Examples of stages, levels and interfaces between levels
Update history:
All kinds of smaller and larger additions before Feb 06.
Februari 2006: added links to concentric man and some text
May, 2006: link to John G. Bennett's systematics added. See near end of article. Added two pages summarizing Miller's writings on the levels of cell and organism.

Now, finally, let's have a look at some illustrative material.
I will choose some physical, physiological/biological and psychological examples from several articles and books and try to place them on the seven-staged arc. Some attention to interfaces between the levels will be given, since these levels are integrated  and coordinated in real-life examples. This is a work in progress. First have a look at two basic examples.

Introductory examples:

basic businesscycle (Simplified)

Arthur Young's example of communication
P.S. You can position "meaning" (a multi-faceted term) also on the sixth stage as is done in the TOP-poster. The sixth stage is on the second level, the "social level"

A truely interesting book on 'fractality'/parallel development in the human being

Onno Damsté's free book The concentric man is truely enlightening in comparing the development of genetic, immune-, neurological and language-system. Keywords: adaptation, defense, learning. Coupled oscillations belong to the essence of the workings of the body, confirming the age-old notions of Yin and Yang. Whether we talk about stimulation vs. inhibition, vegetative vs. animal function, it is all about complementary, c.q. antagonistic function. Form and function as occurring on different time-scales (in different time-frames) is discussed in this book too. Very interesting.

A short intermezzo: Fritjof Capra gives some interesting info in his books "Web of Life" and "The Hidden Connections". In "Web of Life" he gives three factors to take into account in science/biology: relational/informational pattern (corresponding to stage 3 in TOP), maintenance of pattern/organization (stage 5 in TOP) and physical configuration that does work (stage 4). My paraphrase, so don't take it for granted. Maintenance of pattern is also called "bringing forth a world" by Maturana, characterized by negentropy (see link below, principia cybernetica). In Capra's book "hidden connections", Capra adds "Meaning" as a factor/level to his model of reality. Note how closely this corresponds to TOP where meaning is put on the second level (TOP-poster), sixth stage. Now, meaning is a very difficult term to define, and there may be multiple levels of meaning, but that is not the topic of this article. Pattern and information are obviously related, and meaning has to do with value attached to perception or attributed to symbols (language for example!). Some define meaning as a transaction in mind between symbol and object (since meaning is through symbol to the thing meant). What do you think of that?
Capra could have added the idea of the field as a factor in his model, but he doesn't. I would like to add the field as a "seventh stage" factor, the integrative factor. The field encompasses all, in principle and in reality. Even the first "stage" is related to the field in a way to be described later. Some people may like to know that the original model of the seven-stage arc (see "The Mahatma letters to A.P. Sinnett") has the Akashic Field mentioned as the seventh principle. This field integrates and differentiates as it were. Vitvan mentions the Autonomous Field as the first level principle, quite the same idea as the Akashic Field as it seems to me.

BTW, for abundant examples of level 4 and level 3 processing of matter-energy and information/patterns, you could try to procure a copy of James Grier Miller's book "Living Systems". It is out of print, but perhaps you can get it via your local library. I'll try to give some examples from his book later on, in a separate document.
Here is a small taste of his work in the form of two pages, derived faithfully (but slightly adapted and including some comments of mine) from tables in the chapters on the cell and the organism, respectively, showing examples of the 19 critical subsystems of cells and the organism.
Text between square brackets is mine. Note that in a later edition of his work Miller added a "timer" subsystem and other scientists would like to add even more subsystems (e.g. transport). It is a snapshot of knowledge available in 1979, of course.
In the meanwhile you can google for an overview of his work.

Last, but not least, a promising theory of interaction between people has been formulated by Marty Monteiro. His "General Social Model Of The Human Being" comes close to my understanding of interaction. It needs more elaboration, but it seems a promising building block for a comprehensive model of social interaction (more or less level 2 and a bit of level 1 in TOP, depending on how you see the levels).

