There are two main aims of this thesis: the first is to demonstrate that there is an important version of empiricism - "methodological empiricism"- which is a central part of the empiricist tradition ...but has been neglected incurrent philosophy of science. The second aim is to develop methodological empiricism in light of current science. The first aim is met by first articulating what I take methodological empricism to mean, alongside articulating the more dominant version of empiricism - "epistemic empiricism". I explicate both via several characteristics for each, and then trace a history of both positions from Ancient Western philosophy up until current times. Finally, I give evidence of the neglect of methodological empiricism in current philosophy of science. The second aim is met by, first, presenting four criteria for a current version of methodological empiricism that are directly derived from the characteristics of methodological empiricism through its history. I then consider three topics within recent philosophy of science that prima facie pose a challenge to methodological empiricism, all of which can be broadly characterised as appearing to be non-empirical in some way - analogue confirmation, philosophy of computer simulations, and non-empirical theory confirmation. It is argued that, ultimately, analogue confirmation and computer simulation are compatible with methodological empiricism, but that non-empirical theory confirmation is not. I argue that this should give us good reason to reject non-empirical theory confirmation.
Spring wild turkey (Meleagris gallopavo) hunting is a foundational activity for many hunters across North America. Managing turkey hunters and turkey hunting is, therefore, a priority for state and ...provincial fish and wildlife management agencies. Early stages of the current SARS‐CoV‐2 (COVID‐19) pandemic in the United States coincided with 2020 spring turkey hunting seasons across the U.S. Potential effects of increases in peoples' time available for hunting on effort and turkey populations could have been substantial. We surveyed the primary wildlife biologist tasked with wild turkey management for each state and provincial jurisdiction with a huntable wild turkey population to determine turkey hunter and hunting dynamics before and during the spring 2020 turkey season. Biologists in 47 states responded to the survey. Results varied among states but hunting license sales, the number of hunters afield, harvest, total hunter‐days afield, and the number of days individual hunters were afield were greater in 2020 than the mean from the previous 3 years (2017–2019) in many states. Although hunting effort and total reported harvest increased in most states in 2020 from the previous 3‐year average, take‐per‐unit‐effort (i.e., harvest per hunter day) decreased in 93% of jurisdictions from which data were available, supporting the finding that increases in turkey harvest in spring 2020 were a result of a COVID‐related increase in participation and effort and not increases in turkey abundance. We recommend using these reference data for turkey population and turkey hunter monitoring pre‐ and post‐pandemic. Monitoring efforts should include wildlife population and habitat evaluations and study of hunter dynamics in a social science framework.
We evaluated turkey hunter and hunting dynamics before and during the spring 2020 turkey season corresponding with the outbreak of the 2020 COVID‐19 pandemic. Hunting license sales, the number of hunters afield, harvest, total hunter‐days afield, and the number of days individual hunters were afield increased in 2020. Although hunting effort and total reported harvest increased in most states, take‐per‐unit‐effort decreased in 93% of jurisdictions, supporting the finding that increases in turkey harvest in spring 2020 were a result of a COVID‐related increase in participation and effort and not increases in turkey abundance.
Rare copy number variants (CNVs) disrupting ASTN2 or both ASTN2 and TRIM32 have been reported at 9q33.1 by genome-wide studies in a few individuals with neurodevelopmental disorders (NDDs). The ...vertebrate-specific astrotactins, ASTN2 and its paralog ASTN1, have key roles in glial-guided neuronal migration during brain development. To determine the prevalence of astrotactin mutations and delineate their associated phenotypic spectrum, we screened ASTN2/TRIM32 and ASTN1 (1q25.2) for exonic CNVs in clinical microarray data from 89 985 individuals across 10 sites, including 64 114 NDD subjects. In this clinical dataset, we identified 46 deletions and 12 duplications affecting ASTN2. Deletions of ASTN1 were much rarer. Deletions near the 3′ terminus of ASTN2, which would disrupt all transcript isoforms (a subset of these deletions also included TRIM32), were significantly enriched in the NDD subjects (P = 0.002) compared with 44 085 population-based controls. Frequent phenotypes observed in individuals with such deletions include autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), speech delay, anxiety and obsessive compulsive disorder (OCD). The 3′-terminal ASTN2 deletions were significantly enriched compared with controls in males with NDDs, but not in females. Upon quantifying ASTN2 human brain RNA, we observed shorter isoforms expressed from an alternative transcription start site of recent evolutionary origin near the 3′ end. Spatiotemporal expression profiling in the human brain revealed consistently high ASTN1 expression while ASTN2 expression peaked in the early embryonic neocortex and postnatal cerebellar cortex. Our findings shed new light on the role of the astrotactins in psychopathology and their interplay in human neurodevelopment.
