Knowledge Generator

It is what it is
“The individuals credited with the introduction of philosophical thought into human civilizations were men who speculated on what constitutes the objects of human experience in so far as those objects have or involve an existence or being independent of what [any given agent, be it gods or human beings] may think, feel or do. The philosophers, in other words, are those individuals who are credited with introducing into human thought the idea of reality, or something which ‘is what it is’ on its own grounds, regardless of what further relations it may have ‘to us’ or how it may appear in experience.” – John Deely (2001)

It is perhaps more the norm than the exception for university life-science majors to be instructed, at the outset of their studies, that “science only studies observable phenomena. It functions in the realm of matter and energy [and therefore] it is a serious mistake to think that the methods of science can be applied in areas of investigation involving other aspects of human experience, e.g., matters of the mind”. However, “most neuroscientists and philosophers now take for granted that all biological phenomena, including consciousness, are properties of matter . . . and some philosophers and many neuroscientists believe that consciousness is an illusion”. And so a rather fascinating question arises: How did modern science – the communal knowledge-generating system par excellence – arrive at this sterile impasse – one where the investigation of individual knowledge-generating systems (minds) as knowledge-generating systems per se has come to be seen, at best, as a vexingly paradoxical riddle and, at worst, as falling entirely outside the scope of legitimate scientific inquiry?(1a)

A little more concisely: minds are unscientific.
A search using terms describing study of science such as “scienceology” returned only “scientology” entries. Apparently there is no meta-science, or science of science.(note i)

Biological prerequisite for knowledge
“Knowledge-generation requires opportunities for systemic self-correction, recursive iteration, and continual adaptive growth” – Donald Favareau (2010)

Systemic self-correction is exemplified by the proofreading capability of ribosomes, the action of immune systems, the healing of wounds, the regulation of emotions…

Recursive iteration is exemplified by the copying of physical genetic materials (DNA or RNA), its transcription to physical messengers (mRNA), childbirth, trial-and-error…

Continual adaptive growth(note ii) is exemplified by the evolution of species, a tree growing through a fence, the subtle changes in the morphology of quorum sensing signaling molecules that allow for the exclusion of cheaters in a bacterial colony…

These three concepts seem fairly straightforward, and clearly describe aspects of living systems. Indeed one may fairly argue that they are necessary for the continuation of any living system, and so are more than concepts(note iii), they must exist in the reality external to minds.

Knowledge-generation is a rather more mysterious concept, a compound of generation (similar to iteration) and knowledge. The meaning of the latter is not at all clear, and invokes feelings of awareness, consciousness, certainty, and experience – all of which are subjective states of minds. Is knowledge necessary for the continuation of a living system, such as an ant nest? Is knowledge necessary for the continuation of a formal system of logic, such as a computer program? In both cases I would argue that it is, and that examples might be made of the various epigenetic phenomena in living systems, and the symbolic representation of data stored in the working memories of formal systems.

Prior to the Hellenistic period, the word σημεῖον (Latin: semeion) was understood by the Greeks almost exclusively as a medical term, roughly akin to the modern concept of symptom, referring to the outward manifestation of an internal state. A sign – something that suggests the presence or existence of some other fact, quality or quantity.
Donald Favareau
Donald Favareau – circa 2010

Biosemiotics is defined as “the study of the myriad forms of communication and signification observable both within and between living systems. It is thus the study of representation, meaning, sense, and the biological significance of sign processes from intercellular signaling processes to animal display behavior to human semtotic artifacts such as language and abstract symbolic thought. Such sign processes appear ubiquitously in the literature on biological systems. Up until very recently, however, it had been implicitly assumed that the use of terms such as message, signal, code, and sign with respect to non-linguistic biological processes was ultimately metaphoric, and that such terms could someday effectively be reduced to the mere chemical and physical interactions underlying such processes. As the prospects for such a reduction become increasingly untenable, even in theory, the interdisciplinary research project of biosemiotics is attempting to re-open the dialogue across the life sciences – as well as between the life sciences and the humanities – regarding what, precisely, such in eliminable terms as representation, sign of, and meaning might refer to in the context of living, interactive, complex adaptive systems”(1b)

Assuming that human minds did not arise ex nihilo (from nothing), some far more fundamental form of mind (subjective experience) must be occurring within and between living systems. A handful of relatively new fields of study, including: neurophilosophy, evolutionary psychology, dynamic systems theory, cognitive neuroscience, and artificial intelligence/artificial life, are attempting to reframe two age-old questions:
“What is the relation between mental experience, biological organization, and the law-like processes of inanimate matter?” and “How does the human brain produce the mind?”

