Archive

New Publication in Studies in History and Philosophy of Life Sciences

Plasticity, stability, and yield: The origins of Anthony David Bradshaw's model of adaptive phenotypic plasticity

A new paper by Erick Peirson in Studies in History and Philosophy of Life Sciences is available online.

Plant ecologist Anthony David Bradshaw's account of the evolution of adaptive phenotypic plasticity remains central to contemporary research aimed at understanding how organisms persist in heterogeneous environments. Bradshaw suggested that changes in particular traits in response to specific environmental factors could be under direct genetic control, and that natural selection could therefore act directly to shape those responses: plasticity was not “noise” obscuring a genetic signal, but could be specific and refined just as any other adaptive phenotypic trait. In this paper, I document the contexts and development of Bradshaw's investigation of phenotypic plasticity in plants, including a series of unreported experiments in the late 1950s and early 1960s.

For those without an institutional subscription to Elsevier, see the archived preprint.

Austria’s Ahead-of-Its-Time Institute That Was Lost to Nazis

Manfred Laubichler was interviewed for an article by Chelsea Wald about the Biologische Versuchsanstalt in Vienna, published in the recent issue of Nautilus. From the article:

In 1911, Popular Science Monthly published an enthusiastic description of a young, private experimental-biology institute in Vienna, lauding its “remarkable scientific productivity resulting from only eight years of research.”

An early air-conditioning system used to control air temperatures at the Vivarium

The author, zoologist Charles Lincoln Edwards, attributed the success of the Biologische Versuchsanstalt (Insitute of Experimental Biology) to its many advanced experimental devices. The institute, popularly known as the Vivarium, boasted a wide range of terrariums, which housed hundreds of organisms, from glow-worms to kangaroos, at strictly controlled temperatures, humidity, pressure, and light levels. That wasn’t always easy—the Vivarium had to adopt or invent many cutting-edge technologies, including an early air-conditioning system. It was “a pioneer in the use of the carbonic-acid cooling machine for maintaining a cold environment,” wrote Edwards. With the help of circulating salt water and a condenser, four rooms were kept at temperatures ranging from 5°C to 20°C.

The idea of using various apparatuses to control the living conditions of plants and animals for study was new; before that, scientists mainly observed their subjects in nature. At the Vivarium, the focus was on raising many generations under the same conditions in order to probe questions of heredity and development—a unique approach at the time, and one that many consider a precursor to today’s research on evolutionary developmental biology, or “evo-devo.”

Tethne: Geographic Networks in Gephi and Google Earth


Many bibliographic datasets include institutional affiliations for authors. Using geocoding services, such as the Google Geocoding API, we can convert institution names and addresses into geographic coordinates that can be plotted on a map. Tethne provides geocoding services in the services.geocode module.

In this tutorial, we will use the Google Geocoding service to obtain geographic coordinates for authors in a coauthorship network (see Coauthorship Networks) and its derivative, the institutions network (see networks.authors.institutions()). We will then plot those geo-coded networks in Gephi using the Geo Layout plugin, and overlay them on a 3D map of the globe in Google Earth.

This tutorial was developed for the course Introduction to Digital & Computational Methods in the Humanities (HPS), created and taught by Julia Damerow and Erick Peirson.

Click here for the full tutorial.

New Review in Quarterly Review of Biology

Erick Peirson's review of Ted R. Anderson's The Life of David Lack: Father of Evolutionary Ecology was published in the March issue of the Quarterly Review of Biology. See the full review here (paywall).

David Lack (1910–1973) was a British ornithologist whose research on population biology was part of a broader set of attempts in mid-20th century to integrate neo-Darwinian evolutionary theory into explanations of the distribution and abundance of species. In The Life of David Lack, ecologist Ted R. Anderson asserts that Lack should be appreciated as the “father of evolutionary ecology,” pointing to his 1947 book Darwin's Finches and his 1947 paper titled “The Significance of Clutch-Size” as evidence for his claim. Central to both of those works was the idea that the demographic and reproductive characteristics of a species are best explained in terms of maximizing the reproductive fitness of individual organisms, and the idea that the mechanisms of this selective process can be studied through experimental manipulations in the field.

Classroom lessons go global at ASU through technology

The Global Classroom project was recently fingered by ASU News as breaking down the boundaries of the traditional classroom. You can read the entire article here.

One of the most powerful examples of a mediated classroom is located in the C-wing of the Life Sciences building, where “Sustainable Cities: a Contradiction in Terms?” is being taught simultaneously to students at ASU and at Leuphana University in Germany.

