Annotated Bibliography

The most recent exposition of Hierarchy theory of evolution, tightly integrated with network theory, is:

Niles Eldredge developed Hierarchy theory in books and papers, with a constant attention to the historical and epistemological context of Twentieth Century evolutionary biology. The Pattern of Evolution (1999) incorporates most of the intuitions and works that influenced Hierarchy theory since the 1980s, for example the epistemological comparison with other approaches, the ‘sloshing bucket’ model (see below), and the analysis of Darwin’s work. Reinventing Darwin (1995) lays Hierarchy theory down into the most important debates of the Twentieth Century, including that on punctuated equilibria. Eternal Ephemera (2015) locates Hierarchy theory into a still deeper historical context.

The foundational text of hierarchy theory is the highly readable and engaging book Unfinished Synthesis:

From the same years, two other interesting works are a paper and a book:

Unfinished Synthesis argued that the Modern Synthesis ontology (i.e., the “theory of what exists”) was incomplete:

In a nutshell, the synthesis limits its attention to only a few of the biological entities that seem to me to exist in the world and to be involved in the evolutionary process. Genes (in a premolecular phase of understanding of course), organisms, demes (to some degree), and species are explicitly addressed in the writings of the synthesis; monophyletic taxa are but dimly perceived: and ecological entities (populations, communities, and regional biotas) are not even addressed (p. 7).

To complement the synthesis, Eldredge’s book proposed “an alternative approach to the very structure of evolutionary theory”:

That structure is hierarchical. Genes, organisms, demes, species, and monophyletic taxa form one nested hierarchical system of individuals that is concerned with the development, retention, and modification of information ensconced, at base, in the genome. But there is at the same time a parallel hierarchy of nested ecological individuals—proteins, organisms, populations, communities, and regional biotal systems, that reflects the economic organization and integration of living systems. The processes within each of these two process hierarchies, plus the interactions between the two hierarchies, seems to me to produce the events and patterns that we call evolution (p. 7).

The revision of the ontology of evolution was supported by good scientific reasons: there were actual scientific questions left unanswered by the synthesis, such as why sex is prevalent, why relatively large amounts of genetic variation are found within most populations, and whether selection operates at higher levels. Many things were left out, such as all species-level phenomena in the history of life, including trends, “radiations”, and the like; cross-genealogical extinction events (of varying magnitude) that degrade ecological systems; and the likewise cross-genealogical patterns of proliferation following such episodes.

Here we report two pictures from the book. Each shows the two hierarchies, but the two differ with respect to the configuration interactions between the hierarchies.  (see Fig.7.1 & Fig.7.2)


Fig. 1 Fig. 2


In the first picture, all levels interact with all others. In the second one, the only interaction is natural selection. The two situations are the extremes of a continuum. Hierarchy theory is open with respect to the number, nature, and direction of interactions, but reality lies, for Eldredge, somewhere in between, and one of the tasks of hierarchy theory is assessing which interactive processes do tie the two hierarchies together.

Unfinished Synthesis contains the first, full, correct description of hierarchy theory. Earlier attempts can be seen as preparatory. In tracing back the origins of Hierarchy theory, Eldredge often refers the famous punctuated equilibria paper that focused on species and on the paleontological evidence of stasis, advocating implications for evolutionary theory:

Further back, Eldredge sees the paper with Gould as, in turn, a repackaging, with additions, of a previous paper published in 1971:

A literature review on punctuated equilibria would be out of place here. On the one hand, given the sustained attention raised by punctuated equilibria over the years, a review would be too demanding and oversized. See, for example:

On the other hand, Hierarchy theory was actually largely independent from punctuated equilibria – and from Eldredge’s colleague Stephen Jay Gould – both in its origin and in its development.

In Unfinished Synthesis (note 1 on p. 215), Eldredge explains that his initial interest in hierarchies stemmed from arguments with philosopher Stanley N. Salthe, whose paper described a hierarchy of levels (molecular, cellular-organismic, population, community).

Eldredge thought that the notion of hierarchy was valuable, but the hierarchy he used to associate with evolution involved genes, organisms, species, and monophyletic taxa. In the meantime, Eldredge himself had not cleared his mind yet: in 1982, in an attempt of hierarchically expanding punctuated equilibria, he described a hierarchy that included regional biotas above monophyletic taxa (“a vain attempt to incorporate cross-genealogical phenomena such as extinctions”, ibidem).

Eldredge and Salthe eventually published together the paper Hierarchy and evolution (1984), integrating the two systems into a single, coherent framework of two parallel hierarchies, later modified in Unfinished Synthesis.

Salthe autonomously went on developing hierarchical ideas, but his studies went in a different direction from Eldredge’s: more leaned towards a totally ecological, thermodynamical, and ‘cosmic’ view of evolution. See for example:

Eldredge went on to enhance and promote his Hierarchy theory in the books and articles mentioned here in the beginning. One interesting addition was the ‘sloshing bucket’ model, explained in The Pattern of Evolution and in the following papers:

The sloshing bucket (Figure below, from Eldredge 2008) was a way to apply Hierarchy theory to real world considerations, and to show the relevance of Hierarchy theory to other biologists. In the history of life, the magnitude of ecological perturbations match the extent of evolutionary change. Localized ecological disruptions often result in the re-establishment of similar local ecosystems, by recruitment of conspecifics that still live outside the affected area. On the grandest scale, global environmental disruption is coupled with the disappearance of larger-scale taxonomic entities, and, over periods of millions of years (typically 5-10 My), modified species derive from taxa that survived the extinction event. For Eldredge the most interesting situation is the intermediate one, where regional ecosystems are disturbed: the fossil record shows that most speciation events take place as a consequence of regional ecosystemic collapse and multiple extinctions of species across different lineages, and for Eldredge speciation is basically what brings about evolutionary genetic change in the history of life.


Fig. From Eldredge


The emphasis on ‘abiotic control’ was retained also in reapproaching the theme of punctuated equilibria. For example, Eldredge set up a study group on the causes of evolutionary stasis, and the group, ruling out competing hypotheses, was left with physical environmental conditions as causes of stasis and punctuations:

Explicit references to Hierarchy theory were also made by authors developing evolutionary concepts such as turnover pulse, coordinated stasis, macroevolutionary consonance. See for example:

Many advancements of biological sciences—in particular, network theory, complex and dynamical systems theory, computational methods—are intimately connected to Hierarchy theory, although researchers working on them are not fully aware of the theory or of its relevance. To have a picture of this ‘unaware convergent movement’ in the scientific community, the reader will have to wait for the book Evolutionary Theory: A Hierarchical Perspective coming out from our project.

A particular branch of reflection conceptualized social systems and their relationship to biological systems within Hierarchy theory. Such branch was developed by Eldredge and philosopher Marjorie Grene:

Social systems were seen as historical entities that arise from the reintegration of organismic reproductive and economic adaptations. The view contrasted, in particular, sociobiology’s exclusive emphasis on reproductive success.

Finally, there is a sense that human culture would fit into Hierarchy theory better than it does in less pluralistic theories: