Phylogenetic aspects of the concept of intelligent life design

This paper presents a new treatment of molecular evolutionary model as a product of intelligent changes. The aim of this paper is to obtain a life design system, drawing on processes occurring in nature regardless of explanations of the origins of life. The idea of intelligent design and molecular relationship is considered as a basic concept of the intelligent life design system, using some analogies taken from molecular evolutionary models. Three steps of life design system are outlined; however, the main subject is an attempt to find certain similar effects of the design system processes and the processes simulated with basic evolutionary substitution models: Jukes-Cantor; Felsenstein; and Hasegawa, Kishino, and Yano (HKY). An idea of gene reduction has been applied, from more complex (taking into account information density) biological systems to less complex, specialised biological systems. Two steps have been taken into consideration: a test stage in the virtual world and an adaptation finishing process after running the systems in the real world. Two algorithms have been applied. The first one has applied similarity related to an accommodation process to required conditions in the virtual and the real world. The second algorithm has applied accommodation to required conditions separately (expressed as amino acid substitution) in the first step, using a convenient criterion, and further (similar to observable) accommodation in the real world. A phylogenetic tree, similar to a real one, has been calculated using the above method for mammals, for mtDNA, with the maximum likelihood method, and with the aid of PhyML for the HKY model. This paper is an introduction showing an aspect of the life design system, related to phylogenetic relationships.