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Timing adjustment is an important ability for living organisms. Wild animals need to act at the right moment to catch prey or escape a predator. Land plants, although limited in their movement, need to decide the right time to grow and bloom. Humans also need to decide the right moment for social actions. Although scientists can pinpoint the timing of such behaviors by observation, we know extremely little about how living organisms as actors or players decide when to act – such as the exact moment to dash or pounce. The time measurements of an outsider-observer and the insider-participants are utterly different. We explain how such essential operations of timing adjustment and temporal spanning, both of which constitute a single regulated set, can be carried out among organisms. For this purpose, we have to reexamine the ordinary conception of time. Our specific explanatory tools include the natural movement known as the upbeat (anacrusis) in music, a rhythmic push for the downbeat that follows, which predicts future moves as an anticipatory lead-in. The scheme is situated in and is the extension of our formulation of E-series time, i.e., timing co-adjusted through interaction, which is derived from the semiotic/communicative perspectives. We thereby demonstrate that a prediction-based timing system is not mechanical but communicative and entails meanings for future anticipation.

One common denominator between biosemiotics and quantum physics is the participation of agents detecting their surroundings. In biosemiotics, any biological agents as the internal observers including the molecular and cellular ones are involved in detecting their surroundings. Likewise, the physicist as the external observer is also involved in detecting what should be all about the physical world with use of a wide variety of sophisticated measurement apparatuses. On the other hand, the difference between the two is in the nature of the agents of detection involved there. One obvious difference is that although the physicist can report the results of measurement with use of the symbolic language, the biological beings take the indexical act of measurement to simply be a matter of experiencing. The internal observers are phenomenological in constructing something durable as participating in the construction of the phenomenon. In a similar vein, the external observer is also phenomenological in getting into interpreting the constructed durable class property of an object with use of the symbolic language. In particular, the potential use of phenomenology is not limited only to the phenomenologist as the external observer. A possible integration of both the internal and external observers may be sought within quantum phenomenology allowing for the external observer to descriptively make access to the durable objects the internal observers could eventually have constructed. The internal observers are ubiquitous in the environment that functions as the absorbers of whatever quantum particles available there.

Anticipatory acts or predictive behavior are prerequisites for living organisms to sustain their survival when escaping from a predator, catching prey, or schooling. For example, catching prey requires that the predator perform some procedures that are equivalent to estimating the directional movement of the prey, its speed and its distance relative to the predator. Underlying these procedures is time experience, which does not adhere to man-made mechanical clocks. Living organisms keep time based on the local activities of each participant and form ecological clocks together. The timekeeping of ecological clocks has been called E-series time, which is interactive in character and consists of mutual alignment of timing that is co-adjusted to each other’s movements and rhythms. A main objective of our current work is to illustrate how E-series time is used for flows of anticipatory acts. To explain such predictive moves and their efforts based on how the perspective of the immediate future affects the present, we resort to the organismic activity of revising the preceding acts in retrospect and semiotic scaffolding that extends beyond simple linear causality. Special attention is paid to the construction of the notion of retrocausal scaffolding, which is a series of dialogical punctuations or mutual coordination of rhythms for the joint production of the present moment of now. Retrocausal scaffolding is synonymous with negotiated anticipation, which is a semiotic/communicative account of revising the preceding acts in the present moment.

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.

The occurrence of the tenses of past, present and future presumes a subject distinguishing between memory and anticipation in reference to an experience. One possible scheme to recover the reality of time should be sought in naturalization of the subject. A metabolic material body of any sort appearing in the biological realm can be seen as a sentient agent constantly punctuating the intervening material through-flow so as to make both the incoming and outgoing flows balance. The repercussions of the punctuation are thus propagated throughout the biological world. The sequence of events crystallized in the finished record precipitates time to be read out as B-series time, i.e., as a measure for distinguishing between before and after with respect to the events in question.

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.

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.

