139

11

Design Principles of a Cell

Abstract

The design principles of a cell can be bioinformatically decoded in detail by sequence

analyses and more elaborate methods. Regulation, the localization of proteins, their trans­

port and secretion are also precisely encoded in the cell and are crucial for the ordered

structure of the cell. Modern imaging techniques and imaging software help to validate

these predictions. It is also important to classify all cellular processes by analyzing the

gene ontology. Combined with information on the protein-protein interactome, the result­

ing cellular network can be traced using software such as CellDesigner or Cytoscape, e.g.

motor proteins and the actin-myosin cytoskeleton are crucial for cell movement. Metabolic

“design” is quickly queried via databases such as KEGG or more accurately calculated

via metabolic modeling (e.g., with YANA or Metatool). Complex signalling networks are

important for fast responses (stress response, chemotaxis in bacteria) and especially for

multicellularity. They are modelled in detail with dynamic modelling (cell differentiation,

tumorigenesis, embryology, inflammatory processes, nervous system).

Evolution (last chapter) and systems biology (penultimate chapter) work together when

the cell successfully asserts itself in the environment and organisms persist and reproduce.

By combining both factors, cells are amazingly optimally engineered. Cells are and have

always been exemplary “natural engineers”, which once again makes it clear that the ques­

tion of “intelligent design” posed by creationists is unfortunately always completely

wrong. Just when living beings are so wonderfully organized by completely natural pro­

cesses, this should arouse our admiration and sharpen our view for higher and highest

levels of such processes and how wonderful our world is, in which such processes are

naturally possible spontaneously and self-organized. This is no accident, but for this par­

ticular world, selection processes are again at work, but on a truly high level – a truly suc­

cessful creation that subtly defies easy interpretation.

© Springer-Verlag GmbH Germany, part of Springer Nature 2023

T. Dandekar, M. Kunz, Bioinformatics,

https://doi.org/10.1007/978-3-662-65036-3_11