The struggle over consciousness

One of the major themes of Western philosophy since Plato is the elevation and near-deification of consciousness. Conscious thought and reflection have been prized above all else. Suspicion has been directed towards everything that is dark, murky, instinctive, unclear, unreasonable. Spirit has been emphasised above body. Christianity and its penal mechanisms was in no small part the engine used for this process for many centuries.

But what can consciousness really do? Every sequence of words I produce, every line of code I write, every sketch I draw or tune I play on the piano is for the most part not a product of conscious reflection. (Some earlier, unfinished thoughts on the limitations of reason here.) These productions are given to me, just as associations, feelings or moods are given to me – by the Other in me, the unconscious, the body. Through reflection I can remix and arrange these parts, critique them, say yes and no, but I cannot generate these things through purely conscious thought and logic. So what, in fact, was Western society really doing for 2000 years?

Nietzsche heralded the beginning of a reversal of this trend. In him, consciousness turns around, questions itself and finds that in the end, it isn’t all that powerful. A new philosophical school begins: a counter-movement that aimed, and aims to, reaffirm what is unthought, unseen, unreasonable. After him, thinkers like Freud, Jung (with his elaboration of the unconscious and his idea of “individuation”, psychological development understood as a harmonious union with the unconscious), Foucault (whose “History of madness”, if not almost his entire oeuvre, is almost entirely about this theme and the technicalities of how the unreasonable was suppressed) and Heidegger (in part) progressed on this path. But this reversal has only just begun. What are, in the grand scheme of things, the 130 years since Nietzsche’s productive years in the 1880s? The battle over the value of consciousness is in full swing and might be for centuries or millennia yet. And so we find ourselves, for now, living in a schizophrenic society, perhaps on the threshold of crossing over from a value system that praises consciousness to one that gives it a much more modest role.

 

The bounded infinity of language

Works of art, including film, painting, sculpture, literature and poetry, have a seemingly inexhaustible quality. As we keep confronting them, renewing our relationship with them over time, we continually extract more meaning from them. Some works truly appear to be bottomless. Reaching the bottom easily is, of course, a sure sign that a work will not have much lasting value.

Out of the forms listed above, (written) poetry and literature have the particular property that they are crafted out of a demonstrably finite medium: text. A finite alphabet, finite vocabulary, and a finite number of pages. As long as one disregards the effect of details such as paper quality, typography and binding, perfect copies can be made; the text can indeed be transcribed in its entirety without information loss. Somehow, reading Goethe on a Kindle is an experience that still holds power, although he presumably never intended his books to be read on Kindles (and some might argue that reading him in this way is ignoble).

How is it then that the evocative power of something finite can seem to be boundless? This curious property is something we might call the poetic or metaphorical qualities of a text. (Works of film, painting, sculpture and so on most likely also have this power, but it is trickier to demonstrate that they are grounded in a finite medium.) Through this mysterious evocative power, the elements that make up a work of art allow us to enter into an infinity that has been enclosed in a finite space. It will be argued that what is evoked comes as much from the reader as from the text, but this duality applies to all sensation.

With this in mind we turn, once again, to programming and formal “languages”. Terms in programming languages receive their meaning through a formal semantics that describes, mathematically, how the language is to be translated into an underlying, simpler language. This process takes place on a number of levels, and eventually the lowest underlying language is machinery. This grounds the power of a program to command electrons. But this is something different from the meaning of words in a natural language. The evocative power described above is clearly absent, and computer programs today do not transcend their essential finitude. With brute force, we could train ourselves to read source code metaphorically or poetically, but in most languages I know, this would result in strained, awkward and limited metaphors. (Perhaps mostly because programming languages to a large extent reference a world different from the human world.)

