Biological explanation

Biological purpose as expressed in the intricate and mindlessly created design of a goal-directed biological agent (an autonomous organism).
Shared X-Ray image of stingray
Courtesy loctrizzle – http://imgur.com/gallery/bZbHmJA
Accessed – 22 Mar 2019
Living matter persists by exchanging energy, materials, and information with its surroundings and, in this sense, it is continuous with its surroundings. However, among the variety of organic forms, it is organisms that stand out for their bounded individuality and agential autonomy within this organism-environment continuum.
Like other organisms, a stingray displays biological agency, meaning that it acts on and responds to its internal and external conditions in a unified, goal-directed, flexible, and adaptive way. It is this agential autonomy that establishes organisms as primary biological agents.
The stingray is identified by species-specific biological traits that have arisen during its unique evolutionary history. However, it also shares with other organisms many characteristics that are a consequence of common ancestry, and it is these shared characteristics that establish evolutionary relationships. Among the shared characteristics are those that are shared by all organisms – features that can be used to define life itself.
The stingray’s structures, processes, and behaviors are functionally integrated so that they attain the same universal, objective, and ultimate goals as every other living organism – the capacity to survive, reproduce, adapt, and evolve. These behavioral goals are universal, because they are common to all life; objective, because they are a mind-independent empirical fact; and ultimate, because they summarize and unify all proximate goals. So, while the parts of organisms often demonstrate a high degree of independence, self-maintenance, and goal-directed activity, they are ultimately subordinate to the overall goals of entire organisms.
There are many characteristics that are necessary for life to exist, they include structures (like genes and cells), processes (like metabolism, homeostasis, growth and development), and behaviors (like response to stimuli), but it is the unified functional integration of all these factors in entire organisms that most clearly distinguishes the living from the non-living and dead. Thus, the universal, objective, and ultimate behavioral conditions of biological agency – the propensity to survive, reproduce, adapt, and evolve – constitute an essential condition for life, a foundational biological principle of agency that is referred to here as the biological axiom.
Organisms are goal-directed biological agents, so biological explanations often begin with the consideration of ‘ends’ – with what organisms and their structures, processes, and behaviors are ‘for’. This can be confusing because, while biological goals are first in explanation, they are last in causation/realization being natural limits or ends. Prioritizing ends in biology does not mean that biological goals exert a mysterious causal pull from the future, possess a supernatural force, or amount to the reading of conscious human intentions into nature. Acknowledging the purpose of goal-directed behavior is not merely a useful heuristic. Goal-directed (agential) behavior is scientifically proven, causally transparent, and uncontroversial. However, when biology ignores functions and agential goals it risks reduction to an incoherent collection of unrelated facts precisely because it overlooks the purposes of biological entities.
Without agency biology assumes the character of inanimate matter, of purposeless physics and chemistry. This is why it is agency – not the other necessary biological structures, processes, and behaviors – that is fundamental to life. In biological explanation function comes first because it conveys the goals and purposes of agency that give structures, processes, and behaviors their biological meaning.
Stingray traits can be understood and explained from two different evolutionary perspectives: their evolutionary ancestry, and functional role. Our knowledge of the evolution of both species and lineages is steadily improving so we are constantly refining our knowledge of how traits evolved. The biological axiom is not, however, concerned with actual individual structures but universal goal-directed behaviors in general (functions, purposes, goals) and, as we have seen, it is ends that have priority in biological explanation. Each organism has a unique set of traits that manifests the same functional ends as other organisms. Importantly, functionally equivalent ends are not necessarily attained using evolutionarily related structures. For example, all wings facilitate flight, but the wings of bats, birds, and butterflies have different evolutionary origins.
Human agency and human cognition are highly evolved forms of biological agency and biological cognition: they can be understood in terms of both their evolutionary (structural) ancestry, or functional roles. Each has on the one hand, a physical manifestation that has an evolutionary history and, on the other hand, physical traits that have functional equivalents in other organisms. For example, talk of plant intelligence from a strictly structural perspective is straightforward cognitive metaphor, but from a functional perspective it is expressing a real functional equivalence, albeit using confusing language.
The goal-directed behavior of biological agents is generated by functionally integrated internal processes that are referred to here as biological cognition, with human cognition just one of its species-specific and highly evolved forms. The generalized (universal) function of biological cognition is to access, store, retrieve, process, prioritize, and communicate information. These universal functional characteristics of organisms are expressed in structurally and evolutionarily diverse but functionally equivalent ways across the Tree of Life. While we regard the mental faculties of reason, value, knowledge, memory, learning, communication, perception, experience, sentience, subjectivity, etc. as being properties largely associated with human (or sentient) forms of cognition and their unique evolutionary history, they also, of necessity, share the universal properties of biological cognition. That is, uniquely human mental traits have shared functional equivalents in other organisms: the unique properties of human cognition are a subset of the universal properties of biological cognition.
Human thought, action, and language (human agency) are just one species-specific form of more general and functionally equivalent biological cognition, behavior, and communication (biological agency).
Concerning the challenge we just faced about how to describe things in numbers and definitions, What is the reason for a unity/oneness? For however many things have a plurality of parts and are not merely a complete aggregate but instead some kind of a whole beyond its parts, there is some cause of it since even in bodies, for some the fact that there is contact is the cause of a unity/oneness while for others there is viscosity or some other characteristic of this sort. But a definition [which is an] explanation is one [thing] not because it is bound-together, like the Iliad, but because it is a definition of a single thing’
Aristotle, Metaphysics 8.6 [=1045a], c. 350 BCE
Often translated as ‘The whole is greater than the sum of its parts’
Περὶ δὲ τῆς ἀπορίας τῆς εἰρημένης περί τετοὺς ὁρισμοὺς καὶ περὶ τοὺς ἀριθμούς, τί αἴτιον τοῦ ἓν εἶναι; πάντων γὰρ ὅσα πλείω μέρη ἔχει καὶ μή ἐστιν οἷον σωρὸς τὸ πᾶν ἀλλ᾿ ἔστι τι τὸ ὅλον παρὰ τὰ μόρια, ἔστι τι αἴτιον, ἐπεὶ καὶ ἐν τοῖς σώμασι τοῖς μὲν ἁφὴ αἰτία τοῦ ἓν εἶναι, τοῖς δὲ γλισχρότης ἤ τι πάθος ἕτερον τοιοῦτον. ὁ δ᾿ ὁρισμὸς λόγος ἐστὶν εἷς οὐ συνδέσμῳ καθάπερ ἡ Ἰλιάς, ἀλλὰ τῷ ἑνὸς εἶναι.
My loose translation, with my own words in square brackets –
‘When we intuitively recognize a specific object, what is it that makes us treat it as something discrete and unique? If it is somehow different from an aggregate of parts, then how can we explain that difference? In some cases, the close attachment of parts is enough to make a wholeness [as in a heap of sand grains] but in other cases [as in an organism] there is a more complex connection between the parts. When we provide a definition (explanation) of something that is new and unique we are not drawing attention to the mere aggregation of parts (like the many pages that make up a book, [or the grains of sand in a sand heap]) but to some property that exists beyond the aggregation itself.’
This article is one of a series investigating a 'new biology' that gives full consideration to biological agency and its relationship to human agency. These articles are introduced in the article on biological explanation which considers the forward-looking biological explanatory emphasis on ends, goals, purposes, functions, and agency. Much of the discussion revolves around the scientific appreciation and accommodation of real (genetically inherited) purposive (teleological, teleonomic) goal-directedness (agency) that is a universal distinguishing feature of life. The series also discusses the nature of biological classification and the way we classify 'everything' in our worldviews and modes of representation.
Human agency is a limited, conscious, and highly evolved form of biological agency. While it is currently conventional to treat biological agency as a human creation - the reading of human intention into nature - this website explores the claim that it was biological agency that gave rise to human bodies and human subjectivity - that, in this temporal sense, biological agency is prior to human agency.
The suite of articles exploring biological agency ranges across topics in theoretical biology and the philosophy of biology, including:
Processes - how biology is more concerned with process than structure or things.
Synthesis and analysis - the biological legacy of analytical reductionism.
What is life? - the crucial role of organisms and their agency agency in determining purpose, values, and what it is to be alive. How agency gives meaning to biological structures, processes, and behavior and must therefore take precedence in biological explanation.
Biological axiom - how this biological principle establishes the necessary behavioral (agential) conditions for all life as the universal, objective, and ultimate biological goals that give organisms - including their structures, processes, and behaviors - biological meaning.
Purpose - the history of the notion of purpose (teleology) including eight potential sources of purpose in biology.
Biological agency - as an account 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 goal-directed organismal behavioral propensities that express a universal behavioral orientation or perspective on existence (biological normativity).
Evolution of biological agency - the actual evolutionary emergence of human agency out of biological agency.
Plant sense, Plants make sense, and Plant intelligence addressing the rapidly developing research field of pre-cognitive agency in plants.
Biological hierarchy - the explanatory problem of levels, scales, and perspectives in biology.
The organism - the case for an organism-centered biology in which organisms as biological agents are the foundational functional units of biological organization.
Structures, processes, and behaviors - an introduction to biology that avoids the confusion of 'levels of existence'.
The biological axiom establishes the necessary behavioral (agential) conditions for all life. These are the universal, objective, and ultimate biological goals that give structures, processes, and behaviors biological meaning. Without at least an implicit understanding of these goals, biological explanations are an incoherent collection of unrelated facts so, in this sense, agency and function take explanatory precedence in biology. The structures, processes, and behaviors that make up the subject matter of biology may be compared in terms of both their structural-evolutionary history and functional equivalence.
The internal processing required to generate the organismal behavior summarized in the biological axiom can be conceptually framed as biological cognition. On this understanding human cognition is a species-specific and highly evolved form of biological cognition. Theoretical biology does not have a terminology to distinguish between structurally different but functionally equivalent forms of biological cognition. It therefore resorts to the terminology of human cognition (as cognitive metaphor). Though word meanings cannot be changed at will, in science it is possible to refine categories and concepts to better represent the world.[73]
Introduction – The Study of Life
Biological science is currently at a crossroads as it adjusts to two major changes in philosophical outlook.
a) the elevation of biology within the sciences as the traditional emphasis on physics and chemistry, associated with the philosophy of analytical reductionism, comes under increasing critical scrutiny
b) the profound consequences of the reinstatement, after over two millennia, of agency as a defining characteristic of all life
This article is a brief consideration of biological explanation as it relates to these two issues in biology.
Biology is the scientific study of life and living organisms, encompassing their structure, function, growth, evolution, distribution, and taxonomy. It explores the molecular mechanisms underlying cellular processes, the genetic basis of inheritance, and the complex interactions within ecosystems. Biology integrates principles from various scientific disciplines, including chemistry, physics, and mathematics, to understand the fundamental processes that govern life. Through research and experimentation, biologists seek to unravel the mysteries of life, from the molecular level to entire ecosystems, providing insights into the diversity and interconnectedness of all living beings.
– A consensus account of biology provided by AI –
Biology, as the study of life, has struggled with its definition. What do we mean by ‘life’, what distinguishes life from non-life, and how do we separate the living from the inanimate and dead? And isn’t life, ultimately, just physics and chemistry?
Current attempts to find a single critical ingredient or feature of life have failed, so we fall back on a shortlist of life’s essential conditions – those structures, processes, and behaviors that appear necessary for life. Prominent among these are structures (like genes and cells), processes (like metabolism, homeostasis, reproduction, growth, and development), and behaviors (like adaptation and response to stimuli). Rather than saying what life is, it is easier – like the AI summary above – to describe what biologists do.
The problem of definition is discussed in detail in the article ‘What is life?‘ where it is argued that the historical extension of biology into micro- and macro-scales has taken researchers away from the organism as the center of biological study. Critical though studies of genes, cells, physiology, and ecology might seem, biology finds its focus in organisms. This is because organisms, more than any other biological factor, are physically bounded, functionally integrated, and autonomous biological agents. They are therefore centers of biological activity: independent causal hubs to which biological structures, processes, and behaviors – as organism parts – must ultimately defer.
Biological agency, which is most clearly demonstrated in organisms, is the propensity to survive and reproduce (expressed through the key biological concepts of adaptation and evolution). These goals are objective (an empirical fact), universal (occur in all organisms), and ultimate (a summation and limit for all proximate goals).
Life can therefore be defined in terms of the agency of organisms, and biology the study of organisms, their structures, processes, behaviors, and communities.
This is organism-centered biology with the individuation of organisms established by their physical bounds and agential focus (survival, reproduction, adaptation, evolution) to which three key biological phenomena – structures, processes, and behaviors – are subordinate.
Goal-directed organisms are necessarily explained and understood by first – implicitly or explicitly – acknowledging their objective, universal, and ultimate goals, and therefore their agency. That is, goals – though last in causation/realization – are necessarily first in explanation. This is the significance of teleology for biology: without understanding, or presuming, what things are ‘for’, biology becomes an incoherent collection of unrelated facts.
Organism-centred biology – biology studies organisms, their parts, and their communities. This is the foundational principle of organism-centered biology. The organism is a fundamental analytical, methodological, epistemic, and ontological biological category. As the basic unit of biological classification (the species is a group of similar organisms), ecology, and evolution, the organism is a reference point for biological description and explanation. While parts of organisms often demonstrate a high degree of independence, self-maintenance, and goal-directed activity, they are ultimately subordinate to the goals of the functionally integrated and self-determining adaptive agency of whole organisms. Organisms thus express greater agential autonomy than their parts or communities, being major causal hubs within the biological network of causal connection.
Structures, processes, and behaviors – the study of biology requires an explanatory categorization of its major scientific phenomena. The traditional conceptual framework of the hierarchy of biological organization introduces unnecessarily ambiguous and complicated philosophical ideas. Biological understanding can be built around organisms (their parts and communities) and the categories of structure, process, and behavior. While engaging fewer categories this offers a more comprehensive, simple, and dynamic conceptual framework that reflects the nature of contemporary biological investigation.
Structures: the tangible physical components of biology, ranging from sub-organismal entities like molecules, genes, cells, tissues, and organs, to supra-organismal entities such as colonies, populations, ecosystems, and the biosphere.
Processes: the biochemical and physiological activities that sustain life, such as photosynthesis, homeostasis, growth, metabolism, and reproduction. Also the long-term changes addressed by evolutionary biology. These dynamic activities are often obscured when focusing solely on structural descriptions.
Behaviors: the actions and responses of organisms within their environment. These can be both minded and mindless, in both organisms and their parts, and are often goal-directed, even in a minimal sense, by having specific functions.
These three categories reflect the historical development of biological investigation as it passed from being an inventory of static structures (histology, anatomy, morphology, taxonomy), to dynamic functional processes (physiology, developmental biology, ecology, evolutionary biology, systems biology), and then behaviors and agency (ecology, ethology, psychology, cognition).
This progression of investigative categories shows how biology has increasingly integrated the concepts of time, change, function, and agency through the interplay of physical structures, processes, and adaptive behaviors. These three categories provide a conceptual tool of interrelated categories that effectively abstract the complexity of biological systems.
It is conventional in biology to contrast structures with functions. Dividing biology into structures, processes, and behaviors offers a broader perspective on its phenomenal scope: structures focus on physical organization, processes on biochemical and physiological mechanisms, and behaviors on actions and interactions of organisms to provide a more dynamic, processual, and adaptive account of life.
Biological agency – the structures, processes, and behaviors of organisms combine to express a functionally integrated unity of purpose – the universal, objective, and ultimate behavioral 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. These are not only the defining conditions of biological agency they are the natural limits or ends that establish the behavioral conditions that define all life and the motivating force of evolution that drives the continuous development and diversification of organisms. Biological agency does not entail deliberate intention. Human agency is a highly evolved and species-specific form of biological agency.
Primacy of agency – agency is a necessary behavioral condition for life but many other necessary factors may be given elevated status, most notably genes and cells. What is special about agency? Goal-directedness in organisms is an objective fact. These goals are the natural ends or limits to behavior. Without understanding these ends biological explanations do not make sense.
