Genomics & Informatics Vol. 2(4) 167-173, December 2004 The Atom of Evolution Jonghwa Bhak¹ , ² , ³ ,4  , Dan Bolser³ ,5 , Daeui Park 4 , Yoobok Cho 4 , Kiesuk Yoon 4 , Semin Lee¹, SungSam Gong¹, Insoo Jang², Changbum Park¹, Maryana Huston³ and Hwanho Choi³ ¹Biomatics Lab, BioSystems, KAIST, Daejeon 305-701, Korea, ²NGIC, KRIBB, Daejeon 305-333, Korea, ³BiO Institute, Daejeon 305-701, Korea, 4 OITEK Inc. Daejeon 305-701, Korea, 5 MRC-DUNN, Cambridge CB2-2XY, England, United Kingdom. 3) Abstract The main mechanism of evolution is that biological entities change, are selected, and reproduce. We propose a different concept in terms of the main agent or atom of evolution: in the biological world, not an individual object, but its interactive network is the fundamental unit of evolution. The interaction network is composed of interaction pairs of information objects that have order information. This indicates a paradigm shift from 3D biological objects to an abstract network of information entities as the primary agent of evolution. It forces us to change our views about how organisms evolve and therefore the methods we use to analyze evolution. Introduction Bioinformatics is a scientific discipline that analyzes, seeks understanding of, and models all life as an information processing phenomenon on utilizing energy with methods from philosophy, mathematics, and computer science using biological experimental data. Due to its information processing nature, bioinformatics is one of the broadest and deepest scientific disciplines. All biological research is, aiming to understand the architecture of information processing in life. For example, the analysis of genomes and genes is to  discover the underlying linguistic rules of molecules (Searls, 1993) and the concept of proteins as computational elements (Bray, 1995). In this sense, the shortest possible definition of bioinformatics is: Bioinformatics is Biology and Biology is Bioinformatics. In the next 20 years, bioinformatics will become the core of biological education even in secondary school biology courses. The early 2000s is at the point where the conventional views of molecular biology should change with new revolutionary views in biology. One of them is the transition from the conventional object-oriented understanding of biology to an interaction-oriented understanding. The concept of evolution is the backbone of modern biology (Darwin, 1859). Evolution is used to explain development and change in many different areas of human society. The word evolution is from the Latin evolvere meaning “unfold”. It succinctly means “descent with modification of objects”, whatever the objects are. For example, although a car is not a self-replicating organic organism, an evolutionary process appears to have occurred in car models. The cars were duplicated, changed, and selected as a result of the interaction of manufacturers and users: by observing the users’ selection and through market research, the manufacturers made design decisions for each new model. As abstract information objects, the cars evolved as much as human hair evolved over time. Hair is a product of hair cells while cars are the product of human brain cells. Here, the more influential factors in development are the interaction and information rather than the objects themselves. This leads us to the question of what the fundamental evolutionary unit is in interaction processes. Discussion Among many biological information object levels, cell-cell interactions are not the most basic unit of evolution, as non-cellular entities, such as molecules and viruses, show evolutionary processes. Use of the