Biological agency – test

Carter – test no action required.

 The stingray is a biological agent. As an individual organism it is a physically bounded and functionally integrated unit of life with an autonomous agency. The structures, processes, and behaviors of the stingray are unified in their support of the flexible, adaptive, and goal-directed behavior of the organism as a whole as it acts on, and responds to, its conditions of existence. 

Goal-directed behavior in biology is agential and purposive behavior – it is behavior that has natural limits or ends. These ends are causally transparent and without mystery; they do not necessarily imply supernatural influence, conscious intention, or backward causation.

Stingray behavior expresses many proximate goals but these are subordinate to the universal, objective, and ultimate goals of all organisms – the propensity to survive, reproduce, adapt, and evolve – as necessary conditions for biological agency. They are universal because they are expressed by all organisms; objective because they are a mind-independent empirical fact; and ultimate because they are a summation, unification, and limit for all proximate goals.^[77] 

The intricate and evolving design of functionally organized organisms exceeds human ingenuity. This design was generated by the agency of non-cognitive goal-directed behavior, the same non-cognitive agency that, through a long evolutionary process, gave rise to the human body, human brain, and human subjectivity.

Organisms, as paradigmatic biological agents, are information processors with a behavioral orientation (the propensity to persist by self-replication and the capacity for flexible adaptation to their conditions of existence).  These agential characteristics are what most obviously distinguish organisms from inanimate objects and the dead. When science ignores the universal and purposive goals of biological agency, life assumes the character of inanimate matter, of purposeless physics and chemistry, and biology becomes a goalless collection of unrelated facts.

Aristotle established biological agency (telos) as the driver or cause (the explanatory end) of biological activity and therefore the most appropriate necessary and sufficient defining condition for life. Aristotle’s agency was an animating principle for life, but it did not address the question of evolutionary change. This was provided later by Darwin’s account of natural selection. Aristotle described the necessary agency required to drive both life and evolution: Darwin described the mechanism of evolutionary change.

The Modern Synthesis is a detailed account of the mechanism of evolution based on gene frequencies in populations. The Extended Evolutionary Synthesis enriches Darwin’s account by acknowledging both Aristotelian agency and its dispersion through organismal structures, processes, and behaviors rather than being located uniquely in genes. 

Human agency is a highly evolved and cognitive form of universal biological agency.

Shared X-Ray image of a stingray by loctrizzle

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) but mindless (non-cognitive, ?teleonomic) goal-directedness (agency) that is a universal feature of life. Biological agency is treated as having cognitive and non-cognitive (pre-cognitive) components. The non-cognitive agential traits, as evolutionary precursors to cognitive traits, are referred to here using the general term pre-cognition. 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 non-cognitive biological agency that ‘created’ 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 investigtion 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.

Describing real but non-cognitive agential biological traits (goal-directed behavior) using the language of human cognition results in cognitive metaphor. This has created profound philosophical and semantic confusion (see human-talk).  Formal scientific recognition of pre-cognitive biological agency is, therefore, a combined philosophical, linguistic, and scientific challenge. Though word meanings cannot be changed at will, in science it is possible to refine categories and concepts to better represent the world.^[73] It is being increasingly acknowledged that human agency is a limited, specialized, and highly evolved form of more general biological agency. However, without a formally developed and descriptive technical terminology, the agential properties of organisms are frequently described using language conventionally restricted to human agency – essentially the language of human cognition and intentional psychology. Thus, the increasing scientific application of words like ‘agency’, ‘purpose’, ‘cognition’, ‘intelligence’, ‘reason’, ‘memory’, and ‘learning’ across biology is broadening their conventional semantic range to include all organisms, and the treatment of such usage as cognitive metaphor is declining.

For a summary of the findings and claims made in these articles see the evolving article called biological desiderata.

Introduction

Agency, as activity and influence, is everywhere.

Aristotle believed that philosophy must provide an account of change, and this was one of his major philosophical endeavors. What is it that generates activity in the universe and has causal efficacy . . . what makes things happen? The universe must have had a prime mover, or first cause that gets everything going.

Today’s science tells us that we live in a universe with a default condition of flux. People, mountains, and stars are all just temporary manifestations, ephemeral concentrations of stuff in the vast swirl of cosmic time. Life itself is a glaring example of a brief and dynamic process. So, the crucial question has now become . . . how do we account for stability, permanence, stasis, and our need for the enduring security of ‘things’? How can we talk of rocks, trees, genes, and molecules as if they were eternal?

Nature, in a broad sense, is full of powerful and terrifying forces (agencies): earthquakes, tsunamis, storms of thunder and lightning, fiery conflagrations, floods, plagues, famines, and disease. Who or what is the agency behind all these phenomena? Change can imply a mysterious, possibly supernatural force of some kind, so it is hardly surprising that we personify nature by attributing such events to punishing and rewarding human-like Gods.

The history of science can be understood as a progressive exorcism of agential spooks. It has always struggled with the intangibility of natural forces which are difficult to explain because they cannot be seen, smelled, heard, or touched, even those of foundational physics. Some forces, for example, have an immaterial and mysterious capacity to act at a distance – which is especially spooky.  Newton accounted for the effects of gravitation while refusing to speculate on what it was, and only relatively recently have we come to grips with the strange invisible attractive phenomena associated with electro-magnetism, while finding new puzzles like quantum entanglement.

There are agents of all kinds in the world, but how are we to understand the notion of agency in biology? More specifically, what is it that animates living things – that gives them ‘life’? What exactly is the drive and ‘vitality’ that so obviously leaves a body when it dies?

When our scientific predecessors treated the goal-directed biological agency of non-cognitive organisms as a creation of the human mind, they were treating biological agency like all the other spooks, as something with no mind-independent existence. They may have exorcised one spook too many.

The idea of agency in biology has its origins in Aristotle’s telos (hence teleology) – his investigation of the ‘final causes’, ‘ends’, or ‘purposes’ of things – his ‘that for which‘.

In his treatise ‘On the soul’ (De Anima) Aristotle described the soul^[79] as a principle of life and individuation – a goal-directed and internally derived animating principle that organizes the matter of living bodies in a manner that distinguished them from inanimate objects. His concept of the soul corresponds closely with what, today, we call agency. Though Aristotle pointed out that his principle was not independent of the body, interpreters have tended to treat it as a philosophically ambiguous or supernatural force.

Later, influential Enlightenment philosopher Immanuel Kant, while endorsing Aristotle’s views concerning the inner source of functional organization in self-organizing beings, regarded this as an as if (what he called ‘regulative’) necessity of explanation, rather than something that actually existed in nature. It is this Kantian view of biological purpose and agency as a metaphor or heuristic that still holds sway today.

Aristotle

Considered the founder of biological science, Aristotle noticed how, in the biological world especially, explanations of organisms – including, their structures, processes, and behaviors – became dissociated facts unless the question ‘what is it for‘ was answered. This was a cogent question precisely because all organisms are goal-directed (agential, purposive) in a way that inanimate objects are not. It makes sense to ask what an eye or a wing is ‘for’, when the same question asked about a rock, or the moon seems like nonsense.

Teleology has a vast literature and the article on purpose provides an introduction to its history, literature, and contest of ideas, including eight different proposed sources of purpose in the world.

Aristotle’s teleology (specifically his formal and final causes) was rejected by the Scientific Revolution because it seemed philosophically obscure with the goals of organisms exerting a mysterious and unscientific causal pull from the future. These goals were like strange supernatural forces that were not amenable to empirical investigation. Moreover, they could be convincingly explained as the reading of human intentions and aspirations into goal-less matter. These philosophical difficulties were compounded by a pre-Darwinian anthropocentrism that understood organisms as the unique products of Special Creation by God not, as Darwin later claimed, connected by evolutionary descent with modification from common ancestors.

Aristotle’s logic and philosophical rigor had overlooked the scientific value of experiment and observation, and it was this that was avidly embraced by the Scientific Revolution. Credibility for the revolutionary new scientific empiricism was gained, in part, by a rejection of the old sources of authoritative knowledge, the Bible and Aristotelian philosophy. Exorcising strange out-of-body forces from non-human organisms was considered a scientific duty. Francis Bacon, who headed the charge against Aristotelian teleology, called Aristotle’s final causes  ‘barren virgins dedicated to God‘.

The Scientific Revolution’s interpretation of biological agency and purpose as the reading of human cognitive sentiments into non-human organisms (like Kant’s heuristic interpretation) has persisted to the present day. Its philosophical and scientific ramifications are discussed in detail in the articles listed at the head of this page. 

Seemingly a semantic problem, this is a metaphysical debate concerning the reality or not of purpose and agency in organisms.

Over the last few centuries, the objections to teleology (its implication of backward causation, inference to the supernatural, anthropomorphism, and philosophical obscurity) have all been met with compelling refutations, so the time is now right to examine how biology looks when, once again, it accepts Aristotle’s vision of the subject as he presented it over 2000 years ago – a vision of biology saturated with functions and goals – of life suffused with agency, where ‘nature does nothing in vain‘.

Darwin

Enlightenment philosopher Immanuel Kant, like Aristotle, had recognized that the teleology of machines was extrinsic (derived externally) while the purposive nature of self-organizing biological structures, processes, and behaviors was an intrinsic teleology. However, it was customary at this time to study and explain the obvious goal-directedness of nature by reference to the purposive wisdom of an external supernatural Creator. This was, for example, the natural theology followed by Linnaeus and made famous by clergyman William Paley.^[108] The possibility of mindless (non-cognitive) purpose and agency was not countenanced at a time when people believed that these were properties breathed into humans by God at the Creation. Darwin was uncommitted in his views about purpose (teleology) in nature (see Charles Darwin).

Darwin provided a causally transparent mechanism for evolution. It was assumed that his theory of natural selection had removed any need for not only supernatural explanations of life but also all talk of agency and purpose in biological systems. When we explain the mechanical operations of the heavens there is no necessity to add the complications of purpose and agency. If, then, we provide a mechanical account of evolution are purpose and agency equally dispensable?

The purpose we attribute to organisms derives from their goal-directed agential behavior, a natural feature that is absent from the lifeless heavens. In providing a mechanical explanation of evolution, Darwin did not explain purpose and agency away.

While Darwin’s theory of natural selection provided a scientifically compelling account of the origin of species, it lacked a fleshed-out empirical account of the mechanism of inheritance. With the development of genetics, and specifically population genetics in the 1920s, and the cracking of the genetic code in 1953, evolutionary explanation took on a gene-based character now known as the Modern Synthesis or Neo-Darwinism. The overwhelming explanatory power of genetics and the genetic code seemed to put a final nail in the coffin of agency and purpose.

The assumption that biology is grounded in genes, with organisms the epiphenomena of genetic programs, occurred during a historical phase of 20th-century analytic and reductionist exuberance that is now drawing to a close.

There has, in recent times, been a lack of conceptual synthesis in biology, probably due in part to the increasing isolation and proliferation of new and developing biological subdisciplines in the microbiological and cognitive sciences. Each discipline has carved out a unique and special place, or silo, for its own subject matter. Perhaps it is time to re-group.

Biological agency and purpose are once again acquiring respectability as science explores a new biological paradigm – the Extended Evolutionary Synthesis (EES). This drive for a new evolutionary synthesis has unleashed a host of ambitious new perspectives on old themes including, for example, the Agency Perspective, the Philosophy of Organismal Biology, Systems Biology, Complexity Science, Enaction, Field Theory, phenotypic plasticity, niche construction, epigenetics, and so on.^{[58,61,62,64,66,72,74,78,86,103,104]}

While goal-directed behavior is a real, indeed, obvious, and pervasive feature of living organisms, biology has never established clarity in its description of this phenomenon. The old suspicion related to Aristotle’s ‘teleology’ has prompted a 20th-century neologism ‘teleonomy’, variously defined, but recently revisited and re-defined as ‘evolved biological purposiveness.‘^[69] This is like a Darwinian extension of Aristotle’s basic idea of purpose and agency but within the context of evolutionary biology.^[89]

Biological agency, minimally defined as the goal-directedness of living organisms, is an obvious feature distinguishing life from non-life. Its traditional denial diminishes our scientific understanding of nature, and reduces our respect for non-human life as we perceive non-human organisms more in terms of the inanimate and purposeless world of physics and chemistry than the human world of purposive and agential intention.

Formal scientific recognition of biological agency is long overdue, but this requires an understanding of the evolving history of ideas and a close examination of what is meant by the biological agent, its mission, and its means of pursuing that mission. Above all, there must be clarity about the confusing relationship that exists between biological agency and human agency. On the genetic front there is gathering evidence, in a range of disciplines, for the inheritance of acquired characteristics, a Lamarckian idea that was once lampooned but now also gathering respectability. The exploration of these ideas is likely to involve a protracted period of discussion in the scientific literature unless expedited by a formal process addressing problems of terminology, definitions, principles, etc.

These are the questions that biologists and philosophers are currently investigating as they reconsider the foundations of the study of life.

Before Darwin, there was no scientific explanation for the goal-directedness in nature that was so evident to everyone. Who, or what, put this purposiveness into living things? For most people there was only one answer, God.

Darwin combined heritability, genetic variation, differential reproduction, adaptation to the environment, selection pressures, and random events to produce the gradual change of species that was necessary to generate the entire community of life. He provided a compelling naturalistic (scientific, mechanistic) explanation of evolution that did not depend on supernatural intervention and in so doing many believed that he had, in the process, simultaneously removed any hint of purpose. But the goal-directedness so intimately associated with purpose and agency was still present, just as it had been in the first organism at the origin of life. Darwin provided a scientific explanation for purpose and agency, but he did not explain them away.

This article explores some of the logical space available within the categories ‘biological agent’, ‘biological goal’, and the ‘means’ used by biological agents to pursue their goal(s).

The Standard Model

Skepticism about agency and purpose in biology, combined with a gene-centered interpretation of evolution (the Modern Synthesis or Neo-Darwinism) are the current biological orthodoxy. This is what is referred to here as the Standard Model: it is the mainstream textbook representation of biology that developed out of the Scientific Revolution and the 20th-century genetic elaboration of Darwinian ideas. It may be characterized roughly as follows:

The concepts of agency and purpose when used in biology are best confined to the realm of uniquely human conscious intentions and rational deliberation. The agency we see in nature, and which we sometimes describe with the use of human-talk (anthropomorphism, mostly as cognitive metaphor) is our reading of human conscious intentions into organisms which, since they have no cognitive faculties, can have no intentions and therefore no agency or purpose. The attribution of agency and purpose to non-human organisms may assist biological explanation and therefore have heuristic value, but these properties are not there in reality.

There are many reasons why this interpretation of the relationship between human minds and the behavior of non-cognitive organisms is misleading:  it ignores the likely evolutionary path of human cognition; it misinterprets the implications of human-talk and cognitive metaphor for biological agency; it avoids scientific and semantic confusions concerning the distinction between biological and human agency; it ignores the lack of scientific-technical vocabulary available for the description of biological agency. These matters are discussed in articles listed at the top of this page.

Combined with this suspicion of agency in biology there is a growing dissatisfaction with a mainstream gene-centric view of biology as expressed through the Modern Synthesis characterized loosely as follows:

Darwin gave no experimentally based analysis of inheritance. The genetic foundations of evolution were established much later. The Modern Synthesis combines the Darwinian theory of evolution by natural selection with modern genetics by pointing out that genetic variation within populations, driven by mutation and recombination, is the raw material for the natural selection that leads to the evolution of species over time. It is these genetic changes within populations that lead to the diversification and adaptation of species, so natural selection is best conceptualized as a struggle between genes, usually through the effects they have on organisms, and for their replication and transmission to the next generation. The primacy of genes derives from the fact that evolutionary novelty can only occur when genetic information passes from germ cells to somatic cells and not vice-versa – that is, there is no inheritance of acquired characteristics – changes in somatic cells are not passed on to offspring.

This emphasis on genes not only ignores the role of biological agency and behavior in evolution, it also ignores many other non-genetic factors that can influence the evolution of species.

Problems with the Standard Model

Biology is currently undergoing a paradigm shift in philosophy as its metaphysical emphasis shifts from things to processes, the notions of purpose and agency are rejuvenated, and the reductionist model of genes ‘pulling the strings’ of life is revised.

Inversion of reasoning – there is a mistaken assumption that since biological goals can only be understood (represented) in human minds and language, then they can only exist in human minds, and are therefore a creation of human minds . . . that biological agency is therefore not real. 

Reality of agency & purpose in biology – goal-directed behavior demonstrates both agency and purpose as an objective fact. All organisms express biological agency by acting on, and responding to, their conditions of existence with flexible and adaptive behavior that influences both their immediate lives and evolutionary future. The minded goal-directed behavior we associate with human agency is a cognitive evolutionary development of the mindless non-cognitive (?teleonomic) but purposive and agential behavior of mindless organisms.  

Behavior & biological causation – organisms may be treated scientifically as either objects or subjects. Studied as objects their behavior is regarded in a detached way as the product of either internal or external causes such as changes in the environment or the activity of genes. This tacitly suggests internal and external causes as the primary, original, or ‘real’ source of agency and change. Studied as subjects it is clear that the behavior of organisms is always and ultimately a consequence of the internal reconciliation (functional integration at an organismal scale) between the organism’s behavioral propensities (goals) and its conditions of existence (triggers in the internal and external environments) that may help or hinder these goals. Treating the organism as a subject rather than an object converts its role from a passive recipient of impersonal causal factors to a self-determining agent. The agential reality of organisms has been known for a long time (Aristotle regarded organisms as ‘causes of themselves’; Kant recognized that ‘a thing exists as a natural end if it is cause and effect of itself’), but there have been historical changes in explanatory traditions and emphasis, at least in part resulting by a suspicion of biological agency. The underlying point remains. Behavior (which we and other organisms use to assess agency) may be indirectly triggered by internal or external causes but it is ultimately (most directly) a consequence of an internal reconciliation between an organisms natural propensities and its conditions of existence.

The metaphor fallacy – 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 (see metaphor fallacy).

Converse reasoning – by treating the minded language of biological agency as cognitive metaphor rather than biological simile we treat biological agency as a creation of the human mind whereas in fact, and conversely, human agency evolved out of (was ‘created by’) real and mindless biological agency. Scientifically it is more productive to describe human agency as an evolutionary development of biological agency than to explain biological agency in the uniquely cognitive terms of human agency.

The mind/no mind mistake – products of biological evolution simultaneously possess – not theoretically, but in reality – both uniquely defining characteristics and characteristics that are shared with other organisms (the characteristics that indicate common ancestry). So, when locating biological objects (structures, processes, behaviors – and even biological concepts) within an evolutionary context, we must be aware that, in nature, uniquely defining characteristics are associated with other characteristics that are shared with evolutionary relatives. Biological agency and human agency are not mutually exclusive properties in the same way that organisms with minds may be considered distinct from those without minds. Human agency is just one of many evolutionary expressions of biological agency (albeit a complex and minded one) and it therefore shares universal agential features with other organisms. 

Conflation of human agency & biological agency – human agency is, of necessity, an evolutionary development of biological agency. Human agency, though associated with uniquely human cognitive faculties, also shares with all organisms the ancestral propensity to survive, reproduce, and flourish.  Because of this evolutionary connection, concepts we usually associate with minded agency (e.g. reason, knowledge, value) can resonate with evolutionarily antecedent properties of mindless biological agency (e.g. adaptation, information-processing, and behavioral orientation). We fail to recognize that much of the intentional language of human-talk, interpreted as cognitive metaphor, is referencing properties that exist universally in nature and are physically expressed by degree.

Anthropocentrism – consider the sentence:

The design we see in nature is only apparent design

Insisting that ‘agency’ and ‘purpose’ are strictly cognitive concepts is a form of anthropocentrism.  We say that design in nature is only apparent design (not real) because it is not human design, it has not been created by human minds. But nature and organisms are replete with (real) designed structures that are far more complex, beautiful, and ordered than anything produced by humans. Mindless nature created/designed the human body, and the human brain with its capacity to contemplate itself.
The problem is that, for many people, words like ‘design’ (and other words like ‘purpose’, ‘reason’, ‘knowledge’ and ‘value’, even ‘creation’) are only meaningful in the context of human cognitive faculties. Organisms cannot manifest design because they have no cognitive faculties.
But here lies the intellectual challenge of the cognitive metaphor. Because nature’s mindedness is unreal (hence the cognitive metaphor) this does not mean that the design is unreal. Our anthropocentrism simply refuses to countenance the possibility of mindless design. But, following philosopher Dan Dennett’s mode of expression . . . ‘purpose’, ‘reason’, ‘knowledge’, ‘value’, ‘design’, and many other concepts attributed to human intention ‘bubbled up from the bottom, not trickled down from the top‘. That is, we would find it more scientifically productive to view human subjectivity through the real lens of biological agency than to try and understand biological agency through the metaphorical lens of human subjectivity. If we reject this form of language use then what words are we to use to describe real mind-like properties that exist objectively in nature?
The usual scientific solution to such a problem is to devise a technical vocabulary that discriminates between nature’s real and mindless design and the minded artifacts of human creation. But this has never been adequately achieved. It would be impractical and the threat to human dignity too embarrassing.

Absence of technical terminology – If words like ‘purpose’ and ‘agency’ are inappropriate for non-human (non-cognitive) organisms, then we must find some way of referring to the real goal-directed agential behavior that distinguishes this group of organisms from, on the one hand, inanimate nature and, on the other hand, those organisms with cognitive faculties. That is, we would need a new vocabulary of agential but non-cognitive terms. Introducing such a terminology seems both unwieldy and unlikely. In the meantime, we refer to real organismal agency using the language of cognitive psychology which is therefore open to the accusation of being cognitive metaphor. Real agency is thus reduced to figurative agency (see metaphor fallacy above).  

Scale & the reification of hierarchical levels of organization –
The proliferation of biological disciplines over the last century, most notably those in the microbiological and cognitive sciences, has created specialized academic silos, each with its own principles, technical terms, and a sense of their crucial place within biology as a whole. Uncritical (intuitive) acceptance of the metaphor of disciplines and their subject-matter as representing the real metaphysical hierarchical organization of the biological world has reified/ontologized these ‘levels’ (both sub- and supra-organismal), investing them with an empirically and philosophically unjustified degree of independent significance. They have become equivalent levels of both reality and evolutionary selection leading to a pluralism more appropriate to inert matter than goal-directed life. It is unclear, for example, whether biology currently regards the cell, gene, organism (or none of these) as a basic unit of biological science. When each discipline claims either agential precedence or metaphysical equivalence for its own ‘level’, the scientific significance of physically bounded and functionally organized autonomous organisms is diminished or ignored.
While all scales or levels of biological organization, both structural and functional, incorporate agential, purposive, and evolutionary information, they are ultimately subordinate to the conditions determined at the scale of the autonomously integrated organism. It is the physically bounded and functionally integrated whole organism that is nature’s most clearly individuated biological agent and it is at this scale that the conditions of biological agency most obviously apply. 

Process – goal-directed life is more a process than a thing. The reification of levels of organization, neglect of agency, and emphasis on genes are ways in which process can be diminished or ignored. Process philosophy reflects a dissatisfaction with the analytic and reductive notion of the unity of science as grounded in the principles and laws of maths, physics, and chemistry, built on a foundation of fundamental particles – a metaphysics that does not adequately explain the operation of complex and dynamically integrated systems and emergent phenomena, or allow for alternative perspectives on the world

Gene-centrism – the successful ‘reductionist turn’ of the last half-century – which included the cracking of the genetic code and the outstanding success of microbiology and biotechnology that followed (with associated developments in particle physics) – has, in effect, treated organisms as an epiphenomenon of the genetic code and evolution as an existential struggle between individual genes. This historical period corresponds with an ‘analytic turn’ in Western science and philosophy that has invested increasingly small constituents of the world (the parts that make wholes possible) with an unwarranted metaphysical significance as the increasingly small has been tacitly associated with the increasingly real. Since organisms are composed of fundamental particles, it is the particles, not the organism, that are given scientific and philosophical significance. Our one-time intuitive and metaphorical understanding of existence as a ladder of life dominated by the agency of gods, humans, and organisms has been challenged by an equally metaphorical assumption of the foundational metaphysical significance of fundamental particles and genes.