Twenty ASU students sit at tabletop computers surrounded by numerous large screens, taught in person by two of the top professors at ASU. Another 20 are tuned in from Germany. Still another 20 students from each country are in adjoining classrooms working on research projects, as part of a second cohort of the three-semester class.

The Global Classroom, a pilot project funded by a $900,000 award from the Mercator Foundation, utilizes video conferencing; intensive writing assignments and student writing workshops; online exhibits; peer-to-peer mentoring; and in-person international exchange.

Python Class for Accessing Custom DSpace API

By Erick Peirson

The Genecology Project, and other computational HPS projects at ASU, rely on the ASU Digital HPS Community Repository for storing a variety of data and products. An important part of the development process for the repository was producing a REST API that could provide reliable and programmatic access to deposited materials. Since the built-in DSpace REST API didn't quite have all of the functions that we needed (e.g. it didn't have a reliable authentication mechanism, and it ignored access restrictions), we collaborated with programmers at the Marine Biological Laboratory to develop a new API (available here). Since the analysis process in most of our computational projects takes place in a Python environment, we had to develop some simple methods for pulling material from the repository via the API.

A Python class for interacting with our custom DSpace API is available here, and documentation is available here. This is a work in progress, but may be useful for others who adopt similar infrastructure for their digital projects, or who wish to interact with the ASU Digital HPS Community Repository.

New article in Biology & Philosophy

PhD candidate Christopher Dimond is a co-author on a recent paper in Biology & Philosophy, titled "Pluralism in evolutionary controversies: styles and averaging strategies in hierarchical selection theories."

Two controversies exist regarding the appropriate characterization of hierarchical and adaptive evolution in natural populations. In biology, there is the Wright–Fisher controversy over the relative roles of random genetic drift, natural selection, population structure, and interdemic selection in adaptive evolution begun by Sewall Wright and Ronald Aylmer Fisher. There is also the Units of Selection debate, spanning both the biological and the philosophical literature and including the impassioned group-selection debate. Why do these two discourses exist separately, and interact relatively little? We postulate that the reason for this schism can be found in the differing focus of each controversy, a deep difference itself determined by distinct general styles of scientific research guiding each discourse. That is, the Wright–Fisher debate focuses on adaptive process, and tends to be instructed by the mathematical modeling style, while the focus of the Units of Selection controversy is adaptive product, and is typically guided by the function style. The differences between the two discourses can be usefully tracked by examining their interpretations of two contested strategies for theorizing hierarchical selection: horizontal and vertical averaging.

Success! Excellent turn-out for Digital HPS Workshop @ HSS 2013

Photo credit: Center for Biology & Society

The workshop on Digital HPS at the History of Science Society 2013 meeting went off without a hitch! The workshop was organized by the international Digital HPS Consortium, and the ASU Digital Innovation Group. The objectives of the workshop were to expose HSS attendees to some of the cool things happening in the Digital HPS world, and to create an informal, friendly space where people interested in digital approaches can be inspired, discuss ideas, and get more information. Despite starting at 8:45pm, and competing with numerous parallel sessions, the room was packed! Read more to see pictures from the event.

Workshop on Digital HPS @ History of Science Society, 2013

Are you fascinated by the prospect of taking your scholarship into the digital realm, but not quite sure how to get started? Heard lots of buzz, but aren't quite clear about what "digital history & philosophy of science" means in practice? Join us for an informal and informative workshop on digital HPS at the upcoming History of Science Society meeting in Boston! This workshop is a co-production of the international Digital HPS Consortium and the ASU Digital Innovation Group.

What: Workshop F1: Laying the Foundation for Your Digital or Computational Project in the History of Science: an Interactive Workshop
When: Friday, November 22nd, 8:45pm
Where: Alcott Room, Mezzanine Level, Westin Boston Waterfront Hotel

Objectives

  1. To expose HSS attendees to some of the cool things happening in the Digital HPS world, and
  2. To create an informal, friendly space where people interested in digital approaches can be inspired, discuss ideas, and get more information.

(Read more...)

History of the Max Planck Society — Department Baldwin - Introgression in Co-authorship Networks



By Erick Peirson.

An important component of analyzing the causes and dynamics of conceptual change in science is understanding the behavior and influence of individual scientists, in the context of their collaborations and discursive activity. Fleck's concept of Denkkollectiv drew attention to the ways in which patterns of collaboration give rise to specialized Denkstil -- patterns of thought, language, and practice that constitute the lens through which scientists see the natural world and ask questions about it. Consistent with our everyday experience in social situations, Social Network Analysis has shown how power and influence are distributed unevenly among individual actors in collectives, shaping the flow of ideas and information in those social networks. Graph theory gives us a rich collection of concepts and metrics to express such influence quantitatively, based on the structural properties of networks. As historians we are interested not only in the structure of particular social networks, but how those networks evolve. With respect to analyzing the behavior and influence of individual actors, this prompts us to ask how different scientists enter existing collaborative networks, and how their structural position within those networks change over time.

