Semiosis as a Source of Providing Empirical Phenomena with a New Type of Cohesion.

Embodying the indexical signs is vital to semiosis as a cohesive material agency mediating between consequents and antecedents. One unique factor of biology compared with standard physics and chemistry is the cohesion enabling the biological components, codes and organizations to accommodate themselves with a specific material embodiment. Every individual body is uniquely biological and requires a specific cohesion of material origin for its own sake that could not be found in the non-living material world. The relevant cohesion comes from the exchange interaction of the atomic quantum particles, such as the carbon atoms, which is far greater than the electrons as a common exchange mediator adopted for the spatial cohesion ubiquitous in physics and chemistry. What is specific to the temporal cohesion latent in the atomic exchange is the immutable identity of the individual quantum particle surviving only over a limited time, while being constantly alternated with the new ones of the same kinds in a successive manner. Semiosis is supported by the underlying teleonomic cohesion, such that the preceding temporal cohesion may constantly induce the succeeding similar one ad infinitum.

Temporal cohesion as a candidate for negentropy in biological thermodynamics.

Negentropy explored by Schrödinger for saving biology within thermodynamics stands firm on the perpetual temporal cohesion of material origin. The temporal cohesion refers to the cohesion acting between what has been produced and what is going to produce, thus keeping the negentropy as a measure of organization constantly positive in time. Such cohesion is ubiquitous in measurement internal to the material world. Internal measurement in the quantum realm really lets the current "detecting" constantly feed upon some quantum resources available from the preceding "detected" a moment ago. The quantum resources transferred during the cohesive process serve as a physical factor for bridging between the two different temporalities; the present perfect and progressive tenses. What has been detected comes to participate in an attribute of what is going to detect next as constantly following suit. Temporal cohesion is an agential mediator connecting the adjacent temporalities in a manner different from the spatial cohesion observing only the single temporality restricted to the present tense. The activity of enhancing the magnitude of negentropy may have preceded the emergence of something called life phenomenon. Biology feeds upon temporal cohesion.

Approaching biology through the retrocausal apex in physics.

Quantum stochasticity carries two incompatible implications. One is for the statistical divergence upon the prior absence of complete controllability over boundary conditions applied to mechanistic causation. One more alternative is for the statistical convergence upon the posterior decidability of measurement despite the absence of the prior decidability. Decidable measurement lacking the prior decidability is retrocausal. The quantum physical likelihood for the life world may derive from the statistical convergence proceeding in a durable manner. This observation suggests that there must have been some type of observers even internal to the lifeless world, otherwise no likelihood of identifying the objects of interest could be available there. Measurement activity intrinsic to the internal observers is indexical, while the similar activity specific to the external observer like us can be symbolic. The difference is in the phenomenological qualification since both are the observers of different types. A most conspicuous case demonstrating the phenomenological difference is revealed in the different nature of time to be employed and experienced there. Time serves as a principal attribute qualifying the phenomenon to be experienced as such. Qualification of time is observer dependent.

Living with the emergence of agents on physical terms.

Evolutionary emergence of agents in the empirical world is a direct consequence of the indexicality of matter itself. It is grounded upon the act of quantum origin that is accessible indexically with use of our language. One unique aspect of our language rests upon its appraisal of different grammatical tenses, such as the present progressive tense and the perfect one. Both the tenses are indexical in pointing to some movements in progress or registered in stasis as such out there as admitting no anthropocentric interventions. In particular, the material movement mediated by the transfer of the quantum particles is punctuated by the event of the transfer completed so far that can be referred to in the present perfect tense. At the same time, the transfer of the quantum particles can constantly induce the similar transfer in sequence in the following present progressive tense. Constant update of the present perfect tense in the subsequent progressive tense is agential in keeping no inconsistency between the two left behind in the finished record. That is the inconsistency-mediating cohesion acting between the present perfect and the progressive tenses. A most conspicuous case demonstrating the competency of inconsistency-mediating cohesion may be the origins of life. Molecular recognition widely observed in the biological realm is a specific instance of demonstrating such a molecular cohesion.

Biological computation running on quantum computation.

Biological computation supporting biological phenomena functionally practices the underlying quantum computation indexically, rather than symbolically. An advantage of the indexical operation of quantum computation rests upon a significant reduction of the computational complexity compared with the corresponding classical counterpart running exclusively upon the symbol manipulation. The reduction of the complexity is sought in allowing for the participation of multiple processors running concurrently in a parallel manner. The concurrent distribution of multiple processors operating mutually in an inseparable manner lets each processor regard the rest of the distribution as its own environment. The environment thus formed and detected by each processor may differ from the similar ones appropriated to the other individual participants nearby. Both the individual processor and the corresponding environment turn out to be agential. Quantum computation practiced indexically may serve as a precursor agency apt for both forming Jakob von Uexküll's umwelt towards the environment and making use of James J. Gibson's affordance from the environment. The individual environment to each material participant there is already indexically agential in pulling that participant in.

