Manfred D. Laubichler - US grants

The project "Twentieth Century Theories of Development in Context" provides the integration of research, teaching, and outreach called for by the CAREER initiative. Taking developmental biology in the 20th century as its subject matter, the project approaches development from two scholarly and educational angles: theoretical biology and the history of biology. The research project seeks to understand how the theoretical assumptions, analytical categories, and mathematical models of developmental biology arose in interaction with several layers of scientific, socio-economic, political, and cultural contexts. The research project thus focuses from multiple perspectives on scientific change. Its goal is to understand that change historically and conceptually and also to contribute to ongoing scientific debates. The educational and outreach activities are part of the growth and further development of the Biology and Society and History and Philosophy of Science (HPS) programs within the School of Life Sciences at Arizona State University. They include the development of interdisciplinary courses, such as the "Laboratory in the History of Biology," and seminars in history of biology for graduate and undergraduate students and the further development of a graduate and undergraduate curriculum in HPS and Biology and Society as a concentration of biology degrees. All these research and educational projects are geared towards developing a better understanding of how scientific knowledge is generated, and add important perspectives to interpretations of current scientific knowledge and its interactions with societal and policy decisions.

Intellectual Merit:
The Project will accomplish two major intellectual goals. First it will provide a rich understanding of the history and current state of theories of development and the multiple ways how three clusters of factors, (a) Scientific/Technical, (b) Actors/Places, and (c) Social/Cultural, interact in scientific change. Because of the importance of embryo research, this is of powerful intellectual value itself. The project focuses on theories as a lens to study changing patterns of embryo research more generally. Second, the understanding of the history of dynamics of theories of development will also be relevant for current issues of science policy, the public understanding of science, and theoretical discussions within developmental biology itself. The interdisciplinary project thus addresses different intellectual and policy communities.

Broader Impacts:
This project has multiple broad impacts: (1) Due to its interdisciplinary focus, its questions and results will be relevant to multiple disciplinary communities. The project will also demonstrate the value of interdisciplinary research and training. (2) The Virtual Laboratory (VL) digital working environment supports this research and makes all research materials and scholarly interpretations available to multiple users. (3) The research will demonstrate how theories of development change within multiple scientific and societal contexts and include interpretations of the emerging patterns shaping science and societal decisions. This should also inform future decisions processes and policy-making. (4) Educational Materials will be developed for multiple user groups. (5) Graduate students and undergraduates, especially minority students, who are well represented within the Biology and Society program, will all be members of the research team, and each will be trained individually while adding their own results.

For the HSD initiative, Embryo research provides a case study of rapidly changing science within radically contested contexts. As with any science, embryo research is embedded in webs of unsettled ethical, legal, political, religious, cultural, and social negotiations that shape the conduct of science, its diverse meanings, and the spectrum of decisions built upon such understandings. Embryo research starts with a scientific drive to understand development of the individual organism and is shaped by three clusters of factors: (1) technical, including experimental techniques, equipment, and the way results are presented (in publications and presentations) and represented (in images and models); (2) actors, laboratory settings, institutions, and local contexts of scientific and technical work; and (3) social/cultural/ intellectual/economic environments in which the work is done. These clusters of Technical, Actors/Places, and Social/Cultural all impact and are impacted by the science. Understanding each requires different disciplinary research approaches, and understanding interactions requires multi-disciplinary research strategies and methods. The factors combine to serve as "Agents of Change" shaping science in society. This project explores those agents of scientific change in a dynamic, interactive, integrative, interdisciplinary, international research environment. With regards to Intellectual Merit, we will accomplish two major intellectual goals. First is a rich understanding of the history and current state of embryo research, the factors involved, and the multiple contexts in which research is done. Because of the importance of embryo research, this is of powerful intellectual value itself. Furthermore, in bringing together multiple otherwise disparate areas of study related to this particular case, we will achieve a much richer understanding of the Agents of Change influencing each case of scientific change. Our hypotheses focus on selected episodes in which different factors had different relative importance, and we seek to analyze and understand the Agents of Change over time. All results will be part of the digital working environment of the Virtual Laboratory (VL) in collaboration with the Max Planck Institute for the History of Science in Berlin. We will archive research materials to be shared among different working teams, and will add scholarly interpretive essays and articles that will make up an on-line Resource Collection accessible to multiple users, in addition to traditional scholarly publications. With regards to Broader Impacts, this project has a several: (1) Working with a network of nearly 2 dozen collaborators in 6 countries and multiple disciplines, we will develop a true "collaboratory." By sharing materials and research questions, we will ask new questions within each discipline and learn of research materials, questions, and interpretations across disciplines. (2) The VL tested digital working environment makes that research possible by making all research materials and scholarly interpretations available to all users at all times. (3) The research will allow us to demonstrating how Agents of Change affect this case of Embryo Research in its societal contexts, including interpretations of the emerging patterns shaping science and societal decisions. This should also inform future decisions processes and policy-making. (4) In the final stages, we will develop Educational Materials for multiple user groups. A Postdoctoral Fellow, Graduate Student, and Undergraduates will all be members of the research team, and each will be trained individually while helping to add to the accumulating community results.

