Tag Archives: model

Phenotypic variation in ecological setting

phenotypic-ecological.035Organisms are niche constructors: they impact the environment and modify selective pressures that direct their own evolution as well as that of their non-conspecific fellows in ecological systems at various scales. The theoretical acknowledgement of niche construction has inspired many reflections about the active role of organisms in evolution, often proclaiming a revolutionary theoretical change. But if we look at formal models the claim is not yet justified. Ecologists have specified population-scale models of niche construction, but these cannot be adopted as evolutionary models: they don’t incorporate heritable variation nor allow for directional selection and cumulative change. As evolutionists point out, these models are mere phenotype dynamics or population fluctuations with different possible outcomes – extinction or sustainability. Evolutionary models of niche construction, on the other hand, are not so revolutionary in their foundations, often being just classical population genetics provided with feedback loops between loci and selective pressures acting on them. The idea that variation among organisms boils down to genetic differences captured by gene frequencies dates back to the heart of the Modern Synthesis. But niche construction points directly to the world of physical and chemical interactions. This is the world where resource-impacting phenotypes are built through developmental processes, in turn subject and sensitive to the surrounding environment and the resources left over by previous generations. The produced phenotypes and their effects are hardly summarized by gene frequencies, yet evolutionary models need some kind of heritable variation and selection. The future challenge of evolutionary modeling beyond the Modern Synthesis is thus ecological, plastic variation that allows for inheritance with varying degrees and not-always-allelic mechanisms.

Session: Understanding variation beyond the Modern Synthesis


Look for it in the Publications page (with additional links):

Serrelli E (2013). Phenotypic variation in ecological setting: a challenge for evolutionary modeling beyond the Modern Synthesis. Meeting of the International Society for History, Philosophy, and Social Studies of Biology (ISHPSSB), Montpellier, France, July 7-11. [http://hdl.handle.net/10281/46365]

ProgrammeDefinitifISHPSSB2013

Tree and network models in San Francisco

Emanuele Serrelli co-organizes with Nathalie Gontier the session “Tree and network models of micro- and macroevolution” at the 2012 Annual Meeting of the American Anthropological Association (November 14-18, 2012). Developing from phylogenetic methodologies in evolutionary biology, the session examines how cultural trees and networks are composed differently (which data are used to compose trees and networks), what they can and cannot model, how inferences are made, and how they enable theory formation on cultural evolution.

AAA SESSION ON CULTURAL TRANSMISSION STUDIES: TREE AND NETWORK MODELS OF MICRO- AND MACROEVOLUTION, November 15, 8-9:45 AM

Organized by Nathalie Gontier and Emanuele Serrelli and Chaired by Larissa Mendoza Straffon

In biology, phylogenetic tree models (based on shared morphological traits, genes, or proteins) remain the primary methodological tool to reconstruct evolutionary ancestral-descent relationships. Phylogenetic and phylogenomic methodologies are also applied to reconstruct linguistic and cultural descent relationships. Such reconstructions have now advanced up to the point that one can estimate divergence in time, and the rate at which such linguistic or cultural divergence occurred. Both biological as well as sociocultural phylogenetics now demonstrate that besides natural selection, drift and punctuated equilibria theory can explain many of life’s and sociocultural divergences. And comparative analyses demonstrate that ancestral-descent relations of human populations significantly overlap with linguistic family trees and cultural diversification trees. Phylogenetics has also brought to light that horizontal evolution occurs abundantly in life’s evolution, and scholars active in the field have therefore challenged classic tree of life iconography. Today, scholars active in Horizontal Gene Transfer studies are therefore introducing network phylogenies (“webs of life”) that allow the depiction and modeling of reticulate evolution. In the sociocultural sciences, linguists, archeologists and anthropologists have criticized hominin and cultural bifurcating trees because they are unable to depict hominin hybridization and horizontal transmission and diffusion of sociocultural traits. And here too, network models are introduced that allow the formalization and depiction of linguistic and sociocultural interactions through time. In sum, biological and sociocultural sciences both make use of tree and network models to depict biological and sociocultural evolution. We will examine how cultural trees and networks are composed differently (which data are used to compose trees and networks), what they can and cannot model, how inferences are made, and how they enable theory formation on cultural evolution.

