Barham; Part 7; Looking at cells dynamically (Introduction)

by David Turell , Friday, August 21, 2015, 20:06 (3381 days ago) @ David Turell

This is a wholly different way of looking at cells and the way they function:-http://jamesabarham.com/my-blog/40-seeing-past-darwin-vii-some-physical-properties-of-life-"Too often, we envision the cell as a "factory" containing a fixed complement of "machinery" operating according to "instructions" (or "software" or "blueprints") contained in the genome and spitting out the "gene products" (proteins) that sustain life.-"Many things are wrong with this picture, but one of the problems that needs to be discussed more openly is the fact that in this "factory," many if not most of the "machines" are themselves constantly turning over---being assembled when and where they are needed, and disassembled afterwards. The mitotic spindle (top) is one of the best-known examples, but there are many others.-"Funny sort of "factory" that, with the "machinery" itself popping in and out of existence as needed!-***-"Paradoxically, extraordinary advances in our understanding of the parts do not seem to bring about significant progress in our understanding of the whole. In fact, it appears that the design of the cell becomes increasngly elusive as experimental data accumulate. . . . Quantitative visualization of fluorescently tagged proteins inside living cells shows that most, perhaps all, sub-cellular structures and macromolecular complexes exist not as pre-assembled and relatively stable structures, but as highly dynamic steady-state macromolecular organizations, conceptually similar to a treadmilling actin filament but of greater complexity.-***-" ...it should be pointed out that, in reality, the internal resource distribution/transport systems of biological organisms (at all scales) are not mechanistic pipes built according to a preconceived design, but dynamic and adaptive fluxes of energy/matter in themselves, shaped by both internal and external influences. And their main purpose is not to deliver resources and remove waste---that is the limited interpretation of the mechanistic paradigm---but to integrate energy/matter and space into one scale-free continuum of energy/matter circulation.-***-"DNA is a stable template by means of which some proteins generate other proteins, as required. Proteins, not genes, are the active agents in the cell. Therefore, it would be far closer to the truth to say that genes are proteins' way of making more proteins.-"Still closer to the truth, of course, would be to say that both proteins and genes are cells' way of making more cells. But be that as it may, the question that arises from a right understanding of causality within the cell is this: How can proteins be "active agents"?-***-"First, proteins are frustrated systems. "Frustration" is a technical term in physics meaning that a system in incapable of relaxing into a single lowest-energy state. The reason for this is a myriad of competing self-interactions among different parts of the system. As a result, the system as a whole incessantly and rapidly traverses a very large set of nearly isoenergetic, conformational substates.-"In other words, proteins resemble not so much the traditional static structures depicted by X-ray diffraction (which are only averages), as essentially dynamic, writhing masses of fleeting configurations that have been described as "kicking and screaming."-***-"In summary, proteins are far from being the static molecular "machines" of popular imagining. Rather, their behavior is dominated by their intrinsic dynamics (frustration) and thermodynamic coupling to their environment (slaving).-***- "Considered as a whole, cytoplasm must have physical properties that are very different from those of ordinary liquid water---properties that make of cytoplasm an intermediate state of matter in between a liquid and a solid, like a gel or a liquid crystal.-"This is what one would expect on theoretical grounds from the sheer fact of cell crowding, but experimental evidence is also not lacking. For example, relatively large sections of the cell membrane may be excised with no visible effect on the functioning of the cell, and with no leakage of cell contents."-Comment: Living cells are extremely complex and dynamic, not the bobs Darwin envisioned.