Much of the transition from the microbial to the macrobial, from the smaller and less complex to the larger and more complex, can be viewed as transitions in terms of what it means to be an individual. These transitions include ones from free living to existing in symbioses, from "uni-genomed" to possessing endosymbionts, from prokaryotic to eukaryotic, from mononucleated to multinucleated, from unicellular to colonial to multicellular, and from undifferentiated colonies to differentiated multicellular organisms. What, then, is an individual?

Part of what it is to be an individual is physical separation from other individuals. This can be viewed in terms of sharing of phenotype, where a given individual's phenotype is more available to itself than it is to other individuals. The simplest means towards separation of phenotype involves the possession of a plasma membrane by cells. Note that mechanisms by which avoidance of phenotype-sharing is accomplished are not perfect, and therefore inadvertent sharing, such as with parasites or predators, is almost inevitable. Further, it is possible for individuals to extend their phenotypes beyond their own "bodies" (Dawkins, 1999) , e.g., such as with the secretion of extracellular factors, including enzymes or signaling molecules by bacteria. It is more difficult to avoid sharing these unbounded phenotypes, and especially the coordinated sharing of extended phenotype (e.g., quorum sensing) blurs what it means to be an individual.

A second view of what it is to be an individual is genetic. From this perspective, individuals that are genetically identical may, collectively, be viewed as a single individual. If those individuals are colonial, then this a reasonable statement. However, if these clonal entities are physically separated, then their existence as a single individual can be more difficult to defend. Certainly reproductively there should be little difference between separated clonal entities producing progeny versus colonies of clonal entities reproducing. In terms of communication as well as the potential for cooperation (including in terms of not sharing phenotype with other genotypes), there seems to be much distinction between separated clones and clonal colonies. By contrast, two sexually generated members of the same species are considered to be separate individuals even if both are members of the same colony.

A third view of the concept of individual is in terms of linkage. Certainly the genes found within an individual cell are all linked, even as viewed within a population of clonal organisms, so the linkage perspective would seem to encompass the genetic perspective. Linkage, broadly speaking, can go beyond that between genes found within the same organism, however. Thus, it is possible to envisage two organisms that otherwise may be viewed as individuals but which nonetheless together can act as though they were a single individual because they are both physically linked, e.g., host organisms and their microbiome or within microbial consortia. It is unlikely, however, for two individuals to coevolve sufficiently that we may view them collectively as a single individual unless they are also reproductively linked. Thus, acquired rhizobia endosymbionts are not thought of as the part of the same organism as their hosting plants whereas vertically transferred endosymbionts are more reasonably considered to be members of the same individual. Similarly, anything that is directly vertically inherited can viewed as being linked, to some degree, with components that are similarly inherited together.

A fourth view is based on metabolic integration, or more broadly, phenotypic integration. To the extent that this metabolic sharing is less available to other entities that are not members of the same individual (i.e., such that metabolic integration is more than just one otherwise free-living organism living off of the waste products of another), and is coevolved, which is more likely given genetic linkage, then two individuals may more reasonably be described together as representing a single individual. Indeed, it is more difficult for even a clonal group of organisms to achieve metabolic integration, along with a phenotype that is relatively unshared with others, if that group is dispersed rather than clumped. On the other hand, even an aggregation of organisms can be less likely to display metabolic integration, especially in terms of coevolution and cooperation, if the individual components are not closely related. Thus, mixed biofilms as well as pure but planktonic cultures of clonal organisms both are less reasonably viewed as individual organisms than are colonies of cells that developed clonally from a single progenitor cell.

A fifth consideration is collective action or, more simply, emergent properties. Thus, if an entity is relatively discrete in terms of its sharing of phenotype, is clonally derived, is reproductively linked even if consisting of more than one genome, is accommodating to the metabolic needs of its brethren, and in some manner functions differently as a group versus as simply a collection of individual cells, then collectively the entity may be viewed as an individual unto itself, even if parts too may be described also as individuals. How do we consider what constitutes a collective function? The simplest means is a phenotype that has a positive impact on the fitness of the components of an individual but is either not or less available to separated, unintegrated, individual parts. For example, resource acquisition or potential to survive may be enhanced through colonial living. A clonal colony that is fitter than the same clone not existing within a discrete colony thus may represent the simplest example of a multicomponent individual. Such fitness advantages may be seen simply with a microcolony that has formed from a cell that has been fortunate enough to have become anchored to an available substrate in a location where resources are available—retention of that niche could require either shading or not being shaded by one's neighbors, resulting in resource acquisition advantages that are not similarly available to bacteria which are unable to form microcolonies. Such individual colonies, though, may not necessarily be described strictly as multicellular.