  1. THE ‘GLOBAL PHYLOGENY’ AND ITS HISTORY: A CRITICAL APPRAISAL OF A UNIFIEDTHEORY OF HUMAN BIOLOGICAL AND LINGUISTIC CO-EVOLUTION, Frank Kressing, Ulm University
  2. THE CHALLENGE OF TREE-THINKING AND NETWORK-THINKING: CONCEPTUAL ISSUES ACROSS BIOLOGICAL AND CULTURAL DOMAINS, Emanuele Serrelli, University of Milano Bicocca.
  3. COMPARING RATES OF CULTURAL CHANGE ACROSS TREES – DO SOME TRAITS EVOLVE FASTER THAN OTHERS?, Ruth Mace and Tom Currie, London, OXFORDSHIRE
  4. PHYLOGEOGRAPHIC APPROACHES TO TRACING HUMAN CULTURAL ANCESTRY, Quentin Douglas Atkinson, University of Auckland
  5. UNITS, LEVELS AND MECHANISMS OF CULTURAL EVOLUTION, AN APPLIED EVOLUTIONARY EPISTEMOLOGICAL ACCOUNT, Nathalie Gontier, Applied Evolutionary Epistemology Lab, Centre for Philosophy of Science, University of Lisbon
  6. MOSAIC EVOLUTION IN CULTURAL AND BIOLOGICAL FRAMEWORKS: DYNAMICS VARY WITH SCALE, Anna Marie Prentiss and Matthew Joseph Walsh, University of Montana
  7. USING CLADISTICS TO INTERPRET ARCHAEOLOGICAL ASSEMBLAGES: THE SLATE TOOL TRADITION AT BRIDGE RIVER, BRITISH COLUMBIA, Matthew Joseph Walsh and Anna Marie Prentiss, The University of Montana
  8. PLEISTOCENE NETWORK INTERACTIONS AND THE ORIGINS OF VISUAL ART, Larissa Mendoza Straffon, Leiden University
  9. THE ECONOMICS OF CULTURAL TRANSMISSION, Alberto Bisin, New York University

ABSTRACTS

THE ‘GLOBAL PHYLOGENY’ AND ITS HISTORY: A CRITICAL APPRAISAL OF A UNIFIEDTHEORY OF HUMAN BIOLOGICAL AND LINGUISTIC CO-EVOLUTION
Frank Kressing, Ulm University
Starting in the late 20th century, “new” approaches claiming a direct link between the evolution of linguistic and biological diversity in humans received broad attention in the sciences and the general public. Based on an extensive literature review, we claim that, contrary to its supposedly innovative character, the post 1980 ‘new synthesis’ of genetic, linguistic, and archaeological data was based on a well-established western tradition dating back at least until the 18th century. Special emphasis will be put on the importance of interdisciplinary reticulations between scholars in the sciences (such as biology and comparative anatomy) and the humanities (such as linguistics). In our overview, it shall be argued that interdisciplinary contact between these two fields resulted in the construction of links between the classification of languages and the classification of human populations. Furthermore, it shall be stressed that the theory of human biological and linguistic co-evolution was developed in the 18th and 19th century within the framework of anthropology, since this academic discipline evolved as an all-encompassing, integrative science dealing with human nature in its physical and cultural aspects. Finally, 20th-century attempts at the ‘genomization’ of human cultural, ethnic, and linguistic affiliations will be critically analysed, highlighting the fact that theroots of the so-called global phylogeny are ‘once again’ to be found in interdisciplinary scholarly networks transgressing the borders between the sciences and the humanities.

