An analogical "field" construct in cellular biophysics: history and present status

Metabolic Compartmentalization at the Leading Edge of Metastatic Cancer Cells

Despite advances in targeted therapeutics and understanding in molecular mechanisms, metastasis remains a substantial obstacle for cancer treatment. Acquired genetic mutations and transcriptional changes can promote the spread of primary tumor cells to distant tissues. Additionally, recent studies have uncovered that metabolic reprogramming of cancer cells is tightly associated with cancer metastasis. However, whether intracellular metabolism is spatially and temporally regulated for cancer cell migration and invasion is understudied. In this review, we highlight the emergence of a concept, termed “membraneless metabolic compartmentalization,” as one of the critical mechanisms that determines the metastatic capacity of cancer cells. In particular, we focus on the compartmentalization of purine nucleotide metabolism (e.g., ATP and GTP) at the leading edge of migrating cancer cells through the uniquely phase-separated microdomains where dynamic exchange of nucleotide metabolic enzymes takes place. We will discuss how future insights may usher in a novel class of therapeutics specifically targeting the metabolic compartmentalization that drives tumor metastasis.

From protoplasmic theory to cellular systems biology: a 150-year reflection

Present-day cellular systems biology is producing data on an unprecedented scale. This field has generated a renewed interest in the holistic, "system" character of cell structure-and-function. Underlying the data deluge, however, there is a clear and present need for a historical foundation. The origin of the "system" view of the cell dates to the birth of the protoplasm concept. The 150-year history of the role of "protoplasm" in cell biology is traced. It is found that the "protoplasmic theory," not the "cell theory," was the key 19th-century construct that drove the study of the structure-and-function of living cells and set the course for the development of modern cell biology. The evolution of the "protoplasm" picture into the 20th century is examined by looking at controversial issues along the way and culminating in the current views on the role of cytological organization in cellular activities. The relevance of the "protoplasmic theory" to 21st-century cellular systems biology is considered.

Nano-enabled synthetic biology

Biological systems display a functional diversity, density and efficiency that make them a paradigm for synthetic systems. In natural systems, the cell is the elemental unit and efforts to emulate cells, their components, and organization have relied primarily on the use of bioorganic materials. Impressive advances have been made towards assembling simple genetic systems within cellular scale containers. These biological system assembly efforts are particularly instructive, as we gain command over the directed synthesis and assembly of synthetic nanoscale structures. Advances in nanoscale fabrication, assembly, and characterization are providing the tools and materials for characterizing and emulating the smallest scale features of biology. Further, they are revealing unique physical properties that emerge at the nanoscale. Realizing these properties in useful ways will require attention to the assembly of these nanoscale components. Attention to systems biology principles can lead to the practical development of nanoscale technologies with possible realization of synthetic systems with cell-like complexity. In turn, useful tools for interpreting biological complexity and for interfacing to biological processes will result.

The biofield hypothesis: its biophysical basis and role in medicine

This paper provides a scientific foundation for the biofield: the complex, extremely weak electromagnetic field of the organism hypothesized to involve electromagnetic bioinformation for regulating homeodynamics. The biofield is a useful construct consistent with bioelectromagnetics and the physics of nonlinear, dynamical, nonequilibrium living systems. It offers a unifying hypothesis to explain the interaction of objects or fields with the organism, and is especially useful toward understanding the scientific basis of energy medicine, including acupuncture, biofield therapies, bioelectromagnetic therapies, and homeopathy. The rapid signal propagation of electromagnetic fields comprising the biofield as well as its holistic properties may account for the rapid, holistic effects of certain alternative and complementary medical interventions.

Intracellular signalling proteins as smart' agents in parallel distributed processes

In eucaryotic organisms, responses to external signals are mediated by a repertoire of intracellular signalling pathways that ultimately bring about the activation/inactivation of protein kinases and/or protein phosphatases. Until relatively recently, little thought had been given to the intracellular distribution of the components of these signalling pathways. However, experimental evidence from a diverse range of organisms indicates that rather than being freely distributed, many of the protein components of signalling cascades show a significant degree of spatial organisation. Here, we briefly review the roles of 'anchor' 'scaffold' and 'adaptor' proteins in the organisation and functioning of intracellular signalling pathways. We then consider some of the parallel distributed processing capacities of these adaptive systems. We focus on signalling proteins-both as individual 'devices' (agents) and as 'networks' (ecologies) of parallel processes. Signalling proteins are described as 'smart thermodynamic machines' which satisfy 'gluing' (functorial) roles in the information economy of the cell. This combines two information-processing views of signalling proteins. Individually, they show 'cognitive' capacities and collectively they integrate (cohere) cellular processes. We exploit these views by drawing comparisons between signalling proteins and verbs. This text/dialogical metaphor also helps refine our view of signalling proteins as context-sensitive information processing agents.

The topology of perceptive functions as a corollary of the theorem of existence in closed spaces

The capability for a system of perceiving both outer objects and an inner self are two fundamental features of abstract mathematical objects endowed with the properties of topologically closed sets. Such structures exist upon intersection of topological spaces owning different dimensions. Then, the theorem of Jordan-Veblen provides their capability of being observable, while the theorems of Brouwer and of Banach-Caccioppoli provide two kinds of fixed points which account for the properties of so-called right and left brain functions. Fixed points account for the biological 'self', and the system provides theoretical justification for the existence of brain structure/function relationships, including memory, emotion, and respective characteristics of right and left hemispheres. Hence, an abstract topological reasoning based on set properties, provides evidence that the observer's function directly infers from the phenomenon of existence and that it belongs to the same mathematical system as the property of being observable. Order relations are raised from equivalence relations by Poincaré groups, upon mappings on the sets of functions and related homotopic transformations in sequences of intersections. Therefore, time is a construction of abstract brain functions, and a living organism just fills the system with appropriate molecular structures.

The enzymatic basis of information processing in the living cell

Analogies are drawn between the computational aspects of information processing and the enzymatic events of cellular metabolism. The origin thereof is linked to the logic-elements involved in the reaction-diffusion processes of the metabolic operation. It is shown how such function entails a 'molecular machine' quality when associated with organized non-equilibrium energy sources in the cell.

Some computational models at the cellular level

A number of viewpoints on how a cell can be modelled are discussed in this paper in light of the ability it has to process information. The paper begins with a very brief summary of four general types of computation: sequential, parallel, distributed, and emergent. These form the general framework from which a number of comparisons are made. Several metaphors are introduced to enable reflections to be made about cellular computational properties. The most important metaphor, namely the cell as a machine, is discussed, and then a number of other ideas are introduced that complement much current thinking in this area. The idea of networks or circuits in the cell is then developed, as this provides a means of describing the mechanisms within a machine. Following on from this, three further metaphors are applied in order to overcome certain limitations in current machine thinking, cell-as-society, cell-as-text, and cell-as-field.