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We think hierarchically. By this I mean that we prioritize our thoughts: we put them into some sort of order. Mostly this happens unconsciously, but sometimes it requires concentration and conscious effort. Either way, this mode of thinking is part of our human nature; part of our innate cognitive make-up. If we did not order our experience, noting similarities and differences while also ranking some things as more important than others, then we could not operate in the world: all would be confusion.

This article discusses the way that this every-day and every-moment characteristic of our mental life has been incorporated, as metaphor, into the scientific way that we understand and explain the world.

Could science be better served by avoiding the language of hierarchy – and what are the alternatives?

Representing the world

In our everyday lives we do not question the nature of the world around us, what it is ‘really’ like (see manifest image). But the nature of ‘reality‘ is not as obvious as you might think. Below is an image representing one view of the way the world ‘actually is’.

Baron von Mueller

The Natural Order

The Great Chain of Being or Ladder of Life

From Rhetorica Christiana by Didacus Valades (1579).

The world is arranged like the steps of a ladder from:
– higher to lower
– God – to rulers – to common people – to – animals – to plants – to rocks
– perfect to imperfect
– spiritual to material
– rational to irrational
– complex to simple
From God in blissful heaven above, to the Devil in burning hell below.

Everything has a fixed place in an eternal physical, spiritual, and moral Natural Order as determined by God.

The connecting ‘Great Chain of Being’ runs up the centre.
Courtesy Wikimedia Commons – Duncharris – Accessed 29 April 2016

Humanity, in trying to devise the best possible way of representing the way the world as it ‘actually is’, has found that the principles and procedures of science have the strongest powers of prediction, with the further benefit that are open to constant appraisal and improvement as new evidence emerges.

Science attempts to represent (reflect, copy, map, mirror, describe – choose your metaphor) as best it can, the external world that exists beyond our minds. But it can only do this within the constraints of our evolved perception and cognition assisted by the tools of technology (physical technology like microscopes, telescopes, computers; and mental technology like language and mathematics) that enhance our biologically-given senses.

As our understanding of human language, cognition, and perception improve, so we gain increasing insight into the factors governing our metaphysical assumptions (intuitions) about the world. The character of our thought becomes social communication through language and here we can also learn about hierarchy since language is itself organized in a hierarchical way (see classification).


Because science is communicated through a shared scientific language it is not always advanced by adhering to the strict scientific principles of careful observation combined with meticulously designed experiment (with its verification or falsification). Sometimes progress can be made by honing the language we use to convey scientific information and ideas.


We deal with difficult or abstract ideas by making them more concrete and familiar, and we do this by using metaphors or ‘as if’ language. We say, for example, that temperature goes ‘up’, or that something took a ‘long’ time. Here we are describing properties of temperature and time using the more familiar category of space. Temperature does not literally go ‘up’, and we do not usually think of time using spatial properties – this is just a façon de parler, or figure of speech.

In thinking about the relationship between science and language Steven Pinker in ‘The Stuff of Thought’ (2008) shows how we embed key complex and abstract concepts of space, time, matter, and causality in 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. Prepositions express space as places and objects in spatial relationships (on, under, to, from etc.). This language of intuitive physics may not agree with the findings of modern physics but, like all metaphor, it helps us to reason, quantify experience, and create a causal framework for events in a way that allows us to assign responsibility.

Scientific metaphors can be extremely useful by providing mental representations: they give us a mental framework or structure to work with, instead of something abstract or ill-defined, and this helps us to draw inferences and conclusions about the world.

Humanity has invented several popular metaphors to express the operations of the universe in its entirety. So, for example, one early metaphor treated the universe as an unfolding or evolving organism, recently modified as the self-regulating biosphere which creates the necessary conditions for its own persistence, feeding and nurturing us humans in a purposeful way. This is part of the imagery of Mother Earth or Gaia, probably the prevailing view of our prehistoric ancestors.

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, constrained by rigid deterministic and absolute laws. Today the popular metaphors for the universe are the human brain, or a computer.

Metaphors are generally harmless tools: but we must be on our guard, because it is always possible to mistake metaphor for ‘reality’, and in so doing make unjustified inferences. Scientists themselves are especially prone to confusing scientific facts (empirical generalizations) with the objects and circumstances that they purport to represent.

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

But let’s consider a contemporary popular metaphor of wide currency in both science and philosophy. It is pervasive in today’s text-books, as well as scientific and philosophical journals and it is, I believe, obstructing our scientific thinking.

