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Cell duplication, biocybernetics in action


John von Neumann, in his mid-1950s ground breaking studies about the mathematical theory of self-reproducing automata, argued that self-replication basically involves:
— import of materials;
— symbolic description/instructions;
— memory;
— constructor;
— controller.

He developed his theory before the discovery of DNA and the cellular machinery based on information processing. Here I will deal a little with the relations and similarities between such cybernetic theory and the biological process of cellular duplication.

First, we must keep in mind that the biological cell is a natural living thing, a true whole, something characterized by a far higher degree of integration and unity compared to any artificial automaton. This is the reason why in cell division (and in general all what pertain to life) it is more difficult to distinguish parts, functions and roles than in technology. This is especially true for the “controller” top function. In a sense it is the animated cell in its entirety to control and govern the entire process.

Cell duplication involves an organizing power in action similar to the organizing power necessary to origin life itself. In fact, cell duplication, far from being a trivial task, is an extremely complex hierarchy of organizational processes, where equivalents of all the above von Neumann’s functions are involved. Usually the description of its many steps takes several chapters in cellular biology textbooks. Obviously here we can only summarize it in few steps.

In the first step (interphase), at a certain point in its life, the cell begins to increase its mass, thank to previous import of raw molecular materials in its cytoplasm, and synthesize bio-molecules according to the DNA (which stores in memory a library of the necessary symbolic instructions). In this preparatory step the cell must somehow “know” what kinds of molecules and how many of them to produce. It is like a carpenter who sets up a list of materials necessary to construct the artifact he has conceived in his mind. In turn also the DNA contained in the chromosomes is duplicated by the machinery.

In the second step (mitosis) there is the formation of the so called “mitotic spindle”, composed of two organizing “poles”. These poles perform extremely complex functions in a somehow robotic way. They use a big number of microtubules, as robotic arms and communication tools.

Mike Behe explains: “Microtubules serve a number of functions. Among these are formation of the mitotic spindle — the apparatus that, during cell division, pushes one copy of each chromosome into each daughter cell. Microtubules are also the spine of eukaryotic cilia, which, like oars, can move the cell through its environment. […] The motor proteins are known to travel along microtubules, using them as little highways to get from one point to another. […] Finally, microtubules can act as “railroad tracks” for molecular motors to carry cargo to distant parts of the cell.”
(Darwin’s black box, pag. 66, 259)

Each of these poles has the task of taking what each daughter cell needs and assembling the right components in the right place. The perfect separation and segregation in two equal nuclei of the duplicated chromosomes is part of this important task.

The couple composed of the duplicating/constructing machinery of the first step plus the fundamental organizing/assembly role of the mitotic spindle in the second step can be related to the “constructor” function of von Neumann’s schema. The key point is that this couple of constructors necessarily collaborate and act according to a precise plan, something that has a lot to do with what von Neumann called “logical description” or what David Abel in general calls, in a single word, “formalism”.

Von Neumann says: “But it is easier, and for the ultimate purpose just as effective, not to construct an automaton which can copy any pattern or specimen given to it, but to construct an automaton which can produce an object starting from a logical description. In any conceivable method ever invented by man, an automaton which produces an object by copying a pattern will go first from the pattern to a description and then from the description to the object. It first abstracts what the thing is like, and then carries it out. It’s therefore simpler not to extract from a real object its definition, but to start from the definition.” (Theory of Self-Reproducing Automata, IV).

In turn Abel defines “formalism”: “Systems of rules […] involving symbol systems and requiring choices to be made at decision nodes […] formalisms employ conceptual representationalism […] arise out of uncoerced choices in the pursuit of function and utility […] require bona fide decision nodes, not just “bifurcation points”. Language, mathematics, programming and logic theory are all formalisms. […] Formalisms are governed by arbitrary rules, not laws. […] they cannot be encompassed by a consistently held naturalistic worldview that seeks to reduce all things to physicodynamics. (The First Gene, pag. 365).
The F > P Principle states that ‘Formalism not only describes, but preceded, prescribed, organized, and continues to govern and predict Physicality.’ (ibidem, pag. 325).
Formalism organized physicality before the fact of physicality’s existence. (ibidem, pag. 347).”

We see that von Neumann and Abel perfectly agree on the primacy of formalism compared to physicality, — in other words — the superiority of information on matter.

The third final step of cell duplication is “cytodieresis”, the cytoplasm division, which happens only when the two daughter cells are just fully formed and can be divided and enclosed without damage in two distinct cellular membranes.

