Piu Wong. / Thesis submitted in: July 2002. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (leaves 126-146). / Abstracts in English and Chinese. / Thesis committee --- p.i / Statement --- p.ii / Abstract --- p.iii / Acknowledgement --- p.viii / General abbreviations --- p.xi / Abbreviations of chemicals --- p.xiii / List of figures --- p.xv / List of Tables --- p.xvii / Table of contents --- p.xviii / Chapter 1 --- Literature review / Chapter 1.1 --- Overviews --- p.1 / Chapter 1.1.1 --- Nutritional and economical significance of aspartate family amino acidsin human and animal nutrition --- p.1 / Chapter 1.1.2 --- Synthesis of aspartate family amino acids in plants --- p.2 / Chapter 1.2 --- Regulation of aspartate family amino acids between sink and source organs --- p.6 / Chapter 1.2.1 --- Co-ordination of genes/enzymes involved in amide amino acid metabolism to channel aspartate for aspartate family amino acid synthesis --- p.6 / Chapter 1.2.2 --- Sink-source regulation as a general mechanism in plants --- p.9 / Chapter 1.3 --- Source regulation at free amino acid level --- p.11 / Chapter 1.3.1 --- Regulation of free methionine synthesis --- p.11 / Chapter 1.3.1.1 --- Competition for OPHS between TS and CGS --- p.11 / Chapter 1.3.1.2 --- Turnover of CGS mRNA --- p.12 / Chapter 1.3.1.3 --- Post-translational regulation of CGS enzyme --- p.13 / Chapter 1.3.2 --- Regulation of lysine synthesis and catabolism --- p.15 / Chapter 1.3.2.1 --- Feedback regulation loop --- p.15 / Chapter 1.3.2.2 --- Possible intracellular compartmentalization of enzymes and metabolitesin regulating lysine level --- p.21 / Chapter 1.3.2.3 --- Co-ordination of gene/enzyme in aspartate kinase pathway in regulating flux to Lys --- p.21 / Chapter 1.3.3 --- Significance of lysine catabolism in mammals and plants --- p.24 / Chapter 1.3.3.1 --- Complex developmental regulation and stress response of LKR/SDH gene expression --- p.28 / Chapter 1.3.3.2 --- Regulation through a novel composite locus LKR-SDH --- p.28 / Chapter 1.3.3.3 --- Post-translational control of LKR-SDH activity --- p.31 / Chapter 1.3.3.4 --- Implication of two metabolic flux in Lys catabolism --- p.34 / Chapter 1.4 --- Source (free lysine) enhancement in transgenic plants --- p.36 / Chapter 1.4.1 --- Expression of feedback insensitive enzyme in transgenic plants to enhance free lysine supply in transgenic plant --- p.36 / Chapter 1.4.2 --- Reducing or eliminating lysine catabolism to enhance free lysine poolin transgenic plants --- p.40 / Chapter 1.5 --- Sink regulation --- p.41 / Chapter 1.5.1 --- Engineering transgenic plants through expression of seed storage protein (sink) --- p.41 / Chapter 1.5.2 --- "Dynamic relationship between sink protein, nitrogen metabolism and sulphur metabolism" --- p.45 / Chapter 1.6 --- Transgenic plants with improved source or enhanced sinks related to aspartate family amino acids available for our research --- p.47 / Chapter 1.6.1 --- Enhanced source: ASN1 over-expressers --- p.47 / Chapter 1.6.2 --- Enhanced source: metL transgenic plants --- p.47 / Chapter 1.6.3 --- Altered source: RNAi line --- p.47 / Chapter 1.6.4 --- Effective sink: LRP transgenic plants --- p.48 / Chapter 1.7 --- Overall concept of this study --- p.48 / Chapter 2 --- Materials and methods --- p.50 / Chapter 2.1 --- Materials and growth conditions --- p.50 / Chapter 2.1.1 --- "Plants, bacterial strains and vectors" --- p.50 / Chapter 2.1.2 --- Chemicals and reagents used --- p.53 / Chapter 2.1.3 --- Solutions used --- p.53 / Chapter 2.1.4 --- Commercial kits used --- p.53 / Chapter 2.1.5 --- Equipment and facilities used --- p.53 / Chapter 2.1.6 --- Growth condition --- p.53 / Chapter 2.1.7 --- Tagging of A. thaliana siliques of different developmental stage --- p.54 / Chapter 2.2 --- Methods --- p.55 / Chapter 2.2.1 --- Expression pattern analysis --- p.55 / Chapter 2.2.1.1 --- RNA extraction --- p.55 / Chapter 2.2.1.2 --- Generation of single-stranded DIG-labelled ASN1 DNA probes --- p.55 / Chapter 2.2.1.3 --- Testing the concentration of DIG-labelled probes --- p.56 / Chapter 2.2.1.4 --- Northern blot --- p.57 / Chapter 2.2.1.5 --- Hybridization --- p.58 / Chapter 2.2.1.6 --- Stringency washes --- p.58 / Chapter 2.2.1.7 --- Chemiluminescent detection --- p.58 / Chapter 2.2.2 --- Amino acid analysis and nitrogen determination --- p.60 / Chapter 2.2.2.1 --- Free amino acids in A. thaliana --- p.60 / Chapter 2.2.2.2 --- Phloem exudates collection from A. thaliana --- p.60 / Chapter 2.2.2.3 --- Soluble Protein quantitation --- p.61 / Chapter 2.2.2.4 --- Extraction of salt and water soluble protein from A. thaliana seeds --- p.61 / Chapter 2.2.2.5 --- Purification and amino acid analysis of protein extracts from A. thaliana seeds --- p.62 / Chapter 2.2.2.6 --- Total amino acid determination in mature dry seeds --- p.63 / Chapter 2.2.3 --- Generation of crossing progenies --- p.64 / Chapter 2.2.3.1 --- Artificial crossing of A. thaliana --- p.64 / Chapter 2.2.3.2 --- CTAB extraction of genomic DNA --- p.64 / Chapter 2.2.3.3 --- PCR screening for successful crossing --- p.65 / Chapter 2.2.4 --- Generation of transgenic plants --- p.67 / Chapter 2.2.4.1 --- Cloning of E.coli dapA gene --- p.67 / Chapter 2.2.4.2 --- Preparation of recombinant plasmid --- p.68 / Chapter 2.2.4.3 --- Gene sequencing --- p.68 / Chapter 2.2.4.4 --- Homology search of differentially expressed genes --- p.69 / Chapter 2.2.4.5 --- Construction of chimeric dapA genes (TP-Phas-dapA) --- p.69 / Chapter 2.2.4.6 --- Transformation of electro-competent Agrobacterium cell --- p.73 / Chapter 2.2.4.7 --- Transformation of A. thaliana through vacuum infiltration --- p.73 / Chapter 2.2.4.8 --- Selection of hemizygous and homozygous transgenic plants --- p.74 / Chapter 2.2.4.9 --- Expression analysis of homozygous LRP/dapA transgenic plants --- p.75 / Chapter 3 --- Results --- p.77 / Chapter 3.1 --- Characterization of ASN1 over-expressers --- p.77 / Chapter 3.1.1 --- Overexpression of the ASN1 gene enhances the sink-source relationship of asparagine transport under regular daylight cycle --- p.88 / Chapter 3.1.2 --- Spatial distribution of total free amino acids under normal daylight cycle --- p.88 / Chapter 3.1.3 --- Over-expression of the ASN1 gene affects free amino acid level quantitatively under normal daylight cycle --- p.89 / Chapter 3.1.4 --- Over-expression of the ASN1 gene affects composition of total amino acid under normal daylight cycle --- p.89 / Chapter 3.2 --- Construction of dapA transgenic Arabidopsis --- p.91 / Chapter 3.2.1 --- Construction of chimeric gene for expression of the dapA gene --- p.91 / Chapter 3.2.2 --- Transformation of p1300/Phas-dapA into Arabidopsis and selection of homozygous progenies --- p.91 / Chapter 3.3 --- Generation of transgenic plants with altered sink-source relationship through crossing and in-planta transformation --- p.96 / Chapter 3.3.1 --- Rationale in methods for generating transgenic plants with different combination of sources and sinks --- p.96 / Chapter 3.3.2 --- Screening for double homozygous progenies through crossing --- p.98 / Chapter 3.3.3 --- Screening for F1 progenies of successful crossing --- p.100 / Chapter 3.3.4 --- Selection of homozygous crossing progenies --- p.102 / Chapter 3.3.5 --- Screening for homozygous dapA/LRP transgenic plants --- p.104 / Chapter 3.4 --- Amino acid composition analysis --- p.109 / Chapter 3.4.1 --- The change of aspartate family amino acids in mature seeds of transgenic plants with altered sources --- p.113 / Chapter 3.4.2 --- The change of aspartate family amino acids in mature seeds of transgenic plants with improved sink --- p.114 / Chapter 3.4.3 --- The change of aspartate family amino acids in mature seeds of transgenic plants with improved sink --- p.115 / Chapter 4. --- Discussion / Chapter 4.1 --- Characterization of ASN1 over-expressers --- p.116 / Chapter 4.1.1 --- Possible regulation of ASN1 mRNA stability through level of asparagine --- p.117 / Chapter 4.1.2 --- Over-expression of ASN1 gene may improve nitrogen remobilisation from source to sink tissues --- p.118 / Chapter 4.1.3 --- Over-expression of ASN1 gene has modified the composition of amino acidsin sink organs --- p.119 / Chapter 4.2 --- ASN1 RNAi transgenic plants increases the relative contents of lysine in the seeds --- p.122 / Chapter 4.2.1 --- Role of ASN1 in supplying or competing aspartate in developing seeds --- p.122 / Chapter 4.2.2 --- Possible role of glutamate receptor --- p.123 / Chapter 4.3 --- Lysine catabolism may strictly control the level of lysine --- p.123 / Chapter 4.3.1 --- Possible role of lysine-tRNA in protein synthesis --- p.124 / Chapter 5. --- Conclusion and prospective --- p.125 / References --- p.126 / Appendix --- p.147

Yang, Fan. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 111-132). / Abstracts in English and Chinese. / ACKNOWLEDGEMENTS --- p.iii / ABSTRACT --- p.iv / TABLE OF CONTENTS --- p.viii / LIST OF FIGURES --- p.xii / LIST OF TABLES --- p.xv / LIST OF ABBREVIATIONS --- p.xvi / Chapter Chatper 1. --- General Introduction --- p.1 / Chapter Chapter 2. --- Literature Review --- p.5 / Chapter 2.1 --- Facts on food allergy --- p.5 / Chapter 2.1.1 --- Food allergy and its prevalence --- p.5 / Chapter 2.1.2 --- Pathogenesis of food allergy --- p.6 / Chapter 2.1.3 --- Clineal disorders caused and diagnosis of food allergy --- p.8 / Chapter 2.2 --- Allergenicity assessment of genetically engineered food --- p.13 / Chapter 2.2.1 --- The structural and sequence homology of proteins as a criterion for food allergenicity assessment --- p.14 / Chapter 2.2.2 --- Digestion stability as a criterion for food allergenicity assessment --- p.15 / Chapter 2.2.3 --- Animal models for Food Allergenicity Assessment --- p.21 / Chapter 2.3 --- The importance of rice and its nutritional facts --- p.27 / Chapter 2.3.1 --- The importance of rice --- p.27 / Chapter 2.3.2 --- Rice nutritional facts and its relationship with malnutrition --- p.28 / Chapter 2.4 --- Food allergenicity research in rice --- p.30 / Chapter 2.5 --- Glutelin overexpression transgenic rice GT3 --- p.33 / Chapter 2.6 --- Recent and future perspectives for treatment of food allergy --- p.36 / Chapter Chapter 3. --- Materials and Methods --- p.39 / Chapter 3.1 --- Rice Seed Protein Extraction --- p.39 / Chapter 3.1.1 --- Rice varieties for protein extraction --- p.39 / Chapter 3.1.2 --- Protein extraction from rice seeds --- p.39 / Chapter 3.1.3 --- Fractionation of major rice seed storage proteins --- p.40 / Chapter 3.1.4. --- Protein quantification --- p.41 / Chapter 3.1.5 --- Tricine SDS-PAGE --- p.42 / Chapter 3.2 --- Simulated Gastric Digestibility Assay --- p.43 / Chapter 3.2.1 --- Assay System --- p.43 / Chapter 3.2.2 --- Preparation