This dissertation argues that philosophers Barbara Forrest and Robert T. Pennock fail to discredit William A. Dembski's Design Inference as a legitimate scientific program. Chapter 1 is the introduction, explaining the problem and the research methodology used in the dissertation to ascertain a conclusion. Chapter 2 is a background survey and analysis of contemporary Intelligent Design (ID) theory and Dembski's part within the overall schemata of the Intelligent Design enterprise. Particular aspects of Dembski's Design Inference framework and its corresponding "explanatory filter" are explained in Chapter 3. Both Forrest and Pennock had significant influence on the judge's final opinion in the Kitzmiller v. Dover trial, which brought serious scrutiny against ID's scientific merit. Criticism against Dembski was an important part of Forrest and Pennock's respective expert testimony against ID. Based on this trial testimony and their respective academic writings, Chapter 4 therefore argues for the legitimacy of Forrest and Pennock as influential critics when considering Dembski's scientific relevance. The chapter also surveys their substantive arguments against Dembski. Dembski's own response to the categorical criticisms by Forrest and Pennock are addressed in Chapter 5. The concluding analysis is in Chapter 6, arguing that Dembski's Design Inference maintains as viable science, despite the critiques by Forrest and Pennock. / This item is only available to students and faculty of the Southern Baptist Theological Seminary. If you are not associated with SBTS, this dissertation may be purchased from <a href="http://disexpress.umi.com/dxweb">http://disexpress.umi.com/dxweb</a> or downloaded through ProQuest's Dissertation and Theses database if your institution subscribes to that service.

Thesis (Ph.D.)--University of Delaware, 2005. / Principal faculty advisor: J.A. Leo Lemay, Dept. of English. Includes bibliographical references.

Made available in DSpace on 2014-06-11T19:29:44Z (GMT). No. of bitstreams: 0 Previous issue date: 2006-07-18Bitstream added on 2014-06-13T20:19:58Z : No. of bitstreams: 1 souza_ec_me_ilha.pdf: 505202 bytes, checksum: b2e8a6c8e22a5805a00f3381be5d40df (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / O mal-do-fio (ou queima-do-fio) é uma doença causada pelo fungo Basidiomiceto Ceratobasidium sp., que afeta diversas plantas frutíferas nativas ou cultivadas. A doença ocorre com mais freqüência em zonas de alta precipitação e temperaturas elevadas, típicas de regiões de florestas tropicais como a Amazônia e a Mata Atlântica. Em São Paulo, recentemente detectou-se a ocorrência do mal-do-fio, em caquizeiro na região de Mogi das Cruzes. Essa doença pode- se tornar importante com a expansão do cultivo de fruteiras no Estado. A maioria das pesquisas sobre o patossistema focalizou a epidemiologia e o controle do fungo. Entretanto a etiologia do patógeno ainda não está totalmente definida, especialmente para populações do fungo infectando caqui e chá no Estado de São Paulo. Há também pouca informação sobre a divergência genética entre populações do patógeno de hospedeiros distintos como caqui e chá. O primeiro objetivo deste trabalho foi determinar o posicionamento filogenético global de populações de Ceratobasidium sp. do caqui e do chá, em relação a espécies de Ceratobasidium sp. descritas no mundo. Foram analisadas seqüências de DNA da região ITS-5.8S do rDNA, inferindo-se a história dos alelos ou haplótipos deste lócus, por meio de métodos filogenéticos, cladísticos e coalescentes. Observou-se que uso de C. noxium é apropriado para denominar espécies associadas ao mal-do- fio em caqui e chá, apesar de C. noxium do caqui e do chá constituírem populações filogeneticamente independentes, as quais denominamos de Grupo Diospyrus e Grupo Camellia. Este estudo trouxe uma contribuição importante para a compreensão das relações filogenéticas e biologia de populações de C. noxium em caqui e chá. Uma vez esclarecidas as questões filogenéticas, o segundo objetivo deste trabalho foi testar a patogenicidade cruzada de... / The white-thread blight is a disease caused by the Basidiomycete fungus