Retrocausal regulation for the onset of a reaction cycle.

The emergence of a reaction cycle in a mixture of reacting molecules may require naturalized regulation of the constituent material elements. One source of naturalized regulation could be sought in updating the constituent elements through exchanging with those available from the outside under the conditions of unidirectional heat flow. One physical vehicle for implementing constant material exchange could be a durable reaction cycle serving as a necessary precursor to the phenomenon called life. Each constituent element circulating around a durable reaction cycle moves causally until it comes to eventually leave the cycle. At the same time, the circulation is also retrocausal in letting the reaction flow in the downstream pull in and being cohesive to those reactants in the immediate upstream. The onset of a reaction cycle as a precursor to the origins of life must have corresponded to a unique historical event taking advantage of the likelihood of retrocausal cohesion propagating backward along the reaction sequence. Physical underpinning of biology may be found in the operation of retrocausal cohesion.

Time from Semiosis: E-series Time for Living Systems.

We develop a semiotic scheme of time, in which time precipitates from the repeated succession of punctuating the progressive tense by the perfect tense. The underlying principle is communication among local participants. Time can thus be seen as a meaning-making, semiotic system in which different time codes are delineated, each having its own grammar and timekeeping. The four time codes discussed are the following: the subjective time having tense, the objective time without tense, the static time without timekeeping, and the inter-subjective time of the E-series. Living organisms adopt a time code called the E-series, which emerges through the local synchronization among organisms or parts of organisms. The inter-subjective time is a new theoretical dimension resulting from the time-aligning activities of interacting agents. Such synchronization in natural settings consists of incessant mutual corrections and adjustments to one's own punctuation, which is then constantly updated. Unlike the third-person observer keeping the objective time while sitting outside a clock, the second-person negotiators participate in forming the E-series time by punctuating and updating the interface through which different tenses meet at the moment of "now." Although physics allows physicists to be the only interpreters, the semiotic perspective upends the physical perspective by letting local participants be involved in the interpretation of their mutual negotiations to precipitate that which is called time.

From quantum measurement to biology via retrocausality.

A reaction cycle in general or a metabolic cycle in particular owes its evolutionary emergence to the covering reaction environment acting as a measurement apparatus of a natural origin. The quantum measurement of the environmental origin underlying the molecular processes observed in the biological realm is operative cohesively between the measuring and the measured. The measuring part comes to pull in a quantum as an indivisible lump available from an arbitrary material body to be measured. The inevitable difference between the impinging quantum upon the receiving end on the part of the environment and the actual quantum pulled into the receiving end comes to effectively be nullified through the retrocausative propagation of the corresponding wave function proceeding backwards in time. The retrocausal regulation applied to the interface between the measuring and the measured is to function as the organizational agency supporting biology, and is sought in the act for the present in the immediate future within the realm of quantum phenomena. Molecular dynamics in biology owes both the evolutionary buildup and maintenance of its organization to the retrocausal operation of the unitary transformation applied to quantum phenomena proceeding backwards in time. Quantum measurement provides the cohesive agency that is pivotal for implementing the retrocausal regulation. In particular, the physical origin of Darwinian natural selection can be seen in the retrocausal regulation applied to the unitary transformation of a quantum origin.

On the physics of the emergence of sensorimotor control in the absence of the brain.

The evolutionary origin of sensorimotor control requires a sort of physical durability, other than Galilean inertia being accessible in third-person description in the present tense. One candidate to address this need is the 'class property' of a material body's durability remaining invariant during the exchange of component elements. Using grammatical tense as a descriptive attribute, this durability is accessible only in the frequent update of the present perfect tense in the present progressive tense at the 'now' of the present moment. In this view, the update of the perfect tense is equated with the onset and occurrence of on/off switching behavior of physical origin underlying the phenomena of sensorimotor control. Notably, the physical update of the perfect tense is specific only to the 'now and here' that is central in the tradition of phenomenology. The phenomena upholding thermodynamics, when taken apart from its theory, are decisive in facilitating the onset of sensorimotor control. Instrumental to the emergence of both life in general and sensorimotor control in particular may be the occurrence of a 'physical and chemical affinity' of the material bodies of whatever type. Such will let the constant exchange of component elements be feasible, so that the class identity equipped with the capacity for measurement is made available within the phenomenon. Material bodies constantly exchanging such component elements would make the material world open to biology by allowing each element to experience the organizational whole from within. The internal observer responsible for the origins of life may do double duty of letting itself be durable on the material basis while observing the conditions making it durable on the linguistic ground. The origins of life appear to us a material phenomenon when they are approached with use of our linguistic tools that can get rid of the strict stipulation of an abstract nature applied to the description of dynamical laws in physics.