In accordance with modern scientific understanding, the phenotype(note iv) of a living system is the product of its evolutionary and ontogenetic embedding in the environment, and it consists of precisely those sets of systemic relations that serve to organize material substrates into that particular living system. I am speaking of living systems rather than organisms because life rarely, if ever, comprises a single organism. Much more common, if not ubiquitous, are the various forms of symbiosis:

Commensalism – a relationship where one species obtains nourishment and/or shelter from another species, and does not harm or help the other species.
Mutualism – a relationship where both species benefit from the relationship.
Parasitism – a relationship between two species in which one species (the parasite) obtains nourishment and/or shelter to the disadvantage of the other species (the host).(2)

“Biological organization and agency of every kind, is precisely the naturalistic establishment of sign relations that ‘bridge’ subject-dependent experience (such as we find both in animal sensations as well as in human ‘mindedness’) with the inescapable subject-independent reality of alterity – an alterity that all organisms have to find some way to successfully perceive and act upon in order to maintain themselves in existence.”
– Favareau

The narrow path of logic – a short history
Aristotle’s vision of biology (represented as a group of texts titled De Anima) included an interdependent recursivity:
a) A phenotype is the product of a living system’s interaction with the world, and vice-versa.
b) The actions of a living system upon the world (which subsequently change that world) are both enabled by and constrained by the systemic biological constitution of the living system, including its perceptual capacities.
c) As the result of (a) and (b) there is both a “realism” to sign relations and a deep necessity for the joining together of the extra-biological relations of external reality to the embedded biological relations within living systems such that what occurs in the case of the perceiving [system] is conceivably analogous to what holds true in […] the things themselves”.

Anicius Manlius Severinus Boethius was born into the Roman aristocracy, circa 480 AD. BoethiusHis social position ensured that he acquired a thorough grasp of the Greek language and scholastic tradition. It is uncertain whether he traveled to Athens or Alexandria, the sites of the two remaining (Platonic) philosophical schools, but certainly he was acquainted with their works. His life combined stately privileges and duties, and a learned leisure in which he pursued a vast project of translating and commenting on philosophical texts. This undertaking was cut short by his execution, circa 525 AD. It is important to realize that the Aristotelian works which were available to European scholars in the early Middle Ages, included only the six books on logic that had been translated by Boethius. These became the standard text of non-Biblical learning in the thousand years between the fall of Rome and the beginnings of the modern era, and were known collectively as Organon (the “instrument” of knowledge and well-ordered thought). Organon comprises treatises on the internal logic of language and linguistically formed propositions. Aristotle’s more general treatises on biological form, function and development (De Anima), were lost to the West for the first 800 years AD.

Aurelius Augustinus Hipponensis (St. Augustine), circa 400 AD, is presented as the first Western thinker to have discussed the similarities and differences between “natural signs” (signa naturalia) and “given signs” (signa data). The former lead to the knowledge of something other than themselves – one might think of the relations of physical contiguity, such as the relation of smoke to fire, or the relation of a fossil to the phenotype that left it. The latter (signa data) are mutually exchanged by living systems, in order to show, as well as they can, the feelings of their minds, of their thoughts, or more simply of their perceptions.

This Middle Age misinterpretation of Aristotle, by accidental exclusion of De Anima, has resulted in ordo orandi (“order of speaking” – hierarchy of knowledge), through which things of “the external world (res) are signified by mental concepts (intellectus), which are then signified by spoken words (voce) and these, in turn, are signified by written characters (scripta). Supporting this system is the principle that: at the [root] of written and spoken discourse there is a mental speech (oratio mentis) in which thinking is performed”.
hierarchy of knowledge
The hierarchy of knowledge (ordo orandi)

“Spoken words are the symbols of mental experience and written words are the symbols of spoken words. Just as all men have not the same writing, so all men have not the same speech sounds, but the mental experiences, which these directly symbolize, are the same for all, as also are those things of which our experiences are the images…”
De Interpretatione is a part of the Aristotelian Organon, it deals specifically with semantics, hermeneutics and propositional logic; it focuses on signa data via the relations of words and sentences.

Unsurprisingly, ordo orandi has resulted in a top-down hierarchy of knowledge, in which sign relations follow linguistic relations. Of course we now know this to be an evolutionarily impossibility, as language (even oratio mentis) could not have preceded simpler forms of symbolic exchange and interpretation (sign relations). Even so, the habit of attempting to logically derive deep knowledge persists to this day. Herein, I believe, may be embedded the two central problems of modernity:
1) Homo sapiens assume ourselves to be smarter and more important than we are.
– God made the Earth, the plants, and the animals for us, and we are to keep and rule over them.
2) Top-down logic is one-sided and short-sighted.
– nature in composed of bottom-up, top-down, (multi-)lateral, and interconnected (complex) logical structures.
Molecular interaction map of the toll-like receptor (TLR) signaling network(3)
– in reality this set of molecular interactions has no “top”.

