Biological cognition

Human Brain – Epitome of a Cognitive Object – the most highly evolved of the many functionally equivalent organs of biological cognition 

Tesla MRI of the ex vivo human brain at 100 micron resolution (100 micron MRI acquired FA25 sagittal) (downsized, original speed).gif

Courtesy Wikimedia Commons – Accessed 20 September 2021

This article is one of a series investigating biological agency and its relationship to human agency. These articles are introduced in the article on biological explanation.  Much of the discussion revolves around the scientific appreciation and accommodation of real (genetically inherited) purposive (teleonomic) goal-directedness (agency) that is a universal feature of life. Human agency is treated as a limited, conscious and highly evolved form of biological agency. While it is currently conventional to treat biological agency as a human creation – the reading of human intention into nature – this website explores the claim that it was biological agency that gave rise to human bodies and human subjectivity.

The suite of articles on this topic include: What is life? – the crucial role of agency in determining purposes, values, and what it is to be alive; Purpose – the history of the notion of purpose (teleology) including eight modes (claimed sources of purpose) in biology ; Biological agency – an investigation of the nature of biological agency; Human-talk – the application of human terms, especially cognitive terms, to non-human organisms; Being like-minded – the way our understanding of the minded agency of human intention is grounded in evolutionary characteristics inherited from biological agency; Biological values – the grounding of biological values, including human morality, in organismal behavioral propensities (biological normativity); Evolution of biological agency – the actual evolutionary emergence of human agency out of biological agency; Plant sense and Plant intelligence addressing the rapidly developing research field of pre-cognitive agency in plants.

Introduction – Biological Cognition

A recent 2021 Theme Issue of the Royal Society Philosophical Transactions entitled, ‘Basal cognition: conceptual tools and the view from the single cell’, addressed the need for a broader understanding of what we currently understand by ‘cognition’. Specifically, ‘How organisms on the lower branches of the phylogenetic tree . . .  can aid our understanding of . . . organisms that evolved later (including Homo sapiens)’ and to recognize the ‘deep evolutionary inheritance of cognitive behavior’. A research methodology was proposed starting with the smallest and simplest organisms that display the phenomenon of interest, their principles of interaction, and the scaling up of the findings across the community of life in a comparative way. This more biologically generalized approach to cognition was designated ‘basal cognition’.

This website (plantspeopleplanet.au) regards basal cognition as a property of the more general phenomenon of biological agency. Just as human agency is a highly evolved and limited form of biological agency, so human cognition is a highly evolved and limited form of biological cognition (basal cognition).

Conventional cognition treats the brain and nervous system as processing both internal and external information to create internal representations and interpretations that generate output in the form of adaptive behaviors. If organisms are to adapt, then they too must have the capacity, no matter how crude, to both represent and interpret their conditions of existence as a property of their universal biological cognition. This includes the processing triggered by external conditions as significant elements of the organism-environment continuum. Human cognition, from this perspective, is an evolutionarily specialized form of biological cognition with functionally equivalent structures, processes, and behaviors in other organisms. However, use of human cognitive words like ‘experience’, ‘subjectivity’, ‘awareness’, ‘perception’, ‘intelligence’, ‘choice’, ‘decision’, ‘learning’, ‘memory’, etc., is the language used in the sense of functional, not direct evolutionary, equivalence.

The problem for theoretical biology is to find a descriptive language that distinguishes between uniquely human cognition and the functionally equivalent form of biological cognition that is displayed by all organisms in response to the universal evolutionary pressure to survive, reproduce, adapt, and evolve.

Biological cognition, loosely defined, refers to the internal processing through which (mostly) organisms perceive, interpret, and respond to their conditions of existence. It investigates the functional integration of this inner processing as it precedes and motivates the adaptive goal-directed behavior of biological agents (mostly organisms). In more general terms, it considers how organisms access, store, retrieve, process, prioritize, and communicate information in a meaningful way.

Cognitive biology regards strictly human cognition (perception, learning, memory, problem-solving, decision-making, linguistic and other communication, self-awareness, abstract thought, and other factors) as a highly evolved, limited, and specialized form of biological cognition. While human cognition has many uniquely defining features it shares with other organisms a suite of functionally equivalent cognitive properties which, though not a product of direct evolutionary ancestry share biologically universal commonalities of evolutionary pressure.

Such a claim is contrary to orthodox theoretical biology which treats cognition as a human phenomenon based on brains and nervous systems, and mental phenomena as uniquely different from other biological phenomena. Therefore to speak, for example, of plant intelligence is nonsense since plants have neither brains nor nervous systems.

Many of the concepts once regarded as uniquely human can now be usefully applied to all organisms as ‘an epistemic extension of the concepts and explanations we find in the cognitive sciences to biology’^[3] – put simply, biology arrived before brains.

The 18th-century development of philosophical, psychological, and cognitive ideas, especially those of Immanuel Kant (1724-1804), led to an intellectual focus on human subjectivity as the key to our understanding of both scientific inquiry and the world. This human-mind-centred introspection posed the question ‘what are the mental preconditions that make experience possible?‘. Darwin (1809 to 1882), perhaps inadvertently, countered this human self-absorption by looking outward into the operations of nature as a whole. His work engaged with the question posed by German philosopher Friedrich Schelling (1775 to 1854) as a retort to Kant’s question. He turned this question on its head by asking, ‘What is it in nature that makes subjectivity possible?‘. It was this way of thinking that foreshadowed the development of the cognitive sciences, evolutionary biology, evolutionary psychology, and today’s revolution in biological cognition.

Evolution became a serious scientific thesis in the 19th century at a time when most people believed in Special Creation – that each species was created individually by God. Humans were God’s supreme creation and they possessed souls, related to minds, and these souls could persist after death. This was a theory of separation – between unique and immutable species, between humans and other organisms, and between mind and soul. Evolution transformed this perception of life into a theory of organic continuity.

In the mid-20th century, before the cognitive revolution in the sciences, behaviorism had confined mental processes to an unknowable (because empirically inaccessible, it was argued) black box. The operations of the mind itself were best left alone. Today the cognitive properties of non-human organisms have been confined to a similar black box called cognitive metaphor, resulting in major explanatory gaps between our understanding of biological agency and human agency. This has happened because we resort to the language of human cognition when describing real biological agency.

This article is an examination of the emerging field of biological cognition.

Historical background

Biological cognition is an interdisciplinary concept that explores the cognitive processes of living organisms, emphasizing the relationship between biological systems and their cognitive capabilities. The roots of biological cognition can be traced back to early philosophical inquiries into the nature of mind and consciousness, particularly in the works of Aristotle and Descartes, who pondered the relationship between the body and the mind. However, it was not until the 20th century that biological cognition began to emerge as a distinct field of study, influenced by advances in biology, psychology, and cognitive science.