Ceratobasidium sp. that affects several native or cropped tree fruits. This disease frequently occurs in zones of high precipitation and high temperatures typical of the tropical forest regions such as the Amazon and the Atlantic Forest. In São Paulo, the occurrence of the white-thread blight was detected only recently on kaki orchards closer to Mogi das Cruzes. That disease can become important with the expansion of the fruit trees cropping areas in the State. Most of the researches about the pathosystem has focused on the epidemiology and control of fungus. However the etiology of the pathogen is not totally defined yet, especially for the fungus populations infecting kaki and tea in São Paulo State. There is also little information available about the biological and genetic divergence between pathogen populations from distinct hosts, such as kaki and tea. The first objective of this research was to determine the global phylogenetic placement of populations of Ceratobasidium from kaki and tea, considering the species of Ceratobasidium described throughout the world. Sequences of the ITS-5.8S region of the rDNA were analyzed, inferring the alleles or haplotypes history for this locus, by phylogenetics, cladistisc and coalescent methods. We observed that the use of C. noxium is appropriate to denominate the fungus species associate with the white-thread blight on kaki and tea, despite the fact that C. noxium from kaki and tea constitutes phylogenetically independent populations, which we denominate Diospyrus and Camellia groups. This study brought an important contribution for the understanding of the phylogenetics and population biology of C. noxium infecting kaki and tea. Once the phylogenetics subjects have been cleared, the second objective of this work was to test the cross-pathogenicity... (Complete abstract, access electronic address below)

Organisms are frequently faced with uncertainty regarding how best to exploit vital resources, and may benefit from collecting information about their distribution through space and time. However, the ways in which competition over resources might systematically facilitate or constrain an individual's ability to use information has been largely overlooked. In this thesis, I develop a conceptual framework for considering how the distribution of limited resources might underpin interdependencies between competition and information use. I focus on the evolutionary ecology of relationships between social dominance and social information use. I begin with an observational study of wild chacma baboons (Papio ursinus) suggesting that, when resources can be monopolised, individuals with low competitive ability are limited in their ability to use social information. Building on these findings, I then develop a general model exploring selection on social information use in a competitive context across three axes of 'resource ecology' (scarcity, depletion rate, monopolisability). This study makes predictions regarding the resource conditions under which competitive ability might constrain social information use, and the potential importance of social information use in the evolution of social dominance. I go on to test these predictions in chacma baboons using a field experiment. This experiment also explores whether the predictability of resource distribution might facilitate the decoupling of social information use from the competitive context in which it was collected. Taken together, these findings provide general insights into the combinations of ecological conditions and behavioural mechanisms that should underpin the benefits of social dominance. I end by building a simple population matrix model to study social dominance using an eco-evolutionary approach, in which feedback loops between ecological and evolutionary processes are considered. By modelling relationships between dominance rank and survival, reproduction, inheritance, and development, I am able to derive estimates of long-term fitness associated with dominance. Using these estimates, I generate predictions regarding how dominance hierarchies should impact the dynamics of group stability, viability, and fission.

