In defense of mechanism

In Life Itself and in Essays on Life Itself, Robert Rosen (1991, 2000) argued that machines were, in principle, incapable of modeling the defining feature of living systems, which he claimed to be the existence of closed causal loops. Rosen's argument has been used to support critiques of computational models in ecological psychology. This article shows that Rosen's attack on mechanism is fundamentally misconceived. It is, in fact, of the essence of a mechanical system that it contains closed causal loops. Moreover, Rosen's epistemology is based on a strong form of indirect realism and his arguments, if correct, would call into question some of the fundamental principles of ecological psychology

The External Tape Hypothesis: a Turing machine based approach to cognitive computation

The symbol processing or "classical cognitivist" approach to mental computation suggests that the cognitive architecture operates rather like a digital computer. The components of the architecture are input, output and central systems. The input and output systems communicate with both the internal and external environments of the cognizer and transmit codes to and from the rule governed, central processing system which operates on structured representational expressions in the internal environment. The connectionist approach, by contrast, suggests that the cognitive architecture should be thought of as a network of interconnected neuron-like processing elements (nodes) which operates rather like a brain. Connectionism distinguishes input, output and central or "hidden" layers of nodes. Connectionists claim that internal processing consists not of the rule governed manipulation of structured symbolic expressions, but of the excitation and inhibition of activity and the alteration of connection strengths via message passing within and between layers of nodes in the network. A central claim of the thesis is that neither symbol processing nor connectionism provides an adequate characterization of the role of the external environment in cognitive computation. An alternative approach, called the External Tape Hypothesis (ETH), is developed which claims, on the basis of Turing's analysis of routine computation, that the Turing machine model can be used as the basis for a theory which includes the environment as an essential part of the cognitive architecture. The environment is thought of as the tape, and the brain as the control of a Turing machine. Finite state automata, Turing machines, and universal Turing machines are described, including details of Turing's original universal machine construction. A short account of relevant aspects of the history of digital computation is followed by a critique of the symbol processing approach as it is construed by influential proponents such as Allen Newell and Zenon Pylyshyn among others. The External Tape Hypothesis is then developed as an alternative theoretical basis. In the final chapter, the ETH is combined with the notion of a self-describing Turing machine to provide the basis for an account of thinking and the development of internal representations

An exploratory comparison of Kentucky public school districts that primarily select the “Compensating Rate”

Public school districts in the Commonwealth of Kentucky are primarily funded from federal, state, and local sources. While the proportion of each of these funding sources differs from district to district, the local property tax is one source that is within the control of locally-elected officials: the members of the local Board of Education. While some Boards of Education choose to increase local tax rates to increase local revenue, others do not. This research suggests that property value assessments and median incomes of districts that choose not to increase tax rates are similar. A majority of the counties studied are under the statewide average in these two measures. This suggests that these two measures are an indicator in a district’s proclivity to increase property tax rates. However, these same districts did not show similarities when comparing unemployment rates and the General Fund Balance as a percentage of expenditures. These two measures are more heterogeneous in their distribution above and below the statewide average line. This suggests that while important financial and economic indicators, they do not appear to be characteristics that would lead to further understanding of Board of Education tax policy trends

An evolutionary perspective on the kinome of malaria parasites

Malaria parasites belong to an ancient lineage that diverged very early from the main branch of eukaryotes. The approximately 90-member plasmodial kinome includes a majority of eukaryotic protein kinases that clearly cluster within the AGC, CMGC, TKL, CaMK and CK1 groups found in yeast, plants and mammals, testifying to the ancient ancestry of these families. However, several hundred millions years of independent evolution, and the specific pressures brought about by first a photosynthetic and then a parasitic lifestyle, led to the emergence of unique features in the plasmodial kinome. These include taxon-restricted kinase families, and unique peculiarities of individual enzymes even when they have homologues in other eukaryotes. Here, we merge essential aspects of all three malaria-related communications that were presented at the Evolution of Protein Phosphorylation meeting, and propose an integrated discussion of the specific features of the parasite's kinome and phosphoproteome

