Biological hierarchy

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 an informal classification of the key elements of theoretical biology expressed in a simple and informative way. It provides a more general and accessible introduction to the subject matter of biological study than the species-focused scientific taxonomy of the Tree of Life.

As a classification system, it presents us with key biological objects to be classified (molecules, cells, tissues, etc.) arranged into groups (ranks or levels) that represent the major objects of biological study. The selection criterion – the reason for arranging these objects into a prioritized sequence of superimposed layers – is usually regarded as their degree of organizational complexity. 

Hierarchy theory classifies biological objects into theoretically stratified levels or ranks that are distributed in metaphorical vertical space. This metaphor represented pictorially elicits the spatial language of ‘up’ and ‘down’, ‘top’ and ‘bottom’, ‘higher’ and ‘lower’, ‘above’ and ‘below’. Also, position within a hierarchy implies a location within a causal chain of command that is related to authority or influence that is either imposed from ‘above’ or supported by its foundations ‘below’.

This impression of interacting hierarchical levels of biological organization seems a harmless heuristic – an explanatory tool to facilitate our understanding of life’s complexity. However, it is often mistakenly treated as reality (reified, ontologized) – as a representation of biological systems that can be used to guide scientific inference.

Biology represented in this hierarchical way is built on a foundation of physics and chemistry. Molecules are the smallest units of biological organization that unite to form cells, which are the basic structural and functional units of life. Cells are then organized into tissues, organs, organ systems, and finally organisms and their aggregates. This is like a causal chain that cascades ‘upwards’ through levels that, reminiscent of evolution, pass from the simple to the complex suggesting that the complex is subordinate to, or grounded in, its simple constituents. 

The levels of the biological hierarchy have a degree of explanatory independence and are, to some extent, expressed in the discrete pluralism of biological subdisciplines (genetics, cytology, anatomy, histology, ecology etc.) each with its own domain of principles and terms.

The conceptual difficulty is that in actuality (in nature) these ingredients of biology are united into complex, dynamic, and goal-directed networks of communication. These systems are unified and functionally integrated as organisms (the canonical autonomous biological agents) whose parts are ultimately subordinate to the goals of the organism as a whole. Represented in this way the biological world does not consist of either ‘equal’ levels of impersonal living matter arranged in order of increasing organic complexity, or of living matter that is grounded in physics and chemistry. Instead, it consists of the processual interactions related to organisms – their parts and their communities.

There is a confusing contrast between the explanatory convenience of hierarchical representation and the picture of the living world that emerges from contemporary scientific evidence. The biological hierarchy is misleading for several reasons: 

• • • It suggests misleading ‘top-down’ and ‘bottom-up’ paths for the flow of causation, explanation, and information.
    • It imposes human ranking (hierarchical) criteria for levels that are not ranked as superordinate and subordinate in nature. 
    • It presents the key ingredients of biology as physical objects (molecules, cells, tissues, etc.) which diminishes biology’s inherent character as dynamic process.
    • It overemphasizes the spatial character of part-whole relationships to the detriment of temporal factors that emphasize biology as dynamic process.
    • It imposes metaphorical and confusing directional thinking on causation, explanation, and information flow.
    • It treats actual physical scales of existence as hypothetical explanatory layers.
      

This article is one of a series considering the nature of classification including the way we classify ‘everything’ in our worldviews and modes of representation.  The framework of hierarchical ideas we use to classify biological science is an informal classification of the living world. More specific articles address the way that we classify plants in both a general and scientific way. The wikipedia article on hierarchy provides some background on the concept of hierarchy and may be read alongside the article on levels of organization in biology in the Stanford Encyclopedia of Philosophy as an introduction to this article.

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.

This was a simple metaphorical representation of everything in the physical, moral, and spiritual world located on the rungs of a ladder-like structure and arranged from top to bottom in what became known as the Great Chain of Being or Ladder of Life (see illustration above).

Confronted by the complexity of existence this metaphorical picture provided a simple and compelling metaphysical (speculative) hypothesis about what existed in the world, how it interacted, what was desirable or undesirable, and what it was all for.

The Great Chain of Being probably influenced Linnaeus’s classification of living organisms into relationships represented by a nested hierarchy of classification categories (ranks). Linnaeus believed in the Special Creation of individual species by God, but his boxes-within-boxes taxonomy anticipated Darwin’s later theory of evolution by modification from common ancestors.

Science rests on metaphysical assumptions about the way things are – our general intuitions about the world. We all have these intuitions, even though we might not be consciously aware of them. We do not question our everyday experience of the world around us (see manifest image) even though science might contradict our common-sense understanding of it (see scientific image).

Metaphysics and empiricism are two distinct explanatory approaches to the world. Metaphysics is the abstraction of empirical findings to a form not accessible to experimental science, but that does not mean it is disconnected from science. Metaphysics deals with speculative questions about the nature of reality, existence, and the ultimate structure of the universe, while empiricism deals with observation, experimentation, and verification through sensory data. Though metaphysics uses concepts that reach beyond empirical observation, empirical evidence can support or challenge these metaphysical hypotheses.

Scientists generally have little time for the seemingly irrelevant and unproductive ruminations of philosophers. This means that scientific time is not wasted on untestable claims, but there is a downside, unverifiable metaphysical assumptions may be accepted without criticism.

The representation of the living world as an interactive hierarchy of levels of biological organization is an excellent example of metaphysical speculation because it prompts questions about the nature of biological reality and the best way of representing it. How are we to represent life, in thought, word, and picture?

This article examines the dangers associated with the uncritical use of a hierarchical metaphor to represent ‘everything’ – especially the theoretical structure and organization of the living world and the academic disciplines that study it.

Biological philosophy

A hierarchy is a system of objects arranged from higher to lower in graded levels or ranks like the rungs of a ladder. A broad definition of a biological hierarchy (their are many minor variations) is that it organizes the elements of life into different levels based on their organizational complexity.

The biological hierarchy is a simple representation of life that provides an explanatory framework of ideas, structuring the complexity of life into a set of manageable interrelated categories.

We need to be clear about the ideas that are embedded in this mental tool because levels of existence are frequently referenced by philosophers and scientists alike, giving the idea authoritative endorsement. But is this endorsement justified?

Science admires the elegance of simplicity. Consider the power of the equation e=mc². Simplicity is achieved by abstraction. Why clutter the world with all sorts of objects, properties, and relations when the many may be reduced to one – perhaps matter, mind, number, energy, or information? An organism is, after all, just a physicochemical process.

There are several problems with this approach: answers must be meaningful;  they must address the problem at its relevant scale, they must address the concept of reality since the claim is that the many are ‘really’ elaborations of the one – that the one can be explained in terms of (reduced to) the one.

This draws our attention to two major factors, one to do with our mental structuring and processing, and the other to do with the external world.

First, the pragmatic or utilitarian nature of mental processing and programs of reduction. What would be achieved by describing a tiger in terms of number or information? And even if we had such a description, would it help us to answer the kinds of questions about tigers that we think are scientifically important?

Second, a sand heap may be just lots of sand grains, but is it helpful to say that a tiger is just a lot of molecules? Here the properties and relations of molecules when aggregated seems very important. A tiger is very different from a heap of molecules: it is not the same kind of aggregation as a heap of sand.

How to describe the nature and direction of their causal relationship. This does (see characteristics of nested hierarchies) is a useful, it does not capture the complexity of non-linear interactions that occur in living organisms. “ (re-express this in normal language).

How do hierarchical language, hierarchical thought, and hierarchical imagery influence the way that we do biology?

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 the flux of sensations, percepts, and concepts flowing through the neurons of our brains into meaningful experiences? Sensations might have no order, but if we are to survive in the world these sensations must be placed in context; they must make sense. And to be meaningful they must be put in order. Science itself is a search for the order in the world external to minds but as interpreted by our minds. We order the world in an infinite number of ways – from formal and deliberate classifications like the scientific Periodic Table of Elements, to the unconscious way we focus our attention when driving.

There are, among our various human mental faculties, four necessary and interconnected preconditions (innate predispositions) that must be present if we are to operate effectively in the world: segregation, focus, classification, and valuation.

To understand and explain what is going on here, we must establish the key ingredients of the mental ordering process.

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 an agent as orderer.

These are crucial 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.

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.

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.

4. Purpose/Valuation (ranking, adaptation) – 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.

These interrelated mental capacities 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. Together they constitute our means of mental adaptation, both unconscious (as our attention constantly shifts from one thing to another), and conscious (as we make intentional decisions).

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).

The mental process that combines segregation, focus, classification, and purpose to provide order is referred to here as hierarchical thinking. These properties of the human mind seem like sophisticated evolutionary developments that are unique properties of complex brains. However, on close inspection, it is evident that they are not just innate predispositions of the human mind, they are preconditions for any biological agent. They are necessary principles of biological cognition that are represented across the community of life in graded physical form as a general-sense cognition that is present in all organisms.

