# Quick and dirty argument for space from chemlambda

One of the least understood ideas of chemlambda is related to this question: which is the space where these artificial molecules live?

There are two different possible applications of chemlambda, each having a different answer for this question. By confusing these two applications we arrive at the confusion about the conception of space in chemlambda.

Application 1 concerns real chemistry and biology. It is this: suppose there exist real chemical molecules which in reaction with real other substances (which play the role of the enzymes for the moves, invisible in chemlambda). Then, from the moment these real molecules and real enzymes are identified, we get *for free* a chemical computer, if we think small. If we think big, then we may hope that the real molecules are ubiquitous in biochemistry and once identified the chemical reactions which represent the chemlambda moves, then we get for free a computational interpretation of big parts of biochemistry. Thinking big, this would mean that we arrive to grasp a fundamental manifestation of computation in biochemistry, which has nothing at all to do with numbers, or bits, or boolean gates, or channels and processes, all this garbage we carry from the experience (very limited historically) we have with computation until now.

In this application 1 space is no mystery, is the well known 3d space, the vessel where real molecules roam. The interest is here not in “what is space”, but “is life in some definite clear way a computational thing?”.

Application 2 resembles more to physics than biochemistry. It aims to answer to the question what is space? Ironically from neuroscience we know that clearly living brains don’t relate with space in any way which involves coordinates and crunching numbers. However, the most fundamental physics never escaped the realm of coordinates and implicit assumptions about backgrounds.

Until now. The idea proposed by application 2 of chemlambda is that space is nothing but a sort of a program.

I try to make this clear by using emergent algebras, and will continue this path, but here is the quick and dirty argument, which appears not to use emergent algebras,  that chemlambda can explain space as a program.

(it does use them but this is a detail, pay attention to the main line.)

OK, so the artificial molecules in chemlambda are graphs. As graphs, they don’t need any space to exist, because everybody knows that a graph can be described in various ways (is a data structure) and only embeddings of a graph in a space need ahem … space.

Just graphs, encoded in .mol files, as used by the chemlambda visualiser I work on these days.

What you see on the screen when you use the visualiser is chemlambda as the main engine and some javascript salt and pepper, in order to impress our visually based monkey brains.

But, you see, chemlambda can do any computation, because it can do combinatory logic. The precise statement is that chemlambda with the reduction strategy which I call *the most stupid” is an universal computer.

That means that for any chain of reductions of a chemlambda molecule, there is another chemlambda molecule whose reductions describe the first mentioned reductions AND the javascript (and whatnot) computation which represent the said first chain of reductions on the screen.

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# Why computing with space?

Where is this fascination about UD from? Think about it a bit from a visual point of view (and mind that I am not writing about the exact, whatever it turns out to be, algorithm, but about principles). The information coming to the brain by the visual path is ridiculously small compared to the complexity of the world. Yes, when we look at something, the world takes care of the intricacies of ray-tracing for us. But what about the visual world reconstructed in our brains? There is no ray-tracing, there are no octrees, nor coordinates. Again, I repeat that despite all the very useful knowledge people have about robotic vision, this knowledge fails spectacularly to explain how we, humans, or simple creatures like flies, see.  This cartezian point of view, based on coordinatizing the exterior world and treating it like a given geographical space, is not, neuroscience tells us, how we manipulate space in the brain. Again , I repeat that algorithms, which are devices invented to solve problems, are not the right mean for trying to understand this problem, despite the amazing ideas that CS might give concerning the understanding of the world as some big system which we act upon and which it acts upon us. That is because our little grey cells (but let us not forget about those of the humble fly) don’t work by proposing themselves to solve problems. This is just another disease inflicted by the cartezian viewpoint. (I hope that at this stage you can still make the difference between mine and the average crackpot’s talking.)

If we look at the other side, the one of neuroscience, what we find? Sloppy data, compared to physics, due to the complexity of the systems studied, lack and even despise of mathematical knowledge, again compared with physics, due to the fact that these new sciences are in their infancy.

But somehow, as it has always been, somewhere there is an armchairian (word invented by Scott Aaronson), an ancient greek philosopher kind, which could get rid of the cartezian disease and see clearly  a system through the huge pile of data. My bet goes to a mathematician, but I may be biased.

