Maladaptation and the paradox of robustness in evolution

Background. Organisms use a variety of mechanisms to protect themselves against perturbations. For example, repair mechanisms fix damage, feedback loops keep homeostatic systems at their setpoints, and biochemical filters distinguish signal from noise. Such buffering mechanisms are often discussed in terms of robustness, which may be measured by reduced sensitivity of performance to perturbations. Methodology/Principal Findings. I use a mathematical model to analyze the evolutionary dynamics of robustness in order to understand aspects of organismal design by natural selection. I focus on two characters: one character performs an adaptive task; the other character buffers the performance of the first character against perturbations. Increased perturbations favor enhanced buffering and robustness, which in turn decreases sensitivity and reduces the intensity of natural selection on the adaptive character. Reduced selective pressure on the adaptive character often leads to a less costly, lower performance trait. Conclusions/Significance. The paradox of robustness arises from evolutionary dynamics: enhanced robustness causes an evolutionary reduction in the adaptive performance of the target character, leading to a degree of maladaptation compared to what could be achieved by natural selection in the absence of robustness mechanisms. Over evolutionary time, buffering traits may become layered on top of each other, while the underlying adaptive traits become replaced by cheaper, lower performance components. The paradox of robustness has widespread implications for understanding organismal design

Charged Magnetic Brane Solutions in AdS_5 and the fate of the third law of thermodynamics

We construct asymptotically AdS_5 solutions to 5-dimensional Einstein-Maxwell theory with Chern-Simons term which are dual to 4-dimensional gauge theories, including N=4 SYM theory, in the presence of a constant background magnetic field B and a uniform electric charge density \rho. For the solutions corresponding to supersymmetric gauge theories, we find numerically that a small magnetic field causes a drastic decrease in the entropy at low temperatures. The near-horizon AdS_2 \times R^3 geometry of the purely electrically charged brane thus appears to be unstable under the addition of a small magnetic field. Based on this observation, we propose a formulation of the third law of thermodynamics (or Nernst theorem) that can be applied to black holes in the AdS/CFT context. We also find interesting behavior for smaller, non-supersymmetric, values of the Chern-Simons coupling k. For k=1 we exhibit exact solutions corresponding to warped AdS_3 black holes, and show that these can be connected to asymptotically AdS_5 spacetime. For k\leq 1 the entropy appears to go to a finite value at extremality, but the solutions still exhibit a mild singularity at strictly zero temperature. In addition to our numerics, we carry out a complete perturbative analysis valid to order B^2, and find that this corroborates our numerical results insofar as they overlap.Comment: 45 pages v2: added note about subsequent results found in arXiv:1003.130

Permeability and acoustic velocity controlling factors determined from x-ray tomography images of carbonate rocks

Carbonate reservoir rocks exhibit a great variability in texture that directly impacts petrophysical parameters. Many exhibit bi- and multimodal pore networks, with pores ranging from less than 1 μm to several millimeters in diameter. Furthermore, many pore systems are too large to be captured by routine core analysis, and well logs average total porosity over different volumes. Consequently, prediction of carbonate properties from seismic data and log interpretation is still a challenge. In particular, amplitude versus offset classification systems developed for clastic rocks, which are dominated by connected, intergranular, unimodal pore networks, are not applicable to carbonate rocks. Pore geometrical parameters derived from digital image analysis (DIA) of thin sections were recently used to improve the coefficient of determination of velocity and permeability versus porosity. Although this substantially improved the coefficient of determination, no spatial information of the pore space was considered, because DIA parameters were obtained from two-dimensional analyses. Here, we propose a methodology to link local and global pore-space parameters, obtained from three-dimensional (3-D) images, to experimental physical properties of carbonate rocks to improve P-wave velocity and permeability predictions. Results show that applying a combination of porosity, microporosity, and 3-D geometrical parameters to P-wave velocity significantly improves the adjusted coefficient of determination from 0.490 to 0.962. A substantial improvement is also observed in permeability prediction (from 0.668 to 0.948). Both results can be interpreted to reflect a pore geometrical control and pore size control on P-wave velocity and permeability