Hierarchical thinking – the capacity of an agent to discriminate objects of experience, focus on those that are significant to its umwelt, and then to classify and prioritize them as a guide to behavior – is a universal characteristic of biological cognition and biological agents. It is a necessary cognitive precondition for adaptive goal-directed behavior. 

Hierarchical thinking is deeply embedded in human patterns of thought. It is, for example, apparent in the structure of our language.

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

Metaphors

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, they can also misguide and confuse.

The Ladder of Life is clearly a metaphor: is the Ladder of Biology a metaphor?

Everything

The Great Chain of Being is an attempt to classify everything that there is. It is a hierarchy of being, existence, or reality, and is therefore hierarchical thinking at its most abstract and generalized extreme.

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 number, information, space-time, energy, quantum field fluctuations, elementary particles, or mental sensations. Is the universe more like an organism, a clock, a ladder, a tree, a web, a brain, or a computer?  Who decides, and on what grounds?

Aristotle claimed that all explanations (answers to the question ‘why?’) can lead to an infinite regress or vicious circle: thinking can only progress when the securest possible foundation is established. 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.

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? Is there one thing or many – what degree of abstraction or reduction should we accept in explanation?), size (how big is it?), scope (what are the best categories of containment and inclusiveness i.e. where is it located in a system of parts and wholes?), and complexity.

The universe does not categorize and prioritize – that is what agents do. Chemical elements may exist independently of human minds but the Periodic Table does not. All classifications reflect the purposes of agents and human scientific classifications attempt to minimize the impact of subjective interpretation.

Metaphor & Reality

We need to know what exactly the hierarchy of biological complexity tells us about the world – why it should be considered a useful heuristic. Is it just an explanatory tool that shouldn’t be taken too seriously since it operates like a literary device – a metaphor or simile saying that biology is ‘as if’ or ‘like’  this – or does it imply more than this? As a conceptual framework – a set of categories and ideas – is it a reliable representation of the biological world . . .  and does it matter if it isn’t?

Some of the appeal and power of the biological hierarchy derives precisely from its generality: it can be interpreted in many ways. It even manages, in a loose sense, to represent a broad range of academic subdisciplines of biology. Granted some explanatory license in presenting ideas to students of biology, we nevertheless would like such a widely accepted representation to reflect our best science. However, as a generalized representation, it implies (at least) the following:

• • • • kinds of things
      • sizes of things
      • levels of physical organization
      • frames of explanatory reference (degrees of abstraction)
      • degrees of inclusion (part-whole composition)
      • degrees of organic organizational complexity
      • spatiotemporal scales of existence
      • causal pathways

How reliable are these implications? Each of these interpretations needs closer scrutiny, but from this list alone it is clear that a simple clarification or tidying-up of the concept of ‘levels’ is a vain hope.

Biology

How do we decide what is most important in biology . . . . where do we start? What are the characteristics that distinguish the living from the non-living and therefore set biology apart from other academic disciplines, and what are the most illuminating concepts around which biological science can be built?

In one sense this is simply a matter of context, depending on what interests us or seems important at a particular time. However, any introduction to biology, such as a textbook, must attempt an orderly overview of its subject matter.

In the 19th century French philosopher Auguste Comte (1798–1857) in his ‘System of Positive Polity: or Treatise of Sociology’ applied hierarchical thinking to the system of 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, theological explanations in which natural phenomena are rooted in supernatural or divine powers (animistic, polytheistic, or monotheistic) which he treated as being 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, was the positive or scientific stage characterized by reliance on empirical evidence and scientific knowledge, rejecting metaphysical speculation and focusing on observable phenomena and, Comte claimed, epitomized by sociology.

The development of human knowledge 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 moving 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, this is all contentious metaphysics. But this is where science begins . . . with our most general assumptions about the nature of reality, and hierarchical thinking is a powerful intuition.

We need our best possible state-of-the-art representation of the science of biology – but preferably one that is simple and engaging.

The most popular current representation of biology follows the hierarchical tradition of the Great Chain of Being, the Linnaean taxonomic hierarchy, and the Comtian hierarchy of the sciences. It is the hierarchy of the complexity of biological organization.

The conceptual structure – the lens through which the biological hierarchy presents the objects listed above – is a system of ranked (prioritized) levels. The world is not literally composed of physically stratified levels – this is just a preferred way of representing it.

If the world is not literally a layer-cake of matter then how are we to understand what is meant by ‘level’, and what are the crucial criteria that determine what these levels should consist of – what are their selection criteria? 

Levels of organization

Philosophers have tended to address the ambiguities of hierarchy theory under the rubric ‘levels of reality’.^{[8][9][10][11][12][13][14][15][16]}

Biologists no doubt draw intuitive comparisons with the Linnaean system for classifying organisms whose ranks – the levels of the Linnaean nested hierarchy (e.g. order, family, genus, species) – provide the conceptual framework for a classification system of all living creatures, using the species as its basic taxonomic unit.

It is tempting to adapt the ideas of the Linnaean nested taxonomic hierarchy to the biological hierarchy with the levels species, genera, families, orders, etc. having loosely equivalent levels of molecules, cells, tissues, organs, organisms, etc. Though the Linnaean hierarchy has higher and lower levels, it is a classification system that is 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.

If species ground the Linnaean hierarchy then what grounds the biological hierarchy? The present-day intuition suggests that this is whatever sits at the bottom, be it molecules, atoms, or elementary particles.

The most comprehensive contemporary critical account of ‘levels of organization in biology‘ is given in a 2023 updated article in the Stanford Encyclopedia of Philosophy. This encyclopedia article provides a historical account of the topic and outlines its literature.  Three influential papers are examined, that of Oppenheim and Putnam (1958), Craver and Bechtel (2007), and Wimsatt (1994 [2007]).

The biological hierarchy is open to many interpretations (see illustration above). It is, for example, a convenient representation of biological science since it provides an overview of the topics studied, and these, in turn, often relate to specific academic subdisciplines. As an informal system of hierarchical classification, it comprises three structural elements: the taxonomic units (the objects being classified), the taxonomic groups of these objects, and the ranks or levels into which these groups are organized based on agential selection criteria not what is in the world. In the Linnaean hierarchy, for example, species are organized into groups called genera that are given similar ranks regardless of their evolutionary history. Botanically many items might meet the definition of ‘fruit’ as a basic units of classification, these might then be divided into groups called oranges, pears, and apples. We can then rank these groups by color, flavor, size, etc. Though philosophers might disagree, most of us assume that both the fruits and their groupings correspond to things external to the human mind but ranking is not.

Perhaps confusingly, in the biological hierarchy the names of the objects being classified and the groups into which they are placed are the same, so what we name as the rank ‘cells’ refers to cells.

Such an important concept requires justification, and several questions immediately arise:

What are the reasons for selecting these particular taxonomic units?

What are the reasons for the selection criteria of the groups (ranks, levels) chosen?

It is reasonable to ask that biological science provide its best attempt (or focused discussion of) the objects appropriate for such a classification, the groupings they form, and the grouping criteria. Each of these are discussed below.

As a specifically hierarchical (level- or rank-based) classification, it is also appropriate to detail how levels interact with one another, that is, their causal relationships and dependencies.

Classification

Classifications are a way of establishing the relations between objects and they come in many forms most familiar to biologists, linguists, and librarians. The biological hierarchy is an informal classification but it still follows taxonomic rules.  

Hierarchies are just one of many ways of grouping, classifying, and providing pictorial representation. Alternatives might be, for example, the tree as a pictorial representation of life (e.g. modification from common ancestry), or a web/network (e.g. interactions within an ecosystem), or an unprioritized list.

Regardless, the hierarchy of biological organization is a particular kind of classification.

Philosophers speak of prioritization in terms of supervenience. Physicalism, for example, is the view that everything supervenes on the physical – meaning that higher-level properties, entities, or phenomena are ultimately dependent on and determined by the physical properties and arrangements of lowest-level physical entities e.g. subatomic particles. That is, higher-level properties must have corresponding changes in the physical properties of lower levels.

Such mental contortions do not arise when levels are acknowledged as spatiotemporal perspectives that are not always nested in one another (see later).

In hierarchical thinking, the distinction between classification and ranking is imprecise and interconnected. This is because it, confusingly, relates to kinds of purposes.

Classification is more about differentiation (similarity and difference) while ranking (prioritization) is more closely associated with the goals of agents. This is tricky because even the recognition of similarities and differences requires an agent. In a loose sense, classification is the attempt by an agent to establish similarities and differences between objects as they exist independently of the agent while ranking acknowledges the relationship to the agent. Asked to get some tasty fruit from a grocer I might first subconsciously arrange the fruits into different groups based on size, shape, and color (classification) before tasting and ranking them by flavor (rank-value).

