James P. Collins - US grants

A two-year continuation of current research is proposed with projects designed to uncover how variability, inheritance, and differential fitness affect the evolution of morphological variation within species of animals. The polymorphic tiger salamander, Ambystoma tigrinum, will be a model to address three questions. 1). Have changes in timing of development over evolutionary time affected the origin of morphological variation within species? 2) Will simple extensions of genetic models describing continuous variation in species? 3) Is natural selection, especially through competition within species and predictability of the aquatic habitat, a force maintaining morphological variation within and between populations? These questions relate to the general issue of how continuous morphological variation within a species is maintained or converted into discontinuous morphological variation within or between populations. Questions will be studied using laboratory and field experiments and observations. These include morphometric analyses of changes in size and shape as animals grow, complemented by descriptions of geographic variation in morphology. Breeding experiments will quantify genetic and environmental contributions to morphological variation among populations. Finally, several experiments are designed to provide a means for relating variation in anatomy, diet, and fitness. Collectively, the research projects proposed contribute to our developing understanding of the ecological and evolutionary processes relating variation within species and the origin of novel evolutionary forms.

9317340 Grimm

This proposal is submitted under a special pilot program, Undergraduate Mentorships in Environmental Biology. The four year program will offer undergraduate students first hand experience in carrying out ecological research under the mentorships of six active research ecologists. We will aggressively seek to involve groups traditionally under represented in environmental biology, includi ng trainees of Latino, American Indian, and African American backgrounds as well as a number of non minority students. This effort will be aided considerably by close coordination with existing programs that target these minority groups at ASU. The program is a specialized educational track consisting of an integrative first year seminar, early exposure to advanced courses, research involvement at the outset of students' college careers, and continued follow up and support of individual students as they make plans for graduate school and future careers. Careful documentation of the program's successes and failures, support from other research experience programs targeting more advanced undergraduate students, and placement of students in individual laboratories will facilitate the entry of alumni and alumnae of this program into research careers in environmental biology.

Our legal system often requires decision-making. Judges and legislators must often resolve, address, or intelligently incorporate into policy, scientific issues that are themselves hotly debated by knowledgeable scientists. How can we best adjudicate competing scientific claims consistently with democratic values? An historian/philosopher of science, Jane Maienschein, a lawyer, Daniel Strouse, and a biologist, James Collins, have organized this conference in order to formulate a research agenda on questions of how conflicting scientific claims are resolved in a constitutional democracy. Traditionally, scholars in science studies, law, and political philosophy have lacked a common perspective. They have different conceptions of evidence and different approaches to resolution. Nonetheless, the issues overlap all these disciplines and the scientific. legal, and political communities in which such conflict resolution currently proceeds also overlap. Indeed, legal systems and scientific development seem to be central to establishing and stabilizing democracies. Consequently, we need an interdisciplinary study of the adjudication of competing scientific claims in the context of such democratic systems. This workshop promises to develop a research agenda for such interdisciplinary study by identifying researchable questions, promising approaches, and available opportunities. Experts from law, biology, philosophy, the social and behavioral sciences, and history will gather to be held in Phoenix Arizona March 24 and 25 to develop this research agenda.

Collins 9807967 This workshop will examine the apparent causes of global decline of amphibian populations. Participants will examine declines from endocrinogical, immunological, and environmental perspectives. Participants will represent the United States, Europe, Central America, and Australia. The goal of the workshop will be to determine how research on amphibian decline can be more integrated and provide more generic answers.

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Collins et al.