This reductive paradigm is now undergoing a timely revision.

Drilling into biological microstructures has sidelined factors that are now gaining more attention: it is challenging the idea that genes are the ultimate agents of life and evolution. These elements include: environmental factors that influence gene expression and phenotypic outcomes – the way organismal behavior determines the conditions of inheritance; the influence of epigenetics^[75][76] on gene expression without alteration to underlying DNA, especially during development; the contribution of systems biology to the understanding of the intricate connection between genes, proteins, and other molecules with emergent properties arising from the system as a whole rather than exclusively from genes; the influence of non-coding DNA on regulatory functions including gene expression; the influence of groups and populations.

Natural selection, agency & behavior – natural selection, as propounded by Darwin, is currently regarded as the driver, cause, and foundational principle of evolution. Darwin understood natural selection as a behavioral contest which he described, following Herbert Spencer, using the expression ‘survival of the fittest’. After the analytic and genetic turn of the 20th century natural selection is today explained in genetic terms as, for example, ‘the replacement of gene variants (alleles) with those alternatives that shift the average phenotype of a population in the direction in which natural selection is tugging’ (p. 27) or, more simply, as ‘changes in gene frequencies in populations’. This characterization, while technically acceptable, ignores the behavioral arena of organisms pursuing their ultimate goals of survival, reproduction, and flourishing. Gene frequencies change in line with behaviors that generate a survival advantage – improving access to food, avoiding predators, having successful courtship, mating and parenting strategies, enhancing cooperation, coordination, learning, developing social hierarchies that contribute to reproductive success, and meeting environmental challenges. It is behavior, more than genes, that determines the environments of evolutionary adaptation that determine biological traits. Behavior (agency) is thus the driver of natural selection because it directly influences an organism’s ability to survive, reproduce, and flourish, determining the organism’s capacity for adaptation and leading to the evolution of species with traits and behaviors suited to their ecological niche. The grounding of natural selection in either genes (Modern Synthesis) or organisms (Darwin) raises questions about biological priority and the sequence of causation in biological processes. Do genes determine the nature of organisms, or is each genotype ultimately an outcome of organismal behavior that establishes the context of natural selection? Or what? More directly, is natural section the concept that most efficiently crystallizes what we mean by ‘biological evolution’? Scientifically, natural selection is an outcome of the agency of autonomous organisms as they mindlessly reconcile their propensity to survive, reproduce, and flourish with their conditions of existence. Natural selection is therefore as Walsh points out, a by-product of biological agency.
Aristotle identified the driver of life (which, after Darwin, would also become the driver of evolution) as the goal-directed behavior of organisms most parsimoniously described here as biological agency. Darwin explained the principle of its operation (natural selection) in the origin of new species, and the Modern Synthesis provided a genetic account of its mechanism through population genetics.

Evolution – How do we account for evolutionary change – what is the mechanism or driver of the changes that result in the biological process of descent with modification from common ancestors? The traditional answer to this question has been ‘natural selection’ but research over the last century or so has elaborated the answer along the following lines. Biological evolution results from changes in the genetic composition (allele frequency) in populations over time – the result of mutations (the source of genetic variation), genetic drift (random fluctuations of allele frequencies in populations due to chance events), natural selection (the process by which traits that confer a survival or reproductive advantage become more or less common in a population), and gene flow (the transfer of genetic material from one population to another over time). This is a characterization of evolution as a competition between genes.
But evolution can be characterized in other ways. A simpler account might regard evolution as the acquiring of inherited traits through the agential interaction between organisms and their conditions of existence. This is not a passive process but the product of a purposive and agential adaptive reconciliation between the natural goal-directed predisposition of organisms and those conditions of their existence that help or hinder their survival, reproduction, and flourishing. It is this short-term behavior that establishes the organism’s environment of evolutionary adaptation and therefore long-term heritable change. New species arise from the purposive and agential behavior of organisms that leads to the gradual accumulation of heritable variation within populations. This characterization is a move from a gene-centric to an organism-centric interpretation of evolution. The genetic composition of populations is not determined by the selective pressure of environments but by the behavior of organisms resulting from the inner reconciliation between their natural propensities and these environmental factors. This inner agential process shapes adaptive strategies within populations. While it is true that those genes contributing to an organism’s ability to survive and reproduce tend to become more prevalent in the population over time, the struggle for reproductive success is, in the first instance, a struggle between organisms, not a struggle between genes.
The interplay between genes, behaviors, and the environment is complicated and interconnected, but evolutionary processes are most evident in organisms and populations. While genes shape the traits of organisms, the expression of these traits and their impact on reproductive success occurs in organisms. It is organisms, through their behaviors and interactions, that are the immediate agents in the evolutionary process. The struggle for reproductive success results from competition and cooperation between organisms, and the genetic composition of populations is a result of the cumulative effects of these interactions over time.
Evolution is not, in the first instance, a competition between genes or even ‘natural se;ection’, it is a product of the agential and purposive activity of organisms in interaction with their conditions of existence.

The Extended Evolutionary Synthesis

The intellectual exploration of biology, once focused firmly on organisms, has broadened out to include populations and ecosystems, and narrowed down to the microscopic detail of genes.  How do we provide explanatory order to this expansion of knowledge and complexity?

In a complex system of interacting and interdependent factors, how do we decide which factor has causal or explanatory priority, or controlling efficacy? How do we rank the different factors and determine the strength and direction of relationships and dependencies? Which factor is a cause, and which a consequence?

As the focus of research shifts from one factor to another, so too does the explanatory emphasis. The ranking of explanatory categories changes in the light of new evidence and our human need to prioritize.

The Modern Synthesis, as an explanation of evolution, was a product of the genetic revolution that occurred between about 1918 and 1942 during an analytic-reductive turn in thinking that was gathering momentum at this time as scientists and logicians looked for the foundations of the world in its smallest discrete constituents.

Dissatisfaction with the main tenets of the Modern Synthesis began to appear from the 1950s (e.g. organicist Waddington) to 1980s (e.g. evolutionary biologist Gould). These ideas were given expression around 2009^[64] and summarized in a 2010 book by Massimo Pigliucci and Gerd B. Müller, Evolution: The Extended Synthesis whose themes have persisted as the Extended Evolutionary Synthesis (EES).

Dissatisfaction with the Modern Synthesis derived from both theoretical objections and the findings of new research concerned with, among other factors, fitness landscapes, multilevel selection, epigenetic inheritance, cultural evolution, organismal development, developmental plasticity, niche construction, evolvability, phenotypic plasticity, reticulate evolution, horizontal gene transfer, symbiogenesis, and more. A recent synthesis of the EES can be viewed here.

In sum, the EES is an expression of disillusionment with the gene-centered analysis of evolution. It is a movement seeking a revision in the emphasis given to the various factors influencing evolution – those underplayed including organisms, agency, ecology, and the inheritance of acquired characteristics.

The revisionist proposals of the EES fall into two broad camps: those concerned with a modification of our understanding of the inheritance of acquired characteristics, and those concerned with biological agency.

The most comprehensive current discussion of the philosophy and principles of agency in biology is Denis Walsh’s Organisms, Agency, and Evolution (2015). Walsh is a member of a team of four biologists concerned with agency in living systems whose objective is  – ‘To develop a scientific theory of organisms as purposive agents and determine the explanatory concepts and structure of an agent theory in relation to conventional scientific object theories‘.

Walsh outlines his philosophical position as follows:

The ‘Aristotelian purge’ was seen as a pivotal achievement of early modern science. As a consequence of the scientific revolution, the natural sciences learned to live without teleology. Current evolutionary biology, I contend, demonstrates that quite the opposite lesson needs now to be learned. The understanding of how evolution can be adaptive requires us to incorporate teleology – issuing from the goal-directed, adaptive plasticity of organisms – as a legitimate scientific form of explanation. The natural sciences must, once again, learn to live with teleology.^[53]

. . . the capacity of a system to pursue goals, to respond to the conditions of its environment and its internal constitution in ways that promote the attainment, and maintenance of its goals states^[56]

Walsh points out that the purposive activities of organisms have a strong influence on evolutionary outcomes – that evolution is, in this sense, a by-product of organisms’ pursuit of their intrinsic purposes. Evolution is not a product of four discrete and independent processes – inheritance, development, innovations, and biased change. Rather, each of the component processes of evolution—like adaptive evolution itself— is a consequence of what organisms as agents do.

A new biological paradigm

If biology has ignored agency for centuries, if not millennia, then why do we need it now – and how are researchers to adopt it as a relevant, practical, and operational concept?

Science must study agency because it is a critical component of the real fabric of the natural world – it cannot be ignored simply because it was once treated as a philosophically misguided idea. If, indeed, ‘evolution is a by-product of organisms’ pursuit of their intrinsic purposes’ then our historical determination to exorcise purpose and agency from biology must be regarded as a major scientific and philosophical error of judgment.

There was a time when it was considered inappropriate to call humans animals – the meaning of ‘animal’ did not extend comfortably to humans. As biology progressed and the continuity of life was better understood, the word ‘animal’ took on a broader sense with humans accepted as a limited case. In this way, science has shifted our semantics. The same applies to the idea of organisms expressing purpose and agency. As biology has progressed ‘biological purpose’ and ‘biological agency’ have embraced a broader sense, with human agency (as conscious intention) a limited case of biological agency.

Being part of the real fabric of nature, agency has not been ignored by biological science, it has been hidden. The task is to convert the implicit into the explicit – to realize that the technical language of natural selection, adaptation, and fitness maximization tells the truth, but not the whole truth, it is a form of obfuscation and circumlocution – a cryptic terminology that obscures the reality of agency and purpose. It is OK to speak of the purposes of biological entities and what adaptations are ‘for’. This will, by convention, be resisted, and it will be claimed that it is a semantic error – but it will bring humans closer to nature by countering the detached mechanics of physics and chemistry. Being grounded in sound science, it will gradually become accepted.

The concept of agency in biology is gathering support. In a comprehensive philosophical coverage of ‘Agents and Goals in Evolution‘ (2020) with in-depth consideration of agential thinking and the agential idiom in biology, philosopher Samir Okasha cautiously concludes:

‘To the extent that an evolved organism is well adapted to its environment, and thus equipped with phenotypic traits that enhance its survival and reproduction, it can be validly treated as agent-like as long as  a certain empirical precondition is met, at least approximately [the unity of purpose condition]

The reintroduction of agency and teleology to biology requires clarification, consensus, and an understanding of historical problems.

Seeking clarity on the notion of agency in biology Okasha (2023) offers a framework for dialogue that recognizes two roles or motivations for the word ‘agency’: first, as a thesis of agential individuation, that ‘organisms are agents’ (OAT) and, second, as a tool to aid the understanding of evolved biological behavior, the ‘organisms as agents’ heuristic (OAH). He proposes four non-vernacular senses of ‘agency’ and examines their suitability for application in biology: the minimal concept (doing something or behaving), the intelligent agent (having the capacity to adapt: as applied in AI), the rational agent (maximized utility: as applied in economics), and the intentional agent (use of psychological states—beliefs, desires, and intentions: as often applied in philosophy).

Our anthropocentrism drives us to investigate the agency and purpose so obvious in nature through the lens of human agency. So, for example, we ask, ‘Why do we treat organisms as if they experienced cognitive states when clearly they do not?’ Or, ‘Why, do organisms demonstrate behavior that is so similar to human reasoning?‘

This website is concerned primarily with the concept of organisms as agents (OAT). While human agency and metaphor can be useful tools in the study of biological agency this website takes the view that it is more scientifically informative to investigate human subjectivity through the reality of biological agency, than to understand biological agency through metaphorical idioms and lens of human subjectivity – though both approaches can inform.

Much can be learned by looking at human agency through the lens of biological agency – by acknowledging that human agency is an evolutionary elaboration, or limited case, of real biological agency – rather than biological agency being a creation of human minds that must therefore be psychologized.

This is a more empirical approach that prompts scientifically pertinent questions such as, ‘How do we account for the obvious similarity between, on the one hand, the non-cognitive goal-directed behavior found in all organisms and, on the other hand, the uniquely human cognitive faculty of intension?’  or ‘When cognitive metaphor is so patently unscientific, why do we persist in using it?

When we dismiss purpose and agency altogether by treating them as metaphor or heuristic (e.g. the plant wants water) we are mistakenly focusing on the metaphor rather than the agency. Plants have no cognitive faculties, but that does not mean they have no agency (see metaphor fallacy listed above).

Themes investigated on this website include the emphasis on organisms as being real agents, independent of any heuristic considerations relating to non-biological agencies; a close investigation of the relationship between human agency and biological agency and how this, in turn, relates to the minded and mindless in biology (including the actual evolutionary relationship between goal-directedness and cognition).

The analysis of agency in biology has the potential for major scientific contributions to our understanding of the origins and nature of human subjectivity. The benefits of agential studies in biology can flow into many disciplines, including developmental biology, bioengineering, biomedicine, microbiology, robotics, AI, and evolutionary biology.

Agency

What exactly do we mean by ‘agency’ and what are the most effective ways to investigate its relevance to biology? If biological agency is real, then what is its role in evolution?

This overview of agency begins with our general understanding of the notion of agency before looking at agency in nature, the characteristics of human agency, and the relationship between human agency and biological agency. It then focuses on the application of the concept within biological science. 

‘Agency’ is a loosely defined idea with application in many disciplines, so it has a broad semantic compass. Dictionaries tell us that an agent is something that acts, so an agent could, for example, be interpreted in an extremely abstract, and general sense as a cause that brings about an effect. However, we are more likely to think of agency in the familiar and narrowly defined sense of the intentional behavior we associate with human activity.

Agency expresses at least a degree of autonomy and self-determination directed toward specific goals or objectives. An agent initiates or influences events, so its actions cause changes that are not entirely controlled by external factors. We can, however, imagine computer programs such as those of AI that display a non-living kind of agency that is independent of or, at least, superimposed on their human input.

The goals, or objectives of cognitive agents are uncontroversially referred to as ‘purposes’. We speak about the purposes (goals) of inanimate objects like chairs, knives, and guided missiles, but we do so mostly because they infer the human intentions involved in their creation; we do not regard them as independent agents.

Natural agency

Though rarely regarded as a crucial philosophical concept, the notion of agency sits at the center of our religious and scientific understanding of the world. What is it that generates activity in the universe, that initiates change, that has causal efficacy? Change can imply a mysterious, possibly supernatural, force of some kind – and forces are difficult to explain because they cannot be seen, smelled, heard, or touched.

More specifically, what is it that animates living things – that gives them ‘life’? What exactly is the ‘vitality’ that so obviously leaves a body when it dies?

Nature, in a broad sense, is full of powerful and terrifying non-biological forces (agencies): earthquakes, tsunamis, storms of thunder and lightning, fiery conflagrations, floods, plagues, famines, and disease.  Why do these dreadful catastrophes happen, and why must humans suffer their consequences – and who or what is the agency behind them? It is hardly surprising that in such instances we personify nature with events controlled by punishing and rewarding human-like Gods.

The history of science can be understood as a progressive exorcism of agential spooks. It has always struggled with the intangibility of natural forces, even those of foundational physics. Some forces, for example, have an immaterial and mysterious capacity to act at a distance – which is especially spooky.  Newton accounted for the effects of gravitation while refusing to speculate on what it was, and only relatively recently have we come to grips with the strange invisible attractive phenomena associated with electro-magnetism, while finding new puzzles like quantum entanglement.

When we confront the goal-directedness of organisms (biological agency) and their vitality, it too seems to imply some ineffable power – a kind of life force . . . living willpower, motivation, or animating principle. We think we are being detached and scientific when we describe this property in neutral language by saying that life has a disposition or propensity to act in a goal-directed way. But this hardly does justice to the real-time agential immediacy of life that seems much more than a mere propensity.

Such musings are ignored today. The various ‘pushes’ and ‘pulls’ of our lives – the needs, wants, desires, and aspirations that direct our behavior – seem neither mysterious nor unscientific.

While organisms survive, reproduce, flourish, and therefore persist, there is no logical necessity for this. We do not have to breed, or feed, or continue living – but something like a ‘will-to-life’ provides the driving energy, power, or force that keeps most of us going, most of the time.

This applies to all life, and especially mindless life. Very rarely do organisms terminate their lives under-essentially. If we humans suddenly decide to stop our life-affirming activities, then this is considered unnatural: we need professional help.

The ‘will to live’ is an integral part of our inherited biological nature; it no longer needs supernatural explanation. Why should discussing goal-directedness (the agency) of organisms imply the unreal, unscientific, or supernatural?

Minded humans evolved out of mindless organisms. Minded human life-affirming agency evolved out of the mindless life-affirming agency of mindless organisms. Human agency evolved out of biological agency.

Human agency

While human agency is strongly associated with rational considerations and deliberate intention, it is not expressed exclusively through the medium of conscious mental representations.

Human bodies demonstrate biological goals in several additional ways that include: the mindless but integrated and goal-directed biological processes of self-maintenance that include growth, metabolism, homeostasis, homeorhesis, and more. Then there are the minded but unconscious goals associated with our instincts and intuitions including our inherited objective, universal, and ultimate biological propensity to survive, reproduce, and flourish.

Like all organisms, we are engaged in a constant process of adjustment (adaptation) to what is going on both inside and outside our bodies, most notably those conditions that are important for our existence as determined by our human biology. It is these conditions that determine our commonsense reality or umwelt (see manifest image).

Key adaptive ingredients of the human  cognitive agential umwelt include:

Intentionality – our goal-directedness as the purposive focus of our mental activity which we describe using the agential language of intentional psychology.

Conscious self-awareness of our actions and their consequences, so we can reflect on our thoughts, choices, actions, and motivation. This includes an awareness of our capacity for independent (autonomous) decisions that engage rational deliberation.

Capacity for self-regulation based on both individual and collective societal principles, values, norms and ethical precepts.

Creativity and the ability to learn from experience and acquire new skills in adjusting to our environments 

Providing a concise summary of our human mental life is a tall order, but when well-founded, succinct statements – like principles and laws – have great explanatory power. From at least the time of the ancient Greek philosophers, our mental life has been subsumed under three useful categories: knowledge (epistemology), values (ethics), and reason (logic). These three drivers of human behavior will be re-visited at the end of this article. 

Human & biological agency

This website argues at length (see articles listed at head) for the claim that human agency is best understood biologically as a specialized, highly evolved, and minded form of biological agency.

While the idea of evolution suggests transformation, it can also be usefully characterized as adding on to, or supplementing, what is already present. This is how Darwin understood biological evolution – as a process of gradual modification from common ancestors.

The necessity for all life to survive and reproduce, if it is to persist, is an ultimate goal that can be understood as an underlying theme for the vast graduated array of related organisms (with their supporting structures, processes, and behaviors) that make up the community of life.

All organisms, including humans, are subordinate to these ultimate goals of biological agency. However, because humans express their agency in a highly evolved cognitive form these underlying ultimate causes of behavior are concealed in proximate cognitive forms. So, for example, ultimately we eat to survive, but proximately we eat for the biological rewards of smell and taste stimulation, and the satisfaction of hunger. Biologically we have sex for the (ultimate) purpose of reproduction, but our human (proximate) incentive is the pleasure of physical closeness and orgasm . . . and so on.

These examples provide a window into the way that apparently unique human mental faculties are grounded in more general biology. It points to the way that our cutting off of mental faculties from other organisms can be a form of anthropocentrism, of human arrogance. While, after nearly 200 years of Darwinism, we now willingly accept the biological antecedents of our bodily structures we cannot accept that there are aspects or properties of our mental lives that are also shared with the community of life. Human minded agency is just one manifestation of ultimate biological agency and the biological condition of constant adjustment.

More precisely, the features that uniquely define human agency evolved out of the universal, objective, and ultimate characteristics that are common to all biological agents . . . the reason why we intuitively acknowledge plants and animals as fellow agents in a way that rocks are not. This is also the reason why human minded concepts share some characteristics (likenesses) with the mindless concepts we associate with mindless organisms – why there is a set of real properties connecting non-human organisms to human cognitive states.

There are scientifically grounded and real (not fanciful or metaphorical) reasons why we recognize likenesses between the behavior of non-human organisms and, for example, human purpose, agency, reason, value, knowledge, and more.

For those claiming no real connection between biological and human agency, there is the species-specific descriptive language of human intentional psychology. But while dogs and oak trees also express goal-directed behavior (agency) in their own objective and unique way, they do not have corresponding descriptive vocabularies. What words are we to use when trying to describe this real non-cognitive form of agency? Since the reality of objective non-human biological agency cannot be denied, but cannot be described by using the language of human cognitive psychology, what are we to do?

Since it is impractical to devise agential language for each species, but we wish to convey the reality of non-human biological agency, we resort to the use of human cognitive terms. These are then open to accusations relating to cognitive metaphor, heuristics, and so on. That is, real biological agency is described using unreal figurative terms (see metaphor fallacy above). These matters are discussed in the articles human-talk, being-like-minded, and biological values.

Suffice it to say here that we usually use the language of intentional psychology to draw attention to real and universal (shared) biological agency, not to literally imply that non-human organisms have cognitive faculties. We say a plant ‘wants’ water because we know it will die without it, not because we really believe that plants have cognitive faculties.

Conceptual analysis

The rough-and-ready semantic analysis of ‘agency’ given above tells us what we mean by agency in general. But how are we to narrow down these generalities to address the specific question of agency in biology?

One approach might be to first establish a range of different meanings of ‘agency’ and then see how these are applied by practicing biologists. This might help narrow down the field of possibilities when considering a definition.

Philosopher Samir Okasha (2018, pp. 12-15) has investigated four popular senses of ‘agency’ and investigated their appropriateness for application in biology: the minimal concept sense (doing something or behaving), the intelligent agent sense (the capacity to adapt: as used in AI), the rational agent sense (maximized utility: popular in economics), and the intentional agent (use of psychological states—beliefs, desires, and intentions: as used in philosophy).

Okasha himself recognizes the goal-directed behavior of organisms as an empirical fact.^[40] However, while this website regards goal-directed behavior as sufficient to warrant the designation ‘agency’, Okasha embarks on a more rigorous investigation by examining agency through minded concepts of agency, like intelligence, reason, and intention (see above).

This approach proceeds from the popular mainstream assumption that agency is a minded phenomenon. This is, as it were, a ‘top-down’ approach, attempting to understand organisms in general by looking through the lens of human cognitive agency.

This seems unnecessarily conceptually complex when a ‘bottom-up’ methodology could yield valuable empirical insights. But, how could that possibly be done?

This website regards agency as a general biological or organismic phenomenon, not a strictly human characteristic (see, for example, Being like-minded). Human (minded) agency is treated as a highly evolved and limited case of biological agency.

From this perspective, intelligence, reason, and intention are minded cases of biological agency. That is, there is an evolutionary connection between biological agency in general and uniquely minded human agency in particular. It then becomes a productive scientific endeavor to examine the evolution of cognitive agency through an empirical investigation of the graded evolutionary diversity of organisms (including the properties and relations of their structures, processes, and behaviors) as they exist across the community of life. This begins with a determination of features that are shared by both human and biological agency, not those that are unique to humans: it is a study focused on biological agency, not human cognition.

This ‘bottom-up’ approach treats agency as an empirical investigation of real agential characteristics, while a ‘top-down’ approach interprets biological agency through the cognitive filter of human agency with its mind-like heuristics and cognitive metaphors.

In short, we understand the relationship between human agency and biological agency in a more scientifically productive way when viewing human subjectivity through the lens of real biological agency, rather than trying to understand biological agency through the metaphorical lens of human subjectivity (though both approaches may yield insights).