Concerns about destruction of wild turkey (Meleagris gallopavo) nests traditionally restricted the application of prescribed-fire to the dormant season in the southeastern United States. Periodic ...dormantseason burns were used to open forest understories and increase forage and nesting cover for wild turkeys. However, much of the Southeast historically burned during late spring and early summer (i.e., growing season), which tended to decrease understory woody vegetation and promote grasses and forbs, an important spring and summer food for wild turkeys. Despite the potential benefits of growing-season burns, landscapescale application coincident with turkey nesting may destroy nests and reduce or redistribute woody nesting cover. We determined turkey nest-site selection and nest survival in a landscape managed with frequent growing-season burns. We monitored radio-tagged female wild turkeys to locate nests and determine nest survival. We compared vegetation composition and structure at nest sites to random sites within dominant cover types and calculated the probability of nest destruction as the product of the proportion of wild turkey nests active and the proportion of the landscape burned. Females selected shrub-dominated lowland ecotones (a transitional vegetation community between upland pine and bottomland hardwoods) for nesting and avoided upland pine. Ecotones had greater cover than upland pine and estimated nest survival in lowlands (60%) was greater than in uplands (10%). Although approximately 20% of the study area was burned concurrent with nesting activity, only 3.3% of monitored nests were destroyed by fire, and we calculated that no more than 6% of all turkey nests were exposed to fire annually on our study site. We suggest that growingseason burns have a minimal direct effect on turkey nest survival but may reduce nesting cover and structural and compositional heterogeneity in uplands, especially on poor quality soils. A combination of dormant and growing-season burns may increase nesting cover in uplands, while maintaining open stand conditions.
Objective: To compare the frequency of the pathogens of nosocomial pneumonia in a community-based teaching hospital to the frequencies previously published, and to evaluate recommendations for the ...therapy of nosocomial pneumonia in this setting. Design: Retrospective review of prospectively acquired data accrued during 9 randomized single-blinded and 4 single-agent investigational antibiotic studies for the therapy of pneumonia in hospitalized patients between 1981 and 1989. Setting: The study was performed at a university affiliated, community-based teaching Department of Veterans Affairs Medical Center. Patients: Patients were hospitalized on the acute medical/surgical and intermediate medicine wards. Informed consent was obtained prior to enrolling patients into the respective antimicrobial studies. Pneumonia was documented radiographically and clinically for each patient. Results: Two hundred thirty-one episodes of nosocomial pneumonia were treated. Overall, 51% of pneumonias were caused by Streptococcus pneumoniae or Hemophilus influenzae with or without other organisms that were not gramnegative bacilli. Gram-negative bacilli, with or without other organisms, accounted for only 26% of all nosocomial pneumonias. Overall, monotherapy with a cephalosporin (usually a broadspectrum agent) was equally efficacious compared with combination therapy (87% versus 81%, respectively). Cure rates for nosocomial pneumonias from gram-negative bacilli treated with these 2 therapies also were similar (70% versus 60%, respectively). Conclusions: In nontertiary care settings, gram-negative bacilli may cause fewer episodes of nosocomial pneumonia (26% in this study) than noted by previously published reports, which indicated that these organisms account for 50% of nosocomial pneumonias. Further, S pneumoniae and H influenzae may account etiologically for many of these nosocomial pneumonias. Monotherapy with an extended-spectrum cephalosporin may be more appropriate than combined treatment with a β-lactam and an aminoglycoside in a nontertiary care setting, thereby reducing potential toxicity in an older, hospitalized patient population.
Malaria is a deadly disease caused by Eukaryotic, single-cell parasites from the genus Plasmodium, with P. falciparum associated with the most deadly instances of the disease. With 228 million cases ...and over 400,000 deaths in 2018, the continuous rise of anti-malarial resistant P. falciparum parasites is a threat to global health. Research into the parasite’s cellular biology uncovers potential weakness that may be exploited to kill the parasite, but this research has been historically difficult due to the haploid nature of the parasite and its recalcitrance to genetic manipulation. Conditional knockdown systems, in which parasite protein expression is controlled by small molecules, and the adaptation of CRISPR/Cas9 genome editing for use in P. falciparum has recently made research into the parasite’s cellular biology more feasible. This dissertation combines these advances, presenting a detailed protocol for using CRISPR/Cas9 genome editing to introduce conditional knockdown systems into the parasite and demonstrating how those systems were used to investigate a protein exported by the parasite into its host red blood cell. Then, these same methods are used and built upon to provide a detailed investigation of PfJ2, an essential chaperone and thioredoxin-domain protein located in the parasite’s endoplasmic reticulum (ER). The P. falciparum ER is an organelle neglected in research, despite its numerous essential functions. I uncover interactions between PfJ2 and other essential proteins that reside in or pass through the ER, and I leverage the protein’s thioredoxin domain to provide new insights into the process of disulfide bond formation in the oxidative environment of the parasite’s ER. This process likely involved PfJ2 and members of the Protein Disulfide Isomerase (PDI) family, one of which—PfPDI8—I demonstrate is also essential for parasite survival. Finally, I use a chemical biology approach to show that a small molecule can disrupt the redox interactions between PfJ2, PfPDI8, and their substrates. These results suggest that these essential proteins, and the process of disulfide bond formation in the ER, are a new aspect of the parasite’s biology that could be exploited for anti-malarial drug development.
We used aerial surveys and reports from experienced birders and biologists to identify potentially important sites for wintering shorebirds in coastal Florida. We visited 273 sites in November and ...December 1993 to assess use by shorebirds and, based on abundance and number of species, we selected the 60 most important sites. We visited these 60 sites at least 3 times between 16 Dec. 1993 and 1 Mar. 1994 and recorded 25 species among an estimated 30,501 shorebirds wintering at the sites. Dunlin (Calidris alpina), Western Sandpipers (C. mauri), Sanderlings (C. alba), and dowitchers (Limnodromus spp.) were the most commonly observed species. Coastal Florida was winter host to >3% of the estimated North American population of Wilson's Plovers (Charadrius wilsonia), Piping Plovers (C. melodus), and American Oystercatchers (Haematopus palliatus). Fifty-three of the 60 most important sites were on Florida's west coast. St. George Sound, Tampa Bay, and Florida Bay contained sites with the highest numbers and most species of shorebirds.
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