We propose an IRCEB in host-pathogen biology with a strong problem-solving focus designed to enhance collaboration and encourage pursuit of answers beyond the boundaries of traditional scientific disciplines. Host-pathogen interactions alternately fascinate and frustrate biologists. The fascination stems from the opportunities these systems offer as models for understanding at a basic level the complex mechanisms underlying organismal relationships. The frustration stems from not understanding these interactions sufficiently well to anticipate or react to epidemics or epizootics. Ecologists increasingly acknowledge a role for pathogens in population dynamics and in maintaining diverse communities and ecosystems. We have a poor understanding, however, of how pathogens alter host population dynamics, how pathogens infect hosts in a population, and how host and pathogen populations coevolve.
In many populations, hosts and pathogens coexist and each shows regular increases and decreases in population size. At times, however, a pathogen nearly or completely decimates its host population. We propose testing the basic mechanisms underlying each of these patterns using amphibians as a model system. Most amphibian populations regularly fluctuate in numbers of individuals, but beginning about 1989 herpetologists became alarmed by reports that populations and even species were persistently declining, some to extinction. Extreme population fluctuations and declines are centered on a broad region of the Cordilleras of western North America from southern Saskatchewan south to Costa Rica and northern Panama, and the higher elevations of Australia from southeastern to north Queensland. Four main causes seem to be acting alone, sequentially, or synergistically: habitat destruction, exotic species, disease, and anthropogeneic environmental change due to toxic chemicals, UB radiation, or global climate change. Many regions with declines are conservation areas protected from exotic species and habitat destruction suggesting subtle, complex causes like environmental change or pathogens are at work.
We have assembled an international research team to answer the question: Why are pathogens causing some amphibian populations to decline, even to extinction? The evidence suggests a pathogenic chytrid fungus causes populations to plummet, while another pathogen, an iridovirus causes amphibian populations to fluctuate. The proposed research will address the questions: How do pathogens influence host population dynamics? Are these newly-introduced amphibian pathogens, or has the virulence of historically benign amphibian associates changed? Have recent environmental changes altered amphibian-pathogen interactions? Except for some cases involving humans as hosts (e.g., cholera, malaria), few host-pathogen interactions have been dissected from molecular biology to population dynamics. Our team will do just that to advance basic host-pathogen biology with the goal of applying our findings to one of the most significant global biodiversity problems facing us today: Why are amphibian populations declining?
Metaphorically, the declining amphibian problem is like a prism in reverse: instead of dispersing colors, it focuses research disciplines - ecology, evolution, organismal biology, genetics, pathology, and immunology - so that they no longer appear individually. Understanding the basic mechanisms of host-pathogen interactions is central to our proposal and essential for answering the question of why amphibians are declining. The point of this metaphor is that while a spectrum can be "divided" into its colors, the variation is continuous - "divisions" are artificial and at the origin they disappear. Amphibians are integral parts of ecosystems in ways that place them at this metaphorical core. Therefore, we need a diversity of disciplines and a diversity of investigators willing to collaborate on integrative research projects. The declining amphibian case in an exciting, but unfortunate, opportunity to explore the boundaries of host-pathogen biology, and the time is now to understand why amphibians are declining. The point of our IRCEB research program is to meld diverse disciplinary concepts, methods, and traditions in ways that advance our understanding of pathogens as a factor in amphibian declines, a key example of the general loss of biodiversity.

ABSTRACT

The proposed research investigates how disease emerges in populations of salamanders in Arizona, is transmitted among individuals in populations, spreads across populations in a region, and finally, via natural selection, may alter salamander life history. Three hypotheses will be tested. Within a habitat, animals, soil, or water harbor viruses and environmental changes initiate infections by stimulating pathogen growth or weakening host salamanders. Alternatively, salamanders in a habitat are susceptible and disease is introduced from elsewhere. Experiments and field observations will evaluate the roles of salamanders, invertebrates, cows, birds, or humans as possible reservoirs of disease or vectors dispersing virus. Finally, disease selects against cannibalism, accounting for regional variation in salamander life history.
The virus-vector-tiger salamander system is ideal for testing models in disease ecology. Arizona populations are well-studied, the principal viral pathogen is known, infections are frequent, and all habitats for one endangered subspecies where disease is common can be sampled. In the last fifteen years some species of amphibians have declined steadily, even to extinction, and pathogens are a possible cause. This research will advance our understanding of pathogens as a factor in amphibian declines; a key example of the general loss of biodiversity. Proposed experiments and observations incorporate experts in ecology, evolution, pathology, virology, and molecular genetics. Vertically-integrated field and laboratory experiments will untangle complex interactions from molecular genetics to population biology to test general models of disease ecology.

A program is proposed to provide an multifaceted research and educational experience for undergraduate students in environmental biology. The program will attract freshman and sophomore students to experience environmental biology early in their academic careers. A diverse array of environmental biologists will serve as mentors for these students. Students will gain research experience in project ranging from hormonal control of mating behavior to the biogeochemistry of urban environments. Recruiting and retention efforts for this program will be focused on groups that are generally under represented in environmental biology. Participants are expected to include a mixture of Latino, American-Indian, and African-American students. The program will involve careful mentoring not only of students by faculty but by younger students by older students. Careful documentation of student participants will be used to assess and modify the program as a permanent university feature.

Frogs and salamanders are key contributors to many ecosystem functions. It is a concern, therefore, that amphibian species are declining worldwide, some to extinction. Among the suspected causes of amphibian declines is the emergence of infectious diseases. The proposed research will answer a series of questions designed to test how extinction, disease, and environmental change are linked. Do novel, highly virulent pathogens increase the chance of extinction? Does the health of the host change the risk of infection? Are there environmental conditions that increase the likelihood animals become ill? Why do emerging diseases drive some populations or species to extinction but not others? An international team of molecular biologists, immunologists, pathologists, population ecologists, and epidemiologists will use experiments and observations in the field and laboratory to answer these and related questions.