Understanding the goal-directedness of organisms is crucial to biological understanding. Whether the goals of biological agency have proximate ends (the ends of particular instances) or ultimate ends (the ends of all biological activity). Coming first in explanation, goals and agency have a life-defining place in the study of biology and life.
Historical background
The notion of biological explanation has evolved significantly throughout history, reflecting advancements in scientific understanding, philosophical thought, and empirical observations. This concept is rooted in the early inquiries into the nature of life and living organisms, tracing its origins back to ancient civilizations.
In ancient Greece, philosophers such as Aristotle and Hippocrates laid the groundwork for biological thought by proposing naturalistic explanations for biological phenomena. Aristotle, often regarded as the father of biology, categorized living organisms and posited that their forms and behaviors could be understood through systematic observation and classification. His teleological approach, which suggested that organisms exist for particular purposes, established an early framework for understanding biological function and complexity.
The medieval period witnessed a merging of classical biological ideas with theological perspectives, leading to a less empirical approach to biological explanation. However, it was during the Renaissance that a resurgence in scientific inquiry began. Figures such as Andreas Vesalius and William Harvey emphasized direct observation and experimentation, marking a pivotal shift toward a more empirical and mechanistic understanding of biology. Vesalius’s meticulous anatomical studies laid the foundation for modern anatomy, while Harvey’s work on circulation revealed the systemic functions of biological organisms.
The development of the scientific method in the 17th century further refined approaches to biological explanation. Pioneers such as Francis Bacon advocated for an empirical approach to knowledge, promoting observation and experimentation as the cornerstones of scientific inquiry. This period saw the emergence of reductionism, wherein complex biological systems were understood by analyzing their simpler components. This reductionist approach remained prevalent through the Enlightenment, shaping the understanding of life processes.
The 19th century marked a critical juncture with the formulation of evolutionary theory by Charles Darwin. His seminal work, “On the Origin of Species,” introduced the concept of natural selection as a mechanism of evolution, providing a cohesive biological explanation for the diversity of life. Darwin’s ideas challenged prevailing beliefs about the fixity of species and emphasized the importance of adaptation and environmental interaction in shaping biological characteristics.
As biology advanced into the 20th century, the advent of genetics revolutionized the understanding of heredity and variation. Gregor Mendel’s experiments with pea plants laid the foundation for the field of genetics, ultimately influencing biological explanation through the discovery of DNA as the carrier of genetic information. This molecular perspective, coupled with advances in biochemistry, allowed scientists to explain biological phenomena at a cellular and molecular level, shifting the focus from mere observation to the mechanisms underlying life.
The late 20th and early 21st centuries have seen the integration of various biological disciplines, leading to a systems biology approach that emphasizes the interactions and networks within biological systems. This holistic perspective recognizes the complexity of living organisms and the interplay between genetics, environment, and behavior. Furthermore, the rise of computational biology and bioinformatics has enabled researchers to analyze vast amounts of biological data, refining explanations of biological processes.
The history and development of biological explanation reflect a dynamic interplay of philosophical thought and empirical research. From ancient classifications to modern integrative approaches, the concept of biological explanation continues to evolve, providing deeper insights into the complexity of life and the processes that govern living organisms. As our understanding expands, so too does the significance of biological explanation in unraveling the mysteries of life (AI Sider August 2024).
As Aristotle knew over 2000 years ago, it is the goal-directedness of organisms, their purposive behavior (their agency) that differentiates the living from the inanimate and dead. It is universal organismal goals (explicit or implicit) that ground and make coherent all biological explanations. Agency takes precedence in biological explanation, and the definition of life because without understanding the natural ends and limits of organismal behavior (agency), biology becomes a dissociated account of unconnected observations. It is the functionally integrated agential autonomy of organisms that distinguish life from non-life and biology from physics and chemistry.
Biology studies living organisms and their processes, focusing on structure, function, and evolution. The social sciences study human behavior and societies, while physics and chemistry explore the fundamental principles of matter and energy.
For centuries now one major scientific enterprise has entailed the search for scientific meaning, for reality, in the simplest constituents of matter. Our belief in reductive analysis as the single most powerful scientific tool has driven us to every smaller constituent of matter as we drill for the scientific pot of gold, for the basic constituents of everything, and therefore of reality. We see this in the language of fundamental particles and genes as the simplest constituents of life. It is often said that biology is simply complicated but imprecise physics and chemistry – and how can we deny that organisms are an aggregation of physicochemical processes?
The articles on this website investigate what makes life special and different. It concludes that when Aristotle noted how, in living organisms, we see goal-directed purposive behavior and therefore agency.
Aristotle provided a compelling argument that organisms, as functionally organized wholes, cannot be fully explained in terms of their component parts – the functional whole is, as it were, something new – an emergent property that must be included in any scientifically acceptable explanation: it is all the parts – and something more – where the ‘something more’ is real, not a philosophical abstraction or semantic sleight of hand.
Aristotle was drawing attention to the appearance of novelty in the universe. At one time the universe was uniform plasma: it now consists of a myriad of objects with an infinity of properties, and relations.
Aristotle recognized the unity of functional organization of living organisms. They may have been composed of special living matter, but it was their goal-directedness that stood out – the way the potentiality of an acorn was actualized in the form of a mature oak tree with acorns that would repeat the cycle of its biological kind. It was not what an organism was but what it did that mattered. The goal-directedness somehow guided or controlled the matter and, in this sense, it was prior to the matter. Insofar as the parts of organisms – their structures, processes, and behavior – function in support of the organism goals, they are subordinate to them.
Aristotle had singled out a crucial feature of every living organism – its goal-directedness – what today we would call its agency. Organisms act on and respond to, their surroundings in a behaviorally flexible but directed way.
As a grounding for his explanation of biological phenomena this concentration on ‘ends’ became known as teleology. But with the Scientific Revolution came the insistence that ‘goal-directedness’ be empirically justified, and it seemed to fall short. ‘Ends’ were like a mysterious and improbable supernatural life force, an unlikely vitalism. The concern with ends and purposes resembled minded human intentions that could not possibly exist in mindless nature. Today the presence of purpose in non-human organisms seems to hint at its insertion by God: intelligent design. Besides, goals as ‘ends’ cannot be causes, because there cannot be backward causation. In short, teleology was rejected as empirically unjustified – and that is where we are today.
The Scientific Revolution was followed by a methodological scientific preoccupation with analysis, sometimes called analytical reductionism. This was like looking for the prime mover in a causal chain. The smallest part of a substance or process, if it had causal efficacy, was, in effect, its originator and the explanation for all that followed. It was an intellectual foundation stone.
Aristotle had perceived the universe through the metaphor of the whole organism. In a hierarchical world (the great chain of being) God and spirit were at the ‘top’ then came man, sentient animals, plants, with inanimate matter. It is a quirk of the human mind that it ranks the objects of its experience as a prelude to action. The Scientific Revolution turned everything upside down as the smallest conceivable ‘fundamental’ particles of matter, not God, became the explanation for ‘everything’.
This website argues that the Scientific Revolution was an overreaction to Aristotle’s teleology which provided a more compelling account of biological phenomena than the philosophy of biology bequeathed to us by the Scientific Revolution.
The 21st century is acknowledging the inadequacies of analytical reductionism. Science is not served by elevating the significance of small parts of wholes – and this website describes how this is so.
We cannot describe objects in terms of themselves. In describing them using other terms they take on the character of those other terms. If we describe organisms in physicochemical terms, then they take on the character of physics and chemistry, if we explain them in physiological terms, they take on the characteristics of physiology, and if life is viewed as a process it takes on the characteristics of process. Important though ‘parts’ are in our explanation of ‘life’ we intuitively understand its agential focus.
The miracle of DNA coding, the functional power of physiological processes, and the subject matter of the many other academic disciplines studying organism ‘parts’, the origins and directions of causal networks and chains. All are ultimately subordinate to our understanding of the goal-directed operational units we call organisms. These are goal-directed entities that act on, and respond to, their surroundings. Organisms are, to use modern terminology, biological agents – and it is agency that brings us closest to the scientific essence of life.
It is the universal, unified, and objective goals of living organisms that provide the most scientifically satisfying description of what it is to be alive. The academic disciplines of mathematics, physics, and chemistry can be used to study agency but they do not have agency.
Explanation
Dictionary definitions of explanations refer to statements or accounts that make something clear by describing it in detail, and providing reasons or causes. In philosophy, an explanation involves providing a coherent account of the reasons, causes, or mechanisms that clarify why a phenomenon occurs. It aims to enhance understanding by connecting the phenomenon to broader principles or laws, often addressing questions of causality, purpose, and context.
Science today uses various ways to understand, predict, and explain phenomena including the following:
Causal – A causal explanation identifies the cause-and-effect relationship between events. For example, a ball rolls down a hill because gravity acts as the cause.
Deductive-Nomological (DN) – The DN model uses general laws to explain specific phenomena. For instance, the orbits of planets can be explained using Newton’s laws of motion and gravitation.
Statistical – employs probabilistic reasoning to predict the likelihood of events. An example is predicting the likelihood of developing a disease based on statistical data.
Functional – describes the role or function of a component within a system. For example, eyes function to enable vision.
Teleological – refers to the purposes or goals of an organism or system. For example, an organism’s purpose might be to survive and reproduce.
Mechanistic – examines the processes and interactions within a system. For instance, muscle contraction can be explained through the sliding filament model.
Historical – investigates the development and context of events over time. For example, the extinction of dinosaurs is studied by examining the events that occurred around 65 million years ago.
Narrative – uses a story or narrative to illustrate or exemplify a principle or phenomenon. For example, Greek myths can be seen as moral tales that convey ethical lessons.
Ancient Greek philosopher Aristotle noted that explanations answer the question ‘Why?’ and that, like a child, to every answer the question ‘Why?’ can be asked again. If an answer is to be provided then questioning must, at some point, cease. For Aristotle, that moment arrived at the point of secure knowledge. In mathematics, it was the foundational axioms, in today’s science it is in the universe’s physical constants, and so on. In his four (be)causes, Aristotle identified the material, efficient, formal, and final ways of explaining phenomena by determining – what it is made of, how it originated, its unique or essential features (its form, definition, or essence), and what it was for (its purpose).
Aristotle was a biologist, and he was convinced that the most important of his four (be)causes was the final cause, the cause that explained the purpose of biological objects, their goals – what they are ‘for’.
Biological explanation
Aristotle insisted on the special significance of the final cause – the purpose or reason for a biological object – was because biological objects are goal-directed (agential) in their behavior. These goals are natural limits or ends to behavior that may have a mental component in sentient animals, or entail conscious intentions in humans. It is precisely this agency of organisms – including their structures, processes, and behaviors – that accounts for the special, teleological, mode of biological explanation. This is outlined more formally below.
Biological explanations can be classified as either proximate or ultimate. Proximate explanations focus on the immediate mechanisms and processes behind biological phenomena, including genetic, developmental, and physiological factors specific to individuals or species. Ultimate explanations address the evolutionary reasons or adaptive significance behind biological phenomena, focusing on universal principles that apply across species and contexts.
Ultimate explanations in biology emphasize the autonomous behavior of organisms, including their structures, processes, and behaviors, as integrated and unified by the goals of survival, reproduction, adaptation, and evolution. As biological systems are goal-directed (agential), their explanations only make sense when these goals are explicit or assumed. Ignoring these goals leads to incoherent collections of unrelated facts. Teleological explanations in biology, where goals, functions, and purposes are necessarily first in explanation but last in causation/realization (as natural ends or limits to behavior), are a product of biological agency.
Teleology, as the Aristotelian consideration of the way natural processes are directed towards ends (goal-directed) has, since the Scientific Revolution, been regarded by many scientists as an unnecessary philosophical complication. Since the idea of purpose in organisms seems to imply either divine intervention and a mysterious or supernatural life force that is not amenable to empirical investigation. Science subsequently embarked on the attempt to ‘naturalize’ the agency and purpose by providing mechanistic explanations that did not infer controversial philosophical concepts like purpose and agency which were interpreted as the metaphorical reading of human mental properties into nature.
The presence of real agency in organisms has become increasingly obvious as biological investigation has shifted from structures to processes and behaviors. Behaviors, driven by environmental cues and survival needs, demonstrate purposeful actions that move beyond their structural and process-based explanations. Today, the historical philosophical concern the supernatural, mysterious forces, and the reading of human intentions into nature now seem arcane since the meanings of function and purpose have become increasingly detached from their former association with the human and divine.
A major challenge for any explanation is to find the most efficient trade-off between simplicity and generality and detail and specificity – which all depends on the context of the question being asked.
Life can be described at many scales, from many perspectives, and in varying degrees of abstraction.
Because biological objects are goal-directed their description and explanation only becomes meaningful when their goals are known or assumed. A wing, when separated from its context of flying, has no biological meaning so, in this sense, though structure and function must coexist, it is functions that give structures agential meaning. Structures provide the physical basis for life, but their biological role only becomes apparent within the agential explanatory framework of biological activity described in the biological axiom.
In biological explanations ends (goals, functions, and purposes) – what things are for – must always be considered first, even though, as natural ends or limits, they are last in causation (teleology). Without an understanding of goals, biological explanations become disconnected observations that lack coherence. Only when we first grasp the concept of a house (organism) does a heap of building materials (its parts) acquire meaning.
This special characteristic of biological explanation arises out of goal-directed biological agency. This ‘directional’ activity is present in only a minimal sense in the inanimate world. We do not ask what planetary motion is ‘for’ because the inanimate world has no agency.
This uniquely biological mode of explanation is apparent in both ultimate and proximate explanations, although each serves a different biological purpose.
Ultimate explanations take the form of principles – the necessary, general, implicit, or theoretical conditions required for some condition to pertain. Proximate explanations then provide actual, explicit, and observable instantiations of these principles.
Ultimate explanations examine why something exists – what it is for – which, in biology is its evolutionary purpose. Proximate explanations focus on the mechanisms or means of achieving these theoretical ends – on how biological objects work (what they are made of, what they do, and how they do it). The ultimate explanation provides necessary in-principle conditions and the proximate explanation outlines how these conditions are fulfilled in practice. Empirical science may be more concerned with observable instantiations but it also benefits by having a simple and sound theoretical foundation.
Examples of ultimate and proximate explanations can be given in relation to evolution.
Teleology
From at least the time of the ancient Greek philosophers Aristotle has been associated with an emphasis on telos (agency, purpose, function, goals) and the explanatory form now known as teleology.
Biology before the modern era, had no scientific explanation for the purposiveness so evident in organisms. The purpose evident in all aspects of nature was therefore assumed to be either itself supernatural, or inserted by a supernatural being.
Darwinism, many believed, provided a mechanical process that explained why it might seem that organisms pursue goals when, in fact, there was no necessity for anything supernatural but true teleology required an intelligent agent making choices for reasons. An alternative interpretation suggested that, while Darwin had indeed removed the necessity for a supernatural interpretation of purpose, he had not removed the purpose itself which was real in nature since organisms clearly pursue goals. However, this apparent purpose was naturalized in terms of evolutionarily selected traits that served particular functions thus removing the need to invoke purpose. A further popular view was that the attribution of purpose to nature was a reading of human purposiveness and other mental attributes into nature. That is, we interpret organisms, and nature in general, as human-like agents with intention-like goals and functions. While this has a valuable explanatory or heuristic role it has no foundation in biological reality.
Aristotle, over 2000 years ago, had recognized the goal-directed character of organisms as a form of telos, something directed towards ends. These ends became associated with the supernatural (not supported by Aristotle’s work), and were challenged during the Scientific Revolution along with Aristotelian philosophy in general. Teleology remained out of favor up to the present day.
Contemporary biology is now shedding the dense historical argumentation surrounding teleology and simply recognizing the empirical reality of the goal-directed (purposive) behavior of all organisms as supremely exemplified in the highly evolved and conscious behavior of humans.
The challenge for contemporary biology is not the acceptance of function, purpose, and goals but its full implications for theoretical biology.
Naturalizing teleology
Science has strived to naturalize teleology by interpreting goal-directed behavior as a result of natural processes. The theory of natural selection, for instance, elucidates how traits that seem purposefully designed actually emerge from random mutations and survival advantages. Evolutionary biology describes behaviors and physical features as adaptations that increase reproductive success. Furthermore, fields like cybernetics and systems theory view goal-directed systems as complex feedback mechanisms without invoking inherent purpose. This naturalistic approach dispels the need for supernatural explanations, framing teleological phenomena as emergent properties of natural laws and evolutionary pressures.
