No description available.

Call number: LD2668 .T4 1928 R51

No description available.

Thesis (Ph. D.)--University of California, San Diego and San Diego State University, 2003. / Vita. Includes bibliographical references (leaves 219-228).

Lineages of the cyanobacteria Prochlorococcus marinus have diverged into two genetically distinct ‘ecotypes,’ high-light adapted (HL) and low-light adapted (LL), which thrive under different environmental conditions. This type of niche differentiation in prokaryotes is often accompanied by genetic and genomic divergence. Differential selection pressure associated with ecotype divergence can be analyzed using models of codon evolution. However, some characteristics of the Prochlorococcus genome violate underlying assumptions of these models. For example, high levels of recombination between bacterial strains are known to cause false positives for codon models. Therefore, it is important that statistical methods for detecting recombination be reliable. In Chapter 2, I evaluate a set of recombination detection methods under four different scenarios related to functional divergence: 1) varying tree shape, 2) positive selection, 3) non-stationary evolution, and 4) varying levels of recombination and divergence.

This study explores the establishment of the paradigm of evolution by means of natural selection, asserting that Darwin's theories were not scientifically revolutionary because he established rather than overthrew the existing paradigm in biology. Actually Darwin made three more important contributions than the theory of natural selection. He delivered a blow to essentialism, changing the universe from a product into a process. He established the hypothetico-deductive model of the physical sciences for natural history. And he demonstrated that teleological problems could be studied by scientists. The recent controversies in biology are continuations of the old debate over whether evolution is orderly or irregular, controlled by external or internal forces, continuous or discontinuous. The controversies can be separated into four separate challenges to neo-Darwinism: empirical, epistemological, methodological, and teleological. The study concludes that the empirical and teleological challenges do not pose serious threats to the existing paradigm, but unless the epistemological and methodological challenges can be met satisfactorily, the paradigm may be overthrown.This study also explores the differences between the rhetorical and scientific methods of inquiry. Modern science is considered as predominantly empirical, progressing because of the scientists' system of shared, rational values. Actually both metaphysician and physician ponder the same questions, embrace truth with the same assumptions, and operate with the same epistemology. Science is puzzle solving. Rhetoric deals with ill-defined problems, while science turns ill-defined problems into well-defined ones. The danger in separating the scientific and rhetorical methods is that Western man is split into two irreconcilable points of view: the moral and the scientific. The dichotomy arose because of the two fountainheads of Western culture. Plato "solved" the dichotomy by proposing two worlds of Becoming and Ideas. Darwin's solution depends on a different metaphysical pathos which is only now being realized, due to the rethinking of the paradigm as a result of the challenges. Rather than giving us two worlds, Darwin separated the forces of one, completely naturalistic world into a two-step process: chance and necessity. The problem is that many thinkers focus on only one of the processes, sometimes to the exclusion of the other. / Department of English

M.Sc. / The current dogma that dictates that Natural Selection is the driving force behind evolutionary change, is finally being challenged - what with the upsurgence of evidence provided by molecular and developmental biologists. This genetic and ontogenic evidence points towards a far more holistic approach (such as the involvement of the cell as a whole, the external environment as well as a flexible genome) to evolution, in contrast to the previously accepted DNA-centric Mendelian hypothesis. This new wave of thought, together with the re-discovery of 18th and 19th century evolutionary thought that complies with current findings, was the motivation to expose other biological mechanisms that are able to induce evolutionary change. New concepts were introduced (that contradict Neo- Darwinian thinking), with the intention of placing Natural Selection in its rightful position as an adaptive mechanism. Concepts introduced, were firstly, a chapter on how genes produce their effects, and, that by simply reinserting or duplicating existing genes, drastic (macro-evolutionary) change would result. Here the genome is portrayed as a static and dynamic system. The phenomenon of repetition or duplication of existing genes provides evidence of common ancestry, as well as reinforcing the idea of regularity in evolution. Abundant evidence in nature reveals trends of regularity or constraint. Anything is not possible in evolutionary development. The search for laws of form and the reasons for their constraining variables are discussed. The most interesting evolutionary events are those that have led to major changes in the anatomical organisation of animals. These changes are associated with the formation of new phyla. All that remains of such highly significant events are the time-locked tales of fossils. However, the fossil record cannot begin to reveal how these events occurred. The final chapter speculates on how life may have begun in the primordial waters and ends at a hypothesis on the origin of eukaryotes. The scription was an attempt to nudge the prevailing "Darwin" orientated evolutionary paradigm, in order to create space for the arrival of an "Epigenetic" orientated evolutionary paradigm, that is completely able to explain evolutionary procedure.

The bacterial species belonging to the order Mycoplasmatales have highly truncated genomes, and are thus ideal for studying genome evolution patterns. Fourteen members (twelve species) of this order were selected for study of genome evolution based on gene function and phylogeny. A database was constructed that consisting of the set of genes that are common to all of these species, and these genes were further subdivided based on their functions. A Bayesian phylogenetic tree was also constructed from the 16 S ribosomal DNA sequences from these species and robust clades were identified for testing the influence of selection on gene evolution, from which the clades were selected and tested for evidence of natural selection. Two separate statistical techniques, namely the codon substitution models and McDonald-Kreitman tests were used to analyze the presence or absence of selection for genes in different functional categories. The studies demonstrated that the set of genes associated with cellular processes show the highest percentage of selection and are likely to play a crucial role in Mycoplasma evolution (for example, by altering the arrangement of antigens on the cell surface and thus enabling a particular Mycoplasma species to expand its host range). The presence of selection could only be identified at the earliest divisions of the phylogeny. Tests were also performed to detect the presence of a number of neutral genetic processes that can potentially confound detection of patterns of selection. None of these processes were found to affect the results of the analyses. The study has the potential to identify genes, gene complexes or even pathways that may be involved directly or indirectly in speciation.

No description available.

Digitized by Kansas Correctional Industries