Historical contingency and the gradual evolution of metabolic properties in central carbon and genome-scale metabolisms

BACKGROUND A metabolism can evolve through changes in its biochemical reactions that are caused by processes such as horizontal gene transfer and gene deletion. While such changes need to preserve an organism's viability in its environment, they can modify other important properties, such as a metabolism's maximal biomass synthesis rate and its robustness to genetic and environmental change. Whether such properties can be modulated in evolution depends on whether all or most viable metabolisms - those that can synthesize all essential biomass precursors - are connected in a space of all possible metabolisms. Connectedness means that any two viable metabolisms can be converted into one another through a sequence of single reaction changes that leave viability intact. If the set of viable metabolisms is disconnected and highly fragmented, then historical contingency becomes important and restricts the alteration of metabolic properties, as well as the number of novel metabolic phenotypes accessible in evolution. RESULTS We here computationally explore two vast spaces of possible metabolisms to ask whether viable metabolisms are connected. We find that for all but the simplest metabolisms, most viable metabolisms can be transformed into one another by single viability-preserving reaction changes. Where this is not the case, alternative essential metabolic pathways consisting of multiple reactions are responsible, but such pathways are not common. CONCLUSIONS Metabolism is thus highly evolvable, in the sense that its properties could be fine-tuned by successively altering individual reactions. Historical contingency does not strongly restrict the origin of novel metabolic phenotypes

Knowledge and knowers of the past: A study in the philosophy of evolutionary biology.

This dissertation proposes an exploration of a variety of themes in philosophy of science through the lens of a case study in evolutionary biology. It draws from a careful analysis and comparison of the hypotheses from Bill Martin and Tom Cavalier-Smith. These two scientists produced contrasted and competing accounts for one of the main events in the history of life, the origin of eukaryotic cells. This case study feeds four main philosophical themes around which this dissertation is articulated. (1) Theorizing: What kind of theory are hypotheses about unique events in the past? (2) Representation: How do hypotheses about the past represent their target? (3) Evidential claims: What kind of evidence is employed and how do they constrain these hypotheses? (4) Pluralism: What are the benefits and the risks associated with the coexistence of rival hypotheses? This work both seeks to rearticulate traditional debates in philosophy of science in the light of a lesser-known case of scientific practice and to enrich the catalogue of existing case studies in the philosophy of historical sciences

How genetic, social, and evolutionary interactions shape the many levels of biological complexity

Tesis Doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología Molecular. Fecha de lectura: 14-11-2017Esta tesis tiene embargado el acceso al texto completo hasta el 14-05-2019Interactions between genes, between social individuals, and between the results of alternative evolutionary histories reflect the organization and context-dependent properties of each respective level of biological complexity. Genetic interactions modify the combined effect of two genes on the characteristics of an organism. Social interactions develop when some individuals of a population contribute to a common resource at a personal cost. Evolutionary interactions result when adaptation to a particular environment changes survival in unrelated conditions. We studied these three types of interactions with a combination of computational and experimental approaches using microbes. First, we evaluate the stability of interactions between metabolic genes upon changes in the genetic background. We compared the genetic interaction networks of an in silico model of Saccharomyces cerevisiae in two types of backgrounds: single deletions and accumulation of neutral mutations. Network rewiring was strongly associated to catabolic genes, revealing that they can add to an organism’s growth in different configurations thus buffering genetic perturbations. Neutral deletion backgrounds greatly reduced both this genetic buffering and the ability to grow on alternative nutrients, connecting both environmental and genomic robustness. Second, we tracked the sustainability of a microbial community where a social cooperative interaction is essential for survival. Non-cooperative individuals tend to appear and threaten the collective effect by exploting cooperators. Using an engineered interaction between two strains of Escherichia coli we show how feedback between population and evolutionary dynamics, combined with spatial structure, can create a context where invasion by non-cooperators instead preserves the social behavior. We further analyze how the molecular implementation of a social interaction can modify such dynamics, on the synthetic E. coli system and in the natural production of an iron-scavenging molecule by Pseudomonas fluorescens. Third, we assessed the predictability of the effect of an organism’s prior history on its reaction to a novel environment. We contrasted the evolutionary interaction networks associated to the adaptation of a laboratory strain of E. coli to different antibiotic classes. Acquiring resistance to the same drug could nevertheless result in different responses to an alternative compound, including opposite effects on survival. We discuss how a combination of genomic architecture and historical contingency can produce these contrasting outcomes

