Centre for Philosophy of Science Applied Evolutionary Epistemology Lab

Please click the program to expand it or download it here. Abstracts are available bellow. You can also download the conference booklet here.

Preprints of the talks will be made available on the PhilSci-Archive.

Abstracts of the Plenary Talks

Michael Benton

The Tree of Life and Origins of Biodivers\ity

A key question of interest to all evolutionary scientists is to account for modern biodiversity: why are some groups so much more successful than others? Why, for example, are there 25 species of crocodiles and 10,000 species of birds today, when both groups share an ancestor and a history. It is difficult to see how such a question could be answered using traditional approaches, but combining data from biology and palaeobiology may provide some answers. Advances in methods in molecular phylogenomics and palaeobiology, coupled with novel numerical techniques and massive computing power allow us to investigate such questions, which link development, palaeobiology, species numbers, and the roots of adaptation. In this case, the framework is the tree of life, and analysts are producing ever-larger phylogenetic trees – even of all 10,000 species of birds – based on objective analytical protocols. Such trees can then be dated by tying the branching points to a number of confidently dated and located fossils, and then a battery of analytical tools, founded in comparative phylogenetic methods, can be used to explore the tree for unusually high (or low) rates of diversification, patterns of trait acquisition and evolution, and overall morphological variance (disparity) through time, between subclades, and across character sets. Further, feeding and locomotory function can be compared between living and extinct forms, and the timing of acquisition of certain putative ‘key adaptations’ explored.

Tal Dagan

Networks Approach to Evolutionary Dynamics of Genomes and Languages

Phylogenomics is aimed at studying functional and evolutionary aspects of genome biology using phylogenetic analysis of whole genomes. Current approaches to genome phylogenies are commonly founded in terms of phylogenetic trees. However, several evolutionary processes are non tree-like in nature, including recombination and lateral gene transfer (LGT). Phylogenomic networks are a special type of phylogenetic networks reconstructed from fully sequenced genomes. The network model, comprising genomes connected by pairwise evolutionary relations, enables the reconstruction of both vertical and LGT events. Modeling genome evolution in the form of a network enables the use of an extensive toolbox developed for network research. The structural properties of phylogenomic networks open up fundamentally new insights into genome evolution. Genome evolution has a lot in common with language evolution. Both processes entail evolving elements – genes or words – that are inherited from ancestors to their descendents. The parallels between biological and linguistic evolution were evident both to Charles Darwin, who briefly addressed the topic of language evolution in The Origin of Species, and to the linguist August Schleicher, who in an open letter to Ernst Haeckel discussed the similarities between language classification and species evolution. Charles Darwin pictured the history of life as a tree. However, genes can be acquired laterally (not by inheritance), while words can be borrowed between different languages. Phylogenetic trees cannot be used to model such lateral transfers. Phylogenomic networks may offer an alternative model.

John Jungck

Morphing in Morphospace - Mathematical and Philosophical Perspectives on Macroevolutionary Biological Patterns

Evolutionary diversity is filled with myriad forms. G. Evelyn Hutchinson's famous article: "Homage to Santa Rosalia, or Why are there so many kinds of animals?" was cited by Stephen Jay Gould as articulating a fundamental question in biology. However, an important counterpoint has been: why have possible biological forms that could be generated by similar developmental processes based upon related genetic programs never been found in extant or extinct species? Historically this question was framed by David Raup in his analysis of the theoretical morphospace of gastropods, bivavles, brachiopods, and cephalopods. While many readers of his work were impressed that the general morphologies of extant and extinct members of these taxa could be reproduced with just three equations based upon three measurements on specimens, Raup was intrigued more that his three-dimensional plot of these taxa's morphologies showed that most of the morphospace was empty. Were seashells outside of these existing morphospaces too fragile in waves, too susceptible to predation, too constraining on internal organization, etc.? Since then, numerous scientists in theoretical morphology, morphometrics, biomechanics, and bioinformatics as well as artists and architects impressed by the aesthetics of these forms have explored these questions. Recently, economic perspectives of Pareto optimization has been used along with principal component analysis to explore the impact of natural selection of archetypal patterns, hybridization, and intermediate forms. Genomics has been struggling with a similar notion of nullomers. I will illustrate the power of D'Arcy Thompson's bioorthogonal transformations and Sewall Wright's adaptive landscapes in addressing these conundrums.

