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Biological hierarchy

Ladder of life: the template for biological hierarchy

Great Chain of Being – The Ladder of Life – The Natural Order

Illustration of the Ladder of Life from Rhetorica Christiana by Didacus Valades – 1579
A pictorial representation of the world order. Everything is arranged like the rungs of a ladder from top to bottom.
From God – to rulers – to common people – to animals – to plants – to rocks.

top to bottom – higher to lower
perfect to imperfect
spiritual to material
worthy to unworthy

God in blissful heaven above, the Devil in burning hell below

Everything has a God-ordained place in an eternal natural order of matter, moral significance, and spiritual importance

The connecting ‘chain of being’ – like a chain of command – runs up (or down) the center

Courtesy Wikimedia Commons – Duncharris – Accessed 29 Apr. 2016

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‘The necessary hierarchical structuring of our thought, language, and behavior imposes an illusory hierarchical structure on the world.’ 

PlantsPeoplePlanet – September 2024

This article is one of a series considering a ‘new biology’ that gives full consideration to biological agency and biological cognition.  Specialist articles address the way that we classify plants in both a general and scientific way.

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] 

Summary

How should students be introduced to the miracle of life and the foundational concepts of biological science?

The hierarchy of biological organization (biological hierarchy, hierarchy of life) is a popular entry point for the study of biology. The framework of hierarchical ideas we use to classify biological science is an informal classification of the living world that extends into our understanding of the relationship between biology and other sciences. It is embraced and respected by both scientists and philosophers as a valuable conceptual tool. But how accurately and effectively do hierarchical language, hierarchical imagery, and hierarchical thought reflect our current scientific understanding of biology and the world?

Hierarchies are grounded in the key notions of ranking and levels that arise from the process of prioritization that makes human action, thought, and language possible. This is a highly evolved, specialized, and conscious human characteristic that evolved out of the goal-directedness displayed by all biological agents as an inherited aspect of their biological cognition.

The world may be differentiated, but it is not ranked or prioritized – ranking is what we, as biological agents, do.  Without ranking/prioritization (a form of valuation) we cannot think, use language, or act. We therefore assume that ranks are part of the structure of the world. Levels, as hierarchical ranks, are abstract (theoretical, metaphorical, hypothetical) subjective entities that are open to multiple interpretations based on our interests and intuitions; they therefore have great explanatory appeal. When used in the biological hierarchy they provide a flexible and informative alternative to the species-focused scientific taxonomy of the Tree of Life.

Abstraction, however, does not provide a reliable connection to the world and so the overwhelming scientific impulse is to transform this hypothetical hierarchical architecture into something that is scientifically concrete and meaningful: to make the geometry of spatial metaphor a vehicle for scientific inference. And, indeed, when the metaphorical language of ‘up’ and ‘down’, ‘top’ and ‘bottom’, ‘higher’ and ‘lower’, ‘above’ and ‘below’, ‘vertical’ and ‘horizontal’ is translated into the language of  ‘levels of reality’, epistemology has been converted into ontology.

Giving the biological hierarchy scientific substance (reification) begins with the mistaken attribution of objective properties to subjective ranks. Levels are mistaken for things in the world when they assume the properties of the objects they denote (the conflation of ranks and taxa). Some scientific respectability is then maintained by replacing the abstract concept of level with the empirically based property of scale.

The biological hierarchy as a layer-cake ladder of explanatory metaphor separates and individuates (reifies) both the levels themselves and their hypothetical contents which are treated scientifically in the same way as actual objects in nature. This reification of levels results in a strange directional causal geometry – biological causation that proceeds like a chain of command both up and down the levels with the source of causal authority, not a big God at the top, but small foundational particles holding up the entire edifice at the bottom.

This is imagery that does not reflect current research into biological causation. It ignores, or diminishes in significance, the functional integration of molecules, cells, tissues, etc. into organisms as the primary agential units of biology with complex, dynamic, and goal-directed networks of communication.

Is this an apt metaphor? What would a flat or one-layer world be like? Why choose a ladder metaphor rather than a tree, web, or network? Where are processes and time in this spatial world?

These systems are unified and functionally integrated into organisms as primary autonomous biological agents with parts that are ultimately subordinate to the goals of the organism. it only hints at evolution through its layered increase in complexity, and it is grounded in abstract layered things rather than interacting processes. Levels as static hypothetical objects hark back to the old biology of morphology, anatomy, and taxonomy rather than a new biology that includes time and change, and therefore process and evolution – the dynamic processes of physiology, developmental and evolutionary biology, cognitive science, and agency.

Science has attempted to draw the biological hierarchy into its arena of empiricism, but the extreme abstraction of layered existence is a barrier to real-world comparison. The claim that, like other metaphors, this one can simplify, clarify, and facilitate understanding instead add a mostly untranslatable and unnecessary barrier of abstraction to biological explanation. Levels do not improve our understanding of reduction, emergence, biological structures, agency, or organisms. Using the logic of a hierarchical spatial metaphor as the conceptual architecture for scientific inference misleads more than it informs.[9]

Reality is not a multi-layered structure with its causes passing up and down from top to bottom and vice-versa. And biology is not the study of levels of organization such that each level contains the ingredients of its lower level with the entire edifice subordinate to, and supported by, its foundation in physics and chemistry. We need a better metaphor or, preferably, no metaphor at all.

At a minimum, biology investigates the causal interaction of the spatiotemporal structures, processes, and behaviors that engage the agency of organisms, their parts, and their communities.

Introduction – Biological Hierarchy

The notion of life as part of a vast cosmic hierarchy dates back in Western culture to at least the ancient Greek philosophers Plato and Aristotle, notably Aristotle’s scala naturae, which was later adopted and adapted by Medieval Christianity as the Great Chain of Being, or Ladder of Life.

The Ladder of Life is a clever use of abstraction: it simplifies and generalizes information, making it easier to understand, communicate, and manipulate. This hierarchy of being, or existence, conveys its verbal and pictorial message by using the ‘as if’ language of metaphor – everything is arranged from top to bottom on the interconnected rungs of a ladder (see illustration above).

The metaphor of the ladder was extremely effective: it represented everything there was, how it all interacted, what was desirable or undesirable, good or bad, and what it was all for.[21] It was a simple allegory of universal connection – a continuity of the spiritual, physical, and moral domains.

We might think that we have grown out of this metaphorical hierarchical religious image because science now explains the world more directly using the language of empiricism. But science, too, must find ways to represent and explain complexity.

How are scientists to classify everything? Also, where and how does biology fit into this overall scheme of things?

In the face of such generality and the need to find some purchase for our ideas, we fall back on our intuitions about the way the world is, and intuitions follow many paths. We might, for example, believe that everything reduces to numbers, information, space-time, energy, quantum field fluctuations, elementary particles, or mental sensations. Among our most powerful intuitions about the way to classify everything are: size (how big is it?), scope (what are the best categories of containment and inclusiveness i.e. where does it fit in a system of parts and wholes?), and degree of complexity. But does the universe ultimately reduce to one simple thing, or are there many things? Is the universe more like an organism, a clock, a ladder, a tree, a web, a brain, or a computer?  Who decides such ineffable questions, and on what grounds?

These are metaphysical questions that have never been resolved and science, too, must reach into metaphysics to find an explanatory foothold, so early biologists stood on the shoulders of their predecessors by using the conceptual framework of the Ladder of Life as their starting point.

The hierarchy of biological organization replicates the hierarchical conceptual framework of the Great Chain of Being, attempting to squeeze a scientific account of the organization of life into this ancient architecture.

The most widely accepted present-day versions of the biological hierarchy follow the Oppenheim and Putnam representation of hierarchical levels of organization of matter [15] . . . into molecules, genes, cells, tissues, organs, and whole organisms, sometimes extended into populations, ecosystems, biomes, and, ultimately, the biosphere – and sometimes further divided into additional sub-units.

These are the biological levels of popular imagination as illustrated and defined in textbooks and the internet; it is a conceptual framework referred to in the professional literature of both scientists and philosophers.

The hierarchy of biological levels of organization is a versatile and appealing conceptual tool that introduces a biological landscape of structures represented at many scales ranging from atoms to the biosphere.  It is a highly abstract representation of life framed within a metaphorical spatial structure of ranks or levels graded from lower to higher.

Oppenheim and Putnam ‘posited that levels are related via compositional relations that are structured in a stepwise fashion‘ and that ‘all constituents of the objects of study of one branch of science, or, the branch’s ‘universe of discourse’, are exhaustively related as wholes to the parts located at the next adjacent lower level, and as themselves parts to the constituents occurring at the next adjacent higher level‘ (layer-cake) such that ‘levels of science neatly map onto levels of nature‘. This account facilitates the reduction of higher to lower and the unification of science at the lowest level.[1]

Indeed, this is such a powerful abstract representation of biology that its hierarchical ideas and spatial metaphor can take on a life of their own. We can soon get lost in a tangle of explanatory convenience (epistemology) and scientific representation (ontology).

Ranking, as the creation of systems of prioritization – often expressed in human terms using the spatial metaphor of ‘levels’ – is not present in inanimate nature,[23] it is performed by biological agents, typically humans. What, then, is the role of prioritization in biological agency and and how do we account for its operation? This article describes prioritization as an essential component of human thought, language, and behavior – an aspect of the adaptive cognition of our human agency that evolved out of the adaptive goal-directed cognition present in all organisms. In humans, prioritization is both a conscious and unconscious cognitive process that occurs as part of the mental ordering process loosely referred to as classification. It is outlined here, in biologically universal theoretical terms, as ‘hierarchical thinking’.

This article examines the role of biological agency in addressing problems of explanatory abstraction, spatial metaphor, and agential modes of hierarchical thinking. It discusses the role of prioritization (ranking. use of levels) in biological cognition and its relation to the problem of scale in biology. Ways of modifying theoretical biology to address current difficulties and confusions are suggested.

Hierarchies

The wikipedia article on hierarchy provides some background on the concept of hierarchy and it may be read alongside the article on levels of organization in biology in the Stanford Encyclopedia of Philosophy as an introduction to this article. 

Biological hierarchical classification, with organisms organized into levels of increasing inclusiveness and complexity, originated with Aristotle (384-322 BCE) and was later adopted by Linnaeus (1707-1778). Both men pre-dated the ideas associated with Darwinian evolution. Because the Linnaean hierarchy arranged organisms according to their similarities and differences in a boxes-within-boxes (nested) structure it reflected evolution by modification from common ancestors . . . but this fact was coincidental. Though the Linnaean taxonomic hierarchy was evolutionarily informative, Linnaeus intended to provide a practical partitioning of the living world that would facilitate the allocation of names and therefore the business of scientific inventory and communication. Willi Hennig (1913–1976) later shifted emphasis from names and biological inventory to evolutionary relationships using a hierarchical framework of ideas that classified organisms based on the shared derived characteristics that defined clades as branches of evolution based on shared derived traits.

Significantly, the metaphor of levels as graded or prioritized layers is just one way of ordering of things in space. Possibilities are endless although obvious alternatives might include trees, webs, or networks. Our mental spatial imagery of the world can create cognitive dissonance as we picture hierarchy, on the one hand, as a system of nested containment and, on the other hand, a series of levels like the rungs of a ladder. Does science tell us what the world is ‘really’ like?

In the 19th century French philosopher Auguste Comte (1798–1857), in his ‘System of Positive Polity: or Treatise of Sociology’, used hierarchical ideas to express the relationship between academic disciplines. He suggested that science evolved from the simplest and most general scientific discipline to more complex and specialized fields. Comte’s hierarchy was associated with his Law of Three Stages. First are theological explanations in which natural phenomena are rooted in supernatural or divine powers (animistic, polytheistic, or monotheistic), which he treated as anthropomorphic. The second, metaphysical stage shifted explanations from deities to impersonal forces, occult qualities, vital energies, or entelechies (internal perfecting principles).  Comte argued that genuine explanations remained elusive during this phase. Third, the positive or scientific stage is characterized by reliance on empirical evidence and scientific knowledge, rejecting metaphysical speculation and focusing on observable phenomena and, Comte claimed, this was epitomized by sociology.

The development of human knowledge, according to Comte, passed specifically from Mathematics to Astronomy to Physics to Chemistry to Biology to Sociology, each science depending on the one preceding it, so astronomy provides the foundation for physics, which in turn informs chemistry, and so on. The hierarchy also considered the increasing complexity of subjects – maths deals with abstract concepts, while sociology addresses intricate social phenomena.

Today our analytic thinking tends to treat science as grounded in the specifics of chemistry and physics. For Comte, sciences become more specific and less general as you move up the hierarchy. Sociology, as the study of human society, was the most specialized and dependent science. Comte considered sociology the ‘crowning edifice’ of the hierarchy as it connected all sciences within the intellectual history of humanity.

Needless to say, Comte’s fine ideas are not universally accepted. This is because his reasons for establishing this particular hierarchy of levels is wide open to alternative interpretations. It is this subjective generality of hierarchies, as illustrated so well by Comte, that is examined in this article.

We associate science with an inflexible precision that only yields under the weight of evidence. Whatever devices we use to engage an audience, we also need a state-of-the-art representation of the biological world as indicated by our best science.

The hierarchy of biological organization is an abstract structure – a metaphorical spatial framework of interacting and graded levels – just one possible lens through which to view the biological landscape. We must understand the subjectivity of ranked levels their – ambiguities, benefits, and dangers. 

If the world is not literally a layer-cake of matter then what are the crucial criteria that determine the contents of each level (grouping criteria) and the reasons for their prioritization (ranking criteria)?

Hierarchies are agent-produced classifications that rank: they arrange objects into groups according to their similarities and differences (classification) and then organize these groups in prioritized order (ranking). Classification reflects an agent’s assessment of the objective similarities and differences between objects while ranking reflects more closely the arrangement of objects according to the interests (purpose) of the agent.

Metaphor

In science, metaphors[6] (‘as if’ talk) are often used as a way of coming to terms with complexity.

Cognitive scientist Steven Pinker in ‘The Stuff of Thought’ (2008) points out how we embed the difficult scientific concepts of space, time, matter, and causality in our everyday language. 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, and 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 metaphors, 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.’

While metaphors can simplify the world and facilitate creative thinking and empirical research, they can also misguide and confuse.

Spatial metaphor

The biological hierarchy frames biological objects within a spatial metaphor.

Scientific metaphors are useful when they provide insight into the world – when the logic of metaphorical inference guides scientific inference.

More than any other characteristic, it is ranking, as a form of prioritization, that characterizes what we mean by hierarchy. Perhaps surprisingly, prioritization is a pervasive aspect of our lives because the propensity to prioritize is part of our biological nature (biological cognition); it is an essential part of our actions, thoughts, and language (see ranking). To make the rather abstract idea of prioritization more concrete we represent it in metaphorical spatial terms as objects arranged in levels or ranks above and below one another like the rungs of a ladder.

This creates a philosophical dilemma for science as a reliable representation of the world. The contents of the world may be differentiated but they are not prioritized. Prioritization is what we as biological agents do because our biological nature determines that we must prioritize. So, how does our intuitive prioritization influence the scientific way that we represent the world?  Our intuition is to impose a (subjective) hierarchical structure on the world.  This may, of course, be treated as an objective feature of the world but its subjective (non-empirical) nature is always evident through its openness to interpretation.

The logic of the spatial metaphor tempts us to treat hierarchical levels literally as layers or levels of the world, when we know, for example, that although the world contains molecules, cells, tissues, etc., they are not organized into layers as represented in the biological hierarchy. Similarly, causation does not literally go up and down through these layers any more than temperature literally goes up and down. The world is not a layer cake as the biological hierarchy suggests. All this is a spatial metaphor.

Both scientists and philosophers will point out that the biological hierarchy is simply a convenient framework of explanation that is not intended literally (epistemology); it is not making actual scientific claims about the nature of the world (ontology). However. the frequent reference to the biological hierarchy and ‘levels of existence’ in academic literature treat the biological hierarchy as an authoritative representation of the world.

A key element of spatial representation is the depiction of change as a linear progression – which is, essentially, change happening in space. This is, for example, the imagery of the top-down, bottom-up transition of matter and organisms from simple to complex. Darwin unwittingly challenged this representation by representing evolution as change in time.

Metaphor can be useful: the challenge for science is to assess the pros and cons of the biological hierarchy and that is what this article attempts to do.

The biological hierarchy is a spatial metaphor. This article examines how closely this metaphor mirrors what science tells us about the world – whether this metaphor has any scientific value beyond the introduction of biological ideas. 

Scale

Scientifically, the biological hierarchy can only be justified if it informs our scientific understanding of the world.

The great advantage of the biological hierarchy – its abstraction and generality – is also its weakness. This is because the framing of biology within a metaphorical spatial architecture introduces the problem of translation – from metaphor to world. The abstraction of metaphor places no restraint on interpretation and intuition. It is precisely this explanatory freedom that makes the connection to the world so difficult. Translating an open-ended metaphor into a meaningful and uncontroversial account of the world is a major challenge.

Possible interpretations of ‘level’ seem limitless (see later) but clearly levels as ranks relate to degree and gradation (detail or granularity), and this is perhaps best expressed by the concept of scale. The kind of scale is less certain – is it a scale of size, containment, organic complexity – all of these, or more?

Regardless, the notion of scale has put some scientific bones on theoretical geometry. The abstract and almost incoherent concept of ‘level’ has been translated into the empirically meaningful concept of ‘scale’ and a worldly, albeit imprecise, connection has been established.

Levels of reality

We know the world is not literally sliced up into levels, but simply thinking in this metaphorical way can lead to serious scientific confusion.

A biological object, like an organism, can be described at many scales. That is, we can describe and explain it in terms of its molecular composition, its cells, tissues, or maybe its behavior.  These scales, or frames of reference, are not separate realities, they are simply different ways of describing the same thing.

Biological systems are closely integrated, their molecules, cells, tissues, etc., interacting in complex ways. The hierarchical division of biology into levels of organization ignores this integration which is replaced by theoretical layers that, over time, acquire a descriptive and explanatory independence.

Of course, it seems impossible that we could mistake metaphor and reality, but the widespread use of the expression ‘levels of reality’ in philosophy and science shows how readily we can fall into the trap of reification when we treat an abstract concept as if it were a concrete, tangible object.

Science attempts to understand and explain the world at many scales and these can acquire illusory independence as these ‘levels of reality’. So, for example, physics speaks of particles, fields, and forces; biology speaks of cells, organisms, and ecosystems; psychology speaks of mental states, intentionality, and cognition; and the social sciences speak of institutions, norms, and conventions.

These are not separate realities but different perspectives or scales of the same world which we describe in different ways as a matter of convenience – in a form that is appropriate to the questions being asked. Given sufficient computing power we could, in theory, describe a social event in terms of its constituent molecules but it is impractical to do so.

In hard scientific terms, the world is not stratified into levels (the world is not ranked: that is what we do) so there is no ‘fundamental level of reality’ in an ontological sense. Any ranking of the world relates to explanation, not the world itself (it is epistemological not ontological).

Abstraction and reduction provide increased economy, parsimony, and simplicity but can omit the information required for adequate scientific explanation. Knowing that organisms consist of molecules is not scientifically informative for most biologists. Scientific explanations are provided at the scale appropriate to the scientific question being asked.

The major philosophical objection to hierarchies concerns the difficulty of translating a spatial metaphor into a scientifically acceptable representation of the world.  The scientific temptation is to ‘make it real’, by converting hypothetical levels into ‘levels of reality‘, which begins with the synonymizing of ‘level’ and ‘scale’.

Tokens & types

The abstraction of hierarchical levels attracts a confusing range of theoretical objects as we try to distinguish between, on the one hand, tangible physical objects in the world and, on the other, objects denoted in a broad collective sense (including universals and collective nouns), the imaginary objects of metaphor or simile, and hypothetical objects that serve some purpose in description or explanation. For example, in the biological hierarchy, there are levels called ‘cells’, ’tissues’, and ‘organisms’. Are these hypothetical objects or actual objects in the world, or both?