The project is designed to address simultaneously the need of acquiring additional professional experience in informatics in order to advance research in the history and philosophy of science (HPS) and to open up new areas of research and investigation at the intersection of these two areas. As more and more texts, images, and archival sources become available in digital form, history and philosophy of science, and the humanities more generally, are now experiencing a transformation similar to the life sciences during the 1990s and the first decade of the 21st century. While these trends are inevitable, researchers in these areas are ill-prepared to take advantage of the new opportunities or to shape the future development of relevant parts of the emerging new cyberinfrastructure. The post-doc's training in biology and HPS, as well as his work on the NSF funded Embryo Project, has given him a unique perspective on the possibilities and challenges of the upcoming digital era in HPS. With the fellowship he will spend time training with computer scientists and informaticians at the Marine Biological Laboratory in Woods Hole, MA, as well as the Max Planck Institute for the History of Science in Berlin. He will acquire new skills related to developing this cyberinfrastructure, which will then be tested and implemented in the context of the Embryo Project. This professional training fellowship will go beyond supporting research in HPS as the tools and techniques developed will contribute substantially to the digital humanities at large. Presenting HPS related results and information to a multitude of different user groups has enormous educational and outreach possibilities as well, and this depends on a substantially developed cyber-infrastructure to deliver this scholarly content to students, policy makers, judges, and the interested public.

This STS training and research project is supported by the Impacts of Biology on Society (IBS) initiative, which is jointly funded by NSF's BIO and SBE directorates.

The project will provide rigorous interdisciplinary training and research for graduate students and postdoctoral fellows in history and philosophy of the life sciences, with a focus on developmental biology. The program will involve graduate students at Arizona State University (ASU) as well as visiting students from other universities. Participants will receive training in interdisciplinary scholarly research in history and philosophy of science; in addition, they will receive training on digital curating and database managing.

The research theme for this training and research project is provided by the Embryo Project, an ongoing project in history and philosophy of developmental biology at ASU's Center for Biology and Society. The Embryo Project explores historical, philosophical, bioethical, legal, and social aspects of developmental biology and its relations to society, all with a solid grounding in developmental biology and its historical development. It pursues these goals through a set of focused projects directed by individual faculty members at the Center for Biology and Society.

The Intellectual Merits of this IBS supported training and research project lie with research focused on projects within the history and philosophy of developmental biology. Each member of the training group will play a defined role building upon and beyond existing strengths. Each student will develop a focused research project related to individual career directions, and based on that will write a set of related articles to be submitted for review, editing, and publication in the Embryo Project Encyclopedia.

The project's Broader Impacts include the participants learning to communicate research results effectively to multiple user groups, and helping to develop contributions targeted toward K-12 teachers and the broader public, and will take advantage of ASU's outreach activities "Ask a Biologist" and "Chain Reaction." The team-based approach makes it possible for each student to excel in a targeted area while also participating in all other aspects of the project, including outreach.

