Pre-cognition

Venus Flytrap, Dionaea muscipula – showing trigger hairs
Carnivorous plants are stark examples of organisms demonstrating pre-cognitive biological agency and purpose. They have traits that resemble human cognitive traits – they seem to have obvious but mindless ‘goals’, ‘strategies’, and ‘intentions’.

Courtesy Wikimedia Commons
NoahElhardt – Accessed 26 April 2018

Introduction – Pre-cognition

Cognition is a difficult concept that may be loosely defined in a narrow human sense as the mental action or process of acquiring knowledge and understanding through thought, experience, and the senses. It is an extremely useful word indicating the summation of mental faculties and the integration of sensory and other information into meaningful experiences.

It is, however, an ambiguous concept because we treat it as a uniquely human (or sentient animal) mental faculty.  However, we also accept that it is an idea that entails the notions of self-maintenance and regulation – the functional integration of structures, processes, and behaviors that we associate with all organisms, which is cognition as defined in a broad biological sense. So, in a biological context, cognition expresses both difference and similarity – the differences associated with a unique mental faculty and similarities that are a consequence of evolutionary relationships.

The coordinating properties of narrow-sense cognition and its division into functional components such as reasoning, perception, learning, and memory, serve functions that have broad-sense equivalents in all organisms. That is, uniquely human cognitive faculties are just one evolutionary solution to universal biological challenges that all organisms face when adapting to their conditions of existence.

Put simply, mental cognition is a highly evolved and specialized form of more generalized biological cognition – a fact that has yet to be absorbed into the canon of theoretical biology. The cognitive revolution that began in the 1950s is yet to be placed within an overall biological context.

This research agenda has become known as cognitive biology.

Cognitive biology

While biological agency (minimally defined as the goal-directed behavior that we strongly associate with cognition) is widely acknowledged in biology, its scientific investigation has been hampered by its description using the cognitive language of human intentional psychology.

Accounting for agency in biology must involve either the creation of a new scientific vocabulary to describe non-cognitive agential traits, or it must engage and extend the concepts and explanations that are currently employed for human cognition. Cognitive biology assumes that the language of human cognition (terms such as representation, perception, memory, agency, learning, value, purpose etc.) is applied to all organisms, concentrating on their biological basis.

This cognitive transition in biology can be traced in part to the cognitive revolution of the 1950s which challenged behaviorism by examining internal mental states, an approach adopted by a range of scientific disciplines, along with the possibility that these traits might have evolutionary precursors in non-human organisms.

Addressing the agency of organisms using the language of human cognitive psychology, once considered biological heresy, has now become known as cognitive biology. extending to biology in general, cognitive terms such as representation, perception, memory, agency, value, purpose and so on. The application of the agential language of cognitive biology to evolution constitutes a contemporary biological revolution.

The objective display of agential cognitive-like properties in non-cognitive organisms has, for at least 400 years, been regarded as an unscientific figment of the human imagination, damned with the epithet ‘metaphor’ and treated as being of heuristic value at best.

But the agential properties of non-cognitive organisms are not human creations, they are real – they actually exist objectively in the world. All organisms are goal-directed: they are autonomous and intentional units of matter, acting on, and responding to, their conditions of existence as biological agents. Obviously, non-cognitive organisms do not have cognitive faculties but, unlike objects of the inanimate world, they do have real agential traits that resemble those of the cognition that defines human agency (see being like-minded). How are we to distinguish these non-cognitive agential properties?

In trying to come to terms with this problem biology has struggled with the philosophical shackles of teleology, the confusion of its replacement with teleonomy, the difficulty of distinguishing between real non-cognitive biological agency and human cognitive agency, the relationship between goal-directedness and intentionality, and the problem of cognitive metaphor. Collectively these problems have built up an explanatory pressure in biology requiring a resolution akin to a Kuhnian paradigm shift in our understanding of the living world (see the Extended Evolutionary Synthesis in biological agency).

But surely the sentence, ‘That plant wants water‘ is a blatant cognitive metaphor? Isn’t this attribution of cognitive agency to non-cognitive organisms a nonsense that should be removed from biology once and for all?

The metaphor fallacy

It is conventional in science to compare evolutionarily related objects by investigating similarities and differences – the similarities that reflect evolutionary relationships, and the differences that uniquely define a particular feature or trait. So, for example, seemingly unrelated and discrete objects like a human hand, a whale fin, and the leg of a deer all share the evolutionary ancestral ground plan of a pentadactyl limb.

Are there features of non-cognitive biological agency (i.e. non-cognitive agential traits) that are shared with human cognitive agency?

Through a quirk of history, we have not given a crucially important empirical question the attention it deserves . . . What is the evolutionary connection between biological agency and human agency?

This empirical investigation has been avoided because it is conventional to interpret the cognitive-like agential similarities between humans and other organisms through the logic of a literary device, the metaphor.

Biology does not have the language to effectively discriminate between human cognitive biological agency and the real but non-cognitive biological agency of other organisms. We therefore resort to the language of human cognition which then generates cognitive metaphors. These cognitive metaphors intend to draw attention to real non-cognitive biological agency and its physical traits.  However, encouraged by the logic of metaphor in which one of the relata is always figurative (unreal) we make the mistake of assuming that because non-human organisms have no cognitive faculties then they also have no agency. Our mistake is to assume that cognitive metaphors (e.g. that a plant wants water) are intended literally as a serious claim that non-human organisms possess cognitive faculties when, instead, they are drawing attention to non-cognitive agential features that are shared by all organisms.

Treated as creations of the human imagination, non-cognitive agential traits have no technical vocbulary. Instead, they are referenced using the vocabulary of human intentional psychology – words like ‘strategy’, ‘deception’, ‘reason’, ‘favor’, ‘prefer’, and so on. This general referencing of non-cognitive traits using the language of human intentional psychology is referred to on this website as human-talk. In other words, we describe real pre-cognitive biological agency (goal-directed behavior) using cognitive language, and this results in cognitive metaphor. We then mistakenly assume that the unreality of the metaphor entails the unreality of the biological agency and its traits. 

Two important points emerge from this ambiguity. First, since this language intends to draw attention to a real likeness that exists between human and non-human biological agency it would be better expressed through a simile than a metaphor (a plant’s requirement for water is like our wanting water). Then, the inadequacy of both literary devices draws attention to the fact that the similarity reflects an evolutionary connection that is open to empirical investigation.

For example, saying that a plant ‘wants’ water is not intended to literally imply that plants have cognitive faculties, but that plants, like all organisms, need water if they are to survive, reproduce, and flourish. That is, human agency is a cognitive form of biological agency. This is a semantic confusion in which the meaning of ‘wants’ is not intended to be taken literally but as a figurative word of convenience when appropriate terms do not exist.

In short, when we have no words to describe non-cognitive agential traits, we resort to the language of human cognition, thus condemning these traits to the figurative world of metaphor.

