Emergence and Causal Powers

This thesis is concerned with the theory of ontological emergence; a theory that posits a new kind of entity – usually an emergent property – that occurs in complex systems and can explain some system-level behaviour. The theory holds that these emergent entities are dependent on, but novel with respect to, the components of those systems. Such entities have been invoked to explain behaviours as diverse as symmetry breaking in molecular physics to the possibility of personal agency. As a metaphysical theory it is useful wherever there is a lack of understanding about how system-level behaviour can occur based on what we know about the parts of that system. Besides its usefulness, the theory, if true, would profoundly impact our understanding of fundamental ontology. The first half of this thesis aims to do three things: first, identify a problem that emergence can explain; second, identify what emergence must do in order to solve that problem; third, identify a theory of emergence capable of doing it. The first and second of these aims will require us to outline issues in fundamental ontology and metaphysical methodology that are critical to any assessment of the possibility of emergence. They both also require making some commitments on these issues. Among such commitments will be a commitment to an ontology of properties as causal powers. I argue that emergence is a theory of macro-properties and that the primary problem it solves is the Problem of Reduction. I thereafter defend the theory of causal powers emergence against charges that it is incoherent and inconsonant with science and natural unity; these and other conflicts are shown to be unproblematic once the theory is properly explicated. In these respects, this thesis finds no fault with the coherence of emergence. The key claims in the second half of the thesis instead pertain to the necessity of emergence to solve the problem that I have identified. The argument is that even if causal novelty, holistic effects and top-down causation are apparent in a system, a properly developed causal powers ontology can account for them without positing new fundamental properties. I develop an option called non-reductive inherence based on a theory of powers admitting a plurality of compositional principles. The thesis ends by expounding this alternative to emergence and setting out some of the trade-offs between the positions

A National Strategy for the Conservation of Native Freshwater Mollusks

In 1998, a strategy document outlining the most pressing issues facing the conservation of freshwater mussels was published (NNMCC 1998). Beginning in 2011, the Freshwater Mollusk Conservation Society began updating that strategy, including broadening the scope to include freshwater snails. Although both strategy documents contained 10 issues that were deemed priorities for mollusk conservation, the identity of these issues has changed. For example, some issues (e.g., controlling dreissenid mussels, technology to propagate and reintroduce mussels, techniques to translocate adult mussels) were identified in the 1998 strategy, but are less prominent in the revised strategy, due to changing priorities and progress that has been made on these issues. In contrast, some issues (e.g., biology, ecology, habitat, funding) remain prominent concerns facing mollusk conservation in both strategies. In addition, the revised strategy contains a few issues (e.g., newly emerging stressors, education and training of the next generation of resource managers) that were not explicitly present in the 1998 strategy. The revised strategy states that to effectively conserve freshwater mollusks, we need to (1) increase knowledge of their distribution and taxonomy at multiple scales; (2) address the impacts of past, ongoing, and newly emerging stressors; (3) understand and conserve the quantity and quality of suitable habitat; (4) understand their ecology at the individual, population, and community levels; (5) restore abundant and diverse populations until they are self-sustaining; (6) identify the ecosystem services provided by mollusks and their habitats; (7) strengthen advocacy for mollusks and their habitats; (8) educate and train the conservation community and future generations of resource managers and researchers; (9) seek long-term funding to support conservation efforts; and (10) coordinate development of an updated and revised strategy every 15 years. Collectively addressing these issues should strengthen conservation efforts for North American freshwater mollusks

A New Class of Changing-Look LINERs

We report the discovery of six active galactic nuclei (AGN) caught "turning on" during the first nine months of the Zwicky Transient Facility (ZTF) survey. The host galaxies were classified as LINERs by weak narrow forbidden line emission in their archival SDSS spectra, and detected by ZTF as nuclear transients. In five of the cases, we found via follow-up spectroscopy that they had transformed into broad-line AGN, reminiscent of the changing-look LINER iPTF 16bco. In one case, ZTF18aajupnt/AT2018dyk, follow-up HST UV and ground-based optical spectra revealed the transformation into a narrow-line Seyfert 1 (NLS1) with strong [Fe VII, X, XIV] and He II 4686 coronal lines. Swift monitoring observations of this source reveal bright UV emission that tracks the optical flare, accompanied by a luminous soft X-ray flare that peaks ~60 days later. Spitzer follow-up observations also detect a luminous mid-infrared flare implying a large covering fraction of dust. Archival light curves of the entire sample from CRTS, ATLAS, and ASAS-SN constrain the onset of the optical nuclear flaring from a prolonged quiescent state. Here we present the systematic selection and follow-up of this new class of changing-look LINERs, compare their properties to previously reported changing-look Seyfert galaxies, and conclude that they are a unique class of transients well-suited to test the uncertain physical processes associated with the LINER accretion state.Comment: Submitted to ApJ, 31 pages, 17 Figures (excluding Appendix due to file size constraints but will be available in electronic version

Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle

Background Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals. Results Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle. Conclusions This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought

