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The agent-based simulation used by the Village Ecodynamics Project is called "Village" and consists of about 17,000 lines of Objective-C code written for the Swarm simulation platform. This chapter provides an overview of the structure, schedule, main agent actions (methods), and key parameters in the simulation. We show that growth rates exhibited by the agents in the simulation are realistic for Neolithic populations, and that variability in numbers of agents through time introduced by using different random number seeds is relatively small.

The National Science Foundation-funded Village Ecodynamics Project organizes data on the sizes and locations of Pueblo archaeological sites within a 1,817-sq-km portion of southwestern Colorado. The expansion of farmers in this area between AD 600 and 1280 is an example of a worldwide process known as the Neolithic Demographic Transition. We compare the settlement patterns created by these farmers, known through archaeological research, with simulated patterns generated by computerized agents on virtual landscapes (representing households) as the agents attempt to get enough maize, meat, wood, and water to survive under changing climatic circumstances. This will allow us to assess how relevant the concepts of adaptation and optimality are to understanding the changes seen in settlement patterns through time.

Realistic simulation of long-term household settlement patterns is based on spatially and temporally variable supplies of critical natural resources produced by study-area soils. Annual net primary productivity of native vegetation modulated by variability through time in precipitationprovides the basis for estimating supplies of fuelwood and high-quality animal protein required for successful human habitation in this area. This chapter describes soils in Village Ecodynamics Project study area; the native vegetation they supported; the number of deer, hare, and rabbit supported by the vegetation; and the methods by which agents in the simulation harvest fuelwood. Depletion of readily available fuelwood may have influenced long-term human behaviors related to architectural designs and settlement distributions.

We explore how the hunting parameters we vary in the Village simulation affect agent and animal population sizes and hunting return rates. We find that agent populations readily and rapidly deplete deer populations on our simulated landscape under all parameter combinations. Agent populations are consistently lower when agents are required to move to areas where there are local protein resources. Individual protein need is negatively correlated with agent population, while increasing the size of the hunting radius increases agent populations in circumstances in which agents are required to move to areas where hunting can be conducted successfully. The faunal transitions apparent in the northern San Juan archaeological record were plausibly induced by depression of deer populations accompanied by declining return rates for deer hunting.

This chapter discusses the age of dissimulation. During this period, the mask was a matter of survival. Dissimulation provided people with the means to protect themselves. In the age of dissimulation, dissembling was not just about masking the truth. For many, it was about finding a way to do so that was both ethical and protective. Prudence need not to come at the expense of rectitude. As Torquatto Accetto contends in his On Honest Dissimulation, dissembling was not a deceit, rather the mask was sometimes the truth’s only defense. He also asserted a clear distinction between simulation and dissimulation. Simulation according to him was the art of pretending, a show of works and actions. Dissimulation on the other hand withholds the truth, relying instead on silence and omissions. Simulation according to him cannot be called honest, nor can circumstances make it legitimate. It injures both the deceiver and the deceived. Dissimulation by contrast is defensive, a shield and a way of avoiding harm rather than provoking harm. Instead of circulating untruths, dissimulation grants some repose to truth which can be revealed at the proper time. Dissimulation is “a veil of honest obscurity and violent propriety.” This view led to the renewed view of masks not as an accomplice to guile or trickery or intimation of the underworld, but as a modus vivendi, intended to preserve rather than to disrupt. The notion of dissimulation as honesty recast the mask from the devil’s tool to an instrument of virtue.

This chapter examines the processes by which humans make meaning, and thereby illuminates how students learn and how to best structure lessons to achieve maximum understanding. It recommends teaching students to identify and interpret cultural patterns rather than to learn isolated facts. Furthermore, the chapter stresses the importance of developing familiarity with different cultures as an indisputable reality in globally connected twenty-first-century societies. Its emphasis on teaching through patterns is in part a response to what it views as one of the major challenges of globalization: students' inability to make sense of and connect to other cultures. The chapter also develops a powerful argument for the use of instructional technologies to provide students with real-life simulation experiences, opportunities for visualization, and individual tutoring. Finally, it considers the ongoing debate about the appropriate role of advanced technologies in education, claiming that this debate is a symptom of the need for increased research on student learning processes in order to further develop pedagogy based on the needs and learning styles of students in the global world.

Because no large-scale bioterrorist attack has happened in the modern age, planning for bioterrorism requires imagination. Simulations, ranging from computer-generated models to large-scale role-playing events involving thousands of actors, have gained credibility as a scientific tool for calculating the outcomes of violent events. Expanding use of simulation raises questions about how modeling and scenario planning gain tenacity in the current political climate, used by planners and policymakers to generate knowledge of the future. In bioterrorism preparedness, simulations and scenarios matter because they rationalize political actions that manage human life, individually and collectively, in the present moment. A case study of a terrorism training center in Playas, New Mexico, demonstrates the material and political effects of scenarios and simulation.

This chapter examines the increasing role of computer simulation in alignment evaluation, not just for the benchmarking of alignment algorithms but also for exploring the consequences of alignment errors (or use of alternate alignments) in bioinformatic analysis. The quality of an algorithm is often estimated by comparing the results obtained with a predefined benchmark, which provides a set of standard tests used to determine the relative performance of different programs. The chapter discusses multiple alignment benchmarks in detail, first discussing the criteria for benchmark development and issues involved in the definition of a multiple alignment benchmark. It concludes with a discussion on the evolution of multiple sequence alignments since the introduction of benchmarking, and the improvements achieved by the most recent methods.

This chapter discusses the reasons why phylogenetics has barely grown since its inception, and reviews three primary arguments used to justify experimental phylogenetics. It first rejects the perceived inferiority of historical science, and then makes explicit comparisons between experimental phylogenetics and the alternative approach of computer simulation. The chapter also considers the value of experimental phylogenetics for testing methods of phylogenetic inference and then considers whether experimental phylogenetics allows for increased biological realism over computer simulation.

Hydraulic rating methods define the relationship between flow volume (discharge) and the amount and type of habitat provided during the passage of flow along a stream channel. Methods include wetted perimeter or area analysis, flow events method, and various habitat simulation techniques and frameworks. The Instream Flow Incremental Methodology (IFIM) and its core component, the physical habitat modeling platform PHABSIM, are widely used. The main prediction phase of IFIM combines information derived from hydraulic simulation with data on habitat preferences of target species (usually fish), and prediction of habitat availability (expressed as weighted usable area, WUA) at different discharges. A WUA time series plot can be developed to depict changes in habitat over time as a consequence of flow alterations.