Evolutionary connection

The resemblance between cognitive and non-cognitive agential traits across the community of life clearly reflects evolutionary connection. However, the empirical investigation of cognition is, understandably, largely confined to the realm of organisms with narrow-sense cognition – that is, organisms with brains or, at least, neural systems.

Formal recognition of the reality of non-cognitive agential traits – as distinct from human cognitive traits, and absent from the inanimate world – would be facilitated by providing a uniquely defining collective term. This is introduced here by describing these cognitive-like agential traits collectively as pre-cognition,^[1] formally defined here as non-cognitive but real behavioral traits of biological agency that are the evolutionary antecedents of human cognitive states.

Under the broad umbrella of ‘biological cognition,’ this provides a distinction between the cognitive faculties of sentient organisms and the non-cognitive agential faculties of non-sentient organisms. Biological cognition also usefully distinguishes life from non-life.

The evolutionary connection between non-cognitive agential organismal traits and human cognitive traits might appear tenuous with little supporting empirical evidence. As already discussed, the connection results from the role of biological cognition as an evolutionary tool supporting the universal agential traits that produce the functional integration of activity in biological agents.

Plants are excellent examples of organisms without mental faculties but which nevertheless express the agential features of biological cognition. They have:

Systems of communication – signaling and chemical communication in response to environmental cues)
Information processing – using light, gravity, and other factors to optimize growth and survival
Problem-solving (reasoning) – as adaptive behaviors like growing toward light sources or adjusting root growth based on soil conditions
Learning and memory – by the adaptation of responses based on past experiences. And much more (see plant intelligence).

Pre-cognitive agency

The acknowledgment of universal biological agency as ‘the objective capacity of organisms to survive and reproduce while adapting to the conditions of their existence‘ (see biological agency) draws attention to the way organisms display real goal-directed agential traits that are very similar to those we associate exclusively with human agency and subjectivity.

This website regards human agency and human cognition as limited, highly evolved, and specialized forms of more general and universal biological agency and biological cognition. While biological agency refers loosely to the general capacity for goal-directed behavior, biological cognition suggests information processing, decision-making, and problem-solving. If biological agency is a real phenomenon in nature and an evolutionary precursor to human agency then how do we explain the pre-cognitive evolutionary antecedents to human subjective phenomena?

Our intuitive research path for the study of agency and cognition tends to move from the physical construction of the human brain and its cognitive processes to its simpler forms. That is, we explain the non-cognitive in terms of the cognitive as when we use cognitive metaphor. However, we can learn much about cognition by studying its pre-cognitive antecedents.

Pre-cognitive agential traits lack the flexibility of conscious cognitive traits and are usually treated as being more rigidly mechanical. They include instinctual behaviors, reflexes, circadian rhythms, tropisms, chemotaxis, hibernation and dormancy, social hierarchies, and communication signals. They are adaptive responses shaped by evolution, enabling pre-cognitive organisms to meet universal biological needs without relying on conscious cognitive processes – navigating ecological niches, exploiting resources, and fulfilling essential life functions without conscious deliberation.

Pre-cognitive agential traits provide a bridge between the inanimate world and the world of conscious subjectivity.

Purpose, agency, intention

The intentionality of human cognitive agency involves cognition, perception, and decision-making.

These minded traits are grounded in the non-cognitive intentionality of biological agency as mindless behavior that is directed towards objects, properties, or states of affairs involving the acquiring, processing, storing, and usage of information (cognition) the processing of sensory information (perception) and the process of adaptation as the functional integration of the full range of experiential information (the umweldt) of a biological agent as a prelude to behavior (decision-making).

Biological intentionality is demonstrated in something as simple as a plant orientating its leaves towards the Sun.

Language of pre-cognition

Pre-cognitive or instinctive processes resembling human conscious subjective states abound in organisms. It is a relatively easy matter finding, in organisms, processes that resemble human learning, knowledge, memory, values, reason, knowledge, and so on. In frustration with this claim of connection which seems to stretch semantics beyond reasonable bounds, it may be pointed out that there are also correlations in the inorganic world. However, if this is indeed so, they are self-evidently loose, distant, and without the shared history in organic evolution.

The dilemma

Assuming there is a real trait in non-cognitive organisms (not found in inanimate nature) that resembles the human cognitive process we call reason – then what are we to call it? If this is a real trait then we need a scientific designation, but the word ‘reason’ is unacceptable because it is a cognitive word.

This is a major problem because if reason is a strictly human phenomenon, then that word is unavailable. A solution to this problem remains to be found since it is useful for biology to distinguish these pre-cognitive phenomena.

Possible solutions include: science insisting that the concept of reason is not restricted to humans; new words are coined; use of a descriptor such as ‘proto reason’ or ‘natural reason’.

At present this website has adopted different approaches finding it useful, for example, to promote the scientific broadening of the current concepts of purpose and agency to encompass all organisms. This may not be appropriate in other pre-cognitive situations. The coining of the word ‘pre-cognition’ is an early attempt to simplify the explanation of these phenomena.

Origins

How are we to provide an account of non-cognitive agential traits?

One approach is to treat ‘learning’, ‘problem-solving’ etc. as multiply realizable properties that are substrate-independent^[4] – that, for example, there are sentient-like properties displayed by non-sentient and non-neural objects, both organic and inorganic.^[3] That, say, non-neural organisms display response patterns consistent with animal cognition.

The evolutionary approach taken here concentrates on the realm of the living by regarding non-cognitive agential traits as universal properties of biological agents, and cognitive traits as an evolutionary elaboration of these traits of biological agency.

Pre-cognitive faculties

Does it make sense to talk about plants or unicellular organisms ‘learning’, ‘remembering’, or ‘knowing’? The following descriptions illustrate traits found in non-cognitive organisms that resemble and are likely evolutionary precursors to cognitive faculties.

Foresight & hindsight

Both animals and plants exhibit behaviors that suggest they can anticipate future events and plan accordingly. For example, storing food for future consumption, migrating seasonally to exploit favorable environmental conditions, and growing thorns to deter herbivores.

Decision-making

How do organisms demonstrate their non-cognitive traits?

Behavioral orientation

All organisms demonstrate an objective behavioral orientation as their propensity to survive and reproduce. Having this behavioral propensity means that they cannot be indifferent or passive to their conditions of existence because these conditions can influence their lives for ‘better’ or ‘worse’ regarding the pursuit of these goals. Without the exercise of agency they would soon cease to exist.

Obviously the goals of non-cognitive organisms are not conscious intentions but that does not mean that they do not exist: they are clearly manifested in the objective behaviors of these organisms.

This means that all organisms, whether or not they possess minds, have an objective perspective on life. We do not have words to express this behavioral orientation but would describe these goals in human terms as ‘interests’, ‘a point of view’, or ‘values’.

Adaptation

If organisms are to survive and reproduce then they must act on, and respond to, their conditions of existence. It is this process of adjustment to circumstance that endows organisms with the autonomy of agency.

