]. The presence of spatial temperature gradient to be mitigated is thus synonymous to the likelihood of varying the material context specifying its temperature even locally both in space and in time. Temperature gradient manifests an occurrence of the contextual dynamics on specifying and varying its temperature [35]. Temperature dynamics as an instance of contextual dynamics is unique in addressing the intensity specific to the context as a whole in movement. Being different from an extensive quantity such as energy, temperature is an intensive quantitative figure about a material context. As a consequence, the intensive nature of temperature comes to impose upon the contextual elements a selective criterion exclusively of contextual origin. That is to say, no contextual element can belong to two different contexts at the same time. This selective nature of contextual origin is ascribed to the one-way influence such that every contextual element is placed under the constraint of the context, and not the other way around. If a contextual element could belong to two different contexts at the same time, unity of each context would be jeopardized and lost. Selective capacity is physically ubiquitous in the material world even prior to the upcoming of natural selection of biological origin insofar as contextual dynamics is in place. Moreover, the likelihood of contextual dynamics is firmly grounded upon the empirical basis at least as much as temperature empirically holds as a reliable and dependable quantity measuring a contextual intensity. Whenever or wherever a form of contextual dynamics is set in motion, an intensive quantity or intensity unique to the context comes to internally be regulative in exercising an endogenous selective capacity. Any change in the intensity is going to come with the associated changes in the context. Accordingly, the contextual elements are internally subject to selective changes in eliminating those elements not in conformity with the surviving context from the list of the allowed incumbents. A conspicuous example of this sort will be seen in the operation of the time-honored Fourier’s law of heat transfer [22]. Once Fourier’s law of heat transfer receives due attention it deserves, one basic issue comes into focus. Fourier’s law assumes two fundamental quantities. One is temperature, and the other is heat flow,

230

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

as expressed in the form of
Q = κ
T , in which
Q is the rate of heat energy flowing from the higher temperature side to the lower side across the temperature gradient
T marked by its thermal conductivity κ. Between these two quantities, temperature as a quantitative figure is qualitatively different from heat flow as another quantitative figure. Temperature is a figure quantifying the context whose constituent elements, whatever they may be, exhibit a random movement, while heat flow is a quantitative figure being additive even infinitesimally. In short, temperature is intensive, while heat flow is extensive. That implies that Fourier’s law is about a relationship between the context and the contextual elements. As a matter of fact, Fourier’s law addressing heat flow through the interface connecting two different regions at different temperatures is about a dynamic behavior occurring when two different contexts at different temperatures come into contact with each other. In addition, Fourier’s law as a contextual law is already unique in admitting in itself a certain selective capacity. No contextual element can belong to two different contexts at the same time. When a tissue of an organism is at a certain temperature, the temperature of the organs constituting the tissue cannot be different from that of the tissue. When an organ of a tissue is at a certain temperature, the temperature of the constituent organelles cannot be different from that of the organ. Selective capacity latent in Fourier’s law will be more vividly focused when one pays attention directly to two different contexts at different temperatures coming into contact with each other, instead of to the amount of heat flowing through the interface. When the temperatures of the two contexts start varying because of the intervening heat flow through the interface, each context would modify itself or adjust its temperature as fast as possible. This is simply because of the intrinsic affinity between the context and the contextual elements. When the context as a construct from the contextual elements in a bottom-up manner is allowed to change, the realizable change could only be the one proceeding at the fastest rate [35]. There would be no room for the latecomers to take part in since the constituent elements cannot belong to different contexts at the same time. Fourier’s law is contextual. Accordingly, it is intrinsically selective in its operation with regard to the contextual elements. When a small hot body is thrown away into a huge cold surrounding, it can decrease the temperature faster as making the amount of heat dissipation toward the outside less by letting the internally stored latent heat greater. Since the faster temperature drop is selected for on the material and physical basis as implied in Fourier’s law of heat transfer, the greater latent heat substantiating the faster drop should be in accord with the more molecular coordination and synthesis. That is the pruning principle of physical origin. We shall thus require factual evidence on the evolutionary selective capacity latent in Fourier’s law in the presence of temperature gradients. One evolutionary implication of the selective capability latent in Fourier’s law of heat transfer will be seen in chemical evolution in the cosmological context.

3. Chemical evolution in the cosmological context The origin and evolution of biological organizations on the Earth has undoubtedly been put under the cosmological context. The formation of our solar system has been a cosmic event that took place almost 4.6 billion years ago. Formation of small organic molecules that are indispensable for the makeup of

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

231

biological organizations on the Earth could also have been cosmological. One of the likely candidates for cosmological syntheses of small organic molecules, which are conceivable from the framework of temperature dynamics, is the one taking place in interstellar dust grains. In particular, the dust grains having the refractory core mantles, when irradiated by ultraviolet radiation in diffuse interstellar clouds, could make possible to synthesize various small organic molecules (see, for instance, [5,45]). Diffuse clouds keep the water-rich dust grains at temperature in the range 20–100 K. When they are irradiated by ultraviolet radiation, the accompanying photolysis can warm up the ice grains to help form aliphatic –CH2 – and –CH3 groups. As a matter of fact, near-infrared observations reveal the solidstate features due to the presence of dust grains in diffuse interstellar clouds, as pointing out the strong infrared absorption band complex centered around at wavelength 3.4 µm (2955 cm−1 ). The optical depth spectrum of diffuse clouds observed from Galactic Center IRS 6E is found quite close to the spectrum of a laboratory residue produced by the ultraviolet irradiation upon an interstellar ice analog at 10 K, then followed by its warm up to 200 K ([45] and references cited therein). Such a similarity has also been observed with the specimen prepared in the laboratory and then exposed to long-term solar ultraviolet radiation on the EURECA satellite. The products could be nucleobases, sugars, and amino acids when coming into contact with liquid water [14,15]. Furthermore, the similarity of the near-infrared spectrum between the interstellar observations and the ones from a Murchison carbonaceous meteorite suggests a cosmological ubiquity of chemical synthesis of small organic molecules in interstellar ice grains in diffuse clouds. Our Earth is no exception in being subject to the influence from these interstellar ice grains. Another important source for making small organic molecules must have been cosmic rays and the primitive atmosphere of the Earth irradiated by them. Even if the atmosphere was oxidized, cosmic rays might have been a major effective energy source for abiotic formation of amino acids and other bioorganic compounds [23]. When it was tried to synthesize amino acid molecules from carbon monoxide, nitrogen and water as irradiating their gas mixture with high-energy particle beams of protons, helium nuclei or electrons, a considerable amount of the yields was identified. The G-value, that is the number of molecules produced per 100 eV of irradiated energy, of glycine was about 0.02. The present G-value is far greater than that expected from electric discharges. In addition, the G-value did not vary very much depending upon the species of carbon sources in the gas mixture, while it considerably depended upon the species in the discharge experiments. This observation suggests to us that synthesizing small organic molecules including amino acids with recourse to cosmic rays as major energy sources must be cosmic events, and not necessarily be limited to the atmosphere of the Earth. Meteorites and cosmic dusts could have conveyed to the Earth a considerable amount of small organic molecules synthesized elsewhere. Of course, there might have been possibilities of synthesizing amino acid molecules and nitrogen bases through lightning or electric discharge in the primitive atmosphere on the Earth if the atmosphere was reducing. Spark charges in the hydrosphere could have been another possibility for synthesizing small organic molecules on the Earth [39]. Contribution of cosmic rays, radiation and lightning has been registered as significant factors for making feasible the presence of small organic molecules on the primitive Earth. In order to proceed further towards the emergence of life on the Earth, however, we are required to face something more specific to our Earth. Cosmic ubiquity of small organic molecules alone is not good enough for coping with material evolution following the synthesis of those small molecules. In this regard, the contribution of cosmic rays, radiation and lightning is suggestive in sharing one thing in common. That is, the synthesis of small organic molecules could appear in the process of thermal randomization of the primary energy input