Describing goal-directed behavior as ‘purposive’ implies an inherent intention or design, which is scientifically problematic because it suggests a teleological explanation. Science aims to explain phenomena through natural causes and mechanisms. Attributing purpose can introduce elements of subjectivity and anthropomorphism, blurring the distinction between human intentions and natural processes. It risks conflating observable outcomes with intended goals, thereby undermining the objective analysis of how these behaviors arise from evolutionary pressures, biological imperatives, or other non-teleological mechanisms. Essentially, it can lead to the misconception that nature operates with foresight and intent akin to human reasoning.
The term “purposive” can be misleading, as it may inadvertently suggest a form of intrinsic purpose or design.
Teleological explanations in biology explain structures, processes, and behaviors in type terms of their functions, purposes, and goals, such as the function of wings for flight. Some argue that in order for biology to be fully scientific, teleological explanations must be naturalized, reducing them to mechanistic terms. This perspective holds that attributing purposes or goals to biological entities is anthropomorphic and unscientific such that understanding the evolutionary and developmental mechanisms behind traits provides a complete explanation without needing to reference their functions or purposes.
Naturalization involves explaining these phenomena in token (mechanistic) terms without invoking purposes or goals. When we say something is causally transparent, we mean that its causes are straightforward and easily understood without invoking additional explanatory frameworks. For example, each step of photosynthesis is now well-understood, its chemical reactions, physical interactions, specific molecules, enzymes, and conditions required for each stage of the process. Inputs and outputs can be measured, and the process observed in controlled experiments. The process is driven by clear mechanistic pathways, such as the absorption of photons by chlorophyll, the splitting of water molecules (photolysis), and the synthesis of glucose in the Calvin cycle.
Others argue that teleological explanations are inherently part of how we understand biological systems and do not require naturalization because they provide meaningful and coherent explanations. From this perspective, teleological behavior is causally transparent in the sense that understanding the goals and purposes of biological traits and behaviors inherently provides clarity and understanding. This approach emphasizes that biology, unlike inanimate sciences, deals with goal-directed organisms, making teleological explanations both appropriate and necessary.
An integrative approach might involve using teleological explanations where they provide clarity and understanding, while also seeking mechanistic explanations to understand the underlying processes. Teleological and mechanistic explanations can be seen as complementary rather than mutually exclusive. Teleology provides the “why” in terms of function and purpose, while mechanism provides the “how” in terms of processes and structures. Whether there is a need to naturalize teleological causality or whether it is already causally transparent depends on one’s philosophical stance on the nature of biological explanations. Both perspectives offer valuable insights, and integrating them can lead to a richer, more nuanced understanding of biology.
Analysis & Synthesis
The influence of hierarchical ideas on the way we represent and explain biological structures, processes, and behaviors is one of the most controversial topics contemporary science.
Is an organism, when all is said and done, just physics and chemistry? How are we to translate the objects, principles, and terms of one academic discipline into those of another? Should we understand and explain the world ‘top-down’ or ‘bottom-up’ . . . either, neither, or both? And how does all this relate to what is going on in the world?
Biology has a forward-looking character because it deals with organisms as goal-directed agents. Growth, development, survival, and reproduction all project into the future, with natural selection favoring traits that enhance future fitness. Each life stage prepares for the next, ensuring species continuation through reproduction. Processes like homeostasis and metabolism provide stability, while both short-term and long-term behaviors adapt to future conditions.
In sum, biology, as the study of organisms and their systems, is oriented toward future survival, reproduction, adaptation, and evolution. Most importantly, this teleological property of biological systems (its concern with ‘ends’, or what things are ‘for’) does not necessarily imply the foresight or conscious intention we associate with sentience and human cognition.
We are accustomed to explanations proceeding in two (metaphorical) ‘directions’, either ‘top-down’ or ‘bottom-up’. Explanations go ‘up’ when they consider a broader context, and ‘down’ when they examine the contribution of ‘parts’ to a greater ‘whole’. These contrasting explanatory approaches can be referred to as ‘reduction’ and ‘synthesis’.
Reduction explains a ‘whole’ by breaking it down into its constituent parts, focusing on the components themselves. Saying ‘A house is an assemblage of bricks’ is an example of reduction, as it emphasizes the individual elements that make up the structure.
Synthesis explains a ‘part’ in terms of its role, function, or purpose within a greater whole. This approach considers how parts contribute to and interact within a broader context. Saying ‘A house, as an aggregation of bricks that provides shelter and a space for living’ emphasizes the function and relationship of parts to the whole.
These two approaches provide different explanatory perspectives on what it is we want to explain (explanandum) and what it is that provides the explanation (explanans). Reduction explains the whole in terms of its parts: synthesis explains the parts in terms of the whole. Both methods are scientifically important, with reduction revealing the components and synthesis highlighting their roles and interactions within the system.
There are several caveats to this claim. Reductionism can overlook emergent properties of a whole that cannot be understood solely by examining the parts. Synthesis emphasizes function because it looks at how parts contribute to the whole, while reduction focuses on the parts themselves, often ignoring their roles within the broader system. Also, that reduction and synthesis are not mutually exclusive but can be complementary, both explanatory approaches provide insights into the operation of complex systems. In biology, reduction might involve studying genes, while synthesis might investigate how those genes contribute to the organism’s overall function.
Analysis & synthesis
We cannot explain an object in terms of itself and so our explanations of things proceed to either their constituent parts (analysis) or a broader context (synthesis).
This seems to be a feature of our general thinking as we constantly switch between detail and abstraction to create new frames of understanding. We oscillate between accumulating more knowledge and the organization of that knowledge into summary categories and general principles that provide us with a big picture overview. Scientific research, especially, is meticulously recorded and then condensed into theories and models that draw this information into meaningful categories of varying degrees of abstraction.
Almost any item in the universe can be divided into smaller parts or united with a larger whole, and that is how we explain things. Every object is both a whole and a part.
When a whole is explained in terms of its parts we refer to this as analysis which adopts, as it were, the mental perspective of the whole because it is the whole that demands explanation.
When we explain something (as a part) in terms of a greater whole or wider context we can call this synthesis which adopts the mental perspective of a part within something greater. For example, ‘A house is an assemblage of bricks‘ (analysis) but ‘My legs are attached to, and mobilize, my body‘ (synthesis).
Just as we can analyze an object into progressively smaller, less inclusive, and less complex parts in an infinite analytic regress (or until a ‘rock bottom’ foundation is reached), so we can synthesize parts into more inclusive wholes in an infinite synthetic regress (or until an all-embracing ‘rock top’ is reached).
These two modes of explanation have produced two competing systems of scientific metaphysics expressed crudely as follows:
On the one hand, there is reductionism, the view that ultimately biology can be reduced to physics and chemistry. It may be impractical to describe biological systems in physicochemical terms but, in reality, that is what they are.
On the other hand, there is holism, the view that biological objects, especially organisms, are more than the sum of their parts: they are wholes with irreducible properties. This view has also been referred to as organicism and it is associated with the recognition that with increasing complexity come novel structures, properties, and relations – called emergence. A sand heap may be just lots of sand grains, but is it helpful to say that a tiger is just a lot of molecules? Here the properties and relations of molecules when aggregated seem very important. A tiger is not just a heap of molecules – it is a different kind of aggregate than a heap of sand.
Using the spatial metaphor of hierarchy talk these modes of explanation have been given a directional interpretation as proceeding either ‘top-down’ by analysis or decomposition (explaining wholes using the language and ideas appropriate to their constituent parts), or ‘bottom-up’ by synthesis or composition (explaining the parts of objects using the language and ideas of the wholes that they form).
A characteristic scientific example is provided by leading physicist and cosmologist George Ellis who, in describing a hierarchy of scientific disciplines,[13] states:
‘In the hierarchy of complexity, each level links to the one above: chemistry links to biochemistry, to cell biology, physiology, psychology, to sociology, economics, and politics. Particle physics is the foundational subject underlying – and so in some sense explaining – all the others.’
Ellis’s expressed concern though is with causation which he stresses does not flow from the underlying physics (a common assumption) but proceeds both ‘up’ and ‘down’:
‘. . . the challenge to physics is to develop a realistic description of causality in truly complex hierarchical structures’.
This presents us with a historical dichotomy in directional interpretations of the universe – a fascinating chapter in the history of ideas.
In following our intuitions about causation in hierarchies, we have the simple and powerful human example of a chain of command, which traditionally proceeds from top to bottom (the chain in the Great Chain of Being, with everything following what God has ordained). Before the Scientific Revolution, it was God in heaven who was the ultimate reality and prime mover determining the course of all events in the universe, commanding everything from above (on high).
After the Scientific Revolution, as God became a more abstract concept, it was elementary particles, physics, and chemistry that provided the foundation for everything, the new ultimate reality, supporting and pushing or motivating the universe from below.
Among the many unnecessary mental contortions resulting from this hierarchical spatial metaphor is the concern with ‘downward’ causation — the idea that higher-level properties or phenomena can influence and constrain lower-level components or processes within a system, as when a higher-level mental state (e.g. stress) causes changes in lower-level physiological processes, thus demonstrating downward causation.
Emergence is often explained in hierarchical terms as complex systems and patterns arising from the interactions of simpler elements at lower levels of a multilayered framework in which each level of the hierarchy contributes to the emergence of higher-level structures, processes, and behaviors.
We assume that this metaphorical language simplifies, clarifies, or facilitates our understanding of increasing complexity, but talk of levels can be avoided altogether by attempting to describe phenomena directly without the intercession of levels. Novel structures, processes, and behaviors can arise from existing ones through the development of new combinations, collective synergies, and functional organizations. In non-linear systems small changes in initial conditions or interactions can lead to disproportionately large consequences. Feedback mechanisms, along with general conditions of existence, can enhance or dampen these interactions.
Emergence is not a consequence of the interaction of hypothetical layers of existence, it is the creation of novel structures, processes, and behaviors resulting from the intricate web of interactions, dynamics, and feedback systems that establish new relations, systems of organization, functional integration, and collective synergies at multiple scales.
Analysis
We are still living in an age of analysis and reduction in which the prevailing methodology of science is reduction. We take it for granted that phenomena are best explained and understood by examining the structures, properties, and relations of their constituent parts.
English philosopher Bertrand Russell describes this Western preference or bias in ‘direction’ of explanation:
‘. . . the last of my initial prejudices, which has been perhaps the most important in all my thinking. This is concerned with method’ . . . ‘to start from something vague but puzzling, something indubitable but which I cannot express with any precision. I go through a process which is like that of first seeing something with the naked eye and then examining it through a microscope. I find that by fixity of attention divisions and distinctions appear where none were at first visible . . . analysis gives new knowledge without destroying any of the previously existing knowledge. This applies not only to the structure of physical things, but quite as much to concepts . . . belief in the above process is my strongest and most unshakable prejudice as regards the methods of philosophical investigation’.[10]
Russell, a strong advocate of analytic philosophy, was echoing the second principle of Descartes:
‘ . . . to divide each of the difficulties that I was examining into as many parts as might be possible and necessary in order best to solve it’.
Here we have two key proponents of a Western intellectual tradition, sometimes called analytical reductionism and its statement of conviction about a particular manner of intellectual investigation . . . analysis. Logical atomism (the view that the world consists of simple, indivisible facts or ‘atoms’ that can be logically combined to form complex propositions) was in historical lock-step with the scientific search for the smallest particles of matter as the foundation of all science.
We admire the elegance of simplicity and unity which we create by a process of reduction, generalization, and abstraction. A daffodil and the moon are as different as chalk and cheese but all are made of matter.
However, unity and simplicity fail what might be called the principle of complexity. Science must explain the universe in all its variety, a principle that is especially relevant to living systems. But the sameness of generality does not explain anything. Knowing that every organism consists entirely of elementary particles is no explanation of life at all. ‘Eventually everything is held to be explainable in terms of essentially nothing’. [19]Sperry as cited in [18]
A focus on one level of the hierarchy (e.g., genes or cells) can lead to reductionism as the inadequate defining of the whole, the greater context, in terms of its parts. Explaining biological phenomena solely in terms of lower levels ignores the interactions and emergent properties at higher levels leading to incomplete, misleading, or uninformative conclusions, particularly in complex systems. At an absurd extreme we can imagine the explanatory complications of describing a human social event in terms of its constituent molecules.
Does the Periodic Table convey all that we need to know about matter? Is this the single, most economical, and useful classification of matter? Is it fundamental or foundational? Does it ground all science in some way . . . or are there many kinds of classification serving multiple purposes?
Regardless of our opinions about such matters, it is obvious that science requires explanations at many scales.
The fact that hierarchies necessarily rank objects creates an expectation for the ranking criteria that determine what is at the bottom and what is at the top. Though sometimes made explicit, these criteria are often left open to the interpretation of the user. Reductionism, perceived in hierarchical terms, places its rank-value at the point where analysis runs out. In physics this is, more or less, elementary particles. In biology it is, more or less, genes. The rank-value that elevates the significance of elementary particles and genes is not made explicit: perhaps the fact that they are end-points for explanation. But, the search for criteria can lead to contentious assumptions about the causal significance of these end-points.
Analytical reductionism has drilled down to life’s smallest ingredients in a hunt for the holy grail of the universe’s simplest discrete constituents – the foundational layer of elementary particles whose properties and relations support the entire edifice of science. This is close to an ontological assumption that these end-points are, more real than other forms of matter. Elementary particles certainly have explanatory value but a lepton or boson is no more real than a daffodil or an elephant . . . we cannot invest them with special ontological properties.
The most powerful element of human hierarchies is its chain of command. This is what makes things happen in the world and its traditional source of authority was God as prime mover or first cause. Using traditional hierarchical imagery together with with its associated rank-value, modern science has inverted this representation of everything by treating the smallest particles of matter, the hierarchical layer of physics and chemistry, as ‘fundamental’ and ‘foundational’ to science, existence, and change. The ladder of scientific reality is supported by physics and chemistry in control at the bottom, not God pulling the strings from above.
Synthesis
The following thought experiment expands on Russell’s characterization of analysis given above.
Imagine you have an extremely powerful new scientific instrument like a combined microscope and telescope – we can call it a micro-macroscope. You look into the micro-macroscope as it scans extremely small objects and what you see are simple objects with a range of different forms. Let’s call them molecules. But when you zoom out further, you see the molecules seeming to coalesce into a bounded unit, let’s call it a cell, then something like a leg appears. Zooming out further you see that the previous object really was a leg, that the leg belongs to a person, and zooming out even more we see that the person is one among many people living in a city, which is part of a country, which is part of planet Earth, which is part of the solar system, the galaxy, and the universe.
This thought experiment illustrates the way that new objects, properties, and relations arise at different scales, and that these constitute novel frames of reference. Each part can be placed within a broader context that gives us a wider understanding. Scientifically we describe these points of focus as mind-independently as possible given our human umwelt, using distinctive principles and technical language where this facilitates understanding and explanation.
The critical point being made with this thought experiment is that these frames of reference are not separate and independent objects, nor are they above or below one another (the spatial metaphor does not help here), they are different perspectives or points of focus within a spatiotemporal continuum.
Given sufficient technology and computing power, we could describe the molecular composition of any object. However, in living systems, this has limited scientific value because novel properties are associated with different degrees of complexity (emergence). These properties are a consequence of functionally organized wholes and they are neither present nor predictable from their material constituents. An organism is much more than an aggregate of molecules. The ‘more’ here is not a matter of molecules but the relations between the molecules which give rise to novel properties of matter. ‘More’ is not more matter but the properties derived from relations. Organisms are the universe’s supreme examples of functionally integrated units with many novel emergent properties above and beyond those of their constituent parts.
The functions and behaviors of organisms derive from the interaction of their parts rather than the parts themselves.