of Simulated Gastric Fluid --- p.43 / Chapter 3.2.3 --- Assay Procedures --- p.44 / Chapter 3.2.4 --- Results Interpretation --- p.44 / Chapter 3.3 --- Construction of Mouse Models --- p.45 / Chapter 3.3.1 --- Mouse strain and reagents used --- p.45 / Chapter 3.3.2 --- Mouse Model I --- p.46 / Chapter 3.3.3 --- Mouse Model II --- p.50 / Chapter 3.3.4 --- Mouse Model III --- p.51 / Chapter 3.4 --- Bioinformatic Analysis of Glutelin Sequence --- p.52 / Chapter 3.5 --- Epitope Mapping of Glutelin --- p.55 / Chapter 3.5.1 --- Bioinformatic Analysis --- p.55 / Chapter 3.5.2 --- Direct and Competitive ELISA --- p.56 / Chapter 3.5.3 --- Western Blot Analysis --- p.57 / Chapter 3.5.4 --- IgE-binding assay --- p.58 / Chapter Chapter 4. --- Results and Discussion --- p.60 / Chapter 4.1 --- Rice Seed Protein Extraction --- p.60 / Chapter 4.1.1 --- Rice Protein Extraction --- p.60 / Chapter 4.1.2 --- Extraction of rice major seed storage protein fractions --- p.62 / Chapter 4.2 --- Simulated Gastric Digestibility Assay --- p.64 / Chapter 4.2.1 --- Pepsin Digestibility of total protein from GT3 and WT rice seeds --- p.64 / Chapter 4.2.2 --- Pepsin Digestibility of major storage protein fractions in GT3 and WT rice --- p.68 / Chapter 4.2.3 --- Summary of Pepsin Digestibility Assay --- p.74 / Chapter 4.3 --- Mouse Model I --- p.75 / Chapter 4.3.1 --- Protein-specific IgE levels --- p.75 / Chapter 4.3.2 --- Protein-specific IgG1 and IgG2a levels --- p.77 / Chapter 4.3.3 --- Allergic Response Test --- p.79 / Chapter 4.3.4 --- Summary from Mouse Model I --- p.81 / Chapter 4.4 --- Mouse Model II --- p.83 / Chapter 4.4.1 --- Proteins specific IgE levels --- p.84 / Chapter 4.4.2 --- Proteins specific IgG1 and IgG2a levels --- p.85 / Chapter 4.4.3 --- Allergic Response Test --- p.87 / Chapter 4.4.4 --- Summary from Mouse Model II --- p.88 / Chapter 4.5 --- Mouse Model III --- p.90 / Chapter 4.5.1 --- Protein-specific IgE levels --- p.90 / Chapter 4.5.2 --- Proteins specific IgG1 and IgG2a levels --- p.91 / Chapter 4.5.3 --- Allergic Response Test --- p.93 / Chapter 4.5.4 --- Summary from Mouse Model III --- p.93 / Chapter 4.6 --- Potential allergenicity of rice glutelin by bioinformatics and epitope mapping --- p.94 / Chapter 4.6.1 --- Bioinformatic analysis --- p.94 / Chapter 4.6.2 --- ELISA analysis of synthesized epitopes --- p.97 / Chapter 4.6.3 --- Western Blot Analysis --- p.99 / Chapter 4.6.4 --- IgE-binding assay --- p.103 / Chapter Chapter 5. --- Conclusion and Future Perspectives --- p.109 / References --- p.111

Vermont is the first and only state in the US to establish mandatory labels for food containing genetically modified organisms (GMOs). This thesis investigates the impact of the mandatory labeling law as it relates to changes in prices, quantities sold, and opinions of GMOs. First, grocery store scanner data from Vermont and Oregon are compared using triple difference (difference-in-difference-in-difference) models. Next, Vermont, Oregon, and Colorado survey response data are compared using difference-in-difference models. The findings reveal that there is a general price premium for non-GMO goods of $0.05/oz across all states and times, that mandatory labeling laws do not result in a short-term change in quantities sold or prices of GMO products, and that both mandatory labeling laws and failed mandatory labeling referendums cause an increase in support for GMOs in the food supply. The implications of this research are that mandatory GMO labels did not impact short-term prices or sales and increased the level of support for GMOs.