The mid-20th century saw the rise of behaviorism, a psychological paradigm that prioritized observable behavior over internal mental states. This approach, however, faced criticism for neglecting the cognitive processes underlying behavior. In the 1960s and 1970s, cognitive psychology began to gain prominence, focusing on the mental processes involved in perception, memory, and problem-solving. This shift laid the groundwork for a more integrated understanding of cognition that acknowledged the biological underpinnings of cognitive processes.

The advent of cognitive neuroscience in the late 20th century marked a significant turning point in the study of biological cognition. This interdisciplinary field combined principles from psychology, neuroscience, and biology to investigate the neural mechanisms that support cognitive functions. Researchers employed techniques such as functional magnetic resonance imaging (fMRI) and electrophysiology to explore how brain activity correlates with cognitive tasks. This era also saw the emergence of evolutionary psychology, which examined the adaptive significance of cognitive processes in the context of natural selection.

As the 21st century progressed, the notion of biological cognition expanded beyond human cognition to encompass the cognitive abilities of non-human animals and even microorganisms. This broader perspective acknowledged that cognition is not exclusive to humans but is a fundamental aspect of life itself. Researchers began to explore the cognitive capabilities of various species, revealing complex behaviors in animals such as problem-solving in corvids, social learning in primates, and even rudimentary forms of decision-making in simple organisms like slime molds.

Current research in biological cognition emphasizes the role of embodiment and situatedness in cognitive processes. The idea that cognition is deeply rooted in the physical and social environment has gained traction, leading to the development of theories such as enactivism and embodied cognition. These frameworks propose that cognitive processes are not merely located in the brain but are distributed across the organism and its environment. This perspective has profound implications for understanding how organisms interact with their surroundings and adapt to changing conditions.

Today, biological cognition is a vibrant field that continues to evolve. Researchers are increasingly interested in the implications of biological cognition for artificial intelligence and robotics, exploring how insights from biological systems can inform the development of intelligent machines. Additionally, interdisciplinary collaborations are fostering a deeper understanding of the cognitive abilities of diverse organisms, leading to new insights into the evolution of cognition and the nature of intelligence itself.

In conclusion, the notion of biological cognition has undergone significant transformation over the centuries, evolving from philosophical inquiries to a robust interdisciplinary field. As research continues to uncover the complexities of cognitive processes across various biological systems, the understanding of cognition as an integral aspect of life is becoming increasingly refined, opening new avenues for exploration in both scientific and philosophical domains (AI Sider August 2024).

Definition

Conventional understanding of cognition is restricted to its human form as activities that occur in the human brain, such as perception, learning, memory, problem-solving, decision-making, linguistic and other communication, self-awareness, abstract thought, and other factors. However, there is no consensus on what we mean by ‘cognition’ which is currently defined in many ways, extending beyond the human brain and using increasingly inclusive conditions to encompassing a progressively wider range of structures, processes, behaviors, and organisms.

Cognition as restricted to the human brain is cognition in a narrow sense while biological cognition is cognition in its broadest sense, as a property of biological agents. It is treated here as the internal processing that precedes and guides the behavior of biological agents that have the shared (universal) capacity to survive, reproduce, adapt, and evolve.

Ultimate & proximate cognition

A critical distinction may be drawn between ultimate and proximate cognition.

Ultimate cognition (biological cognition) refers to cognitive properties that are shared by all organisms – these are the general (theoretical, in-principle, or universal) conditions of cognition.

Proximate cognition refers to in-practice instances of biological cognition that are localized to actual groups or situations – say, the particular cognition that occurs in humans, primates, cephalopods, birds, spiders, plants, etc. Each proximate cognitive group is united by its unique set of shared cognitive characteristics.

Though there are many forms of proximate cognition there is only one ultimate form. Thus, establishing the ultimate characteristics of biological cognition facilitates the comparison of different kinds of proximate cognition which can be understood as functional equivalents.

Ultimate cognition (biological cognition) – as the internal processing that precedes and guides the behavior of biological agents – can be understood more generally as the way that organisms represent and interpret their conditions of existence. In more abstract general terms, it considers how organisms access, store, retrieve, process, prioritize, integrate, and communicate information in a meaningful way.

Embodied, distributed, extended, situated

Progressively more inclusive definitions of cognition have been distinguished in different ways: distributed cognition as being more systemic and interactive when it includes the body and environment;  embodied cognition as sensory-motor bodily interaction with the world; extended cognition includes external devices, conditions, and environments that aid cognitive processes such as smartphones or the collective behavior of an orchestra or termite mound.^[6,7] Enactivism regards cognition as the entire adaptive and dynamic interaction between an organism and its environment.

Situated cognition maintains that our understanding of cognitive processes is deeply embedded in the context of their occurrence. For example, in humans, it emphasizes that thinking and knowing are inherently linked to the physical and social situations in which they are experienced thus moving away from interpreting cognition as a strictly internal process, emphasizing instead the role of external and social factors in shaping how we think and learn.

The biology of function

Biology is often represented through static structures contrasted with dynamic functions. A more comprehensive perspective might extend the range of biological objects to include processes and behaviors. Biology then becomes a dynamic interplay between these biological objects and their reasons, functions, purposes, or goals (concepts that tend to relate to the complexity of the biological object).

Functions (purposes, goals) are, in an explanatory sense, prior to these biological objects. This is because essentially all biological objects are goal-directed and, to make sense, their explanation must necessarily begin with these goals or ends, with what these objects are ‘for’ (biological goals are natural ends or limits that are first in imagination and explanation, but last in causation). In this sense, functions are prior to structures and processes.

Functions evolve to meet the demands posed by selection pressures. A distinction may be made between two kinds of selection pressure. On the one hand, there are proximate or immediate functions – those responding to specific selection pressures at particular places and times – say, of wings to fly, eyes to see, fins to swim. On the other hand, there are also general biological functional needs, the universal evolutionary behavioral selection pressures to survive, reproduce, adapt, and evolve. While attaining these goals requires not only behavior, but also structures and processes, we intuitively treat behavior as most directly communicating goals and agency.

Though structures and processes are necessary and integral to life it is their integrated behavior (their functions, purposes, and goals) that are crucial and prior. This is not, however, a simple relationship because, while functional needs drive the evolution of biological objects these objects, in turn, determine future functional possibilities in a dynamic and reciprocal feedback loop of co-evolution. For example, there must have been structures in nature that made the evolution of wings possible. However, it is the advantages of flight that drive evolutionary change – consider the coevolution of wings in birds, butterflies, and bats.