Sign-reversal of the in-plane resistivity anisotropy in hole-doped iron pnictides

The in-plane anisotropy of the electrical resistivity across the coupled orthorhombic and magnetic transitions of the iron pnictides has been extensively studied in the parent and electron-doped compounds. All these studies universally show that the resistivity $\rho_{a}$ across the long orthorhombic axis $a_{O}$ - along which the spins couple antiferromagnetically below the magnetic transition temperature - is smaller than the resistivity $\rho_{b}$ of the short orthorhombic axis $b_{O}$, i. e. $\rho_{a}<\rho_{b}$. Here we report that in the hole-doped compounds Ba$_{1-x}$K$_{x}$Fe$_{2}$As$_{2}$, as the doping level increases, the resistivity anisotropy initially becomes vanishingly small, and eventually changes sign for sufficiently large doping, i. e. $\rho_{b}<\rho_{a}$. This observation is in agreement with a recent theoretical prediction that considers the anisotropic scattering of electrons by spin-fluctuations in the orthorhombic/nematic state.Comment: This paper has been replaced by the new version offering new explanation of the experimental results first reported her

Quantum systems in weak gravitational fields

Fully covariant wave equations predict the existence of a class of inertial-gravitational effects that can be tested experimentally. In these equations inertia and gravity appear as external classical fields, but, by conforming to general relativity, provide very valuable information on how Einstein's views carry through in the world of the quantum.Comment: 22 pages. To be published in Proceedings of the 17th Course of the International School of Cosmology and Gravitation "Advances in the interplay between quantum and gravity physics" edited by V. De Sabbata and A. Zheltukhin, Kluwer Academic Publishers, Dordrech

Recent trends in cutaneous malignant melanoma in the Yorkshire region of England; incidence, mortality and survival in relation to stage of disease, 1993–2003

The aim of this study was to investigate recent trends in incidence, mortality and survival in patients diagnosed with malignant melanoma (MM) in relation to stage (Breslow thickness). Cases of primary invasive and in situ MM diagnosed between 1st January 1993 and 31st December 2003 in the former Yorkshire Health Authority were identified from cancer registry data. Over the study period, the incidence of invasive MM increased from 5.4 to 9.7 per 100 000 in male subjects and from 7.5 to 13.1 per 100 000 in female subjects. Most of this increase was seen in thin tumours (<1.5 mm). Thin tumours were more likely to be diagnosed in the younger age groups and be classified as superficial spreading melanoma. In situ melanoma rates increased only slightly. Over the same time period, mortality rates have been relatively constant in both male and female subjects. Five-year relative survival varied from 91.8% (95% CI 90.4–93.1) for patients with thin tumours to 41.5% (95% CI 36.7–46.3) for those with thick tumours. In multivariable analyses, Breslow thickness was the most important prognostic factor. Age, sex and level of deprivation were also identified as independent prognostic factors. The trends in incidence suggest that the increase is real, rather than an artefact of increased scrutiny, implying that primary prevention in the Yorkshire area of the UK has failed to control trends in incidence. Mortality, in contrast, appears to be levelling off, indicating that secondary prevention has been more effective

Cognitive architectures as Lakatosian research programmes: two case studies

Cognitive architectures - task-general theories of the structure and function of the complete cognitive system - are sometimes argued to be more akin to frameworks or belief systems than scientific theories. The argument stems from the apparent non-falsifiability of existing cognitive architectures. Newell was aware of this criticism and argued that architectures should be viewed not as theories subject to Popperian falsification, but rather as Lakatosian research programs based on cumulative growth. Newell's argument is undermined because he failed to demonstrate that the development of Soar, his own candidate architecture, adhered to Lakatosian principles. This paper presents detailed case studies of the development of two cognitive architectures, Soar and ACT-R, from a Lakatosian perspective. It is demonstrated that both are broadly Lakatosian, but that in both cases there have been theoretical progressions that, according to Lakatosian criteria, are pseudo-scientific. Thus, Newell's defense of Soar as a scientific rather than pseudo-scientific theory is not supported in practice. The ACT series of architectures has fewer pseudo-scientific progressions than Soar, but it too is vulnerable to accusations of pseudo-science. From this analysis, it is argued that successive versions of theories of the human cognitive architecture must explicitly address five questions to maintain scientific credibility

Accelerated in vivo proliferation of memory phenotype CD4+ T-cells in human HIV-1 infection irrespective of viral chemokine co-receptor tropism.