Introduction

This award provides support for the first part of an ambitious collaborative informatics project between researchers at Arizona State University and the informatics team at the Marine Biological Laboratory in Woods Hole, Massachusetts (MBL). The full project involves three parts and will lead to informatics infrastructure and training that will be available to the entire STS (Science, Technology, and Society) community. This award provides seed money that will serve to support the first part of the project, which is described in the next section. In the second part, the team will build a centralized repository and adapt and develop informatics tools to allow the History Project to develop new kinds of scholarly data and knowledge. The repository will integrate the MBL History Project into a single, shared resource growing from the repository containing other projects that already reside at the MBL. In the third part, the team will develop a research system to allow any STS researchers to add their materials into the repository (with ownership and intellectual property carefully labeled and protected), then take advantage of participating in a shared system for which each researcher has access to all, and be able to ask new research questions and develop new knowledge as a result. To foster these approaches the team will also develop an education infrastructure for STS informatics.

Intellectual Merit

Scholars will develop new research approaches and findings within the MBL History Project, which brings together existing materials related to biology at the MBL and provides scholarly interpretations of the science, the institution, and its place in society. The MBL has been one of the world's leading biological research and education institutions for over 120 years, and it has had tremendous impact on the life sciences and on society. The team will assemble working groups around four topics: Embryology, Model Organisms, Physiology, and Ecosystems. A team leader has been identified for each working group, and each of them will bring together a small group to help identify materials that will be collected and ingested into the database. These will be combined with materials gathered through MyMBL, an online tool that the team is developing for collecting digital video narratives from living subjects on specific topics; the development of MyMBL is to be supported by this award. Additional (more technical) infrastructure elements are also to be supported, such as the development of a d-space repository for maintaining information in triples that are to be imported from some Fedora databases. All of these elements will serve to provide a "proof of principle" for the full project outlined in the first section above.

Potential Broader Impacts

The impacts of the first part of the project include the scholarly results of the MBL History Project, centered on the repository and Web interface plus more traditional scholarly interpretive publications and presentations. Some steps will be taken to develop the repository and tools that will eventually make research results available through several different Web interfaces to multiple user groups, from scholars to the wider public, including educators and students; undergraduate and graduate students will be able to contribute articles, building on successful existing models. Finally, the informatics team will continue developing plans for offering Informatics Training courses and materials in order to make the shared repository as useful as possible for the STS community and more broadly.

This INSPIRE award is partially funded by the Science, Technology, and Society Program in the Division of Social and Economic Sciences in the Directorate for Social, Behavioral, and Economic Sciences; and by the Advances in Biological Informatics Program in the Division of Biological Infrastructure in the Directorate for Biological Sciences.

Intellectual Merit

This will be the first large scale computational project in Science and Technology Studies. Although the focus of this project is on Biodiversity and on History and Philosophy of science, the approach would extend well beyond these areas. The project will establish a repository and a research system based on computational tools and digital sources, and it will develop education and training modules. The goal is to move beyond separate small collections that reside on individual computers in dispersed places, and bring together the objects of study as well as scholarly interpretations of those objects. The materials are to be openly available for efficiency and also to stimulate new kinds of research and discovery. The repository will link to existing large and widely-used databases such as the Biodiversity Heritage Library and the Encyclopedia of Life. Researchers at Arizona State University and the Marine Biological Laboratory will collaborate in bringing together the robustly integrative methods that combine history and philosophy of science, informatics, and biology of biodiversity. It will transform the way that scholarship and training is done in the areas, and lead to a new kind of scientific history based in open access publishing. The repository, tools, and training modules will be widely available for other projects in Science and Technology Studies for the full range of STEM disciplines.

Potential Broader Impacts

This project will produce scholarly results, a repository, informatics tools, and training manuals for others to customize and contribute their own projects. Scholarly results are to be produces that would be available through different websites for multiple user groups, from specialized scholars to the wider public. For educators and students, the project will connect with Arizona State University's Ask A Biologist project, as well as to Encyclopedia of Life and the Biodiversity Heritage Library, and to other existing databases. Undergraduate and Graduate students will be trained to contribute interpretive articles. Informatics Training courses, manuals, and other educational approaches will make the system and repository available widely.