One way to pursue this question... (read more)

New Course in Digital & Computational Methods


Advances in computational methods have created exciting new opportunities to apply digital methods not only to historical and philosophical research, but also to discovery and meta-analysis in the life sciences. This hands-on course provides an introduction to digital methods — from managing digital data to computational analysis — for advanced undergraduate and graduate students in the humanities and life sciences. Students are introduced to data and metadata management, text-mining, citation analysis, network analysis, data visualization, and other computational methods. The course balances fundamental theory with hands-on sessions geared toward students’ own research projects. This course is suitable for students in both the sciences and the humanities, and is cross-listed for Biology, History & Philosophy of Science, and English.

Digital + Computational Methods in the Humanities (HPS)
Spring, 2014: BIO/HPS/ENG 498/591
Tuesday/Thursday 5:30pm - 7:00pm

For more information, contact Julia Damerow or Erick Peirson.

Global Classroom Update


As part of our Global Classroom Project the Students from Leuphana University have visited Arizona and ASU from Septmeber 14 to 29th. During these two weeks, activities included

1. Developing of Group Project Prospectus for the rest of the Global Classroom:

During Class time and using specific homework assignments, each international team of students will developed a Project Prospectus that contains: (1) the driving question each team wishes to address; (2) a motivations statement that shows why we should care about the question; (3) an analysis of the problems connected to the question; (4) a set of methods that will be employed for the development of the projects.

2. Joint exploration of the main Urban areas in Arizona

Outside of regular class time, students and instructors will visit different areas relevant for the development of the projects. These exploratory activities aim to bridge the different understandings of urban environments in Arizona from the German and American perspectives. In this way, we aim to enhance a shared understanding of urban complexity in the students that will anchor the projects on a more stable and shared ground. These included: (Read more)

Autumn DigInG has Commenced!

The fall semester has commenced, and the Digital Innovation Group programming and research teams are gearing up for another big development push. Here are a few of the things that we're working on:

Vogon is a desktop application to annotate texts with contextualized relationship triples, so-called “quadruples.” This is an important tool for the Genecology Project, which uses Vogon to reconstruct social and institutional networks rooted in specific texts. We're also developing new Vogon manual and tutorial; you can find the latest draft here!

Quadriga is a web-application that acts as a clearing-house for text annotations -- in the form of contextualized triples, or “quadruples,” that form complex graphs -- generated with the Vogon desktop application, and as an environment for managing text-annotation projects. Both Vogon and Quadriga can connect to the Digital HPS Community Repository to pull out texts for annotation. The target release date for Quadriga 1.0 is June, 2014, but keep your eyes open for alpha and beta releases in the coming weeks! (Read more...)

Project Update: Dynamic Social Network from the Genecology Project

(Click for larger view)

This video depicts a small sub-set (616 actors) of the Genecology Project social network, from the mid-1940s through the 1980s. We've been experimenting with dynamic layouts as a way to depict changes in social interactions among participants in the field of plant experimental taxonomy in Britain. Each node is an actor, and each edge represents evidence that the two connected actors interacted in some concrete way. Each node and each relationship is rooted in a specific location in a scientific publication.

Project Update: The Networks of Evolutionary Medicine


by Deryc Painter; edited by Sam Hauserman.

“Research is what I’m doing when I don’t know what I’m doing.” – Wernher von Braun

As the evolutionary medicine project moves forward, it has become apparent that in order to understand what evolutionary medicine is and what effect it has, I need to understand whom people are working with, and what they are working on.  My list (http://www.evolutionarymedicine.org/interested-people) of researchers with interests in evolutionary medicine contains 267 names.  From that relatively small pool, I created a co-author network of 17,908 people containing 413,701 connections.   In these networks, the most central nodes... (more)

Project Update: Five Hundred and Thirteen Disambiguations [Davidson Project]


By Sam Hauserman

We hit an important milestone this week in the Davidson Project: the completion of the Eric Davidson Social Network database.

In last week’s project update, we explained how we generated our bibliographic data set, which will provide some of the raw material that we use to analyze relationships within this community of researchers. My contribution to the dataset was to disambiguate the names and identities of all 513 of Davidson’s coauthors.

Because the authors of scientific papers are typically represented only by a (often un-unique) coupling of initials and surname, we need to establish which individual is the real Davidson coauthor so that our bibliographic information is useful. Once we have established the identities of each individual scientist, we can add them to the Conceptpower authority file so that we have an unambiguous way to refer to them in our data. In this week’s project update, I’ll go into a little detail about what the disambiguation process entails.