Carl Knappett

Using Network Thinking to Understand Transmission and Innovation in Ancient Societies

Are biological models suitable for understanding socio-cultural evolution? While they may have introduced some much-needed methodological rigour into humanities research, and represent an important area of thoroughgoing interdisciplinarity, they fail to capture some key aspects of cultural transmission. In particular, innovations that are combinatorial, or require some depth of learning for adoption, seem largely intransigent to biological models. As innovations of this kind — such as the spread of new technologies like bronze metallurgy or the potter's wheel — are key features of prehistoric social change, we should work on developing models that can capture the dynamics of their horizontal and vertical transmission. I shall argue for a multi-scale cognitive model for innovation that has two central tenets. The first is that learning is critical in innovation, and plays out at three basic levels: that of the individual who must learn the technique, that of the community of practice in which individual learning is invariably embedded, and that of inter-community interactions which allow for innovations to spread from one region to another. The second is that, as a cognitive, decision-making process, it involves a complex interplay of information, data and knowledge.

Daniel McShea

The Evolution of "Insideness" and the Architecture of Purpose

The history of life reveals a trend in the depth of organisms, in the number of levels of things inside of things, parts inside wholes. The eukaryotic cell arose as an association of bacterial cells, cells inside a larger cell. Plants and animals arose as associations of eukaryotic cells, cells inside a multicellular individual. Finally, about 480 million years ago, colonies arose – individuals inside a social whole. Evidence suggests that these "major transitions" involve two sorts of change in organismal architecture: 1) Inside individuals diversify, driven partly by biology's First Law (e.g., in animals, an increase in cell types); and 2) inside individuals lose internal structure, becoming simpler even as they diversify. Thus, in the early stages of transitions, inside individuals are very similar and retain much of their primitive autonomy and complexity (e.g., polyps in a coral colony). In later stages, inside individuals are differentiated but lose much of their autonomy and complexity (e.g., ants in a colony). Speculating, these patterns may have implications for the emergence of apparent goal-directedness or purpose in evolution. Apparently purposeful entities are those that lie within larger wholes and are strongly directed by them but still partly free to act independently. The appearance of purposefulness may be a transitional feature of individuals, arising at a halfway point in major transitions, half way between the cumbersome complexity of solitary life and the empty simplicity of life under rigid social control, at the sweet spot between the anomie of individual freedom and the oppressive orderliness of advanced collectivism.

Alex Mesoudi

The Experimental Study of Cultural Evolution

In biology, one of the key benefits of Darwin's theory of evolution was that 'macroevolutionary' patterns and trends, such as temporal patterns observed in the fossil record or spatial patterns observed biogeographically, could be explained in terms of 'microevolutionary' processes such as selection, drift, mutation or migration. The same benefit can be gained by viewing human cultural change as a Darwinian evolutionary process. Here, 'macroevolutionary' patterns and trends, such as temporal patterns observed in the archaeological record or spatial patterns observed in the ethnographic record, can similarly be explained in terms of 'microevolutionary' processes, sometimes borrowing the same concepts as in biology (e.g. cultural selection or cultural drift) but sometimes introducing novel cultural microevolutionary processes that have no parallel in genetic evolution (e.g. non-random 'guided variation'). As in biology, lab experiments can be used to explicate this macro-micro link, by simulating different microevolutionary processes and comparing the resulting data to real-life macroevolutionary patterns. I will describe a series of experiments that have aimed to do this. These studies have simulated patterns of projectile point variation in the prehistoric Great Basin region of the United States, linking different levels of regional variation to different cultural transmission biases, and exploring the conditions under which we would expect to see the observed patterns of cultural variation. This interplay of experimental methods and real-world data, pursued within an explicit evolutionary framework, promises to significantly enhance our understanding of human cultural change.

Mark Pagel

The Cultural Survival Vehicle

There is agreement that there is something important to explain about human social behaviour. We are distinguished among all animals for living in groups that have forms of cooperation that, on the face of it, pose a challenge to conventional Darwinian accounts of evolution. We routinely help others, we share our knowledge and skills, we give up seats on trains, pay taxes, hold doors for people, give money to charities, and even sometimes risk our health and well-being to fight wars. This remarkable social organization manages to combine the altruism, inventiveness and cohesion of multicellular organisms and the great eusocial insects, even when there is no possibility of our help being reciprocated, and the people we help are not related to us. I call this social structure the cultural survival vehicle and suggest that understanding its origins provides the starting point for a theoretical and empirical investigation of our psychology and morality, social behaviours, our language and our vast range of individual differences within society.