# Carl Einstein on Picasso and the visual brain

The article  “Carl Einstein, Daniel-Henry Kahnweiler, Cubism, and the Visual Brain”  by   made me realize that probably the cubism, invented by Picasso and Gris,  was a logical step further along the path towards the investigation of vision, opened by impressionists.

Indeed, far from being a game of abstraction, multiple viewpoints and other rubbish, it appears that cubism, at least in its first stages, represents the effort of understanding the first stages of vision, as happening in the (artist’s) brain. I find this story amazing, showing how far a brilliant mind (the one of Picasso) could go ahead of its time.

Here is a reproduction of the painting “Guitarist”, by Picasso, 1910, taken from the cited article:

It would be interesting to compare the statistics of edges and corners and blobs  (actually blobs are higher level features) in cubist paintings from this age with the statistics of same features in databases of natural images. My bet is that they are very close.

# A discussion about the structure of visual space

In August I discovered the blog The structure of visual space group and I was impressed by the post The Maya theory of (visual) perception.  A discussion with Bill Rosar started in the comments, which I consider interesting enough to rip it from there and put it here.

This discussion may also help to better understand some of the material from my blog. Several  links were added in order to facilitate this. Here is the exchange of comments.

Me: “I just discovered this blog and I look forward to read it in detail.

Re: “What I am calling into question is the ontological status of a physical world existing beyond the senses.”

Also in relation to the mind-body dualism, I think there is a logical contradiction in the “Cartesian Theater” argument by Dennett, due to the fact that the fact that Dennett’s theater is a theater in a box, already designed for a dualist homunculus-stage space perception (in contradistinction with the older, original Greek Theater).”

Bill Rosar: “Thank you for your posting, Marius Buliga, and welcome! It is great to have a mathematician join us, for obvious reasons, especially since you are interested in problems in geometry.

Your idea of the eye as a “theatron” is interesting, though I do not believe that the brain is computing anything, for the simple reason that it is not a computer, and doesn’t behave like one, as some neuroscientists are now publicly saying. It is people who perform computations, not brains.

Raymond Tallis, who posted “The Disappearance of Appearance” here two years ago, went to some pains to articulate the fallacious reasoning behind the computational metaphor of mind and brain in his marvelous little book WHY THE MIND IS NOT A COMPUTER.

It has long been a truism in cognitive psychology that we do not see our retinal images, and the “function” or process of vision is probably very different from the creation of images, because there is no image in the brain, nor anything like one. If anything, the pattern of stimulation on the retinae is “digested” by the visual system, broken down rather like food is into nutrients (as an alternative, think of chemical communication among insects).

To my knowledge, Descartes did not invoke the analogy of a theater for vision (or perception in general), so for Dennett to construe his ideas on such an analogy is dubious at the outset and, in this instance, just seems to make for a straw man. For that matter, Dennett does not seem to understand the reasons for dualism very fully, and as nearly as I can determine, never bothered to acquaint himself with the excellent volume edited by John Smythies and John Beloff, THE CASE FOR DUALISM (1989). His ill-informed refutations just strike me as facile and unconvincing (and his computational theory of mind has been roundly rejected by Ray Tallis as being fallacious).

My own invoking of theater here as an analogy is to reality itself, not just perception, and is therefore quite different from the view Dennett imputes to Cartesian dualism, though. I propose that physics studies the stagecraft of a reality that only (fully) exists when perceived–which is closer to Berkeley than Descartes, and is a view consistent with John Wheeler’s “observer-participant” model of the universe.

Theoretical physicist Saul-Paul Sirag advanced a “many realities” alternative to the Everett-Wheeler “many worlds” hypothesis, arguing that other realities are mathematically possible. That is why I have tendered the provocative notion that the reality we know is a sort of construction, one that is maintained by the physical constants–or so it seems. Sirag argued that it is not the only possible reality for that reason, and that the constants are comparable to the “chains” that hold the cave dwellers captive to the shadow play on the wall.