Consider how this inability to transcend finitude impacts our ability to model a domain in a given programming language. With an already formal domain, such as finance or classical mechanics, it is simple since what needs to happen is a mere translation. On the other hand, other domains, such as biology, resist formalisation  – and perhaps this is one of their essential properties. Here we would like to draw on the evocative, poetic, and metaphorical capacities of natural language – for the sake of program comprehension and perhaps also to support effective user interfaces – while also writing practical programs. But we have yet to invent a formal language that is both practical and evocative to the point that works of art could be created in it.

an ancient pond / a frog jumps in / the splash of water

(Bashou, 1686)

Science and non-repeatable events

Scientific method is fundamentally concerned with repeatable events. The phenomena that science captures most easily may be described using the following formula: once conditions A have been established, if B is done, then C happens. 

This kind of science is a science of reactions, of the reactive. But what about a science of the active? Is such a science possible?

To phrase what I have in mind in a different way, suppose that there are events in our universe that are not reproducible or repeatable. They would not be the consequence of some stimulus or trigger. But neither would they be the act of some imaginary god. They might simply be part of the same underlying, mysterious generator that is responsible for what we call scientific laws (patterns of reproducibility). (So far we have inferred some of the properties of this generator, but we are very far from apprehending it or understanding its totality and boundaries. Intellectual humility is crucial.) Would science be able to record and theorise about such events? Certainly not. Modern scientific method is firmly aimed at eliminating irreproducible results.

To put it in still another way, we are able to verify determinism in those cases where it holds up, but we are always unable to verify the absence of cases (in the past or in the future) where the deterministic rules break down.

This is a quandary, since it does seem that the world contains phenomena that are difficult to reproduce. The belief that the world can ultimately be reduced to a set of deterministic rules is not at all uncontroversial (and perhaps many physicists have given it up already). Particularly in biology, we constantly struggle to understand phenomena in terms of such rules. However, we can perhaps see biology residing at the boundary between the reactive/deterministic and the active/irreproducible. Gradual determinism? –

Innocent knowing

Megurogawa

Knowledge can be associated with weight, heaviness, obligation, cynicism. Depending on one’s attitude, it can be seen as opposed to more “innocent” qualities such as beauty and play in many cases.

The more we know of our own history, and the more honestly we face it, the more gloomy we might become about the prospects for our future. This is true for individuals and for societies. Truly facing up to our past mistakes might erase all of our faith in a positive future. Thus a negative, passive kind of nihilism is born. On the basis of this, Nietzsche discusses, in “on the use and abuse of history for life”, and in other places, how ignorance actually preserves life and health in many cases. Truth can be a poison. The courage to leap ahead in defiance of the past, trying anew, which is essential for life, can be associated with stupidity as well as with heroism.

The connection between knowledge and guilt/heaviness goes even further back: in the bible, the fall of man in the garden of Eden is associated with the acquisition of knowledge and the shedding of ignorance.

Against this gloomy view Nietzsche later begins to formulate the ideal of “the gay science”, joyful knowing or “wild wisdom”. In Zarathustra he writes:

Three transformations of the spirit I name for you: how the spirit becomes a camel, and the camel a lion, and the lion at last a child.

The meaning of these transformations is mysterious and subject to much interpretation. But it is usually understood that becoming a “camel” involves taking on a heavy load – the burden of knowledge, the burden of history and wisdom. The lion involves attaining the power to create new values. Finally, the child is a regained innocence.

Innocence with knowledge, play with science, beauty with honesty. Is this not one of the most difficult and profound, and also most worthy, formulas to strive for?

 

Small Tools for Bioinformatics

Pjotr Prins has published a Small Tools Manifesto for Bioinformatics, which is well worth a read for anyone who develops bioinformatics software.

In essence it’s about increased adoption of the Unix design philosophy. I fully support the manifesto, which in many ways is reminiscent of the ideas that me and Gabriel Keeble-Gagnere presented in our Friedrich paper at PRIB2012. The idea of designing software as small parts that can be recombined freely, instead of as a huge black box with a glossy surface, is an extremely powerful one, particularly in the research space.

Conceptual meandering