THE CHALLENGE OF TREE-THINKING AND NETWORK-THINKING: CONCEPTUAL ISSUES ACROSS BIOLOGICAL AND CULTURAL DOMAINS
Emanuele Serrelli, University of Milano Bicocca
This talk gives a reflexive outlook on the employment of tree and network thinking to conceptualize and model vertical descent and horizontal transmission of cultural traits. In biology, evolutionary trees are more than tools for researchers across disciplines: they are the main framework within which evidence for evolution is evaluated (Baum et al. 2005). However, several biologists have recognized “tree thinking” as a challenge for students (Gregory 2008, Meisel 2010), lay people (Baum, cit.), and scientists alike (O’Hara 1992), going against our spontaneous cognitive tendencies, e.g., reading along the tips, locating evolution only at nodes, projecting living species backwards to internal nodes. Moreover, common descent, represented by trees, is not the only way in which biological traits are shared: the ubiquity of phenomena like lateral gene transfer is increasing the need for network-based analyses, introducing the conceptual challenge of “network thinking” (Proulx et al. 2005), and the further complexity of conceiving trees and networks together. I focus on which strategies, used and developed in biology, can be implemented in anthropology to address cultural relatedness and common ancestry relationships. Baum DA et al. (2005). The tree-thinking challenge. Science 310(5750):979-980. Gregory TR (2008). Understanding evolutionary trees. Evolution: Education and Outreach 1(2):121-137. Meisel RP (2010). Teaching tree-thinking to undergraduate biology students. Evolution: Education and Outreach 3(4):621-628. O’Hara RJ (1992). Telling the tree: Narrative representation and the study of evolutionary history. Biology and Philosophy 7(2):p.135–160. Proulx SR et al. (2005). Network thinking in ecology and evolution. Trends in Ecology and Evolution 20(6):345-53.

COMPARING RATES OF CULTURAL CHANGE ACROSS TREES – DO SOME TRAITS EVOLVE FASTER THAN OTHERS?
Ruth Mace and Tom Currie, London, OXFORDSHIRE
Ruth Mace and Tom Currie examine the rate of evolution of cultural traits across different phylogenetic trees, to see if cultural traits themselves share any particular properties regarding the rate of change on a tree, or whether traits are simply change according to local ecological conditions or some other factors that are not shared across trees. We use recent phylogenetic methods to estimate rates of change in a range of traits common to most societies.

PHYLOGEOGRAPHIC APPROACHES TO TRACING HUMAN CULTURAL ANCESTRY
Quentin Douglas Atkinson, University of Auckland
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 collaborative research that uses tools from population genetics and phylogeography to analyze spatial information derived from comparative cultural data. This work identifies clear spatial signal in the data that can be used to shed light on the origins of cultural groups.

UNITS, LEVELS AND MECHANISMS OF CULTURAL EVOLUTION, AN APPLIED EVOLUTIONARY EPISTEMOLOGICAL ACCOUNT
Nathalie Gontier, Applied Evolutionary Epistemology Lab, Centre for Philosophy of Science, University of Lisbon
Tree and network models of cultural micro- and macroevolution demonstrate the current scientific need to recognize that a multiplicity of units, levels and mechanisms underlie the evolution of culture. This demand also necessitates a scientific investigation into how these different sociocultural units, levels and mechanisms alternate and interact hierarchically, and together bring forth the phenomenon of evolution. From within an applied evolutionary epistemological approach, I will talk on how theories on the units (replicators, interactors, culturgenes, memes) and levels of evolution can be implemented into micro- and macroevolutionary sociocultural theories; and which evolutionary mechanisms are best able to explain horizontal and vertical transmission.

MOSAIC EVOLUTION IN CULTURAL AND BIOLOGICAL FRAMEWORKS: DYNAMICS VARY WITH SCALE
Anna Marie Prentiss and Matthew Joseph Walsh, University of Montana
There has been significant debate in paleoanthropology and more recently, archaeology, over the concept of mosaic evolution. Essentially, proponents of the concept argue that different aspects of organisms evolve separately while others argue that organisms evolve as integrated entities. Similarly, archaeologists debate the relevance of cultural evolution as a complex multi-scalar process. In this paper we conduct cladistic and network analyses of cultural phenomena ranging in scale from single artifact classes to more complexly integrated cultural packages to examine variability in the evolutionary process. We argue that cultural evolution is simultaneously multi-scalar and that dynamics can vary significantly with different degrees of integration.

USING CLADISTICS TO INTERPRET ARCHAEOLOGICAL ASSEMBLAGES: THE SLATE TOOL TRADITION AT BRIDGE RIVER, BRITISH COLUMBIA
Matthew Joseph Walsh and Anna Marie Prentiss, The University of Montana
In recent years phylogenetic studies have offered a wide range of contributions to explanation of complex evolutionary phenomena in the archaeological record. In this study we apply cladistic and network methods to assess the evolution of slate tools at the Bridge River site in British Columbia. We examine relationships between artifact assemblages from several housepits at the site in order to determine if heritable continuity can be established on an inter- and intra-household basis. This allows us to examine variability in the role of descent with modification manifested in branching versus a range of potential tokogenetic processes. We argue that while distinct household-specific traditions of tool manufacture existed, the data are made complicated by extensive borrowing of ideas and functional differentiation in tool design.

