In silico transitions to multicellularity

The emergence of multicellularity and developmental programs are among the major problems of evolutionary biology. Traditionally, research in this area has been based on the combination of data analysis and experimental work on one hand and theoretical approximations on the other. A third possibility is provided by computer simulation models, which allow to both simulate reality and explore alternative possibilities. These in silico models offer a powerful window to the possible and the actual by means of modeling how virtual cells and groups of cells can evolve complex interactions beyond a set of isolated entities. Here we present several examples of such models, each one illustrating the potential for artificial modeling of the transition to multicellularity.Comment: 21 pages, 10 figures. Book chapter of Evolutionary transitions to multicellular life (Springer

Biology of Applied Digital Ecosystems

A primary motivation for our research in Digital Ecosystems is the desire to exploit the self-organising properties of biological ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex, dynamic problems. However, the biological processes that contribute to these properties have not been made explicit in Digital Ecosystems research. Here, we discuss how biological properties contribute to the self-organising features of biological ecosystems, including population dynamics, evolution, a complex dynamic environment, and spatial distributions for generating local interactions. The potential for exploiting these properties in artificial systems is then considered. We suggest that several key features of biological ecosystems have not been fully explored in existing digital ecosystems, and discuss how mimicking these features may assist in developing robust, scalable self-organising architectures. An example architecture, the Digital Ecosystem, is considered in detail. The Digital Ecosystem is then measured experimentally through simulations, with measures originating from theoretical ecology, to confirm its likeness to a biological ecosystem. Including the responsiveness to requests for applications from the user base, as a measure of the 'ecological succession' (development).Comment: 9 pages, 4 figure, conferenc

Evolving collective behavior in an artificial ecology

Collective behavior refers to coordinated group motion, common to many animals. The dynamics of a group can be seen as a distributed model, each “animal” applying the same rule set. This study investigates the use of evolved sensory controllers to produce schooling behavior. A set of artificial creatures “live” in an artificial world with hazards and food. Each creature has a simple artificial neural network brain that controls movement in different situations. A chromosome encodes the network structure and weights, which may be combined using artificial evolution with another chromosome, if a creature should choose to mate. Prey and predators coevolve without an explicit fitness function for schooling to produce sophisticated, nondeterministic, behavior. The work highlights the role of species’ physiology in understanding behavior and the role of the environment in encouraging the development of sensory systems

Emergence of Self-Organized Symbol-Based Communication \ud in Artificial Creatures

In this paper, we describe a digital scenario where we simulated the emergence of self-organized symbol-based communication among artificial creatures inhabiting a \ud virtual world of unpredictable predatory events. In our experiment, creatures are autonomous agents that learn symbolic relations in an unsupervised manner, with no explicit feedback, and are able to engage in dynamical and autonomous communicative interactions with other creatures, even simultaneously. In order to synthesize a behavioral ecology and infer the minimum organizational constraints for the design of our creatures, \ud we examined the well-studied case of communication in vervet monkeys. Our results show that the creatures, assuming the role of sign users and learners, behave collectively as a complex adaptive system, where self-organized communicative interactions play a \ud major role in the emergence of symbol-based communication. We also strive in this paper for a careful use of the theoretical concepts involved, including the concepts of symbol and emergence, and we make use of a multi-level model for explaining the emergence of symbols in semiotic systems as a basis for the interpretation of inter-level relationships in the semiotic processes we are studying

The Emergence of Symbol-Based Communication in a Complex System of Artificial Creatures

We present here a digital scenario to simulate the emergence of self-organized symbol-based communication among artificial creatures inhabiting a virtual world of predatory events. In order to design the environment and creatures, we seek theoretical and empirical constraints from C.S.Peirce Semiotics and an ethological case study of communication among animals. Our results show that the creatures, assuming the role of sign users and learners, behave collectively as a complex system, where self-organization of communicative interactions plays a major role in the emergence of symbol-based communication. We also strive for a careful use of the theoretical concepts involved, including the concepts of symbol, communication, and emergence, and we use a multi-level model as a basis for the interpretation of inter-level relationships in the semiotic processes we are studying

Fine-Scale Plant Species Identification in a Poor Fen and Integration of Techniques and Instrumentation in a Classroom Setting

Refining carbon flux measurements in the carbon cycle is an ongoing challenge. This study attempted to identify plant species in Sallie’s Fen, a nutrient-poor fen in Barrington, New Hampshire, at a fine scale in order to better model and understand carbon exchange between plants and the atmosphere in this type of ecosystem. A protocol for estimating percent cover of species in plots via ground measurements was developed. The next stage of this project was to compare these measurements with measurements derived from spectral images using ImageJ computer software. Statistical tests of the ground measurement data revealed that patterns of seasonal defoliation had a strong effect on the apparent species richness, evenness, and biodiversity of plants as seen aerially. The presence of Sphagnum mosses excluded the presence of other species, but the presence of other plants only excluded the visibility of Sphagnum since it resides in the understory of the layered community. A regression comparing percent cover of the vascular plant functional group and fractal dimensions from a digital camera was statistically significant, indicating that ground and aerial measurements agree and that spectral imaging can be used to save time in the field in place of ground measurements. Additionally, since ecosystem science is such an interdisciplinary field, it provides the perfect platform around which students can apply their scientific knowledge and understanding. Modifications to this project were suggested so that it can be carried out in a secondary school classroom setting while aligning with the Next Generation Science Standards

Digital Ecosystems: Ecosystem-Oriented Architectures

We view Digital Ecosystems to be the digital counterparts of biological ecosystems. Here, we are concerned with the creation of these Digital Ecosystems, exploiting the self-organising properties of biological ecosystems to evolve high-level software applications. Therefore, we created the Digital Ecosystem, a novel optimisation technique inspired by biological ecosystems, where the optimisation works at two levels: a first optimisation, migration of agents which are distributed in a decentralised peer-to-peer network, operating continuously in time; this process feeds a second optimisation based on evolutionary computing that operates locally on single peers and is aimed at finding solutions to satisfy locally relevant constraints. The Digital Ecosystem was then measured experimentally through simulations, with measures originating from theoretical ecology, evaluating its likeness to biological ecosystems. This included its responsiveness to requests for applications from the user base, as a measure of the ecological succession (ecosystem maturity). Overall, we have advanced the understanding of Digital Ecosystems, creating Ecosystem-Oriented Architectures where the word ecosystem is more than just a metaphor.Comment: 39 pages, 26 figures, journa

Rediscovery of the Florida Scorpionfly, Panorpa floridana Byers (Mecoptera: Panorpidae)

We describe the rediscovery of the Florida scorpionfly, Panorpa floridana Byers (Mecoptera: Panorpidae), at Gold Head Branch State Park, Clay County, Florida, based upon a single, living, adult specimen photographed on 4 November 2010. The hardcopy photographic prints and electronic digital images of this panorpid are the first vouchers for P. floridana in 28 years, the only observation of a living specimen, and the sixth individual known of this seemingly rare Florida endemic