Cellular differentiation can be considered to be the key distinction between consideration of an individual as multicomponent versus multicellular. Cellular differentiation is the generation of phenotypic differences among otherwise genetically identical cells. This may be viewed as an extension of metabolic integration among the parts making up a larger entity. Indeed, it represents an important means by which organismal sophistication may be attained without loss of either clonality or genetic linkage. For example, even if two species should find themselves reproductively linked, such as fungi and algae within lichens reproducing in concert via asexual mechanisms, it can be difficult to assure that one or both lineages are initiated by single cells rather than propagating via an equivalent to serial passage (i.e., which can lead to mutational declines in genetic identity). On the other hand, through differentiation an organism can possess different cell types which are initiated from only a single cell. The distinction nonetheless is subtle. For example, which is the individual, a ruminant, such as a cow, or the cow in addition to its various cellulose-degrading symbionts that are likely maternally acquired and whose presence is essential for breaking down the plant material making up the bulk of a cow's diet? To at least some extent questions such as these, along with the larger question of just what constitutes an individual, can be addressed by employing what is known as multilevel selection theory and the associated idea of a unit of selection (below).

Dawkins (1999) provides an additional and related criterion, and that is that an organism is an entity that displays or indeed is part of a well-defined life cycle. This life cycle can range from being relatively simple, e.g., binary fission in bacteria, to being instead quite elaborate. The latter extreme may be exemplified by cooperative insect colonies where differentiation goes beyond cellular to the organismal such that different members of a colony are specialized for different tasks, with only one of those tasks being reproduction. That is, cooperation seemingly is sustained by these superorganisms by a need to sustain a germ line that is not even found within most of the colony member's own bodies. Nonetheless, these organisms as an entire colony – one often starting with a single mating pair and thus all members are closely related & ndash; go through a well-defined life cycle. These life cycles further may be less ambiguously defined if individuals pass through a single-cell stage, e.g., such as is seen with all sexual cycles, all reproduction mechanisms by single-celled organisms, and also with certain organisms that display parthenogenic reproduction. More ambiguous, in terms of distinguishing among individual organisms, however, are asexual reproductive strategies involving fragmentation, which returns us to our initial concerns about colonial versus dispersed clones as individuals. Consistent with Dawkins' view, however, these more dispersed "individuals" would be seen as having less-well defined life cycles than organisms that develop instead from individual cells (p. 250):

The organism is a physically discrete machine, usually walled off from other such machines. It has an internal organization, often of staggering complexity, and it displays to a high degree the quality that Julian Huxley (1912) labeled 'individuality'—literally indivisibility—the quality of being sufficiently heterogeneous in form to be rendered non-functional if cut in half. Genetically speaking, too, the individual organism is usually a clearly definable unit, whose cells have the same genes as each other but different genes from the cells of other organisms…

Ultimately there is a difference between the evolution of greater size and complexity among groups of individuals and individuals themselves growing to greater sizes and/or developing greater complexity. Consequently, even if it is difficult to precisely define just what an individual represents, it is important to at least try to do so, if only so that the concept of just what is and is not an individual will possess some meaning. This meaning comes about in part because existing as an individual can become more difficult as individuals increase in size and complexity, thus placing constraints on individuals in attaining this greater size and complexity. Nevertheless, in terms of their functioning as a single, well-integrated, and otherwise functionally complex unit, this is more easily attained by individuals than it is by collections of individuals unless similar mechanisms are imposed upon groups to generate an approximation of a collective individuality. Much of the difficulty in understanding how one goes from small and relatively simple to large and relatively complex consequently involves appreciation of how individuality can be sustained despite these changes.