Introduction

This doctoral dissertation improvement grant supports an investigation in the history of cell degeneration research. The dissertation focuses on four historical episodes from the 1930s to 1990s. The first three episodes are largely written in draft form. This grant will support research on the fourth historical episode documenting H. Robert Horvitz's study of cell death in the nematode C. elegans from the late 1970s to the early 1990s. Horvitz, a molecular biologist, shared the 2002 Nobel Prize in Physiology or Medicine with two others. This current proposal requests funding mostly for archival visits and interviews to characterize the fourth historical episode through the early 1990s when Horvitz represented cell death as a specific cellular state of differentiation caused by a network of gene expressions. This development opened the door for future genomic approaches to cell death, aging as well as cancer research through studying the model organism C. elegans.

Intellectual Merits

The specific study supported by this grant and the encompassing dissertation research will serve to provide an analytical account of the emergence of diverse meanings of cell degeneration, such as being a protector of health, a sculptor for development, and a limitation of lifespan, in the contexts of these research programs and broader biomedical concerns. The study will contribute to deeper understandings of the complex history of biomedical research including insights about scientific practice and connections with broader historical backdrops and consequences. The study will also contribute to discussions in history and philosophy of science and science studies on the roles of new biological material, research styles, and priorities in the modern development of biology, especially with the intricate interplay between changing experimental systems and concepts of cell degeneration these systems embodied.

Broader Impacts

History of science projects that contextualize and problematize current knowledge and research programs on a particular topic, in this case cell degeneration, are of substantial interest to scientists in the field (cell biology) and related fields (such as molecular biology, physiology, cancer research, and research on aging). In addition, the results of this project are to be communicated to the public through the online encyclopedia of embryology, the Embryo Project, through an online virtual exhibition about history of biology of aging at the Marine Biological Laboratory Repository, and through a prize-winning podcast by Chemical Heritage Foundation, Distillations.

Introduction

This doctoral dissertation improvement grant supports research in the history of evolutionary ecology. Specifically, it will investigate attempts to integrate models of adaptive phenotypic plasticity into ecological models of species distribution. The project will focus on how specific social, intellectual, and material contexts in which models of plasticity emerged during the 1960s through 1980s shaped their underlying assumptions and commitments. The grant will support travel to multiple sites to retrieve oral histories and to consult specific archival materials that are essential for reconstructing the influential conceptual and theoretical approaches to investigating adaptive phenotypic plasticity.

Intellectual Merit

This project will illuminate an important interface between science and society by placing developments in evolutionary ecology in the context of shifting societal visions of environmental connectivity, vulnerability, and anthropogenic change. It will create new bridges between the history of ecology, environmental history, and the history of genetics and molecular biology, by showing how different visions of environmental change are linked to ideas about genetic mechanisms in ecological and evolutionary processes. It will also contribute to our understanding of trans-disciplinary knowledge transfer by describing the consequences of efforts to integrate theoretical and methodological approaches from ecology and evolutionary biology.

Broader Impacts

By analyzing the complex relationships between theoretical models and empirical research in contextualized investigative settings, this project can generate insights that are highly transferrable to studies of the role and status of models in other scientific fields. In addition, this project has potential to transform the way that scientists think about the broader social and intellectual contexts of their research; the researcher plans to engage ecologists and policy-makers via presentations at scientific meetings, publications in scientific journals, and transdisciplinary workshops. Finally, the results of this project will be used to create educational materials that illustrate science as a practice.

This award will fund a workshop that will bring together key members of the STS community to engage in intensive discussions about data management issues. The need for the meeting is initially driven by a recent requirement implemented by NSF; each research proposal is now required to have a suitably adequate data management plan. The requirement is generally formulated; NSF recognizes that there is a vast array of scientific research cultures with differing practices of data management. Moreover, these many such cultures (including STS) address pertinent data-management issues in widely different ways. Issues include what constitutes data, and how data should be characterized, formatted, securely stored, and made broadly accessible for re-use by others, while also addressing concerns of privacy and the need at times to grant only limited access. The workshop will focus on articulating current needs, as well as proposed responses and solutions, for development of effective data management principles and routines in the STS domain.