In a recent paper philosopher Okasha (2023) asks, ‘What is distinctive about living organisms compared to entities at other hierarchical levels?’ concluding that agency is a ‘candidate for the job’ because organisms exhibit agent-like attributes such as ‘ . . . making choices, learning about the environment, and performing actions, that other biological entities do not’. Apart from his unabashed use of cognitive metaphor, he recognizes two roles or motivations for the word ‘agency’: first, as a thesis of agential individuation, that ‘organisms are agents’ (OAT) and, second, as a tool to aid the understanding of evolved biological behavior, the ‘organisms as agents’ heuristic (OAH).

As indicated before, it is the OAT, that is addressed on this website, with the OAH treated as an empirical, rather then conceptual, challenge.

Biological agency

When asked to name a biological agent we intuitively think of an organism. However, the entry in Wikipedia for ‘biological agent’ describes it as an organism or toxin ‘that can be used purposefully as a weapon in bioterrorism or biological warfare‘ (28 April 2023). There is nothing in that article addressing the matters that are discussed on this website.

Biology has, until recently (when cells and genes have enjoyed a period of ascendency), found little difficulty in allocating organisms a central place in biology. But there is a problem with the word ‘agency’. For many reasons (see articles at the head of this page) notions of biological agency and purpose are currently considered unorthodox biology. For centuries the topic of agency in biology has been swept under the carpet – denied or ignored – it is the elephant in the biological classroom.

Critically, agency is considered by many people as exclusively associated with human cognition.

However, all organisms are goal-directed autonomous biological agents that act on and respond to their conditions of existence. While agency is usually associated with human cognitive traits like intention and deliberation, the presence of agency in non-cognitive organisms confirms the existence of non-cognitive agential traits – a characteristic of non-cognitive organisms that is referred to here as pre-cognition.

Thinking about the agency of organisms forces us to consider their goals or purposes and the characteristics that establish biological objects as discrete individuals or biological categories. Is biological agency a fiction, or is it a critical feature that distinguishes life from non-life? And if all organisms display some form of agency, then what is the difference between this agency and the agency we associate with human intentions?  Does it make sense to speak about cognitive and non-cognitive agency?  And, if it does, could there be an evolutionary connection between the two? It draws our attention to the possibility of an evolutionary connection between the agential behavior of mindless organisms and the intentional behavior of humans but, more importantly, it forces us to reconsider the relative significance and relationship between the key factors of evolutionary theory.

Brainstorming the notion of biological agency gathers ideas that include:  purposeful behavior, self-regulation and homeostasis, response to stimuli, adaptation and evolution, reproduction, energy processing, organizational complexity, information processing, autonomy and independence, and the capacity for learning and adaptation. How can this complexity be condensed into something more simple?

 The view of biological agency presented here is grounded in the general notion of an intentional agent (the organism) performing purposeful actions driven by goals or intentions (the ultimate and mindless goals of survival and reproduction). This theoretical stance can be exemplified in graded physical forms as, say, the minimal agent with the basic capacity for self-regulation and responsiveness, the intelligent agent with cognitive abilities beyond mere responsiveness, and the rational agent capable of decision-making based on reasoning.

Organisms influence their own persistence, maintenance, and function by regulating their structures and activities in response to their conditions of existence. They are not passive elements of environments, they actively engage with them: they not only shape their own evolutionary paths, they contribute to their broader ecological context. That is, they establish the conditions of their own evolution. They regulate their internal environment (homeostasis) and respond to their environmental conditions with physiological adjustments and, over generations, evolutionary adaptations.

The dynamic interplay between organisms and their environmental pressures and conditions determines their evolutionary trajectories as traits that confer advantages in particular environments are passed to future generations by the feedback process of natural selection.  In co-evolutionary terms, each species’ traits and behaviors influence the evolution of other organisms thus helping to shape evolutionary pathways.

These are the questions that will be addressed as this article systematically investigates what is meant by a biological agent, biological goals, and the means used by biological agents to pursue their goals.

Pre-cognition & cognition

Organisms are goal-directed biological agents that act on, and respond to, their conditions of existence. However, we strongly associate all agency with human agency and human cognition, and this means that if we are to accept the agency of non-cognitive organisms then we must also accept that they have non-cognitive agential traits. This is the currently unsettling world of ‘mindless’ biological purpose and biological agency.

This website describes the realm of non-cognitive agential traits as pre-cognition and explores the possibility that the properties of cognition evolved out of universally shared properties of ancestral pre-cognitive traits.

The biological agent

We intuitively treat organisms as the basic operational unit of biological science – the canonical biological agents. Indeed, biology is sometimes defined as the study of organisms.^[99]

The primacy of organisms has, however, been challenged on several fronts as more biologists have accepted that agency is distributed generally through living systems.

This has happened in response to several questions. Why are we to privilege any of the hierarchical levels of biological organization above any other since each level seems to have its own agency, role in evolutionary selection, capacity to adapt, and so on? How are we to distinguish life from non-life? All organisms, we now know, are composed of cells so aren’t cells the foundational units of biology? Or, since genes seem to be crucial component of biological continuity, encoding all the necessary conditions for life, then maybe it is genes that are pulling the strings of life? The seeming independence of many organisms may be challenged by their dependence on populations of associated viruses and bacteria such as the surface and gut organisms that are crucial to the lives of humans to become multi-organisms sometimes called holobionts. Included here are aberrent ‘individuals’ such as clonal forests of trees, the Great Barrier Reef, Portuguese Men ‘o War, and others. It is also evident that organisms as collectives – populations, colonies, swarms etc. – display their own integrated unity such that individual organisms may be subsumed under greater wholes.

Exceptions and gradations have therefore challenged simple notions of a single biological agent, basic biological unit, or of organisms as being exceptional.

This complexity has resulted in an existential pluralism in which the choice of biologically privileged unit and its autonomy becomes a matter of context and convenience, depending on the question being posed. Indeed, biological subdisciplines – genetics, cytology, physiology, ecology etc. – have their own pragmatically determined and preferred biological units.

The remaining part of this section on biological agents considers an unconventional taxonomy of biological objects (useful when addressing other biological questions), before examining the conventional division of biology into hierarchical levels of organization and its challenges to the primacy of the organism.

Biological objects

We like to think that the categories we use to carve up the biological world correspond to the way the world actually is – to reality. It is clear, however, that these categories are, to some degree at least, categories of convenience that arose as a historical legacy. We are, of course, at liberty to divide up the world as we please, and one useful distinction may be drawn between structures, processes, and behaviors (click this hyperlink for a justification of this taxonomy). The utility of this classification is that it embraces the full range of biological phenomena and biological subdisciplines while opening the mind to biological possibilities.

Structures – (both wholes and parts) are the physical ‘things’ of biology that ranging from sub-organismal entities like molecules, genes, cells, tissues, and organs, to supra-organismal entities like colonies, populations, and ecosystems – even mother nature, or planet Earth (Gaia).

Processes – imply the notions of time and change that are obscured in the language of structure. Biological processes occur both inside and outside but in exchange with living systems as open systems. In organisms they include photosynthesis, homeostasis, blood circulation, growth, metabolism and so on.

Behaviors, both minded and mindless in both organisms and their parts, are treated as being goal-directed, at least in the minimal sense of having functions.

This classification loosely reflects the history of biology as it moves from the static description of things (morphology, taxonomy) to their dynamic processes and functions (physiology) to their behaviors (ecology, ethology, psychology). It also reflects a scale of somewhat increasing agency.

The biological hierarchy

The conventional way of investigating biological phenomena is to give serious consideration to the objects of biology’s hierarchical levels of organization.

Biology is traditionally organized into interactive hierarchical levels of organization as levels of increasing physical complexity – from molecules to genes, cells, tissues, organs, organisms, communities, populations, ecosystems, biomes, and biosphere with each level loosely corresponding to a field of study. Each level can then be allocated an individual identity, not only in terms of its organization but also its agency, role in evolutionary selection, and so on.

How are we to distribute agency among this possible range of biological objects?

If organisms are understood as the canonical biological individuals and agents then the agency we might attribute to other biological objects (structures, processes, behaviors) plays a subordinate role to the overarching agency and individuality of the organism.

What is the justification for this claim?

If we take an egalitarian approach to the biological significance of objects of graduated organizational complexity then this leads to an agential pluralism with agency all the way down. 

The organism then becomes a reference point for the categorization of biological objects which extend into the sub- and super-organismal realms.

Autonomy

The human discrimination of objects in the world depends, at least in part, on our human mode of perception and cognition.

How do we justify the individuation of biological objects?^[65]

All objects of the universe are connected in space and time, so no object is autonomous in an absolute sense.

The structural and functional independence of every biological object is clearly a matter of degree. A living heart can only exist outside a body when specially preserved. For scientific convenience, we individuate categories appropriate for study – like organisms, bones, leaves, cells, populations, and ecosystems. Though distinguished as ‘individuals’ they differ widely in their degree of autonomy within the world.

So far biological objects have been classified according to two criteria: physical organization (hierarchical levels of complexity) and mode of existence (structure, process, behavior) with the former providing the conventional metaphorical structure for biological study. Each hierarchical level makes its own unique contribution to a comprehensive or holistic understanding of the biological world with advancements at one level informing the other levels. The significance of each level therefore depends on the specific question or aspect of biology being investigated.

The academic elaboration of this ladder of life followed the historical proliferation of biological disciplines at both micro- and macro-scales, each discipline with its own terminology, principles, and practices. This has resulted, on the one hand, in a perception of biology as a pragmatic pluralism in which no subject or biological object warrants explanatory or physical elevation above any others. On the other hand, some fields promote special status for their preferred individuals.

Are there any biological objects that justify prioritization over others as having an exceptional degree of autonomy?

The most popular of those fulfilling agential and life criteria of being able to survive, reproduce, adapt, and evolve – are cells, genes, and organisms.

Cells are the building blocks of all life that  perform essential life processes. Single cells were the only life forms on Earth for c. 2.5 billion years. However, in multicellular organisms, evolving c. 1.25 billion BP, they form strong dependencies on surrounding tissues and organs.

Genes are the building blocks of heredity containing the instructions for the development, traits, and maintenance of life. However, they are located within cells and other structures, and gene expression is subject to complex regulatory processes.

Organisms can survive, reproduce, and adapt with a degree of physical and functional independence not found in cells and genes although they too are subject to a wide range of external influences. What constitutes an organism is not always clear e.g. lichens, Portuguese Men-o-War, and collectives sometimes display extraordinary degrees of integration e.g. a school of fish, a murmuration of starlings, or the eusociality of termite colonies.^[63]

Walsh (2015, p. 163) contrasted genes and organisms as canonical units of evolution as follows: ‘Genes, on the Modern Synthesis View, are mechanico-computational devices, encoding information, and acting as a centralized command center for the construction of organisms. Organisms are purposive, self-synthesizing, self-regulating entities, open systems, constantly changing matter and energy with their environments. And ‘Agency, like purposiveness, is an observable property of a system’s gross behavior. It consists in a capacity of the system to pursue goals, to respond to the conditions of its environment and its internal constitution in ways that promote the attainment, and maintenance of its goals states‘ (p. 210).

Open systems

Though organisms, as biological agents,  express a high degree of autonomy they are, nevertheless, part of an organism-environment continuum. They are open systems with inputs, outputs, and internal processing. Body processing maintains essential life processes including the functional integration and regulation of flows of energy, information, and materials. Homeostasis, for example, stabilizes the internal environment to maintain conditions conducive to survival.

Inputs from the environment include materials as a source of energy (food), and stimuli that are accessed and processed by a sensory system. Internal processing includes the metabolism and processes needed to complete the organism’s life cycle of growth, maturation, reproduction, senescence, and death. Outputs include material waste, energy, and internally generated behavior that is the organism’s response to its conditions of existence, both internal and external.

While organisms, as open biological systems, have many dependencies, they are exceptional in their agential unity of purpose. This ordered integrity is maintained against the natural tendency of the universe towards disorder (entropy). They do this by taking in energy (sunlight, food) and using that energy to power the processes that sustain their organization.

Though organisms are continuous with their surroundings, they stand out as independent operational units – drawing on their surroundings to maintain this agential independence.

Space & time

Life is a process that takes place in space and time, and part of that process is the autonomous activity that we associate with biological agency. How do these concepts fit into the way that we currently represent biology . . . our metaphysical picture or most general understanding of what biological science is all about?

The prevailing imagery of biology – our way of explaining how the whole subject hangs together – is not presented as process or agency, but as things. Living systems are conceived as arranged into hierarchical levels of biological organization, say – from atoms and molecules to cells, tissues, organs, organ systems, organisms, populations, communities, ecosystems, and the biosphere. Each level of biological organization consists of structures or ‘things’; it builds on the lower levels and exhibits novel (emergent) properties that arise out of the interactions of the components at lower levels.

This hierarchical arrangement of life into a ladder of levels or ranks is a metaphorical tool or heuristic that helps scientists study the complexity of life in all its complexity – from molecules to global ecosystems. It addresses key intuitions about the nature of reality: relative size, progressive inclusion, and increasing complexity. But hierarchy and levels are not part of the world; nature is not inherently ranked into levels of organization like superimposed geological strata. Hierarchy is an explanatory tool, not a statement about the nature of the world (it is an epistemology not an ontology).

Biology would be better served with a metaphysic that excluded hierarchy and its confusing related idea of levels of existence and included the important notions of process and agency.

Roles of agency & process

The philosophy of biology must take account of not only the biological agency that is pervasive in nature, but also the human agency (as human cognition) that influences our interpretation of events and objects in space and time.

Human agency
There are two important aspects to our human spatiotemporal interpretation of the world: first, our uniquely human direct experience of objects in space and time; second, our intellectual capacity to think of and represent the world as process occurring at different spatiotemporal scales.

Human umwelt
Our direct human perception or sense of space, time, and objects is a human perception. It is our species-specific sense of what it means to be ‘here’ and ‘now’ experiencing the objects of a human umwelt (see manifest image).  Human cognition is adapted to (familiar and comfortable with) scales that were important for human survival in ancient environments of evolutionary adaptation.

All organisms adapt to and therefore interact with or ‘perceive’ their conditions of existence, so they must have some kind of spatiotemporal sense. But. whatever the biological ‘here’ and ‘now’ is for a fly, fish, dog, or daffodil, it will be very different from our human ‘here’ and ‘now’. And, just because we have big brains does not mean that our ‘here’ and ‘now’ is the true ‘here’ and ‘now’ . . . it is just the human ‘here’ and ‘now’.

It is the human here and now that frames our contextual understanding of the world.

Spatiotemporal scales

Regardless of what science tells us about the physics of space and time, our brains present the world to us on the stage of human space and time (see Immanuel Kant).

Amazingly we can, almost simultaneously, picture in our minds (in our informed imagination), on the one hand, what is happening in our bodies at an unseen molecular scale and, on the other, the way that life evolved over billions of years. We have the remarkable capacity for abstract thought, foresight (anticipation), and hindsight as informed by knowledge from scientific technology that has allowed us to examine the world at micro- and macro-scales that are far beyond the horizons of our biologically given senses.

We want science to give us the best possible objective representation of the biological world.

The conventional biological hierarchy presents us with timeless objects (presented to us in an abstract or non-specific way): molecules, tissues, populations, and so on. But it is possible to replace what we treat as hypothetical ‘levels of organization’ with ‘spatiotemporal scales of existence’. This has several advantages. It introduces time – and therefore process – into our understanding of biology which becomes the simple and explicit study of life at multiple spatiotemporal scales. It also removes the confusing conceptual baggage associated with hierarchies and brings with it an epistemology that is closer to an ontology while retaining the consideration of size, inclusiveness, and complexity. It recognizes that biology studies the complex, dynamic, and interconnected processes that may be studied and described at different scales of space and time.

Life-lines
The use of spatiotemporal scales allows us to allocate specifiable boundaries to the spatiotemporal existence of any physical object.

The limitations of human cognition become apparent when comparing biological phenomena at extreme scales of space or time relative to human cognition as evidenced in the following examples:

a) comparing extremes of space e.g. we do not describe a landscape in terms of its constituent molecules
b) comparing extremes of time e.g. we account for the anatomical evolutionary changes that occurred in organisms over billions of years in terms of second-by-second activity
c) comparing an extremely short time over a large space e.g. what happens in an ecosystem in a millisecond
d) comparing an extremely long time over an extremely small space e.g. what happens to an organic macromolecule over a billion years.

Each biological object has a spatiotemporal existence, referred to here as its life-line, a concept that allows us to compare scales. The life-line of humans is our cognitive spatiotemporal reference point (what is spatiotemporally real in the human umwelt)  so the life-lines of other biological objects are relative to that. The life-line of a biological macromolecule is thus significantly less than that of a human and the life-line of an ecosystem significantly more.

We think of biological objects as contemporaneous spatiotemporal units: that is, they are objects existing wholly in the present. But we can, at least in theory, hold either space or time constant while considering the effect of altering the other dimension. For example, when we compare molecules to cells to tissues and so on up through the traditional biological hierarchy, the molecule decreases in significance in properties of size, inclusiveness, and complexity.

We have found ways of overcoming the complexities of describing widely divergent lifelines. We have done this by developing separate domains of description, often separate disciplines, that deal mostly with biological objects at a specific spatiotemporal scale although this becomes conceptually complicated by interaction at many scales.

An explanation of the dynamics of an ecosystem must consider the interactions between organisms, abiotic factors, and ecological processes such as nutrient cycling. Attempting to understand these phenomena solely at the molecular scale would overlook the emergent properties that arise from the system as a whole.

The regulation of physiological processes within an organism involves intricate feedback mechanisms operating at multiple scales and a comprehensive understanding of homeostasis requires a knowledge of both the molecular mechanisms underlying cellular function and the integrated responses of organ systems to external stimuli.

Finding the appropriate scale of analysis is crucial for gaining meaningful insights, along with recognizing the limitations of human cognition in dealing with extreme scales of space and time.

Ranked scale

The world itself is not divided into either ‘hierarchical levels of biological organization’ or ‘spatiotemporal scales of understanding’ these are not descriptions of the world but convenient methods of explanation.^[109]

Is there any system of explanatory prioritization that would serve biology? Or, in other words, is there a scale of existence that should be privileged over others when we are doing biology?

This issue might be viewed from different perspectives so, for example: are there particularly significant levels/scales of evolutionary selection; or degrees of agency related to organizational complexity, especially that relating to cognition?

Biology has, for the most part, adopted a pragmatic pluralism with no privileged scale of study. Such questions are usually treated as contextual – depending on the specific question and the nature of the phenomena being investigated. But while scientific research is justified at all scales, and all biological objects exist, as it were, equally – this does not mean that they must be explained as having equivalent biological status – that they are all related equally.

Biological thinking and explanation, both tacit and explicit, use the organism as a reference point. Biology divides simply and naturally into three categories: organisms, parts of organisms, and aggregations of organisms. The parts of organisms are ultimately subordinate to the goals of the organisms of which they are a part. But human cognition can establish its own priorities. Is this classification of the biological world simply the imposition of a human perspective on biology or is this the way the world is?

Purpose, agency, intentionality, and value – including the capacity to adapt and evolve – may be attributed to various scales or levels of biological organization. However, it is organisms – rather than their parts or collectives – that are natural explanatory reference points in biology. As autonomous biological units, they clearly display that propensity to survive, reproduce, adapt, and evolve which makes them the paradigmatic focus of life and agency as they cycle repeatedly through the process of fertilization, growth, maturation and reproduction, senescence, and death.

Scales of space

Science and technology have extended biological science into the micro- and macro- domains – from macromolecules to biomes and the biosphere. This means we can understand and explain the world at many scales, not just the intuitive common-sense scale of our human biology. The bodies of knowledge focused at particular scales have become academic disciplines, each with its own set of structures, processes and behaviors explained with its own principles and terminology.

So, for example, the analytic turn of the last 150 years opened up the new world of microbiology and the conomic benefits of biotechnology. Though biology revolved around organisms composed of cells, it was genes, the new science told us, that were ‘pulling the strings’ of life. Now we are not so sure.

Scales of time

Contemplating time in biological systems draws our attention to change and the fact that life is more a process than a thing. Also, while physical time might have universal properties, the biological time experienced by each organism relates to its umwelt.

So, how does biological science understand and explain its temporal frames?^[97]

Biology must cope with vastly different time scales – from the microseconds of molecular interaction to the instant of an insect’s wing beat, or the depths of geological time.

Static structures undergoing temporal change become processes and behaviors.

Process philosophy draws attention to our understanding, in a general sense, of ‘things’ as regions of temporary stability (life-lines) in the general flux of entangled processes. For humans, ‘things’ represent stasis – as bounded, autonomous, independent, and stable points of reference when viewed from a human temporal perspective. But ‘thingness’ is relative to the timescale – and the human time scale is only the human time scale. Mountains are not necessarily permanent and static objects – they appear, transform, and disintegrate in a brief instant of universal time. Their life-lines are extended only in relation to ours.

For organisms, short-term behavior employs the behavioral language of action and reaction, stimulus, and response. At this scale of time, adaptation to the conditions of existence does not entail inherited traits. But behavior in the present, over longer periods, creates environments of evolutionary adaptation that lead to inherited outcomes. Short-term ethology turns into studies of functional adaptation and evolutionary biology.

An organism does not carry its biological clock like a watch on a wristband: it may have an independent time-keeping mechanism, but that will be part of a functional whole.

Organismal adjustment or adaptation can be related to the behavioral present of the organism’s umwelt and to the long-term genetic changes that occur in geological or evolutionary time. The scale of time relevant to its umwelt might be the time it takes for, say, an insect wing beat, for a flying swallow to catch a fly, or for a bat to avoid other bats in a cloud of its fellows. This is not the same scale as human time.

Biological agency is most evident in the brief moments of adaptive significance in the organism’s umwelt. Biological history is like human history, over the short term we think of people, events, and places but over the long term these factors are swamped by wider environmental factors.

Emergence

The division of existence into wholes and parts (mereology) can be extremely confusing. We tend to think analytically, gaining an understanding of wholes by looking at the operation of their parts. But every part is also a whole so we can proceed, so to say, in the other direction by using synthesis to become progressively more inclusive. Thinking in terms of wholes and parts quickly becomes a hall of mirrors. 

Pondering this conundrum makes us think about what makes some objects more strongly individuated than others, and the factors we use to distinguish wholes from parts (& vice versa).

Humans can think and are composed of molecules: does that mean that molecules can think? An organism consists of molecules: are these molecules aggregated together in the same way that grains of sand are gathered into a heap of sand?

New properties emerge as the structures, properties, and relations of things in the universe change. The universe was once a more or less uniform plasma, but it produced the novelties resulting from reorganization – stars, organisms, and human subjectivity, as matter that is aware of itself. This evolution of novelty in the universe has become known as emergence.

In biology especially, new properties emerge from the interactions of parts that are subordinate to the (usually mindless) goals of the whole. Metabolism is not just matter in motion, it is a miracle of functional integration. The whole organism illustrates better than anything else in nature, the extreme difference between the inert aggregation of grains of sand and the agential aggregation of biological structures, processes, and behaviors.

We are living in an age of analysis and the profound belief that we must understand and explain wholes in terms of their parts.  This methodology has limitations. Are the many physical adjustments we make when driving our cars a whole-of-organism response, or can they, for example, be simplified by analyzing the processing of visual information in our cerebral cortex? Here lies the problem of reduction. Driving requires attention, decision-making, and the coordination of multiple sensory inputs, including those that are visual, auditory, and tactile.

As Aristotle pointed out, in biology the whole is most definitely more than the sum of its parts – not in terms of its physical composition but what emerges out of their functional integration. Paradoxically, emergent properties allow us to explain an organism, not in terms of its parts, but in terms of itself. Emergent properties are whole-of-organism properties superimposed on the various properties of its parts. 

The autonomy of organisms that results from the extreme strength of their functional integration differentiates them from both their parts and other objects in the universe. The biological agency of the individual organism is so powerful and so similar to our human mind-driven autonomous agency that we have fallen into the intuitive habit of calling organisms ‘selves’.

Self & other

Humans have an extremely powerful sense of ‘self’ as a conscious experience of existence that engages a sense of personal identity, cognition, and behavior. 

