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Systematics: harmonizing fact and value
Wednesday, 28 May 2008

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.

Posted by m_euser at 12:31 AM MEST
Saturday, 3 May 2008
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.

Posted by m_euser at 10:22 PM MEST
Friday, 2 May 2008
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 (<a href="http://m_euser.tripod.com/science/table1cellLST.html">Link to cell subsystems</a> and <a href="http://m_euser.tripod.com/science/table2organismLST.html">link to organism subsystems</a>) 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.

Posted by m_euser at 2:57 PM MEST
Sunday, 13 April 2008
substage 5

Substage 5 is about control of form. In humans (level 1, stage 7 Young), creativity shows itself at work (substage 5). Young puts creative genius in this substage. This genius certainly has an ego (quite an ego, at times). The big transformation of the ego/self is something that occurs in substage 6.

In plants (typifying stage 5), there is, in substage 1 of stage 5 of the Young model, the appearance of the cell. First there is the proto-cell, the prokaryote, sometimes called microbe. Later we get the eukaryote. These microbes of substage 1 seem to play a role in the evolution of the cell, as in endosymbiosis - for example, the mitochondrion in the cell. One of the striking features of stage 5 is the presence and activity of membrane organizers. Negentropy or syntropy is only possible if there is some kind of boundary imposed between a center and its environment. Vesicles play an important role in the cell, something to be studied in more detail.

The phospholipid bilayer forms the plasmamembrane, together with certain classes of proteins.These phospholipids can form rings or other closed structures - very interesting indeed. The double feature of hydrophobic tails and hydrophilic heads is something we must keep in mind. Is this bipolarity reproduced in nature on other levels and scales?

On a more esoteric note, the mind has its own enclosure. "Closedmindedness" is not just a linguistic phrase. The human aura is composed of many layers ("membranes") with pores in it, according to the eminent esoterist De Purucker. I suppose that many people would be very surprised if they would get to know more about the functions of the human aura/consciousness. The projections of the mind are many and varied - a subject shrouded in mystery.

Posted by m_euser at 11:59 PM MEST
Wednesday, 27 February 2008
More on level two and three

To continue where I left off in my previous posting: level two seems to entail the source of cycles. Very mystically, the Aeons represent time-periods in which particular facets of consciousness/energy are being developed. We can also expect something like "timers", "pacers", etc., to have their origin here. The notion of recurrence has already been mentioned in respect to hyparxis and autopoiesis. Organisms have to maintain themselves, homeostasis, etc. and they need food/energy from outside sources to do that. Exchange of substances, circulation in a sense is expected to accomplish that feature.

Level three shows the building of form, the organization of form and function, in the Young model there is stage 3, the taking on of a center. In esoteric teaching there is the idea of elementals (micro-elements, life-atoms, whatever you want to call these building blocks of life) taking a form that is organized by some (semi)conscious factor - be it plants, animals or humans. We can take stage 5 and stage 6 as the ensemble of psychophysiological forces, in stage 5 less developed qualities and in stage 6 more or higher developed qualities - something to research a little deeper. Keep in mind that plants are not the stupid creatures one might be inclined to think. No, there is now proof that some plants recognize certain predators and produce chemicals to attract the enemies of such predators. A guy at Wageningen University has researched that stuff, I believe for his PhD. Fascinating.

Stage 4 can be taken as a combination of combinations between "stages" (be it substances, elements, functions). In a simple way one can look at this stage as the infrastructure ("body") of an organism, and look at the psychological/cognitive functions as higher "stages" (or possibilities, spheres, influences, functions, energies) expressing themselves through the body. It all boils down to a very intricate meshwork of hierarchical-heterarchical components forming an ensemble, sometimes designated as holarchy. I suppose that biologists know quite some things about the cell at this point in time (certainly more than about embryology), so this might provide a good starting point for a study of biological process.

Posted by m_euser at 9:18 AM CET
Thursday, 21 February 2008
Comparing Bennett's ideas to Young's work

Comparing the ideas of Arthur Young with John Bennett can be fruitful. It made me realize that Bennett's hyparxis, a time-like power, actually has a lot to do with level two in the Young model. In modern parlance one could say that agency has to do with level two (and with level one). Will, related to the concept of hyparxis, is active on level two. On a similar note, we can say that the Ancients related Kundalini, the Life-force or shakti, to adaptation of and to the environment. As I have written in an evaluative article about Young (see my ebook), level two has to do with interaction with the environment taken in the widest sense.

The 'axis' Level two-Level one seems to me correlated to the inner flow of consciousness. Also, decision making seems to involve level two (emotions, a.o. in the Young model, stage 6) and level one. Lots to research!

On a sidenote: Bennett associates the property of 'spin' with hyparxis (for photons/elementary particles). Something to keep in mind. Light is the connecting factor between the Macro, level 1, and level two ('soul' level in Young's model). Stage six is important in my own fourfold model as it is the intermediate regulating factor between level 1 and the lower levels.

Interaction and events seem primary to time to me. Time looks like an abstraction. Thinking about this, I realized that a proper designation for level two might be something like 'Duration', rather than time. It also is the level where all kinds of elements are unfolded from the bosom of level one. Stage two in Young's model could be correlated with the Serpent force (Kundalini) about which Subba Rao had some interesting things to say. More about him in another posting.