The universal propensity of organisms to survive, reproduce, adapt, and evolve (biological axiom) is a powerful concept that effectively summarizes the drivers of both biological agency and evolutionary change. It establishes the universal selection pressures that determine the universal functional needs of organisms. They are therefore the defining conditions of biological agency and the natural limits or ends of the biological conditions that define life and evolution, driving the continuous development and diversification of life. They provide a comprehensive framework for understanding the mechanisms of evolution and the dynamic nature of life on Earth.

Life consists of autonomous self-sustaining and self-replicating units with metabolic systems that adapt and evolve in response to both internal and external stimuli (the conditions of existence).

Functional equivalence

The diversity of structures, processes, and behaviors we encounter in the community of life can be represented as deriving from the interplay of two complementary kinds of selection pressure, the specific and the general.  Context-specific selection pressures influence particular organisms at the local scales, timeframes, and other conditions of existence (e.g., mostly external factors like predation, competition, and environmental change). General (in-principle or ultimate) selection pressures apply universally in biological systems (e.g., the capacity to survive, reproduce, adapt, and evolve). Specific selection pressures are not merely instances of general selection pressures (a reductionist view), they operate synergistically in an interplay of evolutionary dynamics that links the local and immediate into a broader evolutionary framework without implying any hierarchical order.

These selection pressures shape the evolution of life, influencing the traits that become prevalent in populations. Natural selection is a process driven by the interaction between organisms and their environments, where the behavioral responses of organisms to internal and external factors play a crucial role in shaping evolutionary outcomes. This interpretation of the organism-environment continuum avoids internalist and externalist extremes of view.

Understanding these selection pressures helps explain patterns of biodiversity and the convergent pathways followed by different organisms when faced with similar internal and external challenges.

Just as, in the 1950s, the human cognitive revolution launched an investigation into the internal driving processes of the human brain, the 2020s have launched a corresponding revolution in biological cognition investigating the internal processes driving organism behavior. This transition has been facilitated by recognizing how human cognition encompasses both mental phenomena and bodily processes. Acknowledging the interconnection of mind and body provides a more inclusive understanding of how we think, learn, and interact with the world.

Bird wings and butterfly wings, though they evolved in different ways, did so because of the advantages afforded by flight. Though, in evolutionary terms, these wings are unrelated, in functional terms they are equivalent – they serve the same functional role.

The principles of convergence, while usually applied to physical structures, are equally relevant to mental phenomena. The biologically universal selection pressure to survive, reproduce, adapt, and evolve was resolved by different organisms in different ways.

Biologization

While recognizing the uniqueness of human subjective experience we can understand cognition in a broader biological sense by, as it were, reducing or converting mental states into their biological functional equivalents – by biologizing psychology.

Biologizing human cognitive properties involves understanding human cognitive abilities through the lens of biological processes and principles by emphasizing physiological and anatomical aspects of cognition, such as neural mechanisms, brain structures, and genetic influences. This helps explain the shared biological mechanisms underlying evolutionary continuity and the adaptations providing similar cognitive functions. However, it may be perceived as ignoring, downplaying, or reducing the unique properties of human cognition.

Psychologizing biological cognitive properties applies human psychological concepts to understand the analogous cognitive abilities displayed by non-human organisms.  This provides insights into the behavioral and ecological contexts in which cognition evolves.

Investigating functional similarities shows how different species respond to similar selection pressures. However, treating the cognitive behaviors of other species as analogous to human psychological processes is often treated as an unscientific cognitive metaphor since it attributes uniquely human faculties to non-human organisms.
Approaches may be combined, using biologizing to explore shared biological foundations and psychologizing to highlight the functional and ecological diversity of cognition across species.

There is no universally accepted definition of human cognition which is interpreted in general terms as the mental processes involved in acquiring knowledge and understanding through thought, experience, and the senses. This encompasses a wide range of processes, including perception, attention, memory, reasoning, problem-solving, and decision-making – the integration of sensory information, and use of prior knowledge to navigate and interpret the environment (hindsight and foresight). Also, abstract thought, processing complex ideas, learning from experience, and adapting to new information.

Human cognition evolved out of the same universal biological selection pressures faced by all organisms (survival, reproduction, adaptation, evolution). It is therefore unsurprising that many uniquely human mental faculties have shared and functionally equivalent roles. All organisms, to fulfill universal selection pressures, must be effective biological agents interacting with both their internal and external conditions of existence. This includes the functional equivalents of sensory perception, memory, learning, reason, decision-making, knowledge, value, etc.  . . .  expressed in more abstract terms as the access, storage, retrieval, processing, prioritization, and communication of information. It is the functional integration of these factors that constitutes what we understand as biological cognition of which human cognition is just one limited, specialized, and highly evolved form.  

This mode of cognition does not occur in inanimate matter. While the physical structures of human cognition (e.g. brains and nerves) did not evolve out of the physical structures of biological cognition (e.g., chemical sensing systems in plants or amoeba), they share the important evolutionary property of functional equivalence.

The concept

Biological cognition is a concept that abstracts and generalizes the concepts of human cognition to all organisms by biologizing human psychology. It refers to how living organisms perceive, process, and respond to information about their internal and external environments. It considers the biological manifestation of sensory perception, memory, learning, reason, decision-making, knowledge, value, and other factors that influence the behavior of all organisms through their objective and ultimate propensity to survive, reproduce, adapt, and evolve. These universal purposive goals are manifest through the full range of biological structures found in the community of life. They are a critical part of the functional integration of all biological agents.

Biological cognition is multidisciplinary, combining principles from general biology, neuroscience, psychology, evolutionary biology, ethology, information science, ecology, biosemiotics, developmental biology, etc. in an attempt to understand the internal processes of organisms that guide behavior.

Continuity

Cognition, like consciousness, is most usefully explained as a property that is manifest by degree rather than presence or absence.

The article on biological agency discussed the universal and objective goal-directed (purposive) propensity of all organisms to survive, reproduce, adapt, and evolve.  These biological functions, principles, or purposes are shared by all organisms but expressed physically in the evolutionarily graded structural continuity of the community of life. This agency requires scientific explanation. All these goals involve complex information processing of a kind found in all living organisms but, for historical reasons, they have been described using the terminology associated strictly with human cognition and brains. These real phenomena, described in terms usually restricted to human mental phenomena, have been regarded as cognitive metaphor and therefore ignored.