232

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

whatever it may be. Material evolution requires energies to be thermally randomized [13]. Some energy sources other than those from cosmic rays, radiation and lightning must have been available for driving further material evolution on our Earth. The energy sources specific to the Earth must be quite unique in their inevitable dissipation leading eventually to thermal randomization. At this point, we can see two major sources, each of which is quite specific to our Earth in the framework of temperature dynamics. One is the solar energy impinging on the Earth’s atmosphere, and the other is the geothermal energy erupted into the hydrosphere from the Earth’s mantle. The sunlight reaching the surface of the Earth would soon decrease its temperature from roughly 6000 to 300 K determined by the equilibrium condition of the black body radiation in the latter. Thermal randomization of the solar energy in the Earth’s atmosphere may quite easily be established soon after the solar photons repeat their collisions with material particles constituting the Earth’s environment. The characteristic time for each average solar photon to reach its thermal equilibrium with the surrounding black body is quite small because the time is scaled by the flight time of the photon. Even if there were no special traps of the solar photons available in the Earth’s environment, their thermal randomization would meet no difficulty. In contrast, thermal randomization of the geothermal energy in the ocean is quite different compared to the case of the solar energy in the atmosphere. The thermal relaxation of the geothermal energy in the ocean takes place mainly through the collisions of water molecules. The characteristic time for the heated water molecules to reach a thermal equilibrium with the surrounding cold seawater is significantly greater than the relaxation time for the solar photons to reach their thermal equilibrium with the Earth’s environment. The process is mediated by molecular collisions instead of the flight of photons. The greater thermal relaxation time may provide thermal randomization of the geothermal energy in the ocean with the richer catalogue of the relaxation processes taking place there. The richer catalogue could have facilitated further evolutionary capability in the relaxation of the geological heat in the ocean. The sunlight cannot serve as an energy source to drive the relaxation processes in the ocean, because it is mostly reflected upon the surface of the ocean and back into outer space at temperature far below 300 K. Photosynthesis could have been installed on the Earth’s surface only when there appeared a mechanism of trapping the energy from the solar photons. For this to be accomplished, the trapping of the solar photons has to outstrip the thermal randomization of the photons in the Earth’s environment due to the black body radiation. We cannot rely upon the sunlight as the energy source driving further material evolution until such a fast trapping mechanism of the solar photons emerges. Exactly at this point, the geothermal energy erupted into the ocean becomes significant from the perspective of temperature dynamics. The geothermal environment in the ocean could have been far richer in trying or even tinkering with a lot of evolutionary opportunities. Once there could be synthesized a molecular aggregate or organization in the environment in a time interval shorter than the relaxation time of the hot water molecules, the organization could survive if its decay time is greater than the thermal relaxation time of the water molecules there. The geothermal environment on the primitive Earth could have been a main stage of further prebiotic evolution prior to the emergence of photosynthesis on the Earth’s surface.

4. Chemical evolution in the primitive ocean on the Earth Ever since the ocean was formed around 4.2 billion years ago, off-ridge submarine hot springs interfacing with the surrounding relatively cold seawater in the Hadean Ocean came to provide unique locales

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

233

for further prebiotic synthesis. First of all, the vicinity of the hot springs would have offered protection from bolide-induced vaporization of seawater, cosmic rays, ultraviolet photons, lightning and tidal waves [48]. Circulation of hydrothermal solution around the hot vents could have provided a means of gleaning traces of small organic molecules residing in the crust, that could ultimately have derived from the carbonaceous chondrites, interplanetary dust particles and comets [6,36,43]. What is further unique to the circulation of seawater through the hot vents is the constant geothermal gradient or disequilibrium driving various chemical syntheses. This is the issue of nonequilibrium thermodynamics [46]. Of course, cosmic rays, radiation and lightning can impart their energy to small molecules and drive synthetic reactions in the latter. The energy pathway from the high-energy sources to the end products is definitely in nonequilibrium in the thermodynamic sense. Impinging high-energy particles, whether protons, helium nuclei or electrons, are responsible for making a nonequilibrium situation that can drive synthetic reactions among the available small molecules. Once those high-energy particles are interrupted for whatever reasons, on the other hand, there would be no factors driving such synthetic reactions. Impinging high-energy particles determine the actual synthetic reactions during their inevitable thermal decay. The actual synthetic reactions are associated with realizing the fastest thermal decay or temperature response. In fact, the temperature relaxation process that is actualized is the possible fastest one among the alternatives since there is no chance for the latecomers [35]. This perspective comes to suggest to us that the constant geothermal disequilibrium is really unique in that it would take a considerable amount of time for the hot seawater ejected from the vents to reach a thermal equilibrium with the surrounding cold water. This implies that a synthesized molecule in the hot seawater, if any, can survive in the surrounding cold water if it can hold its own structure while the water droplet including the synthesized product decreases its temperature as contacting the cold surrounding. The constant geothermal disequilibrium due to the mixing of the hot water from the vents with the surrounding cold water provides a selective sieve for the synthesized chemical products when they enter the cold surrounding. Those products that cannot hold themselves during the quenching imputed to the cold surrounding do not have their chance of survival. The dissociation rate of a synthesized product inside or near the hot vent could increase with temperature. If it remains near the vent, the product would likely be dissociated rapidly. On the other hand, if the product is rapidly transferred into the cold surrounding, the dissociation rate of the product is considerably quenched there and its chance of survival in the latter would be greatly enhanced. The constant geothermal disequilibrium thus focuses upon the activity on the part of the lower temperature side in determining the actual temperature relaxation. This exhibits a marked contrast to the case of cosmic rays, radiation and lightning, in which the actual relaxation process is determined by the higher temperature side, that is, impinging high-energy particles. Supply of high-energy particles is met only by those synthetic reactions that could realize the actual fastest temperature relaxation. In contrast, consumption of the geothermal energy from the hot vents by the surrounding cold water is met by the synthetic reactions that could hold the products in the transference. The constant geothermal disequilibrium is maintained independently of the selective sieve acting upon the synthesized products in the hot regions. It can be maintained even if there are no chemicals to be reacted. Independence of the occurrence of the geothermal disequilibrium from the synthetic reactions taking place there now furnishes the reaction products with the selective characteristic imputed to the disequilibrium itself. When there is a dominant relaxation process of an imposed character such as the constant geothermal disequilibrium, it serves as a selective reference against other minor processes of a synthetic character to arise from within. Only those that can live with the dominant relaxation process can survive. Ever since the ocean was formed, the constant geothermal disequilibrium has provided nearby