Our ‘self’ is, in some way, all of our structures, processes, behaviors and cognitive faculties fused into a single intentional entity. As ‘selves’ we do not doubt our capacity to forge our own destinies.

As whole organisms existing as functionally integrated ‘selves’ we never consider our parts as our equals. Why should biology treat ‘hierarchical levels of organization’ as equals when it is entire organisms that determine ultimate goals and give life its meaning? Is it me who decides to take a new job, or is it my genes?

Macromolecules, genes, hearts, tissues, cells, physiological processes, populations, communities, and behaviors all demonstrate a degree of agential autonomy. The sense of ‘self’ and ‘other’ in biological systems is especially pronounced in immunology.But that autonomy refers back to, and is subordinate to, the ultimate ‘self’, the organism as a physically bounded unit of matter with a unity of purpose. A termite colony has collective goals, but it is not a ‘self’.

‘Self’ is a word that we apply to a discrete agent with a special kind of autonomy. It is most obvious to organisms that we apply expressions like ‘self-regulation’, ‘self-organization’, ‘self-maintenance, ‘self-replication’, ‘self-preservation’, ‘self-determination’ etc. Compared to other biological objects organisms are, indeed, more ‘self-contained’.

Use of the prefix ‘self’ reflects our intuitive acknowledgment of both an organism’s agency – its capacity to act on, and respond to circumstances as an expression of its own goals. While such language is used for the goals that exist at any level of the biological hierarchy, these are ultimately subordinate to the agency of individual organisms.

We treat an organism as a ‘self’ because, as a biological agent, it is motivated by the same general biological principles as ourselves. Organisms demonstrate these principles in a more unified and autonomous way than any other biological object.

Actors & objects

An organism can be described from two perspectives – as either a subject or object.

The human sense of ‘self’ and ‘other’ as a demarcation or boundary between an agent and its mission, is readily transposed to the interaction between events and their experiencers – the relationship between organisms and their conditions of existence. While the conditions of existence that determine the behavior of an organism are both internal and external, they are sometimes treated as only external: that the organism is somehow passively molded by its environment.

Is the organism an active participant, a causal factor in its own existence, or is it a consequence of its circumstances?

Subject-orientated (first-person) explanations use agential first-person ‘experiential’ terms relating to the organism’s umwelt as it acts on and responds to its conditions of existence (e.g. the bird sings to seek a mate and to proclaim its territory).

As the object of an external observer, the organism becomes a passive product of internal and external factors that shape its existence – factors that are described in detached third-person terms (e.g. bird singing behavior is driven by the mating and territorial instincts).

This distinction has serious implications for the way we explain evolution.

Object-oriented (third person) evolutionary explanations tend to ignore organismal agency and interests, taking an analytic approach, explaining biological phenomena by looking at simple components and their operations – like cells, genes, and proteins – essentially the elements of molecular biology and genetics. This provides valuable insights into the physical structures and processes involved in evolution and the mechanics of their interaction, but it does not capture the complexity, diversity, and novelty that arises from their integration.

In contrast, subject-oriented (first person) explanations take a synthetic or holistic approach. They are found mostly in evolutionary biology, ethology, and ecology, and they emphasize adaptation and selection pressure, drawing attention to the purpose and agency that becomes more apparent at these scales where individual organisms play a greater role and where emergent properties arising from the functional integration of system components become more apparent.

The agency of non-cognitive organisms derives from their behavioral orientation as a perspective akin to a human ‘point of view’ – the disposition to survive, reproduce, and flourish. And, since this propensity can be ‘helped’ or ‘hindered’ by circumstance, organisms have non-cognitive ‘interests’. Cacti have spines that deter herbivores, and even single-celled organisms respond to stimuli in a manner that expresses ‘self-interest’. When Darwin spoke of a ‘struggle for existence’ and ‘survival of the fittest‘, he was talking of the interaction between organisms (not cells or genes). Organisms influence their evolutionary trajectory by creating their environments of evolutionary adaptation, while genes remain locked inside the cells and fortunes of the organisms of which they are a part. Organisms shape their evolutionary path by creating adaptive environments, while genes remain integral but subordinate to organismal agency.

While some may argue that attributing agency to non-cognitive organisms is anthropomorphic and speculative its acknowledgment gives us a better understanding of how individual organisms actively shape their environments of evolutionary adaptation by influencing the selection pressures that result in heritable traits. If purpose and agency are treated as strictly cognitive phenomena, then biology has no means of describing non-cognitive goal-directed behavior – using terms like ‘natural purpose’, ‘teleonomy’ and resorting to the use of cognitive metaphor. We need agential biological language that does not adopt a human (anthropomorphic) perspective and yet acknowledges the intrinsic goals and behaviors of non-cognitive organisms.

A full account of evolution must adopt both object and subject modes of explanation, including both the analysis and synthesis that incorporates all aspects and disciplines of biology and the multiple organizational scales at which we describe biological structures, processes, and behaviors. By integrating the insights gained from organismal agency with traditional genetic and environmental explanations, we can unlock new insights into the complex processes driving evolutionary change.

The behavior of every organism is an act of agency: it is the external manifestation of an internal resolution between its autonomous behavioral orientation and its constraining conditions of existence (both internal and external). Organisms, as biological agents, initiate change by altering their conditions of existence according to their goals.^[67] 

Evolutionary theory must acknowledge that organisms are autonomous biological agents that actively shape and are shaped by their conditions of existence.

Self-replication

Nature has not produced a living unit of matter that can persist indefinitely without replication. Replication is necessary for the evolutionary continuity of kind over multiple generations.

The reproduction of organisms occurs within a cycle of birth, growth, maturation, reproduction, senescence, and death. Aristotle referred to this as partaking in the ‘eternal and divine’. He was referring to the way that species, like gods, are potentially eternal, passing on their unique characteristics from generation to generation. As a nod to the Modern Synthesis, present-day evolutionary biologist Richard Dawkins refers to this as the ‘immortality of our genes’.^[4]

Replicators can be found at many scales of biological organization. Among the most common are genes, memes (units of knowledge influencing cultural selection), ribozymes, chromosomes, genomes, organelles, and organisms, each with its own characteristics and crucial role in evolution.^[80] All of these, except organisms and memes, are embedded within living tissues.

While this website argues for the central role of organisms in replication, mainstream biology still promotes genes as the primary units of replication, heredity, and natural selection.

Organisms generate new individuals through a complex behavioral process that engages the full range of their conditions of existence.  This involves complex adjustments to the circumstances outside their own bodies while genes and cells, replicate mechanically. Organisms engage in mating, caring for offspring, and adapting to the environment, displaying a form of autonomy that is absent in gene and cell replication does not entail such wide-ranging adaptations.

The organism

As we have seen, nature is replete with agents (actors) of many kinds – from elemental forces to natural selection itself. Every biological structure, process, or behavior displays agency of some sort.

What we call an organism consists of from one to many cells and is an obligately open system existing in a state of symbiotic dependency with other organisms. But it is most obviously a functionally integrated agential unit of matter that has proved an unavoidable reference point for biological explanation.^[105]

The proliferation of biological subdisciplines over the last century has created what has been referred to philosophically as ‘multiple realization’ – the representation of the same objects in many different ways. From this pluralist perspective, the one-time elevated position of organisms begins to recede. Pluralistic biology gives equal epistemological (explanatory) weight to its various hierarchical levels of organization – and sometimes elevates genes and/or cells to a more significant place in biology?

How can the supremacy of the organism in biology be justified? Why should organisms be treated as canonical biological agents when boundaries between themselves and greater wholes might seem so graded and poorly defined?

Biological science proceeds with the tacit assumption that ‘life comes in the form of organisms’.^[81] This is because it seems impossible to engage in biological inquiry without presupposing their existence: they serve as a reference point in biological explanations.^[82] The totality of biology consists in the study of either organisms themselves, their subordinate parts, or their collectives and their interactions (the organismal, sub-organismal, and super-organismal).

Aristotle’s saying, often translated as ‘the whole is greater than the sum of its parts‘ is supremely exemplified through the organism. From the functional integration of organism parts emerges something truly miraculous and novel, with its own unique properties – a biological agent – a unit of matter that has, in its history on Earth, demonstrated a unique capacity to survive, reproduce, adapt, and evolve into a form that is aware of itself.

So, in sum, why is the organism the most individuated of biological objects? The evidence for the primacy of the organism in biology comes from many sources.

In nature, agency, intentionality, structures, functions, and behaviors are physically manifested by degree. However, the physically bounded structural and functional integration of organisms as autonomous biological units with the propensity to survive, reproduce, adapt, and evolve, makes them the paradigmatic explanatory reference point for both life and biological agency.

Their distinctive features include:

• • • While living systems are open systems, each organism is (usually) physically bounded; it has a unique genetic makeup and phenotype that impart an autonomy, individual identity, and physical separation from other biological entities
    • Lifecycles of fertilization, growth, maturation, reproduction, senescence, and death with the potential for indefinite temporal continuity of kind
    • Structural and functional integration exceeding that of their subordinate sub-organismal components and supra-organismal aggregates and collectives
    • Strong autonomy demonstrated in self-replication, self-maintenance, self-organization, and self-preservation
    • Adaptive responses to stimuli that often entails complex traits and behaviors
    • Agency that drives natural selection and genetic drift, thus contributing to genetic diversity and driving evolutionary dynamics
    • They are the focus of energy flow, nutrient cycling, and community dynamics in ecosystems

Origin

Replicators can be found at many scales of biological organization. Among the most common are genes, memes (units of knowledge influencing cultural selection), ribozymes, chromosomes, genomes, organelles, and organisms, each with its own characteristics and crucial role in evolution.^[80]

While the origin and nature of the earliest lifeforms remain a biological mystery, it is life in the form of ‘organisms’ – not just replicating matter, but replicating matter that could survive, reproduce, adapt, and evolve – that was the genesis of the world of biology. This world divides naturally into organisms as functionally integrated wholes, their subordinate parts, and organisms as they exist and interact in communities of various kinds.

Whether the organism preceded natural selection, or was generated by it, remains an open question.

Autonomy

We tend to relate the distinctiveness and individuality of organisms to both their physical and agential autonomy. Physical autonomy includes the truly remarkable continuity of identity through the major physical changes that occur across the organism’s life cycle, including the reduction to gametes and gene transfer. Agential autonomy is demonstrated by individual organism behaviors as they adapt to their conditions of existence across various time scales.

The structures, processes, and behaviors of organisms are subordinate to the overarching and unified goals of the organism as the canonical unit of functional organization.

However, autonomy in biology can differ in both degree and kind cf. viruses and the cellular automata of mathematics and computer science, and various other replicators.

Agency

While the parts of organisms exhibit agential properties that warrant them being treated individually as agents, these agential properties and goals exist in support of (are subordinate to) the universal, objective, and ultimate goals of the organism as a whole.

While the social activity of collectives such as termite colonies, involves a division of labour and specialization among its constituent organisms towards common goals, this cohesion cannot compare with the degree of cohesion that occurs in the functional organization of its component organisms.

Organisms manifest their agency as a high degree of self-determination. As Kant expressed it, organisms are ‘both causes and effects of themselves‘;^[71] they can influence their own destiny.

Organisms are the model biological agents, regardless of scale. Almost any biological object can be ascribed agency and the capacity to adapt but it is the organism that is, both intuitively and empirically, its textbook exemplar. Biological science would benefit by making this fact explicit.

Okasha^[55] points out that while many biological entities have been treated as agents the organism serves as the paradigmatic case. And, though various factors have been used to establish organismic autonomy (e.g. goal-directedness, functional organization, emergence, self-maintenance, and agency itself) he selects three preferred ‘rationales’ for considering organisms as biological agents, as ‘the locus of goal-directed activities‘: goal-directedness, behavioral flexibility, and traits that are adaptations.

For Okasha the notion of agency applies paradigmatically to organisms because it is an ‘implicit theoretical commitment of agential thinking in biology‘. The parts or traits of organisms have evolved ‘because of their contributions to a single overall goal‘. It is the whole organism that expresses most clearly a ‘unity of purpose‘. The meerkat’s warning behavior – like its structures, processes, genes, and component cells – has a function, but it is the meerkat that sees the danger and warns its companions.

Unity of purpose

As biological agents organisms are units of functional organization that demonstrate flexible goal-directed behavior that displays a behavioral orientation (perspective or ‘point of view’), the objective, universal, and ultimate behavioral propensity to survive, reproduce, and flourish.

These goals constitute a unity of purpose towards which all entire autonomous organisms, both minded and mindless – including their subordinated structures, processes, and behaviors – are directed. Other essential structures and processes we associate with life – genes, cells, metabolism, homeostasis, growth, adaptation, and even evolution itself – might be considered subordinate to the objective, ultimate, and universal mission of whole organisms as goal-directed autonomous biological agents.

While the structures, processes, and behaviors of organisms have their own degrees of self-regulation, goal-directedness, biological value (a heart can operate for better or worse in relation to its own persistence), and contribution to evolutionary selection, the meaning of these functions derives from their support for the unity of purpose (the functionally integrated behavior) of the entire organism – which is grounded in its survival, reproduction, and flourishing).

So, for example, meercat warning behavior – like the meerkats structures, processes, genes, and component cells – has a function, but it is the meerkat itself that sees the danger and warns its companions. While genes certainly constrain the range of possible meerkat behavior (its potentiality), it is the functionally integrated behavior of the meerkat that contributes directly to biological outcomes, including the determination of its environment of evolutionary adaptation (the actuality) the broader context in which its structures, processes and future behaviors must also exist.

Put simply, structures (including genes), processes, and behaviors have organismal functions (as adaptive significance) that are subordinate to the goals of the organisms of which they are a part. And, since they have evolved in support of organismal goals it makes sense to treat organisms (not their parts) as biological agents.

Functional integration

One major aspect of biological agency comprises internal processing that integrates multiple cell types, processes, levels of organization, and behaviors into a focus of agency that is manifested as a unity of purpose – the propensity to survive and reproduce. This represents the highest degree of functional integration and autonomy in the biological world as an adaptive emergent property that far exceeds that of cells or genes, and connecting organisms to broader ecological and evolutionary contexts.

Replication

As a unit of reproduction, the organism demonstrates more autonomy than any other replicator, maintaining its identity as it passes through phases of fertilization, growth, maturation, reproduction (with associated genetic transfer), senescence, and death.

Physical separation

Organisms are part of an organism-environment continuum. They are open systems with inputs, outputs, and internal processing of energy, materials, and information.

However, all these flows are functionally integrated, giving rise to a self-maintaining, self-determining, self-replicating and more or less autonomous discrete and physically bounded biological agent, albeit one in constant interaction with its conditions of existence.

Autonomy in biology is always a matter of degree. Organisms exist with a surface flora of microbes and an obligate internal gut flora of independent organisms on which the organism, as a holobiont, depends. The Great Barrier Reef looks like a single organism from space, and what seems like a a forest of maples can be saplings produced from the root system of a single individual (clone). Biology is full of exceptions and gradations.

Regardless, this clearly contrasts with the total dependency of physical connection we see in cells and genes, while the wider frames of social organization including holobionts, colonies, swarms etc. hardly threaten the strength of functional integrity so evident in the individual organism. 

Behavioral units

It is helpful to distinguish between agency as the ability to act and behavior, often treated more specifically, as a particular kind of action performed by an agent. Organisms demonstrate their autonomous agency through the different kinds of behavior they employ while constantly adapting to their conditions of existence. 

This behavior is generated by an internal process of reconciliation between the natural propensity of the organism and the constraints of its circumstances. Of course, such a process could not occur without the contributions of genes, cells, biochemical processes, molecules, and so on – but it is their functional integration that establishes the entire organism (not these supportive, and therefore subordinate, factors) as the canonical biological agent.

Evolutionary selection

The basic unit of evolutionary selection is sometimes treated as a matter of context since selection can act at multiple levels of organization simultaneously, so the level of consideration may vary according to the trait being considered. For example, macromolecules, genes, cells, groups, species, or even ecosystems are all potentially subject to selection pressures based on their heritable traits. Genes may be treated as the primary units of selection when considering phenomena like genetic drift and there is disagreement as to whether group selection or individual selection drives the evolution of traits like altruism.

Organisms may be characterized in evolutionary theory as passive objects programmed by genes and shaped by external evolutionary events whereas they are adaptive systems that influence their own evolutionary paths. It is misleading to point out that genes determine traits and that organismal behavior is therefore, as it were, subordinate to genetics. Genetics sets the parameters or limits to possible behavior, but organismal behavior determines outcomes in real time. Given a particular genotype, it is organisms as biological agents in interaction with their conditions of existence that determine their environments of evolutionary adaptation and therefore the traits that will be encoded in their future genes.

Even so, the organism is generally considered the fundamental unit of evolutionary selection since it is the differential survival and reproduction of individual organisms that drives evolutionary changes from one generation to the next. That is, natural selection acts at the level of the individual organism when, under the classic circumstances, it acts on the characteristics of individual organisms within a population, favoring, over time, those traits that increase the organism’s chances of survival and reproduction. It is the individual organism that expresses the necessary agency, adaptive traits, differential reproduction, and mode of natural selection that promotes the acquisition of advantageous traits in populations.

It is entire organisms – rather than their parts or collectives – that demonstrate what we mean by ‘life’ as they pass through the cycle of life. As physically bounded self-replicating units with a unified functional organization, organisms express a degree of autonomy that is not found in sub-organismal components like organs, tissues, cells, and genes. Nor can such autonomy be attributed to supra-organismal collectives comprised of individual organisms. Indeed it is clear that the components of organisms, while they can be studied in their own right, are ultimately subordinate to the goals of the entire organism which therefore warrants the status of biological agent.

Umwelt

An organism’s umwelt^[94] consists of those conditions of its existence that influence its capacity to survive, reproduce, and flourish. These are the conditions that constitute the organism’s ‘reality’ or way of ‘experiencing’ the world. The umwelt is the interface between an organism and its conditions of existence, shaping its sensory experience, behavior, and evolutionary trajectory.

The human umwelt is our world of common sense (see manifest image) – the world as interpreted through the limitations of our biologically defined human perception, cognition, and sensory system. Evolutionary change can be viewed as changes in the conditions of the organism’s umwelt, often initiated by the organism itself as a biological agent.

The notion of an umwelt helps our understanding of adaptive strategies and the selection pressures influencing evolution.

Affordances

Affordances are the opportunities for an organism to influence its conditions of existence (J.J. Gibson 1970s) or opportunities for action; they are the potential existing between an organism’s capacities and the features of its environment that incline it towards specific behaviors – the circumstances of adaptation. Affordances are a concept of ecological psychology that draw attention to the organism’s ‘perceptions’, ‘cognitions’ and behavior as part of a ‘decision-making’ process.  By understanding the affordances of an organism’s environment, researchers gain insights into how certain species have evolved to, often mindlessly, exploit specific opportunities presented by their surroundings.

The Modern Synthesis encouraged a perception of organisms as passive objects programmed by genes and shaped by external evolutionary events. The Extended Evolutionary Synthesis notes that organisms – through self-organization, self-regulation, and adaptation – exhibit degrees of self-determination, their phenotypic plasticity orientated towards conditions conducive to survival and reproduction.

The concepts of umwelt and affordance draw attention to factors involved in the reconciliation that must occur between the organism, as an autonomous agent, and its conditions of existence. These conditions may influence for ‘better’ or ‘worse’ the organism’s natural behavioral propensity to survive, reproduce, and flourish. The umwelt draws attention to the ‘perspective’ of the organism and those unique physical and sensory capacities that construct its ‘experiential’ world and determine how it ‘interprets’ opportunities as affordances – thus providing insight into the process of adaptation in specific circumstances. This is a feedback loop in which the organism’s actions shape its environment and, in turn, influence its experiences, behaviors, and heredity. Understanding the umwelt of different species helps in understanding the adaptive strategies adopted in diverse ecological settings.

Together, the concepts of umwelt and affordance demonstrate the way that organisms adapt by modifying their conditions of existence in ways that influence their own evolution. This biological fact was neatly captured by philosopher Immanuel Kant in 1790 when he described the organism as a ‘natural end‘ because it is ‘a cause and effect of itself‘.^[95]

Goals (mission)

So far this investigation of biological agency has found the concept of biological agency so broad as to apply to almost any biological structure, process, or behavior. However, it has also been found that the agency of these structures, processes, and behaviors is subordinate to (supportive of) the agency of the organisms of which they are a part.

All parts of organisms are functionally integrated into a single goal-directed agential unit – the organism as the paradigmatic biological agent that acts on, and responds to, its conditions of existence. Indeed, if parts of organisms support the whole, and organisms are the operational units of collectives like colonies, and even ecosystems – then it is hardly surprising that organisms serve as the explanatory reference point for biological systems.

What, then, are the goals of an organism?

This is a devious question open to many interpretations. So, for example, is an organism ultimately about energy distribution, thermodynamics, and entropy? Is it about the organism’s genes producing more copies of themselves? Is it about growing, reproducing, metabolizing, and obtaining food? Is it about modes of information processing?

Aristotle claimed that the purpose of an organism was to maximize its potential – to be itself as best it can. That is what organisms do mindlessly (that is what they show us in their behavior, without words). And this is what humans do under the watchful gaze of their evolved mental faculties and shared symbolic languages.

What is needed here is a practical biological explanation – our best attempt at a scientifically accurate, informative, useful, and concise biological account of what organisms are all about. The answer need not be obscure or philosophical because the goal-directed behavior of organisms is an objective fact.

There are many proximate reasons for an organism’s behavior as it responds to the teeming and random events and conditions going on around it. However, from the earliest days of the subject, biologists have observed that the behavioral response of all organisms may be reduced to the objective and ultimate goals of survival and reproduction.

As a succinct summation of biological agency this unifying principle is often passed over. It is a statement of the purpose (mission) of all organisms, humans included, and is therefore a foundational principle of biology. Its importance to biological science is recognized here by treating it as a major biological principle or axiom.

Since the Scientific Revolution biology has tended to avoid agency and purpose. If a mechanical (?lifeless) account can be given of biological activity, in the same way that we provide a mechanical account of the heavens, then agency and purpose can be explained away and redirected to the human domain.

If agency and purpose are to be returned to their rightful place in biology then their scientific basis needs explanation: what are biological goals; How do goals confer agency; why do these goals need formal recognition; what is the distinction between proximate and ultimate goals; what is the difference between goals, purposes, and functions; what is the role of behavior in communicating goals; how do non-cognitive goals, as a behavioral orientation, relate to human cognitive goals and values?

These are some of the questions addressed in the section below.

The biological axiom

Living organisms are biological agents that express their autonomy as a unity of purpose – the universal, objective, and ultimate propensity to survive, reproduce, adapt, and evolve. These goals are universal because they are a necessary precondition for life itself, objective because they are a mind-independent fact, and ultimate because they are a summation of all proximate goals.

We associate science with the establishment of secure principles and universal laws, like those of physics. These laws resemble the absolute certainties of mathematics which is built on axioms – statements that are taken as self-evident, foundational, and uncontroversial. Examples from Euclid’s geometry would be that ‘Things that are equal to the same thing are also equal to one another’ and that ‘All right angles are equal to one-another’. To deny an axiom is to undermine foundations. If we argue that Euclid’s axioms are mistaken then we are, in effect, challenging the entire enterprise of Euclidian geometry.

We respect the empirical generalizations of science (its principles and laws) because they have predictive power and therefore help us manage the world and our lives. The laws of physics have the properties of axioms because they resist contrary evidence and cannot be altered without transforming our understanding of theoretical foundations.

Can there be principles or axioms like this in biology? Since biology is the study of life, then its axioms would, presumably, set out life’s universal conditions.

Aristotle was a specialist in first principles. He wrote the world’s first systematic treatise on logic, Organon, much of which still stands today as the basis for deductive logic. He understood the importance of axioms as points of stability and reference: that they are a backstop to the tendency for questioning to become diffuse, or circular, or to pass into an infinite regress. Any starting point can be challenged, but we have to start somewhere if we are to develop further reasoning and arguments. It is in this spirit that this foundational biological principle is outlined here. 

