Evolutionary morphogenesis for multi-cellular systems

With a gene required for each phenotypic trait, direct genetic encodings may show poor scalability to increasing phenotype length. Developmental systems may alleviate this problem by providing more efficient indirect genotype to phenotype mappings. A novel classification of multi-cellular developmental systems in evolvable hardware is introduced. It shows a category of developmental systems that up to now has rarely been explored. We argue that this category is where most of the benefits of developmental systems lie (e.g. speed, scalability, robustness, inter-cellular and environmental interactions that allow fault-tolerance or adaptivity). This article describes a very simple genetic encoding and developmental system designed for multi-cellular circuits that belongs to this category. We refer to it as the morphogenetic system. The morphogenetic system is inspired by gene expression and cellular differentiation. It focuses on low computational requirements which allows fast execution and a compact hardware implementation. The morphogenetic system shows better scalability compared to a direct genetic encoding in the evolution of structures of differentiated cells, and its dynamics provides fault-tolerance up to high fault rates. It outperforms a direct genetic encoding when evolving spiking neural networks for pattern recognition and robot navigation. The results obtained with the morphogenetic system indicate that this "minimalist” approach to developmental systems merits further stud

Variable Stars and Stellar Populations in Andromeda XXVII. IV. An Off-centered, Disrupted Galaxy

We present B and V time-series photometry of the M31 satellite galaxy Andromeda XXVII (And XXVII) that we observed with the Large Binocular Cameras of the Large Binocular Telescope. In the field of And XXVII we have discovered a total of 90 variables: 89 RR Lyrae stars and 1 Anomalous Cepheid. The average period of the fundamental mode RR Lyrae stars (RRab) < {P}{ab}> =0.59 {days} (σ = 0.05 day) and the period–amplitude diagram place And XXVII in the class of Oosterhoff I/Intermediate objects. Combining information from the color–magnitude diagram (CMD) and the variable stars, we find evidence for a single old and metal-poor stellar population with [Fe/H] ∼ ‑1.8 dex and t ∼ 13 Gyr in And XXVII. The spatial distributions of RR Lyrae and red giant branch (RGB) stars give clear indication that And XXVII is a completely disrupted system. This is also supported by the spread observed along the line of sight in the distance to the RR Lyrae stars. The highest concentration of RGB and RR Lyrae stars is found in a circular area of 4 arcmin in radius, centered about 0.°2 in the southeast direction from Richardson et al.’s center coordinates of And XXVII. The CMD of this region is well-defined, with a prominent RGB and 15 RR Lyrae stars (out of the 18 found in the region) tracing a very tight horizontal branch at < V({RR})> =25.24 {mag} σ = 0.06 mag (average over 15 stars). We show that And XXVII is a strong candidate building block of the M31 halo. Based on data collected with the Large Binocular Cameras at the Large Binocular Telescope, PI: G. Clementini

Landslide Ground Based Remote Sensing Monitoring: Formigal Case Study (Huesca, Spain)

Galahad is an ongoing Specific Targeted Research Project developed within the EU 6th Framework Programme ¿ Priority 1.1.6.3. The objective is to retrieve, through the use of improved GB-SAR and TLS technologies, field parameters that can be used in prediction algorithms of landslides, avalanches and glaciers related hazards. The landslide study area is located in the ski resort of Formigal, central Pyrenees (province of Huesca, Spain). The excavation of a parking area in the summer of 2004 reactivated a complex paleolandslide creating new sliding surfaces. The movement extends over an area of 0.25 km2 and experienced displacements as large as 0.5 cm/day during the period 2004¿2005. Stabilization engineering solutions were carried out reducing maximum observed displacement to 0.2 cm/day at the end of 2005. Within Galahad performed activities consisted in the collection of data on the landslide useful for its detailed characterization and the execution of a series of site measurement campaigns with GB-SAR, TLS and Differential GPS (D-GPS). The monitoring activities started in May 2006 completing a series of four campaigns with Total Station and D-GPS, a continuous two month data acquisition with GB-SAR and several TLS scans during two different periods from three points of view over the landslide. In this paper data obtained by GB-SAR and TLS are compared with D-GPS data, and a good agreement has been found between data sets. The project is still in progress and new site measurement campaigns with GB-SAR, TLS and D-GPS in 2007 will provide further insight into landslide forecasting models.JRC.H.7-Land management and natural hazard

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Multi-level grounding and self-organization of behaviour through evolution, development, learning and culture

The research topic of this PhD concerns the production of intelligent adaptive behaviour from the embodied perspective. The intelligence seen in biological organisms arises as an emergent property of a complex system displaying multiple levels of adaptive mechanisms. At the bottom, slow changes to the genotype structure are mediated by natural selection. At the top, to cope with more transient factors, faster lifetime transformations are found. Lifetime adaptation also takes place at various levels, from the processes that are responsible for the organism construction and maintenance, to the regulation of behaviour based on instinctive responses, cognitive abilities and social interactions. The traditional GOFAI (Good Old Fashion Artificial Intelligence) stand is based on the view of intelligence as computation taking place on a internal symbolic representations of the outside world. Powered by deductive logic, the classical artificial reasoner is centered on the possibility to describe reality within a symbolic framework. Unfortunately, this approach fails to cope with the ambiguous nature of reality, where good decisions are often based on partial and inconsistent knowledge. In these cases, reasoning could appear irrational, while its rationale is actually found in the necessity to take action. To solve this problem, New AI hypothesizes that intelligent behaviour must be understood within the framework provided by the agent’s physical interactions with the environment: subjective sensations and bodily interactions. The result is a bottom-up exploration, which starts from the lowest adaptive mechanisms to reach the topmost cognitive abilities. The work presented in this thesis follows this hypothesis, analyzing multiple levels of adaptive mechanisms: evolution, development, learning and culture

Evolving a Neurocontroller Through a Process of Embryogeny

We introduce a model of cellular growth that generates neurocontrollers capable of guiding simple simulated agents in a harvesting task. The morphogenesis of the neurocontroller is itself controlled by an evolved artificial neural network. The neural network operates only on local variables and chemical concentrations and is thought as a flexible model of a gene regulatory system and cell metabolism. The model is designed in order to increase the evolvability of the growth mechanism, which constitutes a serious issue in artificial embryogeny. Also, to increase the flexibility of development, organisms are grown in embryonal stages, which allow an incremental refinement of development. Neurocontrollers are organized in horizontal layers, with vertical input and output pathways. Within the same layer, neurons can have only local connections. On one side this limits the information needed for routing and on the other makes the system easy to implement in hardware. Results show that the system is capable of developing appropriate neurocontrollers in most of the evolutionary runs

Evolution and development of a multicellular organism: Scalability, resilience, and neutral complexification

To increase the evolvability of larger search spaces, several indirect encoding strategies have been proposed. Among these, multicellular developmental systems are believed to offer great potential for the evolution of general, scalable and self-repairing organisms. In this paper we reinforce this view, presenting the results achieved by such a model and comparing it against direct encoding. Extra effort has been made to make this comparison both general and meaningful. Embryonal stages, a generic method showing increased evolvability and which can be applied to any developmental model, are introduced. Development with embryonal stages implement what we refer to as direct ‘Neutral Complexification’: a direct genotype complexification mechanisms by neutral duplications of expressed genes. Results show that, even for high complexity evolutionary targets, the developmental model proves more scalable. The model also shows emergent self-repair, which is used to produce highly resilient organisms. 1