The workshop organizers have four distinct goals: (1) to generate provisional templates for data management plans for individual projects across the diverse fields of STS. (2) To produce a workshop report that summarizes the discussions with a focus on current and future needs and existing and possible solutions (including the templates); the report will be made broadly available on an existing secure, open-access repository at Arizona State University. In addition, they will produce two white papers. One white paper is (3) to be circulated to members of the STS community and to other research communities through professional societies to solicit input and work toward a shared understanding of infrastructural needs. Another white paper will (4) outline opportunities for computational work that will become possible only if the communities establish robust data management strategies; it will outline future strategies for taking advantage of opportunities for computational work in the diverse STS fields represented that is predicated on available and accessible data. The white papers will address how STS fields can implement strategies of data driven science and will consider what benefits would accrue from doing so.

This award supports the research of a post-doctoral fellow on a history of biology project that focuses on a variety of different ideas of cooperation that developed during the interwar period (1919-1939). His primary goal is to understand what motivated the work that emphasized cooperation, as well as the nature of that work. He will do so using a set of driving questions and a research plan that utilizes three approaches, which are indicated below. Among the questions that he will pursue are the following. What was cooperation-oriented thinking? To what extent and in what ways was there a shared focus on cooperation and related ideas? What terms in addition to "cooperation" capture this thinking? What motivated researchers to study the biological nature and significance of cooperation during this particular historical period? How did the ideas develop over time, and are there unique features that characterize this period? The results of this project are to be disseminated through both traditional and digital publications, at conferences, and in classrooms. They will be aimed at scientists, scholars, and the general reading public. The postdoc will use his extensive training and experience in digital history to design a blog that showcases pertinent documents, photographs, stories, and novelties that arise out of this project. This website will introduce users to previously overlooked aspects of American biology and international relations.

A working hypothesis of the project is that although biologists during the interwar period used different labels for cooperative behavior including holism, unity, emergence, and organicism, they shared a common underlying goal; namely, to provide a biological explanation for cooperation, of how parts come together as coordinated wholes. The postdoc plans to focus on a specific facet of this goal by examining how this generation of biologists across different fields advanced theories about the evolution and nature of sociality and cooperation (as opposed to competition). His primary goal is to understand how and why these biologists devoted enormous effort and energy to better understanding the origin of social impulses. He will do so by engaging in a close study of the scientific, social, cultural, and political details of the period to obtain a deeper understanding of the ideas of cooperation. He will use archival research, computational methods, and interactions with current researchers in biosocial systems to bring to light what biologists are saying about cooperation today to compare ideas of cooperation across two different time frames; the comparison can both inform the historical study and inform current conceptions.

This award supports the development of an international Research Coordination Network (RCN) for developing computational and big data methods for history and philosophy of science (HPS) research. Such research is beginning to yield novel insights from individual projects. However, an integrated approach is required in order to take full advantage of these methods. The RCN will take some of the steps that are necessary to eventually provide a structured representation of HPS knowledge and the foundation for a data driven computational HPS infrastructure. Given the diversity of contexts, questions, and approaches, it is clear that integration, coordination and standards cannot be imposed centrally, meaning that an RCN is the pertinent mechanism for this type of project. By establishing a new integrative approach to computational and data-driven HPS, the RCN will in turn facilitate an integration of HPS with big-data and data-driven science. In addition, the RCN will lead to new types of questions facilitated by this approach, and thereby increase the relevance of HPS for larger questions at the intersection between science and society. It will also facilitate international collaborations and the inclusion of a diverse group of scholars, particularly many younger scholars; it will do so by promoting commitment to open source, open access, and open education thereby providing broader access to and participation in the HPS community, including members of the general public.