PLEISTOCENE NETWORK INTERACTIONS AND THE ORIGINS OF VISUAL ART
Larissa Mendoza Straffon, Leiden University
In recent years scholars have come to the realisation that models which account for the emergence of behavioural traits, such as visual art, simply in terms of increasing human cognition are not viable. The so-called cognitive models cannot generate falsifiable predictions about the conditions under which such traits would have developed. Equally problematic are evolutionary scenarios of art that put forward some possible adaptive function as cause of its origin (e.g. visual art evolved for mate choice, for ritual, etc.). When contrasted against current evidence from the archaeological record, these postulates generally do not hold. This paper presents an hypothesis for the origins of visual art which incorporates up-to-date archaeological data into a testable evolutionary explanation. This model is based upon specific aspects of Pleistocene human groups, such as group size and social organisation. It is suggested that visual art arose as a signal of identity and an index of reputation under selective pressures towards increasing cooperation and intensified network interactions in the Late Pleistocene. Recognition through style in visual art would have conveyed adaptive benefits by making social interactions more predictable thus reducing risks of conflict and aggression, in turn allowing large-scale reciprocity systems to flourish. In this sense, visual art may be conceived of as a communication signal manifested in stylistic variation in material culture. Finally, the paper shows that this hypothesis is consistent with the archaeological record of visual art.

THE ECONOMICS OF CULTURAL TRANSMISSION
Alberto Bisin, New York University
This paper surveys the recent theoretical and empirical studies on the economics of cultural transmission. The aim of the survey is to emphasize both similarities and differences in the economic analysis of this topic with respect to the literatures in evolutionary biology, anthropology, and sociology.

University of Sydney HPS Research Seminar Series

For 80 years now, a famous and influent picture have been around in evolutionary biology: it is the adaptive landscape, a hilly or rugged surface with peaks and valleys onto which combinations of traits are mapped, the elevation representing the fitness value of these combinations. As a communication and heuristic tool, the adaptive landscape well conveyed several ideas, e.g., adaptation seen as peak climbing. It also set research questions, e.g., how can a population cross a low-fitness valley.
In the mid 1990s, with a certain non-chalance, Princeton mathematician and population geneticist Sergey Gavrilets began to propose an idea which soon several evolutionists regarded as potentially explosive. Gavrilet’s “holey landscapes” were about fitness distribution in the genotype space of a population with realistic number of loci and alleles: backed by newly introduced mathematical methods and empirical evidence, they depicted fitness distribution by means of flat or nearly-flat surfaces drilled with large holes.
The explicit reference and, at the same time, the striking differences between holey landscapes and the adaptive landscape fueled a reflection on crucial themes like the role of adaptation, the extent of neutralism, the meaning of speciation, and even the possibility of non-gradual evolution. Reconsiderations and revisions of the history of adaptive landscapes, since its first introduction by Sewall Wright in 1932, flourished. More deeply, holey landscapes are offering an occasion of rethinking the nature of evolutionary biology as a scientific enterprise.


Look for it in the Talks page (with additional links):

2012, Sep 17 (h.6-8 PM) – Unit for the History and Philosophy of Science, HPS Research Seminar Series Semester Two, University of Sydney, Faculty of Science: Holey landscapes and rethinking evolutionary biology. Seminar.

http://www.mail-archive.com/sydphil@arts.usyd.edu.au/index.html

Guiding extrapolation from model to target

Monika Piotrowska thanks me in her paper:

Piotrowska M (2012). From humanized mice to human disease: guiding extrapolation from model to target. Biology and Philosophy. DOI 10.1007/s10539-012-9323-5.

“I would like to thank Matt Haber, Anya Plutynski, Emanuele Serrelli, Mike Wilson, Rasmus Winther, members of the audience at ISHPSSB 2011 in Salt Lake City, and the editor of this journal for valuable comments”

Thanks to Monika, great friend and admired colleague.

Continue reading Guiding extrapolation from model to target

EGENIS – The ESRC Centre for Genomics in Society, University of Exeter

Ankeny & Leonelli (2011) recently spelled out a number of epistemological characteristics of model organisms which, they think, make them special in the more general category of experimental organisms. In this seminar I show how some similar epistemological characteristics apply to a theoretical model, i.e. the Mendelian population, making it special in respect to other theoretical constructs (equations). Both cases seem to suggest restrictions in the usage of the term “model” to the advantage of a defined model notion. Here I aim to refine and broaden such notion of a model, and explore the epistemological issues it raises.

