1.4 The Organization of This Book

7

Fig. 1.2 Another (partial) ontology for bioinformatics. Information flows are shown by dashed

lines. Note that behaviour can also influence genotype, by determining the selection of mating

partners

1.4

The Organization of This Book

The book is organized into five main parts. Part I essentially expands and continues

this introductory chapter, dealing with the big themes of genome, phenotype and

environment and their interrelationships; regulation (i.e., how the phenotype and

ultimately the genome survive in their environment); evolution (i.e., phylogenetic

adaptation); and the history of life, on Earth and possibly elsewhere, back to its

inception on Earth.

Part II covers, largely heuristically, the concept of information and some essen-

tial basic knowledge associated with it—what one needs to know in order to make

sense of the application of information theory to biology—including elements of

combinatorics and probability theory, pattern recognition, clustering, and so forth.

Complementary to that is Part III, a compact primer on biology, both organismal

and molecular. Part IV covers “omics” and regulatory networks; finally Part V deals

with applications, mainly in the medical field, and concludes with a chapter on the

structure of knowledge, big data and the automation of research. ⁶

For various reasons, including experimental ones, the usual procedure in the phys-

ical sciences, which is first to assign numbers to the phenomenon under investigation

and then to manipulate the numbers according to the usual rules of mathematics, both

operations being publicly declared and publicly accessible, is often confounded in

6 Practical programming and database handling are left out since many books already cover these

topics; even more pertinently, new resources are continually appearing online and the reader would

be well advised to search for appropriate tools when they are required.