Without coordinated authorities and ontologies, data cannot be shared or integrated across individual projects, severely limiting their broader use. Without the benefits of such an economy of scale the transformative impact of computational methods in HPS is limited as the integration and computational analysis of datasets across multiple projects is precisely what enables novel and innovative questions. This RCN addresses the challenges related to authorities and ontologies for computational and digital projects in HPS by conducting research and developing computational solutions for mapping authorities and integrating ontologies across HPS projects through step-wise aggregation and mapping of data models, authorities and ontologies. The international RCN will (1) solidify a working social/organizational network of researchers in computational HPS, including a structured set of educational modules; (2) coordinate research and development of software solutions to address the challenge of data integration across HPS projects; and (3) document and analyze the process of reaching these solutions and integration as an example of how the computational turn affects the development of scientific fields.

This is a project in the history and philosophy of biology that has very substantial ramifications for data-intensive science. The PI will investigate how the history of taxonomy can shed new light on the value of ambiguity for science in the domain of data-intensive science. The project focuses on detecting trade-offs in the value of ambiguity for scientific language as a function of changing social contexts. Accurate disambiguation relies on a shared background of knowledge and abilities, which may prove inadequate as concepts spread into new contexts or a community grows larger and more heterogeneous. The project will fund graduate and undergraduate research assistants to analyze a text corpus drawn from two centuries of history in biological taxonomy. It will also support public events and the creation of educational materials addressing the theme of productive ambiguity in naming and classification.

This project will implement an integrative conceptual framework enabling empirical investigation of ambiguity in linguistic settings. It will use an information-theoretic framework from cognitive pragmatics to quantify ambiguity in a way that is open-ended enough to accommodate a wide range of phenomena shaping human language and communication while also reflecting the specific constraints required by computers. It will provide novel tools for tracking changes in language at the level of populations rather than individuals while remaining sensitive to underlying social institutions and individual differences. Results from this project will open new perspectives on the history of types and subspecies in systematics, and it will inform contemporary debates about the virtues of maximal determinacy in the computational representation of human language and meaning.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

How is knowledge created at the intersections between basic science, biotechnology, and industry? Gene drives are an interesting example, as they combine a long-standing interest with a recent technological breakthrough and a new set of commercial applications. Gene drives are genes engineered such that they are preferentially inherited at a frequency greater than the typical Mendelian fifty percent. During the historical and conceptual evolution of gene drives beginning in the 1960s, there has been many innovations and publications. Along with that, gene drive science developed considerable public attention, explosion of new scientists, and variation in the way the topic is discussed. It is now time to look at this new organization of science using a systematic approach to characterize the system which has enabled knowledge to grow in this scientific field. This project will break new ground in how knowledge advances in genetic engineering science, and how we understand what a “gene drive” is through analysis of language, communities, and social media. In effect, this research will advance multiple fields and enable a deeper understanding of knowledge and complex systems by a wide audience through publicly available dissemination of results through conferences, blogs, GitHub, and scholarly publications.

This project will document patterns of publication, collaborative relationships, social media influence, then combine those factors to characterize the knowledge system into a signal detection algorithm to predict the future trajectory of the larger CRISPR-Cas9 science. The results of computational analysis will provide an in-depth and complete characterization of the structure, dynamics, and evolution of scientific knowledge found in the gene drive technology. In addition, the project will analyze how the public opinion influences the progress of genetic engineering technologies through social media and news platforms. Further, time series analysis of the multiple layers of discourse will enable a diachronic connective mapping of collaborative relationships and track linguistic variation and change, highlighting where ambiguous language may appear. Thus, improving and creating more cohesive scientific language. Overall, depicting the structure, dynamics, and evolution of scientific knowledge during a novel eruption of scientific complexity can shed light on the factors that can lead to: (1) improved scientific communication, (2) reduction of scientific progress, (3) new knowledge, and (4) novel collaborative relationships. Therefore, characterizing the current technological, methodological, and social contexts that can influence scientific knowledge. Research results will reach conferences, blogs, GitHub, and be shared through both traditional and digital publications. Scholarly results will be available through different websites, and as much as possible will be shared for free.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.