The topological dynamics of plant physiology

We have mentioned Goethe's method in the context of the history of phenomenology as well as its connection to the modern topological and geometric theory of differential equations and dynamical systems. Anyone who has studied biology, or plant biology in particular, learnt about the systems of nutrition and transport in vascular plants, the two main types of vascular tissues being xylem and phloem. The first system is easy to understand enough (and its analogy with animal systems obvious) and not incompatible with a general Goethean conception of a plant with its vertically rising gradient. But phloem is a different matter.  Topologically phloem tubes - transporting sugars and amino acids synthesized in the leaves - are spread across the entire plant in a structure analogous to animal circulatory systems - a perplexing situation which begs for deep topological and dynamical questions and explanations. For if we consider the the system of phloem tubes to be topologically equivalent to a closed ball $B^3$, then the circulation of nutrients will define a vector field on $B^3$ which is tangent to its boundary $\partial B^3 = S^2$.  So there must be sources and sinks. We can ask: where are the sources and sinks in the plant? Is there an analogy with animal digestive systems - or even neural pathways? And even more importantly: does this vector field change in time (undergo a continuous bifurcation)? Modern plant biology of course allows us to answer these questions. The point here is the great philosophical and methodological importance of asking precisely these kinds of question and the role of topological-dynamical thinking.

Very short note on formal concepts in science

From whence do we get the impression that some mathematical models are closer to physical and spatio-temporal intuition,  more down to earth and intimately tied to concrete applications, while others hover close to the heights of allegedly less useful  'abstract-nonsense' ? The real numbers and differential equations, these are seen as tied to dynamic-geometric intuition and of vast applicability and interest in engineering and science.  But abstract algebra and category theory appear to have no direct relevance to applicable mathematical models or to their kind of concrete geometric-dynamic intuition. We present here a few short speculations.

Perhaps the abstract models do capture fundamental levels of reality (maybe even more fundamental than the so-called concrete spatio-temporal ones) and what is required is first of all the methodic development of a special kind of intuition or cognition to grasp the planes of reality which they model (maybe something like Goethe's method is called for?). And then further models are required which can effect a mediation or transfer between these two levels, or at least allow a continuity or gradual deformation between concrete spatio-temporal reality and higher levels of reality.

A beautiful illustration of such a meditation and construction is furnished by the double fibration in Penrose's twistor theory which allows a mediation and transfer between physically significant objects on Minkowski space and abstract cohomological objects on the complex algebraic variety $\mathbb{P}^3$.This operation allows solutions to conformally invariant differential equations on spacetime (e.g., Maxwell's equations, Yang-Mills, or linearized gravity) to be identified exactly with Cech or Dolbeault cohomology classes on specific regions of twistor space. This appears to have been Penrose's attempt to give a geometric (topological) interpretation of quantum non-locality. 

Another illustration is the theory of $\mathcal{D}$-modules which presents a mediation between derived categories (and monoidal categories) and concrete models of systems of partial differential equations.

The idea of Kant's schematism of the pure concepts of the understanding can be interpreted as finding the mediation between logic and geometry (including mathematical physics). This is of immense contemporary significance as we find versions of Kantian schematism in topos theory, homotopy type theory and in areas involving monoidal categories in algebra, geometry and physics and in linear logic and computer science. 

There is also apparently a mediation and transition between the theory of bifurcations of smooth vector fields, fundamental  and ubiquitous in concrete applied mathematics,  and monoidal category and operad theory. See also Physics, Topology, Logic and Computation: A Rosetta Stone by John C. Baez and Mike Stay.

An objection can be raised that our concrete allegedly intuitive mathematical models are themselves quite abstract but are only perceived as immediate and intuitive in our present cultural context by a deliberate forgetting of the complexity of their cognitive-historical past and genesis. For instance real numbers are constructed from the rationals by quite abstract, cardinality increasing, procedures involving equivalence classes and identification. And the same goes for the concepts of continuity, differentiability and so forth. Surely the ancient Greeks had other forms of intuitive perception and concreteness in their geometry, physics and engineering. We answer this objection by our arguments that the fundamental dynamic and geometric-topological intuitions of modern science were in fact identical to those of ancient Greece. It is the modern foundations in terms of Dedekind cuts and $\epsilon$s and $\delta$s that can be critiqued from a philosophical and logical point of view and alternative foundations (locales, realizability topoi, synthetic differential geometry, homotopy type theory) can be defended which are also more aligned to the theory of space and change found for instance in Aristotle's Physics.

Meditation, phenomenology and obfuscation

There is an important missing link in the history of philosophy which has significant consequences for the history of phenomenology. This is the work of the young Rudolf Steiner. It is not fair to judge this work by his later abhorrent and manifestly false views as an occultist and cult leader any more than it would be fair to judge Heidegger's Sein und Zeit by his later similar political and cultural-anthropological views. The most important work of the young Steiner (who attended lectures by Brentano) is a work which usually goes under the title of Philosophy of Freedom (1894) but was published and revised numerous times under different titles.  Along with this work there is also much value in Steiner's earlier work on Goethe's scientific method and worldview. 