A Complex Suite of Forces Drives Gene Traffic from Drosophila X Chromosomes

Theoretical studies predict X chromosomes and autosomes should be under different selection pressures, and there should therefore be differences in sex-specific and sexually antagonistic gene content between the X and the autosomes. Previous analyses have identified an excess of genes duplicated by retrotransposition from the X chromosome in Drosophila melanogaster. A number of hypotheses may explain this pattern, including mutational bias, escape from X-inactivation during spermatogenesis, and the movement of male-favored (sexually antagonistic) genes from a chromosome that is predominantly carried by females. To distinguish among these processes and to examine the generality of these patterns, we identified duplicated genes in nine sequenced Drosophila genomes. We find that, as in D. melanogaster, there is an excess of genes duplicated from the X chromosome across the genus Drosophila. This excess duplication is due almost completely to genes duplicated by retrotransposition, with little to no excess from the X among genes duplicated via DNA intermediates. The only exception to this pattern appears within the burst of duplication that followed the creation of the Drosophila pseudoobscura neo-X chromosome. Additionally, we examined genes relocated among chromosomal arms (i.e., genes duplicated to new locations coupled with the loss of the copy in the ancestral locus) and found an excess of genes relocated off the ancestral X and neo-X chromosomes. Interestingly, many of the same genes were duplicated or relocated from the independently derived neo-X chromosomes of D. pseudoobscura and Drosophila willistoni, suggesting that natural selection favors the traffic of genes from X chromosomes. Overall, we find that the forces driving gene duplication from X chromosomes are dependent on the lineage in question, the molecular mechanism of duplication considered, the preservation of the ancestral copy, and the age of the X chromosome

ZTF 18aaqeasu (SN 2018byg): A Massive Helium-shell Double Detonation on a Sub-Chandrasekhar Mass White Dwarf

The detonation of a helium shell on a white dwarf has been proposed as a possible explosion triggering mechanism for Type Ia supernovae. Here, we report ZTF 18aaqeasu (SN 2018byg/ATLAS 18pqq), a peculiar Type I supernova, consistent with being a helium-shell double-detonation. With a rise time of $\approx 18$ days from explosion, the transient reached a peak absolute magnitude of $M_R \approx -18.2$ mag, exhibiting a light curve akin to sub-luminous SN 1991bg-like Type Ia supernovae, albeit with an unusually steep increase in brightness within a week from explosion. Spectra taken near peak light exhibit prominent Si absorption features together with an unusually red color ($g-r \approx 2$ mag) arising from nearly complete line blanketing of flux blue-wards of 5000 \AA. This behavior is unlike any previously observed thermonuclear transient. Nebular phase spectra taken at and after $\approx 30$ days from peak light reveal evidence of a thermonuclear detonation event dominated by Fe-group nucleosynthesis. We show that the peculiar properties of ZTF 18aaqeasu are consistent with the detonation of a massive ($\approx 0.15$ M$_\odot$) helium shell on a sub-Chandrasekhar mass ($\approx 0.75$ M$_\odot$) white dwarf after including mixing of $\approx 0.2$ M$_\odot$ of material in the outer ejecta. These observations provide evidence of a likely rare class of thermonuclear supernovae arising from detonations of massive helium shells.Comment: 10 pages, 6 figures. Submitted to ApJ

Intended Consequences Statement in Conservation Science and Practice

As the biodiversity crisis accelerates, the stakes are higher for threatened plants and animals. Rebuilding the health of our planet will require addressing underlying threats at many scales, including habitat loss and climate change. Conservation interventions such as habitat protection, management, restoration, predator control, trans location, genetic rescue, and biological control have the potential to help threatened or endangered species avert extinction. These existing, well-tested methods can be complemented and augmented by more frequent and faster adoption of new technologies, such as powerful new genetic tools. In addition, synthetic biology might offer solutions to currently intractable conservation problems. We believe that conservation needs to be bold and clear-eyed in this moment of great urgency

The Zwicky Transient Facility: Data Processing, Products, and Archive

The Zwicky Transient Facility (ZTF) is a new robotic time-domain survey currently in progress using the Palomar 48-inch Schmidt Telescope. ZTF uses a 47 square degree field with a 600 megapixel camera to scan the entire northern visible sky at rates of ~3760 square degrees/hour to median depths of g ~ 20.8 and r ~ 20.6 mag (AB, 5sigma in 30 sec). We describe the Science Data System that is housed at IPAC, Caltech. This comprises the data-processing pipelines, alert production system, data archive, and user interfaces for accessing and analyzing the products. The realtime pipeline employs a novel image-differencing algorithm, optimized for the detection of point source transient events. These events are vetted for reliability using a machine-learned classifier and combined with contextual information to generate data-rich alert packets. The packets become available for distribution typically within 13 minutes (95th percentile) of observation. Detected events are also linked to generate candidate moving-object tracks using a novel algorithm. Objects that move fast enough to streak in the individual exposures are also extracted and vetted. The reconstructed astrometric accuracy per science image with respect to Gaia is typically 45 to 85 milliarcsec. This is the RMS per axis on the sky for sources extracted with photometric S/N >= 10. The derived photometric precision (repeatability) at bright unsaturated fluxes varies between 8 and 25 millimag. Photometric calibration accuracy with respect to Pan-STARRS1 is generally better than 2%. The products support a broad range of scientific applications: fast and young supernovae, rare flux transients, variable stars, eclipsing binaries, variability from active galactic nuclei, counterparts to gravitational wave sources, a more complete census of Type Ia supernovae, and Solar System objects.Comment: 30 pages, 16 figures, Published in PASP Focus Issue on the Zwicky Transient Facility (doi: 10.1088/1538-3873/aae8ac

Insights into hominid evolution from the gorilla genome sequence.

Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution