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 | Dynamic Models in Biology |
This file is also available in Adobe Acrobat PDF format Preface In 2001 the United Kingdom suffered a major outbreak of foot-and-mouth disease in livestock. The scientific experts assembled to advise the government included several groups of mathematical modelers. Within weeks of the first case report, modelers had developed systems of equations describing the farm-to-farm spread of infection, and were using them to help devise measures for controlling the outbreak (Ferguson et al. 2001a, b; Keeling et al. 2001). Adapting previous models, Ferguson et al. (2001) classified farms according to disease state: disease-free, infected, and vaccinated or slaughtered, with the infected class subdivided into several stages to represent the degree of infection and whether or not the disease had been detected. Equations were developed to describe how farms become infected, experience a local outbreak, and pass the disease to other farms, with model parameters estimated from the recorded dates and locations of all reported infections. Because the model is based on equations representing the process of disease transmission and spread, it could be modified to incorporate potential control measures and then used to predict their consequences. It was concluded that immediate slaughter of infected herds would slow disease spread but not halt it, and more aggressive measures were needed. Based in part on those analyses, the government instituted a policy of rapidly culling all farms in a ring surrounding a farm where infection is detected. These policies were successful: the disease soon started to decline and the outbreak collapsed within a few months. Detailed modeling and data analyses later confirmed that the control measures had greatly reduced the size of the outbreak, but also suggested that earlier application of the strict control measures that were eventually imposed could have reduced the outbreak by about half (Keeling et al. 2001). The 2001 foot-and-mouth outbreak is a particularly dramatic example of how models, written in the language of mathematics and solved on the computer, are now used throughout biology. Experimental biology is reductionist, disclosing how life works one piece at a time. But at all levels life is complex, meaning that the properties of cells, organisms, populations, and ecosystems reflect the interactions among multiple components. In virtually all areas of biology, models provide the means for putting the pieces together, for example,
In the past, biologists have generally been uninterested in mathematics, but that attitude is changing rapidly. With advances in many technologies, our intuition is no longer sufficient to analyze and interpret data. Quantitative models and methods are needed, sometimes because data are so extensive that automated methods are needed to examine them in detail (e.g., genome sequences) and sometimes because the pheomena are sufficiently complex that computer simulation is the only way to derive predictions from a model. We believe that biology students need to connect what they learn in a required calculus course to biology, and that mathematics students are greatly enriched when they see mathematics connected to real-world problems in a more tangible way than is taught in mathematics courses. These connections come through models, but there are some complex issues that must be addressed to develop an appreciation for them. What are the principles used in developing a model? What simplifications are made to make a model tractable? What measurements are used to estimate model parameters and validate model predictions? How does mathematics help us analyze models, either by hand or through computer algorithms? How robust are the predictions of a model to uncertainties in the structure of the model, errors in our measurements, stochastic fluctuations of the environment, and the individual variability of living organisms? These are all difficult questions, and they deserve sustained attention as students learn the art of modeling biological systems. This text is our attempt to address the lack of curricular materials designed to introduce undergraduate students to dynamic models of biological systems. It is based on a course that we have taught to a diverse audience of students majoring in the biological sciences, computer science, mathematics, engineering, and the physical sciences. We have adopted the following strategies in writing the text:
We require students to do a course project. Their assignment is to choose a published research paper using a dynamic model, implement the model, reproduce the modeling results in the paper, and then take one more step. By this we mean that they should formulate a question that was not fully addressed in the paper, modify or extend the model to do so, and then present their findings. This is a difficult assignment but we have been gratified by the papers that the students have written. Much more than the homework exercises, it prompts students to think creatively and critically about science in a setting in which answers are not absolutely right or wrong. We think computer exercises are essential so that students will have personal experience as modelers and model-users. We use the first three or four computer lab sessions to teach the rudiments of programming and then add a bit each week as new types of models are encountered--how to compute eigenvalues, generate random numbers, solve differential equations, and so on. Our experience is that undergraduate biology students can and do learn how to do real scientific programming. Instructional materials and suggested exercises for computer labs can be downloaded at no cost from this book's web page at Princeton University Press (http://press.princeton.edu/titles/8124.html). There is more in this book than can be covered in a single semester, allowing some flexibility as to the choice of topics and the mathematical level of the course. Here are a few suggestions:
File created: 8/7/2007 Questions and comments to: webmaster@pupress.princeton.edu |