Variations in Ocean Surface Temperature due to Near-Surface Flow: Straining the Cool Skin Layer

The aqueous thermal boundary layer near to the ocean surface, or skin layer, has thickness O(1 mm) and plays an important role in controlling the exchange of heat between the atmosphere and the ocean. Theoretical arguments and experimental measurements are used to investigate the dynamics of the skin layer under the influence of an upwelling flow, which is imposed in addition to free convection below a cooled water surface. Previous theories of straining flow in the skin layer are considered and a simple extension of a surface straining model is posed to describe the combination of turbulence and an upwelling flow. An additional theory is also proposed, conceptually based on the buoyancy-driven instability of a laminar straining flow cooled from above. In all three theories considered two distinct regimes are observed for different values of the Péclet number, which characterizes the ratio of advection to diffusion within the skin layer. For large Péclet numbers, the upwelling flow dominates and increases the free surface temperature, or skin temperature, to follow the scaling expected for a laminar straining flow. For small Péclet numbers, it is shown that any flow that is steady or varies over long time scales produces only a small change in skin temperature by direct straining of the skin layer. Experimental measurements demonstrate that a strong upwelling flow increases the skin temperature and suggest that the mean change in skin temperature with Péclet number is consistent with the theoretical trends for large Péclet number flow. However, all of the models considered consistently underpredict the measured skin temperature, both with and without an upwelling flow, possibly a result of surfactant effects not included in the models

Genome sequence of a gammaherpesvirus from a common bottlenose dolphin (Tursiops truncatus)

A herpesvirus genome was sequenced directly from a biopsy specimen of a rectal lesion from a female common bottlenose dolphin. This genome sequence comprises a unique region (161,235 bp) flanked by multiple copies of a terminal repeat (4,431 bp) and contains 72 putative genes. The virus was named common bottlenose dolphin gammaherpesvirus 1

Convection in a mushy-layer along a heated wall

Motivated by the mushy zones of sea ice, volcanoes, and icy moons of the outer solar system, we perform a theoretical and numerical study of boundary-layer convection along a vertical heated wall in a bounded ideal mushy region. The mush is comprised of a porous and reactive binary alloy with a mixture of saline liquid in a solid matrix, and is studied in the near-eutectic approximation. Here we demonstrate the existence of four regions and study their behavior asymptotically. Starting from the bottom of the wall, the four regions are (i) an isotropic corner region; (ii) a buoyancy dominated vertical boundary layer; (iii) an isotropic connection region; and (iv) a horizontal boundary layer at the top boundary with strong gradients of pressure and buoyancy. Scalings from numerical simulations are consistent with the theoretical predictions. Close to the heated wall, the convection in the mushy layer is similar to a rising buoyant plume abruptly stopped at the top, leading to increased pressure and temperature in the upper region, whose impact is discussed as an efficient melting mechanism

COLLABORATIVE RESEARCH: Microparticle/tephra analysis of the WAIS Divide ice core

