Principia Biro-Informatica: Creative Ideas in Molecular Biology & Bioinformatics

Bioinformatics is a young interdisciplinary science that reached its full potential only after completion of the Human Genome Project in 2003. It was first used for sorting and classifying sequence data. Now that sufficiently large databases of different kinds and easy-to-use database searching methods have been established, the time has come to take the next step and convert the data into information and information into knowledge: data that make sense. This book is a unique collection of in silico experiments that demonstrate the extraordinary power of bioinformatics to turn data into information, when it is used as the extension of (and not as a replacement for) the creative human scientific mind. This is a human-centered book from beginning to end. The author has personally witnessed the development of molecular biology since the structure of DNA was discovered. He has seen biological theories rise and fall and learned not only the strengths but also the weaknesses of major theories in molecular biology. He strongly believes that only information that the human mind is able to process and understand is real knowledge, and scientific truth has to make sense to us humans. Biro was the first scientist who asked the question how is it possible that one of the two virtually identical strands of double-stranded DNA is functionally sense (expressed) while the other (mirror image) is non-sense (silent). This seemed incomprehensible to him. Two decades later, sequencing of several genomes had shown that the sense antisense distinction was erroneous; it became one of the most embarrassing mistakes of 20th century biological science. Using the same logic and equipped with the power of bioinformatics, Biro revisited and researched the major dogmas in molecular biology (developed almost a half century ago) and asked the question: what is their real value today when far more biological data are available to test the limits of their validity? Surprise, surprise: there is a lot of news to tell. Linus Pauling s DNA model is actually not as stupid as James Watson believes. The idea of junk DNA (exons) is actually a junk idea. The connection between codons and coded amino acids is not a frozen accident as Francis Crick so coldly explained, but the result of rigorous co-evolution, and there is a Common Periodic Table of Codons and Amino Acids. The redundancy of codons is not merely a simple information back-up - there is another code in the Genetic Code: The PROTEOMIC CODE. This second code directly predicts the existence of nucleic acid-assisted protein folding: the NUCLEIC ACID CHAPERONS. This book promises a very exciting intellectual trip for students and scientists (from a wide range of different disciplines) who are not afraid of a world outside the box. This book will be the first to describe, with numerous examples, how to use the full power of bioinformatics to gain fundamental new biological knowledge. The first and second chapters explain the birth and development of two interdisciplinary sciences, molecular biology and bioinformatics, and present the basic knowledge and fundamental theories and tools of both discipline. The author systematically prepares the readers (working or studying in a wide range of sciences) to understand the need for regular review and re-search of every existing idea and theory in the science, now matter how well established. This book is the first systematic and critical review of the governing dogmas in molecular biology to be written since enough genome projects have been completed and enough new biological data collected for such a work to be attempted.