Biological science is now investigating and clarifying how cognition can be a universal biological phenomenon. But how can this make sense?

This is described in detail elsewhere by pointing out that in evolution the same property can express both similarity and difference – the difference that makes it a uniquely defining feature and the similarity that demonstrates an evolutionary relationship. The fins of whales, wings of bats, and legs of deer are different structures that share the same evolutionary ground plan, the pentadactyl limb.

Plants do not have brains, but they share many of the properties we associate with cognition. This is, at first, a hard pill to swallow. How can mental phenomena like reason, memory, knowledge, learning, values, and perception possibly have relevance to unicellular organisms: isn’t that either nonsense or playing silly semantic games?

But don’t we need, for example, to clearly distinguish between the sentient and non-sentient? Certainly we need to distinguished the mental from the cognitive and animal cognition from non-animal cognition. Define cognitive categories broadly and their meaning is lost. The concept of agency plays a central role in the developmental turn, and that agency is the converging concept of many conceptualizations of the nature of developmental processes and organismal activities.

The clearest approach to evolutionary theory based on the concept of agency in organisms has been recently developed under the term agential perspective by Sultan et al. (2022; see Moczek and Sultan (2023) for a special issue on Agency in Living Systems).

In the mid-20th century, before the cognitive revolution, behaviorism had confined mental processes to an unknowable black box. Today the cognitive properties of non-human organisms have been confined to a similar black box, resulting in explanatory gaps between our understanding of biological cognition and human cognition, and between the explanatory model of the cognitive sciences and that of biological agency and its information processes.

Biological cognition is the functional integration of a range of pre-cognitive agential traits that are present in all living organisms (supplemented in humans with cognitive traits) and therefore expressed across the community of life in degrees of organic complexity. Pre-cognitive traits were the likely evolutionary antecedents or precursors to human cognition which is a highly specialized evolutionary development.

The belief that cognition requires a nervous system remains the default view embedded in our language, so it will not do to say, without qualification, that, ‘all creatures express cognition’, ‘plants are intelligent’, ‘bacteria can learn’, or  ‘mosses have memories’ . That is because this kind of language is almost exclusively applied in circumstances that relate to human cognition which opens such language, with good reason, to the charge of being cognitive metaphor (not related to real factors in the world).

This website claims that human cognition is one aspect of universal, ultimate, and objective biological agency as the propensity (behavioral orientation) of all organisms to survive, reproduce, and flourish. Human cognition is an agential trait that evolved out of non-cognitive agential biological antecedent conditions. However, there are real traits in non-human organisms that, due to common ancestry, closely resemble these human cognitive traits. So, for example, cognitive concepts such as ‘sensing’, ‘memory’, ‘learning’, ‘communication’, and ‘decision making’ can be applied non-metaphorically to the behaviour of bacteria.

This leads to a potentially confusing taxonomy that, once mastered, becomes straightforward:

All organisms share the universal traits of biological agency. Human cognitive agency is a highly evolved and limited case (subset) of biological agency. We therefore need a term to conveniently and succinctly distinguish between those biological agents that have cognitive faculties and those that do not. Since human cognition evolved out of these pre-cognitive agential traits, the word chosen to represent them is pre-cognition.

It is also claimed that there are some agential expressions, like ‘biological agency’, that represent real and universal biological conditions: they are not metaphors or heuristics. However, their acceptance is contrary to semantic convention. Biology cannot change the common usage of words but it can provide empirical support for technical redefinition.

In short, there are empirically-based connections between human cognitive expressions (like agency, intelligence, learning, and memory) and real pre-cognitive states that do not occur in the inanimate world. Having no accepted technical terminology for these pre-cognitive states, we refer to them using the cognitive metaphor of human cognition.

So, what is biological cognition and how is it related to human cognition and other biological pre-cognitive traits?

Evolution of cognition

By historical tradition, we have explained the world in strictly human terms using anthropomorphism, personification, and cognitive metaphor. This is an anthropocentric (top-down) mode of explanation whereby the biological world is explained/understood/created/derived from a human perspective.

We must, however, remind ourselves that our mental faculties do not create nature, nature created our mental faculties: our mental world has biological origins.

More simply, we have cognitive properties that, on the one hand, uniquely define human cognition and, on the other, demonstrate our relationship to other organisms by common ancestry.

There are several critical consequences of this claim.

1. 1. The shared characteristics are grounded in evolution and are therefore evolutionary precursors to later developments.
   2. They are real – they are not figurative, metaphorical, or of merely heuristic value.
   3. Some of these shared characteristics are non-cognitive agential characteristics that distinguish the animate from the inanimate.
   4. Real and shared characteristics as precursors to cognitive characteristics can be described scientifically as pre-cognitive traits (so biological cognition includes both cognitive and pre-cognitive traits) – though, in the absence of technical terms, these are currently described using the language of human intentional psychology.
   5. Though there is a strong case for much greater scientific emphasis on pre-cognitive traits this will initially be resisted with the persistence of cognitive metaphor.
   6. Science cannot change the meaning of words in common usage, but it can adjust the meaning of technical terms to better reflect the world

The suggestion of an evolutionary connection between human cognitive traits and pre-cognitive general biological traits might seem both tenuous and contentious.

The task remains to assemble and extend the current body of empirical evidence. For example, it has recently been found that potassium ion channels in the Shaker family existed in microscopic single-celled organisms long before the emergence of the common ancestor to all animals – suggesting that many of the building blocks for the nervous system were present in our protozoan ancestors.^[4]

Theoretical evidence for the biological generalization of cognitive concepts is strong (see articles on this website on biological agency, biological purpose, and biological value).

Human cognition includes the capacity to perceive, feel, or experience subjective sensations and emotions; to know, think, and respond to conditions of existence based on sensory input and internal processing; the use of sensory perception, learning, memory, problem-solving and decision-making (as ways of assessing impediments to goals and determining courses of action).

While subjectivity, as some form of conscious awareness, is crucial to our understanding of sentience, there are sentience-like functional equivalents shared by non-cognitive and non-neural organisms. These properties, we must assume, reflect generalized (ancestral) evolutionary precursor conditions to animal sentience. These properties, referred to here as biological cognition, include the capacity to respond to their environments in a way that reflects an internal awareness, reality, or umwelt. While organisms do not ‘experience’ the world in a subjective human-like way they can access and interpret environmental cues in ways that encompass a diverse array of information processing and ‘decision-making’ that facilitates their survival, reproduction, and adaptation. This is a real, not metaphorical, element of every organism’s existence and science needs a simple way of referring to it. It involves It also encompasses a broad spectrum of behaviors, from simple reflexes and instinctual responses to complex learning, memory, and problem-solving abilities, all of which contribute to the organism’s ability to interact with and adapt to its surroundings.

