Underground railroads: citizen entitlements and unauthorized mobility in the antebellum period and today

In recent years, some scholars and prominent political figures have advocated the deepening of North American integration on roughly the European Union model, including the creation of new political institutions and the free movement of workers across borders. The construction of such a North American Union, if it included even a very thin trans-state citizenship regime, could represent the most significant expansion of individual entitlements in the region since citizenship was extended to former slaves in the United States. With such a possibility as its starting point, this article explores some striking parallels between the mass, legally prohibited movement across boundaries by fugitive slaves in the pre-Civil War period, and that by current unauthorized migrants to the United States. Both were, or are, met on their journeys by historically parallel groups of would-be helpers and hinderers. Their unauthorized movements in both periods serve as important signals of incomplete entitlements or institutional protections. Most crucially, moral arguments for extending fuller entitlements to both groups are shown here to be less distinct than may be prima facie evident, reinforcing the case for expanding and deepening the regional membership regime

Phylogenetic representativeness: a new method for evaluating taxon sampling in evolutionary studies

<p>Abstract</p> <p>Background</p> <p>Taxon sampling is a major concern in phylogenetic studies. Incomplete, biased, or improper taxon sampling can lead to misleading results in reconstructing evolutionary relationships. Several theoretical methods are available to optimize taxon choice in phylogenetic analyses. However, most involve some knowledge about the genetic relationships of the group of interest (i.e., the ingroup), or even a well-established phylogeny itself; these data are not always available in general phylogenetic applications.</p> <p>Results</p> <p>We propose a new method to assess taxon sampling developing Clarke and Warwick statistics. This method aims to measure the "phylogenetic representativeness" of a given sample or set of samples and it is based entirely on the pre-existing available taxonomy of the ingroup, which is commonly known to investigators. Moreover, our method also accounts for instability and discordance in taxonomies. A Python-based script suite, called PhyRe, has been developed to implement all analyses we describe in this paper.</p> <p>Conclusions</p> <p>We show that this method is sensitive and allows direct discrimination between representative and unrepresentative samples. It is also informative about the addition of taxa to improve taxonomic coverage of the ingroup. Provided that the investigators' expertise is mandatory in this field, phylogenetic representativeness makes up an objective touchstone in planning phylogenetic studies.</p

The Complexity of Approximating complex-valued Ising and Tutte partition functions

We study the complexity of approximately evaluating the Ising and Tutte partition functions with complex parameters. Our results are partly motivated by the study of the quantum complexity classes BQP and IQP. Recent results show how to encode quantum computations as evaluations of classical partition functions. These results rely on interesting and deep results about quantum computation in order to obtain hardness results about the difficulty of (classically) evaluating the partition functions for certain fixed parameters. The motivation for this paper is to study more comprehensively the complexity of (classically) approximating the Ising and Tutte partition functions with complex parameters. Partition functions are combinatorial in nature and quantifying their approximation complexity does not require a detailed understanding of quantum computation. Using combinatorial arguments, we give the first full classification of the complexity of multiplicatively approximating the norm and additively approximating the argument of the Ising partition function for complex edge interactions (as well as of approximating the partition function according to a natural complex metric). We also study the norm approximation problem in the presence of external fields, for which we give a complete dichotomy when the parameters are roots of unity. Previous results were known just for a few such points, and we strengthen these results from BQP-hardness to #P-hardness. Moreover, we show that computing the sign of the Tutte polynomial is #P-hard at certain points related to the simulation of BQP. Using our classifications, we then revisit the connections to quantum computation, drawing conclusions that are a little different from (and incomparable to) ones in the quantum literature, but along similar lines

Detecting Network Communities: An Application to Phylogenetic Analysis

This paper proposes a new method to identify communities in generally weighted complex networks and apply it to phylogenetic analysis. In this case, weights correspond to the similarity indexes among protein sequences, which can be used for network construction so that the network structure can be analyzed to recover phylogenetically useful information from its properties. The analyses discussed here are mainly based on the modular character of protein similarity networks, explored through the Newman-Girvan algorithm, with the help of the neighborhood matrix . The most relevant networks are found when the network topology changes abruptly revealing distinct modules related to the sets of organisms to which the proteins belong. Sound biological information can be retrieved by the computational routines used in the network approach, without using biological assumptions other than those incorporated by BLAST. Usually, all the main bacterial phyla and, in some cases, also some bacterial classes corresponded totally (100%) or to a great extent (>70%) to the modules. We checked for internal consistency in the obtained results, and we scored close to 84% of matches for community pertinence when comparisons between the results were performed. To illustrate how to use the network-based method, we employed data for enzymes involved in the chitin metabolic pathway that are present in more than 100 organisms from an original data set containing 1,695 organisms, downloaded from GenBank on May 19, 2007. A preliminary comparison between the outcomes of the network-based method and the results of methods based on Bayesian, distance, likelihood, and parsimony criteria suggests that the former is as reliable as these commonly used methods. We conclude that the network-based method can be used as a powerful tool for retrieving modularity information from weighted networks, which is useful for phylogenetic analysis