Catalyzing Inquiry at the Interface of Computing and Biology

CULTURE AND RESEARCH INFRASTRUCTURE 337

10.2.2.3.3 Computer Science Finally, the BIO2010 report noted the importance of information technol-
ogy-based tools for biologists. It recommended that all biology majors be able to develop simulations of
physiological, ecological, and evolutionary processes; to modify existing applications as appropriate; to
use computers to acquire and process data; to carry out statistical characterization of the data and
perform statistical tests; to graphically display data in a variety of representation; and to use informa-
tion technology (IT) to carry out literature searches, locate published articles, and access major data-

Box 10.1

Engineering for Life Science Majors

One example of an engineering topic suitable for inclusion in a biology curriculum is the subject of long-range

neuron signals. Introducing such a topic might begin with the electrical conductivity of salt water and of the lipid

cell membrane, and the electrical capacitance of the cell membrane. It would next develop the simple equations

for the attenuation of a voltage applied across the membrane at one end of an axon “cylinder” with distance

down the axon, and the effect of membrane capacitance on signal dynamics for time-varying signals.

After substituting numbers, it becomes clear that amplifiers will be essential. On the other hand, real systems

are always noisy and imperfect; amplifiers have limited dynamical range; and the combination of these facts

makes sending an analog voltage signal through a large number of amplifiers essentially impossible.

The pulse coding of information overcomes the limitations of analog communication. How are “pulses”

generated by a cell? This would lead to the power supply needed by an amplifier—ion pumps and the Nernst

potential. How are action potentials generated? A first example of the transduction of an analog quantity into

pulses might be stick-slip fraction, in which a block resting on a table, and pulled by a weak spring whose end

is steadily moved, moves in “jumps” whose distance is always the same. This introduction to nonlinear

dynamics contains the essence of how an action potential is generated.

The “negative resistance” of the sodium channels in a neuron membrane provides the same kind of “break-

down” phenomenon. Stability and instabilities (static and dynamic) of nonlinear dynamical systems can be

analyzed, and finally the Hodgkin-Huxley equations illustrated.

The material is an excellent source of imaginative laboratories involving electrical measurements, circuits,

dynamical systems, batteries and the Nernst potential, information and noise, and classical mechanics. It has

great potential for simulations of systems a little too complicated for complete mathematical analysis, and thus

is ideal for teaching simulation as a tool for understanding.

Other biological phenomena that can be analyzed using an engineering approach and that are suitable for

inclusion in a biology curriculum include the following:

• The blood circulatory system and its control; fluid dynamics; pressure and force balance;


• Swimming, flying, walking, dynamical description, energy requirements, actuators, control; material prop-
  erties of biological systems and how their structure relates to their function (e.g., wood, hair, cell membrane
  cartilage);


• Shapes of cells: force balance, hydrostatic pressure, elasticity of membrane and effects of the spatial depen-
  dence of elasticity; effects of cytoskeletal force on shape; and


• Chemical networks for cell signaling; these involve the concepts of negative feedback, gain, signal-to-
  noise, bandwidth, and cross-talk. These concepts are simple to experience in the context of how an electrical
  amplifier can be built from components.

SOURCE: Adapted from National Research Council, BIO2010: Transforming Undergraduate Education for Future Research Biologists, The

National Academies Press, Washington, DC, 2003.