Conformon-driven biopolymer shape changes in cell modeling

Molecular mechanisms of encoding and decoding information in cell computing

The process of computing may be defined simply as the goal-directed selection process (GDSP) that selects m out of n possible choices to achieve some desired goals, thereby generating or utilizing the amount of Shannon information, I, that can be approximated as I = - log₂ (m/n) bits. There are at least 3 distinct kinds of the physicochemical systems that can execute GDSP; (i) enzymes (i.e., microscopic or molecular computers), (ii) living cells (as mesoscopic computers), and (iii) brains (as macroscopic computers). In order to help define the principles and mechanisms underlying cell computing, it was thought necessary to compare cell computers with molecular computers (e.g., enzymes) on the one hand and with the macroscopic computers (e.g., Turing machine) on the other. It was concluded that all these different kinds of computers are ultimately driven by the information-energy particle called gnergons, consistent with the Gnergy Principle of Organization formulated by the present auditor in 2018. Also, it was concluded that to delineate how cells compute supported by enzymes necessitated treating enzymes not only as particles but also as standing waves, thus leading to the postulate of the wave-particle duality of enzymes formulated in this paper for the first time, in analogy to the wave-particle duality of light formulated in physics about 100 years ago.

What are melanocytes really doing all day long...?

Everyone knows and seems to agree that melanocytes are there to generate melanin - an intriguing, but underestimated multipurpose molecule that is capable of doing far more than providing pigment and UV protection to skin (1). What about the cell that generates melanin, then? Is this dendritic, neural crest-derived cell still serving useful (or even important) functions when no-one looks at the pigmentation of our skin and its appendages and when there is essentially no UV exposure? In other words, what do epidermal and hair follicle melanocytes do in their spare time - at night, under your bedcover? How much of the full portfolio of physiological melanocyte functions in mammalian skin has really been elucidated already? Does the presence or absence of melanocytes matter for normal epidermal and/or hair follicle functions (beyond pigmentation and UV protection), and for skin immune responses? Do melanocytes even deserve as much credit for UV protection as conventional wisdom attributes to them? In which interactions do these promiscuous cells engage with their immediate epithelial environment and who is controlling whom? What lessons might be distilled from looking at lower vertebrate melanophores and at extracutaneous melanocytes in the endeavour to reveal the 'secret identity' of melanocytes? The current Controversies feature explores these far too infrequently posed, biologically and clinically important questions. Complementing a companion viewpoint essay on malignant melanocytes (2), this critical re-examination of melanocyte biology provides a cornucopia of old, but under-appreciated concepts and novel ideas on the slowly emerging complexity of physiological melanocyte functions, and delineates important, thought-provoking questions that remain to be definitively answered by future research.

Protein linguistics — a grammar for modular protein assembly?

The correspondence between biology and linguistics at the level of sequence and lexical inventories, and of structure and syntax, has fuelled attempts to describe genome structure by the rules of formal linguistics. But how can we define protein linguistic rules? And how could compositional semantics improve our understanding of protein organization and functional plasticity?

"Live memory" of the cell, the other hereditary memory of living systems

We propose to designate by the term "live memory" of the cell, the cytoplasmic memory. This phenomenon consists of non-genetic memory, but nevertheless includes transmission function, which may be "hereditary" via the ovum, from mother cell to daughter cell, or simply within the same cell from instant t to instant t+1. To understand this notion of "live memory", its role and interactions with DNA must be resituated; indeed, operational information belongs as much to the cell body and to its cytoplasmic regulatory protein components and other endogenous or exogenous ligands as it does to the DNA database. We will see in Section 2, using examples from recent experiments in biology, the principal roles of "live memory" in relation to the four aspects of cellular identity, memory of form, hereditary transmission and also working memory.