Food for Thought: Genetically Modified Seeds as De Facto Standard Essential Patents

For several years, courts have been improperly calculating damages in cases involving the unlicensed use of genetically-modified (GM) seed technology. In particular, when courts determine patent damages based on the hypothetical negotiation method, they err in exaggerating these damages to a point where no rational negotiator would agree. In response, we propose a limited affirmative defense of an implied license due to the patent’s status as a de facto standard essential patent. To be classified as a de facto standard essential patent, the farmer must prove three elements that reflect the peculiarities of GM seeds used in farming: (1) dominance, (2) impracticability, and (3) necessary to fulfill a basic need. Based on the approaches used by courts and standard setting organizations in licensing standard essential patents in technological fields such as cell phones and software, designation of some GM seeds as standard essential patents allows the courts to imply a license from patentees to farmers on reasonable and non-discriminatory (RAND) terms. Doing so shifts the case from a tort-based patent infringement suit to a breach of contract dispute and alters the damages regime from one based in compensation, deterrence, and punishment (a tort approach) to one based solely in compensation (a contractual approach). As a result of this novel proposal, the damages calculations in these suits return to economic reality

The Sunyaev Zel'dovich effect: simulation and observation

The Sunyaev Zel'dovich effect (SZ effect) is a complete probe of ionized baryons, the majority of which are likely hiding in the intergalactic medium. We ran a $512^3$ $\Lambda$CDM simulation using a moving mesh hydro code to compute the statistics of the thermal and kinetic SZ effect such as the power spectra and measures of non-Gaussianity. The thermal SZ power spectrum has a very broad peak at multipole $l\sim 2000-10^4$ with temperature fluctuations $\Delta T \sim 15\mu$K. The power spectrum is consistent with available observations and suggests a high $\sigma_8\simeq 1.0$ and a possible role of non-gravitational heating. The non-Gaussianity is significant and increases the cosmic variance of the power spectrum by a factor of $\sim 5$ for $l<6000$. We explore optimal driftscan survey strategies for the AMIBA CMB interferometer and their dependence on cosmology. For SZ power spectrum estimation, we find that the optimal sky coverage for a 1000 hours of integration time is several hundred square degrees. One achieves an accuracy better than 40% in the SZ measurement of power spectrum and an accuracy better than 20% in the cross correlation with Sloan galaxies for $2000<l<5000$. For cluster searches, the optimal scan rate is around 280 hours per square degree with a cluster detection rate 1 every 7 hours, allowing for a false positive rate of 20% and better than 30% accuracy in the cluster SZ distribution function measurement.Comment: 34 pages, 20 figures. Submitted to ApJ. Simulation maps have been replaced by high resolution images. For higher resolution color images, please download from http://www.cita.utoronto.ca/~zhangpj/research/SZ/ We corrected a bug in our analysis. the SZ power spectrum decreases 50% and y parameter decrease 25

Supervoid Origin of the Cold Spot in the Cosmic Microwave Background

We use a WISE-2MASS-Pan-STARRS1 galaxy catalog to search for a supervoid in the direction of the Cosmic Microwave Background Cold Spot. We obtain photometric redshifts using our multicolor data set to create a tomographic map of the galaxy distribution. The radial density profile centred on the Cold Spot shows a large low density region, extending over 10's of degrees. Motivated by previous Cosmic Microwave Background results, we test for underdensities within two angular radii, $5^\circ$, and $15^\circ$. Our data, combined with an earlier measurement by Granett et al 2010, are consistent with a large $R_{\rm void}=(192 \pm 15)h^{-1} Mpc$ $(2\sigma)$ supervoid with $\delta \simeq -0.13 \pm 0.03$ centered at $z=0.22\pm0.01$. Such a supervoid, constituting a $\sim3.5 \sigma$ fluctuation in the $\Lambda CDM$ model, is a plausible cause for the Cold Spot.Comment: 4 pages, 2 figures, Proceedings of IAU 306 Symposium: Statistical Challenges in 21st Century Cosmolog

Fast and Credible Likelihood-Free Cosmology with Truncated Marginal Neural Ratio Estimation

Sampling-based inference techniques are central to modern cosmological data analysis; these methods, however, scale poorly with dimensionality and typically require approximate or intractable likelihoods. In this paper we describe how Truncated Marginal Neural Ratio Estimation (TMNRE) (a new approach in so-called simulation-based inference) naturally evades these issues, improving the $(i)$ efficiency, $(ii)$ scalability, and $(iii)$ trustworthiness of the inferred posteriors. Using measurements of the Cosmic Microwave Background (CMB), we show that TMNRE can achieve converged posteriors using orders of magnitude fewer simulator calls than conventional Markov Chain Monte Carlo (MCMC) methods. Remarkably, the required number of samples is effectively independent of the number of nuisance parameters. In addition, a property called \emph{local amortization} allows the performance of rigorous statistical consistency checks that are not accessible to sampling-based methods. TMNRE promises to become a powerful tool for cosmological data analysis, particularly in the context of extended cosmologies, where the timescale required for conventional sampling-based inference methods to converge can greatly exceed that of simple cosmological models such as $\Lambda$CDM. To perform these computations, we use an implementation of TMNRE via the open-source code \texttt{swyft}.Comment: v2: accepted journal version. v1: 37 pages, 13 figures. \texttt{swyft} is available at https://github.com/undark-lab/swyft, and demonstration code for cosmological examples is available at https://github.com/acole1221/swyft-CM

The Periodic Standing-Wave Approximation: Overview and Three Dimensional Scalar Models