Aristotle noted that to continue existing (to survive by perpetuating their kind) living beings must reproduce. He summarized this principle by saying that all living creatures ‘partake in the eternal and divine’. By this, he meant that organisms can potentially replicate their kind (species) indefinitely (eternally) provided they can survive.

Today, having access to sophisticated technology, we might use different words that express the same sentiments, like evolutionary biologist Richard Dawkins who refers to the ‘immortality of our genes’. Or we might try to fit in more information with, for example, what has been referred to elsewhere on this website as the algorithm of life, that, ‘organisms are autonomous units of matter that self-replicate while incorporating feedback from their conditions of existence (adapting), thus facilitating beneficial [in relation to their behavioral propensities or goals] change and potential continuity of kind’. There are many distillations of ‘life’ expressed along these lines.

Biologists today think little of Aristotle, or axioms, or final causes, but any cursory examination of modern biological texts reveals an acceptance of the significance of survival and reproduction. This is an unspoken assumption within the tradition of biology but hardly expressed as a necessary first principle. Their reiteration through history vindicates their utility.

However, for the pragmatic convenience of informative communication between biologists, life may be considered as expressing four key propensities: survival, reproduction, adaptation, and evolution. These are interconnected concepts, the first three being agential properties and the fourth their consequence.

While there is a conflation of concepts within these categories, in combination they represent a powerful synopsis of our understanding of the living world.

Flourishing

Survival and reproduction have been grounding principles of biology since its inception,^[37] so the introduction of a third term seems unjustified, controversial, and unnecessary. Why suggest this?

There is a finality and absoluteness about ‘survival and reproduction’ that misrepresents what goes on in most organism’s lives. Much biological time is spent in the pursuit of proximate goals. Biology may have ‘fooled’ us humans into thinking that we are less constrained by our biology than we actually are but, even so, much of our lives is spent in activities that are only obliquely (proximately) concerned with survival and reproduction – like reading, playing with our phones, watching TV, playing sport. While other organisms do not engage in such peripheral activities their lives, similarly, are not always focused on mating or the urgency of survival. The more mundane aspect of ‘simply making things better or more comfortable’ seems only loosely connected to survival. Just living is referred to here as ‘flourishing’.

This point is best illustrated with the human case. Biology might prioritize survival and reproduction as ultimate conditions of life, but religion and philosophy have emphasized mental needs that crystallize around notions of happiness, pleasure, and wellbeing. In the last few decades it has been the word ‘wellbeing’ that appears most frequently in official documents as a universal human goal, probably because it seems to encompass (like the ancient Greek word ‘eudaimonia’) a form of collective as well as individual happiness – individuals in harmony with their societies. In the biological axiom, this notion is conveyed through the broader concept of flourishing.

Certainly, the chances of survival are enhanced by adaptation to environmental factors in an ultimate way, but organisms do not merely survive and reproduce, they can also flourish.^[52]

Biological principles

Biology, of necessity, rests on a foundation of general principles. These principles are rarely presented to students as an explicit system of underlying assumptions about life. Instead, they are left as implicit consequences of empirically based theories. Devising a system of biological principles that include all biological scales might be a useful project for philosophers of biology but, being contentious and therefore potentially unproductive, it is a project avoided by practising biologists.

The following is a brief synthesis of today’s implicit biological principles.

Cell theory, that all living organisms consist of cells—the fundamental units of structure and function; gene theory, that traits are inherited through genes on chromosomes; evolution, that genetic changes occur within populations over multiple generations by natural selection that drives the adaptation of species; homeostasis, that organisms maintain stable internal conditions despite external fluctuations; thermodynamics, that organisms maintain structure through energy flows operating against a thermodynamic equilibrium. 

If this is an accurate representation of biological principles, then does biological agency warrant inclusion?

Here, it is claimed that biological agency not only warrants inclusion, it takes precedence. Biological organisms, as paradigmatic biological agents, subsume cells, genes, and homeostasis as phenomena that are supportive of, and therefore subordinate to, their autonomous objective, ultimate, and universal agential goals. Life is most directly, informatively, and usefully recognized, defined, understood, and explained, through its agency.

Unity of purpose

The biological axiom expresses an objective, universal, and ultimate unity of purpose and agency that is most clearly expressed in nature through the autonomy of individual organisms. It is shared by all organisms as a specific behavioral orientation – a ‘mindless perspective’ that in its highly evolved and human minded becomes a ‘point of view’ or universal set of values that can be ‘helped’ or ‘hindered’ by circumstances.

This unity of purpose was present in organisms before the evolution of the human mind which is not the only form of agency but an evolutionary enhancement of a pre-existing mindless goal-directedness. More specifically, it was this autonomous, mindless, and goal-directed agency of living organisms with a unity of purpose that, over time, gave rise to human subjectivity and conscious intention.

Biologists and philosophers have long denied that life has ‘purpose’ while, at the same time, proceeding in their research as though the goals of life are self-evident. Read any biological text and you will find the explicit or implicit assumption that life is founded on self-preservation and continuity – survival, reproduction, and flourishing – both within a single generation and over many generations. Without this collective and ultimate unity of purpose life would cease. This agency must be a powerful ‘force’ since it has lasted for more than 3.5 billion years, giving rise to the entire community of life, including the human body and brain.

Biological structures, processes, and behaviors may each be telic or ‘for’ something in a functional sense (a heart is for pumping blood etc.) but it is the whole organism that, in a more clearly circumscribed way, has ‘objectives’, ‘preferences’, and ‘interests’ that can be ‘helped’ or ‘hindered’. The parts of organisms are, in this sense, subordinate to and supportive of the goals of the organism as a whole – they have functions within a purposive and agential whole. It is this condensed unity of purpose and individuality that makes an organism an autonomous agent in a way that a heart or metabolism (clearly a part of a greater whole) are not. It is also why the biological axiom is most apt when applied to organisms, not genes, groups, collectives etc. The class of telic objects, even by a scale-independent assessment, divides neatly into sub-organismal and super-organismal groups with organisms themselves as the reference point or standard. 

The expressions ‘biological purpose‘, ‘biological goal‘, and ‘biological agency‘ are related concepts best applied at the canonical scale of the organism, but each with its own nuanced meaning.

The biological purpose of an organism is equated with the overarching evolutionary reason for its existence – ultimately its survival, reproduction, and flourishing.

Biological goals are both the proximate and ultimate natural ends or limits (objectives) of organismal structures, processes, and behaviors that contribute to biological purpose. These goals are typically associated with essential processes such as growth, development, homeostasis, and reproduction such as seeking and consuming food, avoiding predators and finding mates which all contribute to the ultimate goals of survival, reproduction, and flourishing.

Biological agency then refers to the internally generated capacity of living organisms to act purposefully in pursuit of biological goals – as autonomous biological agents, acting and reacting to their conditions of existence with flexible and adaptive behavior that enhances their chances of survival and reproduction.

Biological necessity

Biology is full of exceptions and gradations; single organisms die, and even species and lineages draw to a close – but survival and reproduction are necessary preconditions for life itself. They are not logically necessary but they are biologically necessary because without them there would be no life.

We cannot expect logical certainty in biology, but the biological axiom is a simple and easily comprehended necessary and sufficient agential condition for life in general, even though there are exceptions as individuals fall by the wayside. The principle observes that though organisms, as agents, differ greatly in kind, complexity, and means of attaining their ultimate goals, they share the characteristics expressed in the biological axiom as an ultimate ‘unity of purpose’ grounding the physical diversity of organisms, including their structures, processes, and behaviors. It is these goals that give life agency, that drive or motivate life; they are what makes life vital, powering the engine of evolution and showing how organisms are different from, or a special kind of, mechanical process. 

As preconditions for life – both non-cognitive and cognitive: they define life’s biological purpose, what it is ‘for’. These were the goals present in the first simple organisms at the dawn of life – the goals that made evolutionary elaboration possible, including eventually the emergence of human subjectivity as matter that is miraculously self-aware.

Most importantly, life has a perspective on the universe. In a world of perspectiveless facts there can be no logical grounds for value. But life takes a position on its existence. As Aristotle observed, there is a biologically necessary normative perspective on ‘life’. . . that – ‘It is better to exist than not exist’ and ‘it is better to live than not live’ (Aristotle, GAi23, 731 a24-b8; GAi4,717a21-22; GAii1,731 b20-21) because life, though not logically necessary, persists. Life, unlike the constants of physics, or the detachment of mathematics, assumes a ‘point of view’.[34] All life manifests this ‘point of view’, not as a (subjective) mental representation, but as an (objective) behavioral orientation. 

This objective behavioral orientation distinguishes non-cognitive organisms from inanimate objects. As a behavioral orientation, it resembles a human value, but as a behavioral orientation, it is an objective fact. In this sense it expresses both fact and value. 

Denying the biological necessity of the biological axiom is logically possible, but it is biologically incoherent in the same way that our human desire for health and happiness is not logically necessary, but self-evident.

Aristotle noted that we do not ask ‘Why do organisms try to survive and reproduce?’ because we understand that to deny survival and reproduction is to cease to exist – and that does not make biological sense. Organisms that do not, or cannot, survive and reproduce die out – and in ceasing to exist they become biologically irrelevant.

Today, if we are asked ‘Why do organisms need to survive and reproduce?‘ we might answer, along with Darwin, and Aristotle’s biographer, evolutionary biologist Armand Leroi, ‘Because natural selection made them so‘. But isn’t Darwin’s natural selection predicated on Aristotle’s agency? This is a question that remains unresolved.

Goals, purposes, functions, intentions

When applied in a loose sense the words ‘goal’, ‘purpose’, ‘function’, and ‘intention’ may be used interchangeably. Only when we have our academic biological and philosophical hats on do we look more critically at a sentence like, ‘The goal/purpose/function/intention of the heart is to circulate blood‘.

All these philosophically charged words imply the notion of goals and goal-directedness. One way of reducing this complication is to treat the study of goal-directed behavior as a study of biological intentionality, of which human conscious intentionality is just one instance.

Intentionality

We speak of human intentionality in two senses. First, to do something on purpose or with intent. And, in a second philosophical or psychological sense, as the power of the mind to point beyond itself – for mental states to be about, to represent, or to stand for something, the way our thoughts, beliefs, desires, and perceptions tend to focus on something external to us.

In both of these cases there is a strong sense of goal-directedness such that the word ‘intentionality’ serves as a portmanteau term conveniently and expressively encompassing ‘functions’, ‘goals’, and ‘purposes’, not just in the human world of cognition but the non-cognitive living world as well.

Goal-directed behavior does not necessarily entail conscious deliberation or intention. Instinctive behaviors, automated responses, and innate mechanisms can all generate non-cognitive goal-directed behavior directed toward objects, properties, or states of affairs. It is this intentionality, as the non-cognitive pursuit of goals, that underpins biological agency, adaptation, and evolution.

The word ‘intentionality’ expresses clearly the goal-directedness of all living organisms and, on this website, it joins ‘agency’ and ‘purpose’ in the toolbox of terms that express a universal reality across the community of life.

Human cognitive intentionality is a highly evolved and limited instance of the universal biological intentionality that is usually referenced using words like ‘goal’, ‘function’, or ‘purpose’.

Biological goals

Explanations of biological phenomena – perhaps a mating display, an eye, photosynthesis, a dog wagging its tail  – don’t just tell us what these entities do, as they would for, say, a molecule or the moon. Rather, because they are goal-directed (agential) phenomena, they also tell us, in addition, what they are for.

The expression ‘goal-directed’ is rather detached and impersonal, while the word ‘intentional’ conveys more vividly the way the behavior of all organisms is directed towards objects, properties, or states of affairs. Organisms, unlike inanimate objects, express intentionality. Human intentionality involves cognition, perception, and decision-making. The intentionality of biological agency involves 

The intentionality of functionally integrated and autonomous living organisms, as manifested in their behavior, is what gives them both purpose and agency. While goals can be loosely attributed to any biological object they are most closely associated with organisms as paradigmatic biological agents. We tend to think of goals as conscious representations (intentions) in human minds. However, goals are present in nature independently of any human observer. There were goals in nature from the time of the emergence of the first organism – before humans evolved.

Biological goals are the ends that have for over 400 years been perceived as ‘teleological’ in the pejorative sense of being considered unscientific – partly because ends cannot be causes, and partly because ends are often perceived as differentiating the intentional mind (either human or supernatural) from a mechanical process.

However, there is no problem in finding criteria or principles that identify when and how teleological explanations are warranted within a naturalistic and scientific worldview (see the section below discussing purpose).

Goal-directed behavior, considered from a dynamical systems perspective, is uncontroversial. It has been defined as ‘The persistent and concerted action to attain and maintain a goal state in the face of perturbations’.^[96] This behavior does not imply mysterious design, retro-causality, a vital force, or conscious intention; it complements causal explanations by pointing out likely final states that cannot be predicted by computing trajectories from initial states; it can be used to formulate falsifiable predictions about the behavior of a goal-directed system; it can be formalized and operationalized using the dynamical systems notions of attractors and basins; and it is also possible to explain how goal-directedness may have originated and evolved.^[96]

Biological goals, then, are the proximate or ultimate objectives or ends towards which the behavior of biological agents is directed, These ends follow straightforward and transparent causal pathways. For an individual organism, a proximate end might include maintaining homeostasis, or  attaining maturity, an acorn becoming a mature oak tree. And for all organisms the ultimate ends are ‘survival and reproduction’. Though goals are the natural end-points or limits to natural processes and behaviors they may be inferred from behavior, and are not necessarily attained or maintained.^[68]

We think of goals from a human perspective with the brain as a decision-making command center. Organisms with central nervous systems have provided us with the example of behavioral unification, or functional integration, from a central hub. But there is no reason to suppose that, in a highly integrated system like a living organism, goals need to flow from a single source or have a single nature. Plants are highly integrated biological agents united with the community of life by having universal biological goals. But they have no centralized control system.

Goal-directed behavior is a precondition for both life and its agency. If organisms cannot survive and reproduce then they cease to exist.

Proximate & ultimate goals
Proximate behavior deals with the immediate demands of the present – a rise in temperature, the appearance of a predator, a feeling of hunger. Ultimate behavior refers to the ultimate reasons for proximate behavior.  Proximate explanations focus on short-term causal factors while ultimate explanations place this behavior in a long-term evolutionary context in terms of survival and reproduction. Both perspectives and time-frames are essential for a comprehensive understanding of biological phenomena.

Proximate goals seem temporary, opportunistic, circumstantial, and therefore devoid of direction. In contrast, universal biological goals reflect the inherited disposition of all organisms to survive, reproduce, and flourish as the objective, universal, and ultimate goals that are a necessary precondition for life itself. They give organisms a behavioral orientation or directionality that would be described by human-talk as a value, perspective, or point of view. It is what most organisms do mindlessly, but which humans do and describe with the assistance of their evolved cognitive faculties and language.

Biological purposes

The article on purpose discusses the distinctions between internal and external teleology, between teleolological explanation and teleology as a phenomenon in the world, and eight factors that have, in the course of history, been proposed as sources of purpose in the world.

The concept of a purpose in biology falls within the general semantic scope of purpose as – ‘the object for which anything is made, or done, or for which it exists‘ (Oxford English Dictionary). Living beings display purposive behavior that is distinctive by being generated internally, even though it may have been prompted by an external trigger. Artifacts and machines (chairs and guided missiles) acquire their purpose from an extrinsic source.

While ‘purpose’ is usually associated with human conscious intentions there is little justification for ignoring the goal-directed but mindless purpose of other organisms. It is hardly controversial to point out that the purpose of the ‘propellers’ on the seeds of maples is to catch the wind. There is, of course, a distinction between conscious intention and objective but mindless goal-directed behavior and traits. This is sometimes identified using expressions like ‘natural purpose’ or ‘teleonomy’ but on this website is called pre-cognition.

Human purposes are simply the cognitive instances of more general non-cognitive purposes exhibited by all organisms. Indeed, the universal ultimate goals demonstrated by organisms may be regarded as the paradigmatic instantiation of biological purpose.

The use of the word ‘purpose’ in biology might seem harmless (e.g. the purpose of eyes is to see), but historically it has been rejected because of its associations with teleology which is rejected for its implied introduction of supernatural forces, backward causation, and the reading of human intentions into nature.

Much of the philosophical concern over teleology in recent times, including the industrial-scale discussion of ‘function’ in biology (‘function’ as a non-teleological or anodyne homonym of ‘purpose’) involves the distinction between teleology as a form of explanation, versus teleology as a phenomenon to be explained.^[90]

Teleology as a form of explanation uses purpose or goal-directedness as an explanation for phenomena (eyes are for seeing; leaves are for manufacturing food) such that the purpose explains their existence or structure.

Teleology as a phenomenon seeks to understand why and how teleological features emerge rather than assuming purposefulness as an explanation. Science has room for both, without any need for scientific or philosophical concern.

Teleology is naturalized when we acknowledge that there are natural endpoints (goals) to natural processes. 

There are natural purposes.

Backward causation
Aristotle’s telos, the ends that drive the existence of living organisms, seems to defy science. The future cannot cause the present: nature cannot operate with foresight as the language of purpose implies (e.g. wings are for flying).

Aristotle pointed out that, just as a natural end (e.g. the maturing of an oak tree) must be last in a causal sequence, so it must also be first in explanation. To understand what a pile of construction materials means, we must first have the concept of a house. The counterintuitive assertions of teleology are described by contemporary philosopher Mariska Leunissen as follows:

Final causes explain the presence of features, but exert no ‘mysterious pull’ from the future. They rather function quite literally as the direction-givers and the ends and limits of developments necessitated by formal-efficient or material-efficient causation. In this way, they provide both the first component of a teleological explanation and the heuristic starting point for investigations that will lead to a statement of the complete teleological explanation of the phenomenon in question. This does not mean, however, that final causes have only a heuristic value: since in demonstrations of the teleological type the final causes are part of the conclusion that is being demonstrated, the practice of Aristotle’s natural science demonstrates the very existence of natural teleology.

Mariska Leunissen. 2015.

The apparent foresight of teleology is a result of its requirement for explanatory primacy, not causal primacy.^[21]

We intuitively understand that ends cannot be causes and this is why the the putative implication of ‘backward causation’ has been a major reason for the rejection of teleological explanations. While biological goals, ends, or objectives – being the ends of natural processes – are last in a natural causal sequence, they must be first in explanation. Only when the goals of whole organisms are known can their necessitating conditions be understood.

In biological science, natural ends must be last in causal sequence but first in explanation: organisms can be ‘for’ without foresight.

The supernatural
Supernatural mysteries hidden in biology were rightfully resisted by the Scientific Revolution. But instead of prohibition there was also the possibility of naturalization.  It was, for example, assumed by some that Darwin eliminated the need for ‘purpose’ by providing a naturalistic explanation for purpose in nature. Though he did indeed provide a naturalistic explanation, this did not explain purpose away. Real purpose in nature remained.

Aristotle’s inner dynamism, animating principle, or entelechy, seemed to infer a scientifically unacceptable vitalism: a strange force breathed into matter from outside, and not amenable to empirical investigation. Today, the idea of behavior generated by internal processes is uncontroversial. We are unlikely to resist the idea that the genetic code acts as life’s ‘inner nature’ or, to use Aristotle’s analogy, the ‘inner craftsman’ that provides the critical information whereby ‘like begets like’. This was an answer to Aristotle’s superficially simple and silly (but biologically crucial) question ‘Why do neither snakes nor stars have feet‘?^[17]

Even Darwin could not give a scientific account of this genetic fact. We now recognize ‘like’ organisms and their intergenerational similarity as a consequence of fully scientifically accountable genetics.

Similarly, the idea of ‘ends’ in nature now carries no supernatural stigma. The acorn matures into an oak tree, cells transform into tissues etc. Nature is saturated with ‘natural ends’ that occur in causally transparent ways.

Darwin’s account of natural selection as a mechanical process that was indifferent to outcomes effectively removed agency and purpose from the process of natural selection itself. Natural selection has no intrinsic goals or direction, it just happens. This is very different from organisms that do have intrinsic goals and purposes. It is possible to provide a mechanistic explanation of these goals, but that does not mean that these goals no longer exist. Biological goals as ends and limits of natural processes are objective components of the world.

As cognitive metaphor
By far the greatest objection to ‘purpose’, ‘agency’, and other words associated with human cognition is that they are strictly cognitive words. They are a reading of human cognitive faculties into mindless nature. They are therefore being used in an as if or metaphorical way (see Kant’s claim described in the introduction). Purpose, on this account, exists in human minds (subjectively), not in nature (objectively) (but see the metaphor fallacy described as a criticism of the Modern Synthesis above).

From the Scientific Revolution to Darwin and beyond, teleology was regarded as an Aristotelian error. How can nature display purpose when purpose is something that can only exist in human minds? The solution to purpose-talk was therefore to exorcise it altogether from academic discourse.

A philosophical industry, still active, was built around the reduction of ‘purpose’ to ‘function’. Talk of purpose could perhaps be avoided altogether by ignoring what things are ‘for’ and, instead, simply stating what they ‘do’.

The use of teleological language (human-talk) in biology has, however, refused to go away, not least because goal-directed (agential) behavior is a pervasive and objective biological fact. And if the objectives of agents are not purposes then we are confronting serious semantic problems.

It will not do to say that Darwin naturalized teleology by showing that the teleological ‘for’ or ‘in order to’ so often applied to organisms (including their structures, processes, and behaviors) is ‘really’ the way that we link a trait’s function to its adaptive significance and that this is why talk of function, design, and purpose is legitimate.

It is argued on this website that purpose and agency in nature are real. The purpose and agency we see everywhere in nature – the obvious reasons/purposes of structures (wings, fins, hearts), processes (metabolism, photosynthesis), and behaviors (courtship displays, hunting) – are not explained away by providing scientific descriptions of how they arose or what they do. The reasons why they exist in nature are not just in our minds: they are not our purpose, they existed in nature at the dawn of life, billions of years before humans evolved.

Natural selection itself is mindless, unintelligent, and without foresight . . . it cannot possibly have purposes and goals. And yet the products of natural selection, organisms, clearly do exhibit purpose. Only humans (not the organisms themselves) are aware of these purposes and goals, but the words ‘function’ and ‘adaptation’ do not capture their reality in the way that the words ‘purpose’ and ‘agency’ do.

The shocking realization, so difficult for most of us (including scientists) to accept, is that the entire designed and purposive community of life was created by a non-intelligent process. This cognitive dissonance arises from what philosopher Dan Dennett has called a curious ‘inversion of reasoning’.

. . . Purpose, agency, and design ‘bubbled up from the bottom, not trickled down from the top‘ – they existed in nature before, and independently of, minds. They created minds: minds did not create them.

The insistence that organisms have no intrinsic goals, only mechanical processes or automated processing, reflects the conviction that goals entail conscious intentions. But the processes of the mind are as mechanistic as the processes of organisms, 

The stark fact is that non-cognitive organisms demonstrate natural ends or goals and therefore both purpose and agency. Adaptation, as a biological behavioral orientation, is a consequence of this agency. 21st century science shows that there is no supernatural mystery, backward causation, or metaphorical cognition associated with this agency and purpose.

Teleology has been naturalized.

Biological functions

A biological ‘function’ is the specific task or role that a structure, process, or behavior serves within an organism’s body, usually supporting the organism’s life, growth, development, and reproduction in some way. We are inclined to speak of these roles as goals or purposes (e.g. the purpose of the heart is to pump blood) but biology has elected to use ‘function’ as a convenient teleologically innocuous circumlocution. Functions can be observed, measured, and tested empirically so, while they are biologically respectable, their obvious connection to ‘purpose’ has been a topic of extensive philosophical debate. So, for example, if ‘purpose’ is instantiated by goal-directed structures, processes, and behaviors, then, for example, is it possible to avoid the teleological ‘for’ and simply describe what things ‘do’?

