Bacterial motors carefully studied (Introduction)

by David Turell , Sunday, July 04, 2021, 14:57 (1238 days ago) @ dhw

A new engineering study, first part of three:

https://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2021.1/BIO-C.2021.1

"Systems biology [1] employs methodology and techniques typical of systems engineering. Similarly, reverse engineering the features of biological organisms leverages both biology and engineering disciplines. Specifically, the systems engineering perspective on bacterial motility detailed in Parts 1, 2 and 3 studies the purpose, functions, components, and structure of a typical bacterial flagellum and the flagellum’s assembly stages. The dynamic operation and control of this motility organelle is also studied. This study takes two essentially independent approaches below. One is a constructive approach, which this
Part 1 covers; the other is an analytical approach to be covered in Part 2. The first, constructive approach is a top-down specification. It starts with specifying the purpose of a bacterial motility organelle, the environment of a bacterium, its existing resources, its existing constitution, and its physical limits, all within the relevant aspects of physics and molecular chemistry. From that, the constructive approach derives the logically necessary
functional requirements, the constraints, the assembly needs, and the hierarchical relationships within the functionality. The functionality must include a control subsystem, which needs to properly direct the operation of a propulsion subsystem. Those functional requirements and constraints then suggest a few—and only a few—viable implementation schemata for a bacterial propulsion system. The entailed details of one configuration
schema are then set forth. This constructive approach is analogous to how a myriad of
theorems, definitions, and constructions of plane geometry are derived from the few basic axioms and the rules of logic. A sincere attempt has been made to keep the elaboration of this constructive approach logical and as independent as possible from knowledge of the actual flagellar structure. The analytic approach of this study will be covered in Part 2 and is a bottom-up deconstruction of a typical flagellum. The bacterial flagellum is a well-researched molecular subsystem, and Part 2 draws its information from many cited papers. It documents the known 40+ protein components and the observed and inferred structure, assembly, and control of a typical flagellum. However, in Part 2 the protein and assembly relationships will be illustrated graphically in a form and detail not found in any previous paper. After the constructive and analytic approaches are presented, they will be compared in Part 3 along with a set of fresh concluding observations. The comparison is appropriate, because engineers regularly specify and design systems top-down, but they construct those systems bottom-up. Then the resulting implemented system is evaluated against the specification."

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OBSERVATIONS
"Regarding the foregoing derivation of requirements and Figures 2 to 4, we see intricate coherence which is essentially irreducible. It is hard to imagine that a motility system (comprising control, propulsion, and redirection subsystems) could function at all without each of those details present. Current evolutionary biology proposes that the flagellum
could have been “engineered” naturalistically by cumulative mutations, by horizontal gene transfer, by gene duplication, by co-option of existing organelles, by self-organization, or
by some combination thereof [10, p. 210]. See the summary and references by Finn Pond [11]. Yet to date, no scenario in substantive detail exists for how such an intricate propulsion
system could have evolved naturalistically piece by piece. Can any partial implementation of a motility system be even slightly advantageous to a bacterium? Examples of a partial system might lack sensors, lack decision logic, lack control messages, lack a rotor or stator, lack sealed bearings, lack a rod, lack a propeller, or lack redirection means. Would such partial systems be preserved long enough for additional cooperating components to evolve? Further observations will conclude Parts 2 and 3. They will include suggestions for further research into the molecular details of proteins composing the bacterial flagellum, as detailed in Part 2."

Comment: I just copied out the beginning and the end of an enormous technical engineering can analysis of the flagellum. Note my bolds. The point of this paper is always the same as the poster child for design. There must be an engineering designer.