Explanations of human cognition struggle to make sense without reference to their more general relationship to bodily functions. This extension of the notion of cognition beyond the human brain into the human body links cognition to the bodies of other organisms.

The universal or in-principle biological functional equivalent of human cognition has been described as basal cognition with a working definition ‘the cognitive abilities present in simple organisms, such as prokaryotes and single-celled eukaryotes’. These researchers then provide ‘a behavior-generating toolkit of capacities that comprise the function (e.g. sensing/perception, memory, valence, learning, decision making, communication’ that may be investigated to include a ‘suite of common biophysical mechanisms found throughout the domains of life . . .’.^[2]

Cognition & agency

Biological cognition is a critical component of biological agency because, like human cognitive agency, it creates functionally integrated and meaningful ‘experiences’. It combines information processing as the capacity of organisms, especially animals, to perceive, process, store, and use information as part of their process of adaptation to their conditions of existence. This involves cognitive capacities that include sensory perception, learning, memory, decision-making, problem-solving, and social behavior, all of which are influenced by biological mechanisms with varying degrees of physical complexity (e.g. neural and hormonal systems).

While there are many non-cognitive agential biological processes active in animals, biological cognition often involves the study of how the brain and nervous system process sensory information, encode memories, and generates behavioral responses. Researchers investigate the underlying neural circuits, neurotransmitter systems, signalling networks, and genetic factors that contribute to cognitive functions as represented in different biological systems.

Interdisciplinary investigation along these lines helps researchers gain insights into fundamental questions about the nature of cognition and its evolutionary origins.

Matter, Energy, & Information

It is conventional for science to understand and explain biology in terms of its material constituents and structures. The organization of life into ‘hierarchical levels of organization’, each loosely corresponding to a biological sub-discipline, is our historical legacy from this mode of thinking.

But biological knowledge has accumulated at both the micro- and macro-scales and research is exploring new ideas. Our traditional taxonomy of living matter (metaphysics of biological objects) was based on three key categories: material scale, degree of complexity, and inclusivity. All three of these categories are evident in the academic metaphor of life existing in ‘hierarchical levels of organization’. But there are other ways of categorizing biological objects that also correspond loosely to the way biological subdisciplines are organized. So, for example, another classification of biological objects might consist of structures (including organisms), processes, and behaviors. Such a move has probably been resisted because, apart from other reasons, it moves away from the secure world of solid ‘things’ into a biological world of increasing abstraction.

This biological world of increasing abstraction is now attracting more research as investigation focuses more on biological purpose, agency, and process. In trying to come to terms with life and evolution the gene is no longer regarded as ‘pulling the strings’ in the way it was 50 years ago. We are coming to terms with life as more a ‘process’ than a ‘thing’. These are just a few aspects of a gathering paradigm shift in biological thinking that has become loosely designated as the Extended Evolutionary Synthesis.

Regardless of our personal opinions on biological metaphysics, research is moving strongly in this direction. Biological research has, in a general sense, moved from a 19th-century evolutionary study of the biological diversity found in the vast tree of life as portrayed in zoos and botanical gardens (descriptive and taxonomic inventory), to 20th-century genomics, DNA and the genetic code, and its spinoffs in biotechnology (microbiology). In the 21st century research is focused on the human brain and consciousness as a last biological frontier, but microbiology is taking on a different face as broader, more encompassing general concepts take center stage as the study of life is redefined in 21st-century terms.

Life, as a process, is a flow of matter, energy, and information.

Life, as agency, is a process of adaptation that entails information processing, a behavioral orientation, and a compromise between the behavioral propensities of the organism and the constraints of its conditions of existence.

Human cognition involves the functional integration of human cognitive faculties. Biological cognition involves the functional integration of all of an organism’s agential faculties.

Biosemiotics

The notion that cognition can be understood as dispersed through the living world has a history that is generally subsumed under the title cognitive biology.

Biosemiotics^[5] is an, at present, esoteric interdisciplinary subject that studies the production, interpretation, and communication of signs and meanings in living systems. This takes on a practical role as a framework for understanding the fundamental role of communication, information, and meaning in the organization and behavior of living systems. Perhaps unexpectedly this is a form of study that bridges the gap between the natural sciences and humanities.

Biosemiotics regards biological information (the meaningful signals and signs that facilitate communication and interpretation within living systems) is different from the information of telecommunications and information theory (computers and cybernetics). Biological information transfer is not like water flowing along a pipe, it requires interpretation (it must be ‘understood’) by a biological agent, and it can therefore be misunderstood. It is not a material phenomenon, it is also an interactive relational one in which the information takes priority. Semiotic function in biology is a relationship and not present in the individual components of the relationship.

It is from biosemiotics that we see an acknowledgement of the evolutionary familial resemblance of mind-like properties across the living world. This is a recognition that: ‘ . . . there is a continuum of semiotic agents across biology, extending from the first individually competent cells to their colonial aggregations and then further becoming functioning tissue ecologies, multicellular eukaryotic organisms, and holobionic species. This same agency propels collective human thought and our organizations, including nations or political movements’, and that, ‘life and sentience are coterminous. All living organisms, all biological entities, feel, learn, remember, choose, react, and communicate’.

Sentience

This website explores the possibility that there are cognitive concepts that have, by tradition, been applied strictly within the human domain but which make more scientific sense when applied more generally in biology.

Historically we have tended to explain the world in anthropomorphic (human) terms using anthropomorphism, personification, and, especially, cognitive metaphor. The world of biology is, in effect, explained/created/derived from human-like examples and ideas.

We empathize with and connect to the world by showing how it is like us. But this is an explanatory inversion because the world did not arise or evolve out of us or our ideas, we evolved out of it. Rather than using the language of human cognition to describe the biological world, we would do better to understand how human cognition is a specialized form of biological cognition.

We have failed to acknowledge that our uniquely defining human cognitive properties also share characteristics with the rest of the living world. These are concepts that can express both similarity and difference – the uniquely defining characteristics of difference and the shared characteristics that indicate common functional ancestry.

There are several critical consequences of this claim.

The evolutionary connection between human cognitive traits and, say, plant cognitive traits does not lie in structural evolutionary connection, but in functional lineage for which there is abundant empirical evidence.