Both the informal hierarchy of biological organization and the formal taxonomic scientific Tree of Life are, in taxonomic terms, nested hierarchies. Perhaps something can be learned by examining why we need two hierarchies to describe life.

Classifications are produced by agents for a purpose, so we can safely assume that the Linnaean and biological hierarchies must serve different purposes. What is the purpose of the biological hierarchy of organization and how does it supplement or complement the taxonomic system of scientific classification?

Taxonomic hierarchy

The human purpose for a scientific taxonomy of life is, primarily, to indicate the products of evolution by descent with modification using the species as its basic unit. It organizes and categorizes the diversity of life into meaningful groups based on their similarities and differences – mostly physical and genetic, and the shared characteristics that indicate evolutionary ancestry. It is a grouping that assists predictability by degree of relationship. Combined with the international system of biological nomenclature the Tree of Life provides a universal means of scientific communication that facilitates the documentation of biodiversity and the investigation of its many human applications.

Modern classifications no longer use the traditional Linnaean nested hierarchy, instead using a methodology called cladistics. This is in part because the levels of the Linnaean hierarchy do not translate comfortably into evolutionary history. Certainly, the arrangement of groups according to similarities and differences placed evolutionarily related organisms close to one another. However, the compulsory fitting of organisms into hierarchical ranks e.g. phylum, class, order, family, genus, and species based on their similarities and differences is different from the ranking and categorizing of organisms based on their evolutionary relationships and shared common ancestry as currently used in cladistic taxonomy. For example, each family has its own set of genera but sometimes the characteristics that define genera in one family do not seem equivalent to those in another family: the ranking has imposed artificial levels of equivalence that do not occur in nature. For example, in the order Primates the family Hominidae (great apes and humans) and Cercopithecidae (Old World monkeys) have the same hierarchical level when genera of Hominidae share a more recent ancestor than genera in the Cercopithecidae. Descent with modification leads to graded transitions rather than levels of organization as we try to find order in graded nature.

The Linnaean nested hierarchy thus provides a convenient way of allocating names to groups of organisms, and that is its main function. While its boxes-within-boxes construction reflects evolution with modification, it does not profess to be biology’s most accurate representation of evolutionary history.

Cladistics (phylogenetics, molecular systematics) is based on presumed evolutionary relationships, not on assignment to ranks: it recognizes species but does not use the terms genus, family, order, class, phylum or kingdom. Thus, cladistics has no ranks. A taxon that includes an ancestor and all of its descendants is called a clade.

Biological hierarchy

The hierarchy of biological complexity is neither a means of allocating names to species of organisms – including their groups and subgroups – nor a hypothetical representation of the history of evolution. Instead, it has been used as an explanatory tool that introduces biology students to the key ingredients of theoretical and applied biology. It addresses the complexity of life by suggesting its interconnectedness across levels (scales) of biological organization.

This approach shifts the focus of attention away from the narrow consideration of species to the wider context of biology as it engages fields of study that look at biology from many scales, ranging from molecular biology to global ecology. This introduces the student to living objects at many scales and the academic disciplines that work at these scales.

Comparison

The purpose of the scientific taxonomy of organisms is to facilitate the application of names to groupings of organisms that are based on the best possible evidence concerning their evolutionary history.

The biological hierarchy, while generally presented as being based on organizational complexity, has many demonstrable purposes.

Principle – strict nested hierarchies exhibit:  inclusivity – they are progressively more inclusive as ranks go from bottom to top; exclusivity – an item in a strict hierarchy can only belong to one group at a particular level or rank; transitivity – the properties that define the objects at higher ranks are passed on to the lower ranks; clear boundaries – the properties defining group membership at a particular rank must be both necessary and sufficient (a classical category)

While scientific taxonomy categorizes species and their evolutionary relationships, the organizational hierarchy provides a broader biological context of functional integration. Taxonomy provides the evolutionary framework needed to understand the relationships among species, while the biological hierarchy offers the structural and functional context of not only individual organisms but their interactions with other organisms and the environment. The biological hierarchy documents all aspects of biodiversity, not just the diversity of organisms.

As already explained, this structure does not reflect the world but one way that human agents can arrange to world for explanatory convenience – to reflect human interests, needs, and beliefs.

Science concerns itself with the aspect of classification and hierarchical thinking that involves differentiation, where the differentiated objects are open to empirical investigation. The biological hierarchy can respond to empirical evidence concerning its contents, but their arrangement into ranked levels is a given.

It is the ranking, prioritization, or ordering of things that is at the core of hierarchical thinking. Prioritization occurs when we select particular objects for classification (segregation of objects), not only the kinds of objects, but the particular ones we decide to use (the focus group based on the prioritization of particular selection criteria) the prioritized process of arrangement of the groups (classification) and, most importantly, not just the differentiation of the groups but their arrangement into a prioritized sequence as levels or ranks.
This final rank-order or rank-value depends on the purpose of the agent devising the classification. These are interdependent processes necessary for specific outcomes.)

The contents of the universe may be differentiated into objects that are independent of human minds and open to empirical investigation: but it is not arranged into a system of prioritized hierarchical ranks – that is what agents do. This is the difference between the way the world is, and the way we might explain it – the distinction between epistemology and ontology – although the distinction is not completely clear-cut.

For all biological agents, the evolutionary function of their cognition is adaptation. They must establish objects of experience (segregation), differentiate between them (classification), and determine which are of current concern (focus) given the agent’s goals. While short-term goals will vary with circumstance, long-term ultimate goals are biologically universal (to survive, reproduce, adapt, and evolve). The actual form of each of these factors will depend on the umwelt of the agent concerned.

Regardless of particular circumstances, the ultimate goals of the organism constitute a perspective or ‘point of view’ to which adaptation and classification must conform. This is a property of biological cognition that, in the highly evolved cognitive behavior of humans, is regarded as a demonstration of values (beliefs, desires, and emotions).

All classification establishes relationships. It is done for a purpose and is an activity associated with the adaptation that is a necessary part of the biological cognition of every biological agent. However, ranking is associated with degrees of agential value which may be understood in terms of organismal involvement and dependency.

This is the conceptual structure into which the objects of biology are placed.

characterization of the way 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.

Rank-value

The reason for ranking (the selection criterion used by an agent) is not inherent in the ranked object itself, but in the agent. It is a cognitive dependency that relates to context and can vary with the perspective of the agent. It is a reflection of the interests of the agent (how it influences the agent’s proximate and ultimate goals).

This article draws attention to the insertion of human value (human purposes and prioritizations) into hierarchical thinking. It does this by referring to the ranking of levels as rank-value.

This does not mean that hierarchical thinking is subjective and scientifically unsound. The Ladder of life and biological hierarchy serve the need of our minds to prioritize. They are decision-making tools. As frameworks for ideas, they give our minds something to hold on to. Their strength lies in their broad applicability – their metaphorical explanatory value.

As a metaphor it is an interpretation and we have to investigate how effective it is as an interpretation and if the might be a more scientific interpretation.

Levels of organization

The ranks that form the levels of the Linnaean nested hierarchy (e.g. order, family, genus, species) provide the conceptual framework for a classification that uses the species as a basic unit.

Since the biological hierachy is also treated as a nested hierarchy it is tempting to transpose the ideas of the Linnaean hierarchy to the biological hierarchy. the levels of the biological hierarchy (e.g. organisms, organs, tissues, cells, molecules).

Philosophers have tended to address the ambiguities of hierarchical biology under the rubric ‘levels of reality’.^{[8][9][10][11][12][13][14][15][16]}

The most comprehensive contemporary critical account of ‘levels of organization in biology‘ is given in a 2023 updated article in the Stanford Encyclopedia of Philosophy. This encyclopedia article provides a historical account of the topic and outlines its literature.  Three influential papers are examined, that of Oppenheim and Putnam (1958), Craver and Bechtel (2007), and Wimsatt (1994 [2007]).

One strength of the hierarchy is that it is open to many interpretations. It is, for example, a convenient representation of biological science since it provides an overview of the topics studied, and these, in turn, often relate to specific academic subdisciplines.

From another perspective, it is an informal system of hierarchical classification of the biological world consisting of three key structural elements: the taxonomic units (the objects being classified), the groups of these objects (ranks or levels), and the selection criteria used to separate and designate the groups.

Perhaps confusingly, in the biological hierarchy the names of the objects being classified and the groups into which they are placed are the same, so what we name as the rank ‘cells’ refers to cells.

Such an important concept requires justification, and several questions immediately arise:

What are the reasons for selecting these particular taxonomic units?

What are the reasons for the selection criteria of the groups (ranks, levels) chosen?