Believing that ideas about evolution and genetics are playing an increasing role in popular conceptions of who we are and what it means to be human, I sought ways to express this through my art. In particular I tried to articulate these notions through figurative sculpture. As the role of figurative sculpture in expressing current ideas about being human has declined in the West, I saw this as a challenge. It was the intent of my Masters program to reposition the sculpted body back within contemporary western cultural contexts. For an understanding of those contexts I relied heavily on my own culturally embedded experience and observations. I took as background my readings of evolutionary inspired literature and linked it with my interpretations of the genetic mythologies so prevalent in recent movies. The result was an image of contemporary humans as multifaceted, yet subservient to their genes. These genes appear to be easily manipulated and the product of technological intervention as much as, if not more than, inherited characteristics. As part of developing a sculptural form able to manifest this, I investigated some non-western traditions. I used field trips and residencies to research Buddhist and Hindu sculptures of the body and developed an interest in the spatial and conceptual relationships between those bodies. Through making figurative work in the studio, I came to realise the figures' inadequacy in expressing temporal relationships. As temporal change is a fundamental element of evolution and genetics, I needed to explore this element. The result was a number of series; groups of works that create their own context of relationships. Not all these groups use sculptures of the body but they evoke the notion of bodies, naturally or technologically hybridised, mutating, transforming, evolving and related to each other generationaly through time.

<p>This research investigates the nature of the social project surrounding the lawsuit between the organic farmers of Saskatchewan, Canada, and Monsanto and Bayer, the two largest biotechnology companies in Canada. The thesis also explores the culture of organic farming in an era of high technology and globalization. An ethnographic approach is employed in order to address this research aim from the perspective of study participants. Based on interview data, I detail the difficulties facing farmers, especially small organic farmers, in Canada today. I also describe a hope and determination amongst organic farmers who see themselves resisting the erosion of the rural landscape at the hands of powerful corporations and a dominant industrial model of food production. In the end, the organic farmers of Saskatchewan are recognized as part of a broad, coalitional and embryonic new social movement whose lifeworld, or cultural, focus reflects the post-modern character of contemporary society and presents some interesting challenges for social science.</p>

Over the last few years, genome-wide association studies (GWAS) have been used to identify numerous obesity associated SNPs in the human genome. By using linkage studies, candidate obesity genes have been identified. When SNPs in the first intron of FTO were found to be associated to BMI, it became the first gene to be linked to common obesity. In order to look for causative explanations behind the associated SNPs, a re-sequencing of FTO had been performed on the SOLiD sequencing platform. In-house candidate gene, SLCX, was also sequenced in order to evaluate a potential obesity association. The purpose of this project was to analyse the sequences and also to evaluate the quality of the SOLiD sequencing. A part of the project consisted in performing PCRs and selecting genomic regions for future sequencing projects. I developed and implemented a sequence analysis strategy to identify obesity associated SNPs. I found 39 obesity-linked SNPs in FTO, a majority of which were located in introns 1 and 8. I also identified 3 associated intronic SNPs in SLCX. I found that the SOLiD sequencing coverage varies between non-repetitive and repetitive genomic regions, and that it is highest near amplicon ends. Interestingly, coverage varies significantly between different amplicons even after repetitive sequences have been removed, which indicates that it is affected by features inherent to the sequence. Still, the observed allele frequencies for known SNPs were highly correlated with the SNP frequencies documented in HapMap. In conclusion, I verify that SNPs in FTO are associated with obesity and also identify a previously unassociated gene, SLCX, as a potential obesity gene. Re-sequencing of genomic regions on the SOLiD platform was proven to be successful for SNP identification, although the difference in sequencing coverage might be problematic.

