Emergent processes as generation of discontinuities

In this article we analyse the problem of emergence in its diachronic dimension. In other words, we intend to deal with the generation of novelties in natural processes. Our approach aims at integrating some insights coming from Whitehead’s Philosophy of the Process with the epistemological framework developed by the “autopoietic” tradition. Our thesis is that the emergence of new entities and rules of interaction (new “fields of relatedness”) requires the development of discontinuous models of change. From this standpoint natural evolution can be conceived as a succession of emergences — each one realizing a novel “extended” present, described by distinct models — rather than as a single and continuous dynamics. This theoretical and epistemological framework is particularly suitable to the investigation of the origin of life, an emblematic example of this kind of processes

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps

Molecular biology knowledge can be systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist a number of maps of molecular interactions containing detailed description of various cell mechanisms. It is difficult to explore these large maps, to comment their content and to maintain them. Though there exist several tools addressing these problems individually, the scientific community still lacks an environment that combines these three capabilities together. NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. NaviCell combines three features: (1) efficient map browsing based on Google Maps engine; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting the community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of their interest in the context of signaling pathways and cross-talks between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive fashion due to an imbedded blogging system. NaviCell provides an easy way to explore large-scale maps of molecular interactions, thanks to the Google Maps and WordPress interfaces, already familiar to many users. Semantic zooming used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization meaningful to the user. In addition, NaviCell provides a framework for community-based map curation.Comment: 20 pages, 5 figures, submitte

Large D/H variations in bacterial lipids reflect central metabolic pathways

Large hydrogen-isotopic (D/H) fractionations between lipids and growth water have been observed in most organisms studied to date. These fractionations are generally attributed to isotope effects in the biosynthesis of lipids, and are frequently assumed to be approximately constant for the purpose of reconstructing climatic variables. Here, we report D/H fractionations between lipids and water in 4 cultured members of the phylum Proteobacteria, and show that they can vary by up to 500‰ in a single organism. The variation cannot be attributed to lipid biosynthesis as there is no significant change in these pathways between cultures, nor can it be attributed to changing substrate D/H ratios. More importantly, lipid/water D/H fractionations vary systematically with metabolism: chemoautotrophic growth (approximately −200 to −400‰), photoautotrophic growth (−150 to −250‰), heterotrophic growth on sugars (0 to −150‰), and heterotrophic growth on TCA-cycle precursors and intermediates (−50 to +200‰) all yield different fractionations. We hypothesize that the D/H ratios of lipids are controlled largely by those of NADPH used for biosynthesis, rather than by isotope effects within the lipid biosynthetic pathway itself. Our results suggest that different central metabolic pathways yield NADPH—and indirectly lipids—with characteristic isotopic compositions. If so, lipid δD values could become an important biogeochemical tool for linking lipids to energy metabolism, and would yield information that is highly complementary to that provided by ^(13)C about pathways of carbon fixation

Formal methods for modeling and analysis of hybrid systems

A technique based on the use of a quantifier elimination decision procedure for real closed fields and simple theorem proving to construct a series of successively finer qualitative abstractions of hybrid automata is taught. The resulting abstractions are always discrete transition systems which can then be used by any traditional analysis tool. The constructed abstractions are conservative and can be used to establish safety properties of the original system. The technique works on linear and non-linear polynomial hybrid systems: the guards on discrete transitions and the continuous flows in all modes can be specified using arbitrary polynomial expressions over the continuous variables. An exemplar tool in the SAL environment built over the theorem prover PVS is detailed. The technique scales well to large and complex hybrid systems

Prospective Longitudinal Study of the Pregnancy DNA Methylome: The US Pregnancy, Race, Environment, Genes (PREG) Study