There can be no doubt that The Philosophy of Freedom, like Sein und Zeit, is a very important work and one of the masterpieces of phenomenological philosophy. In this work (and in portions of his later books such as the one on "Initiation") we find something similar to an exposition of the approach and methodology involving the transcendent self-transparency and self-illumination of thought and consciousness which we have repeatedly attempted to expound, the correct combination of "epokhê" and "satipatthâna".  

Equally important is Steiner's Goethean method of variation and "imagination". This seems to us to be the original and correct form of what later was called the method of "eidetic variation" (and the affinity for Ruskin's approach in Modern Painters seems to have gone unnoticed).  But the consequences are enormous. The combination between the philosophical-spiritual insight offered by Steiner's exposition of the Goethean method on one hand and on the other the development of modern geometric and topological theory of differential equations and dynamical systems would have been a "marriage made in heaven", two complementary aspects of the same essence,  whose union would have furnished the key to a powerful new science.

But the harmful influence of 20th-century materialist cults and their pseudoscientific dogmas (Freudian psychoanalysis, evolutionary psychology) hindered the emergence of such a science. This is the tragedy of René Thom whose work flawed by Freudian and materialist-evolutionary dogma did indeed point to such a qualitative topological science with a method based on developing higher dimensional dynamic and geometric intuition. The fact that Thom never mentioned Theodor Schwenk's Sensitive Chaos: The creation of flowing forms in water and air (preface by Jacques Cousteau) which predates Structural Stability and Morphogenesis can only be seen as an example of intellectual dishonesty. As far as I know, Thom never referred to the wonderful book by A.T. Winfree, The Geometry of Biological Time (1980) which shows how advanced topological concepts in applied science can be presented in an accessible, rigorous and clear way (cf. the explanation of phase singularities on p.26).

A major fault of René Thom was also ironically to be found on the mathematical plane. Thom, like V.I. Arnold, engaged in obfuscation and sloppy presentation of mathematical ideas.

An expert in a field has all the right to develop a conceptual shorthand for their own use or that of fellow experts. In particular, a shorthand for writing down ideas to be developed and unfolded in lectures. Such texts can also employ beautiful drawings and diagrams which may impress even the non-expert. However all this has nothing to do with writing a book whose aims is to open the gates of a knowledge to those who, while not having such a knowledge, seek earnestly for it. A book that is a genuine introduction (i.e. initiation) in the full sense of the word, and which does not only "bring in" the neophyte but presents the beauty, clarity and order of the temple in all its details and adornments.  This is the kind of book, the kind of spirit, style and approach, which every student deserves, and certainly the kind of spirit. style and approach which should be employed when presenting important philosophical, scientific and mathematical ideas to the world. To present the young student with any other kind of book can only be considered a pernicious and immoral act of deliberate obfuscation and perversion. On another occasion we hope to develop the topic of cryptography, deliberate obfuscation and "secrets of the trade". Let it just be said that this has traditionally been a not infrequent vice of academia, the deliberately ponderous, opaque, pedantic jargon which not only hinders understanding of comparatively simple concepts and arguments but also masks the author's debt (or even plagiarism) to their contemporaries or predecessors. The aim is also to appear outwardly as outstandingly intelligent, original and sophisticated and to close the doors of science to anyone outside a select few.

Besides in phenomenological philosophy and Goethean science, a tragedy occurred regarding "meditation".  There is no such thing as "meditation" in the popular sense, there is no secret powerful technique of self-help where one sits down, closes their eyes, breathes in and out, focuses their mind or attempts to detach themselves from troubling thoughts, and thus finds a cure for mental anguish or a way to gain paranormal faculties or blissful states. This goes in particular for everything connected to the term "mindfulness".  And there is evidently no easy quick philosophical-phenomenological method for the self-observation and self-transparency of consciousness.

This is not what "bhavana" or "katharsis" as in neoplatonism and the ancient mysteries was about. Rather bhavana can be likened to the building of a beautiful high-towered palace or temple, including the preparation and purification of all the materials needed as well as the ground and foundations. The "mindfulness" at work here cannot be separated from action. The popular concept of "meditation" actually only corresponds to the final royal stage in which one enters the newly built palace and climbs up many flights of stairs to survey the beauty of all the sparkling rooms and luminous windows until reaching the most wonderful of all views at the top. Before that it is the long toil and active work of the artisan and soldier - which can be be interwoven with periods of peaceful surveillance and contemplation of yet unfinished work. We do not meditate as some kind of easy, all-sufficient, way to overcome our desires, rather we first diligently and actively uproot desire-images-complexes in order to attain the peace and illumination of "meditation".  Using a software engineering metaphor, we must start with cultivation at the abstract object-oriented level before proceeding to reverse engineering at the assembly level. Thus taught both the Pali suttas and Plotinus.