The major objective of this study was to produce synthetic genotypes of Brassica juncea from its parental species <i> B. rapa </i> and <i> B. nigra </i> via somatic and sexual hybridization. As prerequisites for somatic hybridization experiments, methods were developed to improve the culture of mesophyll and hypocotyl protoplasts of <i> B. nigra </i> and <i> B. rapa </i>, to obtain reliable plant regeneration from mesophyll protoplast cultures of <i> B. nigra </i>, and to fuse protoplasts of <i> B. nigra </i> and <i> B. rapa </i>. A modified Kao's medium (1977), was found suitable for the culture of mesophyll protoplasts of <i> B. nigra </i> and <i> B. rapa </i>. At a density of approximately $110\sp5$ protoplasts/ml within a culture plate insert surrounded by culture medium, mesophyll protoplast cultures of <i> B. nigra </i> accessions R890, R1819, R3392 and U1218 and <i> B. rapa </i> cvs. R500 and Wong Bok formed colonies. Genotypic differences in cell division and colony formation were observed. Hypocotyl protoplasts of <i> B. nigra </i> and <i> B. rapa </i> were successfully isolated from 6 day-old seedlings cultured in a modified Kao's medium (1977). With <i> B. nigra </i> accession R890 and <i> B. rapa </i> cv. R500, cell division and colony formation were optimal when hypocotyl protoplasts were cultured at a density of 0.5 to $1.010\sp5$ protoplasts/ml within a culture plate insert surrounded by a nurse culture of 4 to 6 day-old mesophyll protoplasts of <i> B. nigra </i>. Plant regeneration was obtained from mesophyll protoplast-derived calli of <i> B. nigra </i> accession R890 originally cultured in inserts; a shoot regeneration frequency of 8.1% was obtained on a medium containing the salts and vitamins of medium K3 (Nagy and Maliga 1976) with 3 g/l sucrose, 18.2 g/l mannitol, 2 mg/l ZR, 0.1 mg/l NAA, 10 g/l agarose, pH 5.6. For somatic hybridizatian studies, methods were developed to select out parental protoplasts using iodoacetic acid and to efficiently fuse protoplasts on the bottom of a petri dish using PEG. Twenty-nine plants were recovered from fusion experiments between mesophyll protoplasts of <i> B. nigra </i> accession R890 and hypocotyl protoplasts of <i> B. rapa </i> cv. Tobin. The somatic hybrid plants resembled natural <i> B. juncea </i>, had $2n=36$ chromosomes and had pollen viabilities ranging from 30 to 45%. Twenty-one plants, derived from one callus colony, possessed the mitochondrial and chloroplast genomes of <i> B. rapa </i>, as found in natural <i> B. juncea </i>. Eight plants, derived from another callus, had a novel cytoplasmic combination consisting of the mitochondrial genome of <i> B. rapa </i> and the chloroplast genome of <i> B. nigra </i>. Synthetic genotypes of <i> B. juncea </i> were also produced from reciprocal sexual crosses between <i> B. rapa </i> and <i> B. nigra </i>. Seventy-eight interspecific hybrid plants from the cross <i> B. rapa </i> x <i> B. nigra </i> and six hybrid plants from the reciprocal cross were identified by their morphology, pollen viability and chromosome number. The colchicine-induced allotetraploids resembled natural <i> B. juncea </i> in morphology, had 18 bivalents at metaphase I, and had between 35 and 70% pollen viability.

<p>This research investigates the nature of the social project surrounding the lawsuit between the organic farmers of Saskatchewan, Canada, and Monsanto and Bayer, the two largest biotechnology companies in Canada. The thesis also explores the culture of organic farming in an era of high technology and globalization. An ethnographic approach is employed in order to address this research aim from the perspective of study participants. Based on interview data, I detail the difficulties facing farmers, especially small organic farmers, in Canada today. I also describe a hope and determination amongst organic farmers who see themselves resisting the erosion of the rural landscape at the hands of powerful corporations and a dominant industrial model of food production. In the end, the organic farmers of Saskatchewan are recognized as part of a broad, coalitional and embryonic new social movement whose lifeworld, or cultural, focus reflects the post-modern character of contemporary society and presents some interesting challenges for social science.</p>

<p>This dissertation explores philosophical problems in biology, particularly those relating to macroevolutionary theory. It is comprised of a series of three papers drawn from work that is currently at the publication, re-submission, and review stage of the journal refereeing process, respectively. The first two chapters concern the overarching contours of complex life, while the third zeroes in on the short and long-term prospects of human evolution.</p><p>The rhetorical journey begins with a thought experiment proposed by the late paleontologist Stephen Jay Gould. Gould hypothesized that replaying the "tape of life" would result in radically different evolutionary outcomes, both with respect to animal life in general and the human species in particular. Increasingly, however, biologists and philosophers are pointing to convergent evolution as evidence for replicability and predictability in macroevolution. Chapters 1 and 2 are dedicated to fleshing out the Gouldian view of life and its antithesis, clarifying core concepts of the debate (including contingency, convergence, constraint and causation), and interpreting the empirical data in light of these conceptual clarifications. Chapter 3 examines the evolutionary biological future of the human species, and the ways in which powerful new biotechnologies can shape it, for better and for worse. More detailed chapter summaries are provided below.