Tyler Volk

Levels, realms, and metapatterns in biological and cultural evolution

The universe seems to be arranged in levels of basic types of being, from elementary particles to atoms to cells, then organisms, and human states. Are there overarching patterns within and among the levels? Of interest is the fact that these levels can be arranged in a time sequence, in which former whole systems become parts within the next, higher level of system. We might term this process "syneosis," from "together" and "new." Given the conference focus on comparing the two great pattern-creating realms biological and cultural evolution, I will examine processes and structures for each level's origin, evolution, and emergence to the next level, for prokaryotic cells, eukaryotic cells, multicellular organisms, animal societies, human bands of conscious individuals in cultural fields, agricultural villages, and states. All these levels of syneosis potentially contain 3 scales of metapatterns: (1) within-level, (2) across-level and within realm, and (3) across-realm. Within-level metapatterns can derive from evolutionary convergences that achieve similar advantages from getting larger. Across-level metapatterns (but still within the realms biological or cultural evolution) can derive from fundamental dynamics that are used at the levels within a given realm. Finally, across-realm metapatterns can derive from commonalities generated by any evolution-type process that uses a logical skeleton of propagate-vary-select. In this talk I will lay out this general model of 3 scales of metapatterns for examining levels in the realms of biological and cultural evolution, with an eye to opportunities for future work.

Richard A. Watson

The Evolution of Symbiotic Partnerships and the Algorithmic Principles underlying the Major Evolutionary Transitions

The evolution of symbiotic partnerships has had dramatic consequences for evolutionary history and a significant role in the origins of biological complexity. In some cases the evolution of such partnerships has been instrumental in the major evolutionary transitions by creating new selective units, e.g., via the vertical transmission of a symbiont. Rather than treating the unit of selection as a fixed parameter, the evolution of such symbiotic partnerships requires that we treat the unit of selection as a dynamic variable, affected by the evolving relationships between species. Moreover, the selective pressures on those relationships are in turn determined by their ecological context. These interactions are not easily accommodated in existing ecological or evolutionary models. Here we begin to explore the interaction of symbiotic partnerships and ecological dynamics given individual traits that change the unit of selection. We find that, under some ecological conditions, the potentially complex eco-evolutionary interactions involved can be understood using simple principles of associative learning that are well understood in the context of neural networks – thus, in a manner analogous to 'neurons that fire together wire together' here species that assort together (i.e., co-occur at high density in the ecological dynamics) 'wire' together via evolved partnerships. This is essentially a very simple positive feedback principle acting on inter-specific relationships, but the algorithmic capabilities of such a system, involving processes that dynamically restructure the unit of selection, are significantly different from those with fixed units of selection. In fact, the ecosystem of evolving partnerships collectively implements a quite sophisticated distributed optimisation algorithm that discovers and exploits implicit modularity in the network of fitness dependencies between species. This suggests that there are general organisational principles that can help us understand how ecological and evolutionary dynamics interact – and specifically, interact in a manner that systematically predisposes the formation of new evolutionary units that are adaptively significant at a higher level of biological organisation. Far from being aberrant curious in an otherwise exclusively gradual picture of evolutionary change, this suggests that the major transitions in evolution may admit systematic algorithmic descriptions that expand our understanding of evolutionary adaptive processes into a multi-scale framework.

Abstracts of the Invited Talks


Tracing Human Cultural Ancestry in Time and Space

Recent work on cultural evolution has successfully applied phylogenetic methods from biology to comparative cultural and linguistic data to test hypotheses about cultural ancestry, chronology and sequences of change. However, relatively little attention has focussed on explicitly modelling large-scale spatial processes of cultural change. Here I report results from a range of collaborative research projects that uses tools from population genetics and phylogeography to analyze spatial information derived from comparative cultural data. This work identifies the legacy of phylogenetic and spatial processes in a range of cultural data.