The number of species on Earth is diminishing, and these losses affect the capacity of ecosystems to deliver the goods and services required to sustain life. Infectious diseases are likely responsible for species losses in some ecosystems, but relatively little is known about how pathogens increase the risk of extinction. From time to time the decline of a key species, for example the American eagle, signals a degrading environment that also threatens many other organisms. It is important to understand how infectious diseases and amphibian declines are linked if we are to ensure a high quality environment for our generation and those that follow.

A grant has been awarded to Arizona State University under the direction of Dr. Thomas Dowling for the acquisition of a 48-capillary DNA sequencer/genetic analyzer, and an HPLC genotyping and DNA fragment purification system. This instrumentation is essential for efficient completion of the diversity of projects being conducted at ASU, including molecular, evolutionary, ecological, genomic, and bioinformatic studies. Acquisition of this equipment is necessary to handle both increasing demands (number of samples) by existing and new faculty, and will permit investigators to address questions not currently approachable with the existing systems. Research areas that will utilize the instrumentation include: (1) molecular genetics and the evolution of photosynthesis, (2) molecular systematics and evolution of a diversity of organisms (e.g., bacteria, fungi, plants, animals), (3) genetics and management of endangered species, (4) introgressive hybridization and evolutionary genomics, and (5) population biology. The equipment will become part of the DNA sequencing facility at the university. This facility provides support to several educational programs, such as the NSF REU and UMEB programs, which introduce students of diverse backgrounds to careers in science. Central to training these students is exposure to the newest techniques that allow us to obtain previously unobtainable answers. Therefore, addition of this equipment will allow us to better serve the undergraduates and graduates working in our laboratories by exposing them to state of the art technology and techniques.

Pathogens play an important role in the health, welfare, and survival of wildlife, agricultural, and human populations. Only recently, however, has it become evident how quickly pathogens can change, rapidly developing drug resistance, adapting to new hosts, and becoming more (and less) virulent. These changes may be predictable. By understanding how traits beneficial to a pathogen (e.g., reproduction and transmission) are linked to potentially costly traits (like harming one's host), we may be able to explain how pathogens change under certain ecological conditions. The proposed research will first examine the relationship between replication, transmission, and virulence, using a lethal virus of salamanders as a model system. Then, using these relationships among traits, it will assess how this virus changes its level of virulence under conditions favoring or inhibiting transmission. Understanding how and why virulence changes over time can make epidemics predictable, and potentially more easily controlled.

The 1-year UMEB renewal will support four current students for their second year of research. The students are currently engaged in active research programs in laboratories with an emphasis on environmental biology, including molecular systematics of endangered species, community ecology, environmental physiology, and insect behavior. We will continue active monitoring of their progress and mentoring experiences. In addition to their research activities, the students will participate in a seminar series that will expose them to career opportunities and ethical issues in environmental science, and will participate in short field trips. During their final semester, they will complete their projects, analyse data, and write up their results for publication and presentation at a scientific meeting. Assessment tools will be used to determine the extent of their understanding of the scientific method, critical thinking, and development of self confidence. The students will then have the opportunity to move on to other research opportunities within the University.

Ecological research and biodiversity management often raise ethical questions in areas that include responsibilities and duties to the scientific community, public welfare, individual research animals, species, and even ecosystems. Value-laden questions cross multiple ethical domains from traditional (human) ethical theory and research ethics, to animal and environmental ethics. Answering these ethical questions is challenging because ecologists and biodiversity managers do not have the equivalent of bioethics, which is an established field with a support network focused mainly on biomedicine, to guide them in making decisions. Environmental ethics provides some insight into environmental values and the duties these may impose upon human agents. But for the most part the field does not engage many of the common responsibilities and obligations ecologists and managers have to the scientific profession or to public welfare. We propose to bring ethicists, scientists, and biodiversity managers together in a collaborative effort to study and inform the methods of ethical analysis and problem solving in ecological research and biodiversity management. The results of this project will be a new case literature, preliminary ethical framework, and research agenda for a novel field within professional ethics devoted to exploring the ethical problems and questions faced by ecological researchers and biodiversity managers, what we call "ecological ethics." The various domains of theoretical and applied ethics are frequently separated as fields of study. Our project integrates these areas to identify principles that will be grouped in an ethical framework so that ecologists and biodiversity managers can identify relevant moral considerations raised by their research and management activities. Ethical theory has not penetrated ecological research in a significant manner, and the often distinctive, practical issues raised by ecological researchers have, up to now, not informed ethical scholarship as well as they might. Our project will begin with analysis of concrete ethical challenges faced by ecological researchers and biodiversity managers. We turn to ethical theory and traditions of applied ethics for clarification and insight into the specific moral problems presented in eight cases in five general issue areas of ecological research and biodiversity management. These cases will then be analyzed in stage two of our project to begin the creation of an integrative ethical framework which will help managers and scientists identify and clarify the diverse, multi-level ethical questions and issues encountered in biodiversity management and in field and laboratory experiments in ecology. The project will begin to provide ecologists and biodiversity managers with materials upon which they can reflect on the ethical dimensions of their work with the goal of creating a structure for addressing ethical problems.