Levels of organization

We simplify the complexity of biological objects, events, relations, and ideas as we do all the categories of our cognition, not only by metaphor, but by combining them into manageable mental groups or categories.

For the most part the criteria we use to establish groups depend on the purpose we have in mind. So, for example, we might arrange organisms according to their edibility, or their medicinal value. Modern scientific biological classifications are intended to present us with groups that reflect the evolutionary relationships of organisms. Prior to the theory of evolution biological classifications were either artificial (classifications of convenience – like associating all plants with yellow flowers) or more natural (reflecting a close examination of similarities and differences in form and function). Today biological classifications define their groupings using criteria that are presumed to reflect evolutionary relationships.

Sometimes the purpose of a classification is unclear. Running alongside purpose-driven classifications (including those of science) are classifications that lack a ‘purpose’. It is as though they organize objects, not according to some special criterion, but according to the way they really are, the way they actually exist in the world so that the grouping reflects its true nature or being. This is the metaphysical foundation of our science – it is what we take as a foundational ‘given’, an unjustified ‘axiom of existence’ . . . this is our metaphysical intuition about the way the world really is.

Historically, probably the most powerful classification of this kind (because it occurs in one form or another in most cultures) is the Great Chain of Being or Ladder of Life (see illustration above) which organizes the world into a hierarchy. This view of the way the world is has been around for millennia and was articulated by Plato and Aristotle and later absorbed into Christianity (see worldviews). And this is probably how hierarchy became embedded in scientific imagery and explanation.

The Ladder of Life as a series of nested, unfolding cosmic layers or dynamic levels of complexity, has found support from both religious and scientific sources. French scientist-philosopher and Jesuit Catholic priest Pierre Teilhard de Chardin in his posthumously published cosmic theology The Phenomenon of Man conceived an Omega Point or maximum level of complexity and consciousness towards which he believed the universe was evolving orthogenetically. It had started out as the primordial matter of the geosphere, then developed into the biosphere which eventually included the consciousness of humans on its way to a supreme consciousness, the Omega Point.

One carefully articulated modern account that has dominated modern science for about 50 years is that of Oppenheim and Putnam (1958)[16]who pictured nature as a hierarchy of levels of objects that, in turn, defined a hierarchy of distinct sciences. Above the root level each level of objects is composed of objects from the next lower level. This gives rise to systems of ontological levels – of atoms, molecules, living cells, multicellular organisms, and communities etc. (the choice of levels varies somewhat between authors). The sciences are then individuated according to the level they occupy and connected to related levels through bridging principles.

Among many contemporary scientifically based accounts that follow the same general framework of thinking is Tyler Volk’s Quarks to Culture: How We Came to Be. Columbia University Press (2017). This is the prevailing way that we represent, both scientifically and philosophically, the order and pattern of the world around us. The themes of physics, as different from biology, as different from consciousness seems to delineate three separate though intimately connected modes of existence.


The single key characteristic of a hierarchy is that it arranges its members ‘above’ and ‘below’ one-another into a series of levels called ranks, and in this way hierarchies prioritize or rank objects using a powerful spatial metaphor. Objects within the hierarchy are spoken of, and conceptualized, as being arranged on a vertical axis divided into ‘levels’ like the rungs of a ladder, so we speak of a ‘top’ and a ‘bottom’ to the hierarchy and of items that are ‘higher’ or ‘lower’ than others on the ladder.

Our everyday language is shot through with hierarchical talk. Humans are ranked metaphorically into ‘upper’, ‘middle’ and ‘lower’ classes. Think of expressions like: top cat, low life, high society, highbrow and lowbrow, high hopes, bottom dollar, low morals etc.

One contemporary example of this kind of classification, described above (and probably derived from it), is the way scientists and philosophers speak of hierarchical levels of organization of matter [15]. . . into molecules, genes, cells, tissues, organs, whole organisms . . . sometimes extending further into populations, ecosystems, biomes, and eventually the entire biosphere.

A characteristic example comes from leading physicist and cosmologist George Ellis who 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 but proceeds both ‘up’ and ‘down’:

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

Hierarchical talk like this might be an economical way of representing the world in casual conversation, but does it help our scientific thinking? Certainly, the frequency of its use in scientific and philosophical literature would imply its general acceptance. But is the metaphor doing its job well, that is, providing us with the best way of representing material diversity?