Project Update: Building a Bibliographic Dataset [Davidson Project]

By Divyash Chhetri; edited by Sam Hauserman.

One of our exploratory projects in computational HPS is an attempt to leverage patterns from large sets of bibliographic and textual data to provide new perspectives on the content and contexts of the investigative pathway of embryologist Eric H. Davidson. Our aspiration is to use a variety of computational approaches to investigate Davidson’s research, drawing on data about coauthorship, citations, and patterns of language in scientific texts. As we go along, we are learning just as much about the tools and methods at our disposal as we are about Davidson’s work.

Our first step was to collect bibliographic data for as many of Davidson’s papers as we could find. In total, we found data for around 540 publications. We then extracted a list of all of Davidson’s coauthors, totaling 515 unique names. Sam has had the arduous task of “disambiguating” each of these names: identifying each individual, collecting basic biographical information about them, and creating an entry for each person in the Conceptpower authority file.

Project Update: Genecology Project: Testing Dynamic Layouts in Cytoscape

This video depicts a small sub-set (121 actors) of the Genecology Project social network, from 1951 to 1979. We've been experimenting with dynamic layouts as a way to depict changes in social interactions among participants in the field of plant experimental taxonomy in Britain. Each node is an actor, and each edge represents evidence that the two connected actors interacted in some concrete way.

The network data were generated using the Vogon text-annotation tool, transformed to Dynamic XGMML, and visualized in Cytoscape 3.0.1 using the Kamada-Kawai DynLayout.

Project Update: Putting Experimental Taxonomy on the Map

By Erick Peirson

As we work to reconstruct the field of genecology, or experimental taxonomy, in Britain as part of the Genecology Project, we have started by scrutinizing a list of researchers assembled in 1964 by David H. Valentine in the Botany Department at Durham University. The list was meant to be inclusive as possible: graduate students and research staff are listed alongside senior figures in the field, and the list includes researchers who openly and publicly disagreed with Valentine about the nature of genecological research and its core concepts. At least 9 of the 87 researchers on the list are women (many are identified as "Miss" or "Mrs"). Twenty five institutions in Britain, and one (Trinity College) in Ireland are represented.

New Publication in Creative Education: A Global Classroom for International Sustainability Education

Manfred Laubichler and Guido Caniglia are co-authors on a recent paper in the journal Creative Education: A Global Classroom for International Sustainability Education.

A brief review of international sustainability education options currently available to students reveals a gap between the knowledge students may need to succeed in a globalized world and the opportunities available. Into this landscape, we introduce The Global Classroom, an international collaboration between Leuphana Univer-sity of Lüneburg in Germany and Arizona State University in the US. The project strives for an interdis-ciplinary and cross-cultural approach to equipping students with the knowledge, skills, and attitudes re-quired to take on sustainability challenges in international settings. We discuss the structure and organiza-tion of the Global Classroom model and share preliminary experiences. The article concludes with a re-flection on institutional structures conducive to providing students with the international learning oppor-tunities they may need to tackle sustainability problems in a globalized world.

New Publication: Genetic and developmental basis of F2 hybrid breakdown in Nasonia parasitoid wasps

Gibson, J. D., O. Niehuis, B. R. E. Peirson, E. I. Cash, J. Gadau. 2013. "Genetic and developmental basis of F2 hybrid breakdown in Nasonia parasitoid wasps." Evolution: Available Online.

Speciation is responsible for the vast diversity of life, and hybrid inviability, by reducing gene flow between populations, is a major contributor to this process. In the parasitoid wasp genus Nasonia, F2 hybrid males of Nasonia vitripennis and Nasonia giraulti experience an increased larval mortality rate relative to the parental species. Previous studies indicated that this increase of mortality is a consequence of incompatibilities between multiple nuclear loci and cytoplasmic factors of the parental species, but could only explain ∼40% of the mortality rate in hybrids with N. giraulti cytoplasm. Here we report a locus on chromosome 5 that can explain the remaining mortality in this cross. We show that hybrid larvae that carry the incompatible allele on chromosome 5 halt growth early in their development and that ∼98% die before they reach adulthood. On the basis of these new findings, we identified a nuclear-encoded OXPHOS gene as a strong candidate for being causally involved in the observed hybrid breakdown, suggesting that the incompatible mitochondrial locus is one of the six mitochondrial-encoded NADH genes. By identifying both genetic and physiological mechanisms that reduce gene flow between species, our results provide valuable and novel insights into the evolutionary dynamics of speciation.