This award supports a project to perform continuous microparticle concentration and size distribution measurements (using coulter counter and state-of-the-art laser detector methods), analysis of biologically relevant trace elements associated with microparticles (Fe, Zn, Co, Cd, Cu), and tephra measurements on the WAIS Divide ice core. This initial three-year project includes analysis of ice core spanning the instrumental (~1850-present) to mid- Holocene (~5000 years BP) period, with sample resolution ranging from subannual to decadal. The intellectual merit of the project is that it will help in establishing the relationships among climate, atmospheric aerosols from terrestrial and volcanic sources, ocean biogeochemistry, and greenhouse gases on several timescales which remain a fundamental problem in paleoclimatology. The atmospheric mineral dust plays an important but uncertain role in direct radiative forcing, and the microparticle datasets produced in this project will allow us to examine changes in South Pacific aerosol loading, atmospheric dynamics, and dust source area climate. The phasing of changes in aerosol properties within Antarctica, throughout the Southern Hemisphere, and globally is unclear, largely due to the limited number of annually dated records extending into the glacial period and the lack of atephra framework to correlate records. The broader impacts of the proposed research are an interdisciplinary approach to climate science problems, and will contribute to several WAIS Divide science themes as well as the broader paleoclimate and oceanographic communities. Because the research topics have a large and direct societal relevance, the project will form a centerpiece of various outreach efforts at UMaine and NMT including institution websites, public speaking, local K-12 school interaction, media interviews and news releases, and popular literature. At least one PhD student and one MS student will be directly supported by this project, including fieldwork, core processing, laboratory analysis, and data interpretation/publication. We expect that one graduate student per year will apply for a core handler/assistant driller position through the WAIS Divide Science Coordination Office, and that undergraduate student involvement will result in several Capstone experience projects (a UMaine graduation requirement). Data and ideas generated from the project will be integrated into undergraduate and graduate course curricula at both institutions

Thermal Convection over Fractal Surfaces

We use well resolved numerical simulations with the Lattice Boltzmann Method to study Rayleigh-B\'enard convection in cells with a fractal boundary in two dimensions for $Pr = 1$ and $Ra \in \left[10^7, 10^{10}\right]$. The fractal boundaries are functions characterized by power spectral densities $S(k)$ that decay with wavenumber, $k$, as $S(k) \sim k^{p}$ ($p < 0$). The degree of roughness is quantified by the exponent $p$ with $p < -3$ for smooth (differentiable) surfaces and $-3 \le p < -1$ for rough surfaces with Hausdorff dimension $D_f=\frac{1}{2}(p+5)$. By computing the exponent $\beta$ in power law fits $Nu \sim Ra^{\beta}$, where $Nu$ and $Ra$ are the Nusselt and the Rayleigh numbers for $Ra \in \left[10^8, 10^{10}\right]$, we observe that heat transport scaling increases with roughness over the top two decades of $Ra \in \left[10^8, 10^{10}\right]$. For $p$ $= -3.0$, $-2.0$ and $-1.5$ we find $\beta = 0.288 \pm 0.005, 0.329 \pm 0.006$ and $0.352 \pm 0.011$, respectively. We also observe that the Reynolds number, $Re$, scales as $Re \sim Ra^{\xi}$, where $\xi \approx 0.57$ over $Ra \in \left[10^7, 10^{10}\right]$, for all $p$ used in the study. For a given value of $p$, the averaged $Nu$ and $Re$ are insensitive to the specific realization of the roughness.Comment: 15 pages, 13 figure

Objectively measured physical activity and fat mass in a large cohort of children

Background Previous studies have been unable to characterise the association between physical activity and obesity, possibly because most relied on inaccurate measures of physical activity and obesity. Methods and Findings We carried out a cross sectional analysis on 5,500 12-year-old children enrolled in the Avon Longitudinal Study of Parents and Children. Total physical activity and minutes of moderate and vigorous physical activity (MVPA) were measured using the Actigraph accelerometer. Fat mass and obesity (defined as the top decile of fat mass) were measured using the Lunar Prodigy dual x-ray emission absorptiometry scanner. We found strong negative associations between MVPA and fat mass that were unaltered after adjustment for total physical activity. We found a strong negative dose-response association between MVPA and obesity. The odds ratio for obesity in adjusted models between top and the bottom quintiles of minutes of MVPA was 0.03 (95% confidence interval [CI] 0.01-0.13, p-value for trend &lt; 0.0001) in boys and 0.36 (95% CI 0.17-0.74, p-value for trend = 0.006) in girls. Conclusions We demonstrated a strong graded inverse association between physical activity and obesity that was stronger in boys. Our data suggest that higher intensity physical activity may be more important than total activity