Multi-disciplinary Perspectives on Cultural Transmission

Preferences, beliefs, and norms that govern human behavior are partly formed as the result of heritable genetic traits, and are partly transmitted through generations and acquired by learning and other forms of social interaction. Cultural transmission arguably plays an important role in the determination of many fundamental preference traits, like discounting, risk aversion and altruism. It certainly plays a central role in the formation of cultural traits, social norms, and ideological tenets, like e.g., attitudes towards family and fertility practices, and attitudes in the job market. Relatedly, distinct cultural traits determine how individuals interpret and react to common (e.g., strategic) choice environment. We conceptualize cultural transmission as the result of interactions between purposeful socialization decisions inside the family and other socialization processes. We study the determinants of the persistence of cultural traits and more generally the population dynamics of cultural traits. We discuss the links between the economic and other approaches to cultural evolution in the social sciences as well as in evolutionary biology.


Integrative Ecoinformatics of Phototrophic Biofilms: Joining Perspectives on the Dynamics of Cities of Microbes

Biofilms are surface-attached microbial communities, encased in a matrix of extracellular polymeric substances. In natural environments this sessile form of microbial existence is generally dominant over the detached, planktonic form. Understanding the long-term dynamics of these communities requires the integration of knowledge from many heterogeneous, complementary sources. Developing predictive models based on the outcome of i) laboratory studies of molecular regulatory networks, addressing the "how" of microbial behavior, and ii) ecological and biosociological studies of species competition, giving clues to the "why" of the observed community-level processes, involves a significant amount of "science friction" and represents a fundamental challenge to emerging discipline of ecological informatics.

In this context I will present our work related to a former European project on phototrophic biofilms, microbial communities with a significant presence of photosynthesizing organisms. I will present the implementation of a database prototype for semantic data management, the integration of several biostatistical studies in a qualitative model and the quantitative minimal description of the often observed boom-and-bust growth dynamics. Considering these different tools as nodes in a knowledge network, I will discuss the role of semantic annotations and metadata as possible links between the nodes and their capacity to catalyze the evolution of systems-level knowledge in biofilm research.


Tempo and Mode in Evolution of Complex Organisms

Most evolutionary biologists appear to believe that populations and species are well adapted to their environment, as the result of continuous action of natural selection on all their traits. In complex organisms, however, many traits do not experience the outside environment: their environment consists of other traits. This implies that fitness is not determined exclusively by how well traits fit the external environment, but also by how well traits are adapted to each other. I will discuss whether the existence of co-adapted trait complexes determines the tempo and mode in evolution of their component traits, and discuss how we could distinguish the extrinsic and intrinsic components of fitness in phylogenetic and experimental studies.


Modeling Biocultural Evolution

There have been a number of attempts in recent years to integrate biological evolution and cultural change. Richard Dawkins introduced the 'meme' as a cultural analog to the gene and the 'science' of memetics was off and running. E. O. Wilson proposed that a biological approach to human social behavior and culture – sociobiology - would be fruitful because the 'genes hold culture on a leash.' In the aftermath of criticism of Wilson's original program sociobiology has morphed into the growing field of evolutionary psychology. Richerson and Boyd, in a number of papers and books, have promoted what they call a dual inheritance model of gene-culture coevolution. What exactly is the relationship between biology and culture? [1] Culture is one (albeit complex) product of biological evolution [the 'leash' option]; [2] Culture is grounded in biology but 'evolves' more or less independently of biological constraints [the 'cultural memes' option]; [3] Culture and cultural change interacts with and helps shape biological evolution (the 'dual inheritance' model; [4] Although culture would not exist if biological organisms did not exist evolutionary models of culture and cultural change are neither fruitful nor particularly insightful [the 'metaphor gone awry' option]. What, exactly, can we hope to expect from such efforts? Are the mechanisms underlying biological evolution and cultural change sufficiently similar to warrant thinking of cultural change as cultural evolution or is these, at best, a suggestive metaphor or analogy that connects the two processes? Dobzhansky once famously remarked 'Nothing in biology makes sense except in the light of evolution.' To what extent can it be truly said that 'Nothing in culture makes sense except in the light of biology?'

Maurizio Casiraghi

Who are You? The Biological Entities in the 21st Century Biology

The identification and classification of living beings is a challenging issue in biology. Since Linnaeus we do have a hierarchical framework universally adopted. However, the currently biologists face several dualisms that needs further consideration: (1) species are the core level of classification, but natural selection is acting largely on individuals or other ranks rather than species. (2) Genome sequencing clearly evidenced that lateral gene transfer and transposition are common events in genome evolution; it seems clear that boundaries among species, at least at the genomic level, are not so strong. (3) Symbiosis deeply challenges the concept of individual; individuals are really evolving alone (i.e. is the real level on which selection acts?) or individuals are rather groups of living beings evolving as a single unit? (4) Since Linnaeus identification and classification of living beings are concurrent, but nowadays identification is separated from classification in many molecular approaches. (5) Is the biodiversity really represented by the three domains of life? Metagenomic approaches on different matrices (ranging from sea water to gut content) reveals the existence of a not negligible quote of biodiversity not clearly falling among Bacteria, Archaea or Eukarya. What is this "biological dark matter"? Is it one (or even more) new domain of life? The overall scenario is much more "fluid" than previously thought. In evolution, the dichotomy among the practical and theoretical contents of classification is well known. However, this is the time in which theoretical issues are deeply influencing practical applications of taxonomy.


The Emergence of Self and Other in Collective Systems: From the Vertebrate Immune System to Distributed Robotic Systems

Understanding how individuality and identity emerge in collective systems is one of the greatest challenges for natural, biological or human sciences alike. The immune system of the vertebrates has a remarkable capacity to eliminate invading microorganisms and extraneous transplanted tissues, while being tolerant to the body's tissues. Tolerance to body's tissues is not hardwired in the organism's genome. It is a developmental process arising from interactions between circulating lymphocytes. This developmental process is so robust and inconspicuous that one only notices it when it fails during so called autoimmune pathologies in which the lymphocytes orchestrate the destruction of organism's tissues. In my seminar I will provide a quantitative framework to understand the causal mechanism of this immunological proto-self. I will first discuss a simple mathematical model describing the ecoevolutionary dynamics of lymphocytes in vertebrates which explains tolerance to body tissue and immunity to invading pathogens. I will then discuss the application of this model to the design of multiagent robotic systems capable of distinguishing self from other.


The Logic of Gene Regulatory Networks

Over the last decade, great progresses have been made to elucidate intricate regulatory networks that orchestrate core cellular processes. Although structural analysis provides valuable insights, it is not enough to fully understand how these networks control cell behaviours depending on external environment. In this context, logical modelling proved useful to convey qualitative, dynamical analysis of regulatory networks. I will briefly present the mathematical formalism and discuss current challenges for analysing the dynamical properties of large regulatory networks. I will then illustrate how simple regulatory modules behave differently, depending on the regulatory functions that define, for each gene, the contributions from its regulators. I will particularly focus on regulatory circuits known to play a crucial role in the dynamics, and prove that variation in regulatory functions may greatly impact crucial properties related to multi-stability and sustained oscillations.


The Language Boundary in Cultural Transmission: Helicopters, Games and Script

In the dispersal of cultural traits, language differences are generally considered a boundary that impedes (horizontal) transmission. Although language differences are not necessarily impossible to overcome, it seems obvious that they do not facilitate transmission processes. Recent studies on the distribution and development of technology, ancient gaming and the adoption of writing systems shed new light on the role of language in facilitating and/or obstructing cultural transmission processes.


Lateral and Vertical Transfer in Biology, Linguistics and Anthropology – an Account of Widely Neglected Ideas in the Formation of Evolutionary Theories

Models of biological and cultural evolution that developed from the 19th century onward are in their majority centered on the unilinear transmission of cultural and biological replicators as well as on phylogenetic images of descent – the tree of life and the tree of languages metaphors. But not all biologists, linguistics and anthropologists of the 19th century subscribed to the idea of human development in the sole form of unilinear evolution in successive stages, leading from inferior to superior states. Competing with the prevailing theories of evolutionism, the idea of diffusion in regard of words, grammatical features, cultural traits, and whole cellular organs played a considerable role in the realms of both linguistics and biology, and later cultural anthropology. The scope of this paper is to give an historical account regarding the idea of transmission by diffusion, of vertical transfer in biology, linguistics, and cultural/social anthropology. Historical and contemporary examples are the idea of Sprachbund (areal typology) and mixed languages (pidgins, creoles) in linguistics, endosymbiosis in biology, and diffusionism in cultural anthropology (Kulturkreise, culture areas).


