Do functions explain? Hegel and the organizational view

In this paper I return to Hegel's dispute with Kant over the conceptual ordering of external and internal purposiveness to distinguish between two conceptions of teleology at play in the contemporary function debate. I begin by outlining the three main views in the debate (the etiological, causal role and organizational views). I argue that only the organizational view can maintain the capacity of function ascriptions both to explain the presence of a trait and to identify its contribution to a current system, for it is the only view that considers teleology as a natural cause. To establish how teleology can be considered as a natural cause, advocates of the organizational view return to Kant's analysis of internal purposiveness. However, while Kant identifies the requirements that an object must meet to satisfy the demands of teleological judgment, I suggest that he denies that we can know whether they are truly met. I argue that Hegel's philosophy of nature is better equipped to determine how internal purposiveness can be considered as a natural cause, for it grounds organization in a form of purposiveness that is more fundamental than a designer's intention

Decline in condition of northern bluefin tuna (Thunnus thynnus) in the Gulf of Maine

The northern bluefin tuna (Thunnus thynnus) is a highly mobile apex predator in the Gulf of Maine. Despite current stock assessments that indicate historically high abundance of its main prey, Atlantic herring (Clupea harengus), commercial fishermen have observed declines in the somatic condition of northern bluefin tuna during the last decade. We examined this claim by reviewing detailed logbooks of northern bluefin tuna condition from a local fishermen’s cooperative and applying multinomial regression, a robust tool for exploring how a categorical variable may be related to other variables of interest. The data set contained >3082 observations of condition (fat and oil content and fish shape) from fish landed between 1991 and 2004. Energy from stored lipids is used for migration and reproduction; therefore a reduction in energy acquisition on bluefin tuna feeding grounds could diminish allocations to growth and gamete production and have detrimental consequences for rebuilding the western Atlantic population. A decline in northern bluefin tuna somatic condition could indicate substantial changes in the bottom-up transfer of energy in the Gulf of Maine, shifts in their reproductive or migratory patterns, impacts of fishing pressure, or synergistic effects from multiple causes

Nicotinic α7 acetylcholine receptor-mediated currents are not modulated by the tryptophan metabolite kynurenic acid in adult hippocampal interneurons

The  tryptophan  metabolite,  kynurenic  acid (KYNA),  is  classically  known  to  be  an antagonist  of ionotropic glutamate receptors. Within the last decade several reports have been published suggesting that KYNA also blocks nicotinic acetylcholine receptors (nAChRs) containing the α7 subunit (α7*). Most of these reports involve either indirect measurements of KYNA effects on α7 nAChR function, or are reports of KYNA effects in complicated in vivo systems.  However, a recent report investigating KYNA interactions with α7 nAChRs failed to detect an interaction using direct measurements of α7 nAChRs function.  Further, it showed that a KYNA blockade of α7 nAChR stimulated GABA release (an indirect measure of α7 nAChR function) was not due to KYNA blockade of the α7 nAChRs. The current study measured the direct effects of KYNA on α7-containing nAChRs expressed on interneurons in the hilar and CA1 stratum radiatum regions of the mouse hippocampus and on interneurons in the CA1 region of the rat hippocampus.  Here we show that KYNA does not block α7* nACHRs using direct patch-­clamp recording of α7 currents in adult brain slices

The Effect of Phosphorylation on the Electron Capture Dissociation of Peptide Ions

The effect of site and frequency of phosphorylation on the electron capture dissociation of peptide ions has been investigated. The ECD of a suite of synthetic peptides (APLSFRGSLPKSYVK; one unmodified, three singly-phosphorylated, three-doubly phosphorylated, and one triplyphosphorylated); two tryptic phosphopeptides (YKVPQLEIVPNpSAEER, α-casein and FQpSEEQQQTEDELQDK, β-casein) and their unmodified counterparts, were determined over a range of ECD cathode potentials. The results show that, for doubly-charged precursor ions, the presence of phosphorylation has a deleterious effect on ECD sequence coverage. The fragmentation patterns observed suggest that for peptides with multiple basic residues, the phospho-groups exist in their deprotonated form and form salt-bridges with protonated amino acid side chains. The fragmentation observed for the acidic tryptic peptides suggested the presence of noncovalent interactions, which were perturbed on phosphorylation. Increasing the ECD electron energy significantly improves sequence coverage. Alternatively, improved sequence coverage can be achieved by performing ECD on triply-charged precursor ions. The findings are important for the understanding of gas-phase fragmentation of phosphopeptides