Philosophy, believing it is providing a service to biology by purging purpose from all biological discourse, has generated a vast philosophical industry exploring the notion of function in biology via Selected Effects Theory, Generalized Selected Effects Theory, Etiological Theories, Causal Role Theory, neo-teleology, teleosemantics, and more.^[48]

This website claims that biological goals, as natural ends, may be legitimately called purposes – that minded goals are simply limited cases of highly evolved but mindless antecedent biological goals – in the same way that human limbs are simply highly evolved and limited instances of the more general pentadactyl limb. However, there is a proviso.

Almost any biological structure, process, or behavior can be assigned a goal or purpose. So, is agency and purpose distributed equally through all of biology’s ‘hierarchical levels of organization’? Is it purpose and agency all the way down?

Philosopher Samir Okasha distinguishes between the goals of structures, processes, and behaviors (functions) and the goals of entire organisms (purposes). The word ‘function’ suggests a role within a broader context, while the integrity, autonomy, individuality, and independence of a living organism – its ‘unity of purpose’ (Okasha) gives the organism, as a paradigmatic biological agent, something more than ‘function’. And, since the goals of entire organisms determine the ‘goals’ of their parts (because the parts support the organism in the attainment of its goals) then it makes sense to treat the operations of structures, processes, and behaviors as functions. Function talk, then, is most at home when applied to traits (which are subunits of, and subordinate to, the organism as a greater whole with a unity of purpose). Parts achieve sub-goals of the organism whose ultimate goals are to survive, reproduce, and flourish. Aristotle regarded teleology as having two aspects, the ‘of which’, aim, or function (say, of an eye ‘to see‘, of a heart ‘to pump blood‘) and the ‘for which’ that has a beneficiary, which Aristotle considered to be the organism that derived the benefit. In modern terms, he noticed that the ‘for’ or purpose that exists in nature is of two kinds: the goals of organisms, and the functions of their parts.

The parts of organisms are thus subordinate to the whole organism both in terms of their evolutionary origin^[100] and their ultimate goals. It makes biological sense for organisms to be regarded as having goals and purposes while their parts have functions – even though common usage of terms might operate differently.

Following this convention, it is the function of an eye to see, the purpose of a web (designed by a whole organism) to catch flies, and the function of a heart to pump blood.

Functional statements are critical to evolutionary biology, anatomy, developmental biology, molecular biology, physiology, and much more because they are grounded in the objective reality of agency and purpose. If, as is claimed here, purpose in biology is real, then trying to exorcise teleological language is a vain enterprise.

Describing goal-directed behavior

The goal-directed behavior of organisms is an objective fact: all organisms display a propensity to survive and reproduce. This biological agency is what distinguishes the living from the inanimate and dead. This website recognizes human cognitive agency as a limited and highly evolved form of this more general biological agency – that biological agency is expressed in both cognitive and non-cognitive forms.

Are there different kinds of goal-directed behavior displayed by the world’s organisms and, if so, what are the words that we use to describe them?

The language of human agency has a rich vocabulary of descriptive terms, mostly those of intentional psychology, like ‘want’, ‘need’, ‘like’, ‘prefer’, ‘interest’, ‘strategy’, ‘goal’, ‘love’, ‘deceive’, ‘consider’, ‘desire’, ‘know’, ‘learn’, ‘remember’, and so on . . . the list is a long one. These words denote human intentions and, significantly, these intentions may be either conscious or unconscious.

We know that all organisms share the universal propensity to survive and reproduce. This means that all organisms share the same general needs although, for humans, these needs are expressed in cognitive form.

All life depends on water if it is to persist. This need for water can be described in cognitive terms as ‘thirst’. However, in biological terms the need for water is biologically universal but we cannot say that a plant is ‘thirsty’ because ‘thirsty’ is a strictly human word that implies a cognitive process. So what word do we use to describe the ‘thirst’ of a plant?

There is no vocabulary for the many different kinds of pre-cognitive agency, and so we resort to the rich vocabulary of human intentional psychology because it describes cognitive human agency in all its differentiated variety.

But, using the vocabulary of intentional psychology to describe the behavior of non-cognitive organisms is cognitive metaphor.

This is the state of biology today. How, then, are we to describe non-cognitive agential behavior?

Means

A compelling description of biological agency must provide a scientific account of what is meant by the biological agent, its mission (goals), and its means of addressing or achieving these goals.

So far, it has been found that, while purpose and agency can be attributed to most biological structures, processes, and behaviors, these biological objects display these properties in supportive subordination to the goals of the organism as a whole. Also that, while aggregations of organisms into colonies, populations, ecosystems and other collectives can also demonstrate a unification of agential properties, they do not approach the same degree of functional integrity as the organisms of which they are composed. 

The mission (goals) of organisms as canonical biological agents was then found best summarized in the form of a biological axiom or foundational principle of biology – the inherent objective, universal, and ultimate propensity of all living organisms to survive, reproduce, and flourish. A term like ‘fitness maximization’ may have contextual value but it does not capture the immediacy of organismal autonomous biological agency.

It now remains to establish the means used by organisms to pursue these ends.

Adaptation

The notion of adaptation assumes goal-directed behavior – to adapt is to adopt a behavioral orientation – and in this sense adaptation implies both agency and purpose. Without this assumption, adaptation is an incoherent idea.

All organisms are constantly adjusting to their conditions of existence in a feedback loop of organismal ‘experience’. As agents they ‘act’ and ‘behave’, but these words do not capture the way this adjustment is an expression of a behavioral orientation – the pursuit of goals. Goals may be facilitated or impeded by circumstance and so the organism is constantly ‘negotiating’ a ‘compromise’ between its own goals and the constraints of its circumstances. This is the fate of every living organism, and it is referred to here as the biological condition.

The word used by biology to describe the adjustment of organisms to their conditions of existence is ‘adaptation’. Though this may be defined as the process by which organisms adjust to their environment in ways that enhance their survival and reproduction the word is used almost exclusively for long-term genetically inherited traits referred to as ‘adaptations’. We do not have a simple expression to designate short-term agential behavior. This is unfortunate because it is the short-term behavioral adjustments resulting from the inner functional integration of the organism’s umwelt that influence the longer-term environments of evolutionary adaptation that entail genetic change. It is in the immediacy of short-term adjustment (defined by Walsh as ‘the response of organisms to affordances‘) that an organism’s agency is evident.

The degree of impact of an organism’s agency on its life situation is difficult to assess and can even be diminished or ignored in the face of a pseudo-environmental agency in which the environment is regarded as molding the organism. This may occur when organisms are perceived as mechanical and passive aggregates of functional adaptive traits. This ignores the fact that every organism is itself a unit of adaptation that not only combines but transcends its aggregate of long-term adaptations through short-term agential adjustments to not only external environmental factors but also internal physiological, genetic, and other factors.

Evolutionary theory currently emphasizes the long-term mechanical role of natural selection acting on heritable variation over many generations, producing changes in gene frequencies in populations. This account makes natural selection and genes the key ingredients of evolution.

A more realistic representation of evolution would establish the role played by short-term organismal agency generated by an inner process of functional integration. For example, the competition for resources may over the long term resolve into genetic change – but it is organisms, not genes, that fight the battles for these resources and guide the outcomes.

Empirical ingredients

The concepts of action, behavior, adjustment, and adaptation provide an in-principle account of the means that organisms use to pursue their goals but they are not very scientifically helpful ideas.
Given every organism’s unity of purpose as the behavioral predisposition to survive, reproduce, and flourish, is it possible to find more tangible, essential, and empirically investigable features?

This might seem a complex and controversial undertaking but some features, though interrelated, stand out as being operationally essential given the conditions of biological agency established so far.

Behavioral orientation – goal-directed behavior with a unity of purpose is not random behavior, it has an orientation or direction like a human ‘perspective’ or ‘point of view’

Information processing – if the organism is to demonstrate a unity of purpose then there must be an integrating system of communication connecting the organism to its conditions of existence, both internal and external. That is, there must be – a capacity to gather, store, process, and retrieve information about both its own body and external environment. The integration of this information is a necessary precursor to activity.

Functional integration – the critical point of agency for every organism is focused on the reconciliation that occurs between the organism’s behavioral propensity and the constraints imposed by its conditions of existence. In human talk, this is ‘decision-making’ or ‘problem-solving’ process’ as a compromise between the ‘interests’ of the organisms and the constraints of its conditions of existence that is very similar to the ‘self-correcting’ we associate with human ‘reason’. This is the process that precedes the organism’s behavior as the public manifestation of its agency.

Behavioral orientation

The behavior of biological agents is a special kind of behavior. It is not a passive process, like stones warming in the Sun, it is an internal agential process involving a reconciliation of the organism’s natural disposition with its conditions of existence and manifested externally in its behavior. In a general sense, organisms pursue their goals by acting or behaving. Plants may appear relatively inert and immobile in human time, but on the time-scale of time-lapse photography, their non-cognitive agential traits are blatant.

All organisms are goal-directed and therefore display biological agency. However, just a few kinds of organisms- most notably ourselves – have a highly evolved and limited form of biological agency that employs conscious intentions, and this we call human agency.

This creates a crude world taxonomy: on the one hand there are inanimate objects and, on the other, there are goal-directed living organisms, some of which have conscious intentions. If we place a heavy emphasis on organisms with conscious intentions then those that are goal-directed but without conscious intentions tend to take on the characteristics of inanimate objects. This leads to a reductive biology that is purposeless, devoid of agency, and explicable mostly in terms of physics and chemistry.

To restore life to biology we must gain a better understanding of the goal-directed agential behavior of non-cognitive organisms.

The most difficult intellectual hurdle here is to acknowledge that non-cognitive organisms are on a mission. It is, as it were, a mindless mission . . . but it is a mission nevertheless: and mindless goals have a mindless point of view.

The behavior of organisms demonstrates objective value by having an orientation, a mindless ‘preference’, ‘perspective’, or ‘point of view’ – the objective disposition to survive, reproduce, and flourish. You demonstrate your values by the way you behave (more by what you do, than what you say or think) and that is how organisms display their values. The cognitive dissonance arises here because we place so much emphasis on our uniquely human mode of expressing value through symbolic language and abstract thought. This is a form of anthropocentrism and human arrogance. A universal biological behavioral orientation is a universal biological value.

Of course, there is a difference between human minded values and the mindless values of non-cognitive organisms, but the biological fact remains: uniquely minded human values are a limited and highly evolved instance of more general biological values.

For many people the notion of biological value will be too much: what is important is the acknowledgment of life’s objective behavioral orientation.

Behavioral flexibility

American philosopher and psychologist William James famously and neatly captured an important characteristic of life by defining intelligence as ‘the ability to reach the same goal by different means’.

The goals of organisms may be facilitated or impeded by circumstances and so flexible behavior increases the possibility of their fulfillment cecause flexibility allows species to thrive and adapt in diverse and changing environments, and it is greatly enhanced when behaviors can be learned and modified within a single generation based on experience. 

The possibilities of behavior for each organism are constrained by two major factors, its uniquely evolved biology (its genetic constitution or genotype) in interaction with its conditions of existence (its internal and external circumstances). A bird cannot live underwater and a fish cannot fly.

This may be crudely expressed by saying that the behavior of organisms is genetically determined (an underlying assumption of the modern synthesis). But this is grossly misleading. While undeniably true this is a characterization that ignores the range of behavior available to each organism as an independent agent. What happens in real-time (though constrained by the possibilities presented by the genotype) is determined by the responses of the phenotype. The genotype constrains possibilities but it does not determine actual outcomes.

Organisms, as autonomous units of matter, adapt to their conditions of existence in a flexible way. This capacity to ‘self-correct’ is referred to more formally as phenotypic plasticity.

In theory, an organism can (mindlessly) increase its chances of survival and reproduction (maximize its fitness) by expanding its behavioral repertoire. Expressed in human-talk, an organism makes ‘choices’ to overcome ‘challenges’ by influencing its conditions of existence – and therefore its own destiny.

degree of freedom to evolve according to conditions determined by its internal bodily demands rather than conditions determined by its external environment?

How, in theory, could an organism (mindlessly) preference conditions conducive to its internal behavioral propensities over conditions imposed by its external environment?

Answering this question opens a door to the history of evolution.  If biological agency is the main driver of evolution then any inherited increase in behavioral flexibility increases the capacity for evolutionary exploration.

So how is behavioral flexibility increased?

The list is a long one: improvement in the speed and efficiency of bodily communication systems; the capacity to learn and remember (memory) culminating in the mental capacity for hindsight and foresight. While degrees of behavioral freedom may be expanded, these are still constrained by bodily limits. Humans have evolved brains that open up infinite possibilities that are constrained by human physical limits. Technology, as applied science (microscopes, telescopes, particle accelerators) attempt to extend natural physical limits and overcome these physical constraints.

Like all organisms, we humans are motivated by the need to survive, reproduce, and flourish. We assume that we have adjusted to this biological condition by using our brains in three key ways that evolved out of mindless precedents.

First, the accumulation of knowledge – which evolved out of the organism’s capacity to absorb, process, and act on information about both itself and its surroundings.

Second, the orientation of behavior according to values and ethical systems – which evolved out of the organism’s behavioral orientation towards survival, reproduction, and flourishing.

Third, the use of reason – which evolved out of the short- and long-term propensity of all organisms to constantly adjust, adapt, and self-correct in relation to their conditions of existence.

Biological evolution has delivered to us from our ancestors not only physical traits, but  also mental traits, notably the capacity for knowledge, values, and reason.

Organisms evolve by taking advantage of situations as they arise – the affordances that are relevant to their own particular umwelt. The more ‘options’ available to an agent – expressed as degrees of structural, processual, and above all, behavioral flexibility – the greater the likelihood of it finding ‘solutions’ to their biological condition, the need to survive, reproduce, and flourish. Flexibility, then, is a measure of the ability of an organism to take advantage of its situation – its adaptability.

Most organisms are mindless but, just as they are ‘competent without comprehension‘ and ‘for without foresight’ they also ‘explore’ an infinity of mindless ‘strategies’, both short- and long-term. Part of the mindless evolutionary process, we might then assume, would be a mindless increase in flexibility since those organisms with greater adaptability will tend to survive.

But evolution is a complex system of ad-hoc trade-offs. Organisms successfully adapt to particular conditions by developing specialized traits, but the fact that these are specialized traits decreases the organism’s overall flexibility.

So what mindless strategies did nature adopt?

One way to survive is through simplicity, when adaptation involves minimal physical adjustment. The success of the microbial world is a testament to this strategy.

But, at the other extreme, we have ourselves as, arguably, the dominant life form – a species that has spread across the world to dominate its environments and resources. Clearly, the development of complexity has been successful, even though that success may be short-lived in evolutionary time.

There is also the special significance of motility. Motility allows an organism to not only explore a variety of environments but to ‘choose’ those that it ‘prefers’.

The diversity of environmental information that requires rapid processing no doubt led to the development of sophisticated and centralized sensory systems and, eventually, to brains. Brains that can ‘learn’ in the course of a single generation clearly have a greater capacity to respond to immediate circumstances than those that only change in evolutionary (genetic) time. The capacity for conscious deliberation (the mental representation of the consequences of behavioral possibilities) adds yet more degrees of freedom to behavioral flexibility.

Sedentary plants have no motility, an obscure sensory system, and no brain. Their behavioral options seem limited, but they are all around us. But, clearly in adjusting to the biological condition, they have done well, just look around!

Biological value

The goals of non-human organisms are non-cognitive natural limits or ends to biological processes; they express non-cognitive behavioral propensities as natural non-cognitive agential traits. These goals can be facilitated or impeded by the organism’s conditions of existence.

Human-talk would treat this as a value since the goals may be ‘helped’ or ‘hindered’ by circumstance. That is, a behavioral orientation in non-human organisms when transposed into the human circumstance would be regarded as a value.

Information processing

To behave in an autonomous and meaningful (goal-directed and therefore orderly) way in the world, organisms must gather and process information about their conditions of existence – both the conditions existing within their bodies and outside in the environment.

It is an incessant process that operates in a constant feedback loop that expresses organismal autonomy within the organism-environment continuum: the organism as an open system.

There must therefore be an internal information transport and communication system connecting all body parts significant to the organism’s umwelt.

While organisms possess a wide range of transport systems – like blood circulation, the distribution of chemicals, and fluids – for an organism to behave in a coordinated way the communication system must carry information about the system as a whole.

The concept of information is abstract and difficult to describe but it is the most efficient way of describing the ‘something’ that is needed for all parts of a living body to behave in a coordinated way. And informaton must be stored. processed, and retrieved.

Functional integration

The internal process of functional integration is a critical aspect of what it is to be a biological agent (see biological objects) since it is the means (see later) by which the organism pursues its goals. This was acknowledged by the philosophers Aristotle (organisms are ‘causes of themselves’) and Kant (‘a thing exists as a natural end if it is cause and effect of itself’).

As already discussed – goals, purposes, and agency may be attributed to biological structures, processes, and behaviors of organisms but they are subordinate to the overriding and regulating goals of the entire organism.

Consider the following claims: ‘hunger is caused by a physiological process’, ‘hunger is a physiological process’, ‘love is just oxytocin in action’, and ‘humans are really just DNA’s way of making more DNA’. When we realize that we understand ‘hunger’, ‘love’ and ‘being human’ as concepts that are unified and functionally integrated by our brains to be demonstrated in behavior, then their reductive emptiness becomes clear.

It is helpful to distinguish between those biological outcomes that are a consequence of agency and those that are a consequence of constraint. Environments (excluding organisms) have no agency, their influence is in constraining the possibilities available given the organism’s agency. Similarly, genes set the constraining boundaries of behavioral possibility – what happens in real-time is a consequence of short-term internal processing (functional integration).

This is crucial for biological explanation. We must be wary of dichotomies expressed in terms of inner/outer, internal/external, organism/environment, genes/behavior because behavior is, of necessity, a reconciliation between the organism’s propensities and its conditions of existence – even though the influence of triggers may exist by degree. For example, consider the nature/nurture debate: is our human behavior a consequence of our genes or our upbringing? Our behavior is a consequence of their functional integration. While genes establish the organism’s inherent propensities as an arena of behavioral possibility (potentiality) it is the interaction of propensities with the conditions of existence that generates actual behavior (actuality) with both genes and conditions of existence influencing by degree.

The internal cognitive generators of human behavior – our attitudes, beliefs, reasons, and desires – are a highly evolved and limited instance of the universal inner processing of all biological agency.

Is behavior controlled by (subordinate to) genes?

This is a misleading simplification because all behavior is ultimately a reconciliation between the organism’s propensities (genetics) and its conditions of existence. Potential behavior may be constrained by genetics, but it is the functionally integrated behavior of entire organism in a moment of time that more directly determines biological outcomes. Behaviors that enhance an organism’s fitness establish the conditions for the establishment of new traits that are more likely to be passed on to future generations.

Behavior is a powerful driver of change in its own right: it shapes the processes of natural selection and adaptation by influencing an organism’s capacity to survive and reproduce. While genes establish the boundaries within which behavior is possible, it is the organismal integration of behavioral propensities (goals) with the immediate conditions of existence that determines biological outcomes in real time.

Accepting the reality of goal-directedness brings with it three interrelated behavioral properties: adaptive flexibility, a behavioral orientation or perspective, conditions that can facilitate or impede that behavioral orientation (for better or worse, life-affirming or life-negating).

The process of constant adjustment is a feature of all biological agents that is referred to here as the biological condition echoing the notion of a human condition.

(Functional integration is a compromise between the organism’s goals and its conditions of existence. These conditions can facilitate or impede the attainment of these goals.  Since these conditions can their While this process of adjustment occurs in all organisms, we are most familiar with the human circumstance in which information processing is focused within the highly evolved and conscious brain. We describe our constant human mental adjustment as ‘self-correction’, ‘problem-solving’, ‘decision-making’, ‘reasoning’, ‘preferring’. ‘making choices’, ‘selecting’, and so on.)

The biological condition

The organism, as an autonomous agent or ‘self’, is mindlessly (genetically) imbued with the goals of survival, reproduction, and flourishing. It is therefore in a state of constant tension with its conditions of existence as it mindlessly attempts to equilibrate its own propensities with its conditions of existence.

Following criticism of the cognitive metaphor ‘natural selection’ (nature has no conscious choice or purposeful design) Darwin adopted  Herbert Spencer’s expression, ‘survival of the fittest‘ to describe his theory of natural selection. The word historically selected by biology to describe the constant and necessary process of adjustment or ‘self-correction’ was ‘adaptation’.

Like ‘natural selection’, ‘adaptation’ might also be regarded as a minded word . . . but no one has bothered to complain: resistance to the obvious connections between biological and human agencies eventually becomes tedious.

What precisely constitutes an ‘adaptation’ in biology may be disputed but it is an invaluable concept referring to a trait or characteristic that has evolved through natural selection to become common in a population for its functional benefit. But giving an (etiological) account of the historical pathways that have influenced a trait’s development over time or, say, the conditions that gave rise to agency, does not dissolve that agency away.

The notions of both adaptation and adaptive function have embedded value derived from their agency – that features are advantageous for the survival and reproductive success of a species, or have functional benefit. It is simply not possible in biology to avoid the implication of ‘advantage’ and ‘disadvantage’ – that the conditions influencing an organism can ‘help’ or ‘hinder’ its existence.

Biological agency refers, in a minimal sense, to the autonomous capacity of organisms to act on and respond to their circumstances of existence. However, while there are many reasons for the proximate behavior of organisms these are grounded in the ultimate goals of survival, reproduction, and flourishing. It is these ultimate goals that constitute a universal organismal behavioral orientation that resembles a human value, perspective, or point of view.

The agency of biological systems is closely linked to the concept of adaptation which can, confusingly, refer to either a process or a physical outcome (trait). A chameleon adapts to its surroundings by changing color (a process) which involves cells with the capacity to alter their pigmentation (a trait).

Natural selection acts as a bridge between agency and adaptation since organisms with effective agency are more likely to pass on their genes. There is, however, a causal priority here since it is adaptive agential behavior that determines the circumstances under which genetic change occurs. That is, the process of adaptation as orientated agential behavior has a strong influence on the evolution of adaptations (as traits) that shape the future expression of agency.

Adaptation as a process engages organismal agency in both short-term behavioral, and long-term genetic, adjustment to circumstance.

Much of the discussion concerning teleonomy, phenotypic plasticity, dynamic systems, and the influence of organisms over their own futures adds little to old ideas of adaptation – it simply acknowledges that the adaptive process can be re-interpreted from a more organism-centred (all behavior, regardless of its causal source, is a product of internal processing), goal-directed, and purposive perspective.

Adaptation has two key features of profound significance for biology described here as behavioral flexibility and behavioral orientation as biological values.

Behavior

Behaviors must be placed within their temporal scale. For every behavior there is a proximate reason (its immediate mechanism or cause) and an ultimate reason (the evolutionary or historical reasons for its origin over time).

It is the functionally integrated and goal-directed inner processing of organisms that generates the behavior that demonstrates agency and purpose.

While the internal process of functional integration is the engine of agency, it is its behavioral manifestation that communicates agency between organisms, supplemented, in humans, by the use of symbolic language as an evolutionary cognitive development.

Because the inner processes responsible for behavior are difficult to access and study scientifically, behavior is often assumed to be what agency is – that to understand behavior it must be observed directly without considering its relationship to internal states. This was a principle accepted by the school of human psychology called behaviorism in the 19th and 20th centuries, and it persists more generally in biology today.

Behavior influences the capacity of the organism to survive, reproduce, and flourish – how it forages, mates, seeks shelter, deals with predators, or how it responds to changes in environmental conditions, engages in social interaction and engages both individual and group learning. Behaviors that increase an organism’s fitness are more likely to be passed on to future generations, leading to the evolution of behavioral traits over time.

The human superimposition of rapid cultural evolution on slow biological evolution marked a remarkable new phase of evolution in which the accumulation of information occurred, not in genes, but in the communication of memes as spoken, written, printed, and electronic units of knowledge. An example of the inheritance of acquired characteristics.

