A mutation rate refers to the frequency at which DNA mutations occur in an organism over time. In organisms, mutations are the ultimate source of genetic variation on which selection may act. However, a large number of mutations over time can be detrimental to the cell. Mutation rates are the frequency at which these new mutations arise over time. This can give great insight into DNA repair mechanisms abilities as well as the mutagenic abilities of selected factors. CRISPR-Cas9 is a powerful tool for genome editing, but its off-target effects are not yet fully understood and studied. With its increasing implementation in science and medicine, it is crucial to understand the mutagenic potential of the tool. S. cerevisiae is a model organism for studying genetics due to its fast growth rate and eukaryotic nature. By integrating CRISPR-Cas9 systems into S. cerevisiae, the mutational burden of the technology can be measured and quantified using fluctuation assays. In this experiment, a fluctuation assay using canavanine selective plates was conducted to determine the mutational burden of CRISPR-Cas9 in S. cerevisiae. Multiple trials revealed that various strains of CRISPR-Cas9 had a mutation rate up to 3-fold higher than that of wild-type S. cerevisiae. This information is essential in improving the precision and safety of CRISPR-Cas9 editing in various applications, including gene therapy and biotechnology.

Throughout history, music has evolved. Composition and songwriting have changed in order to create fresh and original sounds. However, production has been emphasized more than ever in the modern music industry. Due to the fact that music generated with an instrument can only be organized using a specific range, diversity can be limited. Musical production and audio editing introduced an innovative solution. After the creation of the Digital Audio Workstation (DAW), recording transitioned from “being primarily a technical to an artistic matter” (Moorefield). Technology that established reverb, pitch shift, loop, pan, and countless other effects broadened melodic horizons and changed the way that musicians practiced their craft. Notably, once the recording process had been polished by the 1960s, the music industry entered an experimental phase. The term “producer” gained traction along with engineers. To this day, artists prioritize the individuals they choose to produce their album because this factor will drive the overall sound of a song or project. Moreover, an artist may choose to produce their own music as they grow more comfortable with creating music and working with editing software. There is an abundance of music being released into the world on an annual basis. Without production, the community would come to a monotonous halt, making music production the driving force behind musical evolution.

Previous recombination rate estimation studies in rhesus macaques have been mostly restricted to a singular approach (e.g., using microsatellite loci). Here, we employ a bilateral method in estimating recombination rates—pedigree-based and linkage-disequilibrium-based—from whole-genome data of rhesus macaques to estimate CO and NCO recombination events and to compare contemporary and historical rates of recombination.

Discussions of the nature of time can be enriched using insight from the field of biology. In the evolution of our species, biological timekeeping mechanisms have been honed to a fine point and can accurately adhere to a 24-hour cycle. When considering that these timekeeping mechanisms would only have evolved if they were reasonably accurate, it must be the case that our timekeeping systems are measuring a genuine feature of reality. This thesis explores this idea by discussing the veridicality of the circadian clock and contrasting it with the physiological origin of feelings of duration. As it turns out, duration can not be accounted for by the circadian clock, implying that the felt ‘flow’ of time is a cognitive illusion rather than a feature of objective reality. Given this, our knowledge of biology reconciles best with the Static View (B-theory) of time.

The study of macaque monkeys harbors advancements in the field of biomedical research. It is imperative to understand the genetic composition of different species of macaques to assess their accuracy as non-human primate (NHP) models for disease detection and treatment assessments. We sought to characterize the hybridization and admixture of the Southeast Asian macaques using single nucleotide polymorphism markers and analyzing the populations on the mainland and the island. Using AMOVA tests and STRUCTURE analysis, we determined that there are three distinct populations: Macaca mulatta, M. fascicularis fascicularis, and M. f. aurea. Furthermore, the island species holds an isolated population of M. f. aurea that demonstrate high inbreeding and genetic uniqueness compared to the mainland species. Findings from this study confirm that NHP models may need to be modified or updated according to changing allelic frequencies and genetic drift.