Summarizing this section it is concluded that the universe may be differentiated but it is not ranked because ranking is not what the universe does, it is what agents do. Neither temperature nor biological causation go literally up or down: the spatial talk associated with the biological hierarchy is metaphor. It is unhelpful metaphor primarily because it is scientifically impotent: what makes it a hierarchy – the criteria used to rank phenomena – are closed to empirical investigation. It also represents levels as discrete elements of the world that are, more accurately, just different explanatory perspectives (macro-microscope). Hierarchy necessarily imposes rank value that grades top to bottom with the methodology of analytic reductionism investing greatest significance on the lowest level of the hierarchy

Perspective & Scale
The classification of different kinds of biological explanations faces a bewildering array of different approaches. Not only can life be considered from a seemingly infinite number of perspectives, its subject matter includes physical scales that range from molecules to the biosphere.
Perspective
Is it possible to devise a taxonomy of modes of biological explanation?
Biological explanations must consider both theory and practice, considering different scales and perspectives.
Perspectives include the following: mechanistic explanations that focus on the detailed processes and interactions within biological systems; teleological explanations that explain traits or behaviors by their purpose or goal-oriented functions e.g. the function of the heart is to pump blood, which circulates oxygen and nutrients throughout the body; functional explanation describes the roles or activities of biological structures and how they contribute to the organism’s survival and reproduction; evolutionary explanation showing how traits or behaviors are based on their evolutionary origins and the adaptive advantages they confer; developmental explanation of the processes by which organisms grow and develop, explaining how traits arise during an organism’s lifecycle; phylogenetic explanation s which use the evolutionary history and relationships between species to explain traits and behaviors; complex systems explanation focuses on the interactions and emergent properties of complex systems.
Biological systems are uniquely goal-directed and, because of this agency, biological explanation takes a teleological form by necessarily establishing ends before investigating their means (see later).
Explanations in biology can be informatively divided into three categories of progressively decreasing abstraction:
1) A general ultimate explanation for all traits and behaviors (the biological axiom as the behavioral propensity of all organisms to survive, reproduce, adapt, and evolve – treated by evolutionary biology as maximizing fitness). This is the universal and foundational biological principle for life, agency, and evolution – it provides the general context for specific ultimate and proximate explanations.
2) Specific ultimate explanations – the evolutionary reasons for particular traits or behaviors e.g. birds have wings because of the advantages of flight.
3) Proximate explanations – the immediate physiological, genetic, and developmental mechanisms underlying a trait or behavior.
The general ultimate explanation (biological axiom) is a universal behavioral principle that applies to all organisms. It provides a framework for understanding evolutionary processes and biological agency – the grounding characteristics that maximize fitness. Specific ultimate explanations focus on particular traits or behaviors within a broad biological context, explaining their evolutionary significance. Proximate explanations concentrate on immediate physiological, genetic, and developmental mechanisms, how they work and function.
These three modes of explanation can be applied, for example, to behavior, function, development, evolution, agency, purpose, etc.
Biological explanations are greatly enhanced by distinguishing between these three modes of explanation that treat biological phenomena with increasing specificity. This is illustrated in the following examples:
Category | Explanation Type | Example |
Development | General Ultimate | Human brain development enhances overall fitness and reproductive success. |
Specific Ultimate | Human brain development enhances cognitive abilities necessary for social interaction. | |
Proximate | Development of the prefrontal cortex influences decision-making skills. | |
=========== | ================================================================ | |
Behavior | General Ultimate | Migration behaviors evolve to maximize survival and reproductive success. |
Specific Ultimate | Birds migrate to warmer climates to avoid harsh winters. | |
Proximate | Hormones like melatonin regulate migratory timing. | |
=========== | ================================================================ | |
Function | General Ultimate | The human eye evolves to enhance overall fitness by improving visual perception. |
Specific Ultimate | The human eye’s ability to detect a wide range of colors aids in identifying food and avoiding predators. | |
Proximate | The lens and retina of the eye focus light and convert it into neural signals. | |
=========== | ================================================================ | |
Evolution | General Ultimate | Evolutionary processes favor traits that enhance survival and reproduction. |
Specific Ultimate | Bacteria evolve resistance mechanisms to survive in the presence of antibiotics. | |
Proximate | Genetic mutations introduce variations that confer antibiotic resistance. | |
=========== | ============ | ================================================================ |
Agency & Purpose | General Ultimate | Tool use evolves because it provides significant survival advantages. |
Specific Ultimate | Tool use by primates, such as using sticks to extract termites, improves food acquisition. | |
Proximate | Cognitive processes in primates enable problem-solving and tool use. |
These explanations combine theoretical and functional principles with mechanistic applications that provide evolutionary, short- and long-term perspectives on biological phenomena.

Evolution
Evolution may be interpreted as an interplay between structures and their functions. It is now apparent that biological explanation, which, for historical reasons, has focused on the solid foundation of physical features, is now engaging with more abstract functional characteristics.
While physical structures offer a tangible record of evolutionary history, functional explanations illuminate the adaptive significance and selective pressures driving those changes.
Structural explanation
A structural explanation of evolution focuses on the physical characteristics and anatomical traits of organisms. This includes: morphological traits including the shape, size, and structure of organisms and their parts; the comparative anatomy of different species as an indication of common ancestry and adaptive change; exploration of the fossil record to trace evolutionary history through structural change over time; the identification of structures that share a common origin but may serve different functionshomo;logies) in different species, highlighting evolutionary relationships (e.g., the forelimbs of vertebrates); also analogous structures that perform similar functions although evolving independently in different lineages thus demonstrating convergent evolution (e.g., wings in birds and insects); developmental biology uncovering patterns of structural formation and differentiation that provide insights into evolutionary processes; the depiction of evolutionary relationships based on structural traits, illustrating the branching patterns of lineage divergence; exploration of the genetic and molecular bases for structural traits, linking genotype to phenotype and understanding how genetic changes lead to morphological evolution; investigation of physical and mechanical constraints that limit or enable the evolution of new structures, leading to innovations in both form and function.
These features provide an account of how organisms evolved based on their physical forms and structures. By examining these structural aspects, scientists can infer evolutionary pathways, relationships, and the adaptive significance of anatomical traits
Functional explanation
It is conventional in biology to consider evolution in terms of the physical gradation of structural emergence over time. This reflects an early concern with substance and physical change. But how does evolution appear when viewed through the lens of functions?
Functional explanations can be applied across a range of species and contexts, highlighting similarities in how different organisms solve similar biological challenges, despite structural differences. For instance, the function of respiration can be compared across mammals, birds, and insects, even though their respiratory structures differ significantly. Functional explanations emphasize how biological traits contribute to an organism’s survival, reproduction, adaptation and evolution. This approach aligns with the core principles of natural selection, making it easier to understand the adaptive significance of traits. Functional explanations connect biology to other disciplines like ecology, behavior, physiology, and cognition. By focusing on the role traits play in an organism’s life, scientists can better integrate findings from various fields. Understanding the functional role of traits can shed light on evolutionary processes. For example, knowing the function of a bird’s beak in feeding can help explain the evolutionary pressures that shaped its structure.
The evolutionary emergence of an increasing diversity of physical structures was a mindless evolutionary exploration of the universal functional requirement to survive, reproduce, adapt, and evolve. Structural evolution therefore has implicit functional demands that include: functional adaptations that improve their ability to survive and reproduce in specific conditions; functional equivalence when different organisms evolve distinct structural solutions to achieve similar functions as when unrelated species develop similar functional traits, like wings in birds and bats for flight; evolutionary trade-offs where the evolution of one function may compromise another. For example, the development of large antlers in male deer for mating displays may reduce mobility and increase energy demands; focus on efficiency and optimization as natural selection favors traits that optimize an organism’s performance. Functions that enhance efficiency in energy use, resource acquisition, and reproduction are likely to be preserved and refined through evolution; functional traits can exhibit plasticity, allowing organisms to adapt to varying conditions. This principle underscores the importance of flexible responses to environmental changes, such as changes in metabolism or behavior in response to food availability.
Functional explanations provide a comprehensive understanding of the evolutionary dynamics shaping organisms, they offer a practical framework for examining the adaptive significance of traits and diversity of approaches to universal biological dmands.
Functional equivalence
All organisms have the behavioral propensity to survive, reproduce, adapt, and evolve (biological axiom). The specific structures, processes, and behaviors of individual species are shaped by their unique evolutionary histories in relation to these universal conditions. Human cognitive phenomena, like the behaviors and traits of other organisms, are adaptations to these universal conditions and therefore have functional equivalents in other organisms. While the physical manifestations of human cognition—such as experience, perception, and reasoning—are distinctively human (or limited to sentient beings), their functional roles have parallels in other organisms, regardless of their evolutionary lineage.
Without a standardized terminology for universal cognitive functions, scientists use anthropocentric terms like ‘plant cognition,’ interpreted as metaphors describing phenomena that have no scientific basis, even though they indicate genuine functional equivalence. This equivalence pertains to functions, as analogs, rather than evolutionary structures, processes, and behaviors as homologs. This lack of functional terminology leads to philosophical misunderstandings and resistance to the scientific acknowledgement of functional equivalence. For example, all organisms use adaptive strategies akin to ‘decision-making’ in human terms. While ‘decision-making’ when applied to non-human organisms is a cognitive metaphor, it highlights the real functional similarity of different adaptive strategies. In functional terms, human cognition is one species-specific specialized form of universal biological cognition. This highlights the need to distinguish between metaphorical language and actual functional similarities. Using human terms for non-human cognition implies functional, not physical, equivalence.

Proximate & Ultimate Explanation
The biological axiom is a general principle of biology that can be empirically derived by inductive reasoning – by observing how specific instances all conform to its general conditions (deductive reasoning starts with a general principle and applies it to each specific case).
In biology a useful distinction is made between proximate and ultimate explanations (although they can be applied more broadly). Proximate explanations focus on the immediate causes or mechanisms of a phenomenon. They tend to be ‘how’ questions dealing with the short-term here and now, such as ‘How do spiders catch flies?’ (spiders in general or this spider)” questions.
In contrast, ultimate explanations tend to be ‘why?’ questions that take a broader and long-term perspective, looking for the evolutionary reasons or purpose of the phenomenon. For example, ‘Why do spiders catch flies?’ (for food as a source of energy that helps the spider etc.).
In humans examples might be that we eat for not only the proximate reasons of satisfying our hunger and the pleasure of the smell and taste of food, but also the ultimate reason of our survival. We have sex not only for the proximate pleasures of orgasm and the comfort of close physical contact, but also the ultimate reason of reproducing our kind.
This is an important distinction, especially when it is investigated as an account of biological agency as the ultimate defining principle for life – the biological axiom which is presented below in both simple and formal forms.
Life is most evident in the autonomous behavior of living organisms, whose structures, processes, and behaviors work together toward a unified purpose: to survive, reproduce, adapt, and evolve. These goals are universal (essential for life), objective (a mind-independent fact), and ultimate (encompassing all proximate goals).
Life is most apparent in the autonomous agency of living organisms whose structures, processes, and behaviors express a functionally integrated unity of purpose – the universal, objective, and ultimate behavioral 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 and unification of all proximate goals. These are the defining conditions for biological agency whose natural limits or ends are the biological conditions that define life and the trajectory of evolution.
While many essential properties of life are evident in structures (genes, cells), processes (metabolism, homeostasis, growth and development, reproduction) and behaviors (response to stimuli, adaptation) these are all subordinate to biological agency – the unified and functionally integrated activity of entire living organisms. Without agency, biology assumes the character of inanimate matter, of purposeless physics and chemistry. This is why it is agency – not the other necessary biological structures, processes, and behaviors – that best expresses the nature of life. In biological explanations functions, purposes, and goals necessarily precede discussion of structures, processes, and behaviors. Without first understanding goals (biological agency) biology loses meaning and becomes a collection of dissociated facts. The biological axiom is a behavioral account of life’s agency that encompasses the ends of all biological activity – life’s biological purpose.
Evolution
A proximate explanation of evolution provides a ‘how’ account of the mechanism of evolution whereby genetic variations arise through mutations, gene flow, and genetic drift, leading to changes in allele frequencies within populations.
But what is the ultimate explanation for evolution itself – its overarching reason or purpose?
Evolution doesn’t have a purpose beyond the adaptive and reproductive advantages it confers on organisms within their environments. But, while natural selection itself is not goal-directed, it has produced units of matter that are goal-directed (living organisms as biological agents). A mindless process has produced units of matter that – expressed in the most succinct but biologically informative form – can survive, reproduce, adapt, and evolve. This capacity is not a conscious intention, but a mindless goal-directed agency – a behavioral orientation that has generated life in all its manifestations, including human subjectivity.
So, while natural selection has no purpose, the behaviors and actions of organisms do.
Evolutionary theory often emphasizes natural selection’s role in shaping biological phenomena. However, it is crucial to note that natural selection is not an agent in itself; rather, it is a process that arises from the dynamic interactions between organisms—viewed as biological agents— and their conditions of existence. Specifically, it is the interplay of an organism’s genetic variation, phenotypic traits, and environmental conditions that drives evolutionary change. This is an unconventional characterization of evolution that emphasizes the reciprocal influences among organisms, their traits, and environmental factors, and offering a more nuanced understanding of evolution that moves beyond a simplistic view of natural selection as the evolutionary causal hub.
Evolution is a complex process driven by the interactions between organisms, their traits, and their environments. While natural selection is a key mechanism shaping evolutionary change, it is not an agent itself, but a result of these dynamic interactions. Organisms exhibit goal-directed behaviors to enhance their survival and reproduction, which are adaptations to their environments. This continuous interplay of genetic variation, phenotypic traits, and environmental conditions drives evolutionary change, emphasizing both the adaptive significance of traits and the reciprocal influences among organisms and their surroundings.
Comparison
Proximate and ultimate modes of explanation are generally treated as scientifically complementary with ultimate explanations providing general context and proximate explanations their instantiations, with neither taking precedence. There is no inherent priority when comparing a broader explanation and a narrower more detailed one since they serve different purposes. There is simply a trade-off between the simplicity and generality of ultimate explanations, and the precision of detail but increasing complexity of proximate explanations. So, for example, scientific laws (as ultimate explanations) do not take precedence over the phenomena they describe; rather, they arise from and depend on these phenomena.
The precedence we sometimes ascribe to ultimate explanations lies in their ability to summarize and generalize thus providing broad context, direction, and predictive power; they establish the natural limits or ends of all circumstances while proximate explanations offer insights into immediate processes and mechanisms. Therefore, ultimate explanations best serve as theoretical principles – even though they remain grounded in the empirical reality of the phenomena themselves.
In biology, as elsewhere, ultimate explanations are grounded in the phenomena they describe but, as outlined above, their goal-directedness infers natural ends or limits that must be understood (considered first) if biology is to make sense. Whether these are proximate ends (the ends of particular instances) or ultimate ends (the ends of all biological activity), they must come first in explanation, and in biology, it is ultimate ends that provide the general theoretical principles for life.
In early biological history, a firm distinction was drawn between the special and unique agency of humans and the lives of other organisms. Over time the biological grounds for this distinction were reduced culminating with the theory of evolution that connected all organisms. The increasing concern in biology for agency, functions, purposes, and goals reflects the historical shift in research focus from structures to the functional processes of physiology, evolutionary biology, behavioral ecology, and cognitive studies.
Biological phenomena are conventionally divided into structures and functions, but this division may be combined with the classification of biology into structures, processes, and behaviors to yield a classification of biological explanations as follows:
Structures:
Proximate Explanation: Describes the immediate genetic, developmental, and physiological mechanisms forming the physical features of organisms.
Ultimate Explanation: Explains the evolutionary significance of these physical features and how they contribute to the organism’s survival and reproduction.
Processes:
Proximate Explanation: Focuses on the biochemical and physiological processes occurring within organisms that enable life functions.
Ultimate Explanation: Addresses the evolutionary origins of these processes and how they enhance the organism’s adaptability and fitness.
Behaviors:
Proximate Explanation: Details the neurological and hormonal mechanisms triggering specific behaviors in organisms.
Ultimate Explanation: Investigates the evolutionary advantages of these behaviors, considering their role in survival, reproduction, and ecological interactions.