The thesis is that contrary to the received popular wisdom, the combination of David Hume's sceptical enquiry and Charles Darwin's provision of an alternative theoretical framework to the then current paradigm of natural theology did not succeed in defeating the design argument. I argue that William Paley's work best represented the status quo in the philosophy of biology circa 1800 and that with the logical mechanisms provided us by William Dembski in his seminal work on probability, there is a strong argument for thr work of Michael Behe to stand in a similar position today to that of Paley two centuries ago. The argument runs as follows: In Sections 1 and 2 of Chapter 1 I introduce the issues. In Section 3 I argue that William Paley's exposition of the design argument was archetypical of the natural theology school and that given Hume's already published criticism of the argument, Paley for one did not feel the design argument to be done for. I further argue in Section 4 that Hume in fact did no such thing and that neither did he see himself as having done so, but that the design argument was weak rather than fallacious. In Section 5 I outline the demise of natural theology as the dominant school of thought in the philosophy of biology, ascribing this to the rise of Darwinism and subsequently neo-Darwinism. I argue that design arguments were again not defeated but went into abeyance with the rise of a new paradigm associated with Darwinism, namely methodological naturalism. In Chapter 2 I advance the project by a discussion of William Dembski's formulation of design inferences, demonstrating their value in both everyday and technical usage. This is stated in Section 1. In Sections 2 and 3 I discuss Dembski's treatment of probability, whilst in Section 4 I examine Dembski's tying of different levels of probability to different mechanisms of explanation used in explicating the world. Section 5 is my analysis of the logic of the formal statement of the design argument according to Dembski. In Section 6 I encapsulate objections to Dembski. I conclude the chapter (with Section 7) by claiming that Dembski forwards a coherent model of design inferences that can be used in demonstrating that there is little difference between the way that Paley came to his conclusions two centuries ago and how modem philosophers of biology (such as I take Michael Behe to be, albeit that by profession he is a scientist) come to theirs when offering design explanations. Inference to the best explanation is demonstrated as lying at the crux of design arguments. In Chapter 3 I draw together the work of Michael Behe and Paley, showing through the mechanism of Dembski's work that they are closely related in many respects and that neither position is to be lightly dismissed. Section 1 introduces this. In Section 2 I introduce Behe's concept of irreducible complexity in the light of (functional) explanation. Section 3 is a detailed analysis of irreducible complexity. Section 4 raises and covers objections to Behe with the general theme being that (neo-) Darwinians beg the question against him. In Section 4 I apply the Dembskian mechanic directly to Behe's work. I argue that Behe does not quite meet the Dembskian criteria he needs to in order for his argument to stand as anything other than defeasible. However, in Section 5 I conclude by arguing that this is exactly what we are to expect from Behe's and similar theories, even within competing paradigms, in the philosophy of biology, given that inference to the best explanation is the logical lever therein at work. / KMBT_363 / Adobe Acrobat 9.54 Paper Capture Plug-in

Proposes a new model for teaching inquiry and critical thinking in the middle school science classroom. This model will assist students in learning the evidence for evolution for themselves, as well as assisting them in developing skills in critical thinking and inquiry. The objective of this model is to create a more scientifically literate student body who can go on to pursue an even greater understanding of the nature of science.

The purpose of the study was to evaluate the teaching of evolution in selected grade 10 classrooms in Namibia. Some teachers from Oshikoto region in Onyaanya circuit have indicated the difficulties they have encountered when teaching the topic in Life Science of Namibian curriculum. Moreover, the teaching of evolution has a great practical value for student directly or indirectly, evolutionary biology has made many contributions to society. An understanding of evolution is essential in finding and using natural resources and it will be indispensable to establish sustainable relationship with the natural environment. Specifically, this study examined a set of variables including teachers’ understanding of evolution. The data were collected from Life Science teachers through administration of evolution content knowledge. Qualitative case study approach was employed. The population comprised of three Life Science grade 10 teachers from three schools. Three teachers were selected by using a purposive sampling technique. The sampling technique was chosen because is relevant to the conceptual framework and the research questions addressed by the research. The qualitative research was executed by applying the phenomenological method. Mason (2012) claims that: “qualitative research is used when the research wishes to understand meanings, beliefs and values”. The study was drawn from the theory of social constructivism theory by Vygotsky, 1978. According to Vygotsky, (1978) “much