This confusion can be alleviated by making a distinction between a token and a type – this is an ontological distinction between a general or abstract sort of thing (token) and its particular concrete instance (type). This is a critical difference between something in theory and something in the world.

In the Linnaean hierarchy the difference between a taxon e.g. Eucalyptus regnans, as a group of specified individuals in the world (type) and objects of this kind referred to in general terms using the word ‘species’, a designation known in taxonomy as a rank. This is a crucial distinction.

Hierarchical discussion must distinguish between theoretical and actual objects – between tokens and types. In the Linnaean hierarchy, ranks are token taxa while in the biological hierarchy no distinction is made between ranks and taxa (between tokens and types).

Hierarchical thinking

We think hierarchically.

This is a strange claim that needs some explanation, but it is important because hierarchical thinking influences the way we perceive the world – both the world of our human senses (human umwelt) and the world as interpreted by our best science.

How do our minds convert into meaningful experiences the flux of sensations – percepts, and concepts – that flows through the neurons of our brains? Sensation has no order, but if we are to survive in the world sensations must be given context; they must make sense. And to be meaningful they must be put in order.

The single outstanding feature of hierarchies is their organization into ranks or levels as a form of prioritization. Prioritization of action is a universal feature of the goal-directed behavior of every organism as a biological agent.

Among our various human mental faculties, four necessary and interconnected preconditions (innate predispositions) must be present if we are to operate effectively in the world: segregation, focus, classification, and valuation (prioritization, ranking). It is these mental ordering faculties that structure our mental world into meaningful experiences.

We know these are necessary preconditions because there must be things to be ordered (segregation) that are parts of a wider whole (focus), grouped according to similarities and differences (classification) depending on the purpose of the classification as determined by a biological agent (valuation, prioritization).

This is the way that we describe the differentiated matter that exists external to our bodies. We divide it up into objects/units/categories with varying degrees of autonomy (segregation), we organize these objects by similarity and difference (classification), and we distinguish those classified objects that can influence our lives (focus) according to particular interests or purposes (ranking).

These are critical mental processes influencing the intuitive way that we perceive and represent the world.

1. Segregation – division of the world into meaningful mental categories as representational units, both those of perception (percepts) and those of cognition (concepts) – many of these units we treat as objects in the world that are independent of our minds. Segregation and classification constitute an agent’s interpretation of the world (its umwelt).

2. Focus – our capacity to simplify awareness of the multitude of these mental categories by restricting the focus of our attention at any given time to a small proportion of those that are potentially available to us. That is, mental categories are organized into a foreground and background. Focus and valuation constitute an agent’s orientation (goal-directed perspective) on the world.

3. Classification – mental categories are not experienced passively they are – both consciously and unconsciously – compared and contrasted. They are grouped (classified) according to similarity and difference, depending on the purpose of the classification. Segregation and classification constitute an agent’s interpretation of the world (its umwelt).

4. Purpose/Valuation (ranking, adaptation, prioritization) – as biological agents our lives also depend not only on arranging mental categories into meaningful groups but also on ranking them according to their significance to our lives (our umwelt) – our needs, desires, purposes, reasons, and beliefs. This is done in preparation for action as we adapt to the circumstances of our existence. Focus and valuation constitute an agent’s orientation (goal-directed perspective) on the world.

These interrelated mental capacities (or theoretical principles) seem to operate simultaneously and with varying degrees of consciousness. The fact that they, mostly, take place without conscious effort (and must be present in all humans) suggests that they are innate. Without any one of these, we could not survive. Science itself is a search for order in the world – the order that is external to our minds but interpreted by our minds.

Our persistence as a species indicates that these adaptive faculties were historically useful, supporting our propensity to survive, reproduce, and evolve. We can therefore assume they are an effective means of representing the world (albeit a species-specific or human one).

Collectively, these four faculties (or theoretical principles) are a means of mental adaptation, both unconscious (as our attention constantly shifts from one thing to another), and conscious (as we make intentional decisions). Consider the automatic (unconscious) way we use hierarchical thinking to order our experience when driving a car (the constant interaction of selection, focus, classification, and ranking) as our mental focus constantly shifts from one thing to another. This ordering becomes conscious when we make conscious choices. Consider officially and collectively constructed formal classifications like the Periodic Table, Tree of Life, and train timetables.

We must always be alert to the possibility that the structure of our thought (and our species-specific human umwelt) can influence our conclusions about the structure and operations of the world itself (see Immanuel Kant).

Hierarchical thinking is deeply embedded in human thought patterns and is sometimes referred to using the less refined concept of intentionality.[19] It is our means of cognitive adaptation, our perception of the world as seen through the lens of our human umwelt.

Understanding this cognitive framework of hierarchical thinking in humans has applications in education, psychology, and even artificial intelligence. By recognizing how humans categorize and prioritize information, educators can devise better teaching methods, psychologists can understand biases in thinking, and AI developers can create algorithms that mimic human cognitive processes.

Science could be considered as the study of the relationship between the ordering of things in our minds and the order of things in the world. This is a hazardous process because we are habituated to this mental ordering process, and sometimes the order imposed by our minds does not correspond to the order in the world.

Hierarchies arrange objects into ranks or levels in a subjective and agential process of prioritization (valuation). ‘Hierarchical thinking’ refers to the highly evolved and conscious human form of mental prioritization that shapes our thoughts, structures our language, and guides our behavior – creating meaningful experiences. Without this prioritization, we could not explain, describe, or act. 

The ranking process (valuation) of human conscious hierarchical thinking evolved out of the goal-directedness that gives purpose to every living organism. It is the motivational and objective ‘life force’ that drives all biological agents. 

Parse Tree as a Nested Hierarchy

Parse Tree as a Nested Hierarchy

Hierarchical thinking is evident, for example, in the structure of our language.
Courtesy Wikimedia Commons – Tjo3ya – Accessed 3 January 2021

Biological cognitive adaptation

This account of hierarchical thinking outlines those mental processes necessary for orderly, meaningful, and purposive experience. It is called  ‘hierarchical thinking’ because it involves the ranking or prioritization of its objects: it is a goal-directed or intentional process. Hierarchical thinking is perhaps better described as cognitive adaptation because it summarizes the key characteristics of our constant mental adjustment to internal and external circumstances (our conditions of existence).

Human cognitive adaptation evolved out of more general conditions of biological cognition displayed by every biological agent. The connection between biological cognitive adaptation in general and its limited and highly evolved human form can now be described in more detail.

General biological concepts of agency and adaptation relate most meaningfully – not to cells, tissues, organs, or populations – but to the high degree of functionally integrated autonomy displayed by individual organisms within an organism-environment continuum.

Every organism, as a goal-directed biological agent, must reconcile its independent goals (ultimately its propensity to survive, reproduce, adapt, and evolve) with the constraints of its overall conditions of existence. This is a process of adaptation that involves the functional integration of internal conditions and external constraints and demands. It is this inner processing that precedes and motivates behavior. This is what might be termed an organism’s ‘life force’ – what it is that gives organisms their agency. Once considered a supernatural property, today it is explained by science in a straightforward and causally transparent way.  Though behavior may be ‘triggered’ by external conditions it is always ultimately a consequence of inner processing.

For our purposes, and following common usage, causal patterns that are ‘triggered’ internally (related directly to organismal goals) are treated as being ‘subjective’, while those ‘triggered’ by external sources are ‘objective’.

We associate inner processing with the mental processes of our own human conscious cognition, but the general characteristics of our cognition – the accession, storage, processing, and interpretation of information – are shared by all organisms. Human cognition is simply a highly evolved form of biological cognition that exists in both unconscious and conscious forms. 

The familiar key features of our own cognitive adaptation (hierarchical thinking) are evident in all other organisms.

Every organism must have the cognitive capacity to segregate (‘recognize’) the critical elements of its umwelt. It must also classify (order, process, differentiate between) these elements if it is to respond in a meaningful (adaptive) way: if it does not, then it cannot survive. The functional integration of subjective and objective constraints (the organismal response to both its internal and external conditions of existence) must have both focus (determining current significance and ignoring inconsequential factors) and prioritization (valuation, ranking) as an overall ‘assessment’ in relation to organismal proximate and ultimate goals (values, interests, beliefs, etc.).

In assessing external influences humans have a sophisticated sensory system (sight, sound, touch, taste, and smell, etc.) guiding perception. However, all organisms must interpret and integration objective information with the organism’s subjective proximate and ultimate goals. Thus every organisms has a perceptual and cognitive apparatus, no matter how crude.

The study of biological cognition accounts for the inner organismal functional integration of the internal processes that motivate or drive adaptive goal-directed behavior. It accounts for the way every organism makes sense of the world with its own unique mode of representing or ‘experiencing’ (its umwelt). So, cognitive adaptation encompasses much of what we understand by ‘experience’. In humans, this is not just conscious experience since it includes all the unconscious processing that contributes to experience. In non-sentient organisms this is unconscious experience. Thus human cognition is a highly evolved, limited, specialized, and conscious form of biological cognition.

That is, the universal and ultimate goals of all organisms (survival, reproduction, adaptation, and evolution) are grounded in the universal principles of biological cognition (the accession, storage, processing, and interpretation of information) by a cognitive process of segregation, classification, focus, and valuation (prioritization, ranking). Thus, universal functional principles are expressed by organisms in evolutionarily graded structural forms.

Biological cognition is the internal processing (‘life-force’) that motivates or drives the behavior of all organisms as biological agents – a necessary precondition for adaptive goal-directed behavior.

The study of adaptive biological cognition connects scientific classification systems to evolutionary biology since formal hierarchical scientific classifications use the prioritization (valuation, ranking, levels) of the human cognition that evolved out of adaptive biological cognition.

Hylomorphism - the combination of matter and soul to indicate what today we call 'agency'

Biological agents

Goal-directedness, biological cognition, mental prioritization, and agency

Aristotle used the word ‘soul’ (in De Anima) referring to the vital principle or animating force that imparts life to living beings: as that which distinguishes the living from the non-living. By ‘soul’ he was not implying something mysterious or supernatural like today’s meaning of ‘soul’, he was simply referring to the goal-directed (teleological) functioning and activities found uniquely in living organisms and approximating what today we call ‘agency’. Aristotle noted that the soul (agency) is manifest in different ways in different organisms according to their physical organization. Also, that more complex conditions were superimposed on simpler ones in a way that today we would interpret as a consequence of evolution by modification from common ancestry expressed in the containment of a nested hierarchy. He recognized three kinds of agency: in plants, it was the capacity for reproduction, nutrition, and growth (vegetative soul); to which, in some other organisms, was added the ability to perceive and interact with the world through the senses and movement (sensitive soul); and, in humans, the further capacity for higher mental activity such as reason, intellect, and the ability to think and reflect on the world (rational soul).

Image Courtesy Wikimedia Commons – Ian Alexander

Classification & Ranking

The universe may be differentiated, but it is not ranked or classified – ranking and classification are what evaluative agents do.

We are familiar with the classifications produced by conscious human deliberation, but the account above has shown how human hierarchical thinking is a limited and highly evolved form of the more general adaptive biological cognition that is found in all organisms as a critical element of their purposive (goal-directed) behavior.

As understood by biological cognition, the functional characteristics of classification are manifest in terms of the umwelt of the biological agent: it provides biological agents with meaningful information about their conditions of existence (experience), thus facilitating adaptation.

We engage in informal classification and ranking (both conscious and unconscious) every moment of our lives as we order our experience. In a narrower sense, classification is the differentiation of things according to similarities and differences while ranking is a process of prioritization.

To look more closely at hierarchical thinking in general, and the biological and Linnaean hierarchies in particular, it will help to define the key categories of hierarchical classification:

Purpose – the overall agential reason for the classification
Taxon (taxa) – a taxonomic group at any rank
Taxa selection criteria – reasons for the selection of taxa (explicit/implicit)
Grouping criteria – the characteristics that define group membership
Ranks – the universally generalized subjective (agential) designation for taxa
Ranking criteria – reasons for the  selection of ranks as vastly improved communication (not associated with objective criteria or hierarchical structure)

Unsurprisingly, building a hierarchical classification like the biological hierarchy follows the general pattern of hierarchical thinking. The overall objective, purpose or function of the classification is determined by the agent, in this case, the human agent. Segregation involves the formation of taxa, classification determines the various groupings according to grouping criteria, the focus is all-inclusive, and valuing (ranking, prioritizing) organizes groups into levels (ranks) according to ranking criteria.

The precision and utility of classifications is determined by the semantic depth and breadth of its classification categories.

Precision is achieved by using categories that are necessary and sufficient (classic). Having no semantic overlap, these categories leave no room for interpretation, for example, the classification of elements based on atomic number, but these classifications are quite rare. This contrasts with the commoner situation of fuzzy categories with overlapping meanings that are therefore open to interpretation. This feature is especially relevant to biology when considering evolution by modification from common ancestry. A human and a daffodil are as different as chalk and cheese but their common, though distant, evolutionary ancestry means that they share many genetic and biochemical similarities.

Utility is achieved by being aware of the semantic breadth and depth that is required. Semantic breadth offers multiple choices of entry (diversity of topics). For example, an extremely loose and fuzzy classification of living organisms might include roses, cats, fish, spiders, humans, ferns, and the like, while semantic depth relates to the number of choices for each category e.g. selecting ‘rose’ from this list yielding – floribunda, David Austin, climbing etc. With more choices comes increasing semantic depth.

Thus, a well-structured and user-friendly human scientific taxonomy aligns as closely as possible with its purpose. It selects the most appropriate taxa and grouping criteria, ranks, and ranking criteria. It engages the most penetrating semantic breadth (diversity of topics) and semantic depth (topic subcategories) possible to explore the purpose. It uses classical categories where possible and acknowledges fuzzy categories.

Classification

The philosophical confusion between ‘level’ and ‘scale’ in hierarchy theory is further complicated by another subtle distinction between ‘ranking’ and ‘classification’. This is exacerbated by the casual use of formal taxonomic language.

So, for example, we may differentiate people based on objective features such as height, eye color, or salary range. This differentiation may be referred to casually as ‘ranking’ but, technically, it only becomes ranking when an order of priority is established based on subjective, agential, ranking criteria. Or, we might speak of the objective ranking of balls by size. But, again, this contravenes formal taxonomic principles. Distinguishing different ball sizes is an act of classification based on objective similarity and difference – it is only when the balls are placed in a prioritized order of size that ranking occurs.

This situation can be explained another way. Every classification includes two critical elements: the taxonomic units (the objects being classified), and the taxonomic groups (the groups into which these units are being classified) as in the grouping of balls into different colors or sizes. Colors and sizes are objective criteria open to empirical investigation. However, hierarchies include an additional structuring element, ranking, as the subjective arrangement of taxonomic groups into prioritized levels.

Put simply, a level or rank is not the same as a classification category. In the Linnaean hierarchy this technicality is made obvious because ranks are given names like ‘species’ and ‘genus’ and these ranks contain taxa like Homo sapiens and Homo. However, even professional taxonomists confuse ranks and taxa in casual conversation.

In the biological hierarchy, there is no clear distinction made between ranks and taxa – the rank of ‘cells’ contains the taxa ‘cells’. This adds complication to an already abstract notion of levels. This might seem inconsequential, but it fails to clearly distinguish between cells (as classification categories) which are objective features of the world, and cells (as ranking categories or levels) which are established by human subjective judgment.

Assessing the scientific significance of the relationship between agents, ranking, and classification is a complicated matter. Overall, classification tends to be more objective than ranking because it is usually focused on the grouping of items based on objective criteria and observable characteristics while ranking relates more to agential goals. Classification and ranking each combine objective and subjective elements, depending on their context and purpose, the degree of subjectivity being determined by the extent to which agential perspectives influence judgments and outcomes.

This is important because, both philosophically and scientifically, much turns on the distinction between theoretical concepts and objects in the world. In the Linnaean hierarchy, ranks are conceptual categories, while taxa represent real groups of organisms that exist in the natural world. In the biological hierarchy, the distinction between ranks and taxa is unclear and is assessed by context.

Classification and segregation of the meaningful elements of that organism’s experience (its umwelt) are the way that organisms orientate themselves to the world. 

In scientific taxonomy, the names of ranks denote abstract levels of organization that help build a structural framework to a classification, while the names of taxa usually denote concrete objects (e.g. organisms) in the world. Classification establishes similarity and difference: ranking establishes priority. The objects of classification may be grounded in the world, but ranking, as prioritization, is grounded in the subjectivity of an agent.

Grouping criteria

In a strict Aristotelian nested hierarchy the taxonomic groups are distinguished by essential characters (essentialism)  i.e. conditions that are logically both necessary and sufficient, which ensures that the categories used in the classification are logically mutually exclusive (classical categories). This exclusion criterion for the nested groups of the Linnaean hierarchy makes it ideal for the allocation of names used as unique identifiers but inadequate as a way of distinguishing biological entities that combine uniquely defining characteristics with shared characteristics that are a consequence of common ancestry.

Ideal grouping criteria provide necessary and sufficient (mutually exclusive) conditions, but these conditions cannot be met by objects with common ancestry. 

Ranking

The single factor that distinguishes hierarchical classifications from other forms of classification is the use of graded and prioritized ranks as hierarchical levels.

But, as illustrated by biological cognition, ranking, as prioritization, is not just a pervasive human trait, it is displayed by all biological agents as a critical element of their goal-directed agency. It is closely associated with the more familiar concepts of valuation, adaptation, preference, decision-making, and problem-solving.

In the human case, if everything exists ‘equally’ in our minds, then nothing can happen – there is no motivation for mental activity. Only by prioritizing the objects of our experience can thought proceed. If we cannot prioritize, we cannot think. Thus ranking, as prioritization, shapes our thoughts, structures our language, and guides our actions;  it creates meaningful experiences and is the driver of the goal-directedness that gives purpose to every living organism.

Since prioritization is a cognitive phenomenon that facilitates our orientation to the world by providing focus to our thoughts, behavior, and language and, as it involves the organization and structuring of knowledge, it may be considered strictly an epistemological phenomenon. Science, however, investigates the order (and therefore prioritization) that we assume exists in the world itself as a certain structure or hierarchy in which some factors inherently possess more causal power or significance in the fabric of reality – such as the way living organisms prioritize adaptive responses to their survival.

The philosophical and scientific difficulty with ranks and levels (and their ranking criteria) relates to the many different senses, applications, and degrees of subjectivity with which these words are employed as epistemology and ontology become intertwined.

What counts as empirical evidence for ‘levels’?

Ranking criteria

There is a distinction between reasons for classifying (grouping criteria), and reasons for prioritizing (ranking criteria).

(Ranking criteria – The discussion of ranking (above) concluded that the use of ranking terms facilitate abstract or universal communication about groups of organisms (taxa) in their objectively determined and graded scales.

Ranking has no objective criteria, nor does it constitute a structural division within a classification system. It is simply an abstraction that facilitates communication. In both the Linnaean and biological hierarchies this relates to scale. We cannot communicate effectively about organisms by always considering them as units – sometimes we need to speak in abstract terms about their broader groupings. These broader groupings are, on the one hand, classification categories based on shared and diagnostic objective characteristics e.g. the genera Eucalyptus and Homo.  One major difficulty is that the subjective imposition of levels or layers on the structure of nature does not translate comfortably into tree-like evolutionary patterns. For example, the characteristics that define genera in one floral family may not seem equivalent to those in another family. Descent with modification leads to graded transitions, not levels of organization.)

The conditions that determine or define a rank or level in a hierarchy are known as ranking criteria and these may be as many as there are agential goals.

Significantly, The International Code of Nomenclature for Algae, Fungi, and Plants does not define ‘rank’ but its Preamble points to nomenclature as ‘dealing on the one hand with the terms that denote the ranks of taxonomic groups or units, and on the other hand with the scientific names that are applied to the individual taxonomic groups’. 