Functions:
Proximate Explanation: Examines how structures and processes combine to perform specific biological functions, like respiration or reproduction.
Ultimate Explanation: Analyzes the evolutionary importance of these functions and their contribution to the overall fitness and success of the species.
The advantage of such a classification derives from: its comprehensiveness, since it captures a wide array of biological phenomena, recognizing that not all biological aspects can be neatly categorized into just structures or functions; detailed insights from the inclusion of processes and behaviors, providing a more nuanced understanding of the immediate (proximate) mechanisms and evolutionary (ultimate) reasons behind biological phenomena; acknowledgment of interconnectedness since it emphasizes the interactions between structures, processes, and behaviors, reflecting the integrated and holistic nature of biological systems; and inclusion of goal-directedness that highlights the agential aspects of organisms that are critical to the understanding their evolutionary and adaptive significance.
Structure & Function
In biological explanations structure and function seem inextricably intertwined. Considering structures without understanding their functions presents an incomplete picture of life. Structure describes the physical components and arrangements, while function explains their purposes, activities, roles, and goals. Without connecting these two aspects, biology would lack a critical dimension. We are inclined to treat structures as fundamental since form determines an object’s role and capacities, with functions then giving these structures purpose and context. However, in biological explanation function (purposes, goals, roles) must always come before structure if the structures are to be meaningful and, in this sense, it is function that is fundamental.
A whole must be comprehended if its parts are to make sense. A heap of building materials becomes vastly more significant when we have a concept of ‘house’. This claim to the primacy of function over structure is not an empirical claim about the world, it is a claim about the necessary form of scientific explanation, and therefore the way we do biology.

Token vs Type
Explanations in biology can be divided into two kinds – those based on general theory or principle, and those based on particular examples or instantiations. These are sometimes distinguished as ultimate and proximate explanations. A simpler terminology might refer to token explanations and type explanations.
The type-token distinction is a powerful tool in biology that distinguishes between general categories and specific instances.
A type is a general category or kind of thing. It refers to the abstract, general form or idea of a thing e.g. plant as a type refers to the concept of a plant in general, not any specific plant. Types are general ideas or categories that can be instantiated many times. A typecould be “apple” while a token would be a specific apple, such as a particular Granny Smith apple from the grocery. This specific apple is an instance or instantiation of the appletype. Each Granny Smith apple you encounter is a different token, but they all belong to the same type.The type rovides a broad category for understanding general characteristics, while the token refers to specific instances that illustrate those characteristics in everyday life. A token is a specific instance or occurrence of a type. It refers to the particular, concrete manifestation of a type. The word ‘rose’ written on a piece of paper in front of you is a token of the type ‘plant’. Each time you encounter the word ‘plant’ you encounter different tokens of the same type. Tokens are used to discuss specific, individual occurrences or examples that instantiate the general types.
The type-token distinction helps clarify discussions about abstract concepts and their particular instances by allowing users to differentiate between general ideas and specific examples thus avoiding ambiguity. For example, when discussing language, it helps distinguish between the general concept of a word (type) and an individual occurrences in speech or writing (token). It also clarifies issues of identity and difference. It helps address questions like whether two instances of the same type are identical (in terms of type) or distinct (in terms of tokens). For example the type ‘function’ refers to the general category of all functions, while a bat wing is a token example of a phenomenon with the function of flying. Beethoven’s Symphony No. 5 is an abstract type composition. Each individual performance or recording of Beethoven’s Symphony No. 5 is a token performance.
Reductionism
Aristotle’s quote at the head of this page expresses a deep philosophical problem that has persisted to this day – a question about wholes and parts . . . their reality, properties, and relations. This is a metaphysical question about both identity and taxonomy, questioning why and how we fragment the world into objects of experience.
On what grounds do we differentiate these objects? How do we group the smaller or less inclusive into the larger or more inclusive ones? How discrete is one object when compared to another? Which of the objects of our experience exist in the world, and which are creations of our minds?[11]
These are not trivial questions because the way we answer reflects our view of what is ‘real’, and therefore worthy of scientific investigation.
Conceptual analysis
There is a lack of clarity in what we mean when we make a statement like ‘the whole is more than the sum of its parts’ – or we say that something has been ‘reduced‘ to something else. Both claims are ambiguous because they can be interpreted in several ways – they have multiple meanings (polysemy).[2]
Aristotle’s simplified statement – that ‘the whole is more than the sum of its parts’ – is one of unhelpful generality because we can defend or deny its claims according to what is meant by ‘whole’, ‘sum’ and ‘part’. The number three, for example, might be considered a combination of the numbers one and two, but to claim that three is more than the sum of one and two does not make sense. In contrast, the unified functional agency of an organism is clearly more than the sum of the heap of molecules out of which it is composed.
Such claims must therefore be examined on their individual merits.
In contemplating parts and wholes, we are immediately confronted by an ancient philosophical paradox (dilemma, contradiction, antinomy) – the problem of the one and the many.
We can, on the one hand, claim with equal validity that the world consists of a variety of things . . . just look around. On the one hand, there is a long philosophical tradition that reduces this complexity to one thing. Perhaps atoms, or maybe energy, number, space-time, or information? The appeal of the ‘one’ is that it provides security – an eternal sameness in a world of apparent difference and change. The ‘one’ provides a bedrock or foundation. It is fundamental or, in philosophical terms, ontologically prior to everything else. The ‘many’ is really only the ‘one’ in many guises.
We will not solve this problem here – but we can look at one of its manifestations.
Part & Whole
Our common sense tells us that objects can be mental and/or physical: that is, they can exist in the world, or in our minds, and perhaps both. When I see a table, I am seeing the image on my retina of a table that actually exists in the world?
To think and experience is to think and experience something. Mental activity is always about something, it is intentional.
We need units of thought – let’s call them concepts. As a matter of psychological necessity, we use concepts of generality and particularity. We might call this the detail or grain of our thought. Examples of very general concepts would be matter, space, time, or music. Then, to establish particularity, it becomes psychologically helpful to break up the generalities into units that act as building blocks out of which we can then construct a framework of thought.
These units are standards or yardsticks against which we measure and construct other things. Sometimes there seems to be a single foundational unit, like the atom of Democritus, the brick of a house, or the biological notoriously-difficult-to-define species. Biologically at the microscopic scale we have cells. Sometimes we just use a range of convenient units without placing emphasis on one as being fundamental to all the others. The unit of music is the crotchet, perhaps (whole note), as a foundational note that can be added to, or subdivided. The unit of time is, perhaps, the second or minute, while ‘now’ is contentious. Number systems seem to rest on the building block of a single unit, number one. Spatial measures, like centimetres, metres, miles and so on, seem to lack a foundational unit.
Perhaps it is a feature of our mental processing that we need objects to which we tether our thoughts. And, since we intuitively recognize the importance of these anchors, they take on special significance in our experience.
Principle 1 – our minds focus on units of experience and thought, some of which are representations of the external world. Science attempts to maximize the intelligibility of the relationship between our representations and the external world
Black-boxing
Another characteristic (innate limitation?) of our human minds is that we cannot think of everything we know and have experienced, all at once. We overcome this by concentrating on particular aspects, events, circumstances, or parts – and that means taking all else for granted. This is sometimes expressed scientifically as the principle of ceteris paribus or other things being equal.
When we assume that the universe is the largest possible physical ‘whole’, everything within it is, in some sense, no matter how obscurely, related to everything else. It follows that if we are to understand and explain the universe in its entirety then the most effective way of doing so is to provide some kind of total circumscription – otherwise we will be leaving some parts out and the explanation will be incomplete. But describing the entire universe scientifically in all its complexity seems an impossible task so, according to cosmologist Stephen Hawking: ‘
Instead, we break up the problem into bits and invent a number of partial theories. Each of these partial theories describes and predicts a certain limited class of observations, neglecting the effects of other quantities . . .’ . . . but . . . ‘ If everything in the universe depends on everything else in a fundamental way, it might be impossible to get close to a full solution by investigating parts of the problem in isolation’.[6]
Our difficulty with this insight is more one of psychological resistance than intellectual persuasion. Aristotle made a compelling argument that an organism, as unit of functional organization, is more than its material constituents. But we still find this a mental barrier – how can the organism possibly be more than its associated parts?
Context, open & closed systems
This presents us with a further philosophical difficulty. What would a total circumscription of the universe look like? And even if physics were to provide a summary of the universe in a neat equation – this would only be a summary of everything as understood by (in the context of) physics.
It seems important to state our particular viewpoint, the context, aspect, or perspective from which we are approaching such a question.
Perhaps another way of expressing this difficulty is to regard it as a matter of context: what exactly is under consideration and what is not? Are we dealing, explicitly or implicitly, with an open or closed system?
This relates to the analytic and synthetic approaches to explanation. To be objective we can study an object or event within its total context, or we can isolate it from this context in order to manipulate or consider a limited range of variables.
Let’s try to tease out some basic distinctions and ideas.
Part – a part is generally related to and explained in terms of the whole of which it is a part. This simply follows the semantics: if it is a part then it is a part of something else; that is, our understanding of a part depends on its role within a wider context. To understand and explain an ant as a part, rather than a whole, we need to know how it interacts with other ants and its environment
Whole – again, following the semantics, a whole is generally (though perhaps not so strongly as the part) related to and explained or analysed in terms of its constituent parts To understand and explain an ant as an individual organism we need to know about its parts and the way they interact
Paradoxically, every[3] object in the universe (apart from the universe itself) can be both a whole and a part. An ant is a whole individual but it is also a part of a colony . . . and so on. This creates a cognitive dissonance since we feel intuitively that something cannot be these two things at the same time, both a whole and a part.
If you break a rock in two, do you then have two rocks – or one rock in two parts? Like a visual illusion this cognitive illusion occurs because we contemplate situations from one viewpoint at a time, not several at once. This situation becomes further complicated when we include the temporal properties of actuality and potentiality. When we ask ‘Which came first, the chicken or the egg?‘ we waver between considering the wider context by ‘looking forward’ to a destination and whole (becoming a chicken), or ‘looking backward’ to an origin and part (the egg) that gave rise to the chicken. Similarly, we might think of an acorn as either having the potential to produce a tree (see purpose) or of a tree as having the potential to produce acorns . . . even though both apply.
Our minds continuously flip-flop between past, present, and future – between history and potentiality, anticipation and retrospection – and between wholes and their parts.
This does not mean it is impossible to consider an object in terms of both its wider context and constituent parts.
There is a famous logical dilemma. Wholes are of two different kinds: those which contain themselves as members and those which do not. The set of all of the people in a room does not contain itself because all the people together do not make another person. However, all the piles of sand in the world put together would constitute an additional collective pile of sand. A proper part of an object is a part that is not identical to the whole. This leads to various errors and ambiguities, notoriously Bertrand Russell’s 1901 paradox in set theory concerning the set of all sets that do not contain themselves as members, such that the condition for a set to contain itself is that it should not contain itself.
Can we draw any general conclusions from these observations about the way the human mind works?
Hierarchical metaphor
The methods of analysis and synthesis attracts hierarchical metaphorical language.
When we proceed from the smaller to the larger, or from the less inclusive to the more inclusive then we compare this metaphorically to movement in space. We are looking in opposite ‘directions’, either ‘up’ (progressive inclusivity) or ‘down’ (progressive division) or maybe ‘forward’ (to greater inclusivity) or ‘back’ (to greater reduction).
With this metaphor of a spatial hierarchy we regard analysis as reduction, a ‘looking downwards towards the bottom’. But when we think synthetically by understanding and explaining how something fits into a wider context we say we are either ‘looking upwards towards the top’. If we can steadily and systematically ‘build up’ the universe from its fundamental particles into greater wholes and their relations, we can also ‘break down’ the universe from its totality into its simplest parts. Our explanations, including our scientific explanations, thus take us ‘up’ and ‘down’ the ladder of life or great chain of being. The scientific consequences of hierarchical thinking are discussed elsewhere.
The holon
The word ‘holon’ was coined by Arthur Koestler in The Ghost in the Machine (1967, p. 48) to designate the part-whole hybrid – something that is simultaneously both a whole and a part. He was clearly thinking in terms of organic systems:
‘Holons are autonomous, self-reliant units that possess a degree of independence and handle contingencies without asking higher authorities for instructions. These holons are also simultaneously subject to control from one or more of these higher authorities. The first property ensures that holons are stable forms that are able to withstand disturbances, while the latter property signifies that they are intermediate forms, providing a context for the proper functionality for the larger whole‘.
For our purposes ‘holon’ is a term expressing a duality of potential explanation of every object as simultaneously a whole that can be subdivided and analyzed in terms of its parts, and a part that can be synthesized into a wider whole.
Principle 2 – every object is a holon – it is simultaneously both a whole and a part: we can understand and explain it analytically, in terms of its constituent parts, or synthetically in terms of its place within a wider context
Principle 3 – the scientific need for explanation (like the philosophical requirement for rational justification or causal origin) leads to an explanatory regress which is either analytic (segregating into ever smaller parts or scope) or synthetic (combining objects into a progressively wider context)
Principle 2 – every object is a holon – it is simultaneously both a whole and a part: we can understand and explain it analytically, in terms of its constituent parts, or synthetically in terms of its place within a wider context
Principle 3 – the scientific need for explanation (like the philosophical requirement for rational justification or causal origin) leads to an explanatory regress which is either analytic (segregating into ever smaller parts or scope) or synthetic (combining objects into a progressively wider context)
More than its parts?
Now let’s look more carefully at the general question ‘In what possible sense can a whole be more than the sum of its parts?‘ How, for example, can a building be more than the materials out of which it has been constructed?
The prime example here is that of an organism. It might be claimed, for example, that an organism is more than the sum of its parts. But, if we remove all the molecules that make up its body then what is left?
Nothing is left.
Consequently, we might conclude that the claim that there is something else, something more, is either false or that the ‘more’ that is being asserted is something mysteriously abstract and immaterial . . . something that either does not really exist, or which should be ignored. If it is immaterial then it is likely some kind of illusion, something that isn’t ‘real’.
However, the ‘more’, it turns out, is not the molecules or matter of the organism but the relationship that exists among these material objects – it is their organization or structure – their particular spatial arrangement and mode of dynamic interaction.
A dead organism is a collection of organic molecules. A living organism is a functional structure with agency – it can reproduce, metabolize, grow etc. It is this functional organization that makes an organism an organism and not a collection of molecules. This is the abstract and immaterial ‘more‘ that turns molecules into a living organism.
Aristotle’s formal cause
For many scientists this is a step too far. The more described here is akin to Aristotle’s form that was rejected by scientists during the Scientific Revolution as being too philosophically abstract. He had postulated four causes (different kinds of reasons that are offered as scientific explanations – the ‘becauses’ of existence and change) – the material, efficient, formal, and final causes. The Scientific Revolution rejected the formal and final causes as too philosophically abstruse, if not outright mistaken. But today, as in Aristotle’s day, and in spite of modern scientific advances, we are still forced to accept that in addition to the matter of the universe there are abstract (immaterial) properties and relations that have causal efficacy and are as real as matter itself.
Though scientific pride might still prevent us from accepting two of Aristotle’s ’causes’ – his formal cause and telos – it is nevertheless time to acknowledge that scientific explanation, especially in biology, incorporates abstract properties and relations within its explanatory realm.
Novelty in nature occurs, not only through the arrival of new matter, but with the emergence of new forms of matter as new properties and relations.
More than this. Immaterial properties and relations have causal efficacy. It is only organic molecules unified and integrated into a particular set of properties and relations that can express agency.
A paper by Walsh and Wiebe[7] suggests that Foundationalist Materialism is the default ontology for contemporary natural and physical sciences. They argue that it cannot accommodate the emergent nature of organisms. While Foundationalist Materialism accounts for the fact that the capacities of organisms derive from their component parts and processes, it cannot countenance the converse fact that the causal capacities of an organism’s components are derived from the organism as a whole. Aristotle’s hylomorphism, however, adequately captures the reciprocity that holds between an organism and its component parts and processes. Hylomorphism makes sense of organismal emergence. The proper scientific study of organisms suggests that they should be considered as interactions between Aristotelian matter and form.
