Encyclopedia of Computer Science and Technology

46 bioinformaticsand a hierarchy of derived classes. A function in the baseclass can be declared to be virtual, and versions of the samefunction can be declared in the derived classes. In this casea statement containing a pointer to the function in the baseclass cannot be bound until run time, because only thenwill it be known which version of the virtual function isbeing called. However, compilers for object-oriented languagescan be written so they do early binding on statementsfor which it is safe (such as those involving staticdata types), but do dynamic binding when necessary.From the point of view of efficiency, early binding is betterbecause memory can be allocated efficiently. Dynamicbinding provides greater flexibility, however, and facilitatesdebugging—for example, because the name of a variableis normally lost once it is bound and the machine code isgenerated.Further ReadingAho, Alfred V., et al. Compilers: Principles, Techniques, and Tools.2nd ed. Reading, Mass.: Addison-Wesley, 2006.Scott, Michael L. Programming Language Pragmatics. 2nd ed. SanFrancisco: Morgan Kaufmann, 2005.bioinformaticsBroadly speaking, bioinformatics (and the related field ofcomputational biology) is the application of mathematicaland information-science techniques to biology. This undertakingis inherently difficult because a living organism representssuch a complex interaction of chemical processes.Understanding any one process in isolation gives littleunderstanding of the role it plays in physiology. Similarly,as more has been learned about the genome of humansand other organisms, it has become increasingly clear thatthe “programs” represented by gene sequences are “interpreted”through complex interactions of genes and the environment.Given this complexity, the great strides that havebeen made in genetics and the detailed study of metabolicand other biological processes would have been impossiblewithout advances in computing and computer science.Application to GeneticsSince information in the form of DNA sequences is the heartof genetics, information science plays a key role in understandingits significance and expression. The sequences ofgenes that determine the makeup and behavior of organismscan be represented and manipulated as strings of symbolsusing, for example, indexing and search algorithms.It is thus natural that the advent of powerful computerworkstations and automated lab equipment would lead tothe automation of gene sequencing (determining the orderof nucleotides), comparing or determining the relationshipbetween corresponding sequences, and identifyingand annotating regions of interest. The completion of thesequencing of the human genome well ahead of schedulewas thus a triumph of computer science as much as biology.Today the systematic search for genetic and metabolic interactionshas been greatly sped up by the use of microarrays,silicon chips with grids of tiny holes that each contain aA scientist observes an experiment performed by roboticequipment. (Andrei Tchernov/iStockphoto)specified material that can be automatically tested for reactionto a given sample.Evolutionary BiologyThe ability to compare genes and to account for the effectsof mutation has also established evolutionary biology on afirm foundation. Given a good estimate of the mutation rate(a “molecular clock”) in mitochondrial DNA, the chronologyof species and common ancestors can be determinedwith considerable accuracy using statistical methods andappropriate data structures (see tree). The results of suchresearch have cast intriguing if sometimes controversiallight on such issues in paleontology as the relationshipbetween early modern humans and Neanderthals. Computationalgenetics can also measure the biodiversity of apresent-day ecosystem and predict the likely future of particularspecies in it.From Genes to ProteinsGene sequences are only half of many problems in biology.Computational techniques are also being increasinglyapplied to the analysis and simulation of the many intricate