This dissertation focuses on creating a pluralistic approach to understanding and measuring interdisciplinarity at various scales to further the study of the evolution of knowledge and innovation. Interdisciplinarity is considered an important research component and is closely linked to higher rates of innovation. If the goal is to create more innovative research, we must understand how interdisciplinarity operates.

I begin by examining interdisciplinarity with a small scope, the research university. This study uses metadata to create co-authorship networks and examine how a change in university policies to increase interdisciplinarity can be successful. The New American University Initiative (NAUI) at Arizona State University (ASU) set forth the goal of making ASU a world hub for interdisciplinary research. This kind of interdisciplinarity is produced from a deliberate, engineered, reorganization of the individuals within the university and the knowledge they contain. By using a set of social network analysis measurements, I created an algorithm to measure the changes to the co-authorship networks that resulted from increased university support for interdisciplinary research.

The second case study increases the scope of interdisciplinarity from individual universities to a single scientific discourse, the Anthropocene. The idea of the Anthropocene began as an idea about the need for a new geological epoch and underwent unsupervised interdisciplinary expansion due to climate change integrating itself into the core of the discourse. In contrast to the NAUI which was specifically engineered to increase interdisciplinarity, the I use keyword co-occurrence networks to measure how the Anthropocene discourse increases its interdisciplinarity through unsupervised expansion after climate change becomes a core keyword within the network and behaves as an anchor point for new disciplines to connect and join the discourse.

The scope of interdisciplinarity increases again with the final case study about the field of evolutionary medicine. Evolutionary medicine is a case of engineered interdisciplinary integration between evolutionary biology and medicine. The primary goal of evolutionary medicine is to better understand "why we get sick" through the lens of evolutionary biology. This makes it an excellent candidate to understand large-scale interdisciplinarity. I show through multiple type of networks and metadata analyses that evolutionary medicine successfully integrates the concepts of evolutionary biology into medicine.

By increasing our knowledge of interdisciplinarity at various scales and how it behaves in different initial conditions, we are better able to understand the elusive nature of innovation. Interdisciplinary can mean different things depending on how its defined. I show that a pluralistic approach to defining and measuring interdisciplinarity is not only appropriate but necessary if our goal is to increase interdisciplinarity, the frequency of innovations, and our understanding of the evolution of knowledge.

This research investigates the biophysical and institutional mechanisms affecting the distribution of metals in the Sonoran Desert of Arizona. To date, a long-term, interdisciplinary perspective on metal pollution in the region has been lacking. To address this gap, I integrated approaches from environmental chemistry, historical geography, and institutional economics to study the history of metal pollution in the desert. First, by analyzing the chemistry embodied in the sequentially-grown spines of long-lived cacti, I created a record of metal pollution that details biogeochemical trends in the desert since the 1980s. These data suggest that metal pollution is not simply a legacy of early industrialization. Instead, I found evidence of recent metal pollution in both the heart of the city and a remote, rural location. To understand how changing land uses may have contributed to this, I next explored the historical geography of industrialization in the desert. After identifying cities and mining districts as hot spots for airborne metals, I used a mixture of historical reports, maps, and memoirs to reconstruct the industrial history of these polluted landscapes. In the process, I identified three key transitions in the energy-metal nexus that drove the redistribution of metals from mineral deposits to urban communities. These transitions coincided with the Columbian exchange, the arrival of the railroads, and the economic restructuring that accompanied World War II. Finally, to determine how legal and political forces may be influencing the fate of metals, I studied the evolution of the rights and duties affecting metals in their various forms. This allowed me to track changes in the institutions regulating metals from the mining laws of the 19th century through their treatment as occupational and public health hazards in the 20th century. In the process, I show how Arizona’s environmental and resource institutions were often transformed by extra-territorial concerns. Ultimately, this created an institutional system that compartmentalizes metals and fails to appreciate their capacity to mobilize across legal and biophysical boundaries to accumulate in the environment. Long-term, interdisciplinary perspectives such as this are critical for untangling the complex web of elements and social relations transforming the modern world.

Understanding changes and trends in biomedical knowledge is crucial for individuals, groups, and institutions as biomedicine improves people’s lives, supports national economies, and facilitates innovation. However, as knowledge changes what evidence illustrates knowledge changes? In the case of microbiome, a multi-dimensional concept from biomedicine, there are significant increases in publications, citations, funding, collaborations, and other explanatory variables or contextual factors. What is observed in the microbiome, or any historical evolution of a scientific field or scientific knowledge, is that these changes are related to changes in knowledge, but what is not understood is how to measure and track changes in knowledge. This investigation highlights how contextual factors from the language and social context of the microbiome are related to changes in the usage, meaning, and scientific knowledge on the microbiome. Two interconnected studies integrating qualitative and quantitative evidence examine the variation and change of the microbiome evidence are presented. First, the concepts microbiome, metagenome, and metabolome are compared to determine the boundaries of the microbiome concept in relation to other concepts where the conceptual boundaries have been cited as overlapping. A collection of publications for each concept or corpus is presented, with a focus on how to create, collect, curate, and analyze large data collections. This study concludes with suggestions on how to analyze biomedical concepts using a hybrid approach that combines results from the larger language context and individual words. Second, the results of a systematic review that describes the variation and change of microbiome research, funding, and knowledge are examined. A corpus of approximately 28,000 articles on the microbiome are characterized, and a spectrum of microbiome interpretations are suggested based on differences related to context. The collective results suggest the microbiome is a separate concept from the metagenome and metabolome, and the variation and change to the microbiome concept was influenced by contextual factors. These results provide insight into how concepts with extensive resources behave within biomedicine and suggest the microbiome is possibly representative of conceptual change or a preview of new dynamics within science that are expected in the future.