The biological term used for this adjustment is ‘adaptation’. This is a word that generally relates to physically inherited traits considered over a geological time-scale but adjustment to conditions occurs over all time-scales.

Behavior

The agency of organisms is communicated through their behavior. This point is not always obvious to humans who are accustomed to thinking of values, intentions, beliefs, attitudes, and interests as internally generated, and communicated through the medium of symbolic language. However, the significance of behavior is not ignored when we say that ‘actions speak louder than words’.

Internal processing

While behavior is the outward manifestation of agency it is always, ultimately, a consequence of inner processing.

The inner processing that is at the core of what it is to be a biological agent is a reconciliation or compromise between the organism’s natural propensities and the constraints placed on these propensities by circumstance.

While we recognize that organismal behavior can be triggered by both internal and external events, it is always most directly and ultimately generated by the process of internal reconciliation. It is, for example, generally accepted that behavior has causes external to the organism e.g. the mouse ran from the cat.
While the cat triggered the behavior, the behavior itself was generated by the mouse. This seemingly trivial and inconsequential point has considerable biological significance since it redirects agency from the cat to the mouse.

Elements of biological agency

Our conviction of the overwhelming importance of human conscious awareness and deliberation leads us to believe that there can be no connection between human cognition and non-cognitive nature. The distinction between the cognitive and non-cognitive (the minded and mindless) seems absolute. Consequently, we tend to think of the origin, development, and evolution of cognition from within its mental context.

But evolution is an expression of physical continuity in which cognitive faculties must have arisen out of non-cognitive faculties. Our task is to explain how this occurred.

Empirical research, for example, in the emerging field of basal cognition studies the scaling of cognition and collective intelligence by considering that the turning of ‘cell-level physiological competencies into large-scale behavioral intelligences is not limited to the electrical dynamics of the brain. Evolution was using bioelectric signaling long before neurons and muscles appeared, to solve the problem of creating and repairing complex bodies.’^[2]

While science is concerned with the empirical question of what happened in fact, it is also informative to determine what was necessary in principle.

The article on biological agency provided a minimal definition of biological agency as the capacity of organisms to survive and reproduce by adapting to the conditions of their existence (both external and internal).

An intuitive breakdown of this idea into simple empirical categories concluded that:

Biosemiotics

All biology can be regarded as cognitive information processing if cognition is treated as self-organization. All received cellular and organismal information must be processeds analyzed to be deployed as cellular problem-solving to maintain an adaptive homeorhetic path.

Biosemiotics explores the communication of information within and between biological agents; this is a system that include chemical, physical, and visual, signs, symbols, and codes used to interpret and adapt to the agent’s conditions of existence. It draws on cognitive science and other disciplines to understand the processes of communication and meaning in living systems, most notably the umwelts of organisms.

In biological semiotics, the functional integration of biological activity of cells and organisms is regarded as a coordinated information system. One proposal treats this system as composed of three kinds of memory that together constitute the informational architecture: the senome (physicochemical sensory system, with embedded signals from the environment), epigenome (non-coding hereditary information), and genome (protein-coding DNA and RNA).^[7]

The Central Dogma represents the flow of information in biological systems in biomolecular terms, passing from genes to proteins and on into more inclusive biological structures.^[8]

Organisms and their cells are sentient, adaptive, and problem-solving biosemiotic agents that feel, learn, remember, value, choose, react, and communicate – a perspective on life that has been codified as the Cellular Basis of Consciousness (CBC).^[5]

This thesaurus of cognitive metaphor is necessary because biological agents share a suite of universal agential characteristics that are currently only described effectively in their human cognitive form. They are the pre-cognitive components of every organism’s experience (its reality or umwelt) – the universal agential characteristics that distinguish life from non-life, their cognitive manifestation being their highly evolved and limited form.

While organisms are canonical biological agents, agency is expressed at other biological scales so that, for example, biosemioticists can recognize cellular sentience and consciousness as meaningful. The sensory apparatus needed to exchange information between the system and its conditions of existence is called the senome. To act effectively on information, cells must be able to assess and measure it in some way.

Information processing

First, for such a system to exist there must be a functionally integrating system of communication involving both internal and external environments. This must entail, no matter how simple, some form of information processing as information storage, retrieval, and processing.

This is the expression of cognition as a non-cognitive biological trait as the processes involved in acquiring, processing, storing, and using information. In evolved forms it includes a wide range of functions and abilities that allow organisms to perceive, understand, and interact with their environment through various sensory modalities such as vision, hearing, touch, taste, and smell. This information is then interpreted, categorized, and integrated into existing knowledge structures.

Perception entails the ability to perceive and interpret sensory stimuli pattern recognition, and the organization of sensory input into meaningful patterns. Memory: Memory engages the encoding, storage, and retrieval of information over time as sensory memory, short-term memory, long-term memory, and working memory, each serving different functions. Attention engages focus on specific stimuli or tasks while filtering out irrelevant information as it relates to learning, memory, problem-solving, and decision-making. Communication conveys information to other organisms esp. language of humans. Problem-Solving and Reasoning creates adaptive strategies or solutions to circumstances. Executive Functions establish goals, self-regulation, inhibition, and flexibility in relation changing conditions of existence.

Human cognition is evolved metacognition as the ability to monitor and regulate cognitive processes. It involves self-awareness including the ability to reflect on and evaluate one’s own thinking and problem-solving strategies.

Agential traits can change and adapt over time in response to experiences, learning, and environmental influences. This property allows for the acquisition of new skills, knowledge, and cognitive strategies throughout the lifespan.

Information

Information is an abstract concept that might seem to have little hard physical impact or presence in the world – a concept with little scientific meaning. It is, however, a concept with increasing significance and relevance in many branches of biology.

Information is any content or signal that can inform, communicate, or reduce uncertainty. It is distinct from knowledge, which represents synthesized understanding, and from mediums and messages, which serve as conduits and specific instances of communication, respectively.

Information is the content of a message, while meaning is the interpretation of the message by a conscious agent. Information can exist without meaning, but meaning cannot exist without information.

Information provides raw data, while meaning is the interpretation or significance assigned to that data, shaped by context, cognition, and culture.

Information in biology is a concept that refers to the way living systems store, transmit, and process data that is essential for the survival and reproduction of organisms.

Information in biology can be found at different levels of organization, such as molecular, cellular, organismal, and ecological. Some examples of biological information are:

• • The genetic code, which is a set of rules that maps sequences of nucleotides in DNA or RNA to sequences of amino acids in proteins1.
  • The epigenetic code, which is a set of modifications on DNA or histones that affect gene expression without changing the DNA sequence2.
  • The neural code, which is a set of patterns of electrical or chemical signals that convey information between neurons in the brain3.
  • The animal communication code, which is a set of signals that animals use to exchange information with each other, such as sounds, gestures, or pheromones4.