I shall argue that representing the natural world as a hierarchy of matter impedes scientific communication in at least four key ways:

      • By implying misleading values
      • By invoking metaphorical structure, objects, and relations
      • By introducing ambiguous causal and other relations
      • By overemphasizing an analytical approach to scientific investigation

Rank & value

Before Charles Darwin‘s On the origin . . . the Aristotelian ladder of life (scala naturae) provided a convenient metaphorical structure for everything in the world – what Aristotle referred to as its objects, their properties and relations. It showed what everything was for (its purpose), and provided a mental image for the way that all the objects of the world were ordered in relation to one-another.

This ancient imagery was incorporated into the Christian world view as a hierarchy that placed a relative cosmic moral value on the various material and spiritual ingredients of the world. Rocks were 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.

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 simply particular organic 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. Science had become detached from questions of value.

Though resistant to a moral ordering of the natural world, Darwin was not averse to making hierarchical judgements about people. In his account of the voyage of the Beagle, he described Australian Aboriginals as follows, using ‘civilization’ as his grouping criterion:

On the whole they appear to me to stand some few degrees higher in the scale of civilization than the Fuegians‘.

Though this could be taken as a factual statement about degree of social complexity, it clearly carries moral overtones.

Old habits and ideas linger on in language. We still speak of ‘higher’ and ‘lower’ organisms. We can feel the attraction of ‘higher’ meaning ‘better’ in some way as the valuing characteristic of hierarchical metaphor remains.

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 prioritizing we are usually placing greater value on one thing over another. So, out of habit alone, ranked scientific objects are often valued by association. This I call rank-value. Objects at the ‘top’ are frequently ‘valued’ differently from objects at the ‘bottom’.

The simple point here is that the injection of value into the mental hierarchies of daily life are all too easily transposed onto the hierarchies of science.

Principle 1- The objects within a classification system, when ranked, are ranked according to the purpose(s) for which the classification was devised. However, ranking alone frequently brings valuation by association, as in daily life.

Metaphorical structure, objects, & relations

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 . . . or are there many kinds of classification serving multiple purposes and each, possibly, of equal worth?

Regardless of our opinions about this, we clearly need to communicate about many objects beyond the elements: we need to speak of planets, stars, organisms, tables, chairs and so on.

How does science deal with this difficulty of multiple objects of many different kinds? We know that all things are connected, but how are we to group or classify ‘everything’?

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.

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?

Ranked matter

Consider a room in parliament where legislation is being enacted. We can describe the objects and events occurring in that room using, as it were, several different languages – different ‘levels’ or realms of discourse – probably all mixed up together: social, psychological, biological, even physicochemical etc. When we talk about these different scientific and linguistic domains (the language and concepts of physics, biology, psychology, sociology etc.) we are inclined to fall back on the hierarchical metaphors of daily life: we use a mental representation of layers or levels . . . as if they were physically superimposed one on another, the layers perhaps interacting causally in ‘top-down’ and ‘bottom-up’ ways. The metaphor encourages us to treat the ‘levels’ as if they were separate physical objects (like the rungs of a ladder, or strata of rock in a geological profile) when clearly we are simply describing the same situation in different ways: we are examining and speaking about the particular situation from different aspects, perspectives, or points of view.

The important point here is that the different descriptions we provide are not descriptions of different objects or existences like superimposed strata of rock. The difference is in mode of explanation (it is epistemological not ontological).

In using the metaphor of hierarchy our logical inferences about the situation follow the logic of the metaphor, in this instance the logic of interacting physical layers.

Principle 2 – following the logic of the hierarchical metaphor we misleadingly treat the world as though it were a series of superimposed and interacting physical layers when, in fact, we simply perceive, understand, and describe the same objects in many different ways

Describing ranks as higher or lower and structuring the world through the metaphor of ranked altitude can therefore be both confusing and unscientific.

So what is it that defines these ‘levels of organization’ – what exactly are their key ranking criteria? What are our intuitions about the nature of these layers?

When we examine this question more closely it emerges that we use at least four classification criteria that blend in a confusing way, so it will help to look at them all in more detail before suggesting an alternative and more scientifically useful language that can achieve the same ends:


a. Size (scale) – objects in the hierarchy are ranked simply larger or smaller: they represent different scales of existence

b. Scope (Inclusion-exclusion, containment) – some objects are contained by, or nested within, other objects. Cells are within tissues, which are within organs, which are within organisms (this is reminiscent of the Linnaeus‘s nested hierarchical classification)

c. Rank value – objects can be arranged in relation to one-another according to some form of valuation

d. Complexity (degree of organization) – ‘levels’ represent irreducible degrees of complexity so, for example, an organism is a highly integrated self-regulating unit, not just an aggregation of molecules.