Principle 4 – only by studying parts and their dynamic relations can we really come to grips with physical reality: parts alone are not sufficient
Principle 5 – a collection of physical objects is not something in physical addition to the objects themselves, what is extra is something abstract (that is real) – it can be regarded as a power or property that is real but not physical
Principle 6 – though all physical objects consist of matter, the abstract (immaterial) organization of this matter generates properties and relations that can have causal influence on physical structure
Now, from Principle 6 we can see that although we can indeed describe social and biological phenomena in terms of their physical components there is additional information, as new properties and relations, that must be accounted for. Further, even given full physico-chemical knowledge it may not be (or would be nigh impossible) to build up from scratch or anticipate these new properties.
Most scientists would agree that a chair and the arrangement of molecules out of which it is made are one and the same. But, as Aristotle pointed out over 2000 years ago, it is not just molecules, but their organization that give rise to the particular immaterial properties and relations (the form) that we call ‘chair’.
A philosophy of biology
Sometimes our thinking is most effectively challenged when presented directly with a dogmatic point of view, rather than a generous consideration of possibilities. The following is such a challenge.
Pluralism – for the purposes of scientific investigation, real scientific entities consist of many kinds of objects, properties, and relations that emerged and evolved out of the point source at the Big Bang.
Privileged ontology – there is no privileged scientific ontology. The fact that an object is smaller, larger, more or less inclusive etc. does not influence its reality. The distinctions between, and ranking of, scientific objects is for the purpose of explanation and understanding (epistemology) not their reality (ontology)
This article has set out one possible metaphysical foundation for biology that is intended to encourage the reader to think through and criticize. Being metaphysical it might seem of little direct relevance to empirical biology – but, being metaphysical, it can also totally change the way we understand and explain the biological world.
To survive in a complex world our minds are continuously establishing units of experience as objects of understanding. These act as points of shifting focus as our priorities change. They are objects that may or may not correspond to physical objects in the world and they are under continuous re-classification and re-prioritization as our minds vacillate between past, present, and future – between actuality and potentiality – between anticipation and retrospection – all within a kaleidoscope of constantly reconfigured wholes and parts.
We explain a part in terms of the whole of which it is a part. This simply follows the semantics: if it is a part then it is a part of something else; that is, our understanding of ‘part’ depends on its role within a wider context. Similarly, a whole is generally (though perhaps not so strongly as the part) related to and explained or analyzed in terms of its constituent parts.
Every object in the universe (apart from the universe itself) can be both a whole and a part. This creates a cognitive dissonance since we feel intuitively that something cannot be these two things at the same time – that is, we tend to assess the situation from the point of view of the whole, or of the part, but not both at the same time. For simplicity we can call an object considered in the context of this cognitive dissonance a holon – it is simultaneously both a whole and a part: we can understand and explain it analytically, in terms of its constituent parts, or synthetically in terms of its place within a wider context.
When a whole is explained in terms of its parts we refer to this as analysis. Analysis adopts the mental perspective of the whole. We can analyze an object into progressively smaller and smaller or less inclusive parts in an infinite analytical regress (or until a least-inclusive ‘rock bottom’ foundational or fundamental situation is reached). It is the whole that is, as it were, demanding explanation. In contrast, when we explain something (as a part) in terms of a wider whole or context we refer to this as synthesis. We can also synthesize parts into ever more inclusive wholes (wider contexts) in an infinite synthetic regress (or until an all-inclusive ‘rock top’ is reached). Synthesis thus adopts the mental perspective of a part examining its role within a broader context.
This discussion on parts and wholes has two important outcomes for science:
First, analysis and synthesis are often described hierarchically in metaphorical spatial terms. This has created a perception of the entire body of knowledge and, indeed, the world as hierarchically organized. We find it natural to view things top-down or bottom-up. Traditionally this hierarchy took the form of Great Chain of Being that expressed moral worth. The unifying God was at the top, followed by humans in their various classes, then animals, followed by plants, then rocks, and the devil in a fiery underworld. Modern science has tended to reverse this ladder with ‘fundamental’ particles the foundation on which all else rests. Historically our scientific emphasis has been on analysis rather than synthesis. For most scientists it is more scientifically significant that we humans are composed of stardust – of simple atoms and molecules – than that life combines these objects into living and unified functional agents.
PlantsPeoplePlanet argues for a flat ontology – that there is no ‘preferred’ viewpoint on existence – see aspect theory.
Second, by looking closely at the more of ‘the whole is more than the sum of its parts’, especially as it applies to living organisms, we are confronted, as was Aristotle, with the fact that immaterial factors, like properties and relations (organization) can have causal efficacy: that formal cause is not, as most scientists have believed since the Scientific Revolution, an immaterial nonsense, metaphysical mystery, or philosophical obfuscation.
Agency & Explanation
The list of necessary conditions for life enumerated on the web, or in any student introductory textbook on biology, is a long one. Trying to circumscribe, in just a few words, what it is to be a living creature may be a vain ambition.
This website argues that the single most obvious universal feature distinguishing life from non-life was identified by the founder of biology, Aristotle, more than 2000 years ago. It is what today is best referred to, in English, as agency.
Organisms are goal-directed in a way that inanimate objects are not. Aristotle noted that it makes sense to ask what biological structures, processes, and behaviors are ‘for‘ (their purpose) and he insisted that ‘nature does nothing in vain‘. We make no such claims for rocks, the moon, or inanimate objects.
This acknowledgment of purpose in biological activity was later referred to as teleology (the study of ends or goals) and rejected by the Scientific Revolution which treated teleology as unnecessarily mysterious and philosophical. There were several problems and implications: that life was powered by an unscientific supernatural force; that the agency and purpose we see in organisms is simply the reading of human conscious intentions into intentionless nature; that it implied causes acted from the future in a kind of backward causation.
Collectively these criticisms have brought us to today’s prevailing view that the agency and purpose we unguardedly attribute to organisms might help us to understand the operations of nature (they have a heuristic value) but they have no foundation in reality.
This website argues that goal-directed behavior is an objective fact and that we therefore need to build a new foundation for biological science based on a foundation of agency.
Biological agency
Agency is about goals, actions, and behavior: it is more about processes than structures.
Biological agency is an inherited and life-defining behavioral property of all living organisms. It is manifested in the autonomous and flexible behavior of organisms acting on, and responding to, their conditions of existence in a unified and goal-directed way. As a behavioral disposition, it is grounded in the universal, objective, and ultimate biological necessity to survive, reproduce, and flourish – a precondition for life itself. These goals 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 to all proximate goals. These universal biological goals constitute a unity of purpose towards which all autonomous organisms, both minded and mindless – including their structures, processes, and behaviors – are directed.
Goals & Purpose
The goals of organisms are the uncomplicated limits or ends to natural processes that follow conventional causal pathways – the formation of an oak tree from an acorn or a chicken from an egg.[6] The term ‘teleology’ is sometimes referred to pejoratively as implying one or more of the following: the influence of God or supernatural forces, the reading of human intentions into nature, or backward causation acting like a mysterious pull from the future. None of these interpretations is necessary.
Goals take precedence in biology as a matter of explanatory priority. Only when the goals of organisms are understood can there be an understanding of structures, processes, and behaviors (hence the ‘final cause’ associated with teleology) but they do not challenge the natural order of cause and effect. Goals must be first in explanation, and last in causal sequence.
Goal-directedness in organisms is an empirical fact and whether goals constitute reasons and/or purposes seems a matter of taste. It is argued on this website that the notion of ‘purpose’ is unnecessarily often , and unnecessarily, linked to the notion of conscious intention.
Without understanding the reasons for (purposes of) an organism’s behavior as goals – including the role played by structures, processes, and behaviors in the attainment of these goals – biological explanation becomes an incoherent list of dissociated facts.
Conditions of agency
How are we to crystallize, in the most succinct way, what we mean by the expression biological agent?
A biological agent is, of course, an organism (see biological agency), but what exactly is it about an organism that warrants the epithet agent? This is not a matter that is simply resolved. This website suggests three conditions that are both necessary and sufficient: there must be a behavioral orientation (the organism must have discernible goals); its behavior must be coordinated and regulated by a system of information flow; and there must be the capacity to change or adapt in relation to the conditions of existence.
Biological explanation
There is a simple and scientifically acceptable and account of what we mean by ‘life’ and therefore ‘biology’.
Organisms are goal-directed biological agents. Each organism is an autonomous combination of structures, processes, and behaviors that share a unity of purpose . . . the behavioral propensity to survive, reproduce, and flourish. We understand this biological agency because. like our own behavior, it is directed towards ends.
When we describe or explain an organ, process or behavior in relation to the organism as a whole we find it almost impossible to avoid asking what it is ‘for’. We say that eyes are ‘for’ seeing. the heart is ‘for’ pumping blood, and so on.
If we have never seen a house but encountered heaps of bricks, windows, and tiles, they have little meaning until we understand what it means to be a house (their end-product). Only when the goals of organisms are understood can we truly comprehend their structures, processes, and behaviors (hence the ‘final cause’ associated with teleology). There is no mystery about biological ends. Your ‘end’ is, so to speak, becoming a mature adult. and you become a mature adult in a process that is explained in a straightforward biological way that does not challenge the natural order of cause and effect. Goals are first in explanation, and last in causal sequence; they do not imply supernatural forces and, more importantly, they do not depend on a human interpretation. Organism goals are real in nature.
Aristotle’s teleology explains what is unique about life and biological explanations. This natural teleology has been expressed in a more formal philosophical way as: ‘. . . the realization of pre-existing internal potential (as formal-efficient and material-efficient causation) through stages framed by conditional necessity’. In other words, there is nothing unscientific about agency and purpose in nature.
The challenge for biology and the philosophy of biology is less the removal of human properties from nature, and more an account of the nature that grounds our humanity. That is what this website tries to do.
Biological metaphysics
How are we to conceptualize, illustrate, and describe the general characteristics of the living world?
This might seem an unnecessary and probably unanswerable philosophical question, but biology textbooks must start somewhere and – whether implicitly or explicitly – they convey to the reader a scientific representation of biology in general, that is, the metaphysical framework of ideas around which the science of biology is built.
We can attempt to define the key characteristics of life, but we are also accustomed to visual or metaphorical representations that make understanding of complex problems easier to grasp. The popular metaphorical representation of biology is a hierarchy of levels of biological organization.
We often answer metaphysical questions like this by falling back on our general intuitions of reality which we, in a loose sense, loosely regard as consisting of things of different sizes, inclusion, complexity, and significance, all arranged in time and space. Things (science prefers static and stable permanent physical objects and their properties, rather than dynamic and changing processes) but either way we must take account of the influence of space and time; size (bigger/smaller); scope, containment, inclusiveness (more/less unity/multiplicity); position (higher/lower) often associated with value (more important/less important); structure or organization (simple/complex). Some of these factors or evident in everyday language. Cognitive scientist Steven Pinker in ‘The Stuff of Thought’ (2008) points out how we embed the key scientific concepts of space, time, matter, and causality in our conversation. Nouns express matter as stuff and things extended along one or more dimensions. Verbs express causality as agents acting on something. Verb tenses express time as activities and events along a single dimension. Prepositions express space as places and objects in spatial relationships (on, under, to, from etc.). This language of intuitive physics may not agree with the findings of modern physics but, like all metaphor, it ‘helps us to reason, quantify experience, and create a causal framework for events in a way that allows us to assign responsibility. Language is a toolbox that conveniently and immediately transfers life’s most obscure, abstract, and profound mysteries into a world that is factual, knowable, and willable.’
Our human intuitions are evident in the conventional textbook arrangement of living objects into hierarchical levels of biological organization with the ranking criteria inconclusively related to physical objects of different scale, inclusiveness, and complexity e.g. the transition from molecules, cells, tissues, organs, organisms, to populations. Then, following the inferential logic of this hierarchical metaphor, it can reify the imagery of existence as interacting physical layers, like geological strata. This confuses a metaphorical device used for explanation and study (epistemology) with a description of the structure of reality (ontology). It treats each layer as a different object and ignores the dynamic interconnectedness of the biological world at all scales.
Traditional hierarchies consist of levels arranged from ‘higher’ to ‘lower’ like the rungs of a ladder. This can lead to misleading attributions of value to the ranks as we do to human hierarchies, for example, confusing epistemological utility with an ontology e.g. treating a simple particle as ‘fundamental’ or ‘foundational’ – a grounding concept for analysis – as more real than a daffodil. [x] Process philosopher of biology John Dupré treats these ‘levels’ as processes synchronized between spatiotemporal scales synchronized from above and below.
In contrast, real emergent properties are manifested at different scales as distinct ontological elements within the flux using criteria of scale, such as inclusiveness or complexity rather than ‘levels’, albeit explanatory ones.
Organisms in the flux
The absence of hierarchical ontological levels does not diminish the significance of organisms as referential causal and agential entities within the framework of biological explanation. Organisms are privileged because they are self-evidently independent and autonomous agents, even though they are integrated within broader biological systems.
Analysis & synthesis, bottom-up top-down
Our preference for analysis means that we tend to explain each biological object in terms of its simpler components when synthetic thinking can explain their significance within larger, more inclusive, and more complex wholes (the fate of organs depends on the fate of the organisms of which they are a part).
Biological objects are most informatively understood, not as static structures but as dynamic processes that we describe at various temporal and spatial scales. So, for example, molecular processes occur on a much faster time scale than the developmental processes happening at the organismal level which, in turn, operate at a vastly different time scale than evolutionary processes spanning generations. Though these different scales may be organized into a hierarchy of temporally and interacting processes. Biological processes at different levels of organization interact dynamically, influencing one another in complex ways. For example, molecular interactions within cells influence cellular behavior, which in turn influences organismal functions and behaviors, and so on.
By conceptualizing biological organization as a dynamic hierarchy of interconnected processes operating across multiple time scales, Dupré provides a framework for understanding the complexity and dynamism of living systems. This approach underscores the importance of process-oriented thinking in biology and highlights the need to consider both the parts and the whole in biological analysis.
Science currently gives us the impression that life is more like a dynamic network of interacting components interacting in complex ways, rather than a nested hierarchy.
Emergent properties, unique to each scale, defy easy ranking. While criteria like scale, inclusiveness, and complexity guide our understanding (epistemological significance), they don’t necessarily reflect absolute ontological truths. Despite this, organisms remain pivotal causal agents within biological explanations. Their autonomy and agency are evident, even as they operate within broader biological systems. By embracing dynamic interactions and moving beyond simplistic hierarchies, we can enrich our understanding of biology.” Dynamic and evolving interactive process. Emergent properties arise from the interactions of components at lower levels of organization but cannot be predicted or reduced to those lower-level components alone. where multiple levels of organization interact synergistically to create emergent phenomena. It ignores context-dependent functioning. Scale can be spatial or temporal.
Spatiotemporal scales
We would do better to treat all hierarchical talk as talk about scale – recognizing that we often describe biological objects using slightly different terms, depending on the scale of explanatory focus.
There is no need for biology to import the confusing notions of ‘levels’, ‘ranks’, or ‘hierarchy’ (probably related to Linnean taxonomy, which Linnaeus probably based on the former Great Chain of Being).
What the hierarchy of levels of organization is attempting to portray is that our human perception, aided by sophisticated technology, allows us to investigate, explain, and understand the processes of the living world on many spatiotemporal scales. Our best science suggests that the living world is a continuum of complex and interacting processes with regions of spatiotemporal stability and agential independence (e.g. organisms). What constitutes a region of stability (a thing) depends on the spatiotemporal perspective that is being used. We would not consider the operation of the molecules in biological processes on a geological timescale any more than we would consider the operation of molecules at the population scale. Thing-like objects such as organisms become more process-like when considered over longer time scales. Our ability to isolate explanatory spatiotemporal scales allows us to reify (make separate, concrete, and thing-like) these explanatory scales by using the misleading metaphor of a layered or ranked hierarchy.