important learning by the child occurs through social interaction with a skilful tutor”. The researcher collected qualitative data by means of classroom observations and semi-structured I with three Life Science teachers from three different schools. The following research questions were attempt to be answered: What is the nature of teacher’s content knowledge on evolution teaching in grade 10? What is the nature of teachers’ instructional strategies during evolution teaching? How does the teachers’ content knowledge and instructional strategies shape the teacher’s interactions and discourse? The collected data was analysed using Classroom Practice Diagnostic Framework (CPDF). Participants used their teaching experiences to teach evolution. This study indicated a lack of content knowledge among teachers and teaching and learning resources at schools. It is recommended that the Ministry of Education allocate enough textbook funds to regions to cater for every learner’s textbook. Life Science education officer should collaborate with biology education officer to organise a workshop for Life Science teacher in their region. The workshop will equip teachers with more information on evolution and will help in the improvement of learners’ performances. / Science and Technology Education / M. Ed. (Natural Science Education)

Indiana University-Purdue University Indianapolis (IUPUI) / SETMAR is a chimeric protein that originates from the fusion of a SET domain to the mariner Hsmar1 transposase. This fusion event occurred approximately 50 million years ago, after the split of an anthropoid primate ancestor from the prosimians. Thus, SETMAR is only expressed in anthropoid primates, such as humans, apes, and New World monkeys. Evolutionary sequence analyses have revealed that the DNA-binding domain, one of the two functional domains in the Hsmar1 transposase, has been subjected to a strong purifying selection. Consistent with these analyses, SETMAR retains robust binding specificity to its ancestral terminal inverted repeat (TIR) DNA. In the human genome, this TIR sequence is dispersed in over 1500 perfect or nearly perfect sites. Given that many DNA-binding domains of transcriptional regulators are derived from transposases, we hypothesized that SETMAR may play a role in gene regulation. In this thesis, we determined the crystal structures of the DNA-binding domain bound to both its ancestral TIR DNA and a variant TIR DNA sequence at 2.37 and 3.07 Å, respectively. Overall, the DNA-binding domain contains two helix-turn-helix (HTH) motifs linked by two AT-hook motifs and dimerizes through its HTH1 motif. In both complexes, minor groove interactions with the AT-hook motifs are similar, and major groove interactions with HTH1 involve a single residue. However, four residues from HTH2 participate in nucleobase-specific interactions with the TIR and only two with the variant DNA sequence. Despite these differences in nucleobase-specific interactions, the DNA-binding affinities of SETMAR to TIR or variant TIR differ by less than two-fold. From cell-based studies, we found that SETMAR represses firefly luciferase gene expression while the DNA-binding deficient mutant does not. A chromatin immunoprecipitation assay further confirms that SETMAR binds the TIR sequence in cells. Collectively, our studies suggest that SETMAR functions in gene regulation.

Sexually selected ornaments are among the most spectacular traits in nature. Indeed, the extreme costs associated with producing sexual traits seem to play a crucial role in their evolution by enforcing honest levels of advertisement: only males with high levels of acquired resources (or high ‘condition’, as it is known in the literature) can afford to produce extravagant signals, a phenomenon which maintains signal reliability in a constant environment. In my thesis I examine many implications of this condition-dependent model of ornament and preference evolution for variation in age-dependent allocation to sexual signals and other life history traits. In Chapter 1, I review theoretical implications of condition-dependent signalling for life history and sexual selection theory. I note that a universal cost of expenditure in sexual advertisement is metabolic in nature: metabolites used to fund ornament expression are by definition unavailable to other life history traits that compete for a limited resource pool. This universal constraint on expenditure does more than maintain honesty (as noted above), however: the reliance of sexual displays on high levels of nutrient acquisition may help maintain genetic variation in sexual signals that would otherwise be eroded by strong mate choice, and without which the selective basis for good-genes choice would disappear. Three mechanisms in particular probably help to maintain genetic variation in acquisition. 1) Because acquiring resources and converting them efficiently to useful forms depends on the high function of many biochemical pathways, condition is undoubtedly highly polygenic, which slows the erosion of genetic variation under strong directional selection by females (especially in the presence of epistatic interactions). 2) The highly polygenic nature of condition also presents a large target for mutation, which continually restores variation at the loci under selection. 