234

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

chemical reactants with the opportunity for taking advantage of the disequilibrium itself for the sake of the synthetic reactions taking place. An essence of the operation of the constant geothermal disequilibrium will further be clarified from the thermodynamic perspective of temperature dynamics. The geothermal environments in the Hadean Ocean could certainly have played a significant role in setting the subsequent stage for prebiotic evolution [20]. This is however not simply a matter of historical contingency unique to our planet Earth. In order to make it possible to have more complex molecules from smaller and simpler ones during chemical evolution, energy sources are definitely required. Energy is required to move chemical reactants away from their thermal equilibrium, in the latter of which no evolution could be envisaged. At this point, there could arise two important issues. One is from where and how the energy sources could be recruited, and the other is about how the energy transaction would proceed in time while activating some of interesting chemical reactants. As for the first question, all of cosmic rays, radiation, lightning and geological heat can be authentic candidate for supplying energy to nearby chemical reactants. For the second question, on the other had, there could appear a sizable difference in specifying the energy transaction especially in how the used energy could be disposed. Among them, the geothermal environments are quite unique in rendering the constant geothermal gradient or disequilibrium to be the dumping site of the used energy. If the disposer of the used energy is the heat reservoir in thermal equilibrium as is most often the case with cosmic rays, radiation and lightning, the way the energy is utilized is limited. Only the fastest relaxation processes towards thermal equilibrium could be actualized. The constant geothermal disequilibrium, on the other hand, provides subsisting chemical reactants with a selective criterion stipulating them to live with the disequilibrium. This is quite different from another selective criterion intrinsic to thermal equilibrium letting the energized species decay towards its equilibrium condition as fast as possible and live with the reservoir indefinitely. Most significant to the occurrence of the geothermal environments in the Hadean Ocean is the installation of a de novo selective criterion applied to reacting chemical species in the environments. The likelihood of the present perspective on the occurrence of a new selective criterion applied to prebiotic evolution can even be demonstrated and tested experimentally. Chemical syntheses leading to the origin and evolution of biological organizations on the Earth do require a selective criterion other than that applied exclusively to thermal equilibrium. The likely candidate is submarine hydrothermal systems that have persisted in existing ever since the ocean was formed on the Earth [9,11,12,47,51]. The hot spring ejected from the hydrothermal vents soon comes to face cold seawater in the surroundings, which serve as the heat sink. Chemical products synthesized in the hot vents undergo abrupt cooling once they are ejected into the cold environment. The surrounding heat sink constantly feeds on the hot water and consumes the heat energy therefrom. In this sense, the contextual dynamics actualizing the fastest temperature relaxation is definitely operative toward the products. Only the products exhibiting the fastest temperature drop could survive there. Reaction products synthesized in the hot vents followed by their rapid quenching in the surrounding cold seawater are both generative and selective. They are generative in facilitating synthetic reactions in the hot vents, and at the same time selective in materializing only those that can decrease their temperature at the possible fastest rate when ejected into the cold environment. Furthermore, continuous circulation of seawater around the hydrothermal vents could make the selective process cumulative as constantly transforming the preceding products into the succeeding reactants even if the cycle time of revisiting any one of hydrothermal vents in the Hadean Ocean would be tens of thousands of years or more. Temperature dynamics applied to continu-

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

235

ous circulation of seawater around the hydrothermal vents in the ocean can sustain selective process on material grounds indefinitely even prior to that Darwinian molecular evolution gets started. We have constructed a flow reactor simulating a submarine hydrothermal system just to examine the appropriateness of temperature dynamics tailoring quantum mechanics for synthesizing prebiological oligomers in the hydrothermal context [29]. Synthesis of oligoglycine from monomeric glycine up to octaglycine was in fact confirmed in the flow reactor [16,17,41]. Hydrothermal vents could also be active for dissociating amino acids into their constituent molecules through, for instance, decaroxylation, deamination or even dehydration because of their high temperatures [2,37]. However, the synthetic reaction could survive despite that if the residence time of the reaction products in the hot vents is limited compared to the total cycle time required for completing the rounding around the vents. Once continuous circulation of the fluid carrying reactants is guaranteed for some time, an autocatalytic or network-catalytic growth of the products [21,27] could naturally be expected thanks to the forced conversion of the preceding products into the succeeding reactants. For the reactants that help producing the products of like kind can increase their yields exponentially in time. In fact, we observed a network-catalytic growth of oligoglycine up to hexamer in the flow reactor [17]. Such a growth of products in the flow reactor also applies to the synthesis of oligopeptides from more than two different kinds of amino acids [41] and to the synthesis of oligonucleotides from monomeric nucleotide molecule AMP (adenosine monophospate) [40]. Even formic and acetic acids were synthesized from carbon dioxide and water when metal oxides were put inside the simulated hot vents [26,53]. Chemical evolution empirically observed so far both in the cosmological and in the geothermal contexts manifests that the selective capacity ascribed to contextual dynamics is certainly operative in the presence of temperature gradient to be mitigated. However, temperature dynamics is not the only candidate for contextual dynamics. Also underlying the contextual dynamics for chemical evolution is quantum dynamics since those chemical species appearing in the process are quantum mechanical in their material makeup. In fact, the contextual underpinning of quantum dynamics goes back to the observation of a quantum originally made by Max Planck.

5. Planck’s context in the evolutionary perspective Atoms and molecules constituting a biological organism are placed within the material context of an extremely specific configuration. Such a specificity of the material context makes biological organization unique compared to nonliving physical organization of atoms and molecules. Needless to say, physics has its own rich history on explicating the nature of whatever material contexts available there. One example of an extreme significance is the material context discovered by Max Planck. When Planck introduced the notion of a quantum for the first time, the relevant empirical fact referred to was that a light-wave emission from and absorption to a black body in thermal equilibrium with its surroundings are punctuated in a discrete manner. The discreteness is associated with the empirical observation that light-wave emission in progress comes to shortly be punctuated by the emission completed, and light-wave absorption in progress similarly comes to be punctuated by the absorption done. There is no indefinite prolongation of light-wave emission and absorption over to an infinite duration in a continuous manner. The punctuated light-wave referred to as a light quantum or a photon carries with itself the context within which continuous light-wave is encapsulated in a coherent manner. In particular, Schrödinger identified that the coherent nature of the encapsulation is due to the occurrence of a standing

236

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

Fig. 1. An image of Planck’s quantum. The context of a Planck’s quantum is an almost complete closure of oppositely propagating de Broglie’s material waves serving as the moving contextual elements. The robust boundary represents the particle nature of the quantum distinguishing between the movement in progress and the movement perfected on its own from within.

wave as a coherent superposition of both the retarded and the advanced waves of material origin, whose schematic representation is displayed in Fig. 1. Unique to the material context upholding a quantum, as coherent encapsulation of the contextual elements is its robustness against adverse perturbations and disturbances coming from the outside. Context as a limiting modifier of the contextual elements, if empirically available, must remain robust to a reasonable extent. Otherwise there would be no possibility for denoting it as such in the empirical domain. Empirical confirmation of the occurrence of such a robust context derives from examining the empirical record of the events of interest. The record is about the events already registered in the present perfect tense, while the ones right in the making are in the present progressive tense. What remains basic to quantum mechanics is the explicit distinction between the present perfect tense and the present progressive tense, the latter of which does necessitate the participation of second person description being responsible for distinguishing between the movement in progress and the movement completed. Empirical underpinning of Planck’s quantum is upon the robust demarcation of the movement in progress from that completed, more than anything else. The demarcation marked by the movement itself is accessible exclusively in second person description. In fact, second person description takes the physical act of measurement for granted, compared to the case of third person description in the latter of which the act of measurement has to be imported externally. What is uniquely specific to the practice of quantum mechanics in the present progressive tense in second person description is the builtin participation of measurement process that is responsible for making a robust quantum from within. That is internal measurement [28]. The robust record rests upon the clear-cut transference of events in the present progressive tense to those in the present perfect one [32]. In fact, quantum mechanics accessible in third person description grounds itself upon the existence of such a robust record derivable from the material act of crossing the different grammatical tenses. The availability of robust record is also conceivable in thermodynamics, though the robustness there is limited only to macroscopic variables. What is specific to thermodynamics is that it introduces those macroscopic variables such as volume, pressure, temperature and entropy without detailing their atomistic makeup at the outset. These macroscopic variables are about the context in which the underlying microscopic elements, whatever they may be, are eventually situated. The contextual dynamics spec-