The relationship between science and religion in the modern day is complex to the point that the lines between them are often blurred. We have a need to distinguish the two from each-other for a variety of practical reasons. Various philosophies, theories, and tests have been suggested on the interaction between the two and how they are subdivided. One of the sets of criteria which has been shown to work was originally introduced in the opinion of Judge Overton in the case of McLean v Arkansas. McLean v Arkansas is a pivotal case in that it gave us a useful definition of what science is and isn’t in the context of the law. It used the already established Lemon test to show what counts as the establishment of religion. Given the distinction by Judge Overton, there are questions as to whether or not there is even overlap or tension between science and religion, such as in the theory of Stephen Jay Gould’s Nonoverlapping Magisteria (NOMA). What we find in this thesis is that the NOMA principle is doubtful at best. Through the discussion of McLean v. Arkansas, NOMA, and the commentaries of Professors Larry Laudan and Michael Ruse, this thesis develops a contextualization principle that can be used as a guide to develop further theories, particularly regarding the divisions between science and religion.

Cells have mechanisms in place to maintain the specific lipid composition of distinct organelles including vesicular transport by the endomembrane system and non-vesicular lipid transport by lipid transport proteins. Oxysterol Binding Proteins (OSBPs) are a family of lipid transport proteins that transfer lipids at various membrane contact sites (MCSs). OSBPs have been extensively investigated in human and yeast cells where twelve have been identified in Homo sapiens and seven in Saccharomyces cerevisiae. The evolutionary relationship between these well-characterized OSBPs is still unclear. Reconstructed OSBP phylogenies revealed that the ancestral Saccharomycotinan had four OSBPs, the ancestral Holomycotan had five OSBPs, the ancestral Holozoan had six OSBPs, the ancestral Opisthokont had three OSBPs, and the ancestral Eukaroyte had three OSBPs. Our analysis identified three clades of ancient OSBPs not present in animals or fungi.

Cancers of the reproductive tissues make up a significant portion of the cancer burden and mortality experienced by humans. Humans experience several proximal causative carcinogens that explain a portion of cancer risk, but an evolutionary viewpoint can provide a unique lens into the ultimate causes of reproductive cancer vulnerabilities. A life history framework allows us to make predictions on cancer prevalence based on a species’ tempo of reproduction. Moreover, certain variations in the susceptibility and prevalence of cancer may emerge due to evolutionary trade-offs between reproduction and somatic maintenance. For example, such trade-offs could involve the demand for rapid proliferation of cells in reproductive tissues that arises with reproductive events. In this study, I compiled reproductive cancer prevalence for 158 mammalian species and modeled the predictive power of 13 life history traits on the patterns of cancer prevalence we observed, such as Peto’s Paradox or slow-fast life history strategies. We predicted that fast-life history strategists will exhibit higher neoplasia prevalence risk due to reproductive trade-offs. Furthering this analytical framework can aid in predicting cancer rates and stratifying cancer risk across the tree of life.

Theories about the human origin in evolution and religion are fundamentally countering beliefs that are still debated to this day. This study continues to explore this relationship in the college population at a public university with the intention of targeting a diverse religious population. This research hopes to answer the question: does having greater literacy in evolution lead to a noninterventionist perspective on evolution? The prediction is that evidence of increased evolution comprehension will influence students to have a more agnostic, or noninterventionist, view on evolution. An evolution class was given a survey that had two parts broken into demographic and evolution sections with one question that asks about compatibility between evolution and religion. This was given twice in a single semester to track the growth of evolution knowledge and any other differences. There were 265 students in the initial survey, but only 223 responses in the post-survey. The compatibility question had 8 statements that range from creationist to atheistic perspectives and was divided into two sides: interventionist (divine involvement) and noninterventionist (deity may be present but does not intervene). More than 70% of the class had a noninterventionist perspective on evolution despite the Christian categories being the second largest group students identified with after agnostic. The agnostic statement was the top choice followed by the atheistic answer on the noninterventionist side. Lastly, there was some growth of evolution knowledge for each religious category in the evolution section but is not significant for interpretation. Based on the collected data, it is not sufficient to answer the question and requires more data collection via a longitudinal study.