The evolutionary origins of hierarchy

Hierarchical organization -- the recursive composition of sub-modules -- is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a cost for network connections. Here we investigate whether such connection costs also tend to cause a hierarchical organization of such modules. In computational simulations, we find that networks without a connection cost do not evolve to be hierarchical, even when the task has a hierarchical structure. However, with a connection cost, networks evolve to be both modular and hierarchical, and these networks exhibit higher overall performance and evolvability (i.e. faster adaptation to new environments). Additional analyses confirm that hierarchy independently improves adaptability after controlling for modularity. Overall, our results suggest that the same force--the cost of connections--promotes the evolution of both hierarchy and modularity, and that these properties are important drivers of network performance and adaptability. In addition to shedding light on the emergence of hierarchy across the many domains in which it appears, these findings will also accelerate future research into evolving more complex, intelligent computational brains in the fields of artificial intelligence and robotics.Comment: 32 page

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

SummaryProteins display a hierarchy of structural features at primary, secondary, tertiary, and higher-order levels, an organization that guides our current understanding of their biological properties and evolutionary origins. Here, we reveal a structural organization distinct from this traditional hierarchy by statistical analysis of correlated evolution between amino acids. Applied to the S1A serine proteases, the analysis indicates a decomposition of the protein into three quasi-independent groups of correlated amino acids that we term “protein sectors.” Each sector is physically connected in the tertiary structure, has a distinct functional role, and constitutes an independent mode of sequence divergence in the protein family. Functionally relevant sectors are evident in other protein families as well, suggesting that they may be general features of proteins. We propose that sectors represent a structural organization of proteins that reflects their evolutionary histories

The Origins of New Industries: The Case of the Mobile Internet

This paper describes a model of new industry formation that is based on evolutionary theories of technical change. It represents the origins of new network industries as the interaction between multiple technological trajectories that are specific to a particular technology or broadly defined technological regime. The speed with which these multiple trajectories cause industry formation depends on their effective application to the most economical applications; this process occurs through the interaction between design hierarchies and market concepts. Growth in these initial applications causes sub-trajectories or sub-regimes, where competition in the new industry initially takes place, to emerge from the main trajectories. The model is applied to the mobile Internet, an industry that has just started to grow particularly in Japan and Korea.Origins, Industry, Technology, Trajectory, Design, Hierarchy, Market, Competition, Cooperation, Disruptive, Mobile, Internet

The Emergence of Canalization and Evolvability in an Open-Ended, Interactive Evolutionary System

Natural evolution has produced a tremendous diversity of functional organisms. Many believe an essential component of this process was the evolution of evolvability, whereby evolution speeds up its ability to innovate by generating a more adaptive pool of offspring. One hypothesized mechanism for evolvability is developmental canalization, wherein certain dimensions of variation become more likely to be traversed and others are prevented from being explored (e.g. offspring tend to have similarly sized legs, and mutations affect the length of both legs, not each leg individually). While ubiquitous in nature, canalization almost never evolves in computational simulations of evolution. Not only does that deprive us of in silico models in which to study the evolution of evolvability, but it also raises the question of which conditions give rise to this form of evolvability. Answering this question would shed light on why such evolvability emerged naturally and could accelerate engineering efforts to harness evolution to solve important engineering challenges. In this paper we reveal a unique system in which canalization did emerge in computational evolution. We document that genomes entrench certain dimensions of variation that were frequently explored during their evolutionary history. The genetic representation of these organisms also evolved to be highly modular and hierarchical, and we show that these organizational properties correlate with increased fitness. Interestingly, the type of computational evolutionary experiment that produced this evolvability was very different from traditional digital evolution in that there was no objective, suggesting that open-ended, divergent evolutionary processes may be necessary for the evolution of evolvability.Comment: SI can be found at: http://www.evolvingai.org/files/SI_0.zi

Hierarchy Theory of Evolution and the Extended Evolutionary Synthesis: Some Epistemic Bridges, Some Conceptual Rifts

Contemporary evolutionary biology comprises a plural landscape of multiple co-existent conceptual frameworks and strenuous voices that disagree on the nature and scope of evolutionary theory. Since the mid-eighties, some of these conceptual frameworks have denounced the ontologies of the Modern Synthesis and of the updated Standard Theory of Evolution as unfinished or even flawed. In this paper, we analyze and compare two of those conceptual frameworks, namely Niles Eldredge’s Hierarchy Theory of Evolution (with its extended ontology of evolutionary entities) and the Extended Evolutionary Synthesis (with its proposal of an extended ontology of evolutionary processes), in an attempt to map some epistemic bridges (e.g. compatible views of causation; niche construction) and some conceptual rifts (e.g. extra-genetic inheritance; different perspectives on macroevolution; contrasting standpoints held in the “externalism–internalism” debate) that exist between them. This paper seeks to encourage theoretical, philosophical and historiographical discussions about pluralism or the possible unification of contemporary evolutionary biology

The sexual selection of hominin bipedalism

In this article, I advance a novel hypothesis on the evolution of hominin bipedalism. I begin by arguing extensively for how the transition to bipedalism must have been problematic for hominins during the Neogene. Due to this and the fact that no other primate has made the unusual switch to bipedalism, it seems likely that the selection pressure towards bipedalism was unusually strong. With this in mind, I briefly lay out some of the most promising hypotheses on the evolutionary origin of hominin bipedalism and show how most, if not all, fail in the face of the need for an unusually strong selection pressure. For example, some hypotheses maintain that hominins became bipedal so they could use their hands for carrying infants, food, or other valuable objects. But extant apes are able to carry objects in one of their front limbs (while walking with the other three), and thus it does not seem plausible that our hominin ancestors went through the troublesome transition to bipedalism just so they could carry objects a little more efficiently. After I show that past hypotheses are wanting in the face of this challenge, I argue that there is only one selection pressure powerful enough to instigate a strange and problematic evolutionary adaptation like bipedalism, and that is sexual selection. Specifically, from the fact that bipedal locomotion is an important strategy for intimidating others and ascending the dominance hierarchy in extant apes, I argue that for no particular selective reason bipedal locomotion became a signal for high fitness (much as a large and intricate tail became a signal for high fitness for peahens), and this led to the trait being continuously reinforced in spite of all its deleterious fitness consequences

Primordialists and Constructionists: a typology of theories of religion

This article adopts categories from nationalism theory to classify theories of religion. Primordialist explanations are grounded in evolutionary psychology and emphasize the innate human demand for religion. Primordialists predict that religion does not decline in the modern era but will endure in perpetuity. Constructionist theories argue that religious demand is a human construct. Modernity initially energizes religion, but subsequently undermines it. Unpacking these ideal types is necessary in order to describe actual theorists of religion. Three distinctions within primordialism and constructionism are relevant. Namely those distinguishing: a) materialist from symbolist forms of constructionism; b) theories of origins from those pertaining to the reproduction of religion; and c) within reproduction, between theories of religious persistence and secularization. This typology helps to make sense of theories of religion by classifying them on the basis of their causal mechanisms, chronology and effects. In so doing, it opens up new sightlines for theory and research