Matching Items (994)
Description
What makes living systems different than non-living ones? Unfortunately this question is impossible to answer, at least currently. Instead, we must face computationally tangible questions based on our current understanding of physics, computation, information, and biology. Yet we have few insights into how living systems might quantifiably differ from their non-living counterparts, as in a mathematical foundation to explain away our observations of biological evolution, emergence, innovation, and organization. The development of a theory of living systems, if at all possible, demands a mathematical understanding of how data generated by complex biological systems changes over time. In addition, this theory ought to be broad enough as to not be constrained to an Earth-based biochemistry. In this dissertation, the philosophy of studying living systems from the perspective of traditional physics is first explored as a motivating discussion for subsequent research. Traditionally, we have often thought of the physical world from a bottom-up approach: things happening on a smaller scale aggregate into things happening on a larger scale. In addition, the laws of physics are generally considered static over time. Research suggests that biological evolution may follow dynamic laws that (at least in part) change as a function of the state of the system. Of the three featured research projects, cellular automata (CA) are used as a model to study certain aspects of living systems in two of them. These aspects include self-reference, open-ended evolution, local physical universality, subjectivity, and information processing. Open-ended evolution and local physical universality are attributed to the vast amount of innovation observed throughout biological evolution. Biological systems may distinguish themselves in terms of information processing and storage, not outside the theory of computation. The final research project concretely explores real-world phenomenon by means of mapping dominance hierarchies in the evolution of video game strategies. Though the main question of how life differs from non-life remains unanswered, the mechanisms behind open-ended evolution and physical universality are revealed.
ContributorsAdams, Alyssa M (Author) / Walker, Sara I (Thesis advisor) / Davies, Paul CW (Committee member) / Pavlic, Theodore P (Committee member) / Chamberlin, Ralph V (Committee member) / Arizona State University (Publisher)
Created2017
Description
The origin of Life on Earth is the greatest unsolved mystery in the history of science. In spite of progress in almost every scientific endeavor, we still have no clear theory, model, or framework to understand the processes that led to the emergence of life on Earth. Understanding such a processes would provide key insights into astrobiology, planetary science, geochemistry, evolutionary biology, physics, and philosophy. To date, most research on the origin of life has focused on characterizing and synthesizing the molecular building blocks of living systems. This bottom-up approach assumes that living systems are characterized by their component parts, however many of the essential features of life are system level properties which only manifest in the collective behavior of many components. In order to make progress towards solving the origin of life new modeling techniques are needed. In this dissertation I review historical approaches to modeling the origin of life. I proceed to elaborate on new approaches to understanding biology that are derived from statistical physics and prioritize the collective properties of living systems rather than the component parts. In order to study these collective properties of living systems, I develop computational models of chemical systems. Using these computational models I characterize several system level processes which have important implications for understanding the origin of life on Earth. First, I investigate a model of molecular replicators and demonstrate the existence of a phase transition which occurs dynamically in replicating systems. I characterize the properties of the phase transition and argue that living systems can be understood as a non-equilibrium state of matter with unique dynamical properties. Then I develop a model of molecular assembly based on a ribonucleic acid (RNA) system, which has been characterized in laboratory experiments. Using this model I demonstrate how the energetic properties of hydrogen bonding dictate the population level dynamics of that RNA system. Finally I return to a model of replication in which replicators are strongly coupled to their environment. I demonstrate that this dynamic coupling results in qualitatively different evolutionary dynamics than those expected in static environments. A key difference is that when environmental coupling is included, evolutionary processes do not select a single replicating species but rather a dynamically stable community which consists of many species. Finally, I conclude with a discussion of how these computational models can inform future research on the origins of life.
ContributorsMathis, Cole (Nicholas) (Author) / Walker, Sara I (Thesis advisor) / Davies, Paul CW (Committee member) / Chamberlin, Ralph V (Committee member) / Lachmann, Michael (Committee member) / Arizona State University (Publisher)
Created2018
Description
Biochemical reactions underlie all living processes. Their complex web of interactions is difficult to fully capture and quantify with simple mathematical objects. Applying network science to biology has advanced our understanding of the metabolisms of individual organisms and the organization of ecosystems, but has scarcely been applied to life at a planetary scale. To characterize planetary-scale biochemistry, I constructed biochemical networks using global databases of annotated genomes and metagenomes, and biochemical reactions. I uncover scaling laws governing biochemical diversity and network structure shared across levels of organization from individuals to ecosystems, to the biosphere as a whole. Comparing real biochemical reaction networks to random reaction networks reveals the observed biological scaling is not a product of chemistry alone, but instead emerges due to the particular structure of selected reactions commonly participating in living processes. I perform distinguishability tests across properties of individual and ecosystem-level biochemical networks to determine whether or not they share common structure, indicative of common generative mechanisms across levels. My results indicate there is no sharp transition in the organization of biochemistry across distinct levels of the biological hierarchy—a result that holds across different network projections.