While Linnaean taxonomists might differ in their interpretation of groupings of organisms (taxa) their reliance on objective similarities and differences means that they carve up the biological world based on objectively justified groups (taxa) that may be empirically refined as more data emerges. Communication about groupings is greatly facilitated by their arrangement into a system of multiple graded scales so that, for example, Eucalyptus regnans, Eucalyptus, Myrtaceae, and Myrtales are the names of progressively more inclusive taxa.

If taxa are so efficiently and objectively divided up at multiple graded scales then what purpose is served by the introduction of subjective/abstract levels?

This question is soon answered when we attempt to communicate about organisms without using ranks (try it). This is because we need to communicate about organisms at various scales and in a general and abstract (token) way without reference to (type) groups as taxa. In everyday conversation, we sometimes want to talk about specific birds like pelicans, budgerigars, and sparrows, and sometimes we want to talk about birds in general. We need simple ways of expressing degrees of abstraction. Scientific groupings are more complex than this but the principle is the same.

The names of taxa (Eucalyptus regnans, Eucalyptus, Myrtaceae) refer to objectively defined groupings of organisms at progressively more inclusive scales, while ranks (species, genus, family) are universal designators. Universals enable broad, abstract discussions that facilitate generalizations and theoretical frameworks while particulars focus on specific concrete instances. Without ranks the living world becomes much more difficult to organize, understand, and explain. We need ranks if we are to communicate efficiently about biodiversity when, for example, we need to speak about organisms in general (as species, genera, etc.) not just particular taxa (like Eucalyptus regnans or Eucalyptus).

Formal taxonomic ranks are based on a scaled measure of subjective (abstract, agential) criteria of an agent, not on the characteristics of the objects being classified. Ranking is a response to the content of classification and is therefore informed by objective factors but its operation does not engage objective factors.

Confusingly, based on formal taxonomic principles a ‘rank’ in the army is a scaled measure of authority, power, or somesuch, it is not the set of group-determining characteristics that determine a Private, Corporal, etc. Army ‘ranks’ are, in strict taxonomic terms, taxa.

We now have sufficient information to define a rank more informative than ‘a level of classification in the taxonomic hierarchy’.

Ranking, in both formal and informal hierarchical systems, is most informatively regarded as a subjectively scaled (graded) arrangement of taxa (the objects of the classification). The scope of scale type is as broad as subjective possibility.  

A rank in the Linnaean hierarchy is an abstract or universal (token) way of denoting objectively informed (type) taxa at graded scales as (degrees of inclusion). The biological hierarchy confuses because its levels are not explicitly token or type, and the subjective scale type is unclear, though generally related to the degree of inclusion, size, or degree of complexity.

Needless to say, this confusion and conflation of ideas and semantics is not helpful.

Taxonomic principles may have clarity but the everyday use of taxonomic language is ambiguous in both formal and and informal contexts – even as used by taxonomists. It is not always clear whether terms are being used in the type sense of taxa, or the token sense of ranks. Are species and genera taxa? Is Eucalyptus regnans a species, a taxon, or both? If ranks and taxa are so distinct then why do we say that the genus Eucalyptus is in the family Myrtaceae?

This difficulty means that we conflate ranks and taxa. But to do scientific taxonomy according to its precepts means that there is a taxonomically correct or incorrect way of doing things. Ranks are not taxa.

Technically, Homo sapiens is a taxon at the rank of species but we are inclined to assume, for example, that species are determined by their morphological, ecological, genetic, etc. characteristics.  But, as we have seen, ‘species’ is a term denoting rank so, technically, this is a crucial error. A textbook might indicate that ‘species’ denotes groups of similar organisms; genera are groups of closely related species that are more similar to each other than to species in other genera; families are groups of related genera that share common characteristics, and so on.

Formal taxonomic concepts are not observed in everyday usage. A cardinal case of ‘rank’ occurs in the army where ranking criteria are defined by factors like time in service, performance evaluations, education, position availability, merit, recommendations, military needs, and promotion boards. But if this is treated as formal taxonomy then the ‘ranks’ of Private, Corporal, Sergeant, etc. must be described as taxa whose ‘ranking criteria’ turn out to be objective grouping criteria. 

What about the ranks used in the Linnaean system of classification and the hierarchy of biological organization?

Ranks do not have objective characteristics as taxa do. But the impulse, especially among scientists, to overcome subjectivity, abstraction, and ambiguity by invoking objective criteria is all but irresistible. When we say ‘ranks represent different levels of organization in the classification of living organisms’ we confront the cognitive dissonance of the implication that ranks are levels of existence, levels of organization, or somehow related to something concrete in the biological world like phylogeny or morphological characteristics.

Formally established ranks are the universals (tokens) of type taxa. They are subjectively (agentially) determined and have no objective properties – no grounding in phylogenetic, morphological, or other objective characteristics, including scale. They do not contribute to the structure of the hierarchy. Ranks are informed by taxa but do not assume their objective characteristics or any structural role within the hierarchy.

Rank-value

The fact that hierarchies are agentially (subjectively) prioritized means that their constituent objects are value-laden by degree. The word ‘value’ implies a cognitive ‘preference’ based on biological goals.

In traditional human social hierarchies – like those of the military, corporations, and the church – the graded ranking criteria relate to moral worth, political power, authority, or functional role. For many people, even today, these hierarchical ranks are not human subjective creations of convenience, they are part of an objective cosmic order.

Our everyday language is saturated with metaphorical spatial hierarchy talk that harks back to these times. Society is ranked metaphorically into ‘upper’, ‘middle’, and ‘lower’ classes. We use expressions like ‘top cat’, ‘low life’, ‘high society’, ‘highbrow’ and ‘lowbrow’, ‘high hopes’, ‘bottom dollar’, ‘low morals’, etc.

We are therefore accustomed to ranking taking on a value and, in general, ‘higher’ is ‘better’. This tendency for hierarchies to value their objects somehow is referred to here as rank-value, which is an expression that emphasizes the agential, goal-directed, and therefore ‘subjective’ character of ranking.

Scientific ranking
Scientific practice contrasts with this familiar everyday use of ranking/valuation because the ranking of items for subjective reasons by an agent does not fit well with scientific ideals.

When Darwin drew in his diary a branching evolutionary tree of life, he understood that living organisms – the plants and animals at the tips of the branches of his tree – were not engaged in a process of moral improvement. They were not aspiring to become more like humans or to get closer to God, they were the organic outcomes of natural selection: responses to the problems posed by their conditions of existence.

Darwin was attempting to represent the community of life dispassionately, without any value judgments – the world as it is, not as we might want or expect it to be. Science attempts to provide us with the best possible representation of the world that exists independently of our minds. But there cannot be a view of the world from no place, at no time, and with no observer – everything as seen from the point of view of the universe. We therefore try to minimize, or make transparent, any subjective influence on our understanding and explanation of the world.

After Darwin, fewer and fewer scientists regarded organisms as existing within some kind of cosmic moral order – they just exhibited evolutionarily related similarities and differences. Ranking, in scientific systems of classification, was based on comparative data, not relative value. Organisms could be more or less complex, perhaps more or less adapted to their environments, but they were not of greater or lesser worth . . . they were simply different in a range of measurable characteristics. Old ideas die hard though, lingering on in diluted form when we speak of ‘higher’ and ‘lower’ organisms.

So, when we rank the universe and its contents – including its living systems – what determines the ranking criteria? To think at all, we must rank. But any ranking/valuation is a human subjective imposition – and as a subjective imposition, it is open to interpretation. Despite this, scientifically we still seek a natural order that will facilitate communication, prediction, and management.

Things may be bigger or smaller in the universe, but the universe does not rank them relative to one another, we do. In the impossible attempt to eliminate the subjectivity of ranking, we fall back on our intuitions about the way the world must be, independent of us. Inevitably this ultimately reflects the structure of human thought, human interests, and human values – utility, interpretation, and context.

So, for example, the ranks used in plant classification put order into the world’s vegetative diversity by providing abstract terms for taxa (our attempt to find the order of the plant world as it exists outside our minds) that facilitate nomenclature, communication, explanation, prediction, and management.

Scientific ranking is often like a pragmatic or utilitarian subjective dimension of organization that is superimposed on objective criteria.

It is interesting to compare the Linnaean hierarchy with the Periodic Table of elements as a way of understanding the critical classificatory ideas of the Linnaean hierarchy. The Periodic Table is a neat classification with elements arranged sequentially by atomic number into 18 vertical columns whose elements share chemical properties due to their filled outer electron shells. Each horizontal row corresponds to a new energy level (shell) for electrons, the atomic number increasing down the table. The table can also be divided into blocks of elements with different electron orbitals. This is a neat division of taxa into practical groupings based on objective characteristics. Though the arrangement is by numerical sequence and there is some spatial arrangement into practical blocks, there is no obvious prioritization in the form of a hierarchical chain of command (causal chain), source of authority, or prioritized level. The Periodic Table does not need hierarchical ideas. There is a limited requirement for universal ranking terms, although sections of the table have collective names e.g. ‘inert gases’.  Formal and precisely defined scientific classifications, like the Linnaean hierarchy, do not use ranks as tools to facilitate classification (a role performed by taxa), instead, ranks become tools that facilitate communication. Ill-defined classifications like the biological hierarchy do not distinguish between ranks and taxa. 

The functional integration that establishes the agential autonomy of every organism is an adaptive reconciliation of its internal goals with its mostly external conditions of existence.

Segregation and classification are concepts that express, in a summary and abstract way, the processing by which an organism establishes its mostly external (objective) conditions of existence. This assessment must then be reconciled with causation generated by internal (subjective) goals as propensities towards particular ends.

Both the organism’s assessment of its external conditions of existence and its internal goals are constrained by the physical features that determine the organism’s umwelt. 

Scientific classifications attempt to minimize subjectivity but agents influence the purpose of the classification, the choice of taxa, and the choice, and interpretation of ranking and grouping criteria.

To better understand what is meant by ‘levels’ in a particular instance of hierarchical classification both the ranking criteria and the grouping criteria must be made explicit.

Ranks and taxa

In formal scientific taxonomy, ‘rank’ refers to the level or position of a taxon (a designated group of organisms) within a hierarchical classification system. Grouping criteria are the objective characteristics used to define or circumscribe a taxon and ranking criteria are the conditions used to assign taxa to specific ranks.

This terminology aligns with what we understand as the necessary conditions of hierarchical thinking – it describes what is going on in the world. Ranking criteria are not the same as grouping criteria, and ranks are not the same as taxa.

Ranking is performed by an agent (typically a human) and it reflects agential goals, not the objective characteristics of taxa. Ranks and ranking criteria are subjective constructs that help to organize information, such as that of biodiversity. While agents perform classificatory grouping, they do so with both groups and grouping criteria justified by objective criteria. All this has important consequences.

Ranks (levels) have ranking criteria that are subjective and obscure, but they are always associated with taxa that are objectively defined. Given the obscurity of ranking criteria, the scientific mind seeks refuge in the security of the objective criteria of taxa so, even in formal taxonomic literature, subjective ranks are sometimes defined using the objective characteristics of taxa (or other factors may be implied).

How does all this cash out in practical terms?

The Linnaean hierarchy represents the biological world using empirically defined taxa expressed at various scales (progressively more inclusive and objectively defined groups) e.g. Eucalyptus regnans, Eucalyptus, Myrtaceae, etc. The ranking terms ‘species’, ‘genus’, ‘family’, etc. associated with these taxa do not extend or add to the structure of the classification; instead, they allow taxa to be discussed in abstract terms. It might seem that ranks address the problem of scale by giving names to groups prioritized by their degree of inclusiveness, but this is already achieved by the scaling of taxa.

In Linnaean classification, ranks as designations associated with taxa, allow taxa to be spoken of in universal terms (the ranking criterion). Thus Eucalyptus (a taxon) is a genus (the name of a rank). The word ‘genus’ facilitates discussion of objects comparable to one another – objects of equal taxonomic status – without naming each taxon individually. Ranking words denote token (theoretical, abstract) taxa rather than type (actual) taxa, but they are not the taxa themselves. Ranks do not have the objective characteristics of taxa.

How does all this transpose to the hierarchy of biological organization?

The ranks of the biological hierarchy are not given rank names: that is, the names of its ranks are the same as its taxa e.g.  ‘molecules’, ‘cells’, ‘tissues’, etc. Ranks and taxa can only be determined by context adding further ambiguity to the distinction between ranks and taxa.

In casual everyday use, terms like ‘level’, ‘rank’, ‘taxon’, and equivalents are used in such a broad sense as to preclude any meaningful distinction.  The conflation of ranks and taxa is so pervasive that the opportunity to distinguish between them only arises under formal conditions. Even among professional taxonomists, there is a confusing and unnecessary conflation of the terms ‘ranks’ and ‘taxa’. It is sometimes said, for example, that ‘genus’ is a taxonomic rank (level) that is used to organize organisms. But levels, as ranks, do not determine the structure of the hierarchy – the structure of the hierarchy is determined by the organization of taxa. Taxonomists claim that they determine the rank of a taxon based on objective characteristics – but on closer inspection, it is not the rank but the taxon that they have established. Even among taxonomists, ranks are connected to taxa in ambiguous ways. For example, if Myrtaceae is a taxon, and family is a rank, the sentence ‘Myrtaceae is a family of flowering plants‘ (which would be universally accepted by botanists) is a confusing shorthand for ‘Myrtaceae is a taxon at the rank of family within the classification of flowering plants’. It is probably for such reasons that the ICN does not define ‘rank’ in its glossary.

In common usage, this conflation is inconsequential but in scientific hierarchies and philosophical discussion, the formal distinction between ranks and taxa distinguishes between subjectively useful categorization and the objectively determined characteristics of organisms – between the epistemological and ontological.

Ranking in a formal sense, as applied in the Linnaean hierarchy, is a form of prioritization that is determined by subjective (internal) agential goals (interests, values). Ranks are a descriptive and explanatory tool that vastly enhances communication. In formal scientific hierarchies ranks are token (abstract or universal) generalized names for taxa. Ranks of the Linnaean hierarchy e.g. ‘species’ and ‘genus’ generalize the names of taxa like Eucalyptus regnans and Eucalyptus. There is no nomenclatural distinction between the token ranks and type taxa of the biological hierarchy which must be established by context.

It helps to distinguish two senses of rank or level, the formal and informal. The formal sense is a subjective generalization of a taxon (a taxon as a universal which may be given an identifying name): it is a subjective deice with no objective associations and no structuring role within the hierarchy. The informal sense assumes additional objective properties and structural roles within the hierarchy. 

The Scientific Universe

What is the hierarchy of biological organization telling us about life and its place within the general scheme of things?

What are the criteria that rank (prioritize, value) one biological object over another?
The abstract spatial notion of ‘level’ is open to seemingly limitless interpretation, most of which relate to scale.

An inventory of kinds of biological things
Spatial extent of these things (size)
Frames of explanatory reference
Nested levels of physical organization (degrees of inclusion)
Degrees of organic organizational complexity
Spatiotemporal scales of existence
Kinds of mechanistic processes
Academic disciplines
Paths of causation (supervenience)
Kinds of functionality

Courtesy Wikimedia Commons

What are biological levels of organization?

It is time to summarize the thinking so far.

The world may be differentiated, but it is not ranked: ranking, as the organization of objects into prioritized levels, is an activity uniquely associated with biological agents, typically humans.

The organization of the world into hierarchical levels can be used as an explanatory or heuristic tool (epistemology) but it does not reflect the way the world actually is (ontology). The world is not literally composed of layers as depicted in the biological hierarchy. Does this spatial metaphor have any scientific value beyond the introduction of scientific ideas? In what ways can it be used to guide scientific inference?

Human understanding of ‘levels of biological organization’ derives partly from the historical intuition that the world consists of ‘levels of existence’ or ‘levels of reality’. Used in this way, the word ‘level’ is a spatial metaphor so abstract and vague in meaning that it borders on incoherence. Because there is no obvious correspondence between ‘level’ and something in the world, it is interpreted in many, sometimes unrelated, ways – albeit ways that often address our intuitions of scale, notably of size, progressive containment, and organic complexity (see illustration above).

If levels of existence are so obscure in meaning, then where does this intuition about the structure of reality come from? We need a psychological (agential) account of this impulse.

Human thought, language, and behavior are only possible because we prioritize some things over others. Our thoughts always have a focus, our language always has a subject, and our behavior always has a goal. Prioritization, as a form of valuation, is therefore an integral part of our cognition. Without prioritization we could not think, speak, or act. Because they are so pervasive in our lives, we assume that prioritization and hierarchy are part of the world rather than convenient explanatory constructs: the hierarchical structuring of our thought, language, and behavior imposes an illusory hierarchical structure on the world.

This mental prioritization is a highly evolved and limited form of the more general goal-directedness of the adaptive biological cognition displayed by all biological agents.

Is it possible to describe, in general terms, how the interaction between a biological agent and its conditions of existence can become a meaningful experience?

Here it is suggested that it is the necessary preconditions for cognitive adaptation that provide a biological account of the impulse to prioritize, rank, or arrange into metaphorical hierarchical levels. Four preconditions for human hierarchical thinking are here treated as highly evolved and interconnected universal principles of biological cognition. These are: segregation into units of experience, classification (arrangement) of these into related groups based (mostly) on their objective characteristics, the focusing on those of significance to the agent, and the functional integration of these elements with agential goals, as a prelude to behavior as prioritization.

The current biological approach has been to clothe the conceptual spatial architecture with scientifically validated ideas in a process of reification.

The approach adopted in this article is a form of clarification or interpretation that subjects the biological hierarchy to a conceptual analysis of its structure as a classification system.

Each of these approaches will be discussed in turn.

Reification

The explanatory freedom of ‘hierarchical levels of organization’ does not translate easily into the world. Our scientific impulse is to transform this metaphor into something more than just a vehicle for ideas: we want to make it ‘real’ by converting conceptual architecture into something objective and tangible – to turn a concept into a thing (reification).

This is where metaphor is most dangerous. Does the structure of this spatial metaphor provide a reliable representation of the structure of the world: can we safely use it to  guide scientific inference?

The reification of ‘hierarchical levels of organization’ begins by replacing the obscure notion of level with the more specific and empirically meaningful idea of scale or degree. Vague ‘levels of organization’ then become more tangible as ‘degrees of organic complexity’, or some such.

Though seemingly unproblematic, this reification of levels of organization (cells, tissues, organs, organisms, populations, etc.) separates and individuates levels/degrees as if they had an independent existence. The existential status of the objects being discussed then becomes confused. This elevates the autonomous significance of biological objects like cells and tissues while, at the same time, diminishing their functional role in the lives of autonomous organisms.

In simple terms, the hierarchical spatial metaphor might indicate critical biological ideas, but it is an inaccurate and confusing depiction of the world.

Conceptual analysis of classification

Faced with the extreme abstraction of hierarchical levels of organization and the failure of reification to give the biological hierarchy scientific teeth, the temptation is to provide interpretive clarification that brings the hierarchy into the empirical arena. But, individual interpretations require strong justification and, given the obscurity of ‘levels’, are unlikely to be accepted.

The approach in this article has been to adopt a different kind of interpretive clarification. It has attempted to provide a biological account of the origins of the hierarchical impulse and the way this impulse is applied during the process of classification. This is an analysis of the conceptual properties of the biological hierarchy as a taxonomic hierarchical classification and, more specifically, the logical conditions of strict nested hierarchies

Only through the formally defined taxonomic terms of scientific classifications is it possible to discriminate meaningfully between the various conceptual elements of hierarchical classification and their connections to biological cognition.

The most important finding from this analysis is that our casual understanding of classification does not discriminate clearly between the groups or objects being classified and their grouping criteria, or between ranks (levels) and their ranking criteria. This close analysis reveals ranks as subjective (agential) elements of classification as distinct from the objects they name (taxa). So, the informal biological hierarchy does not distinguish between ranks and taxa and so ranks are assigned the objective properties of the taxa they denote in a further act of reification. This invites ranks to be treated as part of the structure of reality or the world rather than creations of (subjective, agential) biological cognition.

In a formal taxonomy, such as the Linnaean hierarchy, the word ‘level’ is treated as synonymous with ‘rank’ which, under scrutiny, is determined by subjective agential criteria. But, even in formal taxonomy, ranks are often erroneously linked to the objective criteria of taxa. 

While a casual understanding of ‘level’ assigns it objective characteristics, closer analysis distinguishes between the subjective (agential) notion of level or rank and the objective characteristics of the objects (taxa) it denotes.

Linnaean hierarchy & biological hierarchy

The benefits of studying taxonomic principles become apparent when comparing the generalized hierarchy of biological organization with the formally defined elements employed by the Linnaean taxonomic hierarchy. This gives some conceptual clarity to the discussion.

Unsurprisingly, the general cognitive principles of hierarchical thinking are evident in formal scientific hierarchical classifications like the Linnaean taxonomic hierarchy: the segregation into taxa, the formation of these taxa into groups in a classification system organized according to the purposes (priorities, goals) of a biological agent.

Both the Linnaean hierarchy and biological hierarchy address the problem of scale by considering objects of progressively greater containment. The formal logical conditions of these nested hierarchies provide further insight into the notion of ‘levels’, both those of explanation, and those of existence.

Insights come from two sources: the defining principles of hierarchical classification, and the specific logical principles that apply to strict nested hierarchies – the latter being significant because of the notion of progressive containment usually applied to the biological hierarchy.

Principles of hierarchical classification

The Linnaean hierarchy provides some conceptual clarity be distinguishing between ranks and taxa, together with ranking criteria and grouping criteria. This provides some assistance in determining subjective and objective elements and influences at play in the process of classification – including the purposes or functions of both the overall classification and its parts.

Linnaeus’s classification of living organisms developed out of Aristotle’s use of nested hierarchies to classify living organisms.

Using the species as a basic unit of classification the Linnaean hierarchy classifies organisms into progressively more inclusive taxonomic groups (taxa), each group defined by its shared objective characteristics.

These taxa are named using generalized (universal or token) terms by, for example, referring to taxa of a certain kind as ‘species’ rather than naming individual taxa. This has several advantages: it provides a standardized reference point, and it greatly facilitates communication. The universal designations ‘species’, ‘genus’,  ‘family’, and ‘order’ are thus token taxa called ranks. Ranks are human subjective constructs that facilitate communication about taxa: they do not have the objective properties of taxa, nor do they have any structural role within the hierarchy. That is, the objective properties of the taxa determine the ‘levels’ of the biological hierarchy but, for ease of communication, these are given universal names referred to as ranks. For example, all past and present humans Homo sapiens, Homo floresiensis, etc. are grouped into the taxon Homo with ‘genus’ being the universal term, known as a rank, attributed to groupings of this kind.

Progressively more inclusive taxa fragment the biological world into scaled units, while the use of universal terms facilitates explanation and description. Taxa carve up the biological world into manageable-sized categories whose ranking designations then facilitate identification, nomenclature, and communication. The association of similar organisms adds predictive power. Linnaeus’s skill lay, not so much in the use of binomial nomenclature that preceded him. He established an accepted system of biological cataloging that underpinned the inventory of world biota taking place during the 18th and 19th century period of European colonial expansion and influence.

Both the Linnaean hierarchy and biological hierarchy are classifications of living systems – so what are their separate roles within biology?

Previously it was determined that the scope of a hierarchical classification is determined by its semantic breadth and depth. Semantic breadth refers to the range of meaning encompassed by its various levels (the groupings of taxa) while semantic depth refers to the meaning associated with the range of characteristics used to establish each grouping (level).

The Linnaean hierarchy uses species as its basic unit (a grounding taxon). The levels of this hierarchy are then composed of progressively more inclusive groupings of species. This is a classification built out of species bricks.

The basic unit of the biological hierarchy is not immediately self-evident but hierarchies, by definition, have prioritized ranks (levels). Our reductive analytic scientific perception of the world (wholes are explained in terms of their parts) treats the lowest level of the hierarchy as foundational, accounting for the composition and operation of higher levels.

Scientific classification attempts to minimize subjectivity, but there are many ways that a hierarchical classification can be influenced by the cognitive (subjective) interpretation of the agent. It includes: the original selection of purpose; the choice of taxa (e.g. basic units of life of biological hierarchy and Linnaean hierarchy as gene, cell, or organism/species; the grouping criteria. Choice of taxa and grouping criteria can depend on the subjective interpretation of objective evidence. So, in biological classification, taxonomists might disagree about the choice of characters and their relative biological significance, as they group organisms differently depending on their interpretation of objective data.

Close examination of the notion of ranks (levels) in the Linnaean hierarchy reveals them as universal (token) designations for actual (type) taxa. They are subjectively (agentially) determined and do not assume the objective properties of the taxa that name – they have no grounding in phylogenetic, morphological, or other objective characteristics, including scale, and they have no structural role within the hierarchy. In practice, the concept of a general or universal term is so subjective and obscure that, even among taxonomists, ranks are widely attributed the objective characteristics of the taxa they denote including a structural role within the hierarchy. It is, nevertheless, a distinction worth making since it distinguishes between subjective ranks (epistemological constructs) and ranks as objects in the world (ontological elements).

Strict nested hierarchies

While scientific hierarchical classifications attempt to minimize the subjective influence of the taxonomist, subjectivity enters the process at many points:

Overall purpose of the classification
Choice of ranks and taxa, of grouping and ranking criteria – and their interpretation.
The grounds for the differentiation of ranks and taxa (if any).

In biological classification, this can lead to different classifications for the same organisms, even when based on similar character sets.

The interpretation of hierarchical classifications, hierarchical thinking, and ‘levels’ is clarified somewhat by considering the formal logical conditions of strict nested hierarchical classifications.

Both the Linnaean and biological hierarchies are classifications of progressive containment. However, this containment can be a matter of degree that has consequences for the efficiency, precision, and scientific utility of the classification.

The scientific precision of the classification depends on its degree of compliance with the formal logical conditions of strict nested hierarchies as listed below?

Group membership – the criteria defining group membership at each rank must be both necessary and sufficient (classical categories)
Inclusivity – ascending taxa are progressively more inclusive (e.g. the taxon Myrtales contains more ‘species’ (taxa at the rank of species) than the taxon Myrtaceae, which contains more ‘species’ than the taxon Eucalyptus.
Exclusivity – an item in a strict hierarchy can belong to only one group at a given rank e.g. a species belongs to one genus, a genus to one family, etc.
Transitivity – the defining properties of higher ranks are inherited by lower ranks e.g. all vertebrates (Vertebrata) have a vertebral column no matter how they are subdivided at lower levels.

 

Group membership

The requirement that the conditions of group membership be both necessary and sufficient ensures that the objects being compared are clear and distinct. In biological systems this is immediately problematic. While practical divisions may be made between biological groups evolution by modification ensures to combined presence of both the shared characteristics that indicate evolutionary relationship and the uniquely defining characteristics of particular groups.

This general limiting proviso applies to both the Linnaean and biological hierarchies.

Inclusivity

The formation of progressively more inclusive groups in a strict hierarchy assumes that there is an objective equivalence between the taxa at a given rank. So, Callistemon, Melaleuca, and Eucalyptus are all taxa at the rank of genus. Having the same rank they are assumed to be more or less equivalent entities. However, ranks like these do not translate well into nature because, for example, the kind of characteristics chosen to determine the rank family in one part of the plant kingdom may not be equivalent to those in another part of the plant kingdom. The subjective tiers, rows, ranks, or grades associated with hierarchies do not match nature so well as the spatial branching patterns of evolution.

 

 

 

 

 

Biology must confront several basic questions: what is life? Are there basic units of life? How are we to divide up the living world, and for what reason?

 

 

The biological hierarchy no doubt gathers some authority from its resemblance to the Linnaean system.

The biological hierarchy is only obliquely concerned with names and evolution; it functions as an introduction to biology with an overview of concepts that are used in both theoretical and applied ways across the range of biological disciplines. It does this by organizing the biological world into interacting levels of structures that can be treated as varying in size, inclusiveness, organic complexity, scale, and many other factors.

This approach shifts focus from the narrow consideration of species – their names and evolutionary history – to more generalized biological phenomena and it makes possible the examination of biology at scales ranging from the molecular to the biosphere in its entirety and the way academic disciplines fit into these scales.

The biological hierarchy meets the criterion of inclusivity as it moves upward from molecules to the biosphere but not the demand for exclusivity.  If a species can belong to only one genus, and a genus can belong to only one family how does this requirement transpose to the ranks of the biological hierarchy? Do molecules belong to only one tissue, and do tissues belong to only one organ – they do not. And what about transitivity: do the properties that define organs pass to tissues and molecules – they do not? The requirement for necessary and sufficient conditions of group membership translates to the biological hierarchy (viz. if the conditions defining a genus are necessary and sufficient, are the conditions defining an organ also necessary and sufficient – they are not.

The Linnaean hierarchy has higher and lower levels that are grounded in the species (even though there are sub-specific ranks). This, presumably, is mostly because species, as groups of similar organisms, have greater intuitive appeal (seem more real) than increasingly subjective groupings like genera and families. Cladistic classification uses the clade as the basic unit of classification. So what is the basic unit of the biological hierarchy?

The present-day intuition suggests that this is whatever sits at the bottom of the hierarchy, be it molecules, atoms, or elementary particles. Why not the organism as species representative?

Confusingly, in the biological and Linnaean hierarchies, the names of the objects being classified and the names of their levels or ranks are the same. The genus as a taxonomic group consists of closely related species, while the genus as a rank of classification is a level in the Linnaean hierarchy. This ambiguity of meaning is also associated with words like ‘cell’ and ’tissue’.  There is always potential confusion between theoretical and actual objects (see tokens and types).

In sum, the Linnaean hierarchy is an effective way to allocate names to groups, but the subjectivity of ranks limits its capacity to represent evolutionary relationships. Modern cladistic classifications based on hypothetical evolutionary trees depict evolutionary branches (clades) derived from common ancestors without using levels (ranks). The biological hierarchy arranges the physical structures of biology into theoretical explanatory levels of organization to present a broad range of biological ideas. The subjectivity of ranking creates difficulties of biological interpretation. 

While classifications can relate to the world and be open to empirical investigation, the ranking of biological objects into levels is of explanatory (cognitive)[17] value only, they do not correspond to levels in the world.

What are the explanatory benefits of this theoretical hierarchy?

(the Linnaean system focuses on the classification of organisms, while the biological organization hierarchy emphasizes the relationships and processes within and between levels of biological complexity. Both are essential for a comprehensive understanding of life and biology as a whole.)

(The Linnaean hierarchy categorizes organisms into a system of ranks as a classification of species based on shared characteristics and evolutionary relationships while the biological hierarchy includes a broader range of biological objects that reflects the complexity of biological systems and their interactions. While the Linnaean hierarchy provides a systematic way to identify, name, and classify species, thus facilitating biological communication, the biological hierarchy represents relationships and interactions between different biological entities and processes that reflect the organization and functioning of living systems. Both hierarchies provide order but in different ways.)

(Biological classification begins with our intuitive recognition of actual individual type organisms as the basic (agential) units of life, and therefore classification. Classification then investigates similarities and differences between organisms, forming progressively more inclusive taxonomic groups. Ranking adds the convenience of additional structure to the organization of the taxa generated by classification. 

This invites the leading question posed by the biological hierarchy. What are the subjective ranking criteria humans have used to establish the levels of the biological hierarchy?)

Elements of biology and the biological hierarchy

So far it has been suggested that the strength of the biological hierarchy lies in its flexibility of interpretation and range of ideas, while its weakness lies in the difficulty of making such abstract ideas apply to the world.

What, today, are considered the key ingredients of biology, and how well are they represented by the biological hierarchy?

This section of the article reflects on the biological landscape and how it is represented by the biological hierarchy. 

Purpose

All thinking is classification (in a broad sense) since it orders the world by prioritizing the objects of thought according to agential goals – it is performed by biological agents, typically humans, for a purpose. This is what establishes meaning in the umwelt of the biological agent. It is the purpose that determines the content of the classification. Any confusion or ambiguity about purpose will be reflected in ambiguities within the classification itself.

The Linnaean and biological hierarchies are examples of a historical divergence of intention. The primary role of the Linnaean taxonomy was as a system of nomenclature, identification, and communication that facilitated biological inventory at a time when species were regarded as independent and immutable products of Special Creation. Aristotle and Linnaeus, despite appreciating similarities between organisms, regarded species as discrete and independent units that could be defined using mutually exclusive logical categories. Darwin revealed species as intergrading products of descent with modification from common ancestors. Evolution emphasized the shared characteristics of common descent that challenged logical independence. Many biologists then assumed that the task of classification was to capture groupings that reflected evolutionary relationships.

(While the Linnaean system, built on similarity and difference, reflected evolution, it did not do so efficiently. Organisms sometimes share characteristics due to convergent evolution, parallel evolution, and evolutionary reversals all rendering the possibility of mutually exclusive logical categories impractical. Factors such as hybridization, lateral gene transfer, and adaptive radiations further complicate the simple assignment of organisms to distinct taxonomic groups based on necessary and sufficient characteristics. Thus criteria for group membership are open to interpretation.)

(To overcome this problem cladistics arranges organisms into clades as groups of organisms that include an ancestral species and all of its descendants. A strict nested hierarchy uses categories that are logically mutually exclusive. We can mistakenly assume that this is how the biological hierarchy, even the Linnaean hierarchy, works. But biology is concerned with objects that arose by modification from common ancestors so there will always be shared characteristics as products of relationship, no matter how distant. Logically exclusive categories are not possible in biology because evolution is not amenable to this degree of logical precision.)

(Strict nested hierarchies provide a logically watertight classificatory framework (ideal for the unambiguous allocation of names to groups and ranks) but not ideal as a means of representing organic evolution because evolutionary groups (e.g. species, genera) do not fit neatly into necessary and sufficient categories i.e. key characteristics may not be universally exclusive or definitive.)

Also, the convenient subjective ranking into tiered levels, though an effective way of fragmenting the community of life, does not transpose comfortably into the branching pattern of evolution.

The Linnaean hierarchy, then, carves up the biological world into intellectually digestible pieces that have great practical utility. It is, however, an imperfect way of representing evolution and has been replaced in evolutionary studies by the method of taxonomy called cladistics based on clades. It is also an imperfect way of introducing the diversity of biological objects studied by biological science and has been rep;laced in this role by the hierarchy of biological organization.

Kinds of things

Among our favorite ways of classifying everything are: kinds (what are the things in the world – is all this difference really a manifestation of an underlying sameness?

The question of biological objects relates to the philosophical notion of biological individuals.[5] What should be the basic ingredients or preferred categories chosen to represent the subject, and for what reason (what are their selection criteria)? So, for example, should the categories chosen be defined by their physical boundaries and organization, their function within a biological system, or their agential properties? Are properties, relations, processes, and events secondary or subordinate phenomena? Should priority be given to units of evolution, genetics, development, or metabolism?

If we accept that levels of organization and complexity provide an explanatory entry into the subject then what is the relationship between these levels? Do they exist, as it were, equally or are some more biologically significant than others? If we do rank some biological objects as more significant than others is this just a matter of context or are there more general principles involved? How do categories of the living relate to those of artificial systems and the non-living?

We like the solidity and brute undeniability of physical objects and so we have a traditional respect for things with a physically bounded identity – molecules, cells, tissues, organisms, etc. But biology is more than physical individuals. We know that every living object is connected by evolution and that in biology we don’t just study structures, we also study functions, behaviors, processes, principles, and theories organized into subdisciplines.

Maybe attempts to order and prioritize the biological world are misleading because everything depends on human interests and concerns that are a matter of context. Is the universe an indifferent and purposeless swirl of matter in which the only purpose issues from human conscious intention?

Sorting all this out is a daunting task, but the study of biology must begin somewhere. Textbooks and discussions of biology must provide an overview of their contents and at present the biological hierarchy is the preferred tool for carving up biology – the lens through which we view the living world.

The hierarchy of biological organization presents us with a list of physical objects – roughly,  molecules, genes, cells, tissues, organs, organisms, populations, ecosystems, biomes, and the biosphere – interacting in a layered way. At face value this is a hierarchy of structures – of objects arranged by complexity and spatial scale.

Object to process

We might expect the major metaphors and categories used in biology to reflect the historical development of the subject. But we need ideas to move with the times.

Over the last 50 years or so the general momentum of scientific metaphysics has shifted from notions of the eternal and absolute to more fluid, dynamic, and flexible concepts. Science, once paraded as the ‘study of truth and universal laws’ is now treated more modestly as ‘best explanation’ or somesuch. The impetus to unify science under a single all-embracing theory grounded in physics and chemistry is also losing traction.

The secure philosophical landscape of permanence, substance, the universal, and the eternal is giving way to contemporary scientific evidence that everything is in a state of flux. This shifts the metaphysics of science from the security of permanent substances to the dynamics of process. Put simply, the scientific emphasis today is on processes, rather than things. This is especially pertinent for living systems. Life is more a process than a thing.

This shift in emphasis draws attention to what it is in living systems that generates or motivates change; it highlights life’s agency. It also draws attention to the distinction between structures and functions and whether biologists think that one of these takes priority over the other.

In a general way, the history of biology has passed from the description and classification of structures (material, structural, morphological, anatomical) to the explanation of functions (physiological, developmental, evolutionary) to an understanding of agency (behavior, cognition, information processing). Our intuitive understanding and explanation of life can engage elements of all these domains. This is a move from questions about material composition (structure, form, appearance) to questions of origin and function (as mechanical operation and process), to agency and purpose as the goal-directed information processing we associate with cognition.

‘What is it made of and what does it look like?’  was built on taxonomy, morphology, and anatomy. Taxonomy provided a systematic framework for organizing life forms while morphological and anatomical studies laid the groundwork for understanding diversity and adaptation. ‘What does it do, and how does it work?’ was built on physiology and genetics with physiology elucidating processes like metabolism, respiration, and circulation and genetics unveiling the role of DNA, genes, and mutations in shaping traits. What is it for?’ was built on the behavioral sciences as the study of the adaptive behaviors of organisms. These explore behaviors that enhance survival and reproduction, providing insights into ecological niches, mating strategies, and social interactions, thus bridging the gap between physiological mechanisms and ecological context.

Agency is pervasive in biological systems; it is not just a human mental phenomenon. Human agency is a highly specialized and limited case of biological agency such that many of the characteristics we associate with human cognitive agency (e.g. purpose, intelligence, cognition, memory, reason, learning, and more) share non-cognitive characteristics with other organisms.

Modern biology includes not only structures, and functions, but purpose and agency.

How does all this help us to determine which are the most appropriate categories for the study of life?

This investigation of the content of biology has teased out three realms of investigation – three distinctive kinds of things that are investigated across the range of subjects we call biology.  These may be loosely divided into structures (matter, molecules, genes, cells, tissues, anatomy, morphology, etc.), processes (mechanical operations, functions, physiology, development, evolution, photosynthesis, metabolism, homeostasis, etc.), and behavior (goal-directed information processing, cognition, purpose, agency). Like any intuitive taxonomy, it is open to interpretation (e.g. isn’t behavior a process?) however, it provides a foundation of ideas that moves beyond things to processes and agency, reflecting the current perception of biological science.

While the biological hierarchy acknowledges interaction its emphasis is on physical structures distributed in vertical space (the molecules, cells, tissues, and organs, etc. of anatomy, morphology, etc.) – a perception that ignores, or at least diminishes, the influence of processes in time (development, adaptation, agency, evolution).

Competing classifications

Hierarchies are classifications whose contents are ranked from top to bottom (and vice-versa). How important is the ranking presented to us by the biological hierarchy – does it represent the way the biological world really is, or is it just a convenient explanatory structure? Is there just one system of ranking (set of criteria) for the levels of the hierarchy or are there several?

Ranking prioritizes: are ranked systems always a matter of context and convenience or are there objects in biology that demand precedence?

It has already been established that the reasons (classification selection criteria) for the establishment of levels in the biological hierarchy are unclear (roughly inclusiveness as part-whole composition, organic complexity, size).

How seriously should we take these levels and their ranking when thinking about biology?

It is instructive to make a list of objects given priority in biology and the reasons for their elevation to high status. The subjectivity of ranking (its explanatory contextual utility rather than its correspondence to the world – its epistemic not ontic significance) has already been pointed out, drawing attention to the need for empirical evidence when deciding what is important in biology.

Objects at the top of the biological hierarchy – e.g. humans with brains, conscious awareness, abstract thought, language, a moral sense, and the capacity to reason, are superior to all other life forms
Objects at the bottom of the biological hierarchy – physics and chemistry are the foundations on which everything in the physical world is built. All complexity can be reduced to the simplicity of elementary constituents
Genes – it is genes that have determined the evolutionary history, developmental patterns, and physical characteristics of every living thing
Cells – all living things consist of self-replicating cells that are the fundamental units of all life
Organisms – organisms are physically bounded and autonomous adaptive agential units

While ranking is subjective, there is a hint of non-negotiable hegemony in these claims that needs closer scrutiny: is there an explanatory biological category that should take precedence over other categories, and, if so, with what justification?

The biological hierarchy of levels of graded physical complexity resembles the gradation of evolution. However, any rank-value, significance, or privilege attached to the levels is graded either from top to bottom (or vice-versa), or the levels, though related as superordinate and subordinate, are treated as having equal status. This latter approach is sometimes referred to as biological pluralism. For example, if I am a geneticist then it makes as much sense to regard genes as the key element of life as either cells or organisms. If I am a cytologist then cells take on this role.[7]No object has special existential significance relative to others (cells, tissues, organisms, and genes exist equally) but as biological agents, they have different explanatory significance.

While different classifications can serve different purposes the biological hierarchy has proved the most popular informal classification system. But there are other ways of approaching biology. For example, the elevation in significance of individual biological objects cuts across the notion of multiple levels by prioritizing one object over all others. The most notable candidates here are cells, genes, and organisms, each of which has been considered foundational to the subject at one time or another.

These preferences are treated as a matter of empirical evidence and not relative to context, scale, or explanatory inclination.

Cell
All organisms are made up of at least one membrane-bound cell, this being the smallest unit that can replicate independently as new cells arise from pre-existing cells. Organisms on this view are, in effect, cell colonies such that cell theory treats the cell as the basic structural and functional unit of life. All the essential features of life can exist in a single autonomous cell. The single living cell drives development and is a center for metabolic and sensory processes. As adaptive (goal-directed, problem-solving, intelligent) and self-regulating entities single cells display the universal characteristics of biological cognition and biological agency. However, within multicellular organisms, cells are subordinate to the adaptive goals of the entire organism.

Gene
Causal dependencies in biology are difficult to unravel. Within the cell, the information encoded in replicating genes directs the synthesis of proteins that ground the developmental paths and characteristics of organisms. Genes – their structure and function – are therefore crucial to our understanding of inheritance, evolution, and development. Indeed, the organism is sometimes regarded as a genetic epiphenomenon (humans are just DNA’s way of making more DNA!). While genes are the biological units of heredity and variation, providing the genetic material that is passed between generations, it is organisms that are the primary units of natural selection and adaptation since they are the agential units interacting with their conditions of existence (both internal and environmental), competing for resources, reproducing, and passing on genetic information to their offspring. Genes encode the blueprint for traits, but the expression of those traits and their evolutionary outcomes includes interactions between genes, organisms, and their environments.

Organism
While nature and life present us with continuity and gradation, it is organisms as bounded and autonomous physical entities that constitute the most obvious units of integrated functional organization – exceptional in the degree of unification of their parts. They are discrete biological agents whose structures (including cells and genes), processes, and behaviors are subordinate to the agential goals of the whole organism. Communities of organisms (holobionts, colonies, swarms, populations, ecosystems) while demonstrating their own emergent collective properties, do not do so to the same unified and autonomous degree as individual organisms: they are organism collectives.

In many ways, organisms serve as the basic units of biology, they are points of biological reference, and the focus of biological processes and agential activity.  They are the critical biological objects that help us understand the complexity and diversity of life and the principles that govern biological systems. Regardless of competing ideas, biologists treat organisms as the basic units of ecosystems, evolution, and biodiversity, including the reception and transmission of disease. They are the outcome or end of developmental processes and the ultimate wholes of structural and functional studies in anatomy and physiology. They are the units of which most biological structures are a part, and they are the units chosen for the classification of all life, and its conservation.

Though all ‘levels’ can express their own individuality by degree, it is the organism that stands out as the most discrete unit of agency and evolutionary selection, its parts subordinate to organism goals – and clearly demarcated as an ecological element in the organism-environment continuum.

Biology, on this understanding, is straightforwardly the study of organisms – their parts and their collectives – the organismal, sub-organismal, and super-organismal.

While organisms are distinctive autonomous agential units of life it is the species that is considered the basic unit of biological classification because it is the primary category in the hierarchy of biological classification (a group of similar organisms that interbreed and share a common gene pool, this reproductive isolation restricting gene flow and maintaining genetic identity); it reflects evolutionary relationships as practical adapting units that can be grouped shared characteristics and evolutionary history; it is a unit that is universally recognized and therefore a convenient building block for more inclusive ranks; species have clear roles in the dynamics of ecosystems; they are a practical and units for both study and conservation.  Overall, the concept of species provides a clear, functional, and biologically relevant framework for organizing and studying the vast diversity of life on Earth.

The selection of the species (a group of similar organisms) as a universally accepted unit of biological classification is an implicit acceptance of the organism as the basic unit of life.

Ultimate biological rank-value
While cells demonstrate a high degree of autonomy, they are usually aggregated into, greater wholes (organisms) and subordinate to the agential demands and conditions determined by that greater whole which is the universal, unified, and functionally integrated propensity of every organism to survive, reproduce, adapt, and evolve.

Though both cells and genes have a degree of individuality and independence of operation, it is organisms that we intuitively regard as the canonical units of life.

The development of an organism is a flexible and dynamic process, its parts responding collaboratively and creatively to external cues and internal signals, the genome and its developmental architecture acting more like a musical score that is open to interpretation and adaptation than a rigid instruction manual.

Aristotle provided us with the theoretical foundations of biology over 2000 years ago, but we are only now returning to his thought. While biology is a synthesis of all aspects of the living world, life is most persuasively explained in terms of the agency of entire organisms – not how they originated (evolution), how they operate (the mechanics or functions of their parts), or what they are made of (their structures, including cellular and genetic components) – though these are all necessary – but what they do (their capacity to survive, reproduce, adapt, and evolve – which is what they are for, their biological purpose). Life is a goal-directed and adaptive dynamic process. The formal and universally accepted scientific classification of the living world is not a classification of molecules, cells, or genes – it is a classification of organisms. It is organisms, as biology’s most discrete but agentially unified collections of cells, that are the operational units of biology. We intuitively understand that organisms are the basic units of life.

The key concepts described above – the classification of kinds and categories of investigation, rank, rank-vale, the structure of the biological world. The ambiguity of the relationship between levels has prompted philosophical questions about multiple realization, supervenience, emergence, reduction, and more.

Biology simply does not reflect levels so much as dominant life forms and it is organisms, as biology’s most discrete but agentially unified collections of cells, that are the operational units of biology. Organisms are the operational units in biology, but the division of the world into artificial layers of molecules, cells, tissues etc. imbues these layers with misleading biological significance. Actual molecules, cells, tissues etc. are parts within the integrated activity of organisms, not independent layers. Ranking reifies these hypothetical levels.

Emphasis in biological research has shifted from structures (things), to operations (processes), to biological goals and agency.

Current scientific evidence indicates that the biological world is not stratified into layers of increasing complexity: it consists of organisms whose molecules, cells, tissues, etc. are fully integrated into activities that are ultimately subordinate to the goals of the organisms themselves. Biology is, therefore, best represented by the agency of organisms, including their structures, processes, and behaviors and those of their parts, and including the wider populations of which they are a part – all set within the framing ideas of evolution.

The subjective hierarchical ranking of the elements of biology into layers builds a misleading conceptual framework of hypothetical objects, properties, and relations (see later) that is of doubtful explanatory value.

Spatial extension – Size

The objects listed as comprising levels in the biological hierarchy are graded in size. Molecules are smaller than cells, which are smaller than tissues, which are smaller than organs, which are smaller than organisms, etc.

Size, relative to ourselves, is a powerful intuition about the world that no doubt contributes to the appeal of the biological hierarchy.   

Inclusivity (scope, containment, nesting)

Biology, the living world, is a subset of a greater whole, the physical world. Whatever we think of, apart from the universe itself, is contained within something else such that the notion of  containment has great intuitive appeal.

Since the early 20th century we have known that the complexity of the universe evolved out of the point source of the Big Bang and a more-or-less uniform plasma. From this uniform plasma has emerged the vast range of structures, properties, and relations that we see today and they were not predictable from their prior objects, properties, and relations.

Nesting
Nesting is simply the containment of one entity within another. Hierarchical nesting is ranked nesting in which subordinate parts are contained within superordinate wholes.

Biologists are familiar with the nested (boxes-within-boxes) hierarchy of Linnaean classification in which the world’s species are grouped into genera, genera into families, and so on. The structural principle is of progressive inclusion, proceeding ‘upwards’ from ‘low’ to ‘high’, the most inclusive categories being ‘highest’. This all makes sense, especially as nesting reflects the post-Linnaean Darwinian idea of descent with modification from common ancestors. Wholes at lower levels are parts of the levels above them: higher levels contain lower levels in a gradation of superimposed complexity.

It therefore seems reasonable that biology, as a whole, is organized similarly, and this is what the biological hierarchy tells us. Molecules are nested within cells, that are nested within tissues, within organs, and so on . . .  but this simple picture can be scientifically misleading.

It helps to be reminded of the precise taxonomic conditions of a nested hierarchy:

Inclusivityone group completely contains another group e.g. ranks (levels) are progressively more inclusive as they pass from bottom to top (e.g. species, genus, family, etc).

Exclusivityelements or groups do not overlap or have any shared members e.g. an item in a strict hierarchy can only belong to one group at a particular level or rank (e.g. plants can only belong to one genus at the rank/level of genus).

Transitivityif A is related to B and B is related to C, then A is also related to C.  e.g. the higher the rank, the more inclusive it is so, for example, ‘lions’ are members of the more inclusive group ‘carnivores’ which are part of the more inclusive group ‘mammals’. Organisms in the hierarchy share characteristics with ranks above (broader taxa) and below them (narrower taxa), which helps in defining their placement within the taxonomic system and understanding their evolutionary relationships. By considering shared derived traits inherited from common ancestors (synapomorphies), hierarchical systems maintain the transitive property where subsets within the taxonomy share some characteristics with both the broader ranks above them and the narrower ranks below them in a consistent and predictable way.

Clear boundaries – the properties defining group membership at a particular rank are both necessary and sufficient (classical categories)

There is a logical tidiness to this representation that is not apparent in life itself.

As a system of representation, the use of ranks or levels has several draw-backs:

      • it treats levels as having the autonomy and independence we usually associate with organisms. But organisms have a strength of functional integration that does not occur in their constituent parts e.g. cells and tissues have a greater dependence on their surroundings and are subordinate to the goals of the organism
      •  uncertainty about the level’s grouping criteria – complexity, size, inclusion, etc.
      • it is a theoretical representation that does not transpose easily to actual objects since its emphasis is on objects rather than processes and causation that passes between hypothetical layers.
      • it uses misleading metaphorical spatial language.

Above all, nature is not organized in this stratified way: it is not composed of cells that interact as a level with tissues as a level, and so on. Cells are parts of tissues and biological interactions may be interpreted differently at different physical scales. There is no need to imagine (or model) causation in biology using theoretical layers when it can be modeled in terms of actual interactions.

Complexity

From the time of the Big Bang, and despite the Second Law of thermodynamics, there are parts of the universe that have become increasingly complex. From undifferentiated plasma has emerged elements, compounds, and organic molecules. In the biological world evolution has mostly proceeded, though not in a linear way, from the less to more complex.

Organisms are nature’s most elaborate organization of matter but the biological hierarchy seems to hint at an evolutionary perspective of increasing physical complexity that includes elements of the Linnaean hierarchy of life. Indeed, the levels of the hierarchy loosely correspond to biological disciplines which suggest that both the biological hierarchy and biological subjects might reflect the structure of the living world.

This section has examined the elements of the biological hierarchy – the categories it uses when carving up the living world into meaningful ingredients. It has examined its inferred basic constituents of biology,  the grouping criteria that establish the differences between them, and the ranking criteria that arrange these groups into prioritized superordinate and subordinate levels.

The biological hierarchy implicitly focuses on ‘things’ as its ingredients (molecules, cells, tissues, etc.). The criteria used to group (differentiate or classify) these things is unclear but can be inferred as including size,  degree of physical complexity, and inclusivity (degree of containment). 

These groups are subjectively ranked according to their perceived significance. This too is unclear – partly because it is mistakenly assumed that ranking is based on the grouping criteria, and partly because the actual ranking criteria are unspecified. The subjective purpose of the classification is to provide an explanatory framework of ideas for biological science, but there is confusion over the degree to which this framework reflects the world. At its extreme, there is the implication that it represents actual levels of reality with the lowest level forming a foundation in physics and chemistry. 

The biological hierarchy expresses the tension between old ways of perceiving science and current empirical evidence. Biology is at a crossroads. Following the exuberance of an age of analytical reductionism and gene technology, the theoretical grounds of biology are being reassessed.

Theoretical levels are being replaced by real-world objects. Despite all the information that is locked up in genes, and the autonomy of cells, biologists are returning to the view that the greatest degree of biological individuality is typically exemplified by the agential autonomy of organisms whose parts are ultimately subordinate to organismal goals. Each organism has its own evolutionarily graded realm of cognition (adaptive and goal-directed information processing) – its unique umwelt of significant structures, processes, and behaviors.

The human umwelt includes the attempt to minimize uniquely human perceptions through the use of science which explains the universe from many perspectives and scales. These perspectives and scales are not different layers of reality, they are different ways of explaining the same things. Biological science deals with objects, processes, and behaviors distributed in scales of space and time.

Causal relationships

The reification of the spatial metaphor of hierarchical levels (using the logic of the metaphor to explain what actually occurs in the world) provides a structural framework for biological causation.  Causal flows and feedback mechanisms are perceived as existing within and between levels, but like a chain of command in a human hierarchy that passes up and down through the levels.

The traditional causal path of the Ladder of Life flowed from God as Prime Mover or First Cause. But in the absence of God, how is the chain of causal command to be represented?

There is debate about whether this causal chain of command proceeds strictly ‘bottom-up’ or whether it can also flow ‘top-down’.

Serious talk by biologists, philosophers, and scientists in the professional literature, of bottom-up and top-down causation demonstrates how powerful the reification of levels has become, and how profoundly misleading it can be.

    • It perpetuates the controversial analytic-reductive hierarchical idea that causation must proceed from simple to complex, from molecules to cells and so on.
    • Reification attributes metaphorical levels of organization with the scientific authority usually given to empirical objects. The scientific elevation of levels then diminishes the scientific authority of objects in the world such as organisms.
    • The reification of levels leads to a biological pluralism with each semi-independent level having its own unique properties, principles, and terminology corresponding loosely to academic disciplines (e.g. genetics, cytology, anatomy, psychology etc.). This ignores any prioritization that might exist outside these metaphorical levels.

The traditional object-based hierarchy of molecules, cells, etc. is under challenge as emphasis shifts from objects in space towards processes in time as causes of biological change.

Is it biologically accurate or helpful to consider each level of biological organization as building novel (emergent) properties from lower levels? Is this a handy heuristic that helps scientists study life’s complexity across many scales and degrees of complexity, from molecular interactions to global ecosystems?

Do we need a theoretical structure round which to build a model of biological causation? Why not describe what actually occurs?

Practising biologists investigate biological causation using experimental, observational, and computational approaches. Controlled experiments manipulate variables to establish cause-and-effect relationships, often in natural settings, and using advanced statistical methods. Studies include gene editing, the operation of metabolic pathways, the assessment of dynamic changes over time, comparative studies, and model organisms. Systems biology, in particular, studies causal networks.

Biological systems are often modeled as causal networks where network nodes represent entities (e.g. genes, proteins, organisms), and their edges causal relationships. This helps unravel the complex web of interactions and interdependencies within biological systems. Consideration of theoretical layers of cells, tissues etc. has little relevance here.

Does biology benefit in any way from an account of biological activity as a causal chain of command running within and between levels of biological complexity? Does this causation pass from top to bottom, bottom to top, or both? How does such an account facilitate an explanation of biological causation?

(But what is most important in biology is its agency as causal efficacy and the ultimate causal subordination of organismal parts to organismal goals. Organisms are complex causal systems with a greater degree of agential autonomy than their parts: their goal-directed autonomy, as a unity of purpose, means that it is organisms, rather than their parts or collectives, that are the major biological causal hubs. So, for example, while genes have great causal efficacy they do not operate in isolation, they exist within the context of their surrounding cells and their persistence/survival depends on the survival of the organism of which they are a part.)

Biological causal efficacy

Causation is a vexed philosophical topic that will not be resolved here and, it seems, there is no single, uniquely biological mode of causation (Wikipedia).

Pluralistic hierarchical biology perceives causation as proceeding between levels which, being hierarchical, must be ranked as superordinate or subordinate. It is traditional in science to regard causal efficacy as flowing from a foundational or bottom layer of physics and chemistry.

If we ignore metaphorical layers for a moment, then what is it in nature that causes things to happen; what is the source of biological agency and change?

Organisms are, once again, perceived as centers of biological activity.

Emphasis on organisms as primary biological agents has profound implications for our understanding of biological causation. Individual organisms are nodes of causal focus within the broader network of biological causation that can be considered at many scales. Framing organisms as causal hubs in the web of biological causation highlights their degree of agential autonomy – the way that their integrated functional organization, as a unity of purpose, drives interactions, influencing biological patterns and processes.

The autonomous agency of an organism does not derive from matter alone but from the relations of its matter that give it a unity of purpose (autonomy) out of its functional organization. this is the ‘more’ when we say that an organism is more than the sum of its parts. [22]

Resistance to such an idea comes from many sources, not least of which is the hierarchical analytic reductionism that grounds all  causation in physics and chemistry, together with the reification of levels which emphasises the causal weight of biological sub-systems, organisms comprising just one level of this system of layers. But there is also the complexity of biological systems, the research focus on specific mechanisms, and the strength of differing disciplinary perspectives. All of these have diminished the causal characterization of organisms.

Among the influential ideas associated with causation in biology are the following:

      • Organisms, more than any other biological units, are causes of themselves. They display self-sufficiency by regulating and maintaining their own existence and functionality. This self-causation is a form of biological agency that distinguishes organisms from non-living entities. As independent units of living matter that can survive, reproduce, adapt, and evolve, organisms  demonstrate life’s highest degree of biological autonomy.
      • The influence of historical factors, such as evolutionary history and phylogenetic relationships. The operational mechanics of processes whose parts perform functional operations that are a consequence of their physical organization.
      • As hierarchical layers, each with its own causal processes and interactions.
      • As teleological or agency-based goal-directedness, notably the functional traits and behaviors of organismal parts that contribute overall organismal goals of survival and reproduction.
      • Traits that have been selected for their effects in past generations (etiological)
        The origin of emergent properties arising from the interactions between system components that cannot be predicted solely from the properties of the individual parts.
      • Downward causation refers to the idea that higher-level phenomena (e.g., psychological states or social structures) can influence and constrain lower-level biological processes thus challenging the reductionist view that only lower-level processes can cause higher-level phenomena.
      • Pluralism as a recognition of different types of causal relationships (e.g., genetic, developmental, ecological) each relevant within its own context.
      • Probabilistic views counter the notion of linear billiard-ball causation since in biological systems causation is more probabilistic than deterministic, reflecting the inherent variability and complexity of biological systems and how effects are context-sensitive.

