On the Origin of the Living State

abstract: 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...

Full description

Bibliographic Details
Other Authors: Mathis, Nicholas (Author)
Format: Doctoral Thesis
Language:English
Published: 2018
Subjects:
Online Access:http://hdl.handle.net/2286/R.I.50446
id ndltd-asu.edu-item-50446
record_format oai_dc
spelling ndltd-asu.edu-item-504462018-10-02T03:01:04Z On the Origin of the Living State abstract: 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. Dissertation/Thesis Mathis, Nicholas (Author) Walker, Sara I (Advisor) Davies, Paul CW (Committee member) Chamberlin, Ralph V (Committee member) Lachmann, Michael (Committee member) Arizona State University (Publisher) Physics Computational physics Biology Astrobiology Complex Systems Origin Of Life Prebiotic Chemistry Systems Chemistry eng 127 pages Doctoral Dissertation Physics 2018 Doctoral Dissertation http://hdl.handle.net/2286/R.I.50446 http://rightsstatements.org/vocab/InC/1.0/ 2018
collection NDLTD
language English
format Doctoral Thesis
sources NDLTD
topic Physics
Computational physics
Biology
Astrobiology
Complex Systems
Origin Of Life
Prebiotic Chemistry
Systems Chemistry
spellingShingle Physics
Computational physics
Biology
Astrobiology
Complex Systems
Origin Of Life
Prebiotic Chemistry
Systems Chemistry
On the Origin of the Living State
description abstract: 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. === Dissertation/Thesis === Doctoral Dissertation Physics 2018
author2 Mathis, Nicholas (Author)
author_facet Mathis, Nicholas (Author)
title On the Origin of the Living State
title_short On the Origin of the Living State
title_full On the Origin of the Living State
title_fullStr On the Origin of the Living State
title_full_unstemmed On the Origin of the Living State
title_sort on the origin of the living state
publishDate 2018
url http://hdl.handle.net/2286/R.I.50446
_version_ 1718756989639589888