Finally, I leverage these large biochemical datasets, in conjunction with planetary observations and computational tools, to provide a methodological foundation for the quantitative assessment of biology’s viability amongst other geospheres. Investigating a case study of alkaliphilic prokaryotes in the context of Enceladus, I find that the chemical compounds observed on Enceladus thus far would be insufficient to allow even these extremophiles to produce the compounds necessary to sustain a viable metabolism. The environmental precursors required by these organisms provides a reference for the compounds which should be prioritized for detection in future planetary exploration missions. The results of this framework have further consequences in the context of planetary protection, and hint that forward contamination may prove infeasible without meticulous intent. Taken together these results point to a deeper level of organization in biochemical networks than what has been understood so far, and suggests the existence of common organizing principles operating across different levels of biology and planetary chemistry.
Finally, I leverage these large biochemical datasets, in conjunction with planetary observations and computational tools, to provide a methodological foundation for the quantitative assessment of biology’s viability amongst other geospheres. Investigating a case study of alkaliphilic prokaryotes in the context of Enceladus, I find that the chemical compounds observed on Enceladus thus far would be insufficient to allow even these extremophiles to produce the compounds necessary to sustain a viable metabolism. The environmental precursors required by these organisms provides a reference for the compounds which should be prioritized for detection in future planetary exploration missions. The results of this framework have further consequences in the context of planetary protection, and hint that forward contamination may prove infeasible without meticulous intent. Taken together these results point to a deeper level of organization in biochemical networks than what has been understood so far, and suggests the existence of common organizing principles operating across different levels of biology and planetary chemistry.
ContributorsSmith, Harrison Brodsky (Author) / Walker, Sara I (Thesis advisor) / Anbar, Ariel D (Committee member) / Line, Michael R (Committee member) / Okie, Jordan G. (Committee member) / Romaniello, Stephen J. (Committee member) / Arizona State University (Publisher)
Created2018
Description
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.
ContributorsAiello, Kenneth (Author) / Laubichler, Manfred D (Thesis advisor) / Simeone, Michael (Committee member) / Buetow, Kenneth (Committee member) / Walker, Sara I (Committee member) / Arizona State University (Publisher)
Created2018
Description
This theoretical inquiry is a response to the apparent need for resources on providing music therapy for LGBTQ adolescents, a population facing systematic oppression in their respective homes and communities. Since there are no published research studies on actual clinical work with this population, I investigated the literature of queer theory, an interdisciplinary field that destabilizes sexual categories and challenges the concept of normal and fixed identities, and applied its theoretical concepts to develop music therapy interventions. I was especially influenced by the ideas of foundational queer theorists Michel Foucault, Eve Sedgwick, and Judith Butler, among others. Their perspectives can advance how music therapists currently approach working with this population and interpret music therapy experiences with LGBTQ clients. The theoretical insights of these fields can be applied to impact the LGBTQ movement for social justice by empowering queer youth using music within a therapeutic environment. This interdisciplinary project incorporates queer theory with music therapy theory to develop evidence-based interventions and open up new perspectives in music therapy practice with LGBTQ clients.
ContributorsBain, Candice Lanell (Author) / Crowe, Barbara (Thesis director) / Grzanka, Patrick (Committee member) / Barrett, The Honors College (Contributor) / School of Music (Contributor) / Department of Psychology (Contributor)
Created2014-12
Description
"Trauma transmission" in Holocaust Studies represents a cross-disciplinary method of studying history that focuses on how particular events impact individuals rather than on the events themselves. It refers to the transfer of trauma or its symptoms from Holocaust survivors to children of survivors (COS). In this project, I explore "echoes of trauma," such as an obsession with food or inability to show emotion, in Holocaust survivors and COS that they directly attribute to Holocaust experiences
ContributorsCohen, Tania Frances (Author) / Ingram-Waters, Mary (Thesis director) / Grzanka, Patrick (Committee member) / Barrett, The Honors College (Contributor) / School of International Letters and Cultures (Contributor) / School of Politics and Global Studies (Contributor) / School of Historical, Philosophical and Religious Studies (Contributor)
Created2015-05
Description
Studies in neocortical neurogenesis have experienced an explosive growth since the early 2000s, measured by the increasing number of publications each year. I examine here the influence of Arnold Kriegstein in the field using Topic Modeling, a set of algorithms that can be applied to a collection of texts to elucidate the central themes of said collection. Using a Java-based software called MALLET, I obtained data for his corpus, and compared it to the texts of other researchers in the field. This latter collection, which I dub "General Corpus", was separated by year from 2000 to 2014. I found that Kriegstein's most frequently discussed topic concerned highly unique terms such as GABA, glutamate, and receptor, which did not appear in any of the primary topics of the General Corpus. This was in contrast to my initial hypothesis that Kriegstein's importance stemmed from his examination of different phenomena that constitute the broader aspect of neocortical neurogenesis. I predicted that the terms in Kriegstein's primary topic would appear many times throughout the topics of the General Corpus, but it was not so, aside from the common ones such as neurons, cortical, and development. Taken in tandem with NIH Reporter data, these results suggest that Kriegstein obtains a large amount of research funding because his studies concern unique topics when compared to others in the field. The implications of these findings are especially relevant in a world where funding is becoming increasingly difficult to come by.