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.

The element iron plays a key role in the cellular chemistry of nearly all life forms. Surprisingly, while iron is the fourth most abundant element on Earth, it often limits growth and reproduction of organisms because it is insoluble in water. Parasites face a special challenge in acquiring iron because hosts actively sequester it. To obtain iron, therefore, parasites must take it from host tissues by overcoming an array of host defenses. Changes in host iron levels alter the dynamics of this struggle; for example, there is a tendency for elevated host iron concentration to cause increased parasite virulence across a variety of infectious diseases, including human diseases. To understand iron?s role in the dynamics of an emerging amphibian disease, chytridiomycosis, the proposed study will test experimentally the biological effects of host iron bioaccumulation on the likelihood of acquiring and spreading an infectious disease. The project is a novel analysis of a potentially broad mechanism influencing the spread of disease in populations of diverse organisms.

Results from this research could explain the recent emergence of a suite of wildlife diseases, if iron is, as suggested, increasing in aquatic and terrestrial ecosystems globally. Throughout the study non-scientists will participate in research and the process of discovery. Researchers will engage elementary school students and adults through innovative, university-sponsored outreach programs such as: "Ask a Biologist", a question and answer resource for K-12 students and teachers; "Graduate Partners in Science Education", an after school science program for 7th and 8th graders; and "SHADES", a mentoring program for underrepresented minorities seeking a degree in science, technology, engineering, or math). These activities will engage the public in scientific inquiry and enrich public education, fostering an appreciation of science and conservation.

This is a proposal for a multi-faceted STS study by an interdisciplinary research team to explore the conservation mission of zoos and aquariums focusing on the evolution of the shifting responsibilities of these institutions to animals and to conservation. The team will engage in an ambitious and integrated program of research, conferences, public events, and the development of teaching materials focused on the complex, contested, and changing roles of zoos and aquaria in society.

There is a dual emphasis on engaging the scientific/professional community and the general public, which not only enables the integration of diverse viewpoints, but also serves as a mechanism for increasing public awareness of the goals, tactics, and challenges of zoo conservation. With regards to the public component, the researchers plan to have a broad impact in two distinct ways; the events will take place in different geographic regions (Arizona, New York), and there will be a virtual public exhibit that will be accessible worldwide.

In 1990, the American Association for the Advancement of Science (AAAS) published the groundbreaking document, "The Liberal Art of Science," which recommended that all college students should take more science courses. This book and associated program argued that science pervades all aspects of contemporary human existence and that our nation?s future economy and security and the quality of individual lives depend on the public?s understanding of scientific developments. The importance of science for all remains true today. Since 1990, however, the science and science education communities have made significant discoveries about how students learn, how to engage a broader spectrum of students in science, what are effective pedagogical methods to teach science, and what scientifically literate citizens and future scientists should know and be able to do. In 1990, many Americans were noted to have little understanding of science or how it affected their lives, and many students, especially from underrepresented groups, had limited access to or incentives to pursue science as a degree or career. These major issues still hold true in 2018. Thus, the revision of ?The Liberal Art of Science? is an important and timely endeavor, capitalizing on recent breakthroughs while addressing continuing problems. The workshop will bring together scientists and science educators to outline and begin writing an updated ?Liberal Art of Science? and to plan for the widespread implementation of contemporary recommendations for teaching and learning science by improving existing science courses and not simply trying to add more courses to a student?s already crowded curriculum. Workshop participants will have diverse research interests in science, science education, faculty professional development, and science literacy. They will also represent major scientific and science education organizations and institutional associations actively engaged in professional development of their members.

Participants at the workshop will have significant obligations before attending the meeting at the headquarters of the AAAS in Washington, D.C. Each person will be asked either to draft an outline of a chapter in the new book or prepare a presentation for the workshop itself based on their interests and expertise. In addition, each person will identify one or two exemplary individuals or programs that use active learning methods, increase scientific literacy of students, or focus on learning outcomes that prepare students for a world that is increasingly influenced by science and technology. The workshop, which will extend over parts of three days, will be a series of presentations, discussions, and small working groups and will result in an outline of the entire new document and a plan to disseminate and implement new recommendations for change.

This project is being jointly funded by the Directorate for Biological Sciences, Division of Biological Infrastructure, and the Directorate for Education and Human Resources, Division of Undergraduate Education.

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.