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

237

ifying the values of the macroscopic variables is constantly operative there. Even if the fundamental dynamics of microscopic elements is left unspecified, the contextual specification is to proceed. A molecule in the gas is subject to the temperature of the gas while at the same time the molecule is part of the gas substantiating the same temperature. Thus, any contextual element constituting the context comes to materialize and share the same contextual specification. Thermodynamics is unique in emphasizing the priority of contextual specification over elementary specification of each constituent element. Although mechanics is a theoretical enterprise equating elementary specification of an imposed character literally to contextual one in a crisp manner, thermodynamics is quite different in allowing an under-complete elementary specification whether or not it is of an imposed character. The present contextual specification now provides the interplay between the two of the contextual and the elementary dynamics with a possibility of influencing each other in both ways, namely, from the elementary to the contextual and vice versa. One attempt for relating the elementary to the contextual dynamics is through a statistics of mechanics over an ensemble of elementary specifications. Statistical mechanics is grounded upon the premise that an ensemble of elementary specifications could be a substitute for the interplay between the two specifications, the contextual and the elementary ones. A justification of the ensemble of elementary specifications came from Boltzmann’s Stosszahl Ansatz or hypothesis of a molecular chaos stating that molecules in the gas soon lose their memory of the past collisions with the others except for the latest ones. Those molecules in the gas thus come to have almost no correlation with the others or to move almost randomly with each other. This is equivalent to saying that the context which Boltzmann introduced is the one under which every contextual element moves almost randomly with each other. More specifically, one particular quantitative figure characterizing the Boltzmann’s context is called temperature at least in an operative manner. To be sure, Boltzmann’s context is found ubiquitous in physics. Nonetheless, it is no more than a heuristic candidate for fulfilling the role of contextual specification available to thermodynamics. There certainly is one more candidate for meeting the similar requirement of contextual specification. That is Planck’s context. The context discovered by Planck, or Planck’s context, is the one for those contextual elements moving almost coherently with each other. Planck’s context is just a polar opposite to Boltzmann’s, in the latter of which the contextual elements are taken to move almost randomly in an incoherent fashion with each other. However, the relationship between Planck’s context and Boltzmann’s is not mutually exclusive. Planck’s context is more fundamental and more inclusive in that any material element of whatever sort is a quantum after Planck. In contrast, Boltzmann’s context is subject to Planck’s contexts embedded in it. At the same time, Planck’s context is also subject to influences and the act of measurement coming from its outside, because it always presumes the action of making a sharp distinction between the present progressive and present perfect tense. What is responsible for generating the context is the robust interplay between the inside and the outside through the act of measurement [28]. The present interplay can now furnish a Boltzmann’s context as a source matrix of the measuring agencies toward each Planck’s context residing in its inside, with the possibility of modifying the latter context in time internally. Occurrence of a Boltzmann’s context is in fact an empirical testimony to the observation that the constituent quanta or Planck’s contexts are measuring each other internally, that is to say, involved in internal measurement altogether. In particular, the contrast between Planck’s context and Boltzmann’s will become more conspicuous once the nature of internal measurement involved is focused. Although Boltzmann’s context rests upon the stipulation that each quantum loses the memory of the past measurements of the others shortly,

238

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

Planck’s context is about the persistent memory of the measurement internal to each quantum while distinguishing the movement in the present progressive mode from the one in the present perfect. Planck’s context is for long memory of internal measurement, while Boltzmann’s is for short memory. One agenda of evolutionary significance on the interplay between Planck’s context and Boltzmann’s may be about the relationship between the material context and its constituent elements at the onset of what is called life phenomenon in molecular terms. Replicating molecules such as catalytic RNA molecules must have been a representation of the material context that might have facilitated the onset of life phenomenon, but not the very material context itself. The material context being competent enough for accommodating replicating molecules into it must have been a Planck’s context in an extended sense since the context is about whatever coherent unity of the contextual elements. At issue is the inevitable interplay between an extended Planck’s context of a coherent unity and Boltzmann’s context in thermodynamics. One likely thread connecting Boltzmann’s context to Planck’s is the first law of thermodynamics on energy transformation. An energy quantum as a coherent enclosure of the standing material wave after de Broglie remains robust, but its enclosure is not literally complete. Otherwise, there would be no possibility of energy quanta interacting with each other. This comes to imply that when one applies Fourier’s law of heat transfer to an energy quantum, there may happen to be a case of transforming the quantum with the aid of the underlying dynamics of varying the participating contexts. Prerequisite to such a transformation is the occurrence of heat flow through the interface between different contexts at different temperatures. When a small energy quantum at a certain temperature is suddenly made contact with the environment of almost an infinite heat capacity at a different temperature, Fourier’s law is to implement the first law of thermodynamics through the contextual transformation or transforming the participating quantum. The contact of the quantum with the environment transforms that quantum so that its temperature may approach the environment’s temperature at the possible fastest rate. Fourier’s law materializes in the form of the first law of thermodynamics as being accompanied by its intrinsic selective capacity of actualizing only the fastest contextual change. An energy quantum conceived within the framework of Fourier’s law of heat transfer now suggests such likelihood that an energy quantum may function as a heat engine processing both the incoming and outgoing heat flow there, in contrast to a quantum originally conceived by Planck as an almost complete

Fig. 2. An image of quantum as a heat engine. A good example of quantum as a heat engine is a robust reaction cycle that can take in necessary reactants from the outside and dispose the waste products also to the outside. The robust cycle, if legitimate, should be grounded upon its empirical confirmation, more than anything else.

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

239

encapsulation of internal movements. In order to make the case of energy quantum as a heat engine more solid as figuratively depicted in Fig. 2, we shall need to clarify its quantum-mechanical makeup in more details.

6. Evolutionary quantum as a heat engine Energy transformation requires temperature differences from the thermodynamic perspective, and temperature differences require black body radiations at different temperatures in contact from the perspective of quantum dynamics. In fact, the interaction between an energy quantum and the black body radiation in thermal equilibrium is quite subtle. The energy quantum could transform itself into a robust one as cohering with others or decohering into others [56]. When the temperature of the surroundings is made extremely low, there could happen to occur the coherent condensation of energy quanta on the macroscopic scale. This is the case with superfluidity and superconductivity as met in statistical physics, while such a macroscopic condensation would easily decohere as the temperature increases. Statistical physics has made a convincing case for realizing an ensemble of decohering energy quanta in thermal equilibrium that would not transform itself any further. When they are taken in thermal equilibrium, both quantum coherence and decoherence would have no capacity for further transformation. This has been one instance on the relationship between quantum coherence and decoherence on the one hand and thermal equilibrium on the other. One more instance that could be more relevant to biology is that the realizable quantum coherence remains robust against the interfering quantum decoherence. This perspective is quite different from the one employed in statistical physics, in the latter of which both quantum coherence and decoherence are taken mutually incompatible by definition. Both the coherence and decoherence cannot coexist if each of them is deemed globally homogeneous in space as practiced in statistical physics. Nonetheless, the actual coexistence of both the coherence and decoherence and the interference between the two could be conceivable at least locally in space once such a forced stipulation on global homogeneity is lifted. This is the place where transformation of an energy quantum can be operative even when immersed in a Boltzmann’s context provided externally. There arises the likelihood that quantum coherence may remain robust as being subject to quantum decoherence originating in the environments, that is to say, quantum coherence somewhere may feed on quantum decoherence elsewhere nearby. Quantum coherence that remains robust can be equated to what has been called a classical object [10]. This is just another way of saying that the observed stability of nonbiological and biological material bodies alike is sought in quantum dynamics and ultimately in the stability of each energy quantum. Although the classical objects cannot exhibit quantum coherence between themselves any more, this does not imply that each classical object would also not be of quantum origin. Quite the contrary, the classical object does exhibit quantum coherence in its inside as with the case of each energy quantum while it has already lost the capacity of cohering with the others in its outside. The coherence the classical object maintains internally remains robust and immune to disturbances of the environmental origin. Heat engine is just a particular mode of quantum coherence in the process of generating a robust temperature difference at the interface with the outside at the same time. What makes heat engine unique compared to the static classical object is the persistence of quantum coherence concurrently at the expense of ongoing quantum decoherence being instrumental for the genesis of local temperature dif-