Example level 2: exchange with the environment; binding in the matrix of life; value/valence systems

There are several examples that come to mind here, like the plasmamembrane in the cell and the multi-layered air containing the ionosphere and magnetosphere. Value/valence systems and communication are very important too, as the basis of motivational factors that keep us going. As many of these examples are really complex, a highly simplified description may be given later. For now, I will give you some links that highlight some of the features that I have been discussing in my evaluative article:

Bruce Lipton on the plasmamembrane as a highly integrated, intelligent operating structure performing input and output functions.
His summary of the new biology (http://www.brucelipton.com/newbiology.php)
My personal angle on this: proteins as agents of intelligence (6th stage factor) work as an integral part of what seems to me a 2nd stage aspect: the bilayered membrane. To be researched later in connection with the Young model.

Joel de Rosnay's digitized book "The macroscope" on a systemic view of ecology, economy, biology, "A NEW WORLD SCIENTIFIC SYSTEM".
Social systems, System theory, Energy policy, Communication, Time. Joel sketches flows of energy, substance, and information. The increase of entropy as the breakdown of the bonds of complex molecules proceeds, is discussed, as is the direction of time; issues related to information and energy. A simple model of hydrosphere, troposphere and lithosphere is given in his book. I may add a little to that later.

Principia Cybernetica Electronic Library
free, downloadable copies of basic books on cybernetics and systems science: Shannon, Ashby, Turchin and more! Good intros to related concepts. Turchin is a must for meta-state transitions (a kind of turns on the arc of development). He describes the development of simple relexes to complex reflexes all the way to culture and thought.

Lastly, an interesting discussion of the object-subject dichotomy (including the so-called body-mind "problem") can be found in Anthony McWatt's text on the Metaphysics of Quality (MOQ, a Robert Pirsig philosophy). While studying that you could get interested in quantonics, the integration of quantummechanics into the MOQ.

A slight hint from myself regarding the body-mind "problem": it is typically a pseudo-problem. "Body" does only exist as a thought-concept, ditto the "mind". These "things" are in reality dynamic processes, including dynamically maintained structures, different phases of substance, etc.
Bennett (see below) says that it requires at least three terms to explain body-mind, i.e. one needs to add relationship as the third factor. He uses triads quite often in his work. Starting with the experience as a whole, we can proceed to duality of mind vs. object and then see the relation between the two and establish the triad. There's a whole lot more to it, but that requires a separate article. Bennett rightly distinguishes between the two domains of fact and value. This is an old division in Kabbalah where the lower triangle (triad) is concerned with biological and physico-chemical processes; the middle triangle is concerned with value-judgments (ethical triangle), typical for humans; the upper triangle is truly spiritual in nature and Bennett associates Harmony with this latter triangle. The cosmic and human processes have to do with values that are being realized, value becoming fact so to speak,and vice versa, by action/intermediation of the human being and other factors. The domains of Fact and Value must be harmonized according to Bennett. See Dramatic Universe, volume 2 where these ideas are elaborated.
To round off this paragraph I like to say that the three mentioned triads are connected by one spiritual stream of life/consciousness emanating from deep within, the emanative principle, the tenth (or first) principle.
Vitvan has solved this kind of questions long ago in his writings about the development of substance/light, as have other esoteric (well-grounded) philosophies. See my articles on "Vitvan highlights".

May, 2006.
A couple of weeks ago I discovered the work of John G. Bennett.
An overview can be found at Systematics site.Loosely based on Gurdjieff and Ouspensky, Bennett has developed an elaborate scheme of twelve energy levels, and a host of categories, applicable to the domains of Fact and Value which he wanted to connect. (These are connected BTW, by agents of change - perception and act). His tome (4 vols) "The Dramatic Universe" deals with natural philosophy, moral philosophy, man and his nature, and, history. Quite impressive, I have to say, and the first decent attempt I've seen by someone to develop a philosophical framework that bridges (or tries to) the gap between knowledge and understanding. Besides the three dimensions of space, Bennett introduces three dimensions of time, among which "eternal time" which explains why consistent action is possible. Do pause a little and ponder this over! Include the experience of continuity of the ego in your considerations (each day you wake up your are still you as far as you know..Your body cells change, but your identity remains. How come?
I think forms or patterns have to do with this, but this requires close scrutiny. Where do you think values come from?) Anyway, the work of this man can keep philosophers busy until eternity! I believe there is a practical side to it too, but you have to study it for yourself. There is a Yahoo group dedicated to him (search for Bennett and you will find it). When I can integrate pieces of his work into my own train of thoughts I will write about it.

See my new site or my scribd account for new notes