Chemical affinity is by itself inclusive of the action of a sign. Naturalization of the action of a sign is latent in the material organization holding its own identity by means of the exchange of material. A concrete experimental example is the citric acid cycle running in the absence of biological enzymes. The carbon atoms to be exchanged round the cycle serve as the signs for holding the cycle as a natural system. The action of a sign operates in the present progressive tense and is also descriptively approachable in the same tense, as implying that a natural system holding its own identity assumes the first-person status acting for its own sake. The action of a sign is thus addressable in first person descriptions on the level of the supporting material system that can recognize the sign as such from within. Furthermore, if the action of a sign happens to precipitate the record registered in the present perfect tense, the record itself will be approachable in third person descriptions in the present tense. When one can relate the record of an earlier event to that of a later one, what is called information will come up. Information to be externalized and objectified is about the completed outcome from the action of a sign that is accessible in third person descriptions in the present tense. Conversely, if the action of a sign is carried by a natural system holding its own identity in a manner to be registered in the present perfect tense after the event, information will appear in a proper form of bookkeeping as relating the memory to anticipation on the part of the material agency. Although information in the present has the capacity of relating the past to future in the present tense as avoiding direct confrontation with the dynamic nature of the present or now head on, the action of a sign facing the present squarely is competent enough to address and decipher the generative capacity of information itself operating in the present progressive tense.

The material underpinning of the action of signs is rooted in the priority of interactions. The evolutionary priority of interactions as envisioned from the proto-semiotic perspective renders both space and time as derivable from interactions, as demonstrating a sharp contrast to the classical, physical and theoretical notion of interactions as occurring in a prior transcendental presupposed space and time that are given prior to interactions. The proto-semiotic framework obtains space as resulting from shared resources among the material participants, whereas time is derived from the act of allocating the mutually shared resource. Consequential upon the priority of interactions is a suspension of the principle of contradiction as keeping the on-going action of signification, since time, while presiding over and embodying the allocation, is constantly progressing. The results of the action of signs as registered in the finished record necessarily meet the principle of contradiction. Nonetheless, the fulfilment of the principle right in the process of the on-going action of signification is constantly out of reach because of the inevitable spill-over of those material disturbances perturbing the likelihood of attaining the principle from within. Interacting atoms and molecules, when viewed from the perspective of time as being derived from the interactions, can be seen as agential in precipitating the principle of contradiction in the finished record out of the on-going evanescent dangers of disturbing that principle from within. Naturalization of the action of signs is sought within the natural capacity of time being capable of changing its own tense.

A unified theoretical perspective is presented on the succession of experimentally observed facts ranging from the self-sequencing of amino acids to the simulated protocellular synthesis of peptides and polynucleotides. The recognition that each microsystem arising from material self-assembly incessantly changes its strength of interaction with its exterior so as to maintain the continuity of material flow is a common theoretical denominator for protobiological synthesis. Material flow equilibration underlies the transition from protocells without nucleic acids to those with both nucleic acids and polypeptides whose making is influenced by the polynucleotides. It is claimed that the information specifying the making of protocells capable of synthesis of both polynucleotides and polynucleotide-informed polypeptides was already latent in the self-sequencing of amino acids.

Molecular imprints of organisms serving as both the agents and the products of the underlying sign activities are quantum mechanical in their origins. In particular, molecules in any reaction networks constituting a biological organism are semiotic or context-dependent in the sense that their activities reside within the proper coordination of the entire networks. The origin of life could have been related to a specific aspect of molecular semiotics, especially in the transition from molecules as the physical symbols of material units to molecules as the semiotic signs having the capacity of pointing to something else other than the molecules themselves. Quantum mechanical underpinning of the molecular imprints leading to the emergence of life is in the appraisal of the material capacities of both coherent assimilation and decoherent dissociation already latent in the imprints. One empirical evidence suggesting the likelihood of both coherent assimilation and decoherent dissociation in prebiotic settings could have been found in synthetic chemical reactions running in hydrothermal circulation of seawater through hot vents in the Haedean ocean on the primitive Earth.

Natural dynamics, as manifested in evolutionary processes, refer to material bodies in movement in the present progressive mode. Any interacting material body in the present progressive mode must be sentient to others because there can be no global agency coordinating it to others in a globally synchronous manner. The internalist perspective, or the worm's eye view, referring primarily to the present progressive mode, renders local material bodies, large or small, subject to an inevitable inconsistency among local representations of neighborhood events registered in the local present perfect tense. Any sentient material body experiencing this inconsistency subsequently transforms itself into an inconsistency-free representation. The descriptive scheme unique to the internalist stance is internal and dynamic in the sense that it constantly strives to update constituent local representations, attempting to eliminate any inconsistencies residing within antecedent local representations. Compared to external descriptions of invariable universals grounded upon the Cartesian epistemic split, which are complementary to dynamics, internal description serves as a linguistic means of embodying natural dynamics even without recourse to the notion called forces. This makes our language powerful enough to enclose natural dynamics of material bodies in the empirical domain.

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.

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.

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.