These criteria (often assumed to lie objectively within the world) correspond to common intuitive (possibly innate) ways of perceiving, representing and understanding the world by size (bigger/smaller), scope or containment (more/less), position (higher/lower) often in combination with value (more important/less important), structure or organization (simple/complex).

The hierarchy of organizational levels seems to blend the Great Chain of Being with the Linnaean nested (containment) hierarchical classification of living organisms.

Do you think that in attempting to build a scientific representation of the structure of the universe that one or several of these criteria better represents the way the world ‘actually is’?

a. Size/scale

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’. Of course, scale and size are often also associated with scope and complexity and the distinction between scale and other modes of arranging the natural world is not clear-cut: increasing size does not necessarily entail increasing complexity and as units of scale become progressively more inclusive they do not necessarily become more complex.

b. Scope/inclusion-exclusion/containment/encapsulation/nesting

Biology, the living world, studies a subset of a greater whole, the physical world. In this sense biology is a ‘reduction’ (part of) the physical world as a in the same way that an organ is part of an organism. All physical objects are physical, but not all physical objects are biological. This simple sentence poses a linguistic and logical riddle that needs unpacking. The point is that physically biological objects are not something more, something physically added to the set of physical objects. Instead they are physical objects of a particular kind, with their own defining structures and properties – there is no new matter, only new properties. This can be confusing because although an organism does not add something physical to our concept of physical object it does add information about structure, function, and properties and in this sense it is additive. To all the things we can say about physical objects in general can be added those specific things that characterize biological objects.

There is a critical historical dimension to biology since the arrival of organisms with their increasing complexity took place late in terms of the process of increasing physical complexity in the universe. Biological structures, functions, and properties ’emerged’ from inanimate matter. ‘Emergence’ of new properties, and the relationship between wholes and parts will be discussed later. For now we can simply note the persuasive metaphor of containment. It is ‘as though’ there is a physical world and contained within and part of that physical world there are living organisms. Following the method of nested hierarchical classification this is a view of the world as different kinds of the same substance ‘nested’ within one-another, each kind having its own particular characteristics or boundary conditions, that are supplemented by additional properties with each wider inclusion.

c. Complexity/organization

From the time of the Big Bang and in spite of the Second Law of thermodynamics one aspect of the universe has been the emergence of increasing complexity. From the first 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?

Dubious causation

The notion of causality – of what determines what – is at the core of our understanding of the world in general and our scientific explanations in particular.

Hierarchy theory confronts the ambiguous character of causation since it forces us to consider the objects of causation and their flow from ‘higher’ levels to ‘lower’ and vice-versa i.e. both ‘up’ and ‘down’. This does not marry well with the imagery of a world in which all activity is ultimately grounded in (flows from) its smallest constituents.

Analysis vs synthesis

It is a characteristic of explanation that we do not explain an object in terms of itself: explanations proceed either to component parts or a broader context. Using metaphorical hierarchy-talk, explanations can proceed in two ‘directions’ – by ‘upward’ synthesis or ‘downward’ analysis. Almost any item in the universe can be divided into smaller parts or united into larger wholes, and that is how we explain things.

Analytical reductionism

English philosopher Bertrand Russell describes a 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 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.

It is a method that lies at the core of scientific procedure and gives its name to a strong tradition in Western philosophy – ‘analytic philosophy’. The principle is simple: to comprehend or explain either a physical object or a concept (a whole) we must investigate its parts and their relations.

Let’s extend, using a thought experiment, Russell’s analogy of the microscope as a means of achieving explanatory focus.

Imagine you have an extremely powerful new scientific instrument like a combined microscope and telescope – we can call it a micro-macroscope. The first objects you see as you look into the instrument have no recognizable form. We can call them molecules. But when you adjust the instrument by zooming out you see the molecules seeming to coalesce into something that looks like a leg, then zooming out further you see that the previous object really was a leg, that the leg belongs to a person, zooming out 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. Perhaps you can also imagine a scientific future when further objects can be added at the limits of this caricature – at one extreme much smaller objects, smaller than fermions and bosons, and at the other extreme our universe merging into a multiverse.

The micro-macroscope gives us a way of thinking about and challenging our scientifically learned cognitive categories (see Immanuel Kant) and the way this cognitive focus translates into explanatory focus: it allows us to look at the landscape of the universe both ‘up’ and ‘down’, viewing the same scenery, but from different scales and perspectives.