Information in biology does not entail meaning or interpretation by a conscious agent. Rather, it is a physical property that can be measured, quantified, and manipulated by natural or artificial processes. It is also subject to the laws of thermodynamics, so information can be created, destroyed, or transformed, but not without a cost in terms of energy or entropy. Information in biology is a fundamental concept that helps us understand the structure, function, and evolution of living systems.

Behavioral orientation

Second, the propensity to survive and reproduce confers on organisms a behavioral orientation (like a perspective, point of view or value).

Adaptation

Third, as part of the process of adaptation this behavioral orientation must be reconciled with both external and internal conditions that might ‘help’ or ‘hinder’ the attainment of these goals.

Evolution & agency

Every biological object (organism, structure, process, behavior) is a product of evolution and therefore necessarily expresses characteristics that demonstrate both similarity and difference. The similarity is that of the shared features of common ancestry, the difference is in the uniquely defining features of the object of interest.

Elements of human agency

This website treats human agency as a limited and highly evolved form of biological agency and this immediately raises the question of evolutionary connection between biological agency and human agency, as understood both theoretically and empirically.

Since all organisms are connected by common ancestry it is interesting to speculate on how these three critical criteria of adaptation might be represented in human cognitive form. We know, for example, that while we must eat to survive our biology mindlessly ensures this through the cognitive process of hunger and the sensory stimulus of smell and taste.

Knowing that humans express adaptation in a highly evolved and minded form it is reasonable to ask how the three principles outlined above may be given mental representation?

As basic biological phenomena it is not surprising to find simple mental correlates to the three biological processes that ground the biological condition – the continuous process of organismal adjustment and adaptation – the processes of information processing, behavioral orientation, and functional integration.

Since all organisms are connected by common ancestry it is interesting to speculate on how these three critical criteria of adaptation might be represented in human cognitive form. We know, for example, that while we must eat to survive our biology mindlessly ensures this through the cognitive process of hunger and the sensory stimulus of smell and taste.

Knowing that humans express adaptation in a highly evolved and minded form it is reasonable to ask how the three principles outlined above may be given mental representation?

As basic biological phenomena it is not surprising to find simple mental correlates to these three grounding biological processes of information processing, behavioral orientation, and adaptation.

Information processing correlates with knowledge, behavioral orientation correlates with values, and the process of informational integration and its behavioral manifestation – the process of self-correction in relation to to conditions of existence – correlates with reason. That is, the mental attributes of knowledge, value, and reason which correspond to the traditional mental domains of epistemology, ethics, and logic find their biological origins in information processing, a behavioral orientation, and the process of adaptation.

Knowledge and information (beliefs), behavioral orientation as biological values (desires), and adaptation (reasoning) are strongly associated with entire agential individuals and weakly with their subordinate contributing parts.

The division of human mental experience into the three interrelated categories of knowledge (epistemology), values (ethics), and reason (logic) is a conceptual framework dating back to ancient Greek philosophy. The way that just three categories can cover so effectively the vast landscape of human experience has great appeal. Though not necessarily discrete or independent mental faculties, these three concepts have provided a useful framework for psychology, cognitive science, philosophy, and anthropology since they draw attention to important aspects of our cognition, individual and collective behavior, and decision-making.

But we understand cognitive properties in their own terms. That is we assume that key characteristics of human cognition are grounded in the biological structures and processes of the brain with their expression and development shaped by both cultural and environmental factors. But maybe cognition, like physical structures, has a biological ancestry dating back to organisms without cognitive capacities?

Perhaps these cognitive categories are also evolutionary signposts. While they are shaped by cultural, social, and environmental influences they may be signalling to us something about our real underlying biology? Human cognition and behavior have evolved to enhance the universal values of survival, reproduction, and flourishing as inherited from interaction with ancestral environments.

This is the topic for a major research program, but a quick overview can explore some possibilities.

This perspective suggests that cognition, like physical structures and processes, has built on, and extended, evolutionarily prior pre-cognitive processes. More specifically, cognition has its evolutionary roots in simpler forms of information processing, behavioral orientation, and adaptation.

The following descriptions of knowledge, value, and reason open with a description of their precursor properties in biological agency before considering their highly evolved manifestation in human agency: they are highly evolved adaptive responses to the precursor conditions of information processing, behavioral orientation, and adaptation as crucial factors underlying organismal survival, reproduction, and flourishing. They are cognitive traits inheriting properties from our biological ancestry in exactly the same way that we inherit physical characteristics.

Those characteristics of human agency that we share with biological agency we treat as cognitive metaphor – as creations of the human mind. It is ironic that the uniquely cognitive characteristics of human agency are creations of biological agency.

Cognition

Cognition is an important concept because it signifies the functional integration of a plethora of sensory and other information into a meaningful experience.

Brain functions are closely interconnected and so behavior is generated by the coordinated activity of multiple brain regions. Processes related to reason, knowledge, and values are distributed throughout the brain but some specific areas are particularly relevant.

Short-term human behavioral adjustments are associated with the integrating power of our cognition which turns a world of potentially teeming sensory confusion into a coherent and meaningful experience. This involves physiological processes as cognitive faculties like like learning, remembering, communicating, valuing, social interaction, and physiological changes etc. – our knowledge, beliefs, and values.

Information processing correlates with knowledge, behavioral orientation correlates with values, and the process of informational integration and its behavioral manifestation – the process of self-correction in relation to to conditions of existence – correlates with reason. That is, the mental attributes of knowledge, value, and reason which correspond to the traditional mental domains of epistemology, ethics, and logic find their biological origins in information processing, a behavioral orientation, and the process of adaptation.

Knowledge and information (beliefs), behavioral orientation as biological values (desires), and adaptation (reasoning) are strongly associated with entire agential individuals and weakly with their subordinate contributing parts.

The division of human mental experience into the three interrelated categories of knowledge (epistemology), values (ethics), and reason (logic) is a conceptual framework dating back to ancient Greek philosophy. The way that just three categories can cover so effectively the vast landscape of human experience has great appeal. Though not necessarily discrete or independent mental faculties, these three concepts have provided a useful framework for psychology, cognitive science, philosophy, and anthropology since they draw attention to important aspects of our cognition, individual and collective behavior, and decision-making.

There is a further fascinating correlation that exists between cognition and our ability to perceive, reason, and adapt through memory, decision-making, and problem-solving. The hippocampus is related to memory and knowledge, the amygdala to emotion or biological orientation, and basal ganglia related to decision-making and reason – all as are ancient brain regions. Their conservation underscores shared cognitive foundations.

But we understand cognitive properties in their own terms. That is we assume that key characteristics of human cognition are grounded in the biological structures and processes of the brain with their expression and development shaped by both cultural and environmental factors. But maybe cognition, like physical structures, has a biological ancestry dating back to organisms without cognitive capacities?

Perhaps these cognitive categories are also evolutionary signposts. While they are shaped by cultural, social, and environmental influences they may be signalling to us something about our real underlying biology? Human cognition and behavior have evolved to enhance the universal values of survival, reproduction, and flourishing as inherited from interaction with ancestral environments.