It is reasonable to ask that biological science provide its best attempt (or focused discussion of) the objects appropriate for such a classification, the groupings they form, and the grouping criteria. Each of these are discussed below.

As a specifically hierarchical (level- or rank-based) classification, it is also appropriate to detail how levels interact with one another, that is, their causal relationships and dependencies.

Kinds of things

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? Can biological individuals be properties, processes, and events rather than physical structures? Should priority be given to units of evolution, genetics, development, or metabolism? Do levels of organization and complexity provide a way into the subject and are these levels all equal or are some more biologically significant than others? How do categories of the living relate to those of artificial systems and the non-living? This is a daunting task.

But the study of biology must begin somewhere, and textbooks must provide an overview of their contents. So, what is the most useful and scientifically grounded way of carving up the subject of biology  . . . remembering that the categories we choose will be the preferred lens through which science will view the living world.

We like the solidity and brute undeniability of physical objects and so we have traditionally treated biology as consisting of physical things – cells, tissues, organisms, etc. But biology is more than physical things. We know that every living object is connected by evolution, a crucial concept. But there are many other approaches since we don’t just study structures, we also study functions, behaviors, processes, principles, and theories (like evolution) organized into academic disciplines.

Perhaps any attempt to order the biological world is misleading because everything depends on our particular interests and concerns – it is a matter of context. Undoubtedly there is truth in this, but science must still facilitate our understanding, explanation, and management of life.

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. That seems to have the living world covered doesn’t it?

Kinds of biological objects

Perhaps the major metaphors and categories we use in biology simply reflect the historical development of the subject. If this is so, then how can we adjust these ideas to move with the times?

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

The secure world of permanence and substance (both material and philosophical) is giving way to the scientific evidence that everything is in a state of change. This moves science’s metaphysical ground rules from the security of permanent substances to the dynamic change that defines processes. Put crudely, scientific emphasis is now on processes, not things, and, in science, this is especially pertinent for living systems.

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 structure and function and whether biologists consider one as taking priority over the other.

Our intuitive understanding of the distinction between the living and non-living prioritizes the physical (material, structural, morphological, anatomical) over functional (physiological, developmental, evolutionary) factors relating to process.

This agency is pervasive in biological systems; it is not just a human 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.

In a loose and general sense, biological science has moved from ‘What?’, to ‘How?’, to ‘Why?’ – from questions about material composition and appearance to questions about function, and purpose. This was a transition from composition (structure and form), to processes (as mechanical operations), to agency (as goal-directed behavior and generalized 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.

While modern research integrates all three aspects it is clear that biological science has evolved from mere observation to a holistic approach that now considers not only structure and function but purpose and agency.

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

What it does is provide us with a crude outline of biology and the major generalized concerns of its academic subdisciplines – as structures (matter), processes (operation, function), and behaviors (cognition). While this is a contentious taxonomy it provides a foundation of ideas to include in any overall representation of biological science.

Competing categories & classifications

The biological hierarchy consists of levels of physical objects of graded physical complexity that is reminiscent of the gradation resulting from 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 (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.

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.

Structures and/or Processes
A more inclusive approach to biology would engage not only structures but processes – including functions and behaviors.

Hierarchical thinking results in the prioritization of concepts that, for scientists, will be based on sound scientific principles and evidence. Historically, as we have seen, biological objects (as generalized objects of biological study) have been classified according to the biological hierarchy. But the historical emphasis in biology has shifted from structures (things), to operations (processes), to biological goals and agency.

So, what are the key selection criteria to be used when we make a prioritized list of the objects of biological study? Is it complexity, inclusiveness, size, importance/value. No doubt all of these factors are of interest, but it is organisms that are the supreme exemplars of biological agency.

Selection criteria (scales)

In any classification, we need to know not only the objects being classified and why they were chosen, but also the reasons for their grouping. In hierarchies these are the selection criteria used to group the objects of interest into levels or ranks.

Our hierarchical intuition results in its wide application to phenomena ranging from criteria as broad as being and existence (e.g. the Great Chain of Being), to mechanical hierarchies, hierarchies of composition, hierarchies of evolutionary selection, and so on. In biology, hierarchies are developed for many reasons, not just the biological hierarchy being discussed here.

But what we need to know is the selection criteria for the biological taxonomy that divides the living world into ranks or levels that range from atoms to the biosphere.

Whatever the criterion is, it is clear from the objects chosen that the selection criteria are scaling criteria, the sort of scaling is not clear. While complexity (as organizational complexity) is most frequently quoted as the scaling factor, discussions of hierarchy also bring strong connotations relating to size, inclusivity, and significance.

Biologists accustomed to the Linnaean classification system as a nested hierarchy will notice that the biological hierarchy has a similar structure with molecules nested in cells within tissues and so on.

Our intuition of rank-value treats ‘higher’ levels as not merely different from, but superior/inferior to ‘lower’ ranks – simply because ranking creates superordinates and subordinates.

Physical extent – Size

When we think of objects we are aware of their relative sizes. Molecules are smaller than cells, which are smaller than tissues, which are smaller than organs, which are smaller than organisms, which are smaller than populations, which are smaller than ecosystems, and so on. Size and its close relative, scale, strongly influence our perception of the world as we study, say, molecules, anatomy, or whole organisms. ‘Size’ and ‘scale’ do appear to represent something more concrete than the word ‘level’.

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 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 the time of uniform plasma to the time of complex humans there has emerged structures, processes, and behaviors that were not predictable from their prior objects, properties, and relations. No wonder the idea of containment has appeal.

Biologists are familiar with the nested (boxes-within-boxes) hierarchy of Linnean classification in which the species of the world are grouped into genera, genera into families, and so on, itself an echo of the ladder of life. It makes sense, especially as the nesting reflects the post-Linnaean idea of Darwinian evolution by modification from common ancestors. It seems reasonable that biology as a whole should be organized in a similar way.

There are also echoes of evolution in the informal nested hierarchy of biological complexity as it moves from molecules to cells, tissues, organs, and so on. In this way, hierarchies can be interpreted as progressive inclusion or containment. There is a neatness in the resulting part-whole relationships in which wholes at lower levels are parts of the levels above them – that the higher levels contain lower levels in a gradation of superimposed complexity.

Strict nested hierarchies of scientific taxonomy have precisely defined conditions so how does the biological hierarchy compare?

Inclusivity – they are progressively more inclusive as ranks go from bottom to top (e.g. species, genus, family etc).

Exclusivity – 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).

Transitivity – 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)

The translation of levels of organization into a hierarchy, even where this is its intention, has many difficulties as can be seen when attempting to translate them into a strict nested hierarchy with the properties described here.

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

• • • it treats levels as if they had the strong autonomy and independence that is usually associated with organisms. Organisms have a degree of unity of functional integration that does not occur in their constituent parts – like cells and tissues which have a stronger dependence on their surroundings and subordination to the organism
    •  the complexity criterion for establishing levels is also associated with considerations of size, inclusion, and rank-value
    • it presents biology as being more about theoretically permanent abstract physical objects than actual dynamic processes and change

The Linnaean hierarchy uses progressive inclusion as its principal structural criterion in proceeding from low to high: the more inclusive categories are the ‘highest’. The evolutionary aspect arises incidentally due to similarities and differences that distinguish groups at a given rank. So, for plants, the basic unit is the species, and the highest (most inclusive) category is the plant kingdom. In contrast, evolutionary trees proceed from simple origins their progressive tree-like diversification being based deliberately on unranked characteristics that reflect evolutionary relationships.

Complexity

From the time of the Big Bang, and despite the Second Law of thermodynamics, parts of the universe have become increasingly complex. From undifferentiated plasma has emerged elements, compounds, and organic molecules. In the biological world, from the simplest organisms has evolved, though not in a linear way, more complex structure, function, integration, and self-regulation. The existence of objects of different physical complexity within the world presents us with an obvious means of organizing the natursal world by arranging it in order from the simplest to the most complex. Perhaps, like the ancients, we can regard living organisms as the most elaborate organization of matter as integrated structure and function and elevate their scientific value? How are we to classify, scientifically, the diversity of matter in the universe? Does the Periodic Table convey all that we need to know about matter? Is this the single, most economical, and ‘best’ kind of classification? Is it fundamental or foundational? Does it ground all science in some way . . . or are there many kinds of classification serving multiple purposes?

Regardless of our opinions about such matters (we will not solve them here!) it is clear that science must communicate about many objects beyond the elements: we need to speak of planets, stars, organisms, tables, chairs, different organisms, space, time, and so on.

So, how does science deal with this difficulty of multiple objects of many different kinds?
One approach might be to start with the knowledge that our minds segregate, focus, classify, and rank – and then make a decision on how this processing relates to the world (both an empirical and pragmatic question).
Biology can provide us with a framework for naming and classifying all life according to evolutionary relationships – but how do we classify a geranium in relation to the moon or the city of Venice? This seems a silly question but if things are indeed all connected then science must provide some schema indicating connections, however distant these might be. The empirical properties that unite all life, for example, seem to hold quite well, but how is life connected to non-life in the world? In terms of academic disciplines, how is biology connected chemistry and physics, or psychology, or sociology and economics? Will it do to say that, in the final analysis, all these subjects boil down to subatomic particles?

One way of dealing with this difficulty is, as we have seen, by invoking the metaphor of the Ladder of Life. But science has moved on, and the metaphor that it falls back on today is the ‘hierarchy of levels of organization’.

It then becomes crucial to state clearly what we mean by the expression ‘levels of organization’: what are the criteria we use to distinguish one ‘level’ from another?
Biology is often perceived and studied in terms of hierarchical levels of organization of increasing inclusiveness and complexity. One example would be the series – genes, cells, tissues, organs, organisms, and populations. With the advancement of biological knowledge, each level has assumed the role of a specialist discipline with its own principles and systems of nomenclature, the objects of study assuming their own role in evolutionary selection. The operational units at each level are often regarded as having their own unique functions (purposes) and forms of agency (e.g. the function of the heart is to pump blood).

Importance, authority, function (rank-value)

The single key characteristic of any hierarchy is that the objects of its levels do not form a flat list, they are classified into ranks ‘above’ and ‘below’ one another using a powerful spatial metaphor. Levels of the hierarchy are spoken of, and conceptualized, on a vertical axis like the rungs of a ladder with a ‘top’ and a ‘bottom’, with items that are ‘higher’ or ‘lower’ than others on the ladder.

Our everyday language is saturated with hierarchical talk. Humans are 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.

The levels (ranks) of human hierarchies, like those of corporate or military organizations, are prioritized in terms of their relativ e importance, authority, or function. In these organizations the higher the rank, the greater the authority or power. This reflects the Great Chain of Being in which the ranks are arranged in order of decreasing merit, authority, and value as they pass from high to low.  The investing of ranks with relative value of some kind is referred to here as rank-value and it reflects our natural inclination to prioritize the things we think and do, whether consciously or unconsciously.

Ranking operates both consciously and unconsciously: unconsciously as our mental focus constantly shifts from one thing to another, and consciously when we make deliberate choices.

Do we use rank-value when we describe matter in general or biological objects?

All matter, we must assume, exists equally at all spatiotemporal scales. The universe does not prioritize, we do. How could it be otherwise? We must assume that there are differences and variety in the matter that is external to our bodies, but any ranking of that difference and variety must be a product of the human mind. This does not make the universe a human creation, but a human interpretation. The ranking of matter might be necessary for scientific explanations, but it is in our minds, not the world.

If we, and all organisms, are to persist then we must act as agents. We must have the capacity to identify activity going on both within and around us, discern its significance for us (our umwelt), and devise an appropriate response. That is, we must adapt. The ranking of our experience is therefore a critical aspect of the decision-making procedure that guides our actions and behavior.

This section, which has examined the selection criteria we choose to divide up biology, has examined one philosophical answer (the Ladder of Life) to the questions, ‘How are we to carve up everything? What are the basic constituents of reality? On what grounds do we prioritize or order what there is?’

Biology has chosen to carve up its domain of study based primarily on degrees of physical complexity but also – by association or implication – evolutionary history, size, and inclusiveness. 

This was a historically appropriate to  a difficult, possibly insoluble, problem. Perhaps it is now time to move away from levels to scales – to recognize life as most typically exemplified by the units of agential matter that we call organisms, each with its own umwelt of personally significant objects but set within the universal impersonal arena of space and time (as understood from the perspective of physics and human perception). We humans understand ourselves, other organisms, and the universe from many perspectives and scales. For now, it is most scientifically informative to place the world of familiar biological objects within convenient scales of space and time.

Causal relationships

The Oppenheim and Putnam-like hierarchical construction of reality divides the living world into hierarchical levels of organization of matter ^[15] . . . into molecules, genes, cells, tissues, organs, whole organisms . . . sometimes extending further into populations, ecosystems, biomes and, ultimately, the biosphere. 

While these objects are static concepts, biological systems are in a state of constant dynamic process – the change that shifts conceptual emphasis from objects in space to processes in time, and the reasons (causes) of this change. 

This vertically layered mental representation may be used to infer the real-life modes of interaction between different categories of physical objects, using the metaphorical language of direction in space.

Viewed in this way, each level of biological organization builds on the lower levels and exhibits novel (emergent) properties that arise out of the interactions of components at lower levels. This hierarchical arrangement helps scientists to study the complexity of life across different scales and degrees of complexity, from molecular interactions to global ecosystems. However, the concept of hierarchy, including hierarchical levels or ranks of biological organization, is a tool or heuristic, it is not a part of the world; nature is not inherently ranked hierarchically into levels of organization.

Biological causation

There is no single, uniquely biological mode of causation.

Biological experiments often model biological systems as networks, manipulating one factor at a time to see its effects on one or more others. This helps establish causal relationships. Network nodes represent entities (e.g., genes, proteins), their edges representing causal relationships. These models help unravel the complex web of interactions and dependencies within biological systems.

There are many influential ideas associated with causation in biology:

• • • 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 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 its own particular umwelt.

Problems with levels

How can the metaphor of levels of biological existence influence scientific thinking about the world? In what ways can it facilitate or impede research?

The following questions are relevant here:

1. 1.  Are hierarchical levels real in some sense, or are they just useful explanatory fictions?
   2. Do some levels have more explanatory or existential relevance or biological significance than others, or are all levels of equal biological significance?
   3. How do levels interact and influence each other? How are we to explain and compare, say, the causation occurring between adjacent levels, or between top and bottom levels?
   4. Can higher levels be fully explained in terms of lower levels (reductionism) or do they have additional (emergent) properties e.g. can mental states be reduced to physicochemical processes?’
   5. How can complex systems exhibit (emergent) properties not present at lower levels and how do these emergent properties arise and influence lower levels?
   6. How do we integrate or relate the principles, terminology, and concepts of one level with those of another, especially when they require different methods and theories e.g. on a grand scale, can physics, biology, and sociology be unified into a single coherent framework of understanding?

Whatever our opinions about the framing ideas of the biological hierarchy, the world is not literally layered in this way. As already discussed, ranking or prioritizing is performed by agents. Awareness of this fact allows tentative answers to the questions above.

1. Hierarchical levels are useful fictions that classify the world based on our agential intuitions.

2. As elaborated elsewhere, levels as explanatory fiction may be treated as having equal significance and, insofar as they equate to academic disciplines, they too may be treated as being of equal significance (pluralism). However, theoretical biological levels (e.g. molecules, tissues, populations etc.) are manifest as either sub-organismal parts or super-organismal aggregates with organisms the biological units that express supreme autonomy and biological agency in their unified functional integration. Token hierarchical entities like macromolecules, cells, tissues, and organs can be treated theoretically as discrete entities when in actuality, they occur in type organisms and that are structurally and functionally integrated. In this sense, attributing equal biological significance to these entities is a confusing error.

3. The causal links between theoretical levels are, in actuality, not a linear process in space but a complex web of spatiotemporal interactions.

4. Abstraction and reduction provide increased economy, parsimony, and simplicity but omit the information that is required for scientific explanation. Knowing that organisms are made up of molecules is not scientifically helpful to a biologist.

5. See emergence.

6. Levels are misleading tokens for type biological circumstances that can be described at different spatiotemporal scales. The spatiotemporal scales used are a pragmatic choice – a matter of convenience or context. For example, there is little point in describing sociology in terms of molecules, even if it were possible – although there may be some conceivable utility.

The notion of levels seems superfluous since it is added by the human mind out of our habitual prioritization of all experience. Perhaps that is a good reason to use it on occasion, but not as reliable science.

Why not regard the world as metaphorically flat or one-layered?

If we explain the world in terms of spatiotemporal scales then the notion of levels can be discarded altogether.

Scales may be ranked (classified) relative to one another (smaller, more inclusive, more complex) but this generally satisfies our classificatory need rather than our hierarchical intuition for rank-value.

Proximate & Ultimate Causes

In 1961, the evolutionary biologist Ernst Mayr made a distinction between proximate and ultimate 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 a particular trait rather than another.

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

This distinction also touches on teleological explanation and agency because, while proximate causes focus on mechanisms or functions, 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.

Explanatory direction

Consider the treatment of the matter of the universe in a hierarchical way. When we proceed from the smaller to the larger, or from the less inclusive to the more inclusive then we compare this shift in thinking to a metaphorical movement in space. We are looking in opposite ‘directions’, either ‘up’ (larger, more inclusive, more complex) or ‘down’ (progressive division, etc.) or maybe ‘forward’ (to greater inclusivity, etc.) or ‘back’ (to greater reduction).