Principle 3 – The physical units of matter have no intrinsic (ontological) precedence one over the other: an electron and a marigold possess existence (‘being’) equally

Better science

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, and ultimately the universe, 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 lies in the finest resolution of the analysis.

My claim is that we place greater significance, value, or 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?’

Aspect theory

Science attempts to describe the world in a detached way that minimizes the impact of human subjectivity. But the objects we perceive, the criteria and cognitive faculties we use to discriminate between them, the sense of time in which they are experienced, the scales and aspects from which we view these objects . . . are all influenced by our humanity.

This does not make the world a subjective illusion but, unsurprisingly, it make it our human interpretation.

We have tried to overcome the bias of our human scale of experience by supplementing our biological capacities with technology that peers into the depths of space and drills into the foundations of matter. But we cannot view everything as though there were no time, no place of observation, and no observer.

A perspectiveless world has a flat ontology where everything exists equally: a world without discrimination. In practice, and of necessity, we have evolved biological traits that discriminate our experience of the world and therefore make it meaningful. This is the biological lens through which we view everything; it is our species-specific human reality or umweldt.

But, given a perspectiveless view of the world how could we attempt its scientific description: where do we start? On what grounds is anything prior to something else? Is it structure, function, behaviour, material composition, purpose, energy, information, number . . .?

The ranking criteria we use to intuitively structure the world (those foundational intuitions about the world that we accept in our science) relate to: size (shape and scale); inclusiveness (containment or scope); and complexity.

It is largely on these criteria (with variation in individual emphasis) that the ‘levels of organization’ of academic biology have been founded. The word ‘scale’ is sometimes used, but this emphasizes spatial distribution to the exclusion of the other factors and is one factor influencing ‘smallism‘.

‘Aspect’ is a simple word that captures the flavour of ‘perspective’ or ‘interpretation’ – it implies a view of nature influenced by the human perspective (intuition). Philosophically we are simply referring to what is sometimes known as perspectivism – alternative systems of representation that are equally valid – our preference based on pragmatic factors such as our particular interests or goals. An atom, boson, or fermion is no more ‘real’ than a daffodil or elephant, it is just that science mostly proceeds by analysis which leads us to believe that studying parts (and the smaller the better) will always reveal the secrets of the whole.

Using the expressions ‘aspect’, ‘perspective’, and ‘representational system’, reduces the temptation to apply rank-value: it does not imply a hierarchical layering of the world; it captures the way disciplines study the same objects from different points of view (rather than the layering of reality suggested by the ‘levels’ metaphor); it is a simpler, more parsimonious way of representing the world.

Put simply, biological and other academic disciplines study different aspects of the same world. They study the same world from different perspectives: there is no hierarchy in the world – that is in our minds.

Principle 4 – The word ‘aspect’ captures the sense of viewing the same ‘reality’ from different perspectives; it avoids the conceptual ambiguities associated with the metaphor of hierarchical levels of organization.

Domains of knowledge

The mental structuring of the world into hierarchical units runs in parallel with the way we have organized the system of knowledge into academic disciplines as domains of knowledge and discourse, each with their own principles, procedures, and technical language.

The study of the natural world developed from philosophy, into natural philosophy, then the natural sciences of physics, biology, and geology, before each fragmented into the wide range of (sub)disciplines that we know today. On the one hand this has provided us with a more detailed, finer resolution, knowledge of the world, but it has also tended to separate academia into knowledge domains or silos. There is no doubt that these knowledge domains play an important part in the way we view ‘reality’ and it is an interesting question as to whether we believe that these subject divisions have been constructed as a matter of convenience, or whether they represent our best interpretation of true nature of things.


Human hierarchies are ‘vertical’ authority structures with people ranked ‘above’ and ‘below’ one-another in systems of command and control. To overcome the difficulty of understanding and explaining something so complex as the material world we construct mental images of what we think it must be like. Once we have a mental picture then we have a framework on which build our thinking.

One popular mental representation of the world is as something that is multi-layered – consisting of a hierarchy of integrative levels of organization. Each level has unique and irreducible properties – its own rules and principles of organization. Being hierarchical means that the levels are ordered, or ranked, in some way. The criteria for this ordering process are rarely made explicit and it is, perhaps, assumed that the reasons for the layering lie within the world rather than being imposed on it by our minds. Regardless, on examining a typical biological hierarchy, say one proceeding from molecules, to cells, to tissues, to organs, to organisms the criteria would appear to be based on factors like size, scale, scope, inclusivity, or complexity.