This is the topic for a major research program, but a quick overview can explore some possibilities.

This perspective suggests that cognition, like physical structures and processes, has built on, and extended, evolutionarily prior pre-cognitive processes. More specifically, cognition has its evolutionary roots in simpler forms of information processing, behavioral orientation, and adaptation.

The following descriptions of knowledge, value, and reason open with a description of their precursor properties in biological agency before considering their highly evolved manifestation in human agency: they are highly evolved adaptive responses to the precursor conditions of information processing, behavioral orientation, and adaptation as crucial factors underlying organismal survival, reproduction, and flourishing. They are cognitive traits inheriting properties from our biological ancestry in exactly the same way that we inherit physical characteristics.

Those characteristics of human agency that we share with biological agency we treat as cognitive metaphor – as creations of the human mind. It is ironic that the uniquely cognitive characteristics of human agency are creations of biological agency.

Knowledge

Knowledge, as a fundamental and universal property of biological agency, exists as information acquisition, storage, processing, and retrieval.

Human knowledge, as information about the world, is acquired through sensory experiences, learning, and memory: it includes facts, skills, and conceptual frameworks whose communication through symbolic languages is advantageous for survival and reproduction. In humans, the intergenerational accumulation of knowledge produced cultural evolution as extremely rapid short-term adaptation superimposed on slow genetically-based biological evolution. In human agency these processes have evolved into neural processes in brains with different regions of the brain specialized for different kinds of knowledge, This process involves various brain regions, including the hippocampus for memory formation and retrieval, the prefrontal cortex for higher-order cognitive functions such as decision-making and planning, and distributed networks across the brain for processing different types of information. Neuroplasticity, the brain’s ability to reorganize itself in response to experience, underlies learning and memory formation. Synaptic connections between neurons strengthen or weaken based on experience, leading to changes in knowledge representation while genetic factors influence individual differences in cognitive ability and predispositions for learning and memory.

Knowledge – the temporal lobes are involved in processing sensory information and are crucial for memory formation and storage understanding meanings, recognizing faces, and storing factual information. The hippocampus, which is located within the temporal lobes, plays a central role in the formation of new memories and spatial navigation.

Values

All life, as a manifestation of biological agency, expresses a behavioral orientation as the disposition to survive, reproduce, and flourish.

This goal-directedness can harness knowledge, as information processing, in the attainment of its goals. While humans make a minded (subjective) judgement as to whether these goals are ‘for the better’ or ‘for the worse’, mindless organisms demonstrate these goals as a mindless behavioral propensity. This is akin to an unspoken ‘perspective’ or ‘point of view’. As a behavioral orientation it is an objective fact, but it is, at the same time, a confusingly mindless ‘value’. Biologists and philosophers ignore this dilemma and blithely refer to adaptations that mindlessly ‘favour’ some individuals over others.

The moral and social values of human agency are manifest through mental faculties grounded in neural circuits involved in emotion processing, social cognition, and reward processing. Brain regions such as the amygdala, prefrontal cortex, and ventral striatum play crucial roles in encoding and evaluating moral and social stimuli. Evolutionary psychology suggests that certain values may have adaptive significance and are shaped by natural selection. For example, empathy and altruism may enhance social cooperation and group cohesion, thereby conferring reproductive advantages. Genetic and neurobiological factors contribute to individual differences in moral attitudes and values. Twin and adoption studies provide evidence for genetic influences on moral development and personality traits related to values. Behavioral economics and decision-making research explore how individual and societal values influence preferences, choices, and economic behavior.

Values – the amygdala integrates emotions, emotional behavior, especially fear, and motivation. The insula is the source of disgust, it records pain and physiological states. The periaqueductal grey is also associated with pain, maternal attachment, and anxiety. The limbic system is also associated with emotional and physiological processing.

Reason

Biological agency expresses a constant and universal process of adjustment and adaptation, of ‘self-correction’ or ‘problem-solving’, ‘decision-making’. It is the functional integration of the organism with its conditions of existence.

The word chosen to express this property as it occurs in minded human agency is ‘reason’. The reasoning of human agency involves the ability to think logically, analyze information, make decisions, and solve problems: it is a cognitive adaptation that allows humans to navigate complex environments, anticipate future events, and make adaptive choices. Evolutionarily it would have facilitated finding food, avoiding predators, navigating social dynamics, assisting creative innovation notably that of technology. It involves complex interactions between multiple brain regions and neural networks. Frontal brain areas, such as the prefrontal cortex, play key roles in executive functions such as planning, problem-solving, and cognitive control. Neuroimaging studies have identified neural correlates of logical reasoning, deductive inference, and probabilistic reasoning. These studies reveal the neural substrates underlying different aspects of rational thought. Genetic factors influence cognitive abilities related to reasoning, such as working memory capacity and fluid intelligence. Variations in genes involved in neurotransmitter systems and neural development can impact cognitive functions relevant to reasoning. Experimental studies have examined cognitive biases, heuristics, and logical fallacies that affect human reasoning and decision-making processes. Computational modeling has been used to simulate and understand cognitive processes involved in reasoning, such as Bayesian inference, analogical reasoning, and cognitive control while cross-cultural studies have explored cultural variations in reasoning styles, argumentation patterns, and logical thinking strategies. Reason – the prefrontal cortex is associated with higher-order cognitive functions such as reasoning, decision-making, planning, and problem-solving, playing a crucial role in executive functions such as regulating behavior, making decisions, and prioritizing tasks. Frontal lobe is involved with reasoning, problem-solving, and planning. The parietal lobes process sensory information from the body and the environment facilitating spatial awareness, attention, and mathematical reasoning.

In sum, a living organism is therefore in a continuous state of problem-solving. It is gathering and processing information in ways that conduces to goals that are meaningful in relation to that organism as a ‘self’ – to those specific conditions of existence that can influence its goals (its umwelt). As many have observed: life designs itself. The uniquely defining cognitive domains of knowledge, values, and reason so closely associated with human agency likely evolved as adaptive responses to the challenges faced by pre-human ancestors in ancestral environments. They can be clearly linked to the universal grounding properties of biological agency, subsequently shaped by billions of years of structural evolution, the foundational biological properties of information processing (knowledge), behavioral orientation (values), and adaptation (reason).

At present this model can serve only as a heuristic device awaiting further philosophical and empirical investigation. More discussion can be found in the article reason-values-knowledge.

Commentary

The concept of non-cognitive agential traits relies on a firm understanding of what is meant by agency in a biological context. The article investigating biological agency concluded that a scientifically acceptable account must include a compelling account of what is meant by biological agent, its mission or goals, and its means of pursuing these goals.

The election of organisms as canonical biological agents, and their goals as survival and reproduction are neither controversial nor novel. However, suggestions for the generalized means used by organisms to pursue their goals charted new ground.

