This paper mainly talks about research methodology of synthetic sciences. First, I compare analytic and synthetic sciences and point out the difference of the view point, or the standing point of the researcher. Analytic sciences require exo-system view and methodology, while constructive or synthetic sciences require endo-system view and methodology. To study intelligence, we need a constructive methodology with internal observation (endo-system view). Then, I focus on the methodology of synthetic sciences and point out that the essential driving force of a synthetic methodology is the evolutionary method. It is a loop of generation and selection. I formalize the loop of synthetic methodology that includes analysis as its part. Finally, I layout my current research plan to implement a multi-level emergent system using evolutionary method.

Concerning the studies of life’s origin, there has been a serious dilemma or a chicken-and-egg paradox how does evolution starts out of randomly reacting chemical soup. Actually, evolving units such as self-replicating polymers could not arise without evolving processes, whereas evolving processes would not begin without evolving units. The processes of life’s origin and its evolution can be considered as the continuous complexation of initially nonliving entities leading to highly complex living organisms. A concept of self-replicating polymers alone can not attack the above-mentioned dilemma, because it can not link different levels of the hierarchy and hence no complexation appears. The present paper assumes that self-replicating units may not be the cause of life’s origin, but instead it may be the result emerging from quite different dynamical processes. It is a new paradigm of ‘endo-exo (or self-nonself) circulation’ that was introduced to account for such dynamical processes.

  Unless the stipulation of the detailed balance is forcibly imposed on a theoretical ground of whatever type, chemical reactions proceeding there could already be selective internally. What is in place instead is the detour balance that can allow the participation of intermediary reactions in implementing the overall balancing in the involved chemical reactions. The evolutionary nature of chemical reactions in the absence of the detailed balance rests upon the persistent imbalance, even though the slightest one, between a direct pair of the forward and the backward reactions. Some reaction products being set free from the stipulation of the detailed balance can exhibit the chemical affinities that were not actualized in the initial reactants. The lack of the mutual consistency between the reactants and their chemical affinities makes the reactions internally selective and evolutionary, and could have implemented a selective process even prior to the onset of Darwinian natural selection. One likely candidate for constantly breaking the mutual consistency between the reactants and their chemical affinities on the primitive Earth could have been those chemical reactions riding on hydrothermal circulation of seawater around the hot vents in the ocean.

  One slogan of science of complex networks is “functionality from network topology”. In order to achieve this slogan, many characteristics such as degree distributions, average path length, clustering coefficients, network motifs etc have been introduced. However, these are all based on the “real view” on networks, that is, nodes are just points and an arc or an edge between two nodes indicates existence of some interaction between the two nodes and nothing more. In this paper we introduce “dual views” on networks in contrast to the “real view” in order to promote further achievement of the slogan. In a “dual view” we interpret objects as processes. This is an abstraction from real systems in which each component has its own process. There are infinitely many “dual views”, however, we can show that there is a canonical “dual view” among all possible ones. We explain mathematical idea to formulate “dual views” and discuss its application to the study of complex networks.

  Previously, school, herd and swarm are explained by using a model called BOID and SPP which are based on the coupling of local potential and external perturbation. Perturbation prevents individuals to cooperate with each other to make a swarm. We here propose a model based on internal perturbation which contributes to make a swarm, in studying swarm behavior of soldier crabs. This model should have a wide applicability to study biological collective phenomena in general.