240

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

ferences. A common functional denominator applicable to ubiquitous biological bodies is the operation of heat engine feeding on transforming an energy quantum. Quantum as a heat engine is nothing other than a robust and irreducible functional unit open to energy flow, compared to Planck’s quantum as an almost complete encapsulation of internal movements. It is in essence a naturalized form of quantum heat engine utilizing quantum coherence and decoherence as an effective means of raising or lowering temperatures. Although ubiquity of quantum as a heat engine in the biological realm remains at most a theoretical thesis to be tested, there has already been indirect and circumstantial evidence supporting it empirically. One evidence is on the occurrence of a weak magnetization of an actomyosin complex that is a functional unit of muscle contraction, in the presence of ATP molecules to be hydrolyzed [31]. The robustness of the weak magnetization stands only when there are ATP molecules to be hydrolyzed. Energy from the high-energy phosphate bond is instrumental for holding the magnetization even in the face of thermal agitations from the surroundings. The weak magnetization is not about a coherent condensation of quanta each of which is almost closed to energy flow to and from the outside, but about a robust functional unit open to energy flow. Once such a robust functional unit is available, it can serve as a quantum unit in the sense that it can hold its own identity even in the face of adverse disturbances from the surroundings. This observation will naturally raise a question of what sort of functional unit that may operate as a heat engine could have been likely in chemical evolution leading to the origins of life. Addressing this question of the origins will require further scrutiny of the relationship between quantum mechanics and thermodynamics. That heat engine is quantum mechanical in its origin can readily be seen once one focuses on energy-rich meta-stable molecules to be degraded energetically by whatever means. The energy distribution of the photons emitted from the meta-stable molecules determines the temperature of the radiation field. If the temperature of the surrounding material bodies is different from that of the radiation field of the emitted photons, there could arise a temperature difference between the material bodies in the surroundings and the radiation field. A consequence is the onset of a heat engine feeding on the temperature difference. Releasing photons from meta-stable molecules is in fact quite ubiquitous in chemical reactions. Consider, for instance, the chemical reaction of synthesizing carbon dioxide from carbon monoxide and oxygen molecules. The photon released in this reaction is in the infrared region, whose energy is roughly of order of 0.1 eV or 1000 K in temperature. If the surrounding is at room temperature, the resulting radiation field can certainly provide a necessary condition for implementing a heat engine. Likewise, there could also be a possibility of raising a heat engine upon chemical reactions in which the temperature of the emitted radiation field is far below room temperature in the surrounding. What is important at this point is how could those chemical reactants be supplied on a continuous basis in the natural setting amenable to biological organizations. Unique to the operation of heat engine in the biological realm is the connection between quantum coherence in the product and quantum decoherence in the making. Quantum coherence feeding on quantum decoherence is to relate the present progressive tense in the making to the present perfect tense in the product. Likewise, energy conservation conceived within the first law of thermodynamics through the internal act of energy transformation is to relate the present progressive tense in the local on the spot to the present perfect tense in the global to be registered in the robust record. Quantum as a heat engine thus presumes the internal act for the sake of fulfilling the first law of thermodynamics from within, since the act referable in the present progressive tense is internal to the act without any predetermined guarantee for the global coordination to all of the others on the scene. This will put in focus measurement internal to material bodies as an agency connecting the different grammatical tenses in material terms.

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

241

Measurement, whether internal to any material bodies or limited only to the external anthropocentric observer, is the act of punctuating the present progressive by the occurrence of the present perfect tense. For further elucidation of the subject matter, we shall require more empirical observation. One candidate for this objective from the perspective of chemical evolution leading to the emergence of life may be an experimental likelihood of igniting a citric acid cycle in a bottom-up manner.

7. Toward igniting a citric acid cycle What could have been unique to the transition from prebiotic to protobiological phase in material evolution must be the emergence of reaction cycles that could remain robust against possible disturbances from the outside. Evolutionary onset of reaction cycles of whatever sort must have been a sine qua non for the start-up of protobiological evolution irrespective of whichever could have come first, whether replicating molecules or metabolic reactions. Either of them requires reaction cycles in one form or another for its implementation, in which reaction cycles hold themselves in between the material flow starting from resources till ending up with their disposal. From the perspective of quantum dynamics as an infra-structure upholding the material world, the evolutionary possibility of raising such robust reaction cycles may be an instance of exploring a quantum functioning as a heat engine processing both material and energy through-flow. One likely candidate for the most primitive and simplest reaction cycles, that can also be amenable even to the laboratory experimentation, might be a citric acid cycle (see Fig. 3) running through mono-, di- and tricarboxylic acid or TCA [8,38,42,50]. When pyruvate is available as both material and energy resources, each reaction step around the cycle can proceed if a chemical means for crossing the barrier for activating the reaction is available [49]. Although the citric acid cycle operating in biological organisms is supplemented with enzymes for activating and moving every reaction step along the cycle, prebiotic onset of the cycle could not rely on prior existence of such enzymes of biological origin. One of the possible prebiotic alternatives for activating each reaction might have been available from temperature

Fig. 3. A schematic diagram of the intended citric acid cycle that is oxidative except for the pathway from pyruvate to oxaloacetate due to a possible electrophilic addition of carbon dioxide.

242

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

gradients as expected in the neighborhood of hot vents in the hydrothermal environments in the ocean [29]. If a reaction molecule stays in the high temperature region only for a limited time interval and is soon transferred into the low-temperature surroundings, thermal activation of the molecule could stand the adverse thermal decomposition to a reasonable extent. Furthermore, prebiotic synthesis of pyruvate from methane thiol could be conceivable in hydrothermal environments as a byproduct of carbonylation reactions as using iron monosulphate as a catalyst [7,55]. Major reactants appearing in the citric acid cycle or TCA cycle include citrate, isocitrate, alpha ketoglutarate, succinate, fumarate, and malate, and oxaloacetate. If the reaction cycle is operative, it may be expected that all of these carboxylic acids could survive while each reaction step around the cycle is constantly kept going without suffering depletion of any one of its member carboxylic acid molecules. In order to examine the likelihood of the citric acid cycle on the factual basis, we prepared a reaction solution of the seven member carboxylic acids with the concentration of 1 mM for each and 10 mM pyruvate in the flow reactor simulating hydrothermal circulation of seawater through a hot vent. Our preparation was for the oxidative, instead of the reductive, citric acid cycle with water molecules or carbonate ions as part of possible oxidants. The reactor realized temperature gradient as much as 120 ◦ C over the linear dimension of 1 mm connecting the hot vessel maintained at 120 ◦ C to the cold one at 0 ◦ C. Temporal development of the seven member carboxylic acids is displayed in Fig. 4. Citrate as a key carboxylic acid molecule constituting the cycle was observed to build up at least initially, while its concentration finally started to decrease because of the experimental stipulation of supplying no additional pyruvate in the process except for those prepared initially. In order to confirm the reaction cycle in operation, we then ran the flow reactor with the reaction solution with only the seven member carboxylic acids with the concentration of 1 mM for each and with no added pyruvate. Fig. 5 demonstrates a slight build-up of citrate, but remained far less significant compared to the case in the presence of added pyruvate. Pyruvate was found indispensable for the proper operation of the reaction cycle. Furthermore, we attempted to run the flow reactor in which one of the seven member carboxylic acids was missing in the initially prepared reaction solution. The missing carboxylic acid molecule we focused was alpha ketoglutarate, while the concentration of the other six member carboxylic acids was maintained at 1 mM for each, along with 10 mM pyruvate. The result was also appended in Fig. 5. There was observed no significant build-up of citrate. This observation serves as a testimony to the fact that the build-up of citrate requires an uninterrupted and connected reaction cycle. Nonetheless, if the reaction cycle is really functional in a robust manner, the cycle itself must eventually be able to help synthesizing and recovering the missing member molecule from within. Otherwise, the robustness of the reaction cycle would have to be lost. We certainly observed that the initially missing alpha ketoglutarate could emerge as a member molecule of the cycle at a later stage of the reactor operation. The identified concentration of alpha ketoglutarate was about 0.4 µM roughly 120 minutes after the start of the operation (see Fig. 6(a)), and its concentration increased since then. Furthermore, we examined whether the build-up of alpha ketoglutarate could be accelerated in the presence of carbonate ions that might help letting water molecules to serve as an oxidant, as will be seen soon below, while other conditions were maintained the same. The result is displayed in Fig. 6(b). The synthesis of alpha ketoglutarate in the presence of 2 mM carbonate ions was enhanced roughly 100 times or more compared to the case in the absence of carbonate ions. The likelihood of carbonate ions letting water molecules serve effectively as an oxidant driving the oxidative citric acid cycle may further be examined by measuring changes in the pH value of the standard reaction solution. Fig. 7 displays a time development of the pH value of the reaction solution with further