A central task for historians and philosophers of science is to characterize and analyze the epistemic practices in a given science. The epistemic practice of a science includes its explanatory goals as well as the methods used to achieve these goals. This dissertation addresses the epistemic practices in gene expression research spanning the mid-twentieth century to the twenty-first century. The critical evaluation of the standard historical narratives of the molecular life sciences clarifies certain philosophical problems with respect to reduction, emergence, and representation, and offers new ways with which to think about the development of scientific research and the nature of scientific change.

The first chapter revisits some of the key experiments that contributed to the development of the repression model of genetic regulation in the lac operon and concludes that the early research on gene expression and genetic regulation depict an iterative and integrative process, which was neither reductionist nor holist. In doing so, it challenges a common application of a conceptual framework in the history of biology and offers an alternative framework. The second chapter argues that the concept of emergence in the history and philosophy of biology is too ambiguous to account for the current research in post-genomic molecular biology and it is often erroneously used to argue against some reductionist theses. The third chapter investigates the use of network representations of gene expression in developmental evolution research and takes up some of the conceptual and methodological problems it has generated. The concluding comments present potential avenues for future research arising from each substantial chapter.

In sum, this dissertation argues that the epistemic practices of gene expression research are an iterative and integrative process, which produces theoretical representations of the complex interactions in gene expression as networks. Moreover, conceptualizing these interactions as networks constrains empirical research strategies by the limited number of ways in which gene expression can be controlled through general rules of network interactions. Making these strategies explicit helps to clarify how they can explain the dynamic and adaptive features of genomes.

How fast is evolution? In this dissertation I document a profound change that occurred around the middle of the 20th century in the way that ecologists conceptualized the temporal and spatial scales of adaptive evolution, through the lens of British plant ecologist Anthony David Bradshaw (1926–2008). In the early 1960s, one prominent ecologist distinguished what he called “ecological time”—around ten generations—from “evolutionary time”— around half of a million years. For most ecologists working in the first half of the 20th century, evolution by natural selection was indeed a slow and plodding process, tangible in its products but not in its processes, and inconsequential for explaining most ecological phenomena. During the 1960s, however, many ecologists began to see evolution as potentially rapid and observable. Natural selection moved from the distant past—a remote explanans for both extant biological diversity and paleontological phenomena—to a measurable, quantifiable mechanism molding populations in real time.

The idea that adaptive evolution could be rapid and highly localized was a significant enabling condition for the emergence of ecological genetics in the second half of the 20th century. Most of what historians know about that conceptual shift and the rise of ecological genetics centers on the work of Oxford zoologist E. B. Ford and his students on polymorphism in Lepidotera, especially industrial melanism in Biston betularia. I argue that ecological genetics in Britain was not the brainchild of an infamous patriarch (Ford), but rather the outgrowth of a long tradition of pastureland research at plant breeding stations in Scotland and Wales, part of a discipline known as “genecology” or “experimental taxonomy.” Bradshaw’s investigative activities between 1948 and 1968 were an outgrowth of the specific brand of plant genecology practiced at the Welsh and Scottish Plant Breeding stations. Bradshaw generated evidence that plant populations with negligible reproductive isolation—separated by just a few meters—could diverge and adapt to contrasting environmental conditions in just a few generations. In Bradshaw’s research one can observe the crystallization of a new concept of rapid adaptive evolution, and the methodological and conceptual transformation of genecology into ecological genetics.

This dissertation shows that the central conceptual feature and explanatory motivation of theories of evolutionary directionality between 1890 and 1926 was as follows: morphological variation in the developing organism limits the possible outcomes of evolution in definite directions. Put broadly, these theories maintained a conceptual connection between development and evolution as inextricably associated phenomena. This project develops three case studies. The first addresses the Swiss-German zoologist Theodor Eimer's book Organic Evolution (1890), which sought to undermine the work of noted evolutionist August Weismann. Second, the American paleontologist Edward Drinker Cope's Primary Factors (1896) developed a sophisticated system of inheritance that included the material of heredity and the energy needed to induce and modify ontogenetic phenomena. Third, the Russian biogeographer Leo Berg's Nomogenesis (1926) argued that the biological world is deeply structured in a way that prevents changes to morphology taking place in more than one or a few directions. These authors based their ideas on extensive empirical evidence of long-term evolutionary trajectories. They also sought to synthesize knowledge from a wide range of studies and proposed causes of evolution and development within a unified causal framework based on laws of evolution. While being mindful of the variation between these three theories, this project advances "Definitely Directed Evolution" as a term to designate these shared features. The conceptual coherence and reception of these theories shows that Definitely Directed Evolution from 1890 to 1926 is an important piece in reconstructing the wider history of theories of evolutionary directionality.