Using the metaphor of spatial hierarchy we regard analysis as reduction, a ‘looking downwards towards the bottom’. But when we think synthetically by understanding and explaining how something fits into a wider context we say we are ‘looking upwards towards the top’. We can steadily and systematically ‘build up’ the universe from its foundation of fundamental particles into greater wholes and their relations, but we can also ‘break it down’ from its totality into its simplest parts. Our explanations, including our scientific explanations, thus take us ‘up’ and ‘down’ the ladder of life.

Hierarchical talk is not only an economical way of representing the world in casual conversation, it is a popular metaphor in scientific and philosophical literature.

A characteristic scientific example is provided by leading physicist and cosmologist George Ellis who, in describing a hierarchy of scientific disciplines, states:

‘In the hierarchy of complexity, each level links to the one above: chemistry links to biochemistry, to cell biology, physiology, psychology, to sociology, economics, and politics. Particle physics is the foundational subject underlying – and so in some sense explaining – all the others.’^[13]

Ellis’s expressed concern though is with causation which he stresses does not flow from the underlying physics (a common assumption) but proceeds both ‘up’ and ‘down’:

‘. . . the challenge to physics is to develop a realistic description of causality in truly complex hierarchical structures’.

In following intuitions about causation in hierarchies, we have the simple and powerful human example of a chain of command, which traditionally proceeds from top to bottom (the chain in the Great Chain of Being).

This presents us with a fascinating historical phenomenon. Before the Scientific Revolution, it was God in heaven who was the ultimate reality (or prime mover) determining the course of all the events in the universe by commanding from above. After the Scientific Revolution, it became elementary particles that provided the foundation of everything, an ultimate reality, supporting and pushing the universe from below.

Is this a benign metaphor? Is it really intellectually helpful to assume that everything in the universe proceeds either top-down, bottom-up, or both?  Isn’t there a more scientific way of representing the universe and biology?

Frames of reference

More innocently, the levels or ranks of the biological hierarchy are treated as frames of explanatory reference. Since they represent scale of some kind then they are separated intellectually into domains, both those of the named ranks (e,g. molecules, cells, tissues) or the disciplines that loosely correspond (biochemistry and genetics, cytology, anatomy).

Each level has is own principles, and technical terms as a specific domain of biological knowledge with its own position, both on campus and within the biological curriculum.

They are organized into ranks or levels that are ‘higher’ or ‘lower’.

Ranking is a form of prioritization, but the significance of the ranks depends on context. It may be of little consequence, as when we make a list of people according to their heights, arranged from tallest to shortest, or of hair colors arranged from dark to fair.

However, human hierarchies are generally more strongly value-charged: the higher and lower ranks are associated with social, moral, organizational, or political worth, importance, or significance. That is, we usually 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’ than being lower.

The habit of applying rank-value to hierarchies is difficult to resist. The old hierarchies, based on moral worth, put God on top, followed by humans. Today’s scientific hierarchy has inverted this representation of everything by treating the smallest particles of matter as ‘fundamental’ and ‘foundational’ to both science and existence. They are now on top of the hierarchical ladder of scientific reality. Conversely, biologists still speak of ‘higher’ and ‘lower’ organisms, with a positive spin on those organisms that are more complex and like humans.

The Ladder of Life (Aristotle’s scala naturae) provided a simple image of universal connection – a continuity of the spiritual, physical, and moral. It provided a simple and satisfying spatial representation of the location of everything in the scheme of things.

One major difficulty, though, was that hierarchies ranked things as more or less important or significant. When incorporated into the Christian world view it took on a moral tone. While there were obvious parallels in the world of human hierarchies, these were not so obvious in the natural world. And perhaps even human hierarchies were human creations rather than being part of the cosmic moral order.

The symbolism was strained as it placed rocks as insignificant inanimate objects at the bottom of the ladder of the material world whose rungs stepped up to plants, then animals and birds, then sentient animals, culminating in the pinnacle of earthly organic existence, the people of the world, surmounted only by their social superiors, the rulers, priests, and administrators. Superimposed on this earthly material realm was a spiritual world of bliss (heaven) with God, as pure spirit, at the very ‘top’. Meanwhile, at the very ‘bottom’, was the fiery underworld of Hell and the Devil. With the progress of science all this became unacceptable.

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 of earthly environments.

After Darwin, fewer and fewer scientists regarded organisms as existing within some kind of external or cosmic moral order – they just exhibited evolutionarily related similarities and differences. Ranking, in scientific systems of classification, was therefore based on comparative data. Organisms could be more or less complex, perhaps more or less adapted to their environments, but they were not of greater or lesser moral worth . . . they were simply different in a range of measurable characteristics.

Scientific ranking does not necessarily imply evaluation – as when we rank objects by weight or colour. Nevertheless, in everyday life the process of ranking brings with it an inbuilt valuation. Simply by placing something within a hierarchy we are usually prioritizing by placing greater value on one thing rather than another. So, simply by habit, ranked scientific objects are often also valued. This I call rank-value: objects at the ‘top’ are frequently valued differently from objects at the ‘bottom’. At one time it was God at the ‘top’ pulling the universal strings: today, for some, it is the simplest forms of matter at the ‘bottom’ that are in control of everything.

Ranking is a creation of the human mind, as are scientific hierarchies. While the scientific ranking or prioritization of objects according to purpose is a transparent and legitimate process, ranking within hierarchies brings the danger of unwarranted valuation.

Layered principles & laws

Hierarchical imagery suggests layered modes of interaction. Each level expresses its own independent principles or laws with higher levels imposing constraints on lower levels with wholes at lower levels functioning as parts at higher levels.
This gives rise to several interesting implications:

• • • • That processes at higher levels are slower than those at lower levels.
      • That properties at higher levels are multiply realizable at lower levels.
      • That higher causes are dynamically independent (autonomous).
      • Do higher level properties, theories, or explanations reduce to lower ones?
      • Can higher level entities have causal influence over lower ones?
      • Can one level be elevated above others as being of greater biological importance or are all levels of equal significance?

Levels, when considered independently of functionally integrated organisms, take on their own evolutionary significance. It then becomes meaningful to ask whether natural selection operates, for example, at the level of the gene, cell, organism, population, or other level. That is, there are levels of selection and therefore the need to differentiate the influence of each level with no one level privileged over others.

Modes of Explanation

Regardless of hierarchical ideas, our way of representing and describing interactions between different biological objects at different scales remains among the most profound and controversial problems in science. Are organisms, when all is said and done, just physics and chemistry? How are we to understand and explain the objects and principles of one academic discipline in terms of another: how are we to translate between their languages, and how does all this relate to what is going on in the world?

Almost any item in the universe can be divided into smaller parts or united into larger wholes, and that is how we explain things. It is therefore both a whole and a part.

When a whole is explained in terms of its parts we refer to this as analysis. Analysis adopts the mental perspective of the whole. It is the whole that is, as it were, demanding the explanation.

When we explain something (as a part) in terms of a wider whole or context we refer to this as synthesis. Synthesis thus adopts the mental perspective of a part within something greater.

For example, ‘A house is an assemblage of bricks‘ (analysis). ‘My legs are attached to, and mobilize, my body‘ (synthesis).

As we have seen, almost all objects in the universe (and our minds) are both wholes and parts. So, just as we can analyze an object into progressively smaller and smaller or less inclusive parts in an infinite analytical regress (or until a least-inclusive ‘rock bottom’ foundational or fundamental situation is reached), so we can also synthesize them into ever more inclusive wholes in an infinite synthetic regress (or until an all-inclusive ‘rock top’ is reached).

This has given rise to competing systems of scientific metaphysics expressed crudely as follows:

On the one hand, there is reductionism, the view that ultimately biology must inexorably be reduced to physics and chemistry. It may be impractical to describe biological systems in physicochemical terms but ultimately that is, in reality, what they are.

On the other hand, there is holism, the view that biological objects, especially organisms, are more than the sum of their parts: they are wholes with irreducible properties. This view has also been referred to as organicism with the origin of unique properties referred to as emergence.

Strangely, these two views can be interpreted as using different approaches, perspectives, and methodologies when providing scientific explanations.

In hierarchical terms, these explanations have a directional perspective because they may be  ‘top-down’ (explaining the parts of objects using the language and ideas of the wholes they form). This is a form of explanation referred to here as synthesis. While, in contrast, explanations may be ‘bottom-up’ (explaining wholes using the language and ideas appropriate to their constituent parts). This form of explanation is referred to here as analysis.