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

243

Fig. 4. Time developments of the concentration of each reactant in the operation of the flow reactor, in which the reaction solution initially prepared, consisted of 1 mM of each of citrate, isocitrate, alpha ketoglutarate, succinate, fumarate, malate, oxaloacetate, and 10 mM pyruvate. The temperature of the high temperature chamber was raised from room temperature up to 120 ◦ C over the first 60 minutes linearly and was maintained at that temperature since then. Since there was observed no significant difference between succinate and fumarate in their detection, their detected concentrations were summarized in one display. The observed data included ±1% experimental errors for repetitions.

addition of 2 mM sodium carbonate. The pH value increased from 2.50 up to 2.55 over 180 minutes of the flow reactor operation, whereas for the similar reaction solution with no added sodium carbonate the value increased from 2.03 up to 2.08 over the same time interval (data, not shown). Increase in the pH value implies that water molecules in the aqueous solution may function as an oxidant as

244

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

Fig. 5. Time developments of the concentration of citrate in the operation of the flow reactor. Three cases were compared. The first one denoted by open circles was for the standard reaction solutions consisting of 1.0 mM of each of citrate, isocitrate, alpha ketoglutarate, succinate, fumarate, malate, oxaloacetate, and 10 mM pyruvate in the initial preparation. The second one denoted by squares was for the reaction solution in which only pyruvate was absent initially compared to the standard one. The third one denoted by triangles was for the reaction solution in which only alpha ketoglutarate was absent compared to the standard one. The temperature of the high temperature chamber was raised from room temperature up to 120 ◦ C over the first 60 minutes linearly and maintained at 120 ◦ C since then.

Fig. 6. Time developments of the concentrations of citrate and alpha ketoglutarate in the operation of the flow reactor. The reaction solution initially prepared, consisted of 1.0 mM of each of citrate, isocitrate, succinate, fumarate, malate, oxaloacetate, and 10 mM pyruvate with no sodium carbonate (a) and with 2.0 mM sodium carbonate (b). Alpha ketoglutarate was absent initially. The temperature of the high temperature chamber was raised from room temperature up to 120 ◦ C over the first 60 minutes linearly and maintained at 120 ◦ C since then. The build-up of alpha ketoglutarate was identified roughly 120 minutes after the start of the flow reactor operation.

accepting electrons from elsewhere. And the presence of carbonate ions can further enhance the concentration of hydroxyl ions as transforming themselves into hydrocarbonate ions. These observations, when combined together, come to suggest that water molecules in the whole reaction system may function as an oxidant. The observation that the build-up of alpha-ketoglutarate in the reaction solution in which alpha-ketoglutarate was initially missing was extremely enhanced in the presence of sodium carbonate

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

245

Fig. 7. Time development of the pH of the reaction solution consisting of 1.0 mM of each of citrate, isocitrate, alpha-ketoglutarate, succinate, fumarate, malate, oxaloacetate, and 10 mM pyruvate with 2.0 mM sodium carbonate. The temperature of the high temperature chamber was raised from room temperature up to 120 ◦ C over the first 60 minutes linearly and maintained at 120 ◦ C since then. Measurement of the pH was done at the low temperature chamber maintained at 0 ◦ C.

Fig. 8. Time developments of succinate in the reaction solution consisting of 1.0 mM of each of citrate, isocitrate, alpha-ketoglutarate, succinate, fumarate, malate, oxaloacetate, and 10 mM pyruvate with no added sodium carbonate (a), and with 2.0 mM sodium carbonate (b). The temperature of the high temperature chamber was raised from room temperature up to 120 ◦ C over the first 60 minutes linearly and maintained at 120 ◦ C since then.

(Fig. 6(b)) compared to the one in its absence (Fig. 6(a)) is effectively consistent to that carbonate ions may help enhance the extent of oxidizing the acetyl group derived from pyruvate so as to run the citric acid cycle. One more circumstantial evidence for water molecules serving as an oxidant was available from comparing the synthesis of succinate in the absence of sodium carbonate to that in its presence of 2.0 mM concentration as demonstrated in Fig. 8. The reaction solution was the standard one consisting of 1.0 mM of each of the seven TCA member molecules and 10 mM pyruvate. The synthesis of succinate was

246

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

significantly enhanced in the presence of 2.0 mM sodium carbonate compared to the case in its absence, while no significant enhancement of citrate synthesis (data, not shown) was observed contrary to the case of its enhancement in the absence of sodium carbonate (see Fig. 4). Since the presence of carbonate ions can increase hydroxyl ions in the aqueous solution, it can effectively enhance the extent of oxidation of the reaction solution. Furthermore, since succinate is the major intermediate product of oxidation of the oxidative citric acid cycle, whose biological embodiment is carried out by oxidant NAD+ , the enhancement of succinate production may be consistent with the relative acceleration of oxidation due to the increase of hydroxyl ions owing to the presence of carbonate ions. Our demonstration of an oxidative citric acid cycle in the homogeneous solution in the presence of temperature gradients simulating hydrothermal environments did not have recourse to enzymes of biological origin nor to regiospecific molecular templates. Nonetheless, the demonstration indicates that prebiotic chemistry can not only synthesize chemical products of prebiotic significance but also raise and maintain a robust production process of protobiological relevance, though the robustness identified experimentally was limited only to the ensemble of such reaction cycles. The robustness here means the selective tendency of a material body moving toward its relatively stable target on its own even in the face of hostile or adverse disturbances from the environment. One selective tendency we focused is that when a small hot body is thrown away into the huge cold environment, it decreases its temperature at the possible fastest rate. The reason behind is rather straightforward. Once the faster one takes over, no chance is left for the slower starter to take part in. A chemical reactant, when suddenly thrown away from the hot spot to the cold surroundings, makes its temperature drop faster by making its stored latent heat greater since it can drop its temperature by less heat dissipation toward the outside. In fact, chemical integration or coordinative synthesis accompanied by emergent structuring by means of covalent and non-covalent bonding tends to proceed as making the internally stored latent heat greater rather than less. The faster temperature drop going with the greater stored latent heat is the selective criterion applicable to any material body traversing the temperature gradients from the higher to the lower, even at the stage prior to the emergence of replicating molecules. Even Darwinian molecular selection can be a special case of the operation of the physical pruning principle identified as the faster temperature drop going with the greater stored latent heat. The selective criterion of the faster temperature drop going with the greater stored latent heat is certainly applicable even to a homogeneous solution of various carboxylic acid molecules. Once whatever reaction cycle for production gets started even in the statistically aggregated sense in the homogeneous solution, the ones that could survive would be only those that can exploit the resources at the fastest rate among the competitors aiming at the same ones. Resources for running the citric acid cycle are pyruvate. Exploitation of the resources at the fastest rate is due simply to the fact that there is no leftover to the latecomers. Production process of a lasting nature comes to focus only on those products that would not disturb proper operation of the lasting production. If catalytic RNA molecules are certainly instrumental to substantiating the evolutionary onset of replicating molecules serving also as genetic materials, one of the likelihood for the occurrence might be to take advantage of hitchhiking on the then available reaction cycle of a lasting nature. Robust reaction cycle such as a citric acid cycle operating in the presence of temperature gradients is network-catalytic in letting any one of the cycle members help synthesizing the others in the cycle, rather than template-catalytic. Evolutionary emergence of catalytic RNA molecules may correspond to the emergence of template-catalysts that might have been able to take advantage of the operation of

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

247

network-catalytic reaction cycle if other conditions had been satisfied. Of course, emergence of templatecatalytic molecules will certainly help narrowing the evolutionary track afterward to a significant extent.

