The science of taxonomy has been an integral part of the investigation of nature, at least as far back as Aristotle. Identification and classification being fundamental to the understanding of relationships, the definition of what is animal, in particular, both derives from and shapes our ideas of what we are and how we relate to the world.

Taxonomy and common classification alike have been guided by the identification of organisms as perceived entities, as singular things defined by clear boundaries. Until recent times, such a presumed individual organism might be highly structured, and in fact individual, or it might be an association of microscopic and more or less independent organisms. The science has become much more sophisticated and discriminating with the greater resolution afforded by the microscope and the analysis of molecular, phylogenetic relationships. But except in obvious cases where an entity is single-celled and free-living, or is found to be a colony of identical cells, it is still the composite entity that is usually identified and described, not the individual cells by which it is constituted.

The focus on cellular kinship has generally provided a more reliable basis for the classification of organisms than perceived homologies (or synapomorphies), but with regard to independent cells, organizations of cells, and levels of individuality, taxonomy remains almost entirely indiscriminate. According to both taxonomy and common perception, a tree is an individual plant, not an organization of interdependent cells, if only because it has the appearance of singular thinghood. A jellyfish is considered an individual animal because it appears to be a distinct and motile organism that feeds by ingestion. Until fairly recently, a protozoan was widely considered an individual member of the animal kingdom because, like most animal species, it moves and ingests its food.

While the primary emphasis on phylogeny remains especially advantageous for specialized purposes, its strict observance tends to obscure significant similarities and distinctions in the way organisms are organized that are of fundamental importance to the more universal purposes of taxonomy.

There are two somewhat incongruent aspects of scientific practice that have led to inconsistencies in the classification of organisms as either individual or composite entities. The characteristic empiricism of science has influenced the identification of individual organisms by their evident singularity, but the virtual indifference to a discrimination between apparent singularity and microscopic plurality is contrary to the more typical reductionism of science, whereby a composite organism would be described in any case as no more than an organization of cells.

In standard taxonomic practice, individual protists are distinguished from colonies, and colonies from multicellular organisms. But whether an organism is an individual or a colony is treated as one character among many, not significant enough to qualify as a distinguishing character of a group. Moreover, there is no strict distinction between what might be a multicellular individuality and what might actually be no more than a highly organized association of cells. Metazoans (multicellular organisms) are commonly distinguished from colonies of protista, somewhat arbitrarily, on the basis of their having more than one functional type of non-reproducing cell; but the question of by what criteria multicellular bodies can properly be considered individual organisms, as more than a matter of convenience or convention, has not been decisively raised.

Consistency is a legitimate criterion by which we might evaluate the practice of describing the organizational level of organisms. In this regard it is noteworthy that the individuality of the eucaryotic (non-bacterial) cell is well-established. The metabolism of the cell is recognized as controlled by the nucleus, and it is accordingly considered an organic whole, an individual. The constituent bodies of the eucaryote – even those like the mitochondria, which are believed to be descended from parasitic or symbiotic viruses – are regarded as mere organs of the whole, functioning within the central direction of the nucleus. It might therefore be expected that an individual multicellular organism, as opposed to an interdependent association of organisms, would be exclusively defined as having sub-structures governed by a definite, integrative, central organ. But by this standard of consistency, current procedures in taxonomy can be seen as insufficiently rigorous.

The indifference to the level of organization by which an individual entity is defined in taxonomy is a tendency shared by other branches of science, which may be indicative of an underlying cultural disposition. There is a common assumption that an aggregation of sufficient size and complexity is sufficient to generate a higher-level identity. A most striking example of this can be found in the field of artificial intelligence, where there is an influential belief that if an information system is sufficiently large it is possible that an individual intelligence will spontaneously arise, an entity that exists in no particular element, but which in some way transcends its constituents. In the biological sciences the analogous, usually implicit belief is that a sufficiently large and complex aggregation of cells is capable of generating a singularity that is no longer just an association, but an actual entity that operates as a whole, dependent on, and yet somehow transcendent of its components. This belief is usually, if not always, more than just an expedient manner of treatment. A tree is literally considered a tree, not an organization of specialized and interdependent tree cells, in common parlance and in taxonomy, and for no apparent reason other than the perceived singularity.

Being multicellular rather than colonial is the character that generally defines metazoan animals. Colonies, as aggregations of cooperating individuals, are commonly, if somewhat arbitrarily distinguished from true metazoans by the number of types of specialized cells. Most, if not all the cell-types of colonies must feed themselves, as they possess no effective means of transporting and sharing nutrients. In more rigorous definitions, multicellular organisms are distinguished from colonies for having developed cell junctions, mechanisms for distributing nutrients, and complex organic molecules to mediate intercellular communications (Nielsen 1995, 19).

Sponges are notable as borderline organisms between colonies and more advanced organizations of cells. Being virtually plant-like in appearance, and lacking overt behavior, they weren’t classified as animals until the 18th century, when their generation of internal water currents as a means of gathering nutrients was discovered. Although they are often acknowledged to be aggregations of somewhat independent cells which (as shown by Ruthmann and Terwelp, 1979) have been found capable of rearranging themselves if disassociated, the porifera (sponges) are in their aggregations routinely treated as singular organisms, based, evidently, on their coherence as singular things. The question here is whether the definition of the aggregation of sponge cells as a sponge can be justified as any more than convention, and whether that convenience has led to a broad neglect, if not misunderstanding, of the wondrous capabilities of cellular associations, and the profound significance of multi-cellular individuality.

Consider the ctenophores, the comb jellies for example, a much more complex organization than the porifera, being comprised of a number of highly specialized and interdependent cell-types. Ctenophores are characterized by having two networks of nerve cells operating with, at most, a limited interaction to coordinate feeding and locomotion, and a distinct apical organ at the anterior pole that coordinates balance and orientation. The apical organ is suggestive of a brain, being a distinct organ positioned where a head would be in a typical animal, but it is evidently limited to providing bodily orientation relative to gravity, and to having its determinations communicated, via nerve cells, to other cells in the body responsible for adjusting orientation. Here the question of individuality is more interesting than it is with a sponge: Where is the comb jelly? Is it in any way appropriate to regard the organization of cells that seems to present itself as a discrete, singular organism as more than an association of comb jelly cells? Is there anywhere to be found in its physiology something more involved than a discrete signal from one cell to another, a signal which evokes anything more than a discrete reflex? The ctenophores are capable of a high degree of sensory discrimination and remarkably complex behavior patterns, suggestive of a unified awareness and intentionality, but there is no evident anatomical basis for assuming that such an individuality actually exists. Clearly more than a colony, a ctenophore might best be described as a society of highly organized and interdependent cells.

Where ctenophores may be said to have approached the limits of cooperative social organization, echinoderms – starfish, for example – have achieved a highly effective consolidation of decentralized hierarchies of coordination. They are characterized by two largely independent nerve rings which coordinate overall motor and sensory functions, and five aggregations of ganglial consolidation which serve to actuate their characteristic arms – but they lack anything like an integrative center, or brain. In echinoderms as in ctenophores, cellular interaction is entirely discrete and reflexive. In both of these most complex and intricate coordinated associations of cells there is no physiological basis for more than specific reflexes between individual cells in response to specific types of stimuli.