Purpose The goal of the Pregnancy, Race, Environment, Genes study was to understand how social and environmental determinants of health (SEDH), pregnancy-specific environments (PSE) and biological processes influence the timing of birth and account for the racial disparity in preterm birth. The study followed a racially diverse longitudinal cohort throughout pregnancy and included repeated measures of PSE and DNA methylation (DNAm) over the course of gestation and up to 1 year into the postpartum period. Participants All women were between 18 and 40 years of age with singleton pregnancies and no diagnosis of diabetes or indication of assisted reproductive technology. Both mother and father had to self-identify as either African-American (AA) or European-American (EA). Maternal peripheral blood samples along with self-report questionnaires measuring SEDH and PSE factors were collected at four pregnancy visits, and umbilical cord blood was obtained at birth. A subset of participants returned for two additional postpartum visits, during which additional questionnaires and maternal blood samples were collected. The pregnancy and postpartum extension included n=240 (AA=126; EA=114) and n=104 (AA=50; EA=54), respectively. Findings to date One hundred seventy-seven women (AA=89, EA=88) met full inclusion criteria out of a total of 240 who were initially enrolled. Of the 63 participants who met exclusion criteria after enrolment, 44 (69.8%) were associated with a medical reason. Mean gestational age at birth was significantly shorter for the AA participants by 5.1 days (M=272.5 (SD=10.5) days vs M=277.6 (SD=8.3)). Future plans Future studies will focus on identifying key environmental factors that influence DNAm change across pregnancy and account for racial differences in preterm birth

Effects Of Human-Driven Water Stress on River Ecosystems: a Meta-Analysis

Human appropriation of water resources may induce water stress in freshwater ecosystems when ecosystem needs are not met. Intensive abstraction and regulation cause river ecosystems to shift towards non-natural flow regimes, which might have implications for their water quality, biological structure and functioning. We performed a meta-analysis of published studies to assess the potential effects of water stress on nutrients, microcontaminants, biological communities (bacteria, algae, invertebrates and fish), and ecosystem functions (organic matter breakdown, gross primary production and respiration). Despite the different nature of the flow regime changes, our meta-analysis showed significant effects of human-driven water stress, such as significant increases in algal biomass and metabolism and reduced invertebrate richness, abundance and density and organic matter decomposition. Water stress also significantly decreased phosphate concentration and increased the concentration of pharmaceutical compounds. The magnitude of significant effects was dependent on climate, rainfall regime, period of the year, river size and type of water stress. Among the different causes of water stress, flow regulation by dams produced the strongest effects, followed by water abstraction and channelization.This project was funded by the European Commission under the grant No. 603629 - project GLOBAQUA. VF acknowledges financial support from the Portuguese Foundation for Science and Technology (FCT) through UID/MAR/04292/2013 and IF/00129/2014. The authors acknowledge the support from the Economy and Knowledge Department of the Catalan Government through the Consolidated Research Group (ICRA-ENV 2017 SGR 1124)

Extracting the abstraction pyramid from complex networks

<p>Abstract</p> <p>Background</p> <p>At present, the organization of system modules is typically limited to either a multilevel hierarchy that describes the "vertical" relationships between modules at different levels (e.g., module A at level two is included in module B at level one), or a single-level graph that represents the "horizontal" relationships among modules (e.g., genetic interactions between module A and module B). Both types of organizations fail to provide a broader and deeper view of the complex systems that arise from an integration of vertical and horizontal relationships.</p> <p>Results</p> <p>We propose a complex network analysis tool, Pyramabs, which was developed to integrate vertical and horizontal relationships and extract information at various granularities to create a pyramid from a complex system of interacting objects. The pyramid depicts the nested structure implied in a complex system, and shows the vertical relationships between abstract networks at different levels. In addition, at each level the abstract network of modules, which are connected by weighted links, represents the modules' horizontal relationships. We first tested Pyramabs on hierarchical random networks to verify its ability to find the module organization pre-embedded in the networks. We later tested it on a protein-protein interaction (PPI) network and a metabolic network. According to Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), the vertical relationships identified from the PPI and metabolic pathways correctly characterized the <it>inclusion </it>(i.e., <it>part-of</it>) relationship, and the horizontal relationships provided a good indication of the functional closeness between modules. Our experiments with Pyramabs demonstrated its ability to perform knowledge mining in complex systems.</p> <p>Conclusions</p> <p>Networks are a flexible and convenient method of representing interactions in a complex system, and an increasing amount of information in real-world situations is described by complex networks. We considered the analysis of a complex network as an iterative process for extracting meaningful information at multiple granularities from a system of interacting objects. The quality of the interpretation of the networks depends on the completeness and expressiveness of the extracted knowledge representations. Pyramabs was designed to interpret a complex network through a disclosure of a pyramid of abstractions. The abstraction pyramid is a new knowledge representation that combines vertical and horizontal viewpoints at different degrees of abstraction. Interpretations in this form are more accurate and more meaningful than multilevel dendrograms or single-level graphs. Pyramabs can be accessed at <url>http://140.113.166.165/pyramabs.php/</url>.</p