Sentience is typically associated with the capacity for subjective experiences like sensations, feelings, and consciousness as they occur in organisms with complex nervous systems, such as mammals and birds. Sentience, as a biologically universal functional adaptation, is an awareness of the conditions of existence as constrained by biological possibilities. In the case of organisms, this amounts to the organism’s, or species, umwelt. Just as with agency, purpose, and cognition, sentience may be evident in organism parts but is paradigmatically exemplified in the unity of purpose of individual organisms. This kind of awareness is not found in inanimate matter.

Biologically universal traits of sentience include: basic sensory perception; response to various kinds of stimuli as dynamic interaction with the external and internal worlds as ultimately mediated by internal processing, and conditions that help or hinder their universal biological goals; self-maintenance and functional integration. The evolution of nervous systems and cognitive abilities can be understood as a progressive refinement of functional capacity.

Though the subjective experiences of non-cognitive organisms differ significantly from those of conscious cognitive beings like humans they are connected through functional equivalence. In this way the language of sentience can refer to universal biological properties of which human sentience is just one manifestation.

Among the universal biological physical processes often used to circumscribe life (metabolism, homeostasis, reproduction, growth and development, inheritance) should be included the physical manifestations of universal functional phenomena such as cognition.

This website has emphasized universal biological agency, biological purpose, biological intentionality (goal-directedness), and biological value, but it is becoming evident that the full range of features that uniquely identify human cognition also share grounding traits with all other organisms.

The significance of cognition is that it is generally interpreted as the process that integrates awareness into meaningful experience.

The unified functional integration of information that occurs in all living organisms is a manifestation of biological agency as a process that distinguishes the living from the inanimate and dead.

Biological cognition

Insights into the way information is managed in biological systems can be gained by investigating the operation of its best-known human manifestation – cognition.

A distinction is drawn on this website between two forms of biological cognition: the highly evolved and limited form of biological cognition we associate primarily with humans, nervous systems, and brains, and the pre-cognitive form of cognition we associate with non-cognitive organisms.

Since all life is physically connected through evolution, it may be presumed that human cognition, though having uniquely human characteristics, shares ancestral, or grounding characteristics with biology’s universal information processing systems. These universal non-cognitive traits are easy to find.

Cognition comprises the sensory and other information-processing mechanisms an organism has for becoming familiar with, valuing, and interacting productively with features of its environment [exploring, exploiting, evading] in order to meet existential needs, the most basic of which are survival/persistence, growth/thriving, and reproduction”.(Lyon, 2020, p. 416). Lyon et al. (2021) also offered a companion definition of information: “A state ofaffairs is information for an organism if it triggers a change in physiology or behavior relative to thatstate of affairs. Whatever state of affairs induces a change in physiology or interactive potential in anorganism is information for that organism.

Biological cognition

Biological agency – as a biological agent pursuing goals by specific means – has been summarized on this website in practical biological terms as the capacity of an organism to survive and reproduce by a process of adaptation.

While adaptation is a useful general term it has many meanings in biology. The general process of functional integration used by all  biological agents to pursue their goals is more precisely referred to here as biological cognition which has three key characteristics.

• • • information processing (acquisition, storage, retrieval, and communication)
    • a behavioral orientation (the goal-directedness of behavior that gives life a direction, perspective, or point of view)
    • internal problem-solving (the reconciliation that must occur between the natural propensities of the organism and the constraints of its conditions of existence as a prelude to agential activity).

These three pillars of biological cognition can be recognized in the human cognitive domains of knowledge, values, and reason.

Information processing

The critical elements of information processing include storage, processing, communication, and retrieval.

Biological cognition – as the means whereby organisms adapt – involves the sensory and other information-processing mechanisms required to meet the requirements of all organisms as biological agents to survive and reproduce. As an informational process of functional integration (communication), it establishes the necessary internal ‘compromise’ between the natural propensities of the organism and the constraints of its conditions of existence that must occur as a prelude to activity (agential behavior).

Communication

For each organism to survive and reproduce as an autonomous biological agent, all its parts must unite in a system of communication which, if it is to be meaningful, must share a common language. That is, the instructions that are necessary to attain goals must make collective sense – such that the organism as a whole can adapt to diverse extraneous challenges while maintaining health and homeostasis.

It is assumed that the common language of communication used by organisms to direct all parts towards common goals is biochemical signaling which involves the transmission of chemical signals, such as hormones, neurotransmitters, and other signaling molecules, within and between cells. This signaling coordinates physiological processes and responses to environmental stimuli. So, for instance, hormones released by endocrine glands can travel through the bloodstream to target cells located throughout the body eliciting responses by binding to receptors on cell surfaces or within cells.

This universal language of communication enables organisms to regulate processes such as growth, development, metabolism, reproduction, and responses to stress or injury. It allows for the integration of diverse cellular activities and ensures that the organism functions as a coordinated whole, even though it may consist of many different cell types with specialized functions.

Humans
Since humans are the organizational scale that we understand best, perhaps we can gain insights into more general biological cognition by starting here.

In humans, numerous signaling systems achieve this marvel of regulation and integration by working together to sustain homeostasis while supporting the entire organism in its goals of survival and reproduction. This coordinated network of signaling pathways ensures the efficient regulation and integration of the physiological processes that enable the body to function as a unified and autonomous agential unit.

Nervous System: The nervous system coordinates rapid responses to environmental stimuli and internal changes. It consists of neurons that transmit electrical impulses and release neurotransmitters to communicate with other neurons, muscles, and glands. Through sensory input, processing, and motor output, the nervous system regulates various physiological processes such as movement, sensation, cognition, and behavior.

Endocrine System: The endocrine system produces hormones that act as chemical messengers to regulate metabolism, growth and development, reproduction, and responses to stress. Hormones are released into the bloodstream by endocrine glands such as the pituitary, thyroid, adrenal glands, pancreas, and gonads. They exert their effects on target cells or tissues throughout the body, coordinating long-term physiological processes and maintaining homeostasis.

Autocrine Signaling: Autocrine signaling involves cells releasing signaling molecules that act on receptors located on the same cell or nearby cells of the same type. This self-regulatory mechanism allows cells to modulate their own activities and coordinate responses within local tissue microenvironments.

Paracrine Signaling: Paracrine signaling involves cells releasing signaling molecules that act on nearby target cells, influencing their behavior and functions. Paracrine signaling allows for local communication and coordination of cellular activities within specific tissues or organ systems.
Neuroendocrine Signaling: Neuroendocrine signaling refers to the interaction between the nervous and endocrine systems, where neurons release neurotransmitters that act as hormones upon reaching target cells or tissues. This integration allows for the rapid transmission of signals across long distances and the coordination of complex physiological responses.