8. Concluding remarks The physics for the origins of life is unique in focusing on production process of a lasting nature, rather than on the products then available. This exhibits a marked contrast to the standard practice of physics based upon the state description, whether in classical or quantum mechanics, in which the state is methodologically deciphered in terms of the already finished or completed products of whatever kinds. Physics upon state description takes the context that the state presumes, to be detached from the movement of making the very context, as maintaining the invariable physical object put in the third-person status out there. The context of the third-person description employed for state description in physics remains invariable and accordingly lacks the competence for forming and transforming the material context from within. On the other hand, the major issue on the physical origins of life is about the material capacity of the contextual specification relegated to contextual elements. The descriptive vehicle for the purpose should be second-person description instead of the standard third-person one [32]. This is due simply to the observation that second-person description is competent enough to specify the other party to be pointed out in a concrete and particular manner, though the spatio-temporal horizon unique to the description remains limited and finite compared to a possible infinite horizon available to third-person description. In contrast to third-person description allowing less specific and more abstract descriptive objects, second-person description accommodates in its core the capacity of measurement on the part of any contextual elements. Although quantum mechanics can be concrete enough in focusing on measurement, its standard practice also partakes in state description in the Hilbert space. In other words, there is an issue of measurement in quantum mechanics that can safely be detached from its state description. The physical origins of life thus come to challenge the present methodological separation between the process of measurement and the state description in quantum mechanics. The material capacity of the contextual specification relegated to contextual elements suggests that the process of measurement is internal to any material bodies. Internal measurement is ubiquitous in the material world. The ubiquity of measurement as material process then sets a certain restriction on the extent to which theoretical articulation of explicating the origins of life could be made possible. Thirdperson description in the present tense as a common descriptive vehicle of theoretical enterprise can be general and universal, but is not concrete particular enough. Concrete and particular aspects of the origins of life would have to have recourse to the act of internal measurement on the part of available small molecules, whether inorganic or organic. What we have observed so far is about the possible evolutionary relevance of a quantum as a heat engine to the physical origins of life. That is, a reaction cycle constantly recruiting resources from the outside and disposing the products toward the outside. If the concrete particular nature of a quantum as a heat engine is empirically rich enough, one may be able to theoretically generalize the implications in the standard third person description only with a few additions of concrete specification of theoretical nature if necessary, and without recourse to any further empirical act of concretization. The present optimism may reflect the historical parallel with the early theoretical development of quantum mechanics grounded upon Planck’s quantum. A photon as a light quantum is empirically concrete particular and rich enough to

248

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

identify itself as a robust encapsulation of moving contextual elements. A pressing agenda on the origins of life perceived from our present perspective turns out whether a quantum as a robust heat engine could also be empirically legitimate and fundamental in addressing the issue as much as a quantum as a robust encapsulation of contextual elements has been so in the standard practice of physics. That is to say, quantum as a heat engine is a robust transformer of Planck’s quantum. In particular, experimental endeavor for addressing the origins of life when viewed from the physical perspective presents a new opportunity of developing physics further for its own sake. A case in point is the issue of intensities. The physics of the origins of life may more readily be approachable by way of the dynamics of intensities or intensive quantities such as temperature and force strengths, compared to the standard dynamics of extensive quantities such as molecule numbers, densities, masses and charges. What is unique to the dynamics of intensities is that it is already contextual in addressing the context under which the intensities in focus are generated and maintained. Although physics has been quite competent in coping with various intensities in the framework of reducing them into renormalized extensive quantities as practiced in quantum electrodynamics, it is not certain whether the carbon chemistry underlying the issue of the origins of life could also be properly renormalized into the mechanistic dynamics of extensive quantities. Until the successful renormalization of the carbon chemistry into a scheme of extensive quantification may become in sight, it would be required to face the dynamics of intensities directly. A most significant intensity to be met in the evolutionary emergence of the phenomenon called life is temperature. Temperature is a quantitative figure about the material context of an intensive implication experienced by whatever bodies. What is unique to temperature dynamics on the relationship between the context and the contextual elements is its intrinsic selectivity in the sense that no contextual element belongs to two different contexts at the same time, since the context is about an organized unity of the contextual elements. Selective capacity of the contextual origin could certainly have been operative at the evolutionary stage even prior to the emergence of replicating molecules such as RNA. We observed several experimental demonstrations on the operation of the intrinsic selective capacity originating in temperature dynamics, especially in the presence of temperature gradients [33,34]. Various synthetic reactions including oligomerization of monomers, phosphorylation of nucleotides [44] and carboxylation of carbohydrates were significantly enhanced when temperature gradients to be removed were present. Temperature changes are nothing but changes in the material context under which the temperature comes to materialize. Hydrothermal environments on the primitive Earth could have been a most likely locale for exercising such a selective capacity of material origin grounded upon the contextual selection in the face of temperature gradient, even without recourse either to regiospecific molecular templates or to the elementary selection due to the difference of the replication rates of the participating molecules. The origins of life must have been an instance demonstrating the significance of the physics of intensities par excellence. The physics of the origins of life anticipates a new type of quantum that can serve as a heat engine. Focused in the physical origins of life is the reshuffling of the fundamental predicates for the purpose. We shall be asked to appraise quantum as a robust transformer of Planck’s quantum much more than the latter alone, which has been so common in the standard practice of the physics of nonliving things. Eventual alternation of the fundamental predicate of Planck’s quantum as an almost complete encapsulation of internal movements by another quantum as a heat engine open to the outside should owe its implementation to the operation of the physical pruning principle identified as the faster temperature drop going with the greater stored latent heat in the presence of temperature gradients to traverse.