One can not help but wonder what the world would be like if medieval (European) scholars, such as Augustine of Hippo, had understood the whole of Aristotle, including that “sign relations are a subset of genuinely causal existential phenomena of relational organization”. Chances are that the modern sciences of physics, chemistry, and biology would not have called solely upon the top-down ordo orandi to explain how a biochemical set of relations (i.e. living systems) could come to know about – much less think about – the set of physical relations existing independently of, and external to, themselves. Perhaps a more realistic method of knowledge generation, and thus a truer knowledge set, may be derived from bottom-up hierarchies, lateral hierarchies, and interconnected parallel hierarchies, as well as top-down hierarchies? It really is mind-bogglingly difficult to step out of what we know, or better, what we think we know, even if we see clearly, as we now do, that our knowledge leads to breakage and discontinuity.

There is, I believe, an important albeit intuitive observation to be made here. It may not be possible for one to understand, come to terms with, and implement this more natural complex of hierarchies, that understanding may necessarily require more than one – person, ant, bacterium… perhaps even more than one species.

If re-oriented, the discoverable relations between system x and entity, state or event y – as those relations become actualized during the course of the interaction whereby y is acted upon as a sign of z for x – can become the focus of empirical and falsifiable scientific investigation. This may sound unworkably complicated, but it is the kind of “enmattered formulable essence” which Aristotle called for in relation biologically [self-] organized systems.

“A physicist would define an affection of soul differently from a dialectician . . . the former assigns the material conditions, the latter the form or formulable essence . . . Thus, [for the dialectician], the essence of a house is assigned in such a formula as ‘a shelter against destruction by wind, rain, and heat’; while the physicist would describe it as ‘stones, bricks, and timbers.’ But there is a third possible description which would say that it was that form in that material with that purpose or end. Which, then, among these is entitled to be regarded as the genuine physicist? The one who confines himself to the material, or the one who restricts himself to the formulable essence alone? Is it not rather the one who combines both in a single formula?” – Aristotle, De Anima

In discussions about a previous post in this series (Governance), a number of my peers have commented that it seems unfair and/or meaningless to compare hierarchical human cultures with anarchic ant mounds or bacterial colonies, because humans are much more complex, more evolved(note v), and because we are self-aware. Biosemiotics fortifies my argument for meaningful analogies between humans and ants in regard to self-organization and self-regulation (i.e. self-governance). Indeed, it would seem to say that because ants and bacteria are closer to the root of the biological system, they may be truer to (less abstracted from) reality.

i) There are references to “science of science policy (SoSP)”, but this is the realm of business and politics – not science. Neither politics nor business are sciences, and the term “political science” is a misnomer.

ii) The assertion “continual adaptive growth” implies continued growth. I find it difficult to accept the relation of those terms and see continued adaptation as real. Continued growth seems to belong exclusively to the realms of cosmology and economy – neither of which are real, but theoretic.

iii) Conceive – from Latin concipere (“to take”), from con- (“together”) + capio (“to take”).

iv) Technically, in modern biology, phenotype is the composite of an organism’s observable characteristics or traits, such as its morphology, development, biochemical or physiological properties, phenology, behavior, and products of behavior (such as a bird’s nest). Phenotypes result from the expression of an organism’s genes as well as the influence of environmental factors and the interactions between the two. – Wikipedia

v) It is physically impossible for humans to be “more evolved” than ants or bacteria. Quite simply, living systems did not stop evolving with the emergence of Homo sapiens.

1a) D. Favareau, “THE EVOLUTIONARY HISTORY OF BIOSEMIOTICS”, chapter one of “Essential Readings in Biosemiotics”, (2010), p.2, Springer,

1b) D. Favareau, “Essential Readings in Biosemiotics”, (2010), preface (not available without login to publisher), Springer,


3) K.Oda and H.Kitano, “A comprehensive map of the toll-like receptor signaling network”, (2006), Nature,


1 thought on “Knowledge Generator

  1. The study of science is undertaken as “science and technology studies” (STS) typically in the social sciences, the work of Latour and John Law, in the field of actor-network theory (ANT) Interesting it was initially controversial, for the reason that scientist believed their work was outside the pail of meta-inquiry.

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