For many scientists this multilayered mental structure is like a building that must rest on firm foundations and they find these foundations in the basic constituents of matter, its fundamental particles: these are the components of the physical world on which all else depends.

There are two major confusions created by this hierarchical metaphor. Firstly, like all hierarchies it ranks or grades its contents like the hierarchies of human existence when it is by no means clear that the natural world is ranked in this way. When we rank one kind of matter as more ‘basic’ or ‘significant’ than any other then we at least need to provide a convincing justification for doing so. Secondly, the imagery of interacting layers or strata of the world is misleading as it implies the interaction of different objects when, on reflection, it is clear that we are dealing with the same material explained in different ways. This is a subtle distinction but, for example, we do not have cells on which are physically superimposed tissues, the two interacting like one person interacting with another. Rather, the cells are a part of the tissue itself. What then is the best way of representing causation in hierarchical (or any other) systems. This then draws our attention to thinking about possible alternative representations.

It is now clear that when we imagine the world as consisting of molecules, cells, tissues or organisms it does not consist of these things separately but together. We can describe the entire organic world in terms of the interactions of cells but we find, on occasion, that it is more convenient to describe it in terms of tissues or organisms. We could, given sufficient computing power, describe what goes on in parliament in terms of all the molecules out of which it is composed – but we find it much simpler to talk about people, buildings and events.

Put simply, ‘levels’ are simply perspectives, aspects, or convenient ways of looking at the world. On some occasions it is convenient or useful to consider an organism as a collection of cells: on other occasions it might be easier to consider it as interacting with other organisms and its environment. And on yet other occasions we might take both circumstances into account.
When we study physics or biology, cells or tissues, we are not investigating different things – but different aspects of the same thing. If we replace theories of ‘hierarchical levels of organization’ with ‘aspect theory’ then we eliminate all the problems associated with the ranking of the physical world and the imagination of misleading structures and relations.

For some this is a price too high to pay. It means that all matter is placed on an even footing. All matter exists equally. Elephants are as important as bosons: biology is as important as physics. These are simply different ways of representing the mystery of the same ‘reality’ – and any importance we attach to them will depend on our ‘aspect’ or point of view.

In sum: we intuitively organize the world using categories of scale, scope, complexity, and hierarchy. It is possible to describe the same objects using different terminologies (categories) and therefore different causal relations. The particular language we use for any particular kind of explanation depends on our choice of ‘aspect’ – what is most useful or appropriate to the circumstances. It does not help us to describe a political debate in terms of molecules and energy exchanges. This raises the question of the validity of ‘grounding’, of all things being being ‘ultimately’ one kind of thing.

The criteria defining the organization of academic disciplines reflects a combination of these factors.

Key points

  • The complexity of the natural world is made meaningful by our mental representations which indicate ‘what it is like’, given our human form of perception and cognition. We adjust to complexity by using metaphors.
  • Our survival depends on the prioritization of the objects of our thought which we rank in a hierarchical order of preference, depending on our purpose.
  • The hierarchical ranking of one object of representation over another is imposed by our minds: it does not lie in the world. The physical units of matter have no intrinsic (ontological) precedence one over the other: an electron, an elephant, and a marigold exist equally, the difference between them is in how we understand and explain them – it is epistemological.
  • The metaphor of hierarchical levels of organization misleadingly implies that objects in the world have rank-value and that they are related to one-another in nature like superimposed physical strata.
  • A less confusing and less ambiguous way of capturing our understanding of the world can be achieved by using the word ‘aspect’, which implies a particular perspective on the world.
Media gallery
The video below outlines the conventional interpretation of hierarchy. The stated assumption is that ‘phenomena exhibit hierarchical structure’. Emergent hierarchical systems consist of integrative levels, each level governed by different rules, arranged from higher (more complex) to lower (less complex). ‘Layers’ can interpreted as systems integrated with (encapsulating) subsystems.

Systems Hierarchy & Abstraction

Systems innovation – 2015 – 6:45

First published on the internet – 1 March 2019
. . . revised 2 September 2020


From Ladder to Tree
Charles Darwin’s Tree – 1837
His first sketch of an evolutionary tree – from his First Notebook on the Transmutation of Species
The notes say:

‘I think … case must be that one generation should have as many living as now. To do this and to have as many species in same genus (as is) requires extinction . Thus between A + B the immense gap of relation. C + B the finest gradation. B+D rather greater distinction. Thus genera would be formed. Bearing relation (next page) to ancient types with several extinct forms’

Darwin's Tree
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