Empiricism, Natural Regularity, and Necessity

This dissertation has two parts. In the first, I set out and defend a new empirical method of practicing metaphysics. The method avoids appeals to intuitions, ordinary beliefs, and the like. It does not accept basic principles of simplicity, unity, and the like. Instead, it proceeds from logic, analytic principles, and immediate experience alone. In the second part of my dissertation, I apply this method to the philosophy of laws of nature. I argue that there are excellent empirical reasons to accept governing laws instead of laws that reduce to other features of the world, such as natural regularities or facts about bare dispositions. The central idea is that observed natural regularities constitute strong evidence in favor of governing laws and against all competing theories. Further, I argue that the only intelligible account of governing laws is one according to which the connection between law and regularity is an irreducible necessary connection. Thus, the second part of my dissertation constitutes a new argument for metaphysically interesting a posteriori necessities

Quadrilateral-octagon coordinates for almost normal surfaces

Normal and almost normal surfaces are essential tools for algorithmic 3-manifold topology, but to use them requires exponentially slow enumeration algorithms in a high-dimensional vector space. The quadrilateral coordinates of Tollefson alleviate this problem considerably for normal surfaces, by reducing the dimension of this vector space from 7n to 3n (where n is the complexity of the underlying triangulation). Here we develop an analogous theory for octagonal almost normal surfaces, using quadrilateral and octagon coordinates to reduce this dimension from 10n to 6n. As an application, we show that quadrilateral-octagon coordinates can be used exclusively in the streamlined 3-sphere recognition algorithm of Jaco, Rubinstein and Thompson, reducing experimental running times by factors of thousands. We also introduce joint coordinates, a system with only 3n dimensions for octagonal almost normal surfaces that has appealing geometric properties.Comment: 34 pages, 20 figures; v2: Simplified the proof of Theorem 4.5 using cohomology, plus other minor changes; v3: Minor housekeepin

The virtual Haken conjecture: Experiments and examples

A 3-manifold is Haken if it contains a topologically essential surface. The Virtual Haken Conjecture says that every irreducible 3-manifold with infinite fundamental group has a finite cover which is Haken. Here, we discuss two interrelated topics concerning this conjecture. First, we describe computer experiments which give strong evidence that the Virtual Haken Conjecture is true for hyperbolic 3-manifolds. We took the complete Hodgson-Weeks census of 10,986 small-volume closed hyperbolic 3-manifolds, and for each of them found finite covers which are Haken. There are interesting and unexplained patterns in the data which may lead to a better understanding of this problem. Second, we discuss a method for transferring the virtual Haken property under Dehn filling. In particular, we show that if a 3-manifold with torus boundary has a Seifert fibered Dehn filling with hyperbolic base orbifold, then most of the Dehn filled manifolds are virtually Haken. We use this to show that every non-trivial Dehn surgery on the figure-8 knot is virtually Haken.Comment: Published by Geometry and Topology at http://www.maths.warwick.ac.uk/gt/GTVol7/paper12.abs.htm

Massive Quiescent Cores in Orion. -- II. Core Mass Function

We have surveyed submillimeter continuum emission from relatively quiescent regions in the Orion molecular cloud to determine how the core mass function in a high mass star forming region compares to the stellar initial mass function. Such studies are important for understanding the evolution of cores to stars, and for comparison to formation processes in high and low mass star forming regions. We used the SHARC II camera on the Caltech Submillimeter Observatory telescope to obtain 350 \micron data having angular resolution of about 9 arcsec, which corresponds to 0.02 pc at the distance of Orion. Our analysis combining dust continuum and spectral line data defines a sample of 51 Orion molecular cores with masses ranging from 0.1 \Ms to 46 \Ms and a mean mass of 9.8 \Ms, which is one order of magnitude higher than the value found in typical low mass star forming regions, such as Taurus. The majority of these cores cannot be supported by thermal pressure or turbulence, and are probably supercritical.They are thus likely precursors of protostars. The core mass function for the Orion quiescent cores can be fitted by a power law with an index equal to -0.85$\pm$0.21. This is significantly flatter than the Salpeter initial mass function and is also flatter than the core mass function found in low and intermediate star forming regions. Thus, it is likely that environmental processes play a role in shaping the stellar IMF later in the evolution of dense cores and the formation of stars in such regions.Comment: 30 pages, 10 figures, accepted by Ap

A High-Mass Protobinary System in the Hot Core W3(H2O)

We have observed a high-mass protobinary system in the hot core W3(H2O) with the BIMA Array. Our continuum maps at wavelengths of 1.4mm and 2.8mm both achieve sub-arcsecond angular resolutions and show a double-peaked morphology. The angular separation of the two sources is 1.19" corresponding to 2.43X10^3 AU at the source distance of 2.04 kpc. The flux densities of the two sources at 1.4mm and 2.8mm have a spectral index of 3, translating to an opacity law of kappa ~ nu. The small spectral indices suggest that grain growth has begun in the hot core. We have also observed 5 K components of the CH3CN (12-11) transitions. A radial velocity difference of 2.81 km/s is found towards the two continuum peaks. Interpreting these two sources as binary components in orbit about one another, we find a minimum mass of 22 Msun for the system. Radiative transfer models are constructed to explain both the continuum and methyl cyanide line observations of each source. Power-law distributions of both density and temperature are derived. Density distributions close to the free-fall value, r^-1.5, are found for both components, suggesting continuing accretion. The derived luminosities suggest the two sources have equivalent zero-age main sequence (ZAMS) spectral type B0.5 - B0. The nebular masses derived from the continuum observations are about 5 Msun for source A and 4 Msun for source C. A velocity gradient previously detected may be explained by unresolved binary rotation with a small velocity difference.Comment: 38 pages, 9 figures, accepted by The Astrophysical Journa

Force-controlled pose optimization and trajectory planning for chained Stewart platforms

Introduction: We study optimization methods for poses and movements of chained Stewart platforms (SPs) that we call an “Assembler” Robot. These chained SPs are parallel mechanisms that are stronger, stiffer, and more precise, on average, than their serial counterparts at the cost of a smaller range of motion. By linking these units in a series, their individual limitations are overcome while maintaining truss-like rigidity. This opens up potential uses in various applications, especially in complex space missions in conjunction with other robots.Methods: To enhance the efficiency and longevity of the Assembler Robot, we developed algorithms and optimization models. The main goal of these methodologies is to efficiently decide on favorable positions and movements that reduce force loads on the robot, consequently minimizing wear.Results: The optimized maneuvers of the interior plates of the Assembler result in more evenly distributed load forces through the legs of each constituent SP. This optimization allows for a larger workspace and a greater overall payload capacity. Our computations primarily focus on assemblers with four chained SPs.Discussion: Although our study primarily revolves around assemblers with four chained SPs, our methods are versatile and can be applied to an arbitrary number of SPs. Furthermore, these methodologies can be extended to general over-actuated truss-like robot architectures. The Assembler, designed to function collaboratively with several other robots, holds promise for a variety of space missions

The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference

HLA class I-binding predictions are widely used to identify candidate peptide targets of human CD8+ T cell responses. Many such approaches focus exclusively on a limited range of peptide lengths, typically 9 aa and sometimes 9-10 aa, despite multiple examples of dominant epitopes of other lengths. In this study, we examined whether epitope predictions can be improved by incorporating the natural length distribution of HLA class I ligands. We found that, although different HLA alleles have diverse length-binding preferences, the length profiles of ligands that are naturally presented by these alleles are much more homogeneous. We hypothesized that this is due to a defined length profile of peptides available for HLA binding in the endoplasmic reticulum. Based on this, we created a model of HLA allele-specific ligand length profiles and demonstrate how this model, in combination with HLA-binding predictions, greatly improves comprehensive identification of CD8+ T cell epitopes.Fil: Trolle, Thomas. Technical University of Denmark; DinamarcaFil: McMurtrey, Curtis. Oklahoma State University; Estados UnidosFil: Sidney, John. La Jolla Institute for Allergy and Immunology; Estados UnidosFil: Bardet, Wilfried. Oklahoma State University; Estados UnidosFil: Osborn, Sean C.. Oklahoma State University; Estados UnidosFil: Kaever, Thomas. La Jolla Institute for Allergy and Immunology; Estados UnidosFil: Sette, Alessandro. La Jolla Institute for Allergy and Immunology; Estados UnidosFil: Hildebrand, Willliam H.. Oklahoma State University; Estados UnidosFil: Nielsen, Morten. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas ; Argentina. Universidad Nacional de San Martín; ArgentinaFil: Peters, Bjoern. La Jolla Institute for Allergy and Immunology; Estados Unido