The perils of spatial metaphor applied to actual biological systems are blatantly apparent in the interpretation of biological causation. If organisms are individuated by their extreme agential autonomy within the realm of biological objects (their parts subordinate to organismal ultimate goals), then it is organisms that are hubs of causation within the network of biological interaction. The representation of biological causation as operating between metaphorical levels of molecules, tissues, organs etc. is profoundly misleading.

The organism-environment continuum

The organism exists as an autonomous agent that is, nevertheless, part of an organism-environment continuum.

The general causal conditions of an organism are often explained and understood as arising from either within the organism (internal) or imposed from the outside environment (external). This inside/outside internal/external distinction, while relevant, can also mislead since all behavior is ultimately a consequence of the organism’s synthesis and response to its overall conditions of existence. That is, what causes behavior most directly is not ‘the environment’ but the organism’s agency – its functional integration of all causal factors.

What causes an organism’s behavior is the organism.

Expressed more simply, the organism does not respond passively to external and internal factors (its conditions of existence), it plays an active role in determining outcomes . . . it adapts in an agential goal-directed and flexible way according to the structural, processual, and behavioral conditions of its umwelt.

How an organism behaves is, most directly, its adaptive agential response to a combination of external environmental factors interacting with the organism’s internal environment.

Proximate & Ultimate Causes

In 1961, the evolutionary biologist Ernst Mayr drew a distinction between proximate and ultimate biological causes. Proximate causes refer to the immediate mechanical influences on a trait. For example, they explain how internal (e.g., hormonal) and external (e.g., temperature, day length) factors combine to elicit or generate a specific characteristic or behavior. Ultimate causes provide historical explanations – why an organism possesses one particular trait rather than another.

Mayr associated ultimate explanations with natural selection, although other evolutionary processes (such as genetic drift) may also play a role.

This distinction touches on teleological explanation and agency because proximate causes focus on mechanisms (or functions), while ultimate causes describe the adaptive significance of traits. Understanding why a trait evolved often involves considering its functional benefits in terms of survival and reproduction. A modern alternative to this dichotomy is reciprocal causation which recognizes that causation cycles through biological systems recursively. It emphasizes the interplay between ontogenetic processes (individual development) and evolutionary questions.

This perspective encourages a more holistic view, acknowledging that proximate and ultimate causes are not mutually exclusive but interconnected.

Ultimate causes concern the ultimate, universal, adaptive, long-term goals of all organisms, while proximate causes concern temporary short-term goals related to the umwelt of individual organisms. 

Frames of reference

Taken less seriously, the levels or ranks of the biological hierarchy do not represent the world in any substantive way – they are simply convenient frames of explanatory reference. This facilitates the formulation of a neat theory of biological operation – how biology works as a system.

Each level expresses its own independent principles, laws, and terminology, the higher levels imposing constraints on lower levels, and the wholes at lower levels functioning as parts at higher levels. As scales of some kind these levels can be separated intellectually into domains, both those of named ranks (e,g. molecules, cells, tissues) or the disciplines that, loosely, work at these scales (biochemistry and genetics, cytology, anatomy and histology). Each level then has is own domain and place within the biological curriculum.

This theoretical framework contrasts with our sense of what is actually going on in biology. In nature, molecules, cells, tissues etc., do not exist as independent layers, they are parts of functionally integrated autonomous and agential organisms. Organisms then form collective groups of various kinds.

The problem is that levels can acquire an identity of their own – a thinghood or reification beyond their role in nature. So, for example, they take on an individual evolutionary significance. Every part of an organism is a necessary component of a functional whole so it is meaningful to ask, for example, whether natural selection operates at the level of the gene, cell, organism, population, or other. Hierarchical thinking imposes the need to rank and its subjective ranking criteria.

It is claimed in this article that the ranking of nature is grounded, not in the subjective ranking criteria of theoretical levels, but in the objective grounding of all biological activity in the functional autonomy and adaptive agency of living organisms.

The emphasis on theoretical levels – with organisms just one level among many in the biological system – ignores the integration and focus of biological activity within the agency of functionally integrated organisms. It artificially elevates (reifies) the significance of organism parts and diminishes the significance of the agential autonomy of whole organisms: it misrepresents what happens in nature.

This misrepresentation has likely occurred as a historical consequence of a florishing analytic research program that has focused on organism parts, most obviously microbiology and genes.

This theory has initiated various speculations:

        • The processes at higher levels are slower than those at lower levels.
        • The properties at higher levels are multiply realizable at lower levels.
        • That higher causes are dynamically independent (autonomous).
        • That higher level properties, theories, or explanations reduce to lower ones?
        • That higher level entities have causal influence over lower ones?
        • Hierarchical thinking entails superordinate and subordinate levels. What are the ranking criteria used to prioritize levels (or are levels of equal biological significance)?

It is possible to explain the structures, processes, and behaviors encountered in biology in the straightforward causal terms of living objects existing in space and time.

But how are we to describe nature if – in either theory or practice – it is organized into interacting and prioritized layers?

An extraordinary amount of scholarly time has been spent trying to make biological explanations fit into this hierarchical framework of ideas..

A New Metaphor

Isn’t the hierarchy of biological organization a useful heuristic, despite its metaphorical shortcomings? Besides, what is the alternative?

The way we represent life to biology students and the world must reflect our best science.

Life is investigated today from a multitude of perspectives and scales with many of these embedded in specialist academic subdisciplines of biology, each with its own established domain of principles and terminology.

One insistent theme in contemporary biology is that of life as a process. Early biology was concerned with its descriptive groundwork – the development of a universal terminology for an inventory of structures, organisms, and their classification. Like the biological hierarchy concern was focused around theoretical (abstract, universal, token) physical objects. Only in the 19th century was this science of static and eternal objects supplemented by an investigative concern about function. Biology now took on an experimental and dynamic character as interest shifted from the permanence of token structures to the functional processes of physiology, leading eventually to an acknowledgment of the purposive goal-directedness of biological systems and behavior that led to the 20th-century flourishing of the cognitive sciences.

Contemporary biology is coming to terms with the extension of the notions of agency and cognition beyond humans to all life. Associated with this is the investigation of goal-directed biological processes as complex networks of physical and informational exchange (e.g. interactomics), notably the way information is stored, transmitted, and processed in adaptive biological systems.

In a general sense, the focus of scientific research has shifted from structures in space to functions, then agency, in time.

Time in biology has long been neglected. We tend to think of biological in general or abstract (token) terms. 

Though life itself is a process the subject of process is hidden in the deeper recesses of the interacting layers of the biological hierarchy. Biology is not just about token molecules, cells, tissues, etc., it is also about metabolism, development, photosynthesis, evolution, and agency.

How can our representation of biology do justice to these ideas?

Agency

Is it possible to establish necessary and sufficient conditions for life? (see What is life?).

The dilemma is that life can be viewed from many perspectives and scales, and biology is renowned for its gradations and exceptions, so a biological consensus answer to the question, What is life? seems unlikely. Many properties may be listed that set life apart from the other matter of the universe, including its diversity of form, the processes it displays, and the unique features of its material composition – all at many spatiotemporal scales.

Much of the difficulty has emerged out of the fragmentation of biology into a multitude of subdisciplines that have become academic silos, each staunchly defending its realm as crucial to the subject.

Despite exceptions and gradations, it is becoming increasingly evident that biology is establishing a more secure theoretical foundation under two ancient key ideas. First, that the living world is most obviously differentiated from the non-living by its goal-directed structures, processes, and behaviors, its agency or telos. This is manifested as the critical interconnected preconditions for life: survival, reproduction, adaptation, and evolution (biological agency) all dependent on the transport and communication of matter and information (biological cognition). Survival enables reproduction, allowing genetic traits to be passed on. Adaptation enhances survival in changing environments, while evolution results from the cumulative effects of these adaptations over time. These purposive processes are grounded in the transport and communication of information and materials?

Second, while this agency is evident in all living matter it is expressed at its fullest extreme in the individuated form of living organisms.

The biological hierarchy, though focusing on biological diversity, has diverted attention away from process, agency, and the organisms to which all biological explanation is drawn. It has been attracted to parts of the academic discipline of biology that have forgotten their connection to the organismal whole.

Agency, in a narrow sense, is the capacity to act with intention, purpose, and awareness based on conscious thought processes. In sentient animals, especially humans, agency involves perception, deliberation, and choice as the ability to weigh options based on past experiences and future goals, including the capacity to learn from experience and make ethical decisions. Plants, for example, are incapable of abstract thought, self-reflection, or symbolic language. Without conscious reflection biological processes are simply mechanical operations.

This account of agency fails to recognize the mechanical underpinnings of conscious thought. But, more importantly, it dismisses the real agency of goal-directed behavior as a form of agency that is not found in inanimate objects and the dead.

Organisms without consciousness act on and respond to their conditions of existence in a mind-like way because they have an evolutionarily inherited legacy of biological agency that they share with humans. The concept of agency makes more biological sense when it is associated with goal-directed behavior rather than conscious intention because it is a quantitative rather than qualitative difference – a difference of degree rather than kind.

All organisms – even those without brains and nervous systems – have the goal-directed propensity to survive, reproduce, adapt, and evolve. Their capacity to adapt to their conditions of existence involves the access, storage, and processing of information that establishes a grounding biological cognition that is evolutionarily related to the learning, knowledge, memory, perception, problem-solving and decision-making we associate with sentient animals.

Biological explanation is greatly facilitated when human agency and human cognition are treated as highly evolved, limited, and conscious forms of a more inclusive broad-sense biological agency and biological cognition.

Spatiotemporal objects & scales

A scientific description of the living world might open with the apparently innocuous principle that biological objects (here equated to organic structures, processes, and behaviors) exist within the parameters of space and time. Each biological object occupies a given space and a given time in its worldline of existence.

This relates directly to our intuitions about scale in biology because

The notion of levels introduces unnecessary abstraction to biological discourse. This can be reduced by using the more applied notion of scale.[20]  Biological interactions become more scientifically transparent when treated as occurring between organisms and their parts rather than between levels.

The reification of levels creates a confusing scientific multiplication of the objects of study. The use of scales draws attention to the fact that the same object can be described in many ways, while levels acquire an independent reality. We do not describe ecosystems in terms of tissues, or organisms in terms of elementary particles because even scientific explanation is pragmatic. Its answers adopt a scale that is appropriate to the question being asked.  

Elsewhere it has been argued that the domain of biological objects can be usefully classified under the three categories of structures, processes, and behaviors, reflecting, approximately, the range of biological academic disciplines. Translating processes and behaviors into world lines is challenging but possible.

Interpreted in this way an actual (type) organism is a spatiotemporal unit with a definitive spatiotemporal world line that intersects causally with the spatiotemporal world lines of the objects around it. Its parts have their own causally intersecting timelines, so, for example, molecular processes such as protein synthesis happen in milliseconds to seconds, cellular processes like cell division may take minutes to hours, a human lasts about 73 years, and speciation may take millennia. Organismal processes like growth, development, and behavior can span days, weeks, or years.

We intuitively think spatially and so we represent biology in terms of spatial objects – cells, tissues, organisms, etc. as spatial scales. This translates into the security and seeming permanence of solid objects but to the neglect of change and process. But all objects in the world also exist in time.

A type organism O at time T may be described in terms of different spatial scales. So, for example, given sufficient technological power it would be possible to describe O in terms of its constituent molecules, cells, tissues, organs, etc. As type entities, these constituents do not exist separately but as a unified whole – they are simply different ways of perceiving and describing the same whole object – different aspects or interpretations – of the organism.

As types, these are simply different ways of describing the same thing and, for simplicity, are referred to here as perspectives. As tokens, these scales have independent identities.

Molecules are not separate from cells, they are constituents of them. Likewise, cells are not separate from tissues, they are constituents of them. They are therefore connected in complex spatiotemporal ways. The theoretical way we individuate token biological objects is not possible in the actuality of types. While cells and tissues may be considered separately in theory, in practice they are not only spatiotemporally interactive, they share part of their spatiotemporal identity. In such cases we can confuse a theoretical category (token) with its actual equivalent (type), mixing up the theoretical and actual.

The spatiotemporal existence of a type biological objects cuts across the spatiotemporal existence of another in complex ways. A type organism does not consist of separate superimposed layers, one of molecules, another of cells, another of tissues, and so on – the organism is all of these in combination and interaction. It is just that we can describe the same phenomenon in many ways – from many different perspectives.

The hierarchy of biological organization deals with token biological objects but tempts us to think of levels as types . . . as real, discrete, and independent entities interacting with one another at their interface like actual physical layers of matter. This is treating token levels as types which is obviously mistaken because the biological world is not composed of molecules on which are superimposed cells, on which are superimposed tissues, etc. When we think like this we confuse or conflate the theoretical and the actual: we mistake theory for reality. Type structures, processes, and behaviors all have, in principle, precisely definable spatiotemporal boundaries, even though these may be difficult to define and measure

Adopting this approach takes account of the change that is so evident in living systems.

This is probably why the biological hierarchy of organization is based on the sense of permanency provided by structures (molecules, cells, tissues, organisms, and populations) rather than the shifting change we associate with more time-dependent processes and activities. It is hardly surprising that descriptive studies of morphology and structure preceded experimental studies of physiology and function in the history of science. The spatiotemporal approach establishes the organism as a dynamic process in space and time. We are aware that when we describe the organism at various spatial scales (e.g. molecules, cells, tissues, organs, etc.), as we have seen, these spatial scales are associated with their own temporal scales.

The theory of relativity has consequences for biology in the sense that space and time are relative to the biological object (as ‘observer’). Experienced (psychological, cognitive) time depends on the observer so we can acknowledge that the time of our human umwelt is different from that of other organisms. Humans with sophisticated technology we assume various spatial perspectives, the world of molecules, the world of cells, and so on. Bigger objects deal with longer timeframes so molecules last fractions of a second, the changing biosphere has lasted several billion years.

The synchronization of temporal processes – when they begin and end and how they adapt flexibly to circumstances – is crucial for the proper functioning of biological systems. Disruptions in temporal functioning can lead to developmental abnormalities, diseases, or other maladaptive outcomes. Temporal properties play a crucial causal role in their relationships with other entities, notably the timing of events in development, behavior, and interactions with the environment. These interactions across scales of time can involve feedback loops, signaling pathways, and regulatory mechanisms that coordinate activities at different levels of organization.

How can this complexity be communicated simply to students of biology? What kind of metaphor for ‘everything’ would avoid the pitfalls of hierarchical thinking?

Spatiotemporal scales avoid metaphor and attempt a scientific representation of the world. This acknowledges that we can never view things from the point of view of the universe and that our interpretation of everything is a species-specific perception and cognition of our human umwelt.

We cannot see quarks and their property of spin, which we can hardly comprehend, but each scale has its objects, characteristic kinds of properties and facts, and usually a different profession and community of operants: quantum physicists, solid-state physicists, chemists, biologists, psychologists, sociologists, and so on.

We need a description of life that minimizes metaphor and resembles more closely the physical characteristics of the world, and life as a dynamic, agential, communicating process that we can  investigate scientifically at many spatiotemporal scales.

A more physically compelling and scientific way of representing biology is as a web or network whose nodes are spatiotemporal centers of activity (molecules, cells, genes, organisms etc.) interacting through regulated pathways as systems of information processing. Causation then becomes the influence of information flow across these networks.  So, for example, metabolites flow through interconnected enzymatic reactions with causation as the transfer of metabolites along these pathways. Though more self-contained than other biological nodes, organisms are nevertheless systems open to energy, nutrients, and many other kinds of information flow.
Wimsatt[4] expresses these nodes in abstract terms as ‘local maxima of regularity and predictability in the phase space of alternative modes of organization of matter’.

This is a difficult entry to biology, but by focusing on the structures of biological networks – their connections, interactions, and interdependencies – hierarchical language can be avoided altogether.

As an informal classification of the biological world, the hierarchy of biological organization brings with it all the problems of hierarchical metaphor. Is it possible to develop an informal classification of biology without these constraints?

A contemporary vision of biology recognizes universal biological agency manifested in the typical case through the organism. However, biological science as a domain of study deals with biological objects in a broad sense – not just physical structures and things, but processes, behaviors, (principles, theories), etc. The placing of these objects within space and time would then provide a scientific foundation for biological representation based on our best current science.

The ranks of the biological hierarchy provide an acceptable inventory of physical biological objects, but it needs to be made clear that they exist in time as well as space, which changes their character from abstract and eternal concepts or ‘things’ to real constituents of a world of dynamic process and behavior.

Replacing the concept of hierarchical levels of organization with a focus on biological objects set within spatiotemporal scales provides a more direct and less theory-laden approach to biological phenomena.

However, the limitations of human cognition become apparent when comparing biological phenomena at extreme scales of space or time. Human cognition is adapted to (familiar and comfortable with) scales that were important for human survival in ancient environments of evolutionary adaptation, so the human brain finds the comparison of extremes of space and time either confusing or too complex to contemplate, as illustrated in the following examples:

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

These are not limitations of the world, but limitations of the human mind. Contemplating time in biological systems draws our attention to change and the fact that life is more a process than a thing. And biological time is a different phenomenon in the umwelt of each organism.

How can talk of downward causation be translated into talk of interaction between spatiotemporal objects. By shifting our focus from wholes and parts to variables and their interactions within a spatiotemporal context, we can understand downward causation as a phenomenon of influence between distinct spatiotemporal objects, avoiding the pitfalls of traditional interpretations that rely on problematic part-whole relationships.

Locating biological objects as spatiotemporally bounded units (ST units) within a spatiotemporal scale places them within a biological ontology. This avoids speaking about biological objects in theoretical or token terms.

We think of biological objects as physically contemporaneous units existing wholly in the present. But we can also, at least in theory, consider our understanding of an object when either space or time is held constant, and the other dimension is changed. For example, when we compare molecules, cells, and tissues, up through the traditional biological hierarchy, the molecule diminishes in significance not only in terms of its size, inclusiveness, and complexity but also its spatiotemporal lifetime.

An ecosystem contains STunits of many kinds. Explaining the dynamics of an ecosystem entails interactions between organisms, abiotic factors, and ecological processes such as nutrient cycling. Attempting to understand these phenomena solely at the molecular level would overlook the emergent properties that arise from the system as a whole.

The regulation of physiological processes within an organism involves intricate feedback mechanisms operating at multiple levels, from molecular signaling pathways to organ systems. A comprehensive understanding of homeostasis requires considering both the molecular mechanisms underlying cellular function and the integrated responses of organ systems to external stimuli. Finding the appropriate scale of analysis is crucial for gaining meaningful insights, along with recognizing the limitations of human cognition in dealing with extreme scales of space and time.

The exuberance of the reductive and analytic turn of the last 150 years created an exciting new world of microbiology and the economic benefits that flowed from its applications in biotechnology. Biology, formerly founded on organisms, now tells us it was genes that ‘pulled the strings of life’. Now we are not so sure.

The notion of hierarchy has been present throughout this remarkable transition. Are there physical or explanatory reasons for one scale or level to be privileged over another? Are there levels of evolutionary selection? Are there levels or degrees of agency related to organizational complexity, especially regarding cognition?

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

Biological thinking and explanation, both tacit and explicit, still treat the organism as a critical biological reference point, thus dividing biology into three categories: the organismal, sub-organismal (parts of organisms) and super-organismal (organism aggregates). The parts of organisms are ultimately subordinate to the goals of the entire organisms of which they are a part. While purpose, agency, intentionality, and value may be allocated to any level of biological organization, it is paradigmatically applicable at the scale of the organisms themselves as the focus of all these agential characteristics.

Science attempts total objectivity, but we can never view biology from nowhere, at no time, and with indifference. We cannot see things from the point of view of the universe, so there will always be a degree of human perspective to biology.

So, how does biological science understand and explain its temporal frames?[97]Biology must cope with vastly different time scales – from the microseconds of molecular interaction, to the instant of an insect’s wing beat, or the depths of geological time.
Process philosophy draws attention to our understanding, in a general sense, of ‘things’ as regions of temporary stability within the general flux of entangled processes. For humans, ‘things’ represent stasis – as bounded, autonomous, independent, and stable points of reference when viewed from a human temporal perspective. ‘Thingness’ is relative to the timescale.

