Tag Archives: visualization

Visualizing Macroevolution

fig03b_simpson_modesThe adaptive landscape is an important diagrammatic concept that was conceived in population genetics. During the Modern Synthesis, in the first half of the Twentieth Century, the landscape imagery was used to represent evolution on a large scale, aiding in the construction of a common language for a new evolutionary biology. Not only historic adaptive landscapes by Dobzhansky, Simpson, and others are a record of how macroevolution was thought of in those decades; they stimulate reflection on ‘combination spaces’ that underlie them. In fact, any landscape diagram is the three-dimensional transposition of a multidimensional space of combinations of genes, morphological traits, or other kinds of variables. This is an important and enduring general point of awareness: the diagram displays some aspects of the considered space while hiding others, exposing the author and the user to incomplete understanding and to conflating different spaces. Today, macroevolution is studied as a multifarious exploration of spaces of possibilities of all different sorts, interconnected in complex ways: genotype spaces, molecular spaces, morphospaces, geographical spaces, ecological spaces, genealogical spaces. Actual macroevolutionary stories and outcomes are a subset of what is, in principle, possible in all of these spaces, composed by possible combinations—of genes, nucleotides, morphological traits, environmental variables. Visualizations of macroevolution are a challenge of showing both distinction and correlation between spaces of possibilities.

Keywords: adaptation, speciation, macroevolution, visualization


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

Serrelli E (2015). Visualizing macroevolution: from adaptive landscapes to compositions of multiple spaces. In Serrelli E, Gontier N, eds., Macroevolution: explanation, interpretation and evidence. Interdisciplinary Evolution Research series, Springer, pp. 113-162. ISBN 978-3-319-15044-4 [DOI 10.1007/978-3-319-15045-1_4] [BOA] [Ac] [RG]

The landscape metaphor in development

“It seems that thtowards-theory-developmente landscape metaphor will continue to stay with us, at least for a while”.

We start defining a landscape as a function of multiple variables and show how this can be interpreted as a dynamical system. From the perspective of dynamical systems modelling, we move to analyze Waddington’s ‘epigenetic landscape’ and landscape representations in current developmental biology literature. Then we delve into the problem of models and metaphorical representations in science, which stands out as a crux for assessing the use of landscapes in development, and analyze the somehow parallel stories of Wright’s and Waddington’s landscapes. We conclude with some ideas on developmental landscapes in the context of visualization in science, with a focus on theoretical work in developmental biology.


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

Fusco G, Carrer R, Serrelli E (2014). The landscape metaphor in development. In Minelli A, Pradeu T, eds., Towards a theory of development, Oxford University Press, Oxford, pp. 114-128. ISBN 978-0-19-967142-7 [http://hdl.handle.net/10281/48518]

Criticizing adaptive landscapes, ecology and genealogy

Disentangling ecological vs. genealogical dimensions is a core task of hierarchy theory in evolutionary biology. As Eldredge repeatedly epitomized, organisms carry out (only) two distinct kinds of activities: they survive, and they reproduce.
At the organismal level, the organism stays the same whether we consider it ecologically or genealogically – yet, differences can occur in what features we consider relevant, and what fitness measurement we use.
At higher levels, the two dimensions diverge, realizing different systems. Reproductive (deme) may not coincide with ecological (avatar) population. Further upwards, along the ecological dimension, higher-level systems are grouped by energy- matter interconnection, whereas, along the genealogical dimension, higher taxa are assembled by relatedness.
In Dobzhansky’s (1937) use of the adaptive landscape visualization (Wright 1932), all living species are imagined as distributed on adaptive peaks which correspond to ecological niches in existing environments. Peaks are grouped forming genera and higher taxa (e.g., “feline”, “carnivore” ranges), and geographic speciation is figured out – like adaptation – as movement on the landscape.
In criticizing Dobzhansky’s landscape, Eldredge wrote that species actually do not occupy ecological niches; demes don’t, either; avatars do.
I point out that neighborhood and movement need to be conceived separately in genealogical and ecological spaces. Indeed, ecology should be further split in at least two spaces: geographic and phenotypic/adaptive. Movement in one space may in fact result in stability in the other(s).
I also comment on the adaptive landscape: technical limitations prevent it from being coherently used above the population level, even though as a metaphor. Finally, I emphasize the partiality of any landscape – based on the choice of relevant features and fitness components – and interpret partiality as the way of approaching complex multi- hierarchical structure in evolution.

Emanuele is also organizer of the “Hierarchy theory” session at the conference.


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

Serrelli E (2011). Criticizing adaptive landscapes and the conflation between ecology and genealogy. Meeting of the International Society for History, Philosophy, and Social Studies of Biology (ISHPSSB), Salt Lake City (Utah, USA), July 10-16. [http://hdl.handle.net/10281/28191]

http://www.slideshare.net/eserrelli/criticizing-adaptive-landscapes-and-the-conflation-between-ecology-and-genealogy

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