We must also consider that actually many controls of cell division are yet unknown. It is meaningful that, while the more visible effects have been discovered by means of microscopy and lab experiments the top driving forces/causes at play remain unknown:

Stephen Wolfe admits: “The physical forces that are at the root of this process have been for long time matter of discussion since the mitotic process was discovered and are still only partially known. […] The precise identity and the modalities of action of these controls so far have eluded the strives of the researchers.” (Biology of the cell, 384, 389)

What is in action in cellular division (and many others processes in organisms) is what Abel aptly calls “[protobio]cybernetics”, which implements formalisms as defined above:

The study of the derivation of control and regulation in the first life forms. Cybernetics incorporates Prescriptive Information (PI) into various means of steering, programming, communication, instruction, integration, organization, optimization, computation and regulation to achieve formal function. (The First Gene, pag.376)

Obviously, all biocybernetics processes imply high organization, in the sense I described in my previous posts, here , here , and here . In fact in biocybernetics nested functions, control, communication are involved in an information processing overall framework.

Note that in “self-reproduction” there is the problem of the software startup: what starts the entire process (bootstrap)? In a sense this bootstrap is the decision/instruction #1. In the case of your computer usually the power-on causes also the operating system startup. In the case of an automaton or biological cell the bootstrap could be an instruction scheduled in the automaton itself (by its designer). Eventually this first instruction could be triggered by one or more factors in the environment. Obviously this changes nothing about the necessity of a designer because also the potentiality of a system of being bootstrapped by external signals coming from the environment (or others automata/cells/systems) has to be aptly frontloaded in the automaton/cell just from the beginning.

To sum up, cell duplication is an highly orchestrated operation performed according to a complex plan of organization. Far from being a simple characteristic that might even “evolve by chance”, cell duplication is really an apotheosis of intelligent design. Obviously, biological reproduction becomes yet more complex in multi-cellulars until arriving to the complexity of sexual reproduction in higher organisms, which requires the integrated design of male and female. “Self-reproduction” is a pre-requisite to have any population of living beings. No wonder that no reasonable naturalistic origin-of-life explanation has been provided thus far: in fact just replication at the one-cell level is an advanced fabric that involves cybernetic organization, software processing and robotics features.