Glossary - Biological Agency
Adaptation (biological) – the word 'adaptation' expresses, in the most parsimonious way, the means by which organisms, as biological agents, attain their goals. 'Adaptation' can refer to a structure, process, or behavior (a trait). The process by which populations of organisms change over many generations in response to environmental factors, developing heritable traits that enhance their survival and reproductive success in specific environments; the evolution of traits with functions that enhance fitness (being conducive to survival, reproduction, and flourishing); the capacity for self-correction - in the short-term through behavioral flexibility, leading to long-term genetic change
Agency - (general) the capacity to act on and react to conditions of existence with goal-directed behavior; (biological) the mostly mindless autonomous capacity of biological individuals to act on, and react to, their conditions of existence (both internal and external) in a unified, goal-directed but flexible way (see biological axiom). Agency is the physical manifestation of functionally integrated behavior. Human agency is biological agency supplemented by the evolved resources of the human mind including: language, self-reflective and conscious reason, hindsight, foresight, and abstract thought
Agent - something that acts or brings things about. Mindless inorganic agents include objects like missiles, cities, and computers. In biology - an organism as autonomous matter with the capacity to behave in a unified goal-directed way as stated by the biological axiom (sometimes extended to include genes, groups, or other entities, even natural selection itself) as a (semi)autonomous individual with inputs as flows of energy, materials, and information, internal processing, and outputs as energy, waste, action and reaction in relation to inner and outer environments. An organism motivated by real goals (these may be mindless, that is, without conscious intention); an agent can act and react; it is the instrument or means by which a purpose is pursued
Agential realism - the claim that non-human organisms exhibit agency in a mindless way, and that humans combine both mindless and minded agency: the grounding of cognitive biological metaphors in non-cognitive biological facts
Algorithm of life - life is autonomous and agential matter that self-replicates with variation that, by a process of evolutionary selection, incorporates feedback from the environment thus facilitating its persistence.
1. Endow units of matter with agency as a capacity to adapt to conditions of existence (i.e. to survive, reproduce, adapt, and evolve).
2. Combine the behavioral orientation of 1 with genetic modifications arising in each new generation
3. Expose 2 to evolutionary selection pressures resulting in differential survival
4. Surviving forms return to step 2
Anthropocentric - to view and interpret circumstances in terms of human experience and values
Anthropomorphism - the attribution of human traits, emotions, or intentions to non-human entities
Apomorphy - a specialized trait or character that is unique to a group or species: a character state (such as the presence of feathers) that is not present in an ancestral form
Autopoiesis - self-replication combined with self-maintenance and modification is sometimes referred to as autopoiesis
Behavior (biology) - the outward expression of the internal processes of biological cognition; actions performed by a biological agent (or, more loosely, its parts); the internally coordinated but externally observable response of whole organisms to internal and external stimuli. Behaviour may be: mindless or minded; conscious, unconscious, or subconscious; overt or covert; innate or learned; voluntary or involuntary. Learning capacity is graded in complexity
Behavioral ecology – the study of the evolution of animal behavior in response to environmental pressures
Biological agency - the capacity of autonomous living organisms as biological agents to act on, and respond to, their conditions of existence in a flexible way and with a unity of adaptive purpose - the goal-directed behavioral propensity to survive, reproduce, and flourish; the capacity of living organisms to act with intentionality; a life-defining property of living organisms; the motivation for biological activity as described by the biological axiom; the capacity of organisms to act with purpose and intentionality; the biological principle that has generated the entire community of life; the capacity organisms act intentionally in the sense that their behavior is purposeful and adaptive i.e. directed towards objects, properties, or states of affairs. Externally observable biological agency is generated by the internal processing of biological cognition.
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 as best exemplified by the activity of living organisms as primary biological agents. Organisms express their autonomy as a unity of adaptive purpose – the universal, objective, and ultimate behavioral propensity to survive, reproduce, adapt, and evolve in response to their internal and external conditions of existence (sometimes referred to in evolutionary biology as 'fitness maximization'). These goals 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. The biological axiom outlines the organismal behavioral conditions to which the operations of biological structures, processes, and behaviors are ultimately subordinate. cf. organism, biological agent.
Biological cognition - the accession, storage, interpretation, and processing of information necessary for biological agents to adapt to their conditions of existence. In its highly evolved sentient form, this entails the mental processes of perceiving, interpreting, and responding to stimuli that encompasses learning, memory, problem-solving, and decision-making, all grounded in the brain's structure and function as shaped by evolution cf. basal cognition, cognition. Biological cognition is manifested externally as biological agency.
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 normativity - the mostly mindless, universal, objective, and ultimate behavioral rules and standards (conditions) essential to sustain life as the survival, reproduction, adaptation, and evolution of organisms (the biological axiom). The biological axiom is, in effect, a code of behavior for life - the conditions that constrain the possibilities of the structures, processes, and behaviors of organisms and grounding human morality.
Biological norms - the physiological, genetic, developmental, and behavioral ranges and standards of healthy functioning in organisms. The organismal propensity to persist is both a biological necessity driven by evolutionary pressures and a logical necessity contingent on the empirical premise that the goal of life is to continue existing. However, the notion that existence is ‘better’ than non-existence is shaped by subjective human values and the ethical reasoning that is an aspect of our human species-specific form of normativity. The universality of biological normativity and its functional equivalence across species demonstrates how uniquely human values and ethical considerations are grounded in our biological nature.
Biological principle - an underlying regularity of a biological system e.g. evolutionary principles (like natural selection), agential principles (survival, reproduction, adaptation, evolution), biochemical laws (like the laws of thermodynamics), or ecological principles (like the cycles of matter and energy flow). By understanding these principles, scientists can make predictions about biological outcomes and develop theoretical frameworks that explain how and why organisms behave and evolve in particular ways.
Biological simile – a comparison (likeness) of biological phenomena that is based on real evolutionary connection
Bioteleological realism - the claim that purposes exist in nature and that most cognitive metaphors used in science are grounded in non-cognitive biological facts
Biosemiotics - the study of the production, interpretation, and communication of signs and meanings in living systems
Bioteleology - purpose resides in the fact that there are natural ends or limits to biological processes (e.g. the maturing of an acorn into an oak tree; the termination of a mating ritual in copulation), that these ends are objectively goal-directed and therefore purposive. Teleonomy controversially interprets teleology as implying a metaphysically questionable source of purpose. The word teleonomy attempts to replace this purported implication with a naturalistic explanation. The distinction between teleology and teleonomy, and whether that distinction is warranted, remains unclear
Cognition - the internal processing that precedes and guides the behavior of biological agents; the goal-directed and adaptive process of acquiring and interpreting information about the conditions of biological existence; the acquiring, processing, storing, organizing, prioritizing, and communication of information. In its highly evolved and limited human form, it involves perception, memory, reasoning, and problem-solving, allowing individuals to understand their environment, make decisions, and establish knowledge through experiences and interactions with the world cf. basal cognition, biological cognition
Cognitive ethology – the study of the influence of conscious awareness and intention on the behavior of an animal
Cognitive metaphor - a metaphor used in the context of human intentional psychology. When we have no words to describe real pre-cognitive agential traits, we resort to the language of human cognition, thus condemning these traits to the figurative world of metaphor
Complementary properties – the properties instantiated by the relata of a biological simile
Conditions of existence (biology) - those factors influencing the inner processing of organisms including triggers arising from both inside and outside the organism.
Derived concept – a concept with a narrow semantic range
Emergence - as used here - the origin of novel objects, properties, or relations in the universe that warrant human categorization
Environmental factors - the external factors impacting on the existence of an organism
Evolutionary biology – the study of evolutionary processes (notably natural selection, common descent, speciation) that created the community of life
Fitness - a measure of reproductive success (survival) in relation to both the genotype and phenotype in a given environment
Function - also referred to as adaptive significance. Typically, this is the role that the structures, processes, or behaviors of an organism play in the functional organization of the organism as a whole. It helps to regard these characters of organisms as having functions while organisms themselves, as independent agents, have purposes and goals
Functional equivalence - performing the same function through the unique structures, processes, and behaviors of different organisms and species
Genotype - the genetic constitution of an individual organism, encoded in the nucleus of every cell
Grounding concept – the general ideas that underpin more specific (derived) concepts
Heuristic – stimulating interest and investigation
Holobiont – an aggregation of the host and all of its symbiotic microorganisms
Homeorhesis - (Gk - similar flow) a term applied to dynamic systems that return to a specific path or trajectory, in contrast with systems that return to a particular state (homeostasis). Homeostasis refers to the maintenance of a stable internal environment in response to external changes (e.g. body temperature in mammals) while homeorhesis is the adjustment, sometimes changing over time, to meet particular organismal functions or goals (e.g. changes in blood composition that support the fetus during pregnancy).
Homology – a similarity in the structure, physiology, or development of different species of organisms based upon their descent from a common evolutionary ancestor
Human agency - behavior motivated by conscious intention; the uniquely human specialized form of biological agency that is described using the human agential language of intentional psychology; the capacity to act based on reasons as cognitive and motivational states (beliefs, desires, attitudes) (philosopher Kim)
Human-talk - the language of humanization - the attribution of human characteristics to non-human organisms, objects, and ideas. (Biology) the description of non-human organisms using language that is usually restricted to humans and human intentional psychology; the use of cognitive metaphor to describe non-cognitive but real biological agency; the psychologizing of adaptive explanations
Intention - a cognitive goal, or pre-cognitive behavior that is directed towards objects, properties, or states of affairs
Intentional idiom - the use of intentional language in a wide range of contexts including those relating to non-human organisms
Life – units of matter with the agential capacity to survive, reproduce, and flourish (cf. biological axiom) as best exemplified by autonomous organisms. Life processes, such as growth, reproduction, response to stimuli, and metabolism are subordinate to the organismal wholes of which they are a part
Metabolism - the set of processes that sustains an organism (or, more generally, any biological system)
Metaphor - figurative language as ‘nonliteral comparisons in which a word or phrase from one domain of experience is applied to another domain’. An 'as if' direct (not a 'like') comparison that is not grounded in reality e.g. 'You are a rat'.
Natural agency - any agency in the natural world
Natural purpose - the natural goals, ends, or limits of biological agents, both cognitive and non-cognitive
Normative realism - the view that normativity has its origin in biology through the mindless and mindful ultimate goals of survival and reproduction, and proximate goal of flourishing
Organism - unicellular to multicellular life forms that include fungi, plants, and animals. The mostly physically bounded and functionally organized basic unit of life and evolution. As a mostly autonomous biological agent the organism acts on, and responds to, its conditions of existence with flexible but unified and goal-directed behavior that demonstrates the objective, ultimate, and universal propensity of organisms to survive, reproduce, and flourish. While life can be described at many scales and from many perspectives (and the structures, processes, and behaviors of organisms all demonstrate a degree of autonomy), it is the entire organism that provides the agential reference point of life - whose autonomy is both intuitively and scientifically most discrete. Exceptional cases such as lichens, Portuguese Men-o-War, the Great Barrier Reef, sexually aberrant variants etc., do not erode these core characteristics.
Organismal factors - the internal factors impacting the existence of an organism
Personification - the representation of something in the form of a person
Phenotype - the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment
Physical reductionism - the view that biological phenomena can be adequately explained in terms of physico-chemical entities
Pre-cognition - all organisms are goal-directed autonomous biological agents that act on and respond to their conditions of existence in a flexible way. Agency is usually associated with human cognitive traits like intention and deliberation. However, the presence of agency in non-cognitive organisms confirms the presence of non-cognitive agential traits, a characteristic of non-cognitive organisms that distinguishes them from inanimate and dead objects. These non-cognitive agential traits are referred to here as pre-cognition.
Process ontology – it is processes that create phenomena including emergent and ephemeral ‘things’ which are derived from processes as transient and cohesive patterns of stability within the general flux. Thus, things are derivative of processes. In practical terms this does not mean that things do not exist or are not useful concepts. However, instead of thinking of processes as belonging to things, it is more scientifically informative to think of things as derived from processes. Organisms are prime examples of transient things in process
Proximate explanation - an explanation dealing with immediate circumstances: the immediate mechanisms and processes behind biological phenomena, including genetic, developmental, and physiological factors specific to individuals or species
Purpose – the reason (end, aim, or goal) why something exists or is done, made, used etc.; (biology) the goal of a biological agent, paradigmatically a living organism, but also the natural end-state, limit, or reason for a structure, process, or behavior (often referred to in this sense as a function). In humans, purposes can assume a cognitive form as mental representations (conscious intentions); what something is 'for'; Aristotle's final cause or telos. Purposes, as the goals or ends of organisms and their parts, are an emergent and agential property of life that preceded human cognition: causal (etiological) explanations of purpose do not explain it away. Darwin did not remove agency and purpose from nature, he showed how they generated a process of natural selection. Thus purpose, in a broad sense, is what a structure, process, or behavior is ‘for’ – its function, reason, or intention – its adaptive goal. In a narrow human sense, a purpose is the object of conscious intention. A distinction of convenience may be made between the functions of parts (the role of a part within a whole), and purpose (the 'function' of the whole organism - as biology’s canonical agent
Reduction - - a mode of explanation that explains a ‘whole’ by breaking it down into its constituent parts, focusing on the components themselves. Saying ‘A house is an assemblage of bricks’ is an example of reduction, as it emphasizes the individual elements that make up the structure cf. synthesis
Relata – the objects being compared
Semantic range – the degree of generality or abstraction encompassed in the meaning of a word - range of objects and ideas encompassed by its meaning
Synapomorphy - a characteristic present in an ancestral species and shared exclusively (in more or less modified form) by its evolutionary descendants
Synthesis - a mode of explanation that explains a ‘part’ in terms of its role, function, or purpose within a greater whole. This approach considers how parts contribute to and interact within a broader context. Saying ‘A house, as an aggregation of bricks that provides shelter and a space for living’ emphasizes the function and relationship of parts to the whole cf. reduction
Teleology - the philosophical concept of purpose and design in the natural world. The claim that natural phenomena occur for reasons as natural ends or purposes that are neither necessitated by human or supernatural intention nor implying backward causation or foresight. For teleology in biology see bioteleology. The article on bioteleology discusses 8 senses of 'teleology'
Teleonomy - see bioteleology
Trait - a unit of the phenotype (physical or behavioral)
Ultimate explanation - a long-term, often evolutionary, explanation (e.g. in biology the purpose or measure of fitness of a particular trait); the reasons or adaptive significance behind biological phenomena, focusing on universal principles that apply across species and contexts
Umwelt - an agent-centric orientation to the world; the environment of adaptive significance for a particular organism - its unique perspective or 'point of view': those factors important for its survival, reproduction, adaptation, and evolution: its mode of experience or 'reality'. For humans, this is the commonsense world of everyday experience (cf. manifest image) that is mostly a consequence of our innate mental processing which is, in turn, a consequence of our uniquely human evolutionary history
Values – (biological agency) that which ultimately motivates the behavior of biological agents (living organisms), namely the universal and objective goals of the biological axiom. Human agency - the proximate and subjective attitudes, beliefs, and inclinations that guide human behavior
First published on the internet – 11 June 2023
. . . up to 13 June – substantial revision
. . . 10 October 2023 – revision as an attempt to integrate connected articles
Biological Revolution
Theoretical biology is currently experiencing a paradigm shift in its foundational ideas as the concepts of agency and cognition are extended beyond the human (sentient) domain to non-human organisms.
Biological agency is evident in the universal capacity of organisms to act on and respond to their conditions of existence in a unified, goal-directed, and flexible way - as the objective and ultimate capacity to survive, reproduce, adapt, and evolve (the biological axiom).
The observable behavior that establishes biological agency is generated by functionally integrated internal processing. This is a universal form of biological cognition as understood in a broad sense as the means by which organisms access, store, retrieve, process, prioritize, and communicate information as a prelude to goal-directed activity. These same universal characteristics are exhibited by functionally equivalent structures, processes, and behaviors of all organisms with human cognition one highly evolved form.
Human agency and human cognition are highly evolved and species-specific examples of universal biological agency and universal biological cognition. Our anthropocentrism and awareness of our own mental states have led us to describe functionally equivalent adaptations of other organisms using the language of human cognition and intentional psychology. This misuse of language, which also implies evolutionary similarity, is therefore treated as cognitive metaphor. This ignores the fact that functionally equivalent adaptations (expressed in evolutionarily graded form) need not necessarily express direct evolutionary connection and, more importantly, they currently lack an appropriate functionally descriptive terminology. Functional equivalence is a genuine feature of biological systems. Human physical mental faculties (many uniquely human), such as sentience, subjectivity, experience, perception, reason, value, knowledge, memory, learning, communication, etc. have functional equivalents in other organisms that do not, and need not, demonstrate physically direct evolutionary connection. We have a well-established biological language for structural comparison, but no equivalent language for functional comparison.
