life inspired

"Unusual strains of the pathogen Candida albicans have been found that contain a single set of chromosomes. Formation of such haploid strains weeds out damaged copies of genes to promote evolution in the human body. Fungi exhibit the most complex and diverse strategies for mating and sexual reproduction in nature. [...] Hickman et al. report the isolation of C. albicans strains that have shed one copy of each chromosome, leading to a haploid state. These haploid strains can mate to regenerate diploid strains, and can undergo all of the developmental life-cycle stages normally seen in the organism." Full news article @ Nature. Original article: Nature (2013) doi:10.1038/nature11865.

Labels: mating; genome organization;

"In the fire ant Solenopsis invicta, the existence of two divergent forms of social organization is under the control of a single Mendelian genomic element marked by two variants of an odorant-binding protein gene4, 5, 6, 7, 8. Here we characterize the genomic region responsible for this important social polymorphism, and show that it is part of a pair of heteromorphic chromosomes that have many of the key properties of sex chromosomes. [...] most of the genes with demonstrated expression differences between individuals of the two social forms reside in the non-recombining region. These findings highlight how genomic rearrangements can maintain divergent adaptive social phenotypes involving many genes acting together by locally limiting recombination." Full paper @ Nature 493, 664–668

Labels: ants; evolution; social behavior; collective behavior

"We present schema redescription as a methodology to characterize canalization in automata networks used to model biochemical regulation and signalling. In our formulation, canalization becomes synonymous with redundancy present in the logic of automata. This results in straightforward measures to quantify canalization in an automaton (micro-level), which is in turn integrated into a highly scalable framework to characterize the collective dynamics of large-scale automata networks (macro-level). This way, our approach provides a method to link micro- to macro-level dynamics -- a crux of complexity. Several new results ensue from this methodology: uncovering of dynamical modularity (modules in the dynamics rather than in the structure of networks), identification of minimal conditions and critical nodes to control the convergence to attractors, simulation of dynamical behaviour from incomplete information about initial conditions, and measures of macro-level canalization and robustness to perturbations. We exemplify our methodology with a well-known model of the intra- and inter cellular genetic regulation of body segmentation in Drosophila melanogaster. We use this model to show that our analysis does not contradict any previous findings. But we also obtain new knowledge about its behaviour: a better understanding of the size of its wild-type attractor basin (larger than previously thought), the identification of novel minimal conditions and critical nodes that control wild-type behaviour, and the resilience of these to stochastic interventions. Our methodology is applicable to any complex network that can be modelled using automata, but we focus on biochemical regulation and signalling, towards a better understanding of the (decentralized) control that orchestrates cellular activity -- with the ultimate goal of explaining how do cells and tissues 'compute'." Full pre-print:

M. Marques-Pita and L.M. Rocha [2013]. "Canalization and control in automata networks: body segmentation in Drosophila Melanogaster". PLOS ONE, In Press.

Labels: automata, biocomplexity, boolean networks, canalization, complex systems, modularity, self-organization

"Our knowledge of the principles by which organ architecture develops through complex collective cell behaviours is still limited. Recent work has shown that the shape of such complex tissues as the optic cup forms by self-organization in vitro from a homogeneous population of stem cells. Multicellular self-organization involves three basic processes that are crucial for the emergence of latent intrinsic order. Based on lessons from recent studies, cytosystems dynamics is proposed as a strategy for understanding collective multicellular behaviours, incorporating four-dimensional measurement, theoretical modelling and experimental reconstitution." Full paper @ Nature

Labels: develo, self-organization, stem cells

"Researchers have done it again—encoding 5.2 million bits of digital data in strings of DNA and demonstrating the feasibility of using DNA as a long-term, data-dense storage medium for massive amounts of information." News article @ The Scientist Magazine®. Original article:


N. Goldman et al., “Towards practical, high-capacity, low-maintenance information storage in synthesized DNA,” Nature, doi: 10.1038/nature.11875, 2013.

Labels: DNA; memory;

"Dissecting the genetic basis of a species' physical features is regular research fodder. So why not do the same for the inanimate objects that some animals produce, such as beehives or beaver dams? On page 402 of this issue, Weber and colleagues show that the sophisticated burrows of oldfield mice can be understood using straightforward genetics, shedding light on how this classic 'extended phenotype' evolved ()." News article @ Nature. Full article: J. N. Weber et al. Nature 493, 402–405; 2013

Labels: genetics; evolution;

On December 11th, 2012, the Calouste Gulbenkian Foundation hosted The Alan Turing Centenary Symposium, organized by the Instituto Gulbenkian de Ciência, to celebrate Alan Turing's centenary and discuss his legacy. Among the invited speakers were Sidney Brenner, Nobel Laureate in Physiology or Medicine 2002, the writer David Leavitt, and the scientists Luís Rocha (Instituto Gulbenkian de Ciência and Indiana University), António Machiavelo (Universidade do Porto) and Christof Teuscher (Portland State University). A video library with all the talks at this conference is available. The videocasts are also shown below in three blocks:

Labels: artificial intelligence, Artificial Life, biocomplexity, computation, informatics, turing