One more thing: stage six is on the right side of the sevenfold arc as per Young. It seems to have to do with regulation (astrological symbol: planet Mars). Sometimes the ancient symbol of Scorpio (generation) is associated with stage 6 (which can also be taken as transformation in a spiritual sense - when appropriate. There is so much symbology applicable here. Think of the Eagle with the serpent in its claws - the symbol of regulated life-force, ideally spiritual Regeneration.). Stage two has also designated a symbol: Jupiter-Zeus-Chronos (Chronos as Duration rather than time!). How Sagittarius fits in is not entirely clear to me, but it seems to be correlated with the many classes of micro-elements that are generated at this level. In esoterism, the nine prajapatis (with Jupiter making the tenth) seem to be mightily involved with this - the Gnostics have their system of Aeons (Time-Duration again!) which has a whole lot of meanings attached (see Simon Magus in his Gnostic system).

What I am looking for in all this is formost generative force, regulation, interaction, adaptation, selection out of available options, choice, to name a few correlatives to this level. One can expect that biological systems will display some or all of these features. Recurrent life (force) is something that can be correlated with hyparxis too, and it makes sense when we think about autopoietic systems that rebuild themselves constantly.

It pays off to do some study of ancient symbols when researching the fundaments of a true holistic science!

Posted by m_euser at 8:14 AM CET
Updated: Monday, 25 February 2008 3:16 PM CET
Monday, 24 September 2007
substance philosophy

To get a feel for the importance of substance in the continuity of life and many other issues, you could study books like: "The Possibility of Metaphysics: Substance, Identity, and Time" by E. J. Lowe; Clarendon Press, 1998.

For now, I direct my attention to the process of creation as a whole, but I'll come back to considerations of substance when necessary to my investigations. Keep in mind that I use the old Eastern method of study: first get a global picture, then descend into more detailed descriptions. Ponder about these things and your intuition will develop alongside with your experience in life.

Posted by m_euser at 4:44 PM MEST
Thursday, 6 September 2007
Value adding

In my holonic model, value and meaning play a role in the whole of the process of the descent of the micro-element along the arc and the subsequent ascent. The macro-system can perform "judgments" as to what to do (a role for consciousness). The "levels" can in some sense be described as "spheres": on the left there is more emphasis on physical-energetic side (and information), on the right side there is more emphasis on principles of consciousness, although there may be visible expressions, like in (level of ) organization of production and distribution of substance or flow of value (money, esteem, mission statement, moral idea) through a system.

The supervisory role of will, c.q. consciousness, is conform the ideas of Assagioli, and some of that can be found in cognitive models of the mind, like ideas of Baars in his book "In the theater of consciousness". Keep in mind that this pertains to a global function. That is simply necessary to explain the workings of the system, to explain the integrity and autonomy of process. Consciousness as such is whole, transcending earthly time, while attention is partial and in time (transactional, I think).

The idea of substance as eternal and indestructable is very old. It is the necessary ground that makes the value experience possible. It is the only way the qualia problem can be solved! It connects the different levels. On the macro-level it can take the form of a kind of light-substance. Not only ordinary light, but also subtle forms of it exist. This light can carry a pattern (encoded, enfolded), not a strange idea since scientists and technologists have succeeded in artificial encoding of radio and television content as a superimposed signal on broadcast waves. The pattern is unfolded, decoded in later stages, notably levels 3 and 4. But this is all food for research when we research the producer subsystem in conjunction with input system, decoder, converter, etc.

Posted by m_euser at 9:48 PM MEST
Updated: Friday, 7 September 2007 10:40 AM MEST
Saturday, 1 September 2007
Objectification and De-objectification

The left side of the arc shows Objectification, the taking of distinct form, while the right side shows De-objectification, i.e. adding of value to the "object". In economic terms, valuing has to do with pricing, or money. In psychological terms, there's a range of values, especially on the social level (value judgments, norms), beliefs, etc. On the more abstract level there's aesthetic judgment and (internalized) moral values.

This passage from objectification to de-objectification is pretty well established in many quarters, including economy (as in adding value and price), esoteric teaching, and also in such theories as Leontiev's activity theory. See links





I did not convert to dialectical materialism, the thing is simply this: every research angle can yield some useful points of view, elements in the big mosaic of life. It's like the seven blind people touching the elephant in the parable. They each report a different structure of the elephant and couldn't understand each other. They fiercely disagreed as to how the elephant looked like. Yet, they all reported correctly about a small part of reality. So, look at the world from different angles and try to integrate different points of view, as far as is possible, logically and philosophically speaking.

Posted by m_euser at 1:58 PM MEST
Friday, 24 August 2007
Backup blog

On second thought, this blog will serve as a back-up blog for my blogspot blog. You never know what is going to crash when..

 The new blog is all about integrative science & philosophy. It is a natural philosophy about science in general, including the sciences, psychology, biology. A little excursion into spiritual realm and mythology may be made if necessary for the exposition of my ideas.
The main train of ideas comes from researchers like Jim Miller (Living Systems Theory), John Bennett (systematics), and Arthur Young (Theory of Process) or is related to these inputs. My background is physics, psychology and I have a good knowledge of diverse esoteric teachings.

 I am developing a true holonic model (first of its kind, I believe) of the manifest cosmos, especially as seen on our planet Earth. It entails a reinterpretation of Arthur Young's Theory of Process (TOP). As I do this in my free time, progress may be slow. Yet, it already looks very promising. You can have a look at the priliminary model:

There's a lot to be elucidated about the model, like the overlay/interfacing/interweaving of micro-development within the macrosystem, and a whole host of other things, not in the least the emergence of loops (reflexivity),  but I have to do some research on more examples first to make it a little clearer for you and myself.

If you have constructive comments to make, please do so.


Posted by m_euser at 11:06 PM MEST
Updated: Friday, 24 August 2007 11:14 PM MEST

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