Biodiversity informatics: the challenge of linking data and the role of shared identifiers

A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on biodiversity databases. The key to rich integration is a commitment to deploy and reuse globally unique, shared identifiers (such as DOIs and LSIDs), and the implementation of services that link those identifiers

Unifying Parsimonious Tree Reconciliation

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to address this research problem is to describe each individual evolution as a phylogenetic tree and construct a tree reconciliation which is parsimonious with respect to a given event model. Unfortunately, most of the previous approaches are designed only either for host-parasite systems, for gene tree/species tree reconciliation, or biogeography. Hence, a method is desirable, which addresses the general problem of mapping phylogenetic trees and covering all varieties of coevolving systems, including e.g., predator-prey and symbiotic relationships. To overcome this gap, we introduce a generalized cophylogenetic event model considering the combinatorial complete set of local coevolutionary events. We give a dynamic programming based heuristic for solving the maximum parsimony reconciliation problem in time O(n^2), for two phylogenies each with at most n leaves. Furthermore, we present an exact branch-and-bound algorithm which uses the results from the dynamic programming heuristic for discarding partial reconciliations. The approach has been implemented as a Java application which is freely available from http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

Prospects of Detecting Baryon and Quark Superfluidity from Cooling Neutron Stars

Baryon and quark superfluidity in the cooling of neutron stars are investigated. Observations could constrain combinations of the neutron or Lambda-hyperon pairing gaps and the star's mass. However, in a hybrid star with a mixed phase of hadrons and quarks, quark gaps larger than a few tenths of an MeV render quark matter virtually invisible for cooling. If the quark gap is smaller, quark superfluidity could be important, but its effects will be nearly impossible to distinguish from those of other baryonic constituents.Comment: 4 pages, 3 ps figures, uses RevTex(aps,prl). Submitted to Phys. Rev. Let

A window into the neutron star: Modelling the cooling of accretion heated neutron star crusts

In accreting neutron star X-ray transients, the neutron star crust can be substantially heated out of thermal equilibrium with the core during an accretion outburst. The observed subsequent cooling in quiescence (when accretion has halted) offers a unique opportunity to study the structure and thermal properties of the crust. Initially crust cooling modelling studies focussed on transient X-ray binaries with prolonged accretion outbursts (> 1 year) such that the crust would be significantly heated for the cooling to be detectable. Here we present the results of applying a theoretical model to the observed cooling curve after a short accretion outburst of only ~10 weeks. In our study we use the 2010 outburst of the transiently accreting 11 Hz X-ray pulsar in the globular cluster Terzan 5. Observationally it was found that the crust in this source was still hot more than 4 years after the end of its short accretion outburst. From our modelling we found that such a long-lived hot crust implies some unusual crustal properties such as a very low thermal conductivity (> 10 times lower than determined for the other crust cooling sources). In addition, we present our preliminary results of the modelling of the ongoing cooling of the neutron star in MXB 1659-298. This transient X-ray source went back into quiescence in March 2017 after an accretion phase of ~1.8 years. We compare our predictions for the cooling curve after this outburst with the cooling curve of the same source obtained after its previous outburst which ended in 2001.Comment: 4 pages, 1 figure, to appear in the proceedings of "IAUS 337: Pulsar Astrophysics - The Next 50 Years" eds: P. Weltevrede, B.B.P. Perera, L. Levin Preston & S. Sanida

Going nuclear: gene family evolution and vertebrate phylogeny reconciled

Gene duplications have been common throughout vertebrate evolution, introducing paralogy and so complicating phylogenctic inference from nuclear genes. Reconciled trees are one method capable of dealing with paralogy, using the relationship between a gene phylogeny and the phylogeny of the organisms containing those genes to identify gene duplication events. This allows us to infer phylogenies from gene families containing both orthologous and paralogous copies. Vertebrate phylogeny is well understood from morphological and palaeontological data, but studies using mitochondrial sequence data have failed to reproduce this classical view. Reconciled tree analysis of a database of 118 vertebrate gene families supports a largely classical vertebrate phylogeny

Transient Observers and Variable Constants, or Repelling the Invasion of the Boltzmann's Brains

If the universe expands exponentially without end, ``ordinary observers'' like ourselves may be vastly outnumbered by ``Boltzmann's brains,'' transient observers who briefly flicker into existence as a result of quantum or thermal fluctuations. One might then wonder why we are so atypical. I show that tiny changes in physics--for instance, extremely slow variations of fundamental constants--can drastically change this result, and argue that one should be wary of conclusions that rely on exact knowledge of the laws of physics in the very distant future.Comment: 4 pages, LaTeX; v2: added references; v3: more discussion of setting, alternative approaches, now 5 pages; v4: added discussion of the effect of quantum fluctuations on varying constants, appendix added, now 7 pages; v5: new reference, minor correctio

Negative vacuum energy densities and the causal diamond measure

Arguably a major success of the landscape picture is the prediction of a small, non-zero vacuum energy density. The details of this prediction depends in part on how the diverging spacetime volume of the multiverse is regulated, a question that remains unresolved. One proposal, the causal diamond measure, has demonstrated many phenomenological successes, including predicting a distribution of positive vacuum energy densities in good agreement with observation. In the string landscape, however, the vacuum energy density is expected to take positive and negative values. We find the causal diamond measure gives a poor fit to observation in such a landscape -- in particular, 99.6% of observers in galaxies seemingly just like ours measure a vacuum energy density smaller than we do, most of them measuring it to be negative.Comment: 9 pages, 3 figures; v2: minor error fixed (results essentially unchanged), reference added; v3: published version, includes a few clarification

No Time Asymmetry from Quantum Mechanics

With CPT-invariant initial conditions that commute with CPT-invariant final conditions, the respective probabilities (when defined) of a set of histories and its CPT reverse are equal, giving a CPT-symmetric universe. This leads me to question whether the asymmetry of the Gell-Mann--Hartle decoherence functional for ordinary quantum mechanics should be interpreted as an asymmetry of {\it time} .Comment: 14 pages, Alberta-Thy-11-9

Entropy bounds for charged and rotating systems

It was shown in a previous work that, for systems in which the entropy is an extensive function of the energy and volume, the Bekenstein and the holographic entropy bounds predict new results. In this paper, we go further and derive improved upper bounds to the entropy of {\it extensive} charged and rotating systems. Furthermore, it is shown that for charged and rotating systems (including non-extensive ones), the total energy that appear in both the Bekenstein entropy bound (BEB) and the causal entropy bound (CEB) can be replaced by the {\it internal} energy of the system. In addition, we propose possible corrections to the BEB and the CEB.Comment: 12 pages, revte