Causal pathways

The causal pathways relating to behavior are often unclear. It is conventional to say that organism behavior is initiated (caused) either internally (e.g. the cat was hungry) or externally (e.g. the cat saw a mouse). This simple characterization ignores the important scientific point that all organismal behavior, whether prompted by internal or external triggers (whether it is an action or reaction) is, most directly a consequence of functionally integrating internal processes.

It is inner processing, expressed externally as behavior, that imparts biological agency. The direct cause of behavior must always be a functionally integrating process, even though it may be triggered by something internal or external. This does not deny the influence of external and internal factors, which may be by degree, but it counters the perception of the organism as a passive respondent to external causes.

This interpretation condenses a confusing external/internal dichotomy of causation into a single internal cause regardless of its triggers. Questions of internal and external influence are not eliminated, but their emphasis is changed.

This draws attention to the ultimate agency of the organism, not the external or internal trigger. This is important because it is the functional integration that generates the organismal self-determination that we recognize as agency. To locate the cause of behavior outside the organism downgrades the agency inherent in the organism itself.

Real-time behavior (an actuality) is the realization of what was formerly just a possibility (a potentiality). Actual behavior is strongly influenced indirectly by both internal and external triggers. Hunger (an internal trigger) might cause a cat to chase a mouse, while the sight of a cat (an external trigger) might cause a mouse to run – but in both cases the direct cause of behavior was not the triggers but their functional integration within the organism.
While genes determine what is possible (potentiality), functional integration and its behavioral outcomes determine what happens (actuality).

Definition

How, then, do we circumscribe ‘biological agency’ in a way that has utility and application in biological science?

This website claimed at the outset that, to be scientifically acceptable, such a definition must clarify what is meant by the biological agent, its mission (purpose or goals), and its means of carrying out its mission.

A critical examination of these concepts leads to a minimal definition of biological agency as:

The behavioral propensity of organisms to survive and reproduce by adapting to the circumstances of their existence.

The brevity of this definition requires some explanation in view of more elaborate definitions attempting to capture the essential features of biological agency (see below).

• • • It recognizes the organism as the canonical reference biological agent – even though agency, in a more general sense, is pervasive in biology
    • it is a concise and simple definition suitable for students studying biology and therefore much is implied rather than stated – e.g. difficult concepts like autonomy, functional integration, self-maintenance, self-determination, evolution, the role and range of pre-cognition and cognition – all can be expanded indefinitely but are covered by this definition
    • it also establishes the minimal conditions for life and evolution since mere replication and/or persistence are insufficient, and adaptation implies both short-term functional integration and its behavioral outcomes as well as long-term Darwinian inherited adaptations
    • it treats ‘circumstances of existence’ as including factors that are both internal and external to the organism

Given this minimal definition, explanations of the agent, its mission, and its means may be expanded to provide increasingly comprehensive coverage, according to taste and context, with the following factors for possible consideration:

Biological agent – Agency is a broad concept with wide application both inside and outside biology. However, in biology, in spite of the many complicating boundary conditions, it is the organism that is overwhelmingly regarded as having the necessary degree of autonomy required for substantial self-determination. While both sub- and super-organismal biological entities may be treated as agents, they are subordinate to (they are functions of, and evolved in the context of) the functionally integrated purposes of entire organisms. That is, the concepts of purpose, agency, and intention have their greatest utility and biological meaning when applied to entire organisms rather than their parts or aggregates. The capacity for self-determination has been used by Aristotle, Kant, and others to mark out the realm of the living, life, and therefore the scope of biological science: it encompasses many of the ideas associated with an independent individual or ‘self’ with a unity of purpose, notably whole-organism functional integration, self-regulation, self-maintenance, self-replication etc.

Goals – Biological goals, in general, are natural ends or limits. However, the objective and ultimate goal of all organisms is their predisposition (their functional integration towards the overall goal) to survive, reproduce, adapt, and evolve (sometimes called fitness maximization).

Means – All organisms – unlike objects in the inanimate world – are constantly acting on, and responding to, their conditions of existence in an agential way. This process of adjustment can, for convenience, be examined from two time scales. First, there is the constant functional integration of the totality of conditions that occurs within the organism, which generates public agential behavior. Then there is the establishment of long-term inherited physical adaptations or traits.  This website has identified three necessary characteristics of adjustment as it relates to organism agency. First, the whole organism processing of information that is obtained from its conditions of existence (both internal and external). Second, a behavioral orientation (its goals) as a biological value that can be ‘helped’ or ‘hindered’ by circumstance and which provides the basis for organismal adaptation in terms of making ‘choices’, showing ‘preferences’, and as a capacity to ‘self-correct’. Third, the internal process of functional integration within the organism as a prelude to agential behavior.

A more expansive understanding of biological agency comes from looking at the work of other researchers who have defined what is meant by ‘biological agency’. For example, Denis Walsh’s generalized and succinct definition given at the top of this page is repeated here:

. . . the capacity of a system to pursue goals, to respond to the conditions of its environment and its internal constitution in ways that promote the attainment, and maintenance of its goals states^[56]

Simplicity always helps, as the following reduced and refined example given later by Walsh and colleagues shows:

The capacity of a system to participate in its own persistence, maintenance and function by regulating its own structures and activities in response to the conditions it encounters.^[85]

Walsh’s associate Fermin Fulda defines biological individuals as autonomous agents with degrees of independence and offers the following definition:

‘Agency is the gross dynamical capacity of a goal‐directed system to bias its repertoire to respond to its conditions as affordances’^[63]

It is always tempting to be more inclusive – as in the following definition developed from autonomy theory:

Biological agency refers to the capacity of autonomous living beings (roughly speaking: organisms) to purposively and functionally control the interactions with the environment, and to adaptively modulate their own self-determining organization and behavior so as to maintain their own existence, construed as their intrinsic telos.^[84]

Sultan et al. (2022) describe agency as:

‘the capacity of a system to participate in its own persistence, maintenance and function by regulating its own structures and activities in response to the conditions it encounters.’

The following is a recent 2024 definition of biological agency offered in the context of agency in general, and artificial agency in particular:

Biological agency refers to the capacity of living organisms to act autonomously and make decisions based on their internal processes and external stimuli. It encompasses the ability of organisms to sense their environment, process information, and respond to changes in ways that promote their survival and reproduction.^[106]

As a prelude to devising a definition, philosopher Samir Okasha recognizes two broad kinds of biological agency – that which we attribute to individual organisms as products of evolution (which he calls Type 1 as a ‘powerful tool for [sic] understand adaptation‘ p. 10), and that which we associate with natural selection (Type 2, as the process of evolution), both ‘. . .  applied in both literal and metaphorical forms‘.^[39] Type 1 biological agency applies to the products of evolution and Type 2 biological agency applies to the process of evolution. Discussion on this website is concerned primarily with Type 1 agency.

Assembling and comparing the above information and definitions reveals a general consensus of basic ideas except in relation to what constitutes a biological agent.  While this website makes a firm commitment to the organism as biological agent, it notes that it is possible to treat other biological structures, processes, behaviors, and collectives in a purposive and agential way and this pluralist approach to agential systems in biology is adopted by many researchers.

Following Okasha, this website distinguishes between whole-organism ‘purposes’ and part-organism ‘functions’ as a pragmatic way of distinguishing between organisms and other potential biological agents.  Discrepancies in the scope of ‘biological goals’ are minor (mostly regarded as survival and reproduction but as fitness maximization in evolutionary biology and the possible inclusion of flourishing suggested by this website).

It should be noted that biology, as a product of evolution, expresses many of its characteristics by gradation and degree.

Commentary

For Aristotle, the crucial characteristic of life was its ‘soul’, which he understood as an organizing principle or intrinsic, animating, and unifying force that gives organisms their characteristic functions and capacities.

For Immanuel Kant, following Aristotle’s general theme, the critical criterion of life and biological individuality was the internally generated functional integration of its activity (see biological objects).^[83] Both men were alluding to what today we might refer to in loose general terms as biological agency. But, for Kant, purpose, agency, and design in nature were merely an ‘as if’ heuristic. They were the reflective judgment of a subject and therefore useful only as an explanatory tool. This is still the prevailing view in philosophy and biology with agency treated as intimately associated with human cognition.
Kant was a God-fearing man who preceded Darwin. The possibility of miraculous human subjectivity evolving out of mindless nature is challenging today and would have been unthinkable in his day.

This has created a Kuhnian paradigmatic tension in biology as research struggles to account for non-cognitive agency. If the objective (real) goal-directed behavior of organisms that act on, and respond to, their conditions of existence is not agency, then what are we to call it? And if – as we are sure – the objective agential traits of non-cognitive organisms are non-cognitive traits, then what are we to call them? At present, since we have no names for them, so we resort to human cognitive terms which become ‘cognitive metaphor’. Thus, real agential non-cognitive traits are interpreted as the reading of human intentions into nature.

It is now evident that agency is a universal biological phenomenon of which human cognitive agency is just one specialist and highly evolved form. This means that biology and philosophy must come to terms with the fact that there are real non-cognitive agential traits: organisms can express real, but mindless, goals.

The functionally integrated ‘agency’ that Kant treated as defining life is, we now know following Darwin, expressed in physical form as the evolutionary continuum of the community of life.

Within the community of life it is the goals of entire organisms that prevail. While the structures, processes, and behaviors of organisms can express their own identity and agency they are ultimately subordinate to the goals of the organisms of which they are a part. The functional integration of organisms is so strong that communities and collectives of organisms, while also expressing their own cohesion and agency, are more like organismal aggregates than autonomous individuals. The world of biological objects falls naturally into three categories – organisms, the sub-organismal, and the super-organismal.

Darwin described the motivating force that created the entire community of life using the expression ‘natural selection’. His choice of these words was criticized because they implied that nature expressed agency in the form of a human-like choice, which was obvious nonsense. After all, nature has no mental faculties.

Today, science has no difficulty in accepting the goal-directedness of living processes, but it still struggles with the concept of mindless agency. Part of the difficulty stems from the tension between religion (the supernatural) and science. In Darwin’s day, the purpose and agency so obvious in nature – including the human capacity for conscious deliberation – was regarded as a gift from God. Darwin was an unbeliever but struggled all his life, knowing that his theory of natural selection potentially did away with the supernatural; it naturalized biology, and this was unacceptable for many people. For example, he shared the scientific announcement of natural selection with Alfred Russel Wallace.^[91] While Darwin believed that human mental faculties could be fully explained by natural selection, Wallace suggested that the human mind evolved through some other, perhaps spiritual, means. Wallace proposed that mental faculties – like abstract thought and the moral sense – could not be explained by natural selection alone, but probably required a ‘superior intelligence’.^[92] This is still the view of many people today.

Darwin the unbeliever, unlike his great predecessor Aristotle, could not bring himself to acknowledge how the notion of purpose flows so obviously and naturally from nature’s patent agency. People ignored the fact that Darwin’s ‘adaptation’ assumed that things could be ‘for the better’ or ‘for the worse’. On the notion of ‘purpose’, he was agnostic (a term invented by his friend ‘Darwin’s bulldog’ Thomas Huxley), probably because an acknowledgment of purpose would be seen as an acknowledgment of God.

Despite the criticism, Darwin’s choice of the detached words ‘natural selection’ (which he used in contrast with the artificial selection of plant and animal breeders) established a respectable scientific distance between humans and the agential process that created all life – described more directly, colorfully – and perhaps more honestly – using the expressions ‘struggle for existence’ and ‘survival of the fittest’.

But all this talk of adaptation and natural selection was still equivocation about what was really going on at the core of evolution. It was not Darwin, but Aristotle, who pinpointed the driving force sustaining all life and its evolution – he had located the core of life (and unknowingly evolution) in the inner processing of individual organisms that generated behavior promoting survival, reproduction, and flourishing. Not natural selection, but biological agency.

In seeking to answer the vexed question ‘What is life?‘ this website singled out biological agency as its most fitting (among others) necessary and sufficient condition. For the sake of clarity, there must be a consensual understanding of what is meant by not only ‘biological agency’, but also ‘biological agent’, its ‘biological goals’ (mission), and its means of pursuing these goals. These were the objectives of this article.

Expressed in simple terms it was found that biological agency is the goal-directed inner processing of biological agents manifested in the behavior of biological agents as canonically exemplified by organisms with the goals (mission) of survival, reproduction, and flourishing. This is achieved by a process of adaptation involving three factors: an exchange of information with the organism’s conditions of existence, a behavioral orientation, and a process of adjustment (adaptation). Conditions like metabolism, homeostasis, capacity to respond to stimuli, are subordinate to (presuppose) conditions determined by the agency of entire organisms. Even the genetic information encoded in DNA is ultimately determined by the agential interaction of organisms with their conditions of existence.

The acknowledgment of biological agency within the EES enriches our understanding of the dynamics of evolutionary systems by recognizing the pivotal role of organisms in life and therefore biology.

Genetic variation arises primarily through mechanisms such as mutation, recombination, and gene flow and it is these processes that are generally considered to be the raw material on which natural selection must act. However, this is a scientific misplacement of evolutionary causal emphasis in the complex interplay between the genetic variation, organismal agency, and environmental factors that drive evolutionary change. While genetic variation does provide the raw material upon which natural selection acts, it is the agency of organisms that powers natural selection. The behavior of organisms plays a major role in shaping the evolution of populations, determining environments of evolutionary adaptation, and therefore the selection pressures that establish what kinds of genetic variation, as novel adaptive traits, can occur.

Genetic variation sets the stage for evolution, but it is the actions of organisms within their environmental contexts (their umwelts) that determine the direction of evolutionary change.

Historical background

The reductive and analytic turn of the last century or so – our scientific preference for analysis rather than synthesis, for explaining wholes in terms of their parts – has taken biology down the highly productive path of microbiology, DNA, and biotechnology. We can now analyze photosynthesis, the biochemical process that supports all life on Earth, to the finest detail. But this approach has given us a ‘bottom-up’ perspective on matter and life. We have ignored the significance of the integrated agential autonomy (unity of purpose) of discrete organisms as organically concentrated individuality that is not found in the inanimate world, or even in biological entities like genes, cells, organs, termite colonies, or schools of fish.

Scientists are no longer encumbered by Aristotle and his causes. His formal and final causes were abandoned during the Scientific Revolution for their unscientific implications and philosophical obscurity. But the realization that agency in nature is real begs a reappraisal of his teleology as outlined in his Physica Book 2. The following is my clumsy attempt to revisit the mind of perhaps the world’s greatest ever polymath.

Aristotle observed that there are four major kinds of explanation of something, his four (be)causes: how it is structured, what it is made of, how it originated, or what it was for.

Aristotle’s four ‘becauses’ are deceptively inclusive. They are both static and dynamic, incorporating both structure and function. By considering potentiality, actuality, and the temporal sequence of efficient cause, they allow for history and development, past and present, while final cause embraces all these factors within the notions of purpose and agency. They describe the way things are now, but also account for change (Aristotle’s primary objective) by explaining how they came to be. And their meaning allows some flexibility of interpretation (Aristotle pointed out that the Greek word aition as ’cause’ had various senses).

The four causes divide neatly into two pairs. The material and efficient causes (those adopted after the Scientific Revolution) capture an analytic ‘bottom-up’ physical and material perspective on the world and change. Formal and final causes offer a synthetic ‘top-down’, integrating, unifying, agential, and purposive perspective.

Scientists of the Scientific Revolution (mostly astronomer-physicist-mathematicians) abandoned Aristotle’s formal and final causes as too abstract, if not altogether mistaken. These men bequeathed us a mechanistic world of matter in motion.  In this way non-human living organisms were united with the material and efficient. By restricting purpose and agency to humans, and without the benefit of the theory of evolution, this was a distancing of humans from their continuity with the community of life, a distancing that persists today.

Aristotle wanted to know, not just about order in general and the project of science in its entirety. He also wanted to describe what was unique about the particular kind of order, change, and coming to be, that we see in biology.

‘It is not good enough to study the stars no matter how perfect they may be. Rather we must also study the humblest creatures even if they seem repugnant to us. And that is because all animals have something of the good, something of the divine, something of the beautiful’ . . . ‘inherent in each of them there is something natural and marvelous. Nothing is accidental in the works of nature: everything is, absolutely, for the sake of something else. The purpose for which each has come together, or come into being, deserves its place among what is natural and good’ . . . ‘The nature that crafted them likewise provides extraordinary pleasures to those who are able to know their causes and are by nature philosophers.’  

Aristotle – De Partibus Animalium (The Parts of Animals) 645a15

Aristotle’s sentiments are aptly referred to as ‘The Invitation to Biology’.

Aristotle’s central idea – the cement that binds all biology together – revolves around his final cause: it is this that gives life its ‘unity of purpose’. Only now, after over 400 years of complete rejection, this idea is gradually being restored to scientific respectability through a recognition of the limitations of a micro-perspective on life, and the resurgence of a philosophical position reinstating purpose in biology (outlined in the article bioteleological realism). This is a recognition that purpose in nature is real – organisms can be ‘for’ without foresight.^[93] Final causes do not imply the supernatural, or the insertion of human intention into non-human behavior, or backward causation.

It was in the reductive exuberance of the 20^th century analytic turn in science and philosophy that the agential role usually assigned to organisms was transferred to genes. Genes, evolutionary biologist Richard Dawkins claimed in his 1976 book, ‘The Selfish Gene’, ensured their own survival and reproduction by having humans as their survival and replication machines with certain behaviors and traits the strategies employed by genes to increase their chances of being passed on to future generations. It is genes that are the units of natural selection, shaping the behavior and characteristics of organisms to maximize their own survival and replication (not the survival of the organism or species). Satirized as ‘Humans are just DNA’s way of making more DNA’. Dawkins’s claim was founded on the Weismann germ-plasm theory, that genetic information can only pass in one direction, from genes to bodies: there can be no inheritance of acquired characteristics. Francis Crick in 1958 stated this in the form of the Central Dogma which insisted that the flow of genetic information proceeds in one direction only, from DNA to RNA to proteins – there can be no process in biology engaging the inheritance of acquired characteristics. In short, it is genes that are pulling the strings of life. This is still the widely accepted view.

In subsequent years various mechanisms (epigenesis, phenotypic plasticity, niche ecology etc.) have been proposed for the transmission of genetic information from bodies to genes although their influence still appears minor. More important is the return to agential thinking that was derided during the analytic turn. This takes account of the purposive and agential behavior of individual organisms as integrated units of functional organization; the creators of outcomes. Set against this is the view that whole organisms display an agency that influences biological outcomes – that organisms demonstrate a degree of self-determination by shaping their own destinies. But the Modern Synthesis was also a claim about behavior: if ‘genes determine traits‘ (simple stipulative definition establishing the primacy of genetic agency) then they also determine behavior (because genes determine which behavioral traits are most successful at propagating themselves). The behavior of organisms is, therefore, a consequence of selective pressures acting on their genes.

But this characterization ignores the complexity of the interaction between the organism as a biological agent and its conditions of existence (both external and internal) – the reciprocal relationship between genetic predispositions and organismal agency. Certainly, genes determine the range or limits of possible organism behavior. However, given these genetic predispositions, it is the integrated behavior of organisms responding to their conditions of existence that establishes the environment of evolutionary adaptation and therefore the subsequent path of evolutionary development. In this sense, genes are subordinate to organismal agency.

While genes provide the foundation for potential behaviors and traits, it is the active engagement of organisms with their environment that ultimately guides the course of evolution. Organismal behavior influences not only obvious factors such as the availability of its food sources, mating opportunities, the environment in which the organism lives, and its interactions with other organisms. Every organismal act in real-time is an act of adaptation – the external behavioral manifestation of an internally integrated reconciliation between the predispositions of the biological agent and its conditions of existence.

Given a particular genotype, it is organisms as biological agents in interaction with their conditions of existence that determine their environments of evolutionary adaptation and therefore the traits that will be encoded in their future genes.

After 2500 years we are now returning to Aristotle’s way of thinking by reinserting formal and final causes into biological science. True to the Scientific Revolution we acknowledge the importance of describing what something is ‘made of’ (its material cause), and ‘how it arose or was made’ (efficient cause). But we are only just beginning to acknowledge, philosophically, that much of our biology is reverse-engineering – not just the investigation of what living systems and structures ‘do’, but what they are ‘for’ – both individually, and collectively through the unity of purpose expressed in the biological axiom (final cause).

In the absence of this unified agential explanation of life, biology becomes a collection of dissociated facts of the kind we use to describe the inanimate world. It is the purposiveness of biological agency that gives life its meaning through the ultimate goals of survival and reproduction and the proximate goal of flourishing, all as a matter of biological necessity.

A satisfying scientific answer to the question ‘What is life?’ must be a full one. It must involve much more than a response detailing ‘what it is made of’ (material cause) and an assumption that something that is small is more ‘real’ than something that is big. We need more than Aristotle’s material and efficient cause as explanation. Life is more than subatomic particles, energy, or information: it is even more than the genetic code. Also, what an integrated and autonomous functional organism is ‘for’ brings with it a meaning that extends well beyond what it ‘does’.

A full explanation of a chair, we believe, must include a description of what it is ‘for’, its final cause or purpose. Sadly, for many scientists and philosophers, even today, organisms are no more ‘for’ anything than are planets or rocks. A chair has more purpose than an organism.

As complexity increased after the Big Bang, so life emerged as matter with distinctly novel properties and relations. It is argued in this article here, and the article on human-talk that our science would better reflect the world if it treated the categories employed by human-talk as existing in reality by degree, rather than as unreal metaphor.

Today, long after Darwin connected humans to the community of life, and naturalized teleology, we are still struggling to acknowledge the purpose that is inherent in all living organisms, the purpose that is associated with their biological agency.

Using minded human-talk (because we do not have a simple vocabulary to express this in any other way) biological agents, mostly mindlessly, ‘pursue’ their ‘goals’ by adopting ‘strategies’ as a means to ends. To put a strategy into effect requires the integration of internal and external resources and this entails the behavioral management of physical resources.

Cognitive & non-cognitive organisms

Our anthropocentric conviction of the overwhelming importance of human conscious awareness, intention, and deliberation has blinded us to the fact that the miracle of human subjectivity had a mindless origin – the cognitive evolved out of the non-cognitive.

Once botanical science acknowledges the existence of non-cognitive agential traits it must also confront a cluster of fascinating empirical and philosophical questions that are investigated on this website.

If non-cognitive agency is real then:

• • • How did science manage to deny it for so long (see purpose)?
    • How has the claim that non-cognitive traits are cognitive metaphors so cleverly misled us for over 400 years (see pre-cognition)?
    • How are we to interpret the use of anthropomorphic language in biology (see human-talk)?
    • How did cognitive traits evolve out of non-cognitive traits (see evolution of biological agency)?
    • How is goal-directed behavior as a behavioral orientation connected to mindless values as evolutionary precursors to human cognitive values (see biological values)?
    • How can the notion of non-cognitive agential traits be transposed to a biological object as seemingly inert as a plant (see plant intelligence)?

The distinction between the cognitive and non-cognitive (the minded and mindless) seems absolute. How could our understanding of organisms with cognition be enhanced in any way by studying organisms that have no cognitive faculties?

We naturally think of the origin, development, and evolution of cognition within its mental context. For example, the emerging field of basal cognition studies the scaling of cognition and collective intelligence. For example, by considering that the turning of ‘cell-level physiological competencies into large-scale behavioral intelligences is not limited to the electrical dynamics of the brain. Evolution was using bioelectric signaling long before neurons and muscles appeared, to solve the problem of creating and repairing complex bodies.’

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

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

There are organisms with minds and organisms without minds: the idea of finding cognitive properties in non-cognitive organisms is a contradiction in terms. By definition, cognition is concerned with brains and brain-like structures. So, for example, in investigating human values like happiness we might look at cognitive correlates in other primates, but looking for these cognitive characteristics in non-cognitive organisms seems absurd. So, for example, looking to non-human, non-cognitive organisms for real biological connections with the human cognitive properties of knowledge, values, and reason seems nonsensical.