Cell-Cell Communication: Various cell-cell communication mechanisms, such as gap junctions, tight junctions, and extracellular signaling molecules (e.g., growth factors, cytokines, and chemokines), facilitate direct or indirect interactions between neighboring cells. These interactions enable cells to synchronize their activities, coordinate responses to external stimuli, and maintain tissue integrity and function.

Feedback Mechanisms: Feedback mechanisms, including negative feedback loops, feedforward regulation, and homeostatic control systems, play essential roles in maintaining physiological balance and regulating cellular activities. These mechanisms allow the body to sense and respond to changes in internal and external environments, adjusting its functions to maintain stability and optimize performance.

Storage

Ideally, stored Information can be accessed for both short- and long-term reasons. The mode of storage will depend on the biological systems available so, for example, humans store cognitive information within their nervous systems as knowledge, although there is a vast grounding foundation of biological configuration that is a consequence of evolutionary history – which is also a form of information storage.

Systems of information storage include:

Neural Networks: where animals with complex nervous systems, such as mammals and humans store information in the form of neural connections within the brain. Neurons communicate with each other through synaptic connections, and patterns of neural activity are assumed to encode information, forming memories.

Synaptic Plasticity: is the ability of synaptic connections between neurons to strengthen or weaken over time in response to activity. Long-term potentiation (LTP) and long-term depression (LTD) are mechanisms through which synaptic strength is modified, allowing for the encoding and storage of information.

Gene Expression: information can also be stored through changes in gene expression. This is relevant to long-term memory storage in simple organisms like invertebrates, where alterations in gene expression patterns play a role in memory formation and retention.

Epigenetic Changes: Epigenetic modifications, such as DNA methylation and histone modifications, can influence gene expression and contribute to long-term changes in neural circuitry. These changes can affect learning and memory processes, providing another mechanism for information storage.

Behavioral Adaptations: information can also be stored in the form of learned behaviors. Through trial and error, observation, and reinforcement, animals acquire knowledge about their environment and modify their behavior accordingly. This learned information can be retained and used to guide future actions.

How is information stored in organisms unlike ourselves?

Plants lack nervous systems but still store and respond to information. They do this by:

Epigenetic Regulation: storing information through epigenetic mechanisms, such as DNA methylation and histone modifications. These modifications can influence gene expression patterns, allowing plants to remember past environmental conditions and adjust their responses accordingly.

Chemical Signaling: chemical signals, such as hormones and secondary metabolites, transmit information within and between cells. For example, the plant hormone auxin plays a crucial role in various developmental processes and responses to environmental stimuli, including growth, tropisms, and organogenesis.

Electrophysiological Signals: though plants lack neurons, they generate electrical signals in response to various stimuli. These signals (action potentials) propagate through plant tissues and coordinate responses to environmental cues, such as touch or injury.

Memory and Adaptation: forms of memory and adaptation to environmental stimuli result from past exposure to stressors, such as drought or herbivory, and initiate defense mechanisms for future encounters. This memory is often associated with changes in gene expression patterns and epigenetic modifications.

Intercellular Communication: plant cells communicate using various mechanisms such as plasmodesmata (channels connecting adjacent cells) and extracellular signaling molecules. Thus plants to integrate information from different parts of the organism and coordinate responses to environmental changes.

While plants lack a centralized nervous system like animals, they possess sophisticated mechanisms for sensing and adapting to their environment in ways that optimize their growth and survival.

Overall, information storage in organisms is a complex process involving interactions between neural, genetic, and behavioral mechanisms, allowing for adaptation to changing environments and experiences.

Processing

Organisms process information primarily through the mechanisms of sensory perception, neural processing, and ‘decision-making’ which are more elaborate and complex in animals.

Sensory Input: information about the environment is obtained through sensory organs such as eyes, ears, nose, skin, and taste buds which detect various stimuli, including light, sound, chemicals, temperature, and touch.

Sensory Processing: sensory information is transmitted to the nervous system where it is processed by specialized neural circuits. Different regions of the brain are responsible for processing specific types of sensory information.

Integration and Perception: processed sensory information is integrated and interpreted by the brain, leading to perception. Perception involves the brain’s ability to organize and make sense of sensory input, allowing organisms to recognize objects, events, and patterns in their environment.

Memory Formation: information that is perceived and processed can be stored in memory. Memory formation involves changes in neural circuits and synaptic connections, leading to the encoding, consolidation, and retrieval of information. Memory enables organisms to learn from past experiences and adapt their behavior accordingly.

Decision-Making: based on processed information and stored memories, organisms make ‘decisions’ and generate appropriate behavior. Decision-making involves complex cognitive processes, including weighing options, assessing risks and rewards, and selecting the most favorable course of action.

Feedback and Adaptation: there is continuous feedback from the circumstances of existence leading to adjustments in behavior. This feedback loop allows organisms to adapt to changing circumstances, optimize their responses, and enhance their chances of survival and reproduction.

It is helpful to consider how organisms without brains can process information.

Plants process information by sensing environmental cues, integrating signals, and modulating their growth and development accordingly. While plants lack nervous systems they possess sophisticated signaling networks and mechanisms to perceive and respond to their surroundings.

Sensory Perception: detecting environmental stimuli through specialized sensory structures and receptors. Stimuli include light, gravity, temperature, water availability, touch, and various chemicals (such as nutrients, toxins, and signaling molecules from other organisms).

Signal Transduction: signal transduction pathways transmit information from the site of perception to other parts of the plant which involves biochemical reactions that may result in changes in gene expression, ion fluxes, and the production of signaling molecules.

Hormonal Regulation: hormones, such as auxins, cytokinins, gibberellins, abscisic acid, and ethylene regulate growth, development, and responses to environmental stimuli, they act as chemical messengers, coordinating various processes such as seed germination, root and shoot growth, flowering, fruit ripening, and stress responses.

Calcium Signaling: calcium ions (Ca2+) play a crucial role as secondary messengers in plant signaling. Changes in intracellular calcium levels are triggered by various stimuli and regulate cellular processes such as gene expression, ion transport, and enzyme activity.

Epigenetic Regulation: information is stored and transmitted through epigenetic mechanism like DNA methylation and histone modifications. These epigenetic changes can influence gene expression patterns and modulate responses to environmental cues across generations.

Integration and Response: information from multiple environmental cues and hormonal signals may be integrated to adjust their growth, development, and physiological responses. This optimizes resource allocation, maximizes reproductive success, and enhances their resilience to changing environmental conditions.

Though plants lack nervous systems, they possess intricate signaling networks and mechanisms that enable them to perceive and respond to their environment in ways that promote survival, growth, and reproduction.