Symbolic Powers of Monomial Ideals

We investigate symbolic and regular powers of monomial ideals. For a square-free monomial ideal $I$ in $k[x_0, \ldots, x_n]$ we show $I^{t(m+e-1)-e+r)}$ is a subset of $M^{(t-1)(e-1)+r-1}(I^{(m)})^t$ for all positive integers $m$, $t$ and $r$, where $e$ is the big-height of $I$ and $M = (x_0, \ldots, x_n)$. This captures two conjectures ($r=1$ and $r=e$): one of Harbourne-Huneke and one of Bocci-Cooper-Harbourne. We also introduce the symbolic polyhedron of a monomial ideal and use this to explore symbolic powers of non-square-free monomial ideals.Comment: 15 pages. Fixed typ

A kingdom in decline. Holocene range contraction of the lion (Panthera leo) modelled with Global Environmental Stratification

Aim We use ecological niche models and environmental stratification of palaeoclimate to reconstruct the changing range of the lion (Panthera leo) during the late Pleistocene and Holocene. Location The modern (early 21st century) range of the lion extends from southern Africa to the western Indian Subcontinent, yet through the 20th century this range has been drastically reduced in extent and become increasingly fragmented as a result of human impacts. Methods We use Global Environmental Stratification with MaxEnt ecological niche models to map environmental suitability of the lion under current and palaeoclimatic scenarios. By examining modelled lion range in terms of categorical environmental strata, we characterise suitable bioclimatic conditions for the lion in a descriptive manner. Results We find that lion habitat suitability has reduced throughout the Holocene, controlled by pluvial/interpluvial cycles. The aridification of the Sahara 6ka dramatically reduced lion range throughout North Africa. The association of Saharan aridification with the development of pastoralism and the growth of sedentary communities, who practised animal husbandry, would have placed additional and lasting anthropogenic pressures on the lion. Main Conclusions This research highlights the need to integrate the full effects of the fluctuating vegetation and desiccation of the Sahara into palaeoclimatic models, and provides a starting point for further continental-scale analyses of shifting faunal ranges through North Africa and the Near East during the Holocene. This scale of ecological niche modelling does not explain the current pattern of genetic variation in the lion, and we conclude that narrow but substantial physical barriers, such as rivers, have likely played a major role in population vicariance throughout the Late Pleistocene

SUSY Production From TeV Scale Blackhole at LHC

If the fundamental Planck scale is near a TeV, then we should expect to see TeV scale black holes at the LHC. Similarly, if the scale of supersymmetry breaking is sufficiently low, then we might expect to see light supersymmetric particles in the next generation of colliders. If the mass of the supersymmetric particle is of order a TeV and is comparable to the temperature of a typical TeV scale black hole, then such sparticles will be copiously produced via Hawking radiation: The black hole will act as a resonance for sparticles, among other things. In this paper we compared various signatures for SUSY production at LHC, and we contrasted the situation where the sparticles are produced directly via parton fusion processes with the situation where they are produced indirectly through black hole resonances. We found that black hole resonances provide a larger source for heavy mass SUSY (squark and gluino) production than the direct pQCD-SUSY production via parton fusion processes depending on the values of the Planck mass and blackhole mass. Hence black hole production at LHC may indirectly act as a dominant channel for SUSY production. We also found that the differential cross section d\sigma/dp_t for SUSY production increases as a function of the p_t (up to p_t equal to about 1 TeV or more) of the SUSY particles (squarks and gluinos), which is in sharp contrast with the pQCD predictions where the differential cross section d\sigma/dp_t decreases as p_t increases for high p_t about 1 TeV or higher. This is a feature for any particle emission from TeV scale blackhole as long as the temperature of the blackhole is very high (~ TeV). Hence measurement of increase of d\sigma/dp_t with p_t for p_t up to about 1 TeV or higher for final state particles might be a useful signature for blackhole production at LHC.Comment: Final Version, To Appear in Phys. Rev.