Program and Proceedings: The Nebraska Academy of Sciences 1880-2012

PROGRAM FRIDAY, APRIL 20, 2012 REGISTRATION FOR ACADEMY, Lobby of Lecture wing, Olin Hall Aeronautics and Space Science, Session A, Olin 249 Aeronautics and Space Science, Session B, Olin 224 Collegiate Academy, Biology Session A, Olin B Chemistry and Physics, Section A, Chemistry, Olin A Applied Science and Technology, Olin 325 Biological and Medical Sciences, Session A, Olin 112 Biological and Medical Sciences, Session B, Smith Callen Conference Center Junior Academy, Judges Check-In, Olin 219 Junior Academy, Senior High REGISTRATION, Olin Hall Lobby Chemistry and Physics, Section B, Physics, Planetarium Collegiate Academy, Chemistry and Physics, Session A, Olin 324 Junior Academy, Senior High Competition, Olin 124, Olin 131 Aeronautics and Space Science, Poster Session, Olin 249 NWU Health and Sciences Graduate School Fair, Olin and Smith Curtiss Halls Aeronautics and Space Science, Poster Session, Olin 249 MAIBEN MEMORIAL LECTURE, OLIN B Buffalo Bruce McIntosh, Research Ecologist with Western Nebraska Resources Council, The Status of Nebraska\u27s Native Aspen LUNCH, PATIO ROOM, STORY STUDENT CENTER (pay and carry tray through cafeteria line, or pay at NAS registration desk) Aeronautics Group, Conestoga Room Anthropology, Olin 111 Biological and Medical Sciences, Session C, Olin 112 Biological and Medical Sciences, Session D, Smith Callen Conference Center Chemistry and Physics, Section A, Chemistry, Olin A Chemistry and Physics, Section B, Physics, Planetarium Collegiate Academy, Biology Session A, Olin B Collegiate Academy, Biology Session B, Olin 249 Collegiate Academy, Chemistry and Physics, Session B, Olin 324 Earth Science, Olin 224 History/Philosophy of Science, Olin 325 Junior Academy, Judges Check-In, Olin 219 Junior Academy, Junior High REGISTRATION, Olin Hall Lobby Junior Academy, Senior High Competition, (Final), Olin 110 Teaching of Science and Math, Olin 325 Junior Academy, Junior High Competition, Olin 124, Olin 131 NJAS Board/Teacher Meeting, Olin 219 BUSINESS MEETING, OLIN B AWARDS RECEPTION for NJAS, Scholarships, Members, Spouses, and Guests First United Methodist Church, 2723 N 50th Street, Lincoln, N

Spaces of the possible: Universal Darwinism and the wall between technological and biological innovation

Innovations in biological evolution and in technology have many common features. Some of them involve similar processes, such as trial and error and horizontal information transfer. Others describe analogous outcomes such as multiple independent origins of similar innovations. Yet others display similar temporal patterns such as episodic bursts of change separated by periods of stasis. We review nine such commonalities, and propose that the mathematical concept of a space of innovations, discoveries or designs can help explain them. This concept can also help demolish a persistent conceptual wall between technological and biological innovation

Modelling Early Transitions Toward Autonomous Protocells

This thesis broadly concerns the origins of life problem, pursuing a joint approach that combines general philosophical/conceptual reflection on the problem along with more detailed and formal scientific modelling work oriented in the conceptual perspective developed. The central subject matter addressed is the emergence and maintenance of compartmentalised chemistries as precursors of more complex systems with a proper cellular organization. Whereas an evolutionary conception of life dominates prebiotic chemistry research and overflows into the protocells field, this thesis defends that the 'autonomous systems perspective' of living phenomena is a suitable - arguably the most suitable - conceptual framework to serve as a backdrop for protocell research. The autonomy approach allows a careful and thorough reformulation of the origins of cellular life problem as the problem of how integrated autopoietic chemical organisation, present in all full-fledged cells, originated and developed from more simple far-from-equilibrium chemical aggregate systems.Comment: 205 Pages, 27 Figures, PhD Thesis Defended Feb 201

EvoEvo Deliverable 6.8: Final report

Final report of the EvoEvo project