Modeling the peak of emergence in systems: Design and katachi.

It is difficult to model emergence in biological systems using reductionist paradigms. A requirement for computational modeling is that individual entities can be recorded parametrically and related logically, but their transformation into whole systems cannot be captured this way. The problem stems from an inability to formally represent the implicit influences that inform emergent organization, such as context, shifts in causal agency or scale, and self-reference.

Pragmatic phenomenological types.

We approach a well-known problem: how to relate component physical processes in biological systems to governing imperatives in multiple system levels. The intent is to further practical tools that can be used in the clinical context. An example proposes a formal type system that would support this kind of reasoning, including in machines.

A two-sorted logic for structurally modeling systems.

Structural modeling of complex biological systems relies on formalisms inherited from physics. These formalisms scale poorly when dealing with interactions with many variables and agents working in systems that cohere at multiple layers. We propose a two sorted logic that supplements existing formalisms to mitigate these problems.