ContributorsChhetri, Chandra Divyash (Author) / Laubichler, Manfred (Thesis director) / Maienschein, Jane (Committee member) / Aiello, Kenneth (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
The Undoing Project is an ongoing educational feminist YouTube channel that serves as an introduction to feminism and feminist theory. The objective for this project is to present feminist theory and feminist ideology in an accessible and entertaining way. Through this project I sought to accomplish three goals: to challenge the negative image of feminism, bridge the gap between the language of academia and the public, and to acknowledge and unlearn ingrained prejudices. The videos focus on theory, history, legislation, current events, and pop culture. The initial project consists of ten videos addressing the feminist wave models, a brief history of the feminist movement, and discussions of concepts like hegemony, intersectionality, masculinity, femininity, and race.
ContributorsBuchholtz, Kaylee Marie (Author) / Brian, Jennifer (Thesis director) / Grzanka, Patrick (Committee member) / Brouwer, Dan (Committee member) / Barrett, The Honors College (Contributor) / College of Public Service and Community Solutions (Contributor) / School of Social Transformation (Contributor) / Department of English (Contributor)
Created2015-05
Description
With the new independence of adulthood, college students are a group susceptible to adopting unsupported, if not harmful, health practices. A survey of Arizona State University undergraduate students (N=200) was conducted to evaluate supplement use, trust in information sources, and beliefs about supplement regulation. Of those who reported using supplements, college students most frequently received information from friends and family. STEM majors in fields unrelated to health who were taking a supplement were found to be less likely to receive information about the supplement from a medical practitioner than those in health fields or those in non-STEM majors (-26.9%, p=0.018). STEM majors in health-related fields were 15.0% more likely to treat colds and/or cold symptoms with research-supported methods identified from reliable sources, while non-health STEM and non-STEM majors were more likely to take unsupported cold treatments (p=0.010). Surveyed students, regardless of major, also stated they would trust a medical practitioner for supplement advice above other sources (88.0%), and the majority expressed a belief that dietary supplements are approved/regulated by the government (59.8%).
ContributorsPerez, Jacob Tanner (Author) / Hendrickson, Kirstin (Thesis director) / Lefler, Scott (Committee member) / College of Liberal Arts and Sciences (Contributor) / School of Molecular Sciences (Contributor) / Department of Physics (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Recent research on alcohol use among LGB young adults indicates that sexual minority youth are at increased risk relative to their heterosexual peers. One possible contributing factor is that religiosity fails to provide the significant protection for LGB youth that it has been demonstrated to provide in general population samples. Although recent studies provide some support for this hypothesis, there is little research seeking to understand the reasons that religiosity may fail to protect against heavy drinking among LGB youth. The current study attempted to address this gap by examining relations among religiosity, age of self-identification, and alcohol use in a sample of 103 young adults self identified as lesbian, gay, or bisexual. Using multiple regression, we found that religiosity had an indirect effect on alcohol use operating through age of identification as LGB. Higher religiosity was associated with a later age of self-identification, which in turn, predicted greater increases in alcohol use among LGB youth during the transition from high school through college. Exploratory analyses found that gender significantly moderated the influence of age of self-identification on alcohol use such that a later age of self-identification was a risk factor for increased drinking for women, but not for men. The findings have important implications for understanding complex relations between religiosity and alcohol use among LGB youth. In addition, the findings may inform the development of religious support groups for LGB youth that will allow them to experience the benefits of religious involvement that heterosexual youth experience.
ContributorsOng, Thai Quang (Author) / Corbin, William (Thesis director) / Glenberg, Arthur (Committee member) / Grzanka, Patrick (Committee member) / Barrett, The Honors College (Contributor) / T. Denny Sanford School of Social and Family Dynamics (Contributor) / Department of Psychology (Contributor)
Created2013-12