Dynamic range and mass accuracy of wide-scan direct infusion nanoelectrospray fourier transform ion cyclotron resonance mass spectrometry-based metabolomics increased by the spectral stitching method

Direct infusion nanoelectrospray Fourier transform ion cyclotron resonance mass spectrometry (DI nESI FT-ICR MS)offers high mass accuracy and resolution for analyzing complex metabolite mixtures. High dynamic range across a wide mass range, however, can only be achieved at the expense of mass accuracy, since the large numbers of ions entering the ICR detector induce adverse spacecharge effects. Here we report an optimized strategy for wide-scan DI nESI FT-ICR MS that increases dynamic range but maintains high mass accuracy. It comprises the collection if multiple adjacent selected ion monitoring (SIM) windows that are stitched together using novel algorithms. The final SIM-stitching method, derived from several optimization experiments, comprises 21 adjoining SIM windows each of width m/z 30 (from m/z 70 to 500; adjacent windows overlap by m/z 10) with an automated gain control (AGC) target of 1 105 charges. SIMstitching and wide-scan range (WSR; Thermo Electron)were compared using a defined standard to assess mass accuracy and a liver extract to assess peak count and dynamic range. SIM-stitching decreased the maximum mass error by 1.3- and 4.3-fold, and increased the peak count by 5.3- and 1.8-fold, versus WSR (AGC targets of 1 x 105 and 5 x 105, respectively). SIM-stitching achieved an rms mass error of 0.18 ppm and detected over 3000 peaks in liver extract. This novel approach increases metabolome coverage, has very high mass accuracy, and at 5.5 min/sample is conducive for high- throughput metabolomics

Spatially Resolved Galaxy Star Formation and its Environmental Dependence I

We use the photometric information contained in individual pixels of 44,964 (0.019<z<0.125 and -23.5<M_r<-20.5) galaxies in the Fourth Data Release (DR4) of the Sloan Digital Sky Survey to investigate the effects of environment on galaxy star formation (SF). We use the pixel-z technique, which combines stellar population synthesis models with photometric redshift template fitting on the scale of individual pixels in galaxy images. Spectral energy distributions are constructed, sampling a wide range of properties such as age, star formation rate (SFR), dust obscuration and metallicity. By summing the SFRs in the pixels, we demonstrate that the distribution of total galaxy SFR shifts to lower values as the local density of surrounding galaxies increases, as found in other studies. The effect is most prominent in the galaxies with the highest star formation, and we see the break in the SFR-density relation at a local galaxy density of $\approx 0.05$(Mpc/h)$^{-3}$. Since our method allows us to spatially resolve the SF distribution within galaxies, we can calculate the mean SFR of each galaxy as a function of radius. We find that on average the mean SFR is dominated by SF in the central regions of galaxies, and that the trend for suppression of SFR in high density environments is driven by a reduction in this nuclear SF. We also find that the mean SFR in the outskirts is largely independent of environmental effects. This trend in the mean SFR is shared by galaxies which are highly star forming, while those which are weakly star forming show no statistically significant correlation between their environment and the mean SFR at any radius.Comment: 37 pages, 11 figures. Referee's comments included and matches version accepted for publication in the Astrophysical Journal. For high resolution figures, see http://www.phyast.pitt.edu/~welikala/pixelz/paper1

Probing the mechanisms of electron capture dissociation mass spectrometry with nitrated peptides

Previously we have shown that the presence of 3-nitrotyrosine within a peptide sequence severely depletes the peptide backbone fragments typically observed following electron capture dissociation (ECD) mass spectrometry. Instead, ECD of nitrated peptides is characterised by abundant losses of small neutrals (hydroxyl radicals, water and ammonia). Here, we investigate the origin of ammonia loss by comparing the ECD behaviour of lysine- and arginine-containing nitrated peptides, and their N-acetylated counterparts, and nitrated peptides containing no basic amino acid residues. The results reveal that ammonia loss derives from the N-terminus of the peptides, however, the key finding of this work is the insight provided into the hierarchy of various proposed ECD mechanisms: the Utah-Washington mechanism, the electron predator mechanism and the Oslo mechanism