Related papers: Foundations of biology
Purpose and meaning are necessary concepts for understanding mind and culture, but appear to be absent from the physical world and are not part of the explanatory framework of the natural sciences. Understanding how meaning (in the broad…
We formulate physically-motivated axioms for a physical theory which for systems with a finite number of degrees of freedom uniquely lead to Quantum Mechanics as the only nontrivial consistent theory. Complex numbers and the existence of…
The fact that life has evolved in our universe constrains the laws of physics. The anthropic principle proposes that these constraints are sometimes very tight and can be used to explain in a sense the corresponding laws. Recently a…
Category theory has foundational importance because it provides conceptual lenses to characterize what is important and universal in mathematics---with adjunctions being the primary lense. If adjunctions are so important in mathematics,…
It is not currently possible to create a living organism ab initio due to the overwhelming complexity of biological systems. In fact, the origin of life mechanism, this being how biological organisms form from non-living matter, is unknown.…
An adult human body is made up of some 30 to 40 trillion cells, all of which stem from a single fertilized egg cell. The process by which the right cells appear to arrive in their right numbers at the right time at the right place --…
We propose a principle of consistency between different hierarchical levels of biological systems. Given a consistency between molecule replication and cell reproduction, universal statistical laws on cellular chemical abundances are…
We introduce a logic for knowledge representation and reasoning on protein-protein interactions. Modulo a theory, formulas describe protein structures and dynamic changes. They can be composed in order to add or remove static and dynamic…
Motivated by a recent article on open problems in artificial life, here I postulate three laws which form a mathematical framework to describe artificial life evolutionary dynamics. They are based on a continuous approximation of population…
In light of G\"{o}del's undecidability results (incomplete theorems) for math, quantum indeterminism indicates that physics and the Universe may be indeterministic, incomplete, and open in nature, and therefore demand no single unification…
This thesis broadly concerns the origins of life problem, pursuing a joint approach that combines general philosophical/conceptual reflection on the problem along with more detailed and formal scientific modelling work oriented in the…
The theory of natural selection has two forms. Deductive theory describes how populations change over time. One starts with an initial population and some rules for change. From those assumptions, one calculates the future state of the…
The cognitive frame in which most neuropsychological research on the neural basis of behavior is conducted contains the assumption that brain mechanisms per se fully suffice to explain all psychologically described phenomena. This…
The sequence of nucleotide bases occurring in an organism's DNA is often regarded as a codescript for its construction. However, information in a DNA sequence can only be regarded as a codescript relative to an operational biochemical…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
The evolutionary biology of aging is fundamental to understanding the mechanisms of aging and how to develop anti-aging treatments. Thus far most evolutionary theory concerns the genetics of aging with limited physiological integration.…
In this paper we explore the boundary between biology and the study of formal systems (logic). In the end, we arrive at a summary formalism, a chapter in "boundary mathematics" where there are not only containers <> but also extainers ><,…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
Through extensive studies of dynamical system modeling cellular growth and reproduction, we find evidence that complexity arises in multicellular organisms naturally through evolution. Without any elaborate control mechanism, these systems…
Linguistic laws, the common statistical patterns of human language, have been investigated by quantitative linguists for nearly a century. Recently, biologists from a range of disciplines have started to explore the prevalence of these laws…