Dust in Spiral Galaxies: Comparing Emission and Absorption to Constrain Small-Scale and Very Cold Structures

The detailed distribution of dust in the disks of spiral galaxies is important to understanding the radiative transfer within disks, and to measuring overall dust masses if significant quantities of dust are either very opaque or very cold. We address this issue by comparing measures of dust absorption, using the galaxy-overlap technique in the optical, with measures of the dust grains' thermal emission from 50-2000 micron using ISOPHOT on board ISO and SCUBA at the JCMT. We examine three spiral galaxies projected partially in front of E/S0 galaxies --- AM1316-241, NGC 5545, and NGC 5091 (for NGC 5091 we have only optical and ISO data). Adopting an empirical exponential model for the dust distribution, we compare column densities and dust masses derived from the absorption and emission techniques. This comparison is sensitive to the amount of dust mass in small, opaque structures, which would not contribute strongly to area-weighted absorption measures, and to very cold dust, which would contribute to optical absorption but provide only a small fraction of the sub-mm emission. In AM1316-241, we find global dust masses of 2-5 x 10^7 M_solar, both techniques agreeing at the 50% level. NGC 5545 has about half this dust mass. The concordance of dust masses is well within the errors expected from our knowledge of the radial distribution of dust, and argues against any dominant part of the dust mass being so cold or opaque. The 50-2000 micron data are well fitted by modified Planck functions with an emissivity law beta=-2, at 21 +/- 2 K. We also present 12 micron ISOCAM observations of these pairs.Comparison of H-alpha and 12 micron images of NGC 5545 indicate that ISOCAM images are reliable tracers of star formation.Comment: 16 pages, 4 tables, 8 figures, in press for October Astronomical Journa

HLA class I molecules consistently present internal influenza epitopes

Cytotoxic T lymphocytes (CTL) limit influenza virus replication and prevent morbidity and mortality upon recognition of HLA class I presented epitopes on the surface of virus infected cells, yet the number and origin of the viral epitopes that decorate the infected cell are unknown. To understand the presentation of influenza virus ligands by human MHC class I molecules, HLA-B*0702-presented viral peptides were directly identified following influenza infection. After transfection with soluble class I molecules, peptide ligands unique to infected cells were eluted from isolated MHC molecules and identified by comparative mass spectrometry (MS). Then CTL were gathered following infection with influenza and viral peptides were tested for immune recognition. We found that the class I molecule B*0702 presents 3-6 viral ligands following infection with different strains of influenza. Peptide ligands derived from the internal viral nucleoprotein (NP418-426 and NP 473-481) and from the internal viral polymerase subunit PB1 (PB1 329-337) were presented by B*0702 following infection with each of 3 different influenza strains; ligands NP418-426, NP 473-481, and PB1329-337 derived from internal viral proteins were consistently revealed by class I HLA. In contrast, ligands derived from hemagglutinin (HA) and matrix protein (M1) were presented intermittently on a strain-by-strain basis. When tested for immune recognition, HLA-B*0702 transgenic mice responded to NP418-426 and PB1 329-337 consistently and NP473-481 intermittently while ligands from HA and M1 were not recognized. These data demonstrate an emerging pattern whereby class I HLA reveal a handful of internal viral ligands and whereby CTL recognize consistently presented influenza ligands