For organisms, short-term behavior employs the behavioral language of action and reaction, stimulus and response. At this scale of time, adaptation to the conditions of existence does not entail inherited traits. However, over longer periods, behavior in the present creates environments of evolutionary adaptation that lead to inherited outcomes as we move from ethology to the world of functional adaptation, and evolutionary biology.
Static structures under temporal change become processes and behaviors. It is entire organisms – rather than their parts or collectives – that demonstrate what we mean by ‘life’ as they cycle repeatedly through the process of fertilization, growth, maturation and reproduction, senescence, and death. An organism does not carry its biological clock like a watch on a wristband: it may have an independent time-keeping mechanism, but that will be part of a functional whole.

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

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

One general feature of the ranking levels illustrated above, is that they are scaling factors, although the specific kind of scaling is not evident. While complexity is frequently quoted as the scaling factor (it is, after all, a hierarchy of biological organization) discussions of the biological hierarchy also relate to size, compositional factors (inclusivity, part-whole relations, nesting, etc.), and other factors.

(Science describes the world (including biological objects like molecules, cells, organisms, processes, and behaviors, etc.) at spatiotemporal scales appropriate to the context of the questions being asked. Choice of explanatory spatiotemporal scale is a matter of utility. Instead of describing the actual world, the biological hierarchy uses theoretical (metaphorical) levels of progressively greater size, complexity, and inclusion (higher levels) that are reducible to simpler and less inclusive (lower) levels. The explanatory use of real-world spatiotemporal biological objects at different scales avoids the epistemic and ontic confusion associated with the unnecessary theoretical objects, properties, and relations implied by hierarchical thought (levels of existence, domains of discourse, ranks, vertical spatial causal interaction, etc.).

Space & time

Our human brains present the world to us on the stage of space and time (see Immanuel Kant).

Our direct human experience of space, time, and the world is our species-specific perception of ‘here’ and ‘now’ in our human umwelt (see manifest image). All organisms adapt to and therefore interact with or ‘perceive’ their conditions of existence, so they spatiotemporal sense albeit very different from ours. But, whatever the biological ‘here’ and ‘now’ is for a fly, fish, dog, or daffodil, it will be different from our human ‘here’ and ‘now’. And, just because we have big brains does not mean that our ‘here’ and ‘now’ is the true ‘here’ and ‘now’ . . . it is just the human ‘here’ and ‘now’.

There are two key aspects to our human spatiotemporal world: our direct and species-specific experience of objects in space and time (as our human umwelt), and our intellectual capacity for hindsight, foresight and abstraction that allows us to represent the world at different spatiotemporal scales. We can imagine and contemplate the unseen interactions of macromolecules in our bodies, and the unknown evolutionary changes to life forms on planet Earth over billions of years, partly because scientific technology has allowed us to extend our knowledge beyond our immediate and biologically determined spatiotemporal boundaries. Scientific knowledge has extended our spatiotemporal horizons into new micro- and macro-scales. The bodies of knowledge that have accumulated at these scales have become new biological domains and academic disciplines, each with its own focus of structures, processes, and behaviors explained using its own principles and terminology.

Classroom & textbook

Talk of biological objects in space and time is a long way from the actual business of classroom biology. How does all this high-minded theoretical speculation translate into the classroom and biological textbooks?

Biology is greatly simplified when it is acknowledged that life is distinguished by its goal-directedness (its propensity to survive, reproduce, adapt, and evolve) as most obviously exemplified in the high degree of autonomy found in organisms. It is this autonomy that gives biological agents their purpose as objectively manifested in the behavior generated from the organism’s adaptive biological cognition. 

How does the representation of biological science as seen through the lens of spatiotemporal structures, processes, and behaviors improve on its interpretation based on a conceptual framework of hierarchical levels of biological organization?

Is this simply a choice that depends on the context or research question, the complexity of the biological system under study, or the level of detail and integration expected from an analysis?

 

      • it is a representation based on the latest scientific evidence
      • it provides a framework for empirical investigation based on actual objects in the world rather than on a theoretical (hypothetical, metaphorical, abstract) set of ideas
      • It offers greater precision and clarity because it focuses on specific objects with defined spatiotemporal scales and properties, opening the empirical gate to more detailed analysis and explanation of biological phenomena.
      • it replaces talk of hypothetical, metaphorical, or theoretical levels or ranks with empirically investigable objects
      • it allows for the complications associated with complexity
      • it replaces the notion of biological causation as operating in a linear way between levels of organization with causation as web of interaction occurring at many spatiotemporal scales
      • It simplifies ‘levels of organization and complexity’ to a single frame of reference devoid of putative ontological and/or epistemological ranks, making it a more versatile method for studying various biological systems.
      • It facilitates the integration and synthesis of information without the need for hierarchical and spatially charged ranking of levels thus promoting a more holistic understanding of biology,
      • it is an object-oriented approach that encourages interdisciplinary collaboration by providing a common language and framework for communicating shared information.
      • it provides a more comprehensive and insightful analysis of complex biological systems.
      • it provides a perspective that focuses on biology as process – the dynamic nature of living systems, the way they develop, adapt to their environments, and evolve. This leads to a holistic understanding of biology that focuses on the processes of growth, development, adaptation, and evolution that shape the lives of organisms.

A malign metaphor

We use metaphors all the time, not only in daily life but also in science. Why should the metaphor of hierarchical biological organization be considered problematic? A generous interpretation might point to its current acceptance, its few drawbacks, and its many heuristic benefits, not least of these being its educative value as an introduction to biological ideas and the place of biology in the scheme of things.

Metaphors can facilitate or impede our scientific interpretation of the world. They are useful when they encourage creative thinking that improves our scientific understanding, but undesirable when they lead to incorrect or misleading conclusions. Harm can be done when the logic of the metaphor leads to false scientific inference.

The notion of levels of biological organization is an explanatory metaphor that invites three strategies: clarification, an acceptance of its heuristic value, or abandonment. The reader of this article will acknowledge that a simple clarification or tidying up ‘biological levels’ is a vain hope so, providing our own specialist watertight interpretation is unlikely to find general acceptance. Perhaps its ideas can ground a fresh start.

It is the generality and abstraction of the notion of levels that allows such broad interpretation. It even manages, in a loose sense, to represent a range of academic subdisciplines of biology.

A recent publication endorses the overall heuristic benefits and general utility of biological levels. It considers levels of organization, ‘roughly, the idea that the natural world is segregated into part–whole relationships of increasing spatiotemporal scale and complexity’ as a core organizational principle for the scientific image of the natural world and, in general, embracing the idea as delivering on ‘the role of levels in the development and evolution of complex systems; conditional independence and downward causation; and the extension of the concept into the sociocultural realm’. However, the scientific opaqueness of the topic comes through in its analysis . . . the hierarchical image of the world ‘captures a variety of important methodological, epistemic, and ontological patterns in science and in nature,’ . . .  ‘its role in scientific reasoning is as a dynamic, open-ended idea capable of performing multiple, overlapping functions in distinct empirical settings’ . . . it is . . . ‘a dynamic, open-ended idea that evolves along with scientific understanding’.[18]

Levels may be used for various kinds of biological explanation or investigative modeling but, it has been claimed here, they are not empirically validated structures of nature, they derive from ranking criteria that express our metaphysical intuitions about the structure of reality.

Philosophers often address the difficulties of hierarchy theory under the unfortunate rubric, ‘levels of reality’.[8][9][10][11][12][13][14][15][16] A contemporary critical account of ‘levels of organization in biology‘ is given in an article in the Stanford Encyclopedia of Philosophy, updated in 2023. This article provides a valuable historical account of the topic and its literature but it opens with an unfortunate definition – ‘Levels of organization are structures in nature, frequently identified by part-whole relationships, with things at higher levels being composed of things at the next lower level’. There is ‘a strict correspondence between the constituents comprising a level and the predicates and theories linked with these constituents, meaning that levels of science neatly map onto levels of nature‘ – but see also [14][18].

This definition conflates the actual (what occurs in nature) and the theoretical but it does point out that this is ‘frequently a part-whole relationship‘. The article examines three influential papers in an attempt to determine the necessary conditions for a ‘level of biological organization’: those of Oppenheim and Putnam (1958), Craver and Bechtel (2007, 2008), and Wimsatt (1994 [2007]).

 

It is this paper that closely parallels the thinking and representation of the biological hierarchy in modern textbooks. Unsurprisingly, it has been criticized for its abstraction from nature itself. Both the metaphorical spatial levels themselves and the claim that higher levels are composed of entities at lower levels do not transpose easily to nature.

The Craver and Bechtel paper provides a specialist interpretation of levels as levels of mechanisms while the approach of Wimsatt explores the properties of levels as exhibited across different instances, regarding them as a ‘deep, non-arbitrary, and extremely important feature of the ontological architecture of our natural world, and almost certainly of any world which could produce, and be inhabited or understood by, intelligent beings’ and that they are ‘constituted by families of entities usually of comparable size and dynamical properties, which characteristically interact primarily with one another’ and, significantly, that ‘levels of organization can be thought of as local maxima of regularity and predictability in the phase space of alternative modes of organization of matter.

Over the years, science and philosophy have found a solution to the problem of abstraction; they ignore it. Levels have been granted a reality that they do not possess. This reification has resulted in a biological pluralism in which each level has acquired its own unjustified independent identity. Levels become ‘levels of reality’ or ‘levels of existence’ with paths of causation flowing up and down the hierarchy within and between levels like a human chain of command. Structures are interpreted as degrees of material containment. As reified ‘levels of reality’ how are the principles, terminology, and concepts of one level to be integrated with those of another level, and how does an increasing number of levels between two interacting levels influence the operation of biological systems?

The abstraction of theoretical levels is revealed in the difficulty of providing convincing answers to questions like, ‘What are the most significant levels of evolutionary selection?’ or ‘Isn’t agency evident at all levels of the biological hierarchy?’. So, for example, when asked which are the most important levels of evolutionary selection, cases can be reasonably established for genes, organisms, populations, and so on, because all biological levels are necessary for life. We then conclude that evolution operates at multiple levels. But what has happened here is that metaphorical, theoretical or token levels have become elevated in scientific significance to become type scales of existence, the obscurity of theoretical levels replaced by real-world scales. Much level-talk has already been replaced with talk of scales.

It is time to itemize, in summary form, the ways in which the biological hierarchy can mislead and confuse – the reason why science needs a fresh metaphor based on its latest research.

Spatial metaphor

The biological hierarchy offers a conceptual framework for biological ideas – the spatial metaphor of the world as a ladder of interacting structures. It is a traditional historical representation with a powerful intuitive appeal but an imaginary structure that could be replaced by other persuasive spatial metaphors such as trees, networks, and webs. The theoretical generality of its ideas greatly reduces its capacity for scientific application. A seemingly harmless explanatory device, it is a metaphor that misrepresents patterns of causal interaction.  While science today has empirical solutions to the problem of scale, can address must address the problem of scale.  Science can represent the world more directly than through the conflicting and confusing hierarchical spatial imagery of progressive nested containment or levels of organization.

Patterns of causation

In hierarchical biology, molecular processes are frequently presented as being essential to cellular functioning, which, in turn, affects tissue and organ behavior and therefore, ultimately, the organism as a whole. This is a linear relationship with molecular processes directly influencing cellular function, which then cascades through tissues and organs to the entire organism – the biological layer-cake represented pictorially in textbooks and other introductory biological texts. The complex is thus a causal consequence of the simple.

This seemingly innocent way of representing the biological world no longer accords with the latest scientific evidence. Being a hierarchy it seeks a source of authority and a chain of command, finding the source of greatest significance in its smallest analytic components.

What actually happens in biological systems is much more complex. Cells are components of tissues (not a layer of life existing below them) and the processes going on in organisms have repercussions at many interacting spatiotemporal scales. The thought of causation passing up and down levels of organization is not helpful here. Rather than operating as a simple bottom-up organized hierarchy, molecules, cells, tissues, organs, and organisms form functionally integrated systems. This interaction is dynamic and reticulate, more like a network or web where system components engage in complex, feedback-loop-driven relationships. This complexity leads to non-linear interactions that are not captured by this simple hierarchical model.

Contemporary agential biology does not interpret molecular processes as the foundational (most important) supporting layer of life. These layers only exist in a disembodied and theoretical (metaphorical or token) form. In their type form, in actuality, they are the biological ingredients of organisms as functionally integrated agents whose parts are ultimately subordinate to the goals of the organism as a whole (survival, reproduction, adaptation, and evolution).

(There are other pseudo-problems concerning the causal relation between levels, parts, and wholes and serious debate as to whether emergent properties at higher levels of organization can exert causal influence on lower-level components within a system. Does this consideration of causation, operating in a hierarchical mode, provide a greater understanding of complex biological systems?

It is hardly problematic to claim that events in the brain have a causal relation to events in the body – such claims are wide open to empirical investigation. Superimposing concerns about whether these events are passing ‘up’ and ‘down’ or ‘inter-level’ are empty, superfluous, and therefore unnecessary – just additional metaphorical hierarchical verbiage.

Is it scientifically helpful to assume that everything – in either theory or practice –  proceeds either top-down, bottom-up, or both – like the grand old Duke of York? We need a more scientifically mature way of representing the universe and biology.)

Ranks not objects

The hierarchy mistakenly treats molecules, cells, tissues, etc. as ‘levels’ when levels necessarily only exist in ranked arrangements whose ranking criteria are provided by a biological agent.

Reifies theoretical structure

It presents biology as consisting of physical objects arranged into layers of molecules, cells, tissues, etc.) creating the false impression that they can exist separately in this form – that they are separate and distinct when, in nature, they are functionally integrated into organisms. It treats levels as independent stratified objects when, in fact, they are contiguous e.g. tissues are comprised of cells, there are not two objects – cells and tissues.

Things not processes

It emphasizes biology as layers of objects that (secondarily) interact, thus ignoring or diminishing the central feature of biology as activity and process.

Uncertain ranking criteria

It makes explicit (hierarchy of biological organization) complexity as the key ranking criterion but uses size and containment as critical ideas

Hierarchical ranking

evokes ranking criteria associated with human hierarchies: power, authority, or overall significance

Space and time

The spatial imagery of the metaphor (rungs of a ladder) emphasizes the distribution of characteristics in space (size, form, containment): it is about physical structures.
This prioritization of space ignores or diminishes the influence of time and therefore the change and dynamic processes that are so important in biology. So, for example, it may conflate the significance of physical changes resulting from short-term behavior, and those resulting from long-term genetic alteration. It may ignore, for example, the relative times taken for molecular interaction, cell division, reproduction, and speciation.

Causation as command

The spatial imagery combined with the popular idea of hierarchies as chains of command treats causation and explanation as a biological chain of command proceeding ‘top-down’ or ‘bottom-up’.

Distance of causation

It creates an impression of causation separated by linear distance e.g. a short distance between cells and tissues and a long distance between molecules and organisms, ignoring reticulate causation.

Reductionism

Analytic reductionism combined with rank-value influenced by the ranking in human hierarchies encourages the reduction of higher-level structures, processes, and behaviors to those at lower levels which are then regarded as having greater ‘reality’, scientific significance, or foundational support.

Layered empiricism

Layering of biology suggests that biological problems, principles, and questions can be resolved at specific levels, thus ignoring their integration e.g. it may be assumed that evolutionary selection occurs at the molecular ‘level’, or that intelligence, agency, and cognition are properties of sentient organisms with no biological connections to other ‘levels’.

Fragmentation

Emphasizing the discreteness of molecules, cells, tissues, etc., compartmentalizes, isolates, and elevates their biological significance, ignoring the fact that they are subordinate to the goals of functionally integrated organisms as the most strongly and agentially individuated biological agents.

That is, biological phenomena often involve interactions and feedback loops acting simultaneously across many levels of organization and with consequences for multiple timeframes. This dynamic complexity is not captured in a ‘static’ hierarchical framework of biological objects. Levels investigated in theoretical isolation from one another ignore the real-time functionally integrated interactions occurring simultaneously across levels of organization.

Process

The significance of process is diminished. Living systems consist of structures, processes, and behaviors engaged in the general agential processes of survival, reproduction, adaptation, and evolution which include development, homeostasis, and other metabolic processes. Levels of biological organization are listed as objects whose function and process are subordinate to their structure.

Top & bottom

Notions of ‘top’ and a ‘bottom’, ‘higher’ and ‘lower’ create the superordinate and subordinate and associate greater or lesser reality, importance, or significance with rank.

Explanatory direction

It creates a directional explanatory perspective in which the explainer assumes the perspective of the part or whole.  How (more important?) higher levels can be explained in terms of (using the language, principles, and concepts) of their parts, or how the parts (being more important?) can be explained (using the language, principles, and concepts) of their wholes.

explanatory metaphorical levels are a theoretical explanatory metaphor that imposes a misleading conceptual framework on biological science that does not adequately capture the branched structure of evolution. It misrepresents the complexity and dynamism of biological systems as processes. Its representation of causation as passing through metaphorical layers distributed in vertical space  ly spatial layers of the spatial metaphor in a ‘top-down or ‘bottom-up’ way contends that the hierarchical model with its emphasis on levels, ranks, and top-down causation, obscures the interconnectedness and emergent properties of organisms. The author advocates for a more process-oriented approach, focusing on spatiotemporal scales and understanding biological phenomena as dynamic networks of interacting components.

 

This article critiques the use of the biological hierarchy as a framework for understanding life, arguing that it misrepresents the complexity and dynamism of biological systems. It contends that the hierarchical model with its emphasis on levels, ranks, and top-down causation, obscures the interconnectedness and emergent properties of organisms. The author advocates for a more process-oriented approach, focusing on spatiotemporal scales and understanding biological phenomena as dynamic networks of interacting components.

Commentary

This article argues for a deflationary to eliminativist interpretation of hierarchy theory in biological science.  

The hierarchy of biological organization is a tribute to invention and intuition. It is a concept that evolved over time, influenced by various philosophical and scientific ideas. It arose out of the Great Chain of Being as an unchanging hierarchical order of existence. Its philosophical and scientific strength lies in its incorporation of our many intuitions about the graded nature of existence, most notably its historical spatiotemporal progression in size, inclusiveness, and complexity.

During the Renaissance and Enlightenment scientists like Carl Linnaeus (1707-1778) developed systems of classification based on the shared characteristics of species placed in hierarchical groupings. In the 19th century Charles Darwin (1809-1882), with his theory of natural selection transformed the understanding of the permanence of species by introducing the theory of natural selection, common descent, and change over time. Modern developments have continued to built on the idea of life as a dynamic evolutionary process.

Metaphor relates complex and often abstract ideas to familiar experiences and this usually enhances our understanding of the world. The critical study of metaphor in daily life and science did not develop until the late 20th century.

Once the goal-directed organism is accepted as a primary source of biological agency and its goals are understood then levels lose much of their explanatory power. Abstract (token) levels are replaced with (type) spatiotemporal biological structures, processes, and behaviors.  Levels lose significance when the biological world is perceived as organisms, their parts, and their collectives. Token hierarchical levels are replaced by structurally and functionally integrated type organisms and type scales. The biological pluralism of interacting layers is replaced by organisms studied at multiple scales.

Levels of the biological hierarchy are hypothetical structures established by subjective ranking criteria that reflect our interests and general intuitions about the structure of the world. They have, over time, become misleadingly reified, acquiring independent identities.

These hypothetical structures may be replaced by actual spatiotemporal scales that do not have separate identities but reflect different perspectives of the same phenomena. The use of a particular spatiotemporal scale is determined by convenience or context. For example, there is little point in describing sociology in terms of molecules.