3) The many loci underlying condition may also be particularly sensitive to environmental heterogeneity in time or space. By favouring the most ornate males, females acquire high performing genes for their offspring, regardless of the precise allele combinations that have conferred the ability to acquire resources. Selection on specific alleles is liable to fluctuate over time or space whenever allelic performance is strongly context-specific. I close by noting the considerable challenges in advancing research on sexual selection and life history allocation, including the fact that two key processes central to life history (acquisition and allocation) are latent variables that interact in complexways and are intrinsically difficult to measure empirically. In the remainder of my thesis I conduct a series of experiments involving decorated crickets, Gryllodes sigillatus, which are useful models for studying life history because they enable precise measurement of male reproductive effort. Male G. sigillatus face important allocation decisions owing to the highly polyandrous nature of females, and the substantial costs involved in signalling and mating. Chapter 2 examines sex differences in age-dependent reproductive effort as a function of diet and development stage. I reared outbred crickets using four combinations of diet nutritional quality, and studied the effects of these combinations on male and female reproductive effort (calling effort in males and fecundity in females) and longevity. While I expected males to be more sensitive than females to variation in diet and developmental changes in its quality, I actually observed the opposite: males in all treatments increased calling effort over time, exhibiting consistently positive covariance between calling effort and longevity across treatments. By contrast, the relationships between female reproductive effort and longevity changed dramatically across treatments, and females who lived to intermediate ages had the highest fecundity. Although my results support sex-specific selection on life history allocation over time, a compelling additional explanation for my findings relates to the strategic role of calling for achieving male fitness. In the absence of positive feedback from potential mates, perhaps male allocation to sexual advertisement is careful and only increases gradually as a function of accumulating metabolic resources and increasing risk of intrinsic mortality. Alleles underlying condition are expected to be particularly sensitive to environmental heterogeneity. While this sensitivity may help maintain additive variation in male quality (which is essential for the sustenance of adaptive good-genes mate choice, as noted in Chapter 1), too much environmental sensitivity could also underiii mine the signal value of the male trait. For example, if there are strong genotypeby- environment interactions (GEIs) for sexual advertisement, in a rapidly changing environment females risk favouring a male whose alleles are no longer best suited to current conditions. This problem is particularly pressing for animals like crickets where males exhibit a behaviourally plastic sexual display (such as calling), and so may dynamically adjust signalling effort over time. In Chapter 3, I used inbred lines of decorated crickets to quantify age and diet dependent genetic variation in male signalling. I demonstrate that while genetic correlations across diets were quite strong for morphological traits, correlations between measures of the male sexual trait rapidly approached zero as I increased the distance in time (i.e., across widely spaced ages) or diet (i.e., comparing more dissimilar dietary histories) between samples. While extrapolating from my laboratory experiments to nature is difficult, my findings nevertheless cast doubt on the value of behaviourally dynamic signals (such as cricket calls) for reliably indicating genetic quality in realistically complex environments. In Chapter 4 I used physiological assays to evaluate factors affecting metabolite storage and use over time in decorated crickets. I manipulated the acquisition ability of all males using artificial diets that varied linearly in nutrient quality, and manipulated access to female mates over the course of the second week of adult life. By sacrificing crickets at key stages before and after manipulating the diet and social environment, I was able to estimate changes in stored metabolites, and relate these changes to calling effort and longevity. During the first week of adulthood (in the absence of females), higher diet quality significantly increased calling effort and storage of lipid, glycogen, and carbohydrate (but not protein). The presence of females increased both the probability of calling and the amount of calling during the second week, whereas diet quality only improved calling effort. By the end of the second week, calling effort had decreased, even by high quality males in the presence of females, suggesting a depletion of resources. Furthermore, the loss of condition during week 2 covaried with calling effort during the previous week irrespective of diet. Males who started the second week in high condition lost more glycogen and carbohydrate than rivals; meanwhile, lipid accumulation covaried positively with calling effort during week 2. The contrasting patterns of storage and use for lipids compared to the ‘quick-release’ metabolites (glycogen and carbohydrates) affirms starkly distinct functions for the different storage components, and underlines the importance of specific physiological measures in life history research. Finally, in the general discussion, I attempt to synthesise my thesis’s contributions to the study of life history trade-offs involving behavioural sexual displays.

