I would like to elucidate philosophical background behind BioUML. As the beginning of this work I have collected here a number of quotations and references that are relevant to this task. I hope that latter I will be able to formulate my vision more precisely.

Fedor Kolpakov

Epistemology

Epistemology is the branch of philosophy that studies knowledge. It attempts to answer the basic question: what distinguishes true (adequate) knowledge from false (inadequate) knowledge? Practically, this questions translates into issues of scientific methodology: how can one develop theories or models that are better than competing theories?

References:

F. Heylighen, 1993. Epistemology, introduction.
http://pespmc1.vub.ac.be/EPISTEMI.html.

The map is not the territory

... important characteristics of maps should be noted. A map is not the territory it represents, but, if correct, it has a similar structure to the territory, which accounts for its usefulness...

"The map is not the territory" expresses Alfred Korzybski's second principle of general semantics: namely, Non-All-ness. By this Korzybski meant that no word ever says "all" about anything and no map ever represents "all" of any territory. We can profitably use words and maps, Korzybski said, as long as we constantly submit them to rigorous examination so that we may keep them accurate and up-to-date. This helps us avoid constructing maps of territories that do not, in fact, exist.

References:

Alfred Korzybski, 1933. Science and Sanity: An Introduction to Non-Aristotelian Systems and General Semantics.

What is it in the territory that gets onto the map?

"What is it in the territory that gets onto the map?" We know the territory does not get onto the map. That is the central point about which we here are all agreed. Now, if the territory were uniform, nothing would get onto the map except its boundaries, which are the points at which it ceases to be uniform against some large matrix. What gets onto the map, in fact, is difference, be it a difference in altitude, a difference in vegetation, a difference in population structure, difference in surface, or whatever. Differences are the things that get onto a map.

But what is a difference? A difference is a very peculiar and obscure concept. It is certainly not a thing or an event. This piece of paper is different from the wood of this lectern. There are many differences between them—of color, texture, shape, etc. But if we start to ask about the localization of those differences, we get into trouble. Obviously the difference between the paper and the wood is not in the paper; it is obviously not in the wood; it is obviously not in the space between them, and it is obviously not in the time between them. (Difference which occurs across time is what we call "change.")

...

Kant, in the Critique of Judgment—if I understand him correctly—asserts that the most elementary aesthetic act is the selection of a fact. He argues that in a piece of chalk there are an infinite number of potential facts. The Ding an sich [thing as such], the piece of chalk, can never enter into communication or mental process because of this infinitude. The sensory receptors cannot accept it; they filter it out. What they do is to select certain facts out of the piece of chalk, which then become, in modern terminology, information.

I suggest that Kant's statement can be modified to say that there is an infinite number of differences around and within the piece of chalk. There are differences between the chalk and the rest of the universe, between the chalk and the sun or the moon. And within the piece of chalk, there is for every molecule an infinite number of differences between its location and the locations in which it might have been. Of this infinitude, we select a very limited number, which become information. In fact, what we mean by information—the elementary unit of information—is a difference which makes a difference, and it is able to make a difference because the neural pathways along which it travels and is continually transformed are themselves provided with energy. The pathways are ready to be triggered. We may even say that the question is already implicit in them. ...

But there are differences between differences. Every effective difference denotes a demarcation, a line of classification, and all classification is hierarchic. In other words differences are themselves to be differentiated and classified. In this context I will only touch lightly on the matter of classes of difference, because to carry the matter further would land us in problems of Principia Mathematica. ...

Lastly there is that hierarchy of differences which biologists call "levels." I mean such differences as that between a cell and a tissue, between tissue and organ, organ and organism, and organism and society.

These are the hierarchies of units or Gestalten, in which each sub unit is a part of the unit of next larger scope. And, always in biology, this difference or relationship which I call "part of" is such that certain differences in the part have informational effects upon the larger unit, and vice versa"

References:

Gregory Bateson, 1972. Steps to an Ecology of Mind.

http://www.rawpaint.com/library/bateson/formsubstancedifference.html

"universal minima" and meta model

But what is disclosed when comparative ethics and comparative epistemology are set side by side? And when both are combined with economics? And when all is compared with morphogenesis and comparative anatomy?

Such comparison will inevitably drive the investigator back to the elemental details of what is happening. He must make up his mind about the universal minima of the overlapping of all these fields of study. The minima are not parts of any one field; they are not parts even of behavioral science at all. They are parts, if you will, of necessity. Some are what Saint Augustine called Eternal Verities, others are perhaps what Jung called archetypes. These fundamentals, which must underlie all of our thought, are the subject matter of the next section.

Of course, the anthropologist and the epistemologist, the psychologist and the students of history and economics will all have to deal, each in his or her field of concentration, with every one of these Eternal Verities. But the verities are not the subject matter of any special field and are, indeed, commonly concealed and avoided by the concentration of attention upon the problems proper to each specialized field.

I believe that BioUML meta model address this problem and there are something common between "universal minima", "Eternal
Verities" and meta model:

• meta model can be used for description different fields: biology, anatomy, economics and other.
• meta model is not part of any of these fields.

References:

Gregory Bateson, Mary Catherine Bateson, 1987. Angels Fear: Towards an Epistemology of the Sacred.

Two chapters from the book: http://www.oikos.org/angelsfear.htm

Glass Bead Game

Hesse's last novel, 'The Glass Bead Game' (1943), is set in the elite province of Castalia, where scholars devote their lives to the endless ramifications of the Glass Bead Game, a kind of universal matrix of knowledge in which the players make new links between the various scholastic disciplines.

The Glass Bead Game is the artistic, philosophical or cosmological manipulation of the symbolic forms which express these systems of knowledge. These symbolic forms, or what we would call the Glass Beads represent a system of language unknown to all but a few who have searched for or been initiated into this rare and most valuable wisdom. Schwaller de Lubicz called this form of expression "symbolique", or the "Language of the Gods", or the "Language of the Birds". He explains it as a language that uses symbols as letters in an alphabet expressing a unknown language. When one is able to read this language, one can read Egyptian hieroglyphics, Medieval alchemical texts or Gothic cathedrals, and realize that they all say the same thing. He also informs us that there is no way to study "symbolique", but at the same time recommends sacred geometry as the best place to start.

References:

Hermann Hesse, 1943. The Glass Bead Game.

Design patterns

The pattern concept came out of a very wide range of philosophic thinking, going back to Greece. Possibly it starts with the Pythagoreans versus their predecessors, and the argument took the shape of "Do you ask what it's made of—earth, fire, water, etc.?" Or do you ask, "What is its pattern?" Pythagoras stood for inquiry into pattern rather than inquiry into substance.

... to be continued ...