It was first recognized that a fundamental feature of the existence of all organisms (humans included) is their constant adjustment to their conditions of existence. This is, as it were, a non-negotiable aspect of being alive. Adjustment may be short- or long-term but the word used by biology to describe this process is adaptation.  It was referred to on this website as the biological condition, echoing the popular notion of the human condition.

While ‘adaptation’ is a useful portmanteau term, it requires fleshing out if it is to be of use to biology.

What are the essential features needed for adaptation to occur?

There seems to be no empirical way of deciding such a question. Perhaps the answer relates most strongly to utility and pragmatism. The conclusion was that three elements stand out as necessary conditions for adaptation.

First, organisms are information-rich objects: their functional integration necessarily entails a complex system of communication including the collection, storage, and processing of information about both their external and internal conditions.

Second, organisms must necessarily adapt because they have a behavioral orientation or ‘point of view’ that must be reconciled with their circumstances.

Third, the act of adaptation involves a crucial process of internal reconciliation between the behavioral orientation of the organism and its conditions of existence.

This tripartite taxonomy is proposed as an empirically testable account of the foundational characteristics of biological agency. But how can such a taxonomy be justified; where is the evidence for such a claim?

If these are universal characteristics of biological agency then how are they manifested in cognitive form? How do humans achieve their universal biological goals, in cognitive form, by harnessing information processing, their behavioral orientation, and adaptation?

As supportive evidence for this taxonomy, it is pointed out that this problem was resolved unknowingly by ancient Greek philosophy in the fundamental distinction between epistemology, ethics, and logic. This was a convenient taxonomy of the mind that separated knowledge (information processing), value (behavioral orientation), and reason (adaptation).

Pre-cognition glossary

The following glossary draws attention to the grounding of human agency in the universal (shared) characteristics of biological agency and biological cognition. These shared traits are a consequence of common evolutionary ancestry; they do not (meaningfully) occur in inanimate objects.

Non-cognitive but mind-like traits have been widely interpreted as cognitive metaphors. Rather than being creations of the human mind, they are the real non-cognitive evolutionary antecedents to human cognitive traits.

In the absence of a technical vocabulary for these evolutionarily antecedent non-cognitive traits, the conventional cognitive meanings of these words is extended in this glossary to include their non-cognitive precursors.

Cognitive terms are here defined in a broad and narrow sense. The broad sense, given in italics, is the grounding ancestral condition as expressed universally in biological agency, followed by our anthropocentric understanding of these traits expressed narrowly in tin terms of their highly evolved cognitive form.

Adaptation – the adjustment of organisms to their conditions of existence by using information processing, a behavioral orientation, and functional integration.

Agency – The exercise of autonomous goal-directed behavior; the human capacity to act autonomously by, for example, making independent moral judgments.

Biological agency – The capacity to act on, and respond to the conditions of existence in an autonomous and flexible goal-directed way that expresses the universal, objective, and ultimate propensity to survive, reproduce, and flourish

Cognition – The processes and activities guiding the behavior of a biological agent – related to the acquisition, processing, storage, and use of information; the human mental processes and activities related to the acquisition, processing, storage, and use of knowledge through thought, experience, and the senses. It includes the mental faculties of perception, reason, memory, attention, problem-solving, and language comprehension meaningfully integrated to guide behavior.

Consciousness – the capacity of a biological agent to orientate itself to space, time, & its conditions of existence; the human awareness of immediate experiences. Also, the entire range of mental processes, including cognitive functions such as self-awareness, introspection, reasoning, memory, imagination, and the capacity for abstract thought. The totality of an individual’s subjective experiences and mental life.

Communication – the exchange of information. Many species communicate with conspecifics using intricate vocalizations, body language, or chemical signals. Some animals, like dolphins and certain bird species, are capable of complex vocalizations with distinct meanings, while others, like ants and bees, use pheromones to convey information about food sources, danger, or mating opportunities.; the exchange of knowledge between humans by both verbal and non-verbal means.

Epigenome – the sum of all non-coding DNA and RNA-based hereditary information of an organism Besides the machinery regulating the package of DNA into the chromatin and chromosomes, the epigenome includes also all structures acting as templates for their own copying

Experience – the event(s) that influence the umwelt of a biological agent and the way these are processed as information.; event(s) that a human goes through or encounters, often characterized by being special in some way – by, say, uniqueness or personal involvement; sometimes the totality of life events, knowledge, emotions, and perceptions and overall comprehension and awareness of the world.

Human agency – A specialized form of biological agency that uses language and cognition.

Intelligence – the capacity to acquire and process information that facilitates adaptation to the circumstances of existence and the attainment of goals; the ability to acquire, understand and apply knowledge and reason to solve problems and adapt to new situations.

Intention – A goal-directed behavioral orientation; a conscious attitude towards the end or purpose of actions or conduct

Intentionality – behavior that is goal-directed i.e. directed towards objects, properties, or states of affairs; the ‘aboutness’ or directedness of our thoughts, beliefs, desires, and perceptions towards something external to them.

Knowledge – Information accumulated by an agent about its conditions of existence; all forms of human awareness and comprehension of the world, including both subjective and objective aspects of our understanding.

Learning – The capacity to process and accumulate information that may facilitate adaptation to the circumstances of existence and the attainment of goals. Many organisms exhibit the ability to learn from past experiences and modify their behavior accordingly. For instance, classical conditioning, where an organism learns to associate a neutral stimulus with a significant event, has been observed in various species, including invertebrates like fruit flies, molluscs, and even plants; the ability for personal growth and development through the processes of acquiring knowledge and skills.

Memory – the capacity for information storage and retrieval.; the ability of the mind to store and recall information, experiences, and knowledge.

Perception – the processing of the full range of experiential information (the umwelt) of a biological agent; the human processing of sensory stimuli through the sensory system that includes the five traditional senses of sight, hearing, taste, smell, and touch, but sometimes including cognitive factors like mental processes, beliefs, desires, reason and their role in experience.

Purpose – the goal of a biological agent, paradigmatically a living organism, but also the natural end-state, limit, or reason for a structure, process, or behavior (often referred to in this sense as a function); the reason (end, aim, or goal) why something exists or is done, made, used etc.; (human) the object of conscious intention.

Reason (problem-solving) – The capacity to process information in a way that facilitates the attainment of goals. Some animals demonstrate problem-solving skills when faced with novel challenges in their environment. For example, certain bird species, such as crows and parrots, are known for their ability to use tools creatively to obtain food or solve complex tasks; the mental faculty that enables individuals to think, analyze, and draw conclusions logically and rationally – to make sound judgments based on evidence and a structured thought process.

Self – what drives behavior and provides an autonomous subjective identity; the sum of an agent’s integrated sensory information as encoded in the senome, epigenome, and genome.

Sene – a sensory experience of information that is of potential adaptive value

Senome – the adaptively integrated sensory experience of a cell or organism. The senome first feeds back into the epigenome and, then the genome.

Sentience – the capacity to experience and respond to sensations; in evolved cognitive form this is conscious awareness and subjective experience of pleasure, pain, and emotions. Present in organisms by degree.