While non-cognitive organisms rely primarily on instinctual behaviors and basic information processing for their survival, cognitive organisms (essentially humans) possess the capacity for abstract thought, symbolic communication, and higher-level reasoning, that allows them to manipulate and understand their environment in uniquely non-instinctive ways. The evolutionary emergence of cognition would appear to provide adaptive advantage by extending the degrees of freedom available for the organism to tackle complex social and environmental problems.

We assume, for example, that knowledge has nothing to do with an amoeba. Knowledge is about neurons, brain regions, provided with environmental cues – it is an awareness of facts, information, and the skills acquired through experience, learning, and reasoning.

But instincts and innate behaviors are genetically encoded knowledge that helps organisms survive and reproduce. Organisms ‘learn’ from their environment, by adapting their behavior based on previous experience (e.g. birds learning migration routes).

Values relate to our assessment of the importance or worth of something – our subjective judgments about desirability, utility, or significance. But all organisms show value-related behaviors as traits that enhance their fitness (survival, reproduction, and flourishing) traits that are favored by natural selection.

Based on past inherited experience (knowledge), organisms allocate resources (e.g. energy and time) based on their perceived value (e.g. investing energy in reproduction).

Human reason entails logical thinking, inference, problem-solving, and drawing conclusions based on evidence, but simple organisms exhibit basic reasoning (e.g. ants optimizing foraging routes). These properties are e deeply embedded in the biology of all organisms, playing an essential roles in their survival and adaptation,

But there is a difficulty here because non-minded organisms display mind-like characteristics to a degree that has warranted scientific recognition. We talk of organisms adopting ‘strategies’, or ‘deceiving’ other organisms. We dismiss this as a cognitive metaphor but it must have some significance because we would not dream of using such language for rocks. We say that organisms employ ‘strategies’, ‘deceive’ their fellows, ‘learn’ from ‘experience’, ‘know’ how to make webs, have ‘reasons’ for avoiding light, and so on.

This is messy biology, at best, and it has generated large-scale philosophical confusion.

This website claims that human minded (cognitive) agency is a limited and highly evolved form of biological agency. This claim leads to a simple evolutionary consequence. While there are features that uniquely define human agency – such as self-awareness and conscious deliberation – there are also features of human agency that are shared with biological agency, features that indicate their common evolutionary origin and relationship.

Biologically we provide explanations of physical structures by examining their evolutionary origins. The fins of whales and human hands share an evolutionary connection through the pentadactyl limb.  Cognition arose out of pre-cognitive antecedents – so how do we recognize this evolutionary connection?

This is best explained by example.

Life

We understand and explain life at many scales and from many perspectives. There are many necessary (essential) physical and chemical requirements for life, including biologically universal biochemical processes and pathways. But it is agency at the scale of the individual organism that provides the most compelling account of what it is to be alive – to manifest the objective, universal, and ultimate inherited behavioral disposition to survive, reproduce, adapt, and evolve.

This claim approaches a statement of the biological purpose of living organisms and the necessary and sufficient preconditions for life itself.

The biological axiom – that life is predicated on the survival, reproduction, and flourishing of organisms as autonomous agents – is a parsimonious scientific statement of life’s universal, objective, and ultimate preconditions – referred to here as biological agency. Biological agency, as the goals that motivate living organisms, is a crucial concept in biology because goal-directedness in nature is real and, without understanding this unity of purpose expressed by every organism it is not possible to understand how biological structures, processes, and behaviors support the organism in the attainment of these goals. Without understanding how the parts of an organism contribute the organism’s overall goals – what they are  ‘for’ – biological explanations become an incoherent listing of dissociated facts. It is from these universally shared grounding properties of life that human subjectivity evolved, including the uniquely minded (both conscious and unconscious) intentional properties of human agency.’

Living systems are information processors with a behavioral orientation that includes the capacity to adapt according to Darwinian principles. Human agency is a highly evolved and minded form of biological agency. These characteristics are what most obviously distinguish every organism from inanimate objects and the dead. Without an acknowledgment of the universal and purposive goals of biological agency, life assumes the character of inanimate matter, of purposeless physics and chemistry, while biology itself becomes a collection of dissociated facts.

Agency & life

Science attempts to describe the world in a detached way that minimizes the impact of human subjectivity. The view expressed on this website is that biological science does not get closer to biological understanding by drilling ever deeper into the physicochemical constituents of matter. This is because it is functionally integrated autonomous organisms that are both the intuitive and empirical reference point for biological explanation and investigation. Drilling does not get us closer to some kind of biological foundation or reality, but it does provide us with more inclusive explanations of the organisms that are the objects of primary biological interest especially in relation to their structures, processes, and behaviors.

We understand the biological world from multiple perspectives and systems of representation (e.g. structural, functional, physiological, genetic, evolutionary, organicist, materialistic, vitalistic, and so on). We also study it at many scales (hierarchical levels of organization, levels of selection, short-term, long-term) relating to everything from molecules to ecosystems.

The relatively recent fragmentation of biology into subdisciplines has led to the isolation of systems of terminology, principles, and frames of reference, each with its own scientific standards of appraisal. Without a synthetic biological overview, our interpretation of the relative significance of biological objects becomes a pragmatic choice based on our specialist interests.

A question like ‘What is life?’ forces us to consider the grounds on which we might prioritize any particular entity or, indeed, if there is any need to make a selection at all?

With the recent return of purpose and agency to biology, it has become evident that life emerged from inanimate matter when the necessary agential preconditions for life occurred in nature. Natural selection and gene frequencies in populations are the consequences, not the cause, of biological agency.

It is biological agency, as matter that expresses goals (ends or purposes), that provides the best explanation for Darwin’s ‘struggle for existence‘ and for life itself. It follows that it was Aristotle, not Darwin, who laid the foundations for biological science, a conclusion that has taken us nearly 400 years to rediscover.

Humans & other organisms

The paradigmatic biological agent is the autonomous, functionally organized, goal-directed, and therefore purposeful organism that acts on, and reacts to, its conditions of existence (adapting to both internal and external conditions) in a flexible way – as constrained by the limitations imposed of its unique biology and environmental circumstances as it pursues both proximate and ultimate goals.

Universal biological goals are pursued by humans with the aid of highly evolved mental faculties that include the use of symbolic languages and real biological agency is often described using the metaphorical language of human cognition.

The mindless behavior of organisms may understood as a set of mechanical processes set in train by its genetic programming (and therefore purposeless) – but human minded behavior may be characterized in the same way regardless of it being’conscious’ or ‘capable of reason’.

From an evolutionary perspective human agency evolved out of (is a development or subset of) biological agency, and thus the proximate minded goals of human agency are subordinate to the ultimate objective goals of biological agency.

The failure to distinguish clearly between biological agency and human agency has resulted in millennia of philosophical and linguistic confusion. Once biological agency is acknowledged as real, its investigation can be transferred from the realm of philosophical speculation into the domain of empirical science.

Four kinds of ‘mind’ biological agencies can be  usefully distinguished as evolutionarily emergent properties of life as it mostly (but not always) increased in complexity:

First: –  mindless agency – as behaviour uninfluenced by minds, but which occurs in both minded and mindless organisms; second, – unconscious minded agency – as mind-generated but intuitive or unconscious behaviour; third, – conscious minded agency – as behaviour that is a consequence of conscious deliberation; fourth, – collective or cultural agency –  behaviour made possible by symbolic communication and expressed through sociocultural norms such as political, economic, legal, and religious ideologies and conventions. These are discussed in more detail elsewhere.

It helps to think of these more as being superimposed on one another rather than changing from one to another. This helps in understanding human agency as a consequence of evolution by modification from a common ancestor, rather than a uniquely human property (see  agency and evolution.)

Agency & biology

An organism is as real as a molecule. We can understand and explain the world by using either analysis or synthesis, breaking it up into its parts, or seeing how its parts are integrated into larger wholes. We have just passed through a historical phase of analysis referred to here as the analytic turn.  We need a synthetic or holistic overview as well as an analytic and reductionist one. And, for convenience, we need an explanation that is neither anthropocentric nor anthropomorphic but human-friendly.

Aristotle noticed that teleology has two faces, the ‘of which’, aim, or function (say, of an eye ‘to see‘, of a heart ‘to pump blood‘) and the ‘for which’ that ahs a beneficiary, the organism deriving the benefit. In modern terms he noticed that the ‘for’ or purpose that exists in nature is of two kinds: the goals of organisms, and the functions of their parts.

Humans view and interpret nature from a human perspective and human scale. Science tries to overcome this cognitive bias by increasing the perspectives from which we view ‘life’, most notably by using technology to narrow down and widen out.

But organisms are meaningful units regardless of scale and this human bias. Agency (purpose) is both real in nature, and an explanatory lens that is close to our human interest because it draws together in a simple and engaging way what it is that we humans recognize in ‘life’ as distinct from  ‘matter’: it makes intelligible phenomena that would otherwise be dissociated facts of our universe‘.^[18]

Unfortunately, the analysis of his central  biological claim – that biological explanation must revolve around ‘ends’ (his final causes)  is now buried in decades of abstruse and mostly unsympathetic philosophical debate. His simple thesis was that biology, at its core, is a process of reverse engineering . . .  finding out what organisms, their parts, and their behaviour, are for.

In Aristotelian terms, humanity has now located the ‘inner craftsman’ that was scorned by the Scientific Revolution. This was an answer to Aristotle’s superficially simple and silly (but biologically crucial) question ‘Why do neither snakes nor stars have feet‘?^[17]

The question remains. From what perspective are we to take a summary view of life?

We humans have cognitive limitations, and it seems we have reached an impasse. Science has extended our biological knowledge beyond anything Aristotle could have dreamed. We have plumbed life’s structure, function, microscopic material composition, behaviour, dynamic process, energy flows, the communication of information, genetic properties, genomics, informatics, proteomics . . . physics, biochemistry, ecology . . . ? The academic arena is now so vast that it seems impossible to explain life briefly and coherently from this multitude of aspects all at once; yet to omit one is do it a disservice.  The place of whole organisms within their wider environments, including the greater whole – as communities, populations, ecosystems etc. – is as important as the circumscription of their smallest components. Is there a priority of scale when we break down organisms into organs, tissues, cells, and macro-molecules?  We cannot explain an ecosystem in terms of the molecules that make it up, even if this is theoretically possible.

This is where we are at now. If we want to define life, then we must define it as viewed from many aspects. We try to overcome our human ‘subjectivity’, our human focus, by using technology that extends our biologically given senses into unfamiliar worlds, and that is how science has advanced.

But Aristotle gave us an option. If we view must view the world from a human perspective, then perhaps we can use that perspective to its greatest advantage. Central to our humanity is our purposiveness, agency, and intentionality.

In (over)simplified terms: scientists of the early modern period provided scientific explanations that were restricted, in Aristotelian terms, to material and efficient cause i.e. what something is made of (its material composition), and the trigger for it doing whatever it does (today’s understanding of ’cause’). This approach to scientific explanation gave rise to what is characterized in the history of science as a mechanistic world of matter in motion and this conception replaced Aristotle’s world view of a cosmos filled with life-like agency. Only with Darwin was a more organic perception of the world reinstated although the old preoccupation with the physicochemical as somehow prior has persisted.

Aristotle’s third and fourth explanatory (be)causes, which he believed were necessary for a complete scientific explanation, were his formal and final causes. These were considered problematic and therefore best discarded or ignored. Final cause (‘that for the sake of which’ or ‘for’) was problematic in several ways: it implied future causation along with the possibility of supernatural influence and the intrusion of anthropomorphism. Formal cause as ‘that which makes it what it is’ was also an ambiguous, abstract and spooky business, suggesting mysterious philosophical essences or some-such.

Aristotle argued that efficient cause without final cause was like a fire that spreads uncontrollably in all directions, while final cause is an outcome to an ordered (not random or accidental) and efficient process (De Anima II.4,416a15-18). He was also adamant that purpose arose in nature itself; it was not placed there by either God or the human imagination.

It is significant that Aristotle’s four causes divide neatly into two pairs. The material and efficient causes capture an analytic ‘bottom-up’ physical and material perspective on the world and change. Formal and final causes offer a ‘top-down’ synthetic, integrating, unifying, forward-looking, agential, and purposeful perspective on the universe. Aristotle’s telos implied the mesmerizing thought that, at its very simplest, every cause has an effect as a primordial ‘purpose’, however obscure or tiny that might be.

The influence of the Scientific Revolution on contemporary science can be exaggerated, but by emphasizing a mechanistic world of matter in motion, and abandoning Aristotle’s formal and final cause, ‘life’ and ‘agency’ were squeezed out of the scientific world, thus uniting non-human life with the material and efficient, essentially the inorganic. Humans were the only creatures with ‘real’ agency. By restricting purpose and agency to humans, and without the theory of evolution, a gulf was opened up between humanity and the rest of life – a gulf that is yet to be satisfactorily bridged.

Agency & Evolution

Eminent biologist Theodore Dobzhansky once pointed out that ‘Nothing in biology makes sense except in the light of evolution’. Though evolution is central to the study of biology it is not central to life itself. We might offer a riposte to Dobzhansky that ‘Nothing in evolution makes sense except in the light of biological agency’ or, in more direct terms, that ‘it is the purposive activities of organisms that are the principal causes of evolution’.^[101]

Darwin proposed natural selection as the principle underpinning the evolution of species. Because resources are limited in nature, organisms engage in a ‘struggle for existence‘ with a ‘survival of the fittest‘, those organisms with heritable traits favoring survival and reproduction leaving more offspring than their peers, these traits increasing in frequency over many generations. For Darwin it was organisms at the center of evolution, but as research moved into genetics and molecular biology it was genes in populations that seemed to be ‘pulling the strings of life’. But the ‘heritable traits that favor survival and reproduction’ arise out of the goal-directed (teleological and agential) behavior of organisms. There is, indeed, no current consensus on what the unit of evolution is.^[107]

Without agency, natural selection would not be possible. It was Aristotle, not Darwin, who established the necessary pre-conditions for life and evolution, a conclusion that has taken us nearly 400 years to rediscover.

Evolutionary theory juggles complex concepts alongside interacting and interdependent physical factors. How do we decide which factor has causal or explanatory priority, or controlling efficacy? How do we rank these different factors and determine the strength and direction of their relationships and dependencies? Which factor is a cause, and which a consequence, and of what?

Here is a possible list of major factors to consider when explaining evolution: variation, inheritance, adaptation, natural selection, and time. And here is an approximation of their causal relationships. Natural selection acts on variation, preserving advantageous traits that, over time, become more prevalent in the population through the process of inheritance, as individuals with these beneficial traits are more likely to survive and reproduce. Adaptation is a consequence of this process, with populations gradually becoming better adapted to their environments through the accumulation of beneficial traits. Natural selection is the primary driver of evolutionary change, with variation and time as supporting factors that enable and shape the process.

How sure are we that these are the key factors in evolution and that this is our best representation of their relationships? Above all, how secure is natural selection as the driver of evolution?

When, for example, we distill the whole idea of evolution by natural selection into three principles – variation, heredity, and differential fitness – we forget that without organismal agency, evolution would not be possible.

Where should the emphasis lie?

So, what happens when biological agency is incorporated into our understanding of evolution?

Here is a preliminary definition of evolution that acknowledges both the reality and evolutionary significance of biological agency:

Evolution is driven by the adaptive interaction between living organisms and their conditions of existence. These conditions of existence include both the external environment and internal bodily constraints, as well as the individual genetic variation resulting from recombination and mutation, and intergenerational genetic changes that take place within populations, such as genetic drift, and gene flow. Short-term adaptation as phenotypic plasticity (which includes behavior) shapes the conditions of evolutionary adaptation that influence the long-term incorporation of inherited traits. Natural selection preserves those traits that enhance survival and reproduction.

Natural selection & biological agency

The relationship between biological agency and natural selection relates to time scale.

Life originated with the first unit of matter that could survive, reproduce, adapt, and evolve. Did natural selection give rise to that organism or did natural selection follow after its emergence?

Natural selection is a multi-generational long-term process in which heritable traits become more or less common in a population depending on how they influence organismal survival and reproduction. Biological agency influences an organism’s short-term ability to survive and reproduce, thus impacting its fitness and potentially affecting its long-term contribution to future generations. Thus the short-term behavior of organisms can act as a temporal bridge between immediate non-genetic adaptation and the gradual shaping of genetic outcomes over evolutionary time.

How much influence does biological agency have on the course of evolution?

This too depends on our emphasis. Sometimes the impression is given that environments mold the organism (& populations) by presenting conditions that promote particular adaptations. But environments have no agency, their influence lies in how they passively constrain what is possible. What actually happens depends on the agential behavior of the organism as generated by an internal reconciliation between the organism’s natural propensities and the constraints of its conditions of existence (both internal and external). Apportioning causal efficacy becomes very tricky.

The current consensus is that short-term behavior plays second fiddle to long-term heredity, but this could change. Studies in ecology and evolutionary biology show how behaviors such as mate selection, foraging strategies, and social interactions impact population dynamics, gene flow, and ultimately evolutionary trajectories. The behavioral orientation of organisms towards their conditions of existence can influence biological outcomes at the scales of both individuals and populations. The short-term behavior of organisms, both individually and collectively, can strongly influence what become the environments of evolutionary adaptation that drive the long-term patterns of evolution observed in populations and species over geological time scales.

While the theory of natural selection is supported by a vast body of empirical evidence from various fields, including genetics, paleontology, comparative anatomy, and biogeography, this does not preclude consideration of the influence and role of biological agency in its manifestation.

The acknowledgement of biological agency enriches our understanding of the complex interplay between evolutionary processes and organismal behavior. Empirical research in fields such as behavioral ecology, evolutionary psychology, and sociobiology provides insights into how organismal agency interacts with evolutionary mechanisms to shape biodiversity and ecological dynamics. Human cultural evolution is a spectacular example of the way non-genetic factors can impact biological outcomes and evolution.

Conclusion

This website treats human minded agency as a limited instance of biological agency. That is, human cognitive faculties evolved out of, and share characteristics with, mindless (pre-cognitive) organisms.

Properties resembling those of human cognition occur in non-neuronal (non-cognitive) organisms.^[87] Included here is a full suite of faculties that we describe using the human-specific (more or less) language of cognitive psychology. It includes reference to remembering, learning, decision-making, sensing, choosing and preferring, deceiving, favoring, perceiving, anticipating, behaving, and so on.

It is conventional, and helpful, in philosophy to condense this range of faculties into the three human cognitive domains of epistemology (knowledge, beliefs), ethics (values, desires), and logic (reason).

The universal goals of the biological axiom are manifested in matter as the totality of biological structures, processes, and behaviors in a state of graded and evolved complexity. These are nature’s mindless exploration of the physical options available for the attainment of inherited and mindless biological goals – the goals that gave rise to human subjectivity.

The most efficient description of the universal means adopted by organisms to address their goals of survival, reproduction and flourishing entails a behavioral orientation, their capacity for information processing, and the capacity to adapt. These underlying conditions of life can be inferred from the crucial human mental faculties of knowledge, values, and reason.

Key points

Note: human-talk is indicated using quotes.

• Darwin dramatically changed our understanding of organisms as they exist in space and time. He changed them from discrete kinds uniquely created in a single moment, to a community of life that is physically connected across time through the process of graduated organic emergence, divergence, and complexification that is descent from a common ancestor

• Darwin’s On the origin . . . contained two profound insights that have not yet found their way into either biological science or the public imagination. First, he naturalized teleology by demonstrating that, in spite of the metaphorical language frequently applied to nature, goal-directedness (purpose) arises in a natural way, without the need to invoke either the supernatural, or the foresight of human intention. That is, he showed how purpose in nature is real. Second, he demonstrated the close physical connection that exists between the entire community of life through descent from a common ancestor and therefore, incidentally, that life concepts and processes show resemblance that is grounded in reality, in nature itself, not in metaphor.

• Biological agency is manifest through three key elements which, expressed in human-talk, are the agent, its mission, and its means. The mission equates to purposes, goals, or interests, while the means entail strategies that are not mere mental ‘intentions’, but physical activities.

• Organisms are agents that pursue biological interests through the ultimate (long term, multi-generational adaptations) as goals of survival and reproduction as expressed in the biological axiom, and the (short term, single generation phenotypic traits). Goals arise out of the very nature of living matter. In their advanced human form, ancestral goals arise out of their biological evolutionary foundation as the ‘will’, ‘passions’, ‘intuitions’, or ‘appetite’.

• The grounding principles of biological agency are universal though biological agents and their strategies vary in degrees of physical and behavioural complexity

• We acknowledge life through the agency of living organisms with a predisposition to survive, reproduce, and flourish, this being biologically necessary ultimate conditions for their existence (the biological axiom).

• humans pursue the ultimate ends of biological axiom I through the proximate ends of happiness and wellbeing

• We apply a normative idiom to organisms and their traits because organisms, in accordance with the biological axiom, can be beneficiaries of circumstance

• The biological axiom is a statement of both fact and value since it provides the basis for biological activity: it is the grounding for all normativity, including human values.

• Biological agency is expressed in terms of semi-autonomous structural, functional, and behavioural flexibility – the capacity to act and react, to adapt, both short- and long-term. Biological agents exhibit a unified short-term independence by regulating both inner processes, and the interaction with surroundings. Over the long-term self-replication with heritable variation and differential reproduction facilitates adaptation and evolution.

• Living organisms differ from inanimate matter in their autonomy expressed through the capacity to replicate (recreate) themselves and to constrain the circumstances of their existence in a way that promotes their survival, reproduction, and flourishing

• Evolution is a process of selection (natural selection). Where there is selection, there is selection ‘for’. And, in nature, where there is an aim, a telos, or ‘for’, together with a beneficiary (under the value conditions of the biological axiom) then there is purpose, agency and a foundation for normativity that distinguishes the living from the non-living, and is independent of human cognition.

• Today the notion of agency no longer brings with it the implication of mysterious supernatural forces or complex abstractions – it has been thoroughly naturalized. But a few philosophical difficulties remain. Among these is the conflation of nature with human experience, generally regarded as an extension of the old personification of nature and an anthropomorphic cognitive bias. Part of this is the use of anthropomorphic language (human-talk) to bridge the gap between human characteristics and their analogues or evolutionary antecedents as they exist in non-human organisms.

• Biology has inherited two fallacies from the thinkers of the Scientific Revolution: the metaphor fallacy as the claim that all anthropomorphism is metaphor; and the purpose fallacy as a claim that the word ‘purpose’ can only be used meaningfully in the context of mindfulness

Glossary

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

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

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

First published on the internet – 13 Sept 2021

. . . 22 March 2022 – added inversion of reasoning and metaphor fallacy as support for teleology
. . . 8 April 2022 – condensed the paragraph on teleology and added the agency error
. . . 10 May 2022 – added the agential paradigm and refined the 5-point defense of teleology
. . . 9 June 2022 – substantial revision of Epilogue
. . . 2 August 2022 – further revision of Epilogue (Epilogue eventually created as separate article)
. . . 4 August 2022 – added discussion of autonomy as increasing individual behavioural flexibility and freedom
. . . 12 September 2022 – minor edits
. . . 28 November 2022 – reconfigured section on the biological axiom
. . . 14 October 2023 – substantial revision
. . . 14 October 2023 to early 2024 – substantial top-bottom revision
. . . 3 January 2024 – added section on biological causation to critique of Modern Synthesis
. . . 4 April 2024 – added arguments putting biology within a spatiotemporal frame and organisms as grounding agential units

. . . under daily review for a while

—

BIOLOGICAL WONDERS CREATED BY MINDLESS & UNCONSCIOUS NATURE
– FAR SUPERIOR TO ANYTHING INVENTED BY HUMANS

STINGRAY
X-Ray image of stingray
Courtesy loctrizzle – http://imgur.com/gallery/bZbHmJA – Accessed 25 May 2017

HUMAN BRAIN
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