Continuation

To continue my previous posting: what I have described in brief format is a pathway of protein synthesis. There are many pathways in such  syntheses. After the production phase in the narrow sense, where ribosomes have done their work, a  lot of other stuff happens. The comparison with industrial production may be illuminating in this point. After all, the product has to be packaged, tagged, distributed and finally integrated (to play its role) in the structure it is directed to, be it a plasmamembrane or other structure. The same applies to the industrial product: this arrives at the consumer site to be used in the daily process of life. There is of course another side to this production business: it starts and is sustained by the need for certain products. Without a perceived need or anticipation of such a need, production wouldn't start, normally speaking. Analysis of need, necessity, desire, aspiration, etc., is something which is necessary in the development of wholistic models. It fits in the larger context of values, qualities, energies, regulation, decision, meaning, etc. Not an easy thing to do, I suppose. We will see.

Energy is necessary for protein synthesis, as in all production processes. There is a whole field of study in this area alone! Not only are there many types and qualities of energy (vide Bennett's work and previous blogpostings), but the working together of some of these energies effectuate the emergence of other, intermediate energies. The latter idea can be found with Gurdijeff, Bennett and in a related way in the system of Simon Magus (in the gems that are transmitted by tradition about him - do a search on  G. R. S. Mead in that respect). That is all food for research.

Lastly, plant biologists begin to apply the Living Systems Theory of Jim Grier Miller (which I use too)  to their field of study. At last, some of them begin to recognize that plants are intelligent beings, can discriminate between self and non-self, process information, communicate with other plants and animals, have a kind of nervous system (much involved with the root-brain) and exhibit different kinds of movements (from rotation to nutation). Very good. I will give you some more information in another posting.

Addition to previous post

In addition to the previous posting about the protein assemblage, it is stated in the text books that the mRNA template (molecule) specifies precisely in which order aminoacids must be added to the peptidechain. It is a rather linear process, which in Young's model is associated with substage 5 operations.

Furthermore, the correct aminoacids are delivered by transfer RNA. These acids
are attached to tRNA by specific enzymes. Many factors are involved in this process, not dealt with here: initiation, charging, decoding, formation of peptide bonds and subsequent splitting of  the aminoacid from the transfer RNA, multiple proteins being synthesized at the same time, the formation of vesicles, etc.

The question remains how the cell knows which aminoacids to deliver at that junction of time and place and when and where and how the decision to do so takes place. There are still many unknown features as to recognition/
decision capabilities of the cell.

Can one say that the decoding of the template (mRNA) is analogous to processing data? And that substage 5 involves instructions that are executed? It certainly entails a complex organization in order to be able to synthesize proteins. Is the product, a protein, or rather, proteins, to be considered a substage 4 result which is subsequently packaged in a vesicle? We will have to investigate these matters more thoroughly, guided by  Young's model and my own model as well. Analogy in process will be another guideline.

Creation and selection: level 2; production : level 3,4

In my preliminary seven stage, four level model of earth development I follow the general ideas of Kabbalah and theosophy. I also use elements of John Bennett's systematics and Arthur Young's theory of process and some of Jim Miller's Living Systems Theory (and some other stuff).
I prefer to work somewhat with Miller's subsystems (Link to cell subsystems and link to organism subsystems) rather than separate structures/components, simply because it provides a cleaner overview of process. Miller discusses the fact that components of cells can be involved in several subsystems (such is the case with the plasmamembrane) and a subsystem can comprise several components. There is not a 1-1 relation between subsystems and components of a cell. It is a n:m relation. Keep this in mind.
So, we must be careful in putting a component on a certain level or sublevel of Young's model. Rather, I prefer to use my own model (which is in its beginning phase of development) to describe functions and relations to structures/components.

It occurred to me recently that I can fit in some basic aspects of cell function into my model. For example, stage 5 in my model shows development of the cell. As I have stated before, I see substage 1 as an archetype for subsequent stages. It contains the substantial pattern or template that has to be used for manifestation, so to speak. It is a clear matter in the case of cells: DNA contains the information pattern necessary to synthezise proteins. On level 2 there is an interaction of proteins, notably enzymes, with the DNA in the nucleus. In the transciption phase of protein synthesis, a small part of the long DNA strand is transcribed (copied) into a pre-RNA molecule (in case of the eucaryotic cell) which is subsequently processed into a regular mRNA molecule. This is clearly a selection out of many possible patterns that make up the DNA. In this process, information is coupled to substance (the elements that make up the mRNA and pre mRNA, also the energy needed to do the work involved). Note that creation entails limitation. It cannot be otherwise. How could it?