Resumo: O mal-do-fio (ou queima-do-fio) é uma doença causada pelo fungo Basidiomiceto Ceratobasidium sp., que afeta diversas plantas frutíferas nativas ou cultivadas. A doença ocorre com mais freqüência em zonas de alta precipitação e temperaturas elevadas, típicas de regiões de florestas tropicais como a Amazônia e a Mata Atlântica. Em São Paulo, recentemente detectou-se a ocorrência do mal-do-fio, em caquizeiro na região de Mogi das Cruzes. Essa doença pode- se tornar importante com a expansão do cultivo de fruteiras no Estado. A maioria das pesquisas sobre o patossistema focalizou a epidemiologia e o controle do fungo. Entretanto a etiologia do patógeno ainda não está totalmente definida, especialmente para populações do fungo infectando caqui e chá no Estado de São Paulo. Há também pouca informação sobre a divergência genética entre populações do patógeno de hospedeiros distintos como caqui e chá. O primeiro objetivo deste trabalho foi determinar o posicionamento filogenético global de populações de Ceratobasidium sp. do caqui e do chá, em relação a espécies de Ceratobasidium sp. descritas no mundo. Foram analisadas seqüências de DNA da região ITS-5.8S do rDNA, inferindo-se a história dos alelos ou haplótipos deste lócus, por meio de métodos filogenéticos, cladísticos e coalescentes. Observou-se que uso de C. noxium é apropriado para denominar espécies associadas ao mal-do- fio em caqui e chá, apesar de C. noxium do caqui e do chá constituírem populações filogeneticamente independentes, as quais denominamos de Grupo Diospyrus e Grupo Camellia. Este estudo trouxe uma contribuição importante para a compreensão das relações filogenéticas e biologia de populações de C. noxium em caqui e chá. Uma vez esclarecidas as questões filogenéticas, o segundo objetivo deste trabalho foi testar a patogenicidade cruzada de... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The white-thread blight is a disease caused by the Basidiomycete fungus Ceratobasidium sp. that affects several native or cropped tree fruits. This disease frequently occurs in zones of high precipitation and high temperatures typical of the tropical forest regions such as the Amazon and the Atlantic Forest. In São Paulo, the occurrence of the white-thread blight was detected only recently on kaki orchards closer to Mogi das Cruzes. That disease can become important with the expansion of the fruit trees cropping areas in the State. Most of the researches about the pathosystem has focused on the epidemiology and control of fungus. However the etiology of the pathogen is not totally defined yet, especially for the fungus populations infecting kaki and tea in São Paulo State. There is also little information available about the biological and genetic divergence between pathogen populations from distinct hosts, such as kaki and tea. The first objective of this research was to determine the global phylogenetic placement of populations of Ceratobasidium from kaki and tea, considering the species of Ceratobasidium described throughout the world. Sequences of the ITS-5.8S region of the rDNA were analyzed, inferring the alleles or haplotypes history for this locus, by phylogenetics, cladistisc and coalescent methods. We observed that the use of C. noxium is appropriate to denominate the fungus species associate with the white-thread blight on kaki and tea, despite the fact that C. noxium from kaki and tea constitutes phylogenetically independent populations, which we denominate Diospyrus and Camellia groups. This study brought an important contribution for the understanding of the phylogenetics and population biology of C. noxium infecting kaki and tea. Once the phylogenetics subjects have been cleared, the second objective of this work was to test the cross-pathogenicity... (Complete abstract, access electronic address below) / Orientador: Paulo Cezar Ceresini / Coorientador: Alcebíades Ribeiro Campos / Banca: Adriana Zanin Kronka / Banca: Cézar Junior Bueno / Mestre