Philosophical Foundations Of Systems Biology

Molecular Biology and Biochemistry base their research on the molecular in the organic body, so learning the characteristic and nature of minor molecule means we could get the secret of life. But with more and more evidences showing that nonlinear interaction but not molecule themselves plays a more important part in the shaping of life characteristics, the reductionism strategy suffered questions from science and philosophy.The paper pointed that complexity shows at gene level, transcription level, protein level, metabolism level, phenotype level and so on reveals the reductionism in living organism is invalid. On the other hand, reductionism is ambiguous and has many logic bugs through Semantics analysis. So reductionism should be more comprehend as a metaphor which express the meaning of constitution than a valid method in complex system's researching.Systems Biology originated at the end of20th century and it is a cross discipline which employ the knowledge and methods from Maths, Biophysics, Biochemistry, Bio-informatics, simulation modeling based on computer etc. Systems Biology try to overcome the inherent defects through getting a mass of information of minor molecule such as DNA and protein, and use the relevant information to construct Omics. Systems Biology have came up with three methods:mechanism based on living organism, the combination of down-top strategy and top-down strategy, stimulation modeling for the living body.The new mechanism abandon the absolute distinction between reductionism and holism, taking a median route which pay more attention on the relationship of molecular and holism on the ontology aspect instead of a determinate cause-effect relation, and put emphasize on the nonlinear interaction between molecule. This kind of mechanism unify data based on mechanism and mechanism based on data, and put forward a new concept "resolution" to locate a suitable sub-unit to describe the route from simple molecule to complex characteristics.Down-top strategy is a method of naturalism which collect data as more as possible, while top-down strategy combine high level data that refect the outcome of nonlinear interaction with methods and theories from system science in order to track those suitable sub-units.Simulation modeling based on living organism use symbols and model to characterize molecule and mechanism. As the model optimizing, the model itself can forecast some functions of system. Model make cognition of living system deeper but it also confronts some logic problems.The paper also pointed that new methods of System Biology is a kind of limited cognition that compromise with the complex nature world, and this limitation can be attributed to we mankind's limited rationality.