The mRNA molecule is then transported out of the nucleus to the endoplasmatic reticulum where it is processed (its code is translated into aminoacids, constituting the protein, it is coding for). This concerns an assemblyline like processing ("substage 5" like, level 3 which works with a "stage 3" substantial template - mRNA which is transported through a ribosome) which involves decoding (translating) the informationmarkers of the mRNA into the instructions for making the right aminoacids and assembling these into proteins, all done by ribosomes and transfer RNA (these form the producer). Formation of peptide bonds takes place here.

Stage 3, 4 ,5 of my model (and possibly Young's model) can be very loosely mapped onto the subsystems of Miller, as follows: Decoder, Converter, Producer. I said loosely, because a closer study of matter-energy subsystems working in association with information processing subsystems is necessary, and a further development of my model is also necessary. Stage 4 might be the production of the aminoacids which are then assembled into proteins. 3-4-5 works as a whole, together.

Note the different domains where transcription and translation take place: the nucleus versus the cytosol. We may be able to establish an analogy with other processes, like the human act of will or the physiological organism, to name a few, later on.

Adaptive matters...

When the protein has been synthesized it buds off the ER in the form of a vesicle and is transported or moves from the ER to the Golgi-complex (research is still going on in that respect).

The Golgi apparatus is very interesting. It has many functions: from sorting and packaging proteins, to modifying proteins, synthesizing molecules, and a role in apoptosis (decision/choice to die as a cell or not to die is involved), to name some.
This requires discrimination (typically a sixth "stage" function) as will become clear when you reflect on these functions. Remember my previous blogposting where I briefly discussed the Mars and Scorpio functions? If not, have a look again, it contains some very interesting points (likely applicable beyond the cell, to organisms and the human being in its psychological aspects).
Also, after production (synthesis) of a protein, a fifth stage function, ending with bubble like vesicles, one would expect a sixth stage to occur, and this may well be the activity of the Golgi complex. The seventh stage would be activity at the plasmamembrane, something to consider at a later point.


My point in this brief note is to put emphasis on the selection part of level two and the collaboration of left and right parts of the arc of my model. Principles working or being expressed through the elements. Subsystems at work.
On the human level, concerning mind, one can draw a strong analogy with the process of decision making (the act of will, the complete process). First there is a "seed-idea" - level 1, substage 1 - that enters the mind, that may be very general (a purposive thing). It comprises many possible courses of action, subgoals, etc. Before one decides about anything, there is usually a phase of deliberation - level 2, a weighing of alternative ideas, strategies, connected to the main idea or purpose.
Then a decision ("stage 6" function) is made concerning which goal to pursue and how to do it, which strategy/tactics to implement.
This bears on methods, means, etc., so it couples idea to substantial means. It usually involves money too (a kind of bearer of value!) and in general is based on a belief-system, moral values, etc. The decision also involves motivation (energetic aspect). If one has enough motivation or a high sense of duty one will decide positively for a lofty purpose.
Later an action plan is developed ("stage" 5 function: planning function of the mind involves the process of sequencing of steps (ordering). It yields a plan of action, ("stage 3" blueprint). See how the left and right parts of the arc relate to each other here? Finally the actionplan is executed (bound to a particular time and place)("stage 4"), which involves control (feedforward commands, possibly a "stage 6" function but often downwardly dispersed as far as possible in hierarchical systems), and feedback to adjust the execution and plan to circumstances. See also my post on Assagioli - the stages of the act of will.

More study is needed to develop the model. Some insights have been gained as to selection/copy processes on level 2 of the model. Level 3 and 4 are seen to entail decoding/conversion/production, something to consider in more detail.
Analogies can be further developed since they are like the salt in the dinner.
It's all time consuming, a lot of comparitive study necessary, but the rewards of developing insight into the intricate workings of nature on many levels of being is great, I believe.