Social learning – Human cultural evolution is a non-genetic consequence of the cultural accumulation and transmission of information. It has resulted in humans creating their own environments of evolutionary adaptation.
Social animals often learn by observing and imitating the behaviors of others within their social group. This can include acquiring new foraging techniques, communication signals, or even cultural traditions. Chimpanzees, for instance, have been observed to learn tool-use techniques from one another.

Valence – alternative term for biological value as the capacity to respond positively or negatively to circumstance.

Value – A behavioral propensity or disposition (towards); the word ‘value’ can be used as both a verb or a noun. When used in a human context it refers to the importance or significance attached to something based on emotional, objective or other factors. Values can include moral, ethical, cultural, and personal principles that guide behavior and decision-making.

Glossary of biological agency

Glossary

Adaptation (biological) – the word 'adaptation' expresses, in the most parsimonious way, the means by which organisms, as biological agents, attain their goals. 'Adaptation' can refer to both a process or trait. The process by which populations of organisms change over many generations in response to environmental factors, developing heritable traits that enhance their survival and reproductive success in specific environments; the evolution of traits with functions that enhance fitness (being conducive to survival, reproduction, and flourishing); the capacity for self-correction - in the short-term through behavioral flexibility, leading to long-term genetic change
Agency - (general) the capacity to act on and react to conditions of existence with goal-directed behavior; (biological) the mostly mindless autonomous capacity of biological individuals to act on, and react to, their conditions of existence (both internal and external) in a unified, goal-directed but flexible way (see biological axiom). Agency is the physical manifestation of functionally integrated behavior. Human agency is biological agency supplemented by the evolved resources of the human mind including: language, self-reflective and conscious reason, hindsight, foresight, and abstract thought
Agent - something that acts or brings things about. Mindless inorganic agents include objects like missiles, cities, and computers. In biology - an organism as autonomous matter with the capacity to behave in a unified goal-directed way as stated by the biological axiom (sometimes extended to include genes, groups, or other entities, even natural selection itself) as a (semi)autonomous individual with inputs as flows of energy, materials, and information, internal processing, and outputs as energy, waste, action and reaction in relation to inner and outer environments. An organism motivated by real goals (these may be mindless, that is, without conscious intention);  an agent can act and react; it is the instrument or means by which a purpose is pursued
Agential realism - the claim that non-human organisms exhibit agency in a mindless way, and that humans combine both mindless and minded agency: the grounding of cognitive biological metaphors in non-cognitive biological facts
Algorithm of life - life is autonomous and agential matter that self-replicates with variation that, by a process of evolutionary selection, incorporates feedback from the environment thus facilitating its persistence.

1. Endow units of matter with agency as the capacity to adapt to their conditions of existence (to survive, reproduce, and flourish).
2. Combine the behavioral orientation of 1 with genetic modifications arising in each new generation
3. Expose 2 to evolutionary selection pressures resulting in differential survival
4. Surviving forms return to step 2