Identification of direct targets of transcription factor MYB46 provides insights into the transcriptional regulation of secondary wall biosynthesis. doi: 10.1007/s11103-014-0205-x. Secondary wall formation requires coordinated transcriptional regulation of the genes involved in the biosynthesis of the components of secondary wall. it is not known whether MYB46 directly activates the biosynthetic genes for hemicellulose and lignin, which are the other two major components of secondary wall. MYB46 function as a central and direct regulator of the genes involved in the biosynthesis of all three major secondary wall components. http://www.ncbi.nlm.nih.gov/pubmed/24879533 Dionisio
Transcription factors that directly regulate the expression of CSLA9 encoding mannan synthase in Arabidopsis thaliana. Little is known about how expression of the CLSA9 gene is regulated. Taken together, we report that transcription factors ANAC041, bZIP1 and MYB46 directly regulate the expression of CSLA9. http://www.ncbi.nlm.nih.gov/pubmed/24243147 How do those TFs regulate the expression of CSLA9? How do those TFs appear on the scene? when do they appear? Why then? In what amounts try appear? Perhaps the answers to those and other questions are in the same paper or in other papers. Dionisio
Controlled by a tightly regulated choreography that determines what should go up and what should go down, plants develop along a polar axis with a root on one end and a shoot on the other. http://www.salk.edu/news/pressrelease_details.php?press_id=200 Dionisio
Dragonflies on the hunt display complex choreography a dragonfly's movement is guided by internal models of its own body and the anticipated movement of its prey. dragonflies on the hunt perform internal calculations every bit as complex as those of a ballet dancer http://www.eurekalert.org/pub_releases/2014-12/hhmi-dot120814.php# Dionisio
#9 clarification niwrad, The statement starting "If you believe that, then you..." could be rewritten as "If one believes that, then one..." because 'you' does not refer to a particular person, but to anyone. The same statement could have been written "Anyone who believes that, could also believe that..." Dionisio
Recognition, signaling, and repair of DNA double-strand breaks produced by ionizing radiation in mammalian cells: the molecular choreography. doi: 10.1016/j.mrrev.2012.06.002 The faithful maintenance of chromosome continuity in human cells during DNA replication and repair is critical for preventing the conversion of normal diploid cells to an oncogenic state. In mammalian and other vertebrate cells, the elimination of double-strand breaks (DSB) with minimal nucleotide sequence change involves the spatiotemporal orchestration of a seemingly endless number of proteins ranging in their action from the nucleotide level to nucleosome organization and chromosome architecture. DNA DSBs trigger a myriad of post-translational modifications that alter catalytic activities and the specificity of protein interactions: phosphorylation, acetylation, methylation, ubiquitylation, and SUMOylation, followed by the reversal of these changes as repair is completed. "Superfluous" protein recruitment to damage sites, functional redundancy, and alternative pathways ensure that DSB repair is extremely efficient, both quantitatively and qualitatively. ...the nature of the intricate coordination of repair processes with cell cycle progression is becoming apparent. http://www.ncbi.nlm.nih.gov/pubmed/22743550
Wow! How did we get all that functional complexity? Well, the explanation could not have been much simpler than this:
The evolution of higher eukaryotic cells endowed them with a large genetic investment in the molecular machinery that ensures chromosome stability
If you believe that, then you should also believe that the moon is made of cheese. Hey, why not? :) Obviously, please refrain from asking simple questions abut the details of that amazing creativity. Some folks might get offended by such 'childish' questions. :) Now, seriously, I can't wait to read the future research papers revealing more details of those amazing biological systems. Dionisio
Dionisio, good finding from a medical journal. It is about the heart system. However the word occurrence count is: cybernetics 2 times cell[ular] 13 times function 16 times signal[ling] 12 times complex[ity] 13 times molecul[ar] 11 times pathway 5 times. It is obvious that if cell is cybernetics also highly integrated and organized systems of cells (organisms) is cybernetics all the way up. These medicine scientists seem well aware that in biology Occam's razor simplicity exist only in our dreams. Occam's razor is only a symbol of our hope that things be simple, so it is easy for us to know. This so-human modern pseudo "principle" is not the work paradigm of the omnipotent Designer. niwrad
'cellular cybernetics' (over a decade ago):
The challenge of molecular medicine: complexity versus Occam’s razor doi:10.1172/JCI18153. http://www.jci.org/articles/view/18153
It seems the word “orchestration” is used often to express the bio-organization involved… no wonder, also an orchestra is a place where many players (functions) and one director (controller) together play a same music (formalism).
Exactly. Also, an orchestration is generally based on a written musical composition created by someone's inspiration with a purpose in mind. Dionisio
Dionisio Thanks for your useful scouting on this large topic. It seems the word "orchestration" is used often to express the bio-organization involved... no wonder, also an orchestra is a place where many players (functions) and one director (controller) together play a same music (formalism). niwrad
Polarity sets the stage for cytokinesis doi: 10.1091/mbc.E11-06-0512 Cell polarity is important for a number of processes, from chemotaxis to embryogenesis. Recent studies suggest a new role for polarity in the orchestration of events during the final cell separation step of cell division called abscission. Abscission shares several features with cell polarization, including rearrangement of phosphatidylinositols, reorganization of microtubules, and trafficking of exocyst-associated membranes. Here we focus on how the canonical pathways for cell polarization and cell migration may play a role in spatiotemporal membrane trafficking events required for the final stages of cytokinesis. http://www.molbiolcell.org/content/23/1/7 Dionisio
As anyone who has renovated a home knows, the process of remodeling often requires an elaborate orchestration of timing and materials. Remodeling at the molecular level is likewise an intricate process in which macromolecules must adopt particular structures at specific times in order to ensure a successful outcome. How is this coordination achieved, and how are large, stable macromolecules disassembled and then reassembled to form new structures in an energetically efficient manner? Our work highlights how deceptively simple retroviruses can, with just a tiny toolkit of machinery, orchestrate elaborate molecular events that ultimately allow these particles to overtake entire cells and organisms. https://www.mcb.harvard.edu/mcb/news/news-detail/3748/rna-remodeling-by-an-efficient-retroviral-renovator-dsouza-lab/
Structural Choreography of Cellular Self-Digestion http://www.mskcc.org/events/seminar/Structural-Choreography-Cellular-Self-Digestion Dionisio
Cell cycle: A division duet doi:10.1038/nature10828 The orchestration of cell division requires a programme of events choreographed by protein modification. A study shows that the relative activity of a phosphatase enzyme towards its substrates imposes order during the final act of division. http://www.nature.com/nature/journal/v481/n7381/full/nature10828.html

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