Self-identities and durability of biosystems via their abstracting capacity.

Any surviving organism is unique in abstracting and holding its self-identity as experiencing and processing different individual events of a concrete nature. The organism that can survive maintains its self-identity as abstracting its own durability as a class property out of those different individual events to be met and processed. Rather, the organism has the internal propensity of making its own actualization durable while processing the material resources available that are individually distinguishable. Biology is distinctive as compared to physics in availing itself of the synthesis of organization with use of the material act of measurement as a form of abstraction.

Making biological theory more down to Earth.

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.

Chemical evolution as a concrete scheme for naturalizing the relative-state of quantum mechanics.

The evolutionary onset of a reaction cycle such as an autocatalytic cycle requires a reliable framework for protecting the harbinger cycle, once it appears by any chance, against the hostile environments in the neighborhood. One natural candidate for protecting the fragile nascent cycle could be available from the operation of internal measurement envisioned in the relative-state formulation of quantum mechanics. Once every chemical reactant is taken to be relative to every other reactant in the act of measuring each other internally, the relative-state formulation provides the condition for favoring and protecting those events such that the reactions mediating between the reactants and the products may eventually form a reaction cycle.

Forming and maintaining a heat engine for quantum biology.

Chemical reactions upholding biological functions and structures are the process of measurement taking place among the participating chemical reactants. Chemical reactions occurring in thermal environments are either endothermic or exothermic. In particular, exothermic reactions that can live with temperature gradients of exogenous origin could potentially be competent enough to synthesize a robust quantum as a heat engine. Molecular organizations leading to the origin of the phenomenon of life might have been associated with the emergence of a quantum coherence embodied in a robust heat engine feeding on quantum decoherence. Evolutionary maintenance of a robust quantum heat engine, once appeared, can further be empowered by the build-up of temperature gradients of endogenous origin. Biology enriches the repertoire of quantum mechanics so as to include a robust heat engine as a legitimate member of a quantum in addition to the already established member of a quantum including an atom, molecule, and macromolecule.

Evolving lipid vesicles in prebiotic hydrothermal environments.

We compared three different kinds of lipid vesicles made of saturated fatty acids, unsaturated fatty acids, and phospholipids for their evolutionary capabilities in a simulated hydrothermal environment. Encapsulation of the glycine monomers enhanced the oligomerization of peptides in all cases. Fatty acid vesicles remained stable at higher temperatures and efficiently utilized heat energy for this synthetic reaction. Phospholipid vesicles were destabilized by higher temperatures, and thus were found to be better suited to enhance synthetic reactions at lower temperatures.

Enantiomeric excess of amino acids in hydrothermal environments.

In a simulated hydrothermal environment allowing fluid circulation between hot and cold regions repeatedly, D- and L-alanine molecules were racemized differently depending upon the concentration of alanine, whether D or L, present in the solution. In particular, the relative population of L-alanine was slightly more enhanced compared to that of D-alanine when the concentration of alanine increased. Enantiomeric excess of L-alanine was also observed when metallic ions such as zinc were sufficiently present in the environments. Hydrothermal environments in the primitive ocean could have maintained the capacity of selectively retaining enantiomeric excess in favor of L-amino acids once the concentration of amino acids could reach a sufficiently high level.

Fourier's law of heat transfer and its implication to cell motility.

Fourier's law of heat transfer addressing temperature differences is intrinsically selective in favoring the mitigation of the differences proceeding as fast as possible. We present an experimental demonstration of such selective behavior of material origin. When an actin filament equipped with nano-scale heat acceptors was placed under heat pulsation, it demonstrated a unidirectional movement without the presence of myosin or ATP. The prime factor for the unidirectional movement was the temperature differences between the locally heated portions on the actin filament and the cooler material bodies in the surroundings. The unidirectional movement could be enhanced in the process of mitigating the temperature differences as fast as possible.

Phosphorylation of nucleotide molecules in hydrothermal environments.

Phosphorylation of AMP into ADP and ATP, that can outrun their hydrolysis, was made possible in a simulated hydrothermal environment when trimetaphosphate was used as the phosphate source. The best yields of phosphorylated products were obtained when the reaction fluids whose temperature was set at about 100 degrees centigrade was injected into the cold environment maintained at 0 degree in a recycling manner. Hydrothermal environments in the primitive ocean could also have served as prebiotic sites for phosphorylation, among others.