Low demographic variability in wild primate populations: fitness impacts of variation, covariation, and serial correlation in vital rates.

In a stochastic environment, long-term fitness can be influenced by variation, covariation, and serial correlation in vital rates (survival and fertility). Yet no study of an animal population has parsed the contributions of these three aspects of variability to long-term fitness. We do so using a unique database that includes complete life-history information for wild-living individuals of seven primate species that have been the subjects of long-term (22-45 years) behavioral studies. Overall, the estimated levels of vital rate variation had only minor effects on long-term fitness, and the effects of vital rate covariation and serial correlation were even weaker. To explore why, we compared estimated variances of adult survival in primates with values for other vertebrates in the literature and found that adult survival is significantly less variable in primates than it is in the other vertebrates. Finally, we tested the prediction that adult survival, because it more strongly influences fitness in a constant environment, will be less variable than newborn survival, and we found only mixed support for the prediction. Our results suggest that wild primates may be buffered against detrimental fitness effects of environmental stochasticity by their highly developed cognitive abilities, social networks, and broad, flexible diets.

Modeling the evolution of regulatory elements by simultaneous detection and alignment with phylogenetic pair HMMs.

The computational detection of regulatory elements in DNA is a difficult but important problem impacting our progress in understanding the complex nature of eukaryotic gene regulation. Attempts to utilize cross-species conservation for this task have been hampered both by evolutionary changes of functional sites and poor performance of general-purpose alignment programs when applied to non-coding sequence. We describe a new and flexible framework for modeling binding site evolution in multiple related genomes, based on phylogenetic pair hidden Markov models which explicitly model the gain and loss of binding sites along a phylogeny. We demonstrate the value of this framework for both the alignment of regulatory regions and the inference of precise binding-site locations within those regions. As the underlying formalism is a stochastic, generative model, it can also be used to simulate the evolution of regulatory elements. Our implementation is scalable in terms of numbers of species and sequence lengths and can produce alignments and binding-site predictions with accuracy rivaling or exceeding current systems that specialize in only alignment or only binding-site prediction. We demonstrate the validity and power of various model components on extensive simulations of realistic sequence data and apply a specific model to study Drosophila enhancers in as many as ten related genomes and in the presence of gain and loss of binding sites. Different models and modeling assumptions can be easily specified, thus providing an invaluable tool for the exploration of biological hypotheses that can drive improvements in our understanding of the mechanisms and evolution of gene regulation.

Features of programmed cell death in intact Xenopus oocytes and early embryos revealed by near-infrared fluorescence and real-time monitoring.

Factors influencing apoptosis of vertebrate eggs and early embryos have been studied in cell-free systems and in intact embryos by analyzing individual apoptotic regulators or caspase activation in static samples. A novel method for monitoring caspase activity in living Xenopus oocytes and early embryos is described here. The approach, using microinjection of a near-infrared caspase substrate that emits fluorescence only after its proteolytic cleavage by active effector caspases, has enabled the elucidation of otherwise cryptic aspects of apoptotic regulation. In particular, we show that brief caspase activity (10 min) is sufficient to cause apoptotic death in this system. We illustrate a cytochrome c dose threshold in the oocyte, which is lowered by Smac, a protein that binds thereby neutralizing the inhibitor of apoptosis proteins. We show that meiotic oocytes develop resistance to cytochrome c, and that the eventual death of oocytes arrested in meiosis is caspase-independent. Finally, data acquired through imaging caspase activity in the Xenopus embryo suggest that apoptosis in very early development is not cell-autonomous. These studies both validate this assay as a useful tool for apoptosis research and reveal subtleties in the cell death program during early development. Moreover, this method offers a potentially valuable screening modality for identifying novel apoptotic regulators.

American Manna: Religious Responses to the American Industrial Food System

“American Manna: Religious Responses to the American Industrial Food System” is an investigation of the religious complexity present in religious food reform movements. I conducted ethnographic fieldwork at four field sites. These field sites are a Jewish organic vegetable farm where the farmers begin their days with meditation, a Christian raw vegan diet center run by Messianic Jews, a Christian family that raises their cattle on pastures and sends them to a halal processing plant for slaughter, and a Jewish farm where Christian and Buddhist farm staff helped to implement shmita, the biblical agricultural sabbatical year.

The religious people of America do not exist in neatly bound silos, so in my research I move with the religious people to the spaces that are less clearly defined as “Christian” or “Jewish.” I study religious food reformers within the framework of what I have termed “free-range religion” because they organize in groups outside the traditional religious organizational structures. My argument regarding free-range religion has three parts. I show that (1) perceived injustices within the American industrial food system have motivated some religious people to take action; (2) that when they do, they direct their efforts against the American food industry, and tend to do so outside traditional religious institutions; and finally, (3) in creating alternatives to the American food industry, religious people engage in inter-religious and extra-religious activism.

Chapter 1 serves as the introduction, literature review, and methodology overview. Chapter 2 focuses on the food-centered Judaism at the Adamah Environmental Fellowship at the Isabella Freedman Jewish Retreat Center in Falls Village, CT. In Chapter 3, I discuss the Hallelujah Diet as prescriptive literature and as it is put into practice at the Hallelujah Diet Retreat Center in Lake Lure, NC. Chapter 4 follows cows as they move from the grassy hills of Baldwin Family Farms in Yanceyville, NC to the meat counter at Whole Foods Markets. In Chapter 5, I consider the shmita year, the biblical agricultural sabbatical practice that was reimagined and implemented at Pearlstone Center in Baltimore, MD during 2014-2015. Chapter 6 will conclude this dissertation with a discussion of where religious food reform has been, where it is now, and a glimpse of what the future holds.

Psychological and Interpersonal Implications of Believing that Everything is One: Identity, Personality, Values, and Worldviews

For thousands of years, people from a variety of philosophical, religious, spiritual, and scientific perspectives have believed in the fundamental unity of all that exists, and this belief appears to be increasingly prevalent in Western cultures. The present research was the first investigation of the psychological and interpersonal implications of believing in oneness. Self-report measures were developed to assess three distinct variants of the belief in oneness – belief in the fundamental oneness of everything, of all living things, and of humanity – and studies examined how believing in oneness is associated with people’s self-views, attitudes, personality, emotions, and behavior. Using both correlational and experimental approaches, the findings supported the hypothesis that believing in oneness is associated with feeling greater connection and concern for people, nonhuman animals, and the environment, and in being particularly concerned for people and things beyond one’s immediate circle of friends and family. The belief is also associated with experiences in which everything is perceived to be one, and with certain spiritual and esoteric beliefs. Although the three variations of belief in oneness were highly correlated and related to other constructs similarly, they showed evidence of explaining unique variance in conceptually relevant variables. Belief in the oneness of humanity, but not belief in the oneness of living things, uniquely explained variance in prosociality, empathic concern, and compassion for others. In contrast, belief in the oneness of living things, but not belief in oneness of humanity, uniquely explained variance in beliefs and concerns regarding the well-being of nonhuman animals and the environment. The belief in oneness is a meaningful existential belief that is endorsed to varying degrees by a nontrivial portion of the population and that has numerous implications for people’s personal well-being and interactions with people, animals, and the natural world.