Human cognition

While human cognition is related to perception, learning, memory, and decision-making, this is readily generalized to the acquisition, processing, storage, and action generated by the processing of information gleaned from the organism’s conditions of existence.

Level of operation

As with biological agency, biological purpose, biological intentionality, and evolutionary selection, the question arises as to whether there is a privileged ‘level of organization’ at which information processing is focused.
So, for example, some researchers treat the cell as the foundational unit of biological cognition governs the flow of biological information so the new dogma ‘must be a cell theory, not a genetic one’.^[102] that must yield ‘must yield to a modern narrative of the reciprocal flow of information across all biological levels and the absence of privileged levels of causation’ and ‘Accordingly, this renewed Central Dogma focuses on the specifics of the intracellular reception of information, its internal self-referential measured assessment, multilevel reciprocal communication, and patterns of coordinated multicellular deployment to effect collaborative solutions to cellular problems.’ ‘When placed in this framework, biology must be recast in terms of the cognitive assessment of environmental cues as information, and all that follows is the productive processing and management of that information to sustain the instantiated cognitive faculties that define the living system.[1]

Cellular Basis of Consciousness (CBC). In CBC, all aspects of the cell coordinate to support sentience, and all of its internal architecture, including genes, are its tools. CBC asserts that all living creatures are conscious, including plants.[1]

This website recognizes that, due to common ancestry, humans share many physical traits with other organisms. just as there are shared physical characteristics the primacy of the organism in biological systems.

Glossary of bio-cognitive terms

The following glossary draws attention to the grounding of human cognitive agency in the functionally equivalent and biologically universal (shared) characteristics of biological cognitive agency. These shared functional traits reflect an internal awareness, reality, or umwelt.

While organisms do not ‘experience’ the world in a subjective human-like way they can access and interpret environmental cues that encompass a diverse array of information processing and ‘decision-making’ that facilitates their survival, reproduction, and adaptation. This is a real, not metaphorical, element of every organism’s existence and science needs a simple way of referring to it. a consequence of common evolutionary ancestry, they do not (meaningfully) occur in inanimate objects. The physical expression of characteristics frequently demonstrates evolutionary gradation.

These mind-like traits are widely interpreted as cognitive metaphors. But, rather than being creations of the human mind, they are the real non-cognitive evolutionary antecedents to human cognitive traits.

Each entry below begins with our anthropocentric cognitive understanding of the concept and is followed, in italics, by its grounding or ancestral properties as they exist in biological agency.

Adaptation – for some reason we accept that plants can ‘adapt’ both short-term by responding to their conditions of existence, and long-term by genetic alteration. For example, in the short-term, they respond to light direction and intensity in a way that maximizes sunlight absorption. This is driven by a genetic program and not conscious understanding. These strategies could be thought of as a type of accumulated knowledge that has been encoded in their genetic makeup.
The adjustment of organisms to their conditions of existence by using information processing, a behavioral orientation, and functional integration

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

Behavior – the range of actions and reactions of an individual or organism in response to internal or external stimuli.
The external manifestation of the internal processing of biological cognition.

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 human mental processes and activities related to acquiring, processing, storing, and using of knowledge.
The acquisition, processing, storage, and use of information by a biological agent as it adapts to its conditions of existence

Consciousness – 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.
The capacity of a biological agent to orientate itself in relation to space, time, & its conditions of existence

Communication – The exchange of knowledge between humans by both verbal and non-verbal means.
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.

Experience – 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.
The event(s) that influence the umwelt of a biological agent and the way these are processed as information.

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

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

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

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

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

Learning – The ability for personal growth and development through the processes of acquiring knowledge and skills. 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.

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

Perception – 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.
The processing of the full range of experiential information (the umwelt) of a biological agent.

Purpose – the reason (end, aim, or goal) why something exists or is done, made, used etc.; (human) the object of conscious intention.
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).

Reason (problem-solving) – 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.
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.

Sentience – the capacity for subjective experiences like sensations, feelings, and consciousness as they occur in organisms with complex nervous systems, such as mammals and birds.
The capacity of awareness as responding to conditions of existence, as in the umwelt of each organism

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.

Subjectivity – relating to the properties and conditions of human cognition including reflective self-awareness, language, and capacity for abstract thought as conditions of human cognition.
Relating to the properties and conditions of biological cognition

Value – 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.
A behavioral propensity or disposition (towards).

Glossary - Biological Agency

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 a structure, process, or behavior (a 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) - the outward expression of the internal processes of biological cognition; 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 cognition - the accession, storage, interpretation, and processing of information necessary for biological agents to adapt to their conditions of existence. In its highly evolved sentient form, this entails the mental processes of perceiving, interpreting, and responding to stimuli that encompasses learning, memory, problem-solving, and decision-making, all grounded in the brain's structure and function as shaped by evolution cf. basal cognition, cognition
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 principle - an underlying regularity of a biological system e.g. evolutionary principles (like natural selection), agential principles (survival, reproduction, adaptation, evolution), biochemical laws (like the laws of thermodynamics), or ecological principles (like the cycles of matter and energy flow). By understanding these principles, scientists can make predictions about biological outcomes and develop theoretical frameworks that explain how and why organisms behave and evolve in particular ways.
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
Biosemiotics - the study of the production, interpretation, and communication of signs and meanings in living systems
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
Cognition - the internal processing that precedes and guides the behavior of biological agents; the goal-directed and adaptive process of acquiring and interpreting information about the conditions of biological existence;  the acquiring, processing, storing, organizing, prioritizing, and communication of information. In its highly evolved and limited human form, it involves perception, memory, reasoning, and problem-solving, allowing individuals to understand their environment, make decisions, and establish knowledge through experiences and interactions with the world cf. basal cognition, biological cognition
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. Typically, this is the role that the structures, processes, or behaviors of an organism play in the functional organization of the organism as a whole. It helps to regard these 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
Proximate explanation - an explanation dealing with immediate circumstances
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. Thus purpose, in a broad sense, is what a structure, process, or behavior is ‘for’ – its function, reason, or intention – its adaptive goal. In a narrow human sense, a purpose is the object of conscious intention. A distinction of convenience may be made between the functions of parts (the role of a part within a whole), and purpose (the 'function' of the whole organism - as biology’s canonical agent
Relata – the objects being compared
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, often evolutionary, explanation (e.g. in biology the purpose or measure of fitness of a particular trait)
Umwelt - an agent-centric orientation to the world; the environment of adaptive significance for a particular organism - its unique perspective or 'point of view': those factors important for its survival, reproduction, adaptation, and evolution: 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