Metaphor

Plato and Aristotle viewed the universe as a vast organism whose parts contributed to the functional organization of the whole. This imagery has echoed down the ages. The Catholic metaphysician Teilhard de Chardin regarded existence as an evolutionary process of cosmic unfolding. Another image is of a self-regulating biosphere that creates the necessary conditions for its own persistence including natural provision for human beings. This is the imagery of Mother Earth or Gaia, and it probably resembles the view of our prehistoric ancestors and the Christian interpretation of nature as something provided by God to sustain human life.

During the Scientific Revolution, and later Industrial Revolution, a mechanical metaphor seemed more apt as a description of ‘everything’. Everything was purposeless matter in motion, ticking over like a machine that is constrained by rigid deterministic and absolute laws.

Today the universe is often compared to a brain or computer.

Metaphors can be misleading when they are treated as ‘reality’ (a reliable representation of the world) because if we assume they are real, this can lead to unjustified inferences. Scientists, for example, frequently forget that scientific facts (empirical generalizations) are our best possible explanations (hypotheses), not ultimate reality.

Surely, today’s science could not fall into a simple metaphorical trap? But perhaps it could be when the metaphor expresses something that cannot be expressed in any other way.

To understand and explain something complex, like the entirety of the universe or a general concept like ‘life’, we construct mental images of what we think they must be like. Then, once we have established a mental characterization or picture, we have a framework on which to build our thinking.

Finding a place to start might seem a fool’s errand, but biology textbooks must start somewhere and – whether implicitly or explicitly – they convey to the reader a scientific representation of the living world.

Though we can attempt to define the key characteristics of life, we are accustomed to visual or metaphorical representations that make complex problems easier to grasp. The popular metaphorical representation of biology as a hierarchy of levels of biological organization is an example.

But how do we represent the entire universe as everything – including every material object, every form of matter, our conscious experience . . . and so on.

The empirical answer to such questions tends to fall back on what physics tells us about what there is in the world. Our intuitions tend to fall back on sizes, degrees of inclusion (relation of parts and wholes), degrees of complexity, and impact on our lives, all arranged in time and space. Things (science has historically preferred static and stable permanent physical objects and their properties, rather than dynamic and changing processes) but, either way, it helps if the metaphor can account for our grounding ideas of space and time because this is the stage on which everything plays out.

Scientific hierarchies

Social hierarchies and the hierarchies of daily life are overwhelmingly based on functional roles, power, and authority.

In biology and science hierarchies are attempts to represent ‘reality’ as the way the world actually is. But the world is what our biological conditions and intuitions make it. Without prioritization we cannot think. But the world itself is not prioritized, so how do we proceed?  Without prioritizing, we cannot think. But, by prioritizing we distort ‘reality’.

Classification orders things according to some purpose. Groupings of progressive inclusion are a way of addressing scale.

Our human intuitions are evident in the conventional textbook arrangement of living objects into hierarchical levels of biological organization in which the ranking criteria are inconclusively related to physical objects of different scales, inclusiveness, and complexity – as in the transition from molecules to cells, tissues, organs, organisms, and populations. While interaction is implied in this representation,  it is physical objects (things – not processes or behaviors) that dominate this scheme.

Following the inferential logic of this hierarchical metaphor, we can mistakenly reify (ontologize or make real) the imagery of existence as interacting physical layers, like geological strata or a layered cake. 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, independent, and self-justifying object of study while ignoring the dynamic functional integration of these objects within the wholes that we know as organisms.

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.

One consequence of analytical reductionism is the strongly held belief that matter is ‘grounded’ in the fundamental (smallest) particles out of which it is comprised. These small units are the bricks out of which all physical objects, including life, are built.

Interestingly, modern science has inverted the former religious and human hierarchies. In our common-sense world humans are elevated forms of matter with consciousness, moral awareness, the capacity to think and make rational decisions. It is the complexity of matter that exists in human brains that, if there are no gods, is the most complex or ‘highest’ and most significant manifestation of matter.

Yet, today, this emphasis on complexity has been inverted as an analytic reductionist approach to science ascribes to the smallest and simplest possible particles – the greatest scientific significance. The most credible science occurs at the ‘bottom’ of the material hierarchy, and the least credible (most scientifically opaque) at the ‘top’. Humans are of course staggeringly complex but, ultimately, they too are composed of, and grounded in, matter’s simplest constituents, its ‘fundamental particles’. If explanation proceeds analytically then ultimate significance or explanatory power must lie in the finest resolution of the analysis.

Here it is claimed that we place greater significance, value, and importance on one ‘level’ rather than another from our habit of attributing rank value to most of the hierarchies we use in daily life. Scientifically we may ‘ground’ science in physics because of our strong scientific inclination towards analysis and analytical reductionism. However, any prioritization (e.g. level ‘a’ is more fundamental or foundational than ‘b’) is added by us, it does not lie in the world. For the benefit of philosophers, I am advocating a ‘flat ontology’ in which an electron exists equally with an elephant or a geranium. Certainly a geranium is, for example, more complex than an electron – but the choice of the rank-value criterion ‘complexity’, is ours.

Today, following the lead of the Scientific Revolution, many scientists believe they are getting closer to ‘reality’, to the way the world ‘actually is’, by drilling ever deeper into matter.

Is there an echo of the Ladder of Life (inverted) when we locate physics as a foundational science? Are there other misleading hierarchical assumptions built into this picture of the world?

So far it has been claimed that the use of hierarchical metaphor in science causes confusion and error by introducing rank-value along with unnecessary objects, structures, and relations, by creating ambiguous and confusing causal relations, and by unjustifiably emphasizing the process of analysis over that of synthesis.

Clearly, we would be doing science a service to remove all this talk of ‘up’ and ‘down’, ‘higher’ and ‘lower’, and of ‘levels’ and the like.

But, as we have seen, metaphor is a convenient way of dealing with something that is abstract and complex. Perhaps hierarchy-talk serves its purpose by providing a simple mental representation of the connection between all matter?

The leading question now becomes: ‘If there is a better way, what would it be like?’The leading question now becomes: ‘If there is a better way, what would it be like?’

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.

In hierarchies, explanations can proceed both up and down, by both analysis (decomposition) and synthesis (composition). That is, we can explore the world from two perspectives – ‘top-down’ or ‘bottom up’. In a top-down explanation the parts are explained in terms of their relationship to a greater whole. Examples of synthesis are the way our brain influences our bodily behavior, or a project-manager organizes the objectives, milestones, and tasks of an organization to achieve an overall goal.

Synthesis tends to be associated with agency, intention, forward direction, goal-directedness, purpose, adaptation and the disciplines of ecology, ethology, psychology, and sociology, while analysis is associated with notions of grounding, foundation, and reality, and the disciplines of physics, chemistry, and microbiology.

Science benefits from explanation by both analysis and synthesis. Top-down explanations offer a holistic and sometimes simplistic overview of complex systems, while bottom-up explanations may investigate underlying mechanisms and principles in detail that obscures the bigger picture. The reason for selecting one approach over another may depend on context but it needs a clearly articulated justification.

If wholes at lower levels are parts at higher levels then explanations can proceed both up (explaining parts in terms of their relationship to a greater whole) and down (explaining wholes in terms of their constituent parts). This is discussed here as the contrasting relationship between analysis and synthesis (reductionism and holism). The spatial notions of up and down is sometimes associated with science applied backwards or forwards. The intentional and goal-directed life-sciences being forward-looking with physics and chemistry more backward-looking in character.

sociology, psychology, biology, even physics and chemistry.

When we think and talk about these scientific, linguistic, and academic domains using the language of ‘levels of organization’ it evokes physical imagery, like layers of matter on top of each other like geological strata. This physical metaphor gives the layers a separation and independence that is misleading because we are not looking at new things, we are simply shifting our focus – seeing things from a different perspective or point of view. And the selection criteria for this point of view tend to relate to size, inclusivity, complexity, and value (importance, significance).

The way we structure the world reflects the intuitive character of our mental processing – our intuitive segregation, classification, focus, and ranking of the objects of our experience. As biological agents our minds have evolved in support our goals of survival, reproduction, and flourishing: they establish categories of experience that are focused, organized, classified and prioritized in relation to goals, and as a prelude to action.

In establishing a representation of the external world our minds have the capacity to segregate it in many ways. The way we do so depends on our goals. We need a focus of attention relevant to need and then we classify the objects of experience in a way that facilitates the action needed to attain those goals.

The important point is that our different descriptions (domains of experience, discourse, academic disciplines) are not describing different objects, but different modes of perceiving and explaining. The difference is epistemological not ontological.

Hierarchical thinking presents us with a metaphorical structure of biological objects arranged above and below one another in vertical space.

On what grounds do we select the objects to be organized in this way – what is special about these objects rather than others? And on what grounds do we elevate (and sometimes prioritize in significance or rank more highly) one object above another? What are the selection criteria for these levels?

How do we explain the real-life interactions that occur between these explanatory levels?

It is the structuring of ideas into higher and lower levels that is the special feature of hierarchical thinking, and it brings with it a suite of inextricably associated ideas, several of which are profoundly misleading.

First, as a representation of the world, the categories of the metaphor become the lens through which we view – and make inferences about – the world. This is the danger of metaphors: they can be interpreted literally.

This might seem like a simple trap that would be quickly spotted and avoided.

However, it is rarely pointed out that hierarchy, as applied in biology, is a metaphor used as an explanatory heuristic – a convenient way of representing the complexity of life in a simple way that can be given visual representation. The biological world is not literally organized into layers like geological strata, so the biological hierarchy is not attempting to describe the way the world actually is (ontology), it is just a simple way of representing our knowledge of it (epistemology). But science has been lured into following the logic of the metaphor as we frequently both think and speak of phenomena in a top-down and bottom-up way.

But why should this be a problem: science is full of metaphors.

The Stanford Encyclopedia article (mentioned above) opens by stating that levels are ‘structures in nature’ . . . and, whether this is intended as a statement of ontology or epistemology, it is precisely here that trouble begins.

Though ranking, in itself, is a form of prioritization, the significance of the levels may be of little consequence, as when we make a list of people according to their heights, arranged from tallest to shortest, or of their hair colour from the darkest to fairest.

However, human hierarchies are generally value-charged: the higher and lower ranks are associated with social, moral, organizational, or political worth, importance, or significance. That is, by habit we allocate value to the ranks of a hierarchy. This is referred to here as rank-value and, usually, being higher in a hierarchy is ‘better’.

Scientific language evolves, and the perception of biological causation as a linear interaction between objects layered in vertical space will gradually dissolve along with its deeply embedded metaphysical assumptions about the nature of reality.

Utility

How does the biological hierarchy assist biological explanation.

How are levels useful? Higher levels of organization arise from lower components e.g., how cellular functions lead to tissue functions (emergence), and how higher levels can be explained in terms of their units of composition (reduction). It also indicates how changes at one level can affect other levels higher levels e.g. organism health and population dynamics.

 

Hierarchical thinking reflects the mental necessity of prioritization. The world itself is not prioritized but, if it is to be considered in hierarchical terms, then its contents must be prioritized and ranked.  

The impulse of scientific explanation is analytic reduction in which (lower) parts explain, support, and cause the (higher) wholes. Hierarchical thinking misleadingly translates this into a physical world whose ‘reality’ is grounded in physics and chemistry.

How can biology be represented simply and engagingly while being based on scientific evidence that gives due attention to the significance of agency and process in biology?

In actuality biologically causal events do not pass up and down between theoretical levels of organization, they interact at many spatiotemporal scales with feedback loops and consequences for multiple timeframes. A more processual scientific interpretation might consider biological objects as agential spatiotemporal structures, processes, and behaviors that are functionally integrated in their goals of survival, reproduction, adaptation, and evolution.

The notion of levels can be dispensed with altogether and replaced by spatiotemporal scales of explanation that take account of dynamic change and process with space and time interacting to yield system-level behaviors. This integrative view helps bridge molecular details with organismal outcomes. This resembles more closely the physical nature of the world and life as a dynamic, agential, and communicative process that is scientifically investigated at many spatiotemporal scales.

Metaphorical ‘levels’ are more appropriately treated as ‘webs’ or ‘networks’ of communication whose nodes are spatiotemporal centers of prediction, explanation, and activity (molecules, cells, genes, organisms etc.) as systems of regulated pathways of information processing. Causation then becomes the consequence of information flow across these networks.

The focus of biological agency on the ultimate subordination of organism parts to the unified and functional integrated goals of entire organisms reverses the former emphasis of analytical reductionist thinking on basic chemistry and physics.

By focusing on the nodes of biological networks – their connections, interactions, and interdependencies – hierarchical language can be avoided altogether.

Though more self-contained than other biological nodes, organisms are nevertheless spatiotemporal systems open to energy, nutrients, and many other kinds of information flow.

(Aristotle claimed that the question ‘why?’ has no end – it leads to an infinite regress or vicious circle. Thinking can only progress when we establish the most secure foundation possible. Explanations of physical objects, he thought, are our response to four basic questions: ‘What is it made of?’, ‘How did it arise (what was its origin)?’, ‘What are its uniquely defining properties?’, and ‘What is it for?’. He also pointed out that everything seems to reduce to ‘objects, their properties, and relations‘. That’s not bad for over 2000 years ago.)

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

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First published on the internet – 1 March 2019

. . . 15 May 2024 – Transferred and modified from a former article simply headed ‘hierarchy’
. . . May 2024 on – undergoing constant daily revision
. . . 22 August 2024 – begin substantive revision of entire article

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   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.

Hierarchical thinking

The prioritization of actions is a critical ingredient of the goal-directedness of every biological agent as a necessary agential property of adaptation. Every action, of every organism, is ‘about’ or ‘for’ something - that something being the prioritized focus of attention.

In the limited agential case of the human self-conscious intellect, action is supplemented by thoughts and language with every thought and every sentence having a focus. Prioritization makes explanations. descriptions - and indeed thinking itself - possible. When we explain something, we prioritize relevant details and select key points to convey understanding. Similarly, when describing, we choose what to highlight. Without prioritization explanations and descriptions would be chaotic. But, while the prioritization applied by our minds brings order, in daily experience it is constantly adapting to context, re-ranking with our shifting focus of attention.

Ranking is, as it were, a form of prioritization. While prioritization orders things (usually) based on criteria of relative importance, value, authority, or significance, ranking groups things into prioritized levels.

Prioritization/ranking guides our actions, shapes our thoughts, and structures our language; it creates meaningful experiences and is the driver of the goal-directedness that gives all life purpose. Because it is a pervasive feature of our experience we assume it is a part of the world rather than a product of our biological agency.

Tokens & Types

Theoretical biology consists of abstract concepts, theories, models, and principles that provide the foundation for biological practice as the empirical investigation of life. Theory and practice are intertwined and this is a major source of confusion when discussing the concepts of the biological hierarchy.

Ambiguity is reduced by distinguishing between theoretical entities as tokens, and objects in nature as types. For example, the statement that cells have a membrane and nucleus does not refer to actual (specific) cells in the world (types), but to cells in general (tokens). When the concept of 'cells' arises in discussions of the biological hierarchy, it is often unclear whether they are token or type cells.

For our purposes, tokens are theoretical categories used in a general or abstract sense while types are spatiotemporal instantiations of these tokens and therefore open to empirical investigation.

The hierarchy of biological organization misleads because users confuse and conflate the distinctions between levels and scales, ranking and classification, tokens and types. We speak of taxonomic units, taxonomic groups, and taxonomic ranks in both theoretical and applied senses. It is this conflation of the theoretical and actual that is at the heart of the hierarchical dilemma, the confusion between the epistemic and ontic - whether we are discussing biology in theory, or biology in practice.

Supervenience & Multiple Realization

Hierarchical thinking is often invoked in philosophical discussions of supervenience and multiple relization.

Physicalism, for example, is the view that everything supervenes on the physical – meaning, hierarchically, that higher-level properties, entities, or phenomena are ultimately dependent on and determined by the physical properties and arrangements of lower (ultimately lowest-level) physical entities like elementary particles. Where, for example, changes in the supervenient properties (e.g. mental states) depend on changes in the subvenient properties (e.g. physical states). Changes in higher-level physical properties must have corresponding changes in physical properties of lower levels.

Multiple realizability refers to the idea that a particular higher-level property can be realized by multiple different lower-level configurations or types – that different materials, structures, or processes can produce the same higher-level outcome.

Supervenience concerns how higher-level properties depend on lower-level ones, while multiple realizability highlights the possibility that a single higher-level property can be realized through different lower-level instances.

The philosophical tension arises when trying to reconcile hypothetical levels with what is going on in the world. We tend to follow the logic of the hierarchical metaphor of levels, falling back on the hierarchical intuition of causation flowing through metaphorical levels like a top-down or bottom-up chain of command. This degree of abstraction seems to have little practical application except perhaps in mathematical modelling and systems theory.

Taxa and ranks

A taxon (taxonomic group) is a group of organisms classified together based on shared and objective diagnostic characteristics, the grouping criteria. A rank is a theoretical structural element (level) of a hierarchy (or hierarchical classification system). Eucalytus is a taxon at the rank of genus. This apparently straightforward definition conceals the ambiguity of understanding and interpretation of what is meant by ‘rank’.

Scientists prefer objective criteria that are amenable to empirical investigation and so ranking criteria are sometimes incorrectly aligned with objective grouping criteria such as morphological characteristics or phylogenetic relationships. Ranks are a subjective ‘level’ or scale of description – but this needs explanation.

Communication is facilitated by the use words appropriate to the scale of interest. With a person as a basic unit, words like ‘population’, ‘football team’, ‘city’, and ‘community’ are simple summary ways of indicating groups of people that might otherwise require tedious explanation. The words Eucalyptus regnans, Eucalyptus, Myrtaceae, and Mytales designate taxa in a scale of increasing inclusiveness. These words allow us to speak about related objects at progressive degrees of containment or scale.

So, why do we need ranks – after all, the work of dividing up the living world into intellectually digestible units is all done by classification: it does this using objective criteria that establish related taxa over a range of scales?

The use of ranks facilitates communication by adding further abstraction: it allows us to speak of taxa in a more general way by giving them collective names at a particular scale, the scales named, for example, species, genus, family, order.

Ranking words like ‘species’, ‘genus’, ‘family’, and ‘order’ facilitate communication, not by relating to objective criteria like morphological characters or evolutionary relationships, but by establishing the scale of discourse. The capacity to communicate abstractly is lost when only the names of taxa are used. Sometimes we want to talk about herons, starlings, and sparrows, and sometimes we want to talk about birds. Ranks help streamline communication by providing the language that facilitates the discussion of organisms at abstract graded scales.

Levels

Both science and philosophy employ the spatial metaphor of ‘levels of existence’ or ‘levels of reality’. This concept provides a way of picturing and making more concrete (reifying) our concepts of gradation and degree. Vagueness permits the application of ‘levels’ to a wide range of scales, properties, and perceptions. However, the benefit of generality – its wide application – can be seriously misleading when we try to translate this spatial metaphor into a scientifically acceptable representation of the world. 

The hierarchy of biological organization seems to combine considerations of (at least) size, inclusiveness, and organic complexity (individually or in combination) but its versatility permits its application to academic disciplines and domains (physicochemical, biological, psychological, social,  etc. levels) and so on. Though usually applied to structures (molecules, cells, tissues, organisms, etc.) and when related to actual physical properties therefore translates readily from the abstraction of ‘level’ to the empirical properties associated with scientifically measurable ‘scales’ of various kinds that are readily communicated.

The reification of explanatory levels into strata of reality creates a mental representation of the world based on the language of spatial metaphor in which objects of scientific or philosophical investigation are situated in vertical space, being higher and lower than one-another, with causation flowing like a chain of command top-down, bottom-up, horizontal – or some variation of this. This is not a harmless metaphor since it diverges substantially from the contemporary view of causal interaction as usually proceeding more in the form of a network of causally connected hubs.

Science is better served by treating levels as scales, contexts, or perspectives of understanding. Human behavior can, for example, be studied as a chemical, biological, psychological, or social phenomenon without these scales of understanding being ranked against one-another.

Though a potential tool for modelling some complex systems it is a concept best discarded from biology.

The Scientific Universe