These philosophical changes are part of the framework of the Extended Evolutionary Synthesis (EES) which expands on traditional evolutionary theory by incorporating new insights from developmental biology, epigenetics, and ecology, notably the acknowledgment of organisms as active participants in their own evolution, shaping their own developmental trajectories and those of their descendants.
This re-evaluation of the human relationship to other species represents a significant expansion of human knowledge. It opens new research fields, challenges the foundations of theoretical biology, and has ethical implications for the way we interact with other living beings.
The Organism
Biology is the study of organisms, their parts, and their communities. This is the foundational principle of organism centered biology.
The organism is a fundamental analytical, methodological, epistemic, and ontological biological category. It is the basic unit of biological classification (the species is a group of similar organisms), of ecology, and of evolution. The organism is therefore a reference point for biological description and explanation.
While parts of organisms – their structures, processes, and behaviors (including genes and cells) – often demonstrate a high degree of independence, self-maintenance, and goal-directed activity, they are ultimately subordinate to the goals of the functionally integrated and self-determining adaptive agency of whole organisms. Organisms thus express a greater degree of agential autonomy than their parts or communities and act as major causal hubs within the biological network of causal connection.
Emphasis on reductive molecular-genetic and other explanatory ‘levels’ of existence is an aberration of hierarchical thinking (see biological hierarchy).
Organisms are biological agents that act on, and respond to, their conditions of existence in a flexible adaptive way. While agency, in a narrow sense, is associated with sentient organisms, notably the consciousness, intention, and deliberation we associate with human subjectivity, it has its evolutionary origins in the goal-directed behavior of all organisms – their universal, objective, and ultimate propensity to survive, reproduce, adapt, and evolve. Human agency is therefore a highly evolved and limited instance of biological agency.
Adaptation entails both short-term access, storage, and processing (interpretation) of information as a form of universal biological cognition driving behavior, ultimately leading to long-term genetic change. Human cognition is a highly evolved and limited conscious form of biological cognition.
The organism, as functionally equivalent to a subject or biologically cognitive 'self', provides an empirically justified and prioritized scale for biological explanation that is as grounded in the agential process that necessarily defines all life.
What is life?
The biological axiom
The basic unit of biological classification, ecology, evolution (and therefore life) is the physically bounded and autonomous organism. Organisms possess many necessary structures (e.g. genes, cells), processes (e.g. metabolism, homeostasis), and behaviors (e.g. the adaptive response to stimuli) that are necessary for life but all of these organism 'parts' are ultimately subordinate to the agential demands of the entire organism, so it is this agency that provides the necessary and sufficient conditions for all life.
What is this agency that defines life?
Ancient philosopher Aristotle noted that organisms persist by surviving to reproduce, thus perpetuating their kind. He said 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. Biologists have subsequently regarded survival and reproduction, more than any other properties, as crucial characteristics of life.
Charles Darwin, like Aristotle, acknowledged that organisms are not passive; they act on and respond to both their internal and external conditions of existence as biological agents in a 'struggle for existence'. Survival was a process of adaptation that facilitated not only short-term adjustment to circumstance but also the long-term genetic change to populations that we now associate with evolution. Today, the Darwinian concepts of adaptation and evolution are inextricably intertwined with the Aristotelian notions of survival and reproduction as core concepts in biology.
Biological agency, as observable behavior, is generated by internal processes of information collection, retrieval, storage, processing, prioritization, and communication. These biologically universal internal properties are functionally equivalent to the general properties of human cognition.
Organisms are thus distinguished by their biological agency as the functionally integrated (unified) and goal-directed behavioral propensity to survive, reproduce, adapt, and evolve. This agency imbues organisms with a behavioral orientation or 'perspective' on their existence. An organism expressing universal biological agency is functionally equivalent to a human 'self' with 'biological cognition' and 'biological values' that are functionally equivalent to human values. Human agency and human values are thus highly evolved, limited, and species-specific forms of biological agency, biological cognition, and biological values.
Thus it is an internally generated but externally observable behavioral agency that animates, motivates, or drives organisms, providing them with the vitality that distinguishes the living from the inanimate and dead. Agency is not a 'thing' it is a process (in its broadest sense). Agents are goal-directed, so biological science, to be meaningful, must make these goals explicit.
Life is defined by its agency as the capacity to survive, reproduce, adapt, and evolve - referred to here as the biological axiom.
Life is most apparent in the autonomous agency of living organisms whose structures, processes, and behaviors express a functionally integrated unity of purpose – the universal, objective, and ultimate behavioral 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 and unification of all proximate goals. These are the defining conditions for biological agency whose natural limits or ends are the biological conditions that define life and the trajectory of evolution.
While many essential properties of life are evident in structures (genes, cells), processes (metabolism, homeostasis, growth and development, reproduction) and behaviors (response to stimuli, adaptation) these are all subordinate to biological agency - the unified and functionally integrated activity of entire living organisms. Without agency, biology assumes the character of inanimate matter, of purposeless physics and chemistry. This is why it is agency – not the other necessary biological structures, processes, and behaviors - that best expresses the nature of life. In biological explanations functions, purposes, and goals necessarily precede discussion of structures, processes, and behaviors. Without first understanding goals (biological agency) biology loses meaning and becomes a collection of dissociated facts. The biological axiom is a behavioral account of life's agency that encompasses the ends of all biological activity - life's biological purpose.
Ultimate, Proximate, & Universal Explanations
Ultimate and proximate explanations are concepts from biology used to understand the causes and mechanisms of traits and behaviors.
Ultimate explanations take the form of in-principle statements – the necessary, general, implicit, or theoretical conditions required for a condition to pertain. Proximate explanations provide in-practice, actual, explicit, and observable instantiations of these principles.
In biology, a distinction may be drawn between specific ultimate explanations (the evolutionary reasons for particular traits or behaviors) and a general ultimate (universal) explanation for all traits and behaviors (the biological axiom). The universal explanation provides the general context within which specific ultimate and proximate explanations apply.
Ultimate explanations examine why something exists – what it is for – which, in biology is its evolutionary purpose while proximate explanations focus on the mechanisms or means of achieving these theoretical ends – on how biological objects work (what they are made of, what they do, and how they do it). Empirical science may be more concerned with observable cases but it benefits by having a simple and principled theoretical foundation e.g. the laws of physics.
The precedence we sometimes ascribe to ultimate explanations lies in their ability to summarize and generalize thus providing broad context, direction, and, most notably, predictive power; they establish the natural limits or ends of all circumstances, while proximate explanations offer insights into immediate processes and mechanisms. It is therefore ultimate explanations that best serve as theoretical principles – even though they remain grounded in the empirical reality of the phenomena themselves.
In biology, as elsewhere, ultimate explanations are grounded in the phenomena they describe. However, goal-directedness infers natural ends or limits that must take precedence (be considered first) if biological explanations are to make sense. Understanding the goal-directedness of organisms is crucial. Whether these are proximate ends (the ends of particular instances) or ultimate ends (the ends of all biological activity), they must come first in explanation and these ultimate ends are the fundamental biological principles for life.
Theoretical biology, in laying out its general principles, must summarize and generalize, establishing natural limits, must therefore establish ultimate ends as the general theoretical principles for life.
Biological objects
The miracle of life is traditionally presented to student biologists through the categories and concepts of the hierarchy of biological organization. This presents a view of science that is grounded in ancient and ambiguous ideas about the structure of reality. Building biological understanding around the agency of organisms (their parts and communities) and the categories of structure, process, and behavior offers a more comprehensive, simple, and dynamic conceptual framework for contemporary biological investigation that is grounded in current biological research. It balances ontological rigor with pragmatic flexibility, which is important for both educational and research purposes by providing categories that are both philosophically sound and practically useful.
Structures: the tangible physical building blocks of biology, ranging from sub-organismal entities like molecules, genes, cells, tissues, and organs, to supra-organismal entities such as colonies, populations, ecosystems, and the biosphere.
Processes: the biochemical and physiological activities that sustain life, such as photosynthesis, homeostasis, growth, metabolism, and reproduction. Also the long-term changes addressed by evolutionary biology. These dynamic activities are often obscured when focusing solely on structural descriptions.
Behaviors: the actions and responses of organisms within their environment. These can be both minded and mindless, in both organisms and their parts, and are often goal-directed, even in a minimal sense, by having specific functions.
This tripartite classification reflects the historical development of biological investigation - as an inventory of static structures (histology, anatomy, morphology, taxonomy) to dynamic processes and functions (physiology, developmental biology, ecology, evolutionary biology, systems biology), and then behaviors and agency (ecology, ethology, psychology, cognition). It emphasizes that structures support processes and processes drive behaviors in dynamic interactions and responses, capturing the complexity and adaptability of life in a comprehensive way.
This progression of investigative categories shows how biology has increasingly integrated the concepts of time, change, function, and agency through the interplay of physical structures, functional processes, and adaptive behaviors. It is a tool that reflects the character of contemporary biology in a categorization that helps students progress logically from understanding physical makeup to exploring interactions in the real world, which underscores the educational value of the approach.
Functions
'Purpose’ and ‘function’ are similar in meaning, both suggesting ends or goals (‘What something is for’). Purposes in biology are the natural ends, limits, or goals of biological agents and their parts, although 'function' can also be treated mechanistically as ‘What something does’. This nuanced semantics can be accommodated in biology by using ‘purpose’ to indicate the ultimate goals of whole organisms (biological axiom), and ‘function’ to indicate the supporting goals of their parts.
While ‘purpose’ is strongly associated with the subjectivity of conscious intent, it is increasingly used to describe the goal-directed behavior of biological systems at all scales with human intention a species-specific and highly evolved form of goal-directed behavior.
The function of a trait—as shaped by its evolutionary history—is primarily its role within a biological system. Functions or goals express normativity by establishing standards or norms for behaviors required to achieve both proximate ends (such as immediate physiological needs) and ultimate biological ends (survival, reproduction, adaptation, evolution).
Organisms are organic matter with a high degree of agential autonomy within an organism-environment continuum.
In biological explanation, the concept of function plays a central role in understanding how structures, processes, and behaviors contribute to the functionally unified organization and ultimate conditions of organism existence. It is functions (purposes, goals, roles) that give meaning to structures, processes, and behaviors. Without knowing their functions, biological phenomena become incoherent and unconnected facts. In this explanatory sense, function takes priority.
When functions are viewed in this way it is the agency of internally generated processes, manifested as external behavior, that plays a major causal role in both the short-term immediate life of the organism and its long-term evolution.
When functions are viewed only in terms of the history of evolutionary selection (etiologial or selected effects theories) the significance of organismal agency is diminished or subordinated to the external influences of natural selection. (Exceptional cases are encountered).
Functional Equivalence
Biological objects may be compared from at least two evolutionary perspectives – their physical ancestry, and functional equivalence. So, for example, likening the behavior of humans and plants by talking about both plant cognition and human cognition does not necessarily mean that plant experiences are the same as human experiences. This is not an equivalence of evolutionary structures, processes, behaviors, and experiences (homologs) but an equivalence of functions (analogs).
Physical functional equivalence, such as the wings of birds and butterflies, can be empirically validated. However, psychological equivalence is more contentious as it relies on interpretive frameworks influenced by our understanding of consciousness and cognition. So, for example, saying a plant ‘wants’ water seems blatant cognitive metaphor.
Assuming human agency and human cognition are highly evolved forms of more general biological traits, functional equivalence becomes more scientifically meaningful since it is grounded in empirically verifiable traits that conform to the biological axiom (to survive, reproduce, adapt, and evolve). When we say a plant ‘wants’ water, we acknowledge its observable biological behavior in response to water stress. This shifts the perspective from metaphorical fiction to functional equivalence grounded in empirical reality, with metaphor serving as a heuristic tool that resonates with human understanding.
Functional equivalence is the real, observable phenomenon, while metaphor is the figurative language used to describe and relate to it.
Using human psychological terms for non-human organisms infers functional, not physical, equivalence. It does not suggest a meeting of minds but a comparison of strategies used to address the same selection pressures - an equivalence of ultimate biological goals. However, it does create a problem for the semantics of cognitive language (see human-talk).
Biological Explanation
Biological explanations can be classified as either proximate or ultimate. Proximate explanations focus on the immediate mechanisms and processes behind biological phenomena, including genetic, developmental, and physiological factors specific to individuals or species. Ultimate explanations address the evolutionary reasons or adaptive significance behind biological phenomena, focusing on universal principles that apply across species and contexts.
Ultimate explanations in biology emphasize the autonomous behavior of organisms, including their structures, processes, and behaviors, as integrated and unified by the goals of survival, reproduction, adaptation, and evolution. As biological systems are goal-directed (agential), their explanations only make sense when these goals are explicit or assumed. Ignoring these goals leads to incoherent collections of unrelated facts. Teleological explanations in biology - in which goals, functions, and purposes are necessarily first in explanation but last in causation/realization (as natural ends or limits to behavior) - are a consequence of the inherent goal-directedness of biological agency.
Structure & Function
In biological explanations structure and function seem inextricably intertwined. Considering structures without understanding their functions presents an incomplete picture of life. Structure describes the physical components and arrangements, while function explains their purposes, activities, roles, and goals. Without connecting the two, biology lacks a critical dimension. We are inclined to treat structures as fundamental since form determines an object’s role and capacities, with functions then giving these structures purpose and context. However, in biological explanation function (purposes, goals, roles) must always come before structure if the structures are to be meaningful and, in this sense, it is function that is fundamental.
A whole must be comprehended if its parts are to make sense. A heap of building materials becomes vastly more significant when we have a concept of ‘house’. This claim to the primacy of function over structure is not an empirical claim about the world, it is a claim about the necessary form of scientific explanation, and therefore the way we do biology.
Biological Normativity
The biological axiom shows how facts about life processes inherently carry values. Organism behavior is not a neutral occurrence; it reflects flexible but goal-directed behavior (as 'preferences'). This intertwining of fact and value shows how the objective study of biology already includes a value-laden perspective that challenges the traditional separation between facts (what is) and values (what ought to be). Values emerge naturally from the very facts of biological existence.
All life is related through both the physical connections of organic evolution and the universally necessary functional and behavioral requirement of the biological axiom for organisms to survive, reproduce, adapt, and evolve. Evolutionary equivalence describes traits that evolved independently in different species but perform the same function e.g. bird and bat wings (homologous). Functional equivalence focuses on traits that perform the same function, regardless of evolutionary origin e.g. bat and butterfly wings (analogous). Evolutionary connections focus on ancestry and lineage through common ancestors and convergent evolution, while functional connections involve analogous structures and ecological roles based on similar functions.
As autonomous biological units (functionally equivalent to a 'self' with a 'perspective' or 'point of view') all organisms exhibit functional equivalence as their behavior conforms to the conditions of the biological axiom.
The biological axiom establishes natural values as the norms necessary for life to persist, driven by evolutionary pressures and the necessity for survival. It is functionally equivalent to a set of universal natural values such that biological normativity refers to the inherent or necessitating conditions for survival, reproduction, adaptation, and evolution. Universal biological normativity includes behaviors across species promoting these fundamental goals. Human normativity, encompassing norms, values, and rules guiding conduct, is a species-specific expression of the biological axiom.
Human normativity and morality - as the norms, values, and rules that guide and shape conduct, influencing what is judged right or wrong, good or bad, and acceptable or unacceptable - are highly evolved, conscious and deliberative forms of biological normativity, with the biological axiom underpinning human values and morality. From a functional perspective, the uniquely human combination of structures, processes, and behaviors is a highly evolved, specialized, and species-specific expression of the biological axiom, with functional equivalence in other species.
In sum, the biological axiom is functionally equivalent to a biological Code of Behavior, a set of rules and standards that underpin all life, including human values and morality.

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