</p><p>In Chapter 1, I critique a book-length excoriation of Gould's contingency theory written by the paleobiologist Simon Conway Morris, in which he amasses and marshals a good bulk of the homoplasy literature in the service of promoting a more robust, counter-factually stable account of macroevolution. I show that there are serious conceptual and empirical difficulties that arise in broadly appealing to the frequency of homoplasy as evidence for robustness in the history of life. Most important is Conway Morris's failure to distinguish between convergent (`externally' constrained) and parallel (`internally' constrained) evolution, and to consider the respective implications of these significantly different sources of homoplasy for a strong adaptationist view of life.</p><p>In so doing, I propose a new definition of parallel evolution, one intended to rebut the common charge that parallelism differs from convergence merely in degree and not in kind. I argue that although organisms sharing a homoplastic trait will also share varying degrees of homology (given common decent), it is the underlying developmental homology with respect to the generators directly causally responsible for the homoplastic event that defines parallel evolution and non-arbitrarily distinguishes it from convergence. I make use of the philosophical concept of `screening-off' in order to distinguish the proximate generators of a homoplastic trait from its more distal genetic causes (such as conserved master control genes).</p><p>In Chapter 2, I critically examine a recent assessment of the contingency debate by the philosopher John Beatty, in which he offers an interpretation of Gould's thesis and argues that it is undermined by iterative ecomorphological evolution. I develop and defend alternative concepts of contingency and convergence, and show how much of the evidence generally held to negate the contingency thesis not only fails to do so, but in fact militates in favor of the Gouldian view of life. My argument once again rests heavily on the distinction between parallelism and convergence, which I elaborate on and defend against a recent assault by developmental biologists, in part by recourse to philosophical work on the ontological prioritization of biological causes.</p><p>In Chapter 3, I explore the probable (and improbable) evolutionary biological consequences of intentional germ-line modification, particularly in relation to human beings. A common worry about genetic engineering is that it will reduce the pool of genetic diversity, creating a biological monoculture that could not only increase our susceptibility to disease, but even hasten the extinction of our species. Thus far, however, the evolutionary implications of human genetic modification have remained largely unexplored. In this Chapter, I consider whether the widespread use of genetic engineering technology is likely to narrow the present range of genetic variation, and if so, whether this would in fact lead to the evolutionary harms that some authors envision. By examining the nature of biological variation and its relation to population immunity and evolvability, I show that not only will genetic engineering have a negligible impact on human genetic diversity, but that it will be more likely to ensure rather than undermine the health and longevity of the human species. To this end, I analyze the relationship between genotypic and phenotypic variation, consider process asymmetries between micro and macroevolution, and investigate the relevance of evolvability to clade-level persistence and extinction.</p> / Dissertation

Bone tissue engineering is a promising approach to address the limitations of currently used bone tissue substitutes. However, an optimal cell source for the production of osteoblastic matrix proteins and mineral deposition has yet to be defined. In response to this deficiency, ex vivo gene therapy of easily accessible non-osteogenic cells, such as skeletal myoblasts, has become a prevalent strategy for inducing an osteoblastic phenotype. The majority of these approaches focus on constitutive overexpression of soluble osteogenic growth factors such as bone morphogenetic proteins (BMPs). In order to avoid aberrant effects of unregulated growth factor secretion, this work focuses on delivery of the osteoblastic transcription factor Runx2 as an autocrine osteogenic signal under the control of an inducible expression system. The overall objective of this research was to engineer an inducible cell source for bone tissue engineering that addresses the limitations of current cell-based approaches to orthopedic regeneration. Our central hypothesis was that inducible Runx2 overexpression in skeletal myoblasts would stimulate differentiation into a regulated osteoblastic phenotype. We have demonstrated that Runx2 overexpression stimulates transdifferentiation of primary skeletal myoblasts into a mineralizing osteoblastic phenotype. Furthermore, we have established Runx2-engineered skeletal myoblasts as a potent cell source for bone tissue engineering applications in vitro and in vivo, similar to BMP-2-overexpressing controls. Finally, we exogenously regulated osteoblastic differentiation by myoblasts engineered to express a tetracycline-inducible Runx2 transgene. This conversion into an osteoblastic phenotype was inducible, repressible, recoverable after suppression, and dose-dependent with tetracycline concentration. This work is significant because it addresses cell sourcing limitations of bone tissue engineering, develops controlled and effective gene therapy methods for orthopedic regeneration, and establishes a novel strategy for regulating the magnitude and kinetics of osteoblastic differentiation.