Abstract

The development of bioinformatics as an influential biological field should interest philosophers of biology and philosophers of science in general. Bioinformatics contributes significantly to the development of biological knowledge using a variety of scientific methods. Particular tools used by bioinformaticists, such as BLAST, phylogenetic tree creation software, and DNA microarrays, will be shown to utilize the scientific methods of extended cognition, analogical reasoning, and representations of mechanisms. Extended cognition is found in bioinformatics through the use of computer databases and algorithms in the representation and development of scientific theories in bioinformatics. Analogical reasoning is found in bioinformatics through particular analogical comparisons that are made between biological sequences and operations. Lastly, scientific theories that are created using certain bioinformatics tools are often representations of mechanisms. These methods are found in other scientific fields, but it will be shown that these methods are expanded in bioinformatics research through the use of computers to make the methods of analogical reasoning and representation of mechanisms more powerful.