Analysis & synthesis

We cannot explain an object in terms of itself and so explanations of objects proceed to either their constituent parts (analysis) or a broader context (synthesis).

Using metaphorical hierarchy-talk, explanations can proceed in two directions – by ‘upward’ synthesis or composition (explaining parts in terms of their relation to the whole) and ‘downward’ analysis or decomposition (explaining the whole in terms of its parts). In this way, explanations are labeled as either top-down or bottom-up.

These two approaches to biological research have given rise to contrasting philosophical perceptions of the subject – reductionist or holistic.

Our preference for analysis means that we tend to explain each biological object in terms of its simpler components (photosynthesis as the capture of the Sun’s energy in biological chemicals) while synthetic thinking can explain their significance within larger, more inclusive, and more complex wholes (the fate of organs depends on the fate of the organisms of which they are a part).

Analysis

We are still living in an age of analysis and reduction in which the prevailing  methodology of science is reduction. We take it for granted that phenomena are best explained and understood by examining the structures, properties, and relations of their constituent parts.

English philosopher Bertrand Russell describes this Western preference or bias in ‘direction’ of explanation:

‘. . . the last of my initial prejudices, which has been perhaps the most important in all my thinking. This is concerned with method’ . . . ‘to start from something vague but puzzling, something indubitable but which I cannot express with any precision. I go through a process which is like that of first seeing something with the naked eye and then examining it through a microscope. I find that by fixity of attention divisions and distinctions appear where none were at first visible . . . analysis gives new knowledge without destroying any of the previously existing knowledge. This applies not only to the structure of physical things, but quite as much to concepts . . . belief in the above process is my strongest and most unshakable prejudice as regards the methods of philosophical investigation’.^[10]

Russell, a strong advocate of analytic philosophy, was echoing the second principle of Descartes:

‘ . . . to divide each of the difficulties that I was examining into as many parts as might be possible and necessary in order best to solve it’.

Here we have two key proponents of a Western intellectual tradition, sometimes called analytical reductionism and its statement of conviction about a particular manner of intellectual investigation . . . analysis. Logical atomism was in lock-step with the scientific search for the smallest particles of matter as the foundation of all science.

We admire the elegance of simplicity and unity which we create by a process of reduction, generalization, and abstraction. A daffodil and the moon make an unlikely comparison but they are both made of matter. The entire universe has an evolutionary history within which is the evolutionary history of the community of life.

But unity and simplicity are their own worst enemies because they fall to what might be called the principle of complexity. Science must explain the universe in all its variety, a principle that applies especially to life. But the sameness of generality does not explain anything. Knowing that every organism consists entirely of elementary particles is no explanation of life at all. The philosophical conviction that the universe is grounded in elementary particles does not assist us in the explanation of a heart attack.

Does the Periodic Table convey all that we need to know about matter? Is this the single, most economical, and useful classification of matter? Is it fundamental or foundational? Does it ground all science in some way . . . or are there many kinds of classification serving multiple purposes? Regardless of our opinions about such matters, it is clear that science must communicate about many objects beyond the elements and their sub-atomic composition: we need to speak of planets, stars, organisms, legs, photosynthesis, behavioral patterns and so on.

Rank-value is applied to the cosmic hierarchy of matter by placing greatest value on the lowest level of matter. Analytical reductionism has drilled down to life’s smallest ingredients in a hunt for the holy grail of the universe’s simplest discrete constituents – the foundational layer of elementary particles that supports the entire edifice of science. Since everything consists of these fundamental particles and their properties and relations, then they both explain and unify the scientific world.

Elementary particles certainly have explanatory value but a lepton or boson is no more real than a daffodil or an elephant . . . we cannot invest them with special ontological properties. Indeed, it hardly surprizing that we once regarded animals and humans as cosmically (scientifically) more significant than specks of dust.

The problem with reductionism is that science does not deal with one thing, it deals with many. But, aren’t the many ‘really’ just elaborations of the one – the same fundamental stuff but in different forms?
This draws our attention to two major factors, one to do with our mental structuring and processing, and the other to do with the external world.

First, the pragmatic or utilitarian nature of scientific explanation – and indeed – all explanation. What is achieved by describing a tiger in terms of number or information? And even if we had such a description, would it help us to answer the kinds of questions about tigers that we think are scientifically important? If we wish to explain what is happening during a heart attack it does not help us if science tells us that everything consists of number, or information.

Second, is the age-old but compelling argument for the emergence of new properties in integrated wholes, with life its most compelling example. A sand heap may be just lots of sand grains, but is it helpful to say that a tiger is just a lot of molecules? Here the properties and relations of molecules when aggregated seems very important. A tiger is not just a heap of molecules it is a totally different kind of aggregate than a heap of sand.

Today, we must take seriously the following possibilities:
First, the universe may be differentiated but it is not ranked in any way – ranking is a product of human minds.

Second, there is no ultimate reality or, at least, what is significant or of interest depends on our human interests and concerns. Our attempts to be as objective as possible have proved very successful but e can, and never will, see everything from the point of view of the universe. But we can begin by acknowledging that the daffodil and boson run neck and neck in the existence stakes.

Synthesis

The following thought experiment expands on Russell’s characterization of analysis given above.

Imagine you have an extremely powerful new scientific instrument like a combined microscope and telescope – we can call it a micro-macroscope. You look into the micro-macroscope as it scans extremely small objects and what you see are simple objects with a range of different forms. Let’s call them molecules. But when you zoom out further, you see the molecules seeming to coalesce into a bounded unit, let’s call it a cell, then something like a leg appears. Zooming out further you see that the previous object really was a leg, that the leg belongs to a person, and zooming out even more we see that the person is one among many people living in a city, which is part of a country, which is part of planet Earth, which is part of the solar system, the galaxy, and the universe.

This thought experiment illustrates the way that new objects, properties, and relations arise at different scales, and that these constitute novel frames of reference. Each part can be placed within a broader context that gives us a wider understanding. Scientifically we describe these points of focus as mind-independently as possible given our human umwelt, using distinctive principles and technical language where this facilitates understanding and explanation.

The critical point is that these frames of reference are not separate and independent objects, nor are they above or below one another, they are different perspectives or points of focus within the spatiotemporal continuum.

Given sufficient technology and computing power, we could describe the physical composition of any object. However, in living systems this has limited scientific value because novel properties are associated with different degrees of complexity, a property referred to as emergence. These properties are a consequence of functionally organized wholes and they are not present or predictable from their material constituents.

This emergence of novelty in complex systems is often contrasted with the claim that nothing can be more than its material constituents (material reductionism).

Reduction & Emergence

Reduction and emergence are treated as contrasting ideas, like holism and reductionism, analysis and synthesis. They are also associated with the directionality of hierarchical thought, the explanatory direction, with reduction proceeding top-down and emergence proceeding bottom-up.

We do not need the metaphor of directionality here, but the different modes of explanation are important.

A bottom-up (reductive explanation, analysis, decomposition) emphasizes the way that structures, properties, and relations (structures, processes, and behaviors) of parts contribute to our understanding of the whole. That is, the whole is explained in terms of the parts. Examples of analysis include the way genetic information flows from DNA (nucleotides) to RNA to proteins and the way molecular biologists study individual genes, their expression, and how they behave within cells.

Emergence

The study of mereology tells us that wholes and parts are not all the same. The number 2 can be considered as consisting of the parts 1 and 1. Also, a heap of sand is little more than an aggregate of the grains out of which it is composed.

But clearly, an organism is much more than an aggregate of molecules. The ‘more’ here is not a matter of molecules but the relations between the molecules which give rise to novel properties of matter. Organisms are the universe’s supreme examples of functionally integrated units with many novel emergent properties above and beyond those of their constituent parts.

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?

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 as a biological layer-cake represented pictorially in textbooks and other introductory biological texts. The entire edifice of life is therefore built on its foundation of chemical constituents.

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

What actually happens in biological systems is much more complex. 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 emergent properties and non-linear interactions that cannot be 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 that are functionally integrated agents whose parts are ultimately subordinate to the goals of the organism as a whole (survival, reproduction, adaptation, and evolution).

Metaphors can facilitate or impede our scientific interpretation of the world. They are useful when they facilitate creative thinking that improves our scientific understanding, but undesirable when they lead to incorrect or misleading inferences about the world.

Because we think hierarchically, there will be many circumstances in which its use as metaphor is either harmless or beneficial. But at this point in the history of biology, the biological hierarchy of organization is probably generating more confusion than insight.

However, the single major difficulty with the notion of interacting levels of biological organization is that metaphorical epistemic (explanatory) levels are treated literally, as reality (they become reified or ontologized)  – like physical layers interacting vertically in space sometimes called the ‘layered cake’). The danger is that the logic of the metaphor then determines the logic of scientific inference.