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

249

References [1] Bada JL. How life began on Earth: a status report. Earth Planet Sci Lett 2004;226:1–15. [2] Bada JL, Miller SL, Zhao M. The stability of amino acids at submarine hydrothermal vent temperature. Origins Life Evol Biosphere 1995;25:111–8. [3] Braun D, Libchaber A. Thermal force approach to molecular evolution. Phys Biol 2004;1:P1–8. [4] Cech TR. The chemistry of self-splicing RNA and RNA enzymes. Science 1987;236:1532–9. [5] Chiar JE. The nature and evolution of interstellar ices. Origins Life Evol Biosphere 1997;27:79–100. [6] Chyba CF, Sagan C. Endogenous production, endogenous delivery and impact-shock synthesis of organic molecules: An inventory of the origins of life. Nature 1992;355:125–32. [7] Cody GD, Boctor NZ, Filley TR, Hazen RM, Scott JH, Yonder SH Jr. Primordial carbonylated iron-sulfur compounds and the synthesis of pyruvate. Science 2000;289:1337–40. [8] Cody GD, Boctor NZ, Hazen RM, Branders JA, Morowitz HJ, Yonder HS Jr. Geochemical roots of autotrophic carbon fixation: hydrothermal experiments in the system citric acid, H2 O–(±FeS)–(±NiS). Geochim Cosmochim Acta 2001;65:3557–76. [9] Corliss JB, Dymond J, Gordon LI, Edmond JM, von Herzen RP, Ballard RD, Green KK, Williams D, Bainbridge A, Crane K, van Andel TH. Submarine thermal springs on the Galapagos rift. Science 1979;203:1073–83. [10] Davies PC. Does quantum mechanics play a non-trivial role in life? Biosystems 2004;78:69–79. [11] Edmond JM, Von Damm KL, McDuff RE, Measures CI. Chemistry of hot springs on the East Pacific rise and their effluent dispersal. Nature 1982;297:187–91. [12] Ferris JP. Chemical markers of prebiotic chemistry in hydrothermal systems. Origins Life Evol Biosphere 1992;22:109–34. [13] Fox SW. The emergence of life: Darwinian evolution from the inside. New York: Basic Press; 1988. [14] Greenberg MJ, Li A, Mendoza-Gomez CX, Schutte WA, Gerakines PA. Approaching the interstellar grain organic refractory component. Astrophys J 1995;455:L177–80. [15] Greenberg MJ, Krueger FR. From the formation of bioorganics in interstellar dust to the thermodynamics of selforganization in cometary grains as seeds of life’s origins: Are 1025 chances enough? Origins Life Evol Biosphere 1996;26:208–9. [16] Imai E, Honda H, Hatori K, Brack A, Matsuno K. Elongation of oligopeptides in a simulated submarine hydrothermal system. Science 1999;283:831–3. [17] Imai E, Honda H, Hatori K, Matsuno K. Autocatalytic synthesis of oligoglycine in a simulated submarine hydrothermal system. Origins Life Evol Biosphere 1999;29:249–59. [18] Joyce GF. The antiquity of RNA-based evolution. Nature 2002;418:214–21. [19] Joyce GF, Orgel LE. Prospects for understanding the origin of the RNA world. In: Gesteland RF, Atkins JA, editors. The RNA world. Cold Spring Harbor: Cold Spring Harbor Laboratory Press; 1993. p. 1–25. [20] Kändler O. The early diversification of life. In: Bergtson S, editor. Early life on Earth: Nobel symposium 84. New York: Columbia University Press; 1993. p. 152–60. [21] Kauffman SA. Autocatalytic sets of proteins. J Theor Biol 1986;119:1–24. [22] Kawaguchi T, Honda H, Hatori K, Imai E, Matsuno K. Fourier’s law of heat transfer and its implication to cell motility. Biosystems 2005;81:19–24. [23] Kobayashi K, Kaneko T, Saito T, Oshima T. Amino acid formation in gas mixtures by high energy particle irradiation. Origins Life Evol Biosphere 1998;28:155–65. [24] Küppers B-O. Die Kontextabhängigkeit biologischer Information. In: Physik, Philosophie und die Einheit der Wissenschaften. Spektrum (The context-dependence of biological information). Kruger L, Falkenburg B, editors. Grundlagen der exakten Naturwissenschaften, vol. 10. Heidelberg: Akademischer Verlag; 1995. p. 260–77. [25] Lahav N, Nir S, Elitzur AC. The emergence of life on Earth. Progr Biophys Mol Biol 2001;75:75–120. [26] McCollom TM, Ritter G, Simoneit BR. Lipid synthesis under hydrothermal conditions by Fischer–Tropsch-type reactions. Origins Life Evol Bioshere 1999;29:153–66. [27] Matsuno K. Natural self-organization of polynucleotides and polypeptides in protobiogenesis: appearance of a protohypercycle. Biosystems 1982;15:1–11. [28] Matsuno K. Protobiology: Physical basis of biology. Boca Raton, FL: CRC Press; 1989. [29] Matsuno K. A design principle of a flow reactor simulating prebiotic evolution. Viva Origino 1997;25:191–204.

250

K. Matsuno, A. Nemoto / Physics of Life Reviews 2 (2005) 227–250

[30] Matsuno K. Thermodynamics as an interface agency tailoring quantum mechanics for the beginning of biology. In: Diebner HH, Druckrey T, Weibel P, editors. Sciences of the interface. Tübingen, Germany: Genista Verlag; 2001. p. 143–54. [31] Matsuno K. The internalist enterprise on constructing cell motility in a bottom-up manner. Biosystems 2001;61:115–24. [32] Matsuno K. Quantum mechanics in first, second, and third person description. Biosystems 2003;68:107–18. [33] Matsuno K. Prebiotic interplay between fatty acids and amino acids in hydrothermal environments. In: Seckbach J, editor. Origins: Genesis, evolution and diversity of life. Dordrecht: Kluwer Academic; 2004. p. 169–79. [34] Matsuno K. Prebiotic organization of fatty acids and amino acids in the interface zone between the hydro and lithosphere. Adv Space Res 2004;33:95–9. [35] Matsuno K, Swenson R. Thermodynamics in the present progressive mode and its role in the context of the origin of life. Biosystems 1999;51:53–61. [36] Matthews C. Origin of life: Polymers before monomers? In: Margulis L, Oleadzenski L, editors. Environmental evolution: Effects of the origin and evolution of life on planet Earth. Cambridge, MA: MIT Press; 1992. p. 29–38. [37] Miller SL, Bada JL. Submarine hot springs and the origin of life. Nature 1988;334:609–11. [38] Morowitz HJ, Kostelnik JD, Yang J, Cody GD. The origin of intermediary metabolism. Proc Natl Acad Sci USA 2000;97:7704–8. [39] Navarro-Gonzalez R, Romero A, Honda Y. Power measurement of spark discharge experiments. Origins Life Evol Biosphere 1998;28:131–53. [40] Ogasawara H, Yoshida A, Imai E, Honda H, Hatori K, Matsuno K. Synthesizing oligomers from monomeric nucleotides in simulated hydrothermal environments. Origins Life Evol Biosphere 2000;30:519–26. [41] Ogata Y, Imai E, Honda H, Hatori K, Matsuno K. Hydrothermal circulation of seawater through hot vents and contribution of interface chemistry to prebiotic synthesis. Origins Life Evol Biosphere 2000;30:527–37. [42] Orgel LE. Self-organizing biochemical cycles. Proc Natl Acad Sci USA 2000;97:12503–7. [43] Owen T, Bar-Nun A, Keinfel I. Possible cometary origin of heavy gases in the atmosphere of Venus, Earth and Mars. Nature 1992;358:43–6. [44] Ozawa K, Nemoto A, Imai E, Honda H, Hatori K, Matsuno K. Phosphorylation of nucleotide molecules in hydrothermal environments. Origins Life Evol Biosphere 2004;34:465–71. [45] Pendleton YJ. Detection of organic matter in interstellar grains. Origins Life Evol Biosphere 1997;27:53–78. [46] Prigogine I, Defay R. Chemical thermodynamics. London: Jarrold & Sons; 1954. [47] Russell MJ, Hall AJ, Cairns-Smith AG, Braterman PS. Submarine hot springs and the origin of life. Nature 1988;336:117. [48] Russell MJ, Hall AJ. The emergence of life from iron monosulphide bubbles as a submarine hydrothermal redox and pH front. J Geol Soc London 1997;154:377–402. [49] Russell MJ, Martin W. The rocky roots of the acetyl-CoA pathway. Trends Biochem Sci 2004;29:358–63. [50] Schuster P. Taming combinatorial explosion. Proc Natl Acad Sci USA 2000;97:7678–80. [51] Shock EL. Hydrothermal systems as environments for the emergence of life. Ciba Foundation Symp 1996;202:40–60. [52] Sreedhara A, Li Y, Breaker R. Ligating DNA with DNA. J Am Chem Soc 2004;126:3454–60. [53] Terada R, Imai E, Honda H, Hatori K, Matsuno K. Fixation of carbon dioxide in hydrothermal environments: synthesis of formic and acetic acids. Viva Origino 1999;27:197–208. [54] Trevors JT. Early assembly of cellular life. Progr Biophys Mol Biol 2003;81:201–17. [55] Wächtershäuser G. Evolution of the first metabolic cycle. Proc Natl Acad Sci USA 1990;87:200–4. [56] Zurek WH. Decoherence, einselection, and the quantum origins of the classical. Rev Mod Phys 2003;75:715–75.