Abstract
If biological objects are created by natural selection, why are they composed of discrete modules? What has been the nature of mutations since the Darwinian epoch? This paper presents examples of genetic circuits in terms of stochastic -calculus; a new mathematical language for nanosystems. The author used a constructor of five elements such as decay, null gate, gene product, and negative and positive gates. These primitives were applied to design genetic switches, oscillators, feedforward and feedback loops, pulse generators, memory elements, and combinatorial logics. The behaviors of those circuits were investigated – functions, such as oscillations or a spontaneous pulse generation were performed simply, flip-flops between stable states occurred in the noisy environment. The modular essence of -calculus and the following up features of Stochastic Pi Machine (SPiM) programming language allowed us to change the topology of networks that resembled a gene exchange in nature. Other types of mutations were considered as variations in parameters. Perturbations modified system behavior in unpredictable ways that generated diversity for a possible future design by selection of appropriative variants.
Highlights
Biological entities are different from artificial devices because they are developed by an algorithm that Charles Darwin called natural selection
Evolutionary simulations demonstrated that modular structures are rare and less optimal than fully wired counterparts (Poli et al, 2008; Thompson, 1998)
Modular structures can spontaneously emerge if the environment changes over time (Kashtan and Alon, 2005)
Summary
Biological entities are different from artificial devices because they are developed by an algorithm that Charles Darwin called natural selection. Evolutionary simulations demonstrated that modular structures are rare and less optimal than fully wired counterparts (Poli et al, 2008; Thompson, 1998). That is why the masterpiece of biological networks is an entanglement. There are many examples of modular design in evolution; body plans of invertebrates and vertebrates, and modular metabolic networks within bacteria (Kreimer et al, 2008; Parter et al, 2007). Modular structures can spontaneously emerge if the environment changes over time (Kashtan and Alon, 2005). Modularity can dramatically speed up evolution (Kashtan et al, 2007). Modularity is a basis of our ability to divide a problem into parts and to scale up to large systems by a composition of elements
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