CD4(+) T-cell loss is the hallmark of HIV-1 infection. CD4 counts fall more rapidly in advanced disease when CCR5-tropic viral strains tend to be replaced by X4-tropic viruses. We hypothesized: (i) that the early dominance of CCR5-tropic viruses results from faster turnover rates of CCR5(+) cells, and (ii) that X4-tropic strains exert greater pathogenicity by preferentially increasing turnover rates within the CXCR4(+) compartment. To test these hypotheses we measured in vivo turnover rates of CD4(+) T-cell subpopulations sorted by chemokine receptor expression, using in vivo deuterium-glucose labeling. Deuterium enrichment was modeled to derive in vivo proliferation (p) and disappearance (d*) rates which were related to viral tropism data. 13 healthy controls and 13 treatment-naive HIV-1-infected subjects (CD4 143-569 cells/ul) participated. CCR5-expression defined a CD4(+) subpopulation of predominantly CD45R0(+) memory cells with accelerated in vivo proliferation (p = 2.50 vs 1.60%/d, CCR5(+) vs CCR5(-); healthy controls; P<0.01). Conversely, CXCR4 expression defined CD4(+) T-cells (predominantly CD45RA(+) naive cells) with low turnover rates. The dominant effect of HIV infection was accelerated turnover of CCR5(+)CD45R0(+)CD4(+) memory T-cells (p = 5.16 vs 2.50%/d, HIV vs controls; P<0.05), naïve cells being relatively unaffected. Similar patterns were observed whether the dominant circulating HIV-1 strain was R5-tropic (n = 9) or X4-tropic (n = 4). Although numbers were small, X4-tropic viruses did not appear to specifically drive turnover of CXCR4-expressing cells (p = 0.54 vs 0.72 vs 0.44%/d in control, R5-tropic, and X4-tropic groups respectively). Our data are most consistent with models in which CD4(+) T-cell loss is primarily driven by non-specific immune activation

Evaluation of the influence of kyphosis and scoliosis on intervertebral disc extrusion in French bulldogs

Although thoracic vertebral malformations with kyphosis and scoliosis are often considered incidental findings on diagnostic imaging studies of screw-tailed brachycephalic breeds, they have been suggested to interfere with spinal biomechanics and intervertebral disc degeneration. It is however unknown if an abnormal spinal curvature also predisposes dogs to develop clinically relevant intervertebral disc herniations. The aim of this study was to evaluate if the occurrence of thoracic vertebral malformations, kyphosis or scoliosis would be associated with a higher prevalence of cervical or thoracolumbar intervertebral disc extrusion in French bulldogs

Improving SNR and reducing training time of classifiers in large datasets via kernel averaging

Kernel methods are of growing importance in neuroscience research. As an elegant extension of linear methods, they are able to model complex non-linear relationships. However, since the kernel matrix grows with data size, the training of classifiers is computationally demanding in large datasets. Here, a technique developed for linear classifiers is extended to kernel methods: In linearly separable data, replacing sets of instances by their averages improves signal-to-noise ratio (SNR) and reduces data size. In kernel methods, data is linearly non-separable in input space, but linearly separable in the high-dimensional feature space that kernel methods implicitly operate in. It is shown that a classifier can be efficiently trained on instances averaged in feature space by averaging entries in the kernel matrix. Using artificial and publicly available data, it is shown that kernel averaging improves classification performance substantially and reduces training time, even in non-linearly separable data