Ankeny & Leonelli define model organisms as “non-human species that are extensively studied in order to understand a range of biological phenomena, with the hope that data and theories generated through use of the model will be applicable to other organisms, particularly those that are in some way more complex than the original model” (p. 313).

Mathematical population genetics – a major pillar of neo-Darwinian evolutionary theory – is often referred to as a great set or family of models, where “models” mean, arguably, equations of gene frequencies or phenotypic change.

The glaring discrepancy between organisms and equations seems to characterize experimental biology and population genetics by two irreducibly different “modeling strategies”: the material and the empirical (cf. Leonelli 2006). By diverting the attention away from equations, in this seminar I challenge such classical distinction.

I present population genetics in a uncommon way: I dismiss the term “model” for equations, and save it for the Mendelian population, i.e. the fundamental formal combination space population genetics equations are about.

One interesting result of my approach is to liken a formal system to an organic system – at least for some “key epistemological characteristics” (cf. Ankeny & Leonelli, cit.). I explore the notion of a model as a stable target of explanation (cf. Keller 2002) that I think captures both objects, and the related epistemological problems about representation, explanation, and prediction. Models as stable targets of explanation are systems selected for intensive research, yielding their stability and a cost-effective apparatus of experimental resources; they feature some degree of artificiality, and are never exhaustively known, even in case of complete artificiality.

Ankeny, R. a & Leonelli, S., 2011. What’s so special about model organisms? Studies In History and Philosophy of Science Part A, 42(2):313-323.

Keller, E. F. (2002). Making sense of life: Explaining biological development with models, metaphors and machines. Cambridge, MA: Harvard University Press.


Look for it in the Talks page (with additional links):

2012, Jan 23 (h.3:00-4:30 PM) – The ESRC Centre for Genomics in Society (Egenis), University of Exeter: Model as a “stable target of explanation”: Mendelian population like model organisms?. Seminar.

Announcement

PhD Dissertation

This dissertation brings a contribution to the philosophical debate on adaptive landscapes, an influent “model” or “metaphor” in evolutionary biology. Some elements of innovation are: the distinction between native and migrant metaphor; a processual and communicational idea on what the Modern Synthesis was, and on what role a metaphor could have played in it; a view (taken by Richard Lewontin) of the disunity and theoretical structure of population genetics; the distinction between “adaptive surfaces” (mainly metaphors) and “combination spaces”, two terms normally conflated in the word “landscape”; an analysis of what bridges (including heuristics) may be cast between equations of gene frequency and the genotype space that, due to its huge dimensionality, cannot be handled by mathematics; a specified vocabulary to be used to clear the adaptive landscapes debate, accompanied by a plea in favor of a pragmatic approach – for example, the plurality of available notions of model forces us to choose one notion and see where it brings, otherwise we get stuck in confused, endless debates; an updated analytical comment of recent landscapes – Dobzhansky, Simpson, Dawkins but also the proliferation of combination spaces used in evolutionary biology to address a great variety of problems; the vision (got by Sergey Gavrilets) of a patchwork of tools finally making Mendelian population suitable model also for speciation; the exact position of holey landscapes in this patchwork, and the idea that scientists’s questions – like “how possibly” questions – matter in accessing this patchwork and in deciding “what explains” and “what describes” what in the world; the direct response to some mistakes Massimo Pigliucci made, I think, in his assessment of the adaptive landscape; an analysis of the Extended Evolutionary Synthesis project at its present stage, and some reflections on the conditions that will allow such a project to give a fair treatment and a good position to tools from the past, like the adaptive landscapes.


Look for it in the Publications page (with additional links):

Serrelli E (2011). Adaptive landscapes: a case study of metaphors, models, and synthesis in evolutionary biology. PhD Dissertation in Educational and Communicational Sciences, Human Sciences Doctorate School, University of Milano Bicocca, Milan, Italy. [http://hdl.handle.net/10281/19338]

http://www.slideshare.net/eserrelli/adaptive-landscapes-a-case-study-of-metaphors-models-and-synthesis-in-evolutionary-biology