We might deny this trap while still thinking of organisms as if they were composed of interacting physical layers as described in the biological hierarchy. But 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.

Human hierarchies, and hierarchies of thought, are associated with social, moral, and other values. There is therefore a strong temptation to associate biological levels with values. Above all, biological hierarchy is an explanatory tool, not a description of the world, or a theory of biology.

The metaphor misleads in many ways:

1. It treats the physical objects of biological levels (e.g. molecules, genes, cells, tissues) as separate and distinct when, in nature, they are functionally integrated into organisms. This also confuses the separation of biology into discrete disciplines based on these levels and sometimes assumed to be grounded in reality.

2. 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.

3. It treats complexity as the critical factor differentiating levels (the key selection criterion).

4. The spatial superimposition of levels resembling human hierarchies evokes the ranking intuitions associated with the ‘higher’ and ‘lower’ in these hierarchies. What is at the top or bottom of human hierarchies relates to power, authority, or significance. In science, this can define ‘degrees of reality’.

5. 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.

6. The spatial imagery gives an inappropriate spatial dimension to explanation and causation as proceeding ‘top-down’ or ‘bottom-up’ like a chain of command.

5. It creates an impression of causation separated by distance e.g. from cells to tissues, molecules to organisms, etc. in a linear, albeit reticulate, fashion  This clearly bears little relation to what is going on in nature which must resemble more closely a network or web.

6. It encourages an explanatory reduction of higher-level structures, processes, and behaviors to those of lower levels which are then regarded as having greater ‘reality’, scientific significance, or foundational support.

8. It suggests that biological problems, principles, and questions can be resolved at specific levels, thus ignoring their overall 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’.

9. There is a continuity of activity throughout the body of an organism – its explanatory division into molecules, cells, tissues, and organs creates a false individuation or compartmentalization of biological agency and objects when it is the organism that is the most strongly individuated biological object in nature. 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.

10. 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.

11. The mereological part-whole treatment of layers of inclusiveness within a nested hierarchy ignores the different characteristics of the objects represented in the ‘layers’

12. 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.

13. 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.

A New Metaphor

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 is that of process. Early biology was a descriptive subject concerned with the inventory of structures, organisms, their classification, and terminology. This static science took on a more experimental and dynamic character as interest shifted from the permanence of structure to the functional processes of physiology, leading eventually to the purposiveness of behavior and the cognitive sciences.

Contemporary biology is currently coming to terms with the extension of the notions of agency and cognition from 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 including its relationship to intelligence, both organismal and artificial.

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

Process

The biological hierarchy consists of things as concepts. While molecules, cells, and tissues are objects in the world, placed in a hierarchy they take on a timeless, abstract, or eternal character. Thinking in terms of spatiotemporal scales by including time takes account of process.

Because we reify (apply an intuitive conceptual permanence or eternal thingness to) physical objects as in the world, we do not think of spatiotemporal objects as having a lifetime. The human biological agent exists for a lifetime (said to be three score years and ten) which is an insignificant speck in the overall universe of space and time. An individual macromolecule, relative to a human, is extremely small and extremely short-lived.

Thus, biological objects have spatiotemporal boundaries: they exist as spatiotemporal units (STunits).

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.

Theory & Practice

Theoretical biology provides the foundation of principles and concepts that underpin biological practice, these two aspects of biology being connected in complicated ways.

Where possible, it helps to distinguish between theory and practice – between abstract concepts, theories, models, and principles (referred to here as tokens), and actual objects and situations in the world (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). For our purposes, tokens are theoretical categories that are instantiated by types that have a spatiotemporal existence that is open to empirical investigation.

The hierarchy of biological organization misleads by allowing interpreters to confuse and conflate the distinction between biological tokens and biological types.

Agency

We know that life is a special kind of matter. Many properties may be listed that set life apart from the other matter of the universe, including its forms, the processes it displays, and its material composition at many spatiotemporal scales.

However, its most autonomous representation is as organisms that display the critical properties of survival, reproduction, adaptation, and evolution which constitute the agency that most readily separates the living from the inanimate and dead.

Possessing these agential properties engages complex systems of transport and communication.

Spatiotemporal scales

A scientific description of the living world can avoid or, at least, minimize theoretical and philosophical complications by adopting the simplest possible first principle – that biology consists of biological objects arranged on the stage of space and time.

Elsewhere it has been argued that the domain of biological objects can be adequately classified under the three categories of structures, processes, and behaviors, and that these objects do not exist equally but, ultimately, are subordinate to the goals of the type organisms of which they are a part.

Interpreted in this way an actual (type) organism is a spatiotemporal unit with a definitive spatiotemporal lifeline that intersects causally with the spatiotemporal lifelines 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.

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 entire object.

As types (but not tokens) spatial scales provide us with different aspects, interpretations, or ways of describing an organism. Because these are simply different ways of describing the same thing they are, for simplicity, referred to here as perspectives. As tokens, these scales have independent identities.

Just as molecules are not separate from cells, cells are not separate from tissues, they are constituents of them, and therefore spatiotemporally connected in complex ways. The theoretical separation of tokens is not possible in the actuality of types. While cells and tissues may be separated in theory, in practice they are not only spatiotemporally interactive, they share part of their spatiotemporal identity. We are confusing a theoretical category (token) with its actual equivalent (type), mixing up the theoretical and actual.

The perspectives we adopt when providing scientific explanations of organism structures and functions are interpolated and intercalated in complex ways. The spatiotemporal existence of one object cuts across the spatiotemporal existence of another object in complex ways and with complex consequences. A type organism does not consist of separate superimposed layers or levels one of molecules, another of cells, another of tissues, and so on – the organism is all of these in combination. 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. But 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. We are intuitively inclined to think spatially rather than temporally and in science this translates into the security and seeming permanence of solid objects and neglect of change and process. 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 process and activity. 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.) that, 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 are we to represent the entirety of this complexity to students of biology through a simple picture or characterization?

What kind of metaphor for ‘everything’ would avoid the pitfalls of hierarchical thinking that are listed above?

We could begin by minimizing our temptation to view the world through the lens of a metaphor and attempt a best possible scientific representation of the world. This would include acknowledging that we can never view things from the point of view of the universe and that our interpretation of everything has passed through the 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 a characteristic kind of object, characteristic kinds of properties and facts, and usually a different profession for people that study or work with it: quantum physicists, solid-state physicists, chemists, biologists, psychologists, sociologists.

It would be an interpretation that recognizes life as driven by an agential process.

When we describe the differentiated matter external to our bodies we divide it up into units with more or less autonomy and more or less similarities and differences. We name these objects and can assign them spatiotemporal properties.

We need a metaphor that resembles more closely the physical characteristics of the world, and life as a dynamic, agential, and intercommunicating process that we 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.

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

The metaphysical question concerning the basic ingredients of biology, once it has moved beyond life and living organisms, has no simple answer. The contentious solution offered here is a simple classification of biological ‘things’ that differentiates both the objects of study (theoretical constructs) and things in the world (reality) as our best human attempt at describing what there biologically is.

This is a classification of biological objects into structures, processes, and behaviors, all understood by reference to organisms as the foundational units of biology. This is a framework based on spatiotemporal process that allows for matter, structure, agency, and function.

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.

Commentary

Humanity has invented several popular metaphors to express the operations of the universe in its entirety – metaphors that reflect the interests and concerns of the day.

So, for example, Plato and Aristotle viewed the universe as a vast organism whose parts contributed to the functional organization of the whole, later treated by writers like Teilhard de Chardin 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 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 provided by God to sustain human life.

During the Scientific Revolution, and later Industrial Revolution, a mechanical metaphor seemed more apt. 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 because they can be treated as ‘reality’ (reliable representations of the world) and thus lead to unjustified inferences. Scientists, for example, frequently forget that scientific facts (empirical generalizations) are our best possible explanations (hypotheses), not some ultimate reality.

Surely, today’s science could not possibly fall into such a simple metaphorical trap . . . ?

How are we to conceptualize, illustrate, and describe the general characteristics of the living world?

Life (typically the units of matter we call organisms) persisted in the world by mindlessly developing means to survive, reproduce, adapt, and evolve.

To understand and explain something so complex as the world, or life, we construct mental images of what we think it must be like. Once we have established this mental 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 understanding of complex problems easier to grasp. The popular metaphorical representation of biology is a hierarchy of levels of biological organization.

We often answer metaphysical questions like this by falling back on our general intuitions of reality which we, in a loose sense, loosely regard as consisting of things of different sizes, inclusion, complexity, and significance, all arranged in time and space. Things (science 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.

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 it is physical objects that are the dominant ‘things’ in 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.

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.

First published on the internet – 1 March 2019

. . . 15 May 2024 – Transferred and modified from a former article simply headed ‘hierarchy’.