The periodic standing-wave method for binary inspiral computes the exact numerical solution for periodic binary motion with standing gravitational waves, and uses it as an approximation to slow binary inspiral with outgoing waves. Important features of this method presented here are: (i) the mathematical nature of the ``mixed'' partial differential equations to be solved, (ii) the meaning of standing waves in the method, (iii) computational difficulties, and (iv) the ``effective linearity'' that ultimately justifies the approximation. The method is applied to three dimensional nonlinear scalar model problems, and the numerical results are used to demonstrate extraction of the outgoing solution from the standing-wave solution, and the role of effective linearity.Comment: 13 pages RevTeX, 5 figures. New version. A revised form of the nonlinearity produces better result

The Tully-Fisher Relation as a Measure of Luminosity Evolution: A Low Redshift Baseline for Evolving Galaxies

We use optical rotation curves to investigate the R-band Tully-Fisher properties of a sample of 90 spiral galaxies in close pairs. The galaxies follow the Tully-Fisher relation remarkably well, with the exception of eight distinct 3-sigma outliers. Although most of the outliers show signs of recent star formation, gasdynamical effects are probably the dominant cause of their anomalous Tully-Fisher properties. Four outliers with small emission line widths have very centrally concentrated line emission and truncated rotation curves; the central emission indicates recent gas infall after a close galaxy-galaxy pass. These four galaxies may be local counterparts to compact, blue galaxies at intermediate redshift. The remaining galaxies have a negligible offset from the reference Tully-Fisher relation, but a shallower slope (2.6-sigma significance) and a 25% larger scatter. We characterize the non-outlier sample with measures of distortion and star formation to search for third parameter dependence in the residuals of the TF relation. Severe kinematic distortion is the only significant predictor of TF residuals; this distortion is not, however, responsible for the slope difference from the reference distribution. Because the outliers are easily removed by sigma clipping, we conclude that even in the presence of some tidal distortion, detection of moderate luminosity evolution should be possible with high-redshift samples the size of this 90-galaxy study. (Abridged.)Comment: LaTeX document, 55 pages including 18 figures, to appear in A

The DEEP2 Galaxy Redshift Survey: Spectral classification of galaxies at z~1

We present a Principal Component Analysis (PCA)-based spectral classification, eta, for the first 5600 galaxies observed in the DEEP2 Redshift Survey. This parameter provides a very pronounced separation between absorption and emission dominated galaxy spectra - corresponding to passively evolving and actively star-forming galaxies in the survey respectively. In addition it is shown that despite the high resolution of the observed spectra, this parameter alone can be used to quite accurately reconstruct any given galaxy spectrum, suggesting there are not many `degrees of freedom' in the observed spectra of this galaxy population. It is argued that this form of classification, eta, will be particularly valuable in making future comparisons between high and low-redshift galaxy surveys for which very large spectroscopic samples are now readily available, particularly when used in conjunction with high-resolution spectral synthesis models which will be made public in the near future. We also discuss the relative advantages of this approach to distant galaxy classification compared to other methods such as colors and morphologies. Finally, we compare the classification derived here with that adopted for the 2dF Galaxy Redshift Survey and in so doing show that the two systems are very similar. This will be particularly useful in subsequent analyses when making comparisons between results from each of these surveys to study evolution in the galaxy populations and large-scale structure.Comment: 10 pages, 9 figures, Accepted for publication in Ap

Observational Constraints on Red and Blue Helium Burning Sequences

We derive the optical luminosity, colors, and ratios of the blue and red helium burning (HeB) stellar populations from archival Hubble Space Telescope observations of nineteen starburst dwarf galaxies and compare them with theoretical isochrones from Padova stellar evolution models across metallicities from Z=0.001 to 0.009. We find that the observational data and the theoretical isochrones for both blue and red HeB populations overlap in optical luminosities and colors and the observed and predicted blue to red HeB ratios agree for stars older than 50 Myr over the time bins studied. These findings confirm the usefulness of applying isochrones to interpret observations of HeB populations. However, there are significant differences, especially for the red HeB population. Specifically we find: (1) offsets in color between the observations and theoretical isochrones of order 0.15 mag (0.5 mag) for the blue (red) HeB populations brighter than M_V ~ -4 mag, which cannot be solely due to differential extinction; (2) blue HeB stars fainter than M_V ~ -3 mag are bluer than predicted; (3) the slope of the red HeB sequence is shallower than predicted by a factor of ~3; and (4) the models overpredict the ratio of the most luminous blue to red HeB stars corresponding to ages <50 Myr. Additionally, we find that for the more metal-rich galaxies in our sample (Z> 0.5 Zsolar) the red HeB stars overlap with the red giant branch stars in the color magnitude diagrams, thus reducing their usefulness as indicators of star formation for ages >100 Myr.Comment: 18 pages, 11 figures, 3 table

Transcriptomic analysis of field-droughted sorghum from seedling to maturity reveals biotic and metabolic responses.

Drought is the most important environmental stress limiting crop yields. The C4 cereal sorghum [Sorghum bicolor (L.) Moench] is a critical food, forage, and emerging bioenergy crop that is notably drought-tolerant. We conducted a large-scale field experiment, imposing preflowering and postflowering drought stress on 2 genotypes of sorghum across a tightly resolved time series, from plant emergence to postanthesis, resulting in a dataset of nearly 400 transcriptomes. We observed a fast and global transcriptomic response in leaf and root tissues with clear temporal patterns, including modulation of well-known drought pathways. We also identified genotypic differences in core photosynthesis and reactive oxygen species scavenging pathways, highlighting possible mechanisms of drought tolerance and of the delayed senescence, characteristic of the stay-green phenotype. Finally, we discovered a large-scale depletion in the expression of genes critical to arbuscular mycorrhizal (AM) symbiosis, with a corresponding drop in AM fungal mass in the plants' roots