In Silico Biology

Author(s):  
Dimitri Perrin ◽  
Heather J. Ruskin ◽  
Martin Crane

Biological systems are typically complex and adaptive, involving large numbers of entities, or organisms, and many-layered interactions between these. System behaviour evolves over time, and typically benefits from previous experience by retaining memory of previous events. Given the dynamic nature of these phenomena, it is non-trivial to provide a comprehensive description of complex adaptive systems and, in particular, to define the importance and contribution of low-level unsupervised interactions to the overall evolution process. In this chapter, the authors focus on the application of the agent-based paradigm in the context of the immune response to HIV. Explicit implementation of lymph nodes and the associated lymph network, including lymphatic chain structure, is a key objective, and requires parallelisation of the model. Steps taken towards an optimal communication strategy are detailed.

Author(s):  
John H. Holland

‘Agents, networks, degree, and recirculation’ explains that when studying complex adaptive systems (CAS) in a grammar-like way, agents serve as the ‘alphabet’. The hierarchical organization of CAS implies different kinds of agents at different levels, with correspondingly different grammars. The interactions of signal-processing agents at a point in time can be specified by a network—a snapshot of the agents’ performance capability. The combination of high fanout (the richness of an agent’s interactions) and hierarchical organization results in complex networks that include large numbers of sequences that form loops. More complex loops allow the CAS to ‘look ahead’, examining the effects of various action sequences without actually executing the actions.


Author(s):  
Professor Michael E. Wolf-Branigin ◽  
Dr William G. Kennedy ◽  
Dr Emily S. Ihara ◽  
Dr Catherine J. Tompkins

Agent based modeling is one of many tools, from the complexity sciences, available to investigate complex policy problems. Complexity science investigates the non-linear behavior of complex adaptive systems. Complex adaptive systems can be found across a broad spectrum of the natural and human created world. Examples of complex adaptive systems include various ecosystems, economic markets, immune response, and most importantly for this research, human social organization and competition / cooperation. The common thread among these types of systems is that they do not behave in a mechanistic way which has led to problems in utilizing traditional methods for studying them. Complex adaptive systems do not follow the Newtonian paradigm of systems that behave like a clock works whereby understanding the workings of each of the parts provides an understanding of the whole. By understanding the workings of the parts and a few external rules, predictions can be made about the behavior of the system as a whole under varying circumstances. Such systems are labeled deterministic (Zimmerman, Lindberg, & Plsek, 1998).


Author(s):  
Lashon Booker ◽  
Stephanie Forrest

It has long been known that the repeated or collective application of very simple rules can produce surprisingly complex organized behavior. In recent years several compelling examples have caught the public's eye, including chaos, fractals, cellular automata, self-organizing systems, and swarm intelligence. These kinds of approaches and models have been applied to phenomena in fields as diverse as immunology, neuroscience, cardiology, social insect behavior, and economics. The interdisciplinary study of how such complex behavior arises has developed into a new scientific field called "complex systems." The complex systems that most challenge our understanding are those whose behavior involves learning or adaptation; these have been named "complex adaptive systems." Examples of complex adaptive behavior include the brain's ability, through the collective actions of large numbers of neurons, to alter the strength of its own connections in response to experiences in an environment; the immune system's continual and dynamic protection against an onslaught of ever-changing invaders; the ability of evolving species to produce, maintain, and reshape traits useful to their survival, even as environments change; and the power of economic systems to reflect, in the form of prices, supplies, and other market characteristics, the collective preferences and desires of millions of distributed, independent individuals engaged in buying and selling. What is similar in these diverse examples is that global behavior arises from the semi-independent actions of many players obeying relatively simple rules, with little or no central control. Moreover, this global behavior exhibits learning or adaptation in some form, which allows individual agents or the system as a whole to maintain or improve the ability to make predictions about the future and act in accordance with these predictions. Traditional methods of science and mathematics have had limited success explaining (and predicting) such phenomena, and an increasingly common view in the scientific community is that novel approaches are needed, particularly those involving computer simulation. Understanding complex adaptive systems is difficult for several reasons. One reason is that in such systems the lowest level components (often called agents) not only change their behavior in response to the environment, but, through learning, they can also change the underlying rules used to generate their behavior.


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