Group Selection and the Relevance of Hamilton's Inclusive Fitness

In 1964, Bill Hamilton proposed a new framework for thinking about fitness that could account for phenomena such as altruism and eusociality: inclusive fitness and kin selection. This framework had a profound effect on our understanding of the evolution of social behavior, particularly in haplodiploid systems such as ants and bees, and played a role in our thinking of the relative importance attributed to individual versus group selection. Recently, Martin Nowak, Ed Wilson – a significant popularizer of Hamilton's ideas – and others have argued that this approach has limitations and that the standard natural selection, based on a form of group selection, represents a simpler and superior approach. These works have re-launched a debate on the importance of group selection and the relevance of Hamilton's inclusive fitness. We will evaluate the critiques to kin selection and whether it still constitutes a valid and useful approach.


The role of Selection, Chance and History during Adaptation to a Novel Environment

Experimental Evolution is Evolutionary Biology in its most empirical sense, as it allows the direct characterization of micro-evolutionary patterns and processes. It is thus a powerful tool to address essential evolutionary questions such as: How fast do populations adapt to a novel environment? What constrains adaptive evolution? What is the role of History, Chance and Selection during local adaptation? For almost two decades now my team has been studying the evolutionary dynamics of laboratory populations of Drosophila subobscura derived from repeated collections in the wild. The rationale of our studies is that the lab is just a novel environment to which populations may adapt, and as such the analysis of how populations change through time since foundation contributes to a general characterization of evolutionary patterns and processes during adaptive evolution. We show that populations are able to adapt to the novel environment, though evolutionary contingencies due to founder effects and genetic drift during the earliest generations affect the details of the adaptive patterns. We also found that selection is able to overcome the signature of History in populations highly differentiated at the start of colonization. Future studies testing for repeatability of the later findings will allow the study of how much History interacts with Chance events during Adaptation.


Hierarchy Theories: a Comparison

We propose a taxonomy of hierarchy theories, or multilevel approaches to evolution, ordered by theoretical impact: 1) hierarchy of "units of selection" as replicators and interactors at each level; 2) double hierarchy of levels of evolutionary change, respectively in terms of genetic transmission (genealogical hierarchy) and in terms of exchanges of matter and energy (ecological or economic hierarchy); 3) hierarchy of evolutionary systems over the long time of natural history and its major transitions. We try to figure out analogies and differences, and the efficacy of these different multilevel approaches in two fields: the unification of micro and macro-evolution (continuity between levels, autonomy and interdependence, reduction); the outcomes as predictive models to be applied in the parallels between biological and cultural evolution. We argue that the extension and revision of the Neo-Darwinian research programme, labelled "Extended Synthesis", would take advantage of a double-hierarchy frame because it encompasses the plurality of causes and patterns (with their relative frequencies) that explain evolutionary phenomena today. The recent misleading controversy among kin selection vs group selection theorists is a good case-study to test the efficacy of an integrated, multilevel, genealogical and ecological approach to evolution.


Turing's Tape, biosemiotics, and the Cybernetics of Biocomplexity

Many have argued that life and open-ended evolution depend on a semiotic closure, or a complex interplay, between separated symbolic information and molecular dynamics components. Alan Turing also showed that the separation between data and program is essential to achieve universal computation. Many, at least since John Von Neumann, have argued that this separation between information/data and dynamics/program is an evolutionary system that is more general than computation, and indeed defines life as we know it. In this talk I will review this idea and argue that many important systems and events in our evolutionary history constitute a re-discovery of this evolutionary principle of organization. In particular, I will discuss how it manifested in genomic organization, vertebrate immune complexity, human cognition and culture.

Sven Steinmo

Institutional Change as an Evolutionary Process

I argue that institutional change can be understood as an evolutionary process. Whereas it is often suggested that evolutionary theories do not apply to human history or institutions because of our conscious capacities and intelligence, I submit that human's advanced cognitive capacities are key to understanding why human institutions can evolve so quickly. Human beings creative intelligence and proclivity to misunderstand or misinterpret are the key sources of variation in this model. Human's ability to learn from one another is the mechanism for selection. Finally, we build institutions in order to reproduce and reinforce the social rules selected.