Anthropocentric - to view and interpret circumstances in terms of human experience and values
Anthropomorphism - the attribution of human traits, emotions, or intentions to non-human entities
Apomorphy - a specialized trait or character that is unique to a group or species: a character state (such as the presence of feathers) that is not present in an ancestral form
Autopoiesis - self-replication combined with self-maintenance and modification is sometimes referred to as autopoiesis
Behavior (biology) - actions performed by a biological agent (or, more loosely, its parts); the internally coordinated but externally observable response of whole organisms to internal and external stimuli. Behaviour may be: mindless or minded; conscious, unconscious, or subconscious; overt or covert; innate or learned; voluntary or involuntary. Learning capacity is graded in complexity
Behavioral ecology – the study of the evolution of animal behavior in response to environmental pressures
Biological agency - the capacity of autonomous living organisms as biological agents to act on, and respond to, their conditions of existence in a flexible way and with a unity of adaptive purpose - the goal-directed behavioral propensity to survive, reproduce, and flourish; the capacity of living organisms to act with intentionality; a life-defining property of living organisms; the motivation for biological activity as described by the biological axiom; the capacity of organisms to act with purpose and intentionality; the biological principle that has generated the entire community of life; the capacity organisms act intentionally in the sense that their behavior is purposeful and adaptive i.e. directed towards objects, properties, or states of affairs
Biological agent - while biological agency, in a broad sense. can be ascribed to almost any biological structure, process, or behavior, it is the organism that best serves as its exemplar, standard, or prototype cf. organism, biological agency. an organism as an autonomous unit of matter with a flexible and adaptive propensity to survive, reproduce, and flourish (the universal, objective, and ultimate unity of purpose shared by all life); biological agents, organisms are self-replicating units that regulate the internal and external exchange of energy, materials, and information that is required for their autonomous pursuit of goals
Biological axiom – a universal biological principle paradigmatically exemplified by living organisms as biological agents that express their autonomy in a unity of adaptive purpose – the universal, objective, and ultimate behavioral propensity to survive, reproduce, and flourish in the face of their conditions of existence (sometimes referred to in evolutionary biology as 'fitness maximization'). These goals may be met in both cognitive and non-cognitive ways: they are universal because these are characteristics demonstrated by all organisms, objective because they are a mind-independent fact, and ultimate because they are a summation of all proximate goals. While aberrations may be found, the biological axiom is a processual and agential definition that expresses with greater clarity than definitions describing structures, the necessary and sufficient ancestral agential characteristics that define all life. cf. organism, biological agent.
Biological goal - the object towards which the behavior of a biological agent is directed. Biological goals are the natural ends or limits of internally generated biological processes that follow transparent causal pathways - the development of a structure, maturation of an organism etc. Their sources may be mindless, minded but unconscious, or conscious. Short-term proximate goals serve long-term ultimate ends. Goal-directedness confers both purpose and agency. Biological goals are usually observed and studied as the behavioral outcomes of internal processes.
Biological object - something from the living world that can be studied scientifically; taken to be either a structure (whole or part), process, or behavior
Biological simile – a comparison (likeness) of biological phenomena that is based on real evolutionary connection
Bioteleological realism - the claim that purposes exist in nature and that most cognitive metaphors used in science are grounded in non-cognitive biological facts
Bioteleology - purpose resides in the fact that there are natural ends or limits to biological processes (e.g. the maturing of an acorn into an oak tree; the termination of a mating ritual in copulation), that these ends are objectively  goal-directed and therefore purposive. Teleonomy controversially interprets teleology as implying a metaphysically questionable source of purpose. The word teleonomy attempts to replace this purported implication with a naturalistic explanation. The distinction between teleology and teleonomy, and whether that distinction is warranted, remains unclear
Cognitive ethology – the study of the influence of conscious awareness and intention on the behavior of an animal
Cognitive metaphor - a metaphor used in the context of human intentional psychology. When we have no words to describe real pre-cognitive agential traits, we resort to the language of human cognition, thus condemning these traits to the figurative world of metaphor
Complementary properties – the properties instantiated by the relata of a biological simile
Conditions of existence (biology) - those factors influencing the inner processing of organisms including triggers arising from both inside and outside the organism.
Derived concept – a concept with a narrow semantic range
Emergence - as used here - the origin of novel objects, properties, or relations in the universe that warrant human categorization
Environmental factors - the external factors impacting on the existence of an organism
Evolutionary biology – the study of evolutionary processes (notably natural selection, common descent, speciation) that created the community of life
Fitness - a measure of reproductive success (survival) in relation to both the genotype and phenotype in a given environment
Function - also referred to as adaptive significance or purpose. In agential terms it helps to regard the characters of organisms as having functions while organisms themselves, as independent agents, have purposes and goals
Genotype - the genetic constitution of an individual organism, encoded in the nucleus of every cell
Grounding concept – the general ideas that underpin more specific (derived) concepts
Heuristic – stimulating interest and investigation
Holobiont – an aggregation of the host and all of its symbiotic microorganisms
Homeorhesis - (Gk - similar flow) a term applied to dynamic systems that return to a specific path or trajectory, in contrast with systems that return to a particular state (homeostasis). Homeostasis refers to the maintenance of a stable internal environment in response to external changes (e.g. body temperature in mammals) while homeorhesis is the adjustment, sometimes changing over time, to meet particular organismal functions or goals (e.g. changes in blood composition that support the fetus during pregnancy).
Homology – a similarity in the structure, physiology, or development of different species of organisms based upon their descent from a common evolutionary ancestor
Human agency - behavior motivated by conscious intention; the uniquely human specialized form of biological agency that is described using the human agential language of intentional psychology; the capacity to act based on reasons as cognitive and motivational states (beliefs, desires, attitudes) (philosopher Kim)
Human-talk - the language of humanization - the attribution of human characteristics to non-human organisms, objects, and ideas. (Biology) the description of non-human organisms using language that is usually restricted to humans and human intentional psychology; the use of cognitive metaphor to describe non-cognitive but real biological agency; the psychologizing of adaptive explanations
Intention - a cognitive goal, or pre-cognitive behavior that is directed towards objects, properties, or states of affairs
Intentional idiom - the use of intentional language in a wide range of contexts including those relating to non-human organisms
Life – units of matter with the agential capacity to survive, reproduce, and flourish (cf. biological axiom) as best exemplified by autonomous organisms. Life processes, such as growth, reproduction, response to stimuli, and metabolism are subordinate to the organismal wholes of which they are a part
Metabolism - the set of processes that sustains an organism (or, more generally, any biological system)
Metaphor - figurative language as ‘nonliteral comparisons in which a word or phrase from one domain of experience is applied to another domain’. An 'as if' direct (not a 'like') comparison that is not grounded in reality e.g. 'You are a rat'.
Natural agency - any agency in the natural world
Natural purpose - the natural goals, ends, or limits of biological agents, both cognitive and non-cognitive
Normative realism - the view that normativity has its origin in biology through the mindless and mindful ultimate goals of survival and reproduction, and proximate goal of flourishing
Organism - unicellular to multicellular life forms that include fungi, plants, and animals. The mostly physically bounded and functionally organized basic unit of life and evolution. As a mostly autonomous biological agent the organism acts on, and responds to, its conditions of existence with flexible but unified and goal-directed behavior that demonstrates the objective, ultimate, and universal propensity of organisms to survive, reproduce, and flourish. While life can be described at many scales and from many perspectives (and the structures, processes, and behaviors of organisms all demonstrate a degree of autonomy), it is the entire organism that provides the agential reference point of life - whose autonomy is both intuitively and scientifically most discrete. Exceptional cases such as lichens, Portuguese Men-o-War, the Great Barrier Reef, sexually aberrant variants etc., do not erode these core characteristics.
Organismal factors - the internal factors impacting the existence of an organism
Personification - the representation of something in the form of a person
Phenotype - the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment
Physical reductionism - the view that biological phenomena can be adequately explained in terms of physico-chemical entities
Pre-cognition - all organisms are goal-directed autonomous biological agents that act on and respond to their conditions of existence in a flexible way. Agency is usually associated with human cognitive traits like intention and deliberation. However, the presence of agency in non-cognitive organisms confirms the presence of non-cognitive agential traits, a characteristic of non-cognitive organisms that distinguishes them from inanimate and dead objects. These non-cognitive agential traits are referred to here as pre-cognition.
Process ontology – it is processes that create phenomena including emergent and ephemeral ‘things’ which are derived from processes as transient and cohesive patterns of stability within the general flux. Thus, things are derivative of processes. In practical terms this does not mean that things do not exist or are not useful concepts. However, instead of thinking of processes as belonging to things, it is more scientifically informative to think of things as derived from processes. Organisms are prime examples of transient things in process
Purpose – the reason (end, aim, or goal) why something exists or is done, made, used etc.; (biology) the goal of a biological agent, paradigmatically a living organism, but also the natural end-state, limit, or reason for a structure, process, or behavior (often referred to in this sense as a function). In humans, purposes can assume a cognitive form as mental representations (conscious intentions); what something is 'for'; Aristotle's final cause or telos. Purposes, as the goals or ends of organisms and their parts, are an emergent and agential property of life that preceded human cognition: causal (etiological) explanations of purpose do not explain it away. Darwin did not remove agency and purpose from nature, he showed how they generated a process of natural selection.
Proximate explanation - an explanation dealing with immediate circumstances
Relata – the objects of a comparison
Semantic range – the degree of generality or abstraction encompassed in the meaning of a word - range of objects and ideas encompassed by its meaning
Synapomorphy - a characteristic present in an ancestral species and shared exclusively (in more or less modified form) by its evolutionary descendants
Teleology - the philosophical concept of purpose and design in the natural world. The claim that natural phenomena occur for reasons as natural ends or purposes that are neither necessitated by human or supernatural intention nor implying backward causation or foresight. For teleology in biology see bioteleology. The article on bioteleology discusses 8 senses of 'teleology'
Teleonomy - see bioteleology
Trait - a unit of the phenotype (physical or behavioral)
Ultimate explanation - a long-term explanation (e.g. in biology as a measure of the fitness of a particular trait)
Umwelt - the environment of adaptive significance for a particular organism: those factors that are important for its survival, reproduction, and flourishing: its mode of experience or 'reality'. For humans, this is the commonsense world of everyday experience (cf. manifest image) that is mostly a consequence of our innate mental processing which is, in turn, a consequence of our uniquely human evolutionary history
Values – (biological agency) that which ultimately motivates the behavior of biological agents (living organisms), namely the universal and objective goals of the biological axiom. Human agency - the proximate and subjective attitudes, beliefs, and inclinations that guide human behavior

First published on the internet – 20 February 2023

. . . 20 February 2023 – coined the word ‘pre-cognition’ – editing continuing into March