I propose instead that the senses are part of the reality-making “mechanism,” and that vision has more the character of a resolving mechanism than a picture-making one (not quite like the Bohm-Pribram holographic reality/brain analogy, though). That gets rid of the homunculus problem, because it turns the perception process inside out: The person and homunculus are one and the same, and visual space is just where it appears to be, viz. in front of us, not a picture made by the visual system in the brain. The forerunner of this view was James Culbertson. The flaw is that it requires a rejection or modification of the causal theory of perception, as we have discussed here. But causality is a metaphysical principle, not a physical one, and perhaps in this context at least requires some close scrutiny, just as Culbertson gave it.”

Me: “…”…for Dennett to construe his ideas on such an analogy is dubious at the outset and, in this instance, just seems to make for a straw man.” This is my impression also, but what can we learn from this about vision?

As a mathematician, maybe, I am quite comfortable with vagueness. What I get from the greek theater/theater in a box argument is that the homunculus is as artificial as the scenic space, or the outer, physical space. These two notions come in pairs: either one has both, or none. The positive conclusion of the argument is that we have to go higher: there is a relation, akin to a map-territory relation, which has on one side the homunculus and on the other side the space.

Let me elaborate a bit on the map-territory relation. What is a map of a territory? It is the outcome of a collection of procedures agreed by the cartographer and the map reader. The cartographer wanders through the territory and constructs a map by some procedure, say by measuring angles and distances using some apparatus. The cartographer follows a convention of representation of the results of his experiments on a piece of paper, let us call this convention “euclidean geometry” (but it might be “quantum mechanics” as well, or “relativity theory”…). The map reader knows that such convention exists and moreover, at least concerning basic facts, he knows how to read the map by applying the convention (for example, the reader of the map of a city, say, knows that straight lines are shortest on the maps as well as across the city). We may say that the map-territory relation (correspondence between points from the territory – pixels from the map) IS the collection of agreed procedures of representation of experiments of the cartographer on the map. The relation between the particular map and the particular territory is just an outcome of this map-territory relation.

Looking at this level, instead of speaking about the perception of the exterior by the homunculus, it is maybe more reasonable to speak, like in “The structure of visual spaces” by J.J. Koenderink, A.J. van Doorn, Journal of mathematical imaging and vision, Volume: 31, Issue: 2-3 (2008), pp. 171-187, about the structure of the visual space as being the result of a controlled hallucination, based on prior experiences which led to coherent results.

Bill Rosar: “Thank you, Marius! What can we learn from Dennett’s faulty analysis of vision, you ask? The “moral of the story” IMO is that any model based on computation presupposes that we know how people perform computations–or how the human minds does–which is something we presently unknown, because we don’t really know what the “mind” really is–it’s just a name. All a computer does is automate a procedure we humans perform. To assume that Nature makes computers strikes me as a classic example of anthropormorphism, and Ray Tallis would agree. How then to get beyond that fallacy? Or, in the case of vision, to echo John Wheeler’s style of formulating foundational problems in physics, “How do you get vision without vision?”–that is, how to understand vision without presupposing it? That’s quite a feat!

A few months ago when Bob French and I were last debating some of these points I suggested that we turn to the evolution of the eye and see what that tells us. Conveniently the evolution of the eyes has been one of Richard Dawkins’ favorite examples to refute the idea of “intelligent design”.

In light of all the questions the account Dawkins raises but leaves unanswered, intelligent design seems to make more sense (I offer no opinion on that myself). So it is a question of what the simplist eyes do and how the organisms possessing them use them. There is a nice little video on YouTube that highlights all that Dawkins does not explain in his simplist account of the evolution of the eye.

As for the map-territory analogy you suggest, it is comparable to the idea of “cortical maps” but shares the same conceptual pitfall as that of the perspective projection analogy I gave above, because as I noted, unlike being able to compare the flat perspective projection (map) with the 3-D *visual space* of which it is (supposedly) a projection, we cannot do that with visual space in relation to putative physical space, which lies beyond our senses. It seems to me that we are to some extent each trapped solipsistically within our own perceptual world.

Koenderink’s idea just seems like nonsense to me, because we don’t even really know what hallucinations are any more than how a hallucinatory space is created relative to our “normal” waking visual space (BTW we invited Koenderink to join the blog a few years ago, but he never replied). The *concept* of a hallucination is only useful when one has some non-hallucinatory experience to which to compare it–thus the same problem as the projection analogy above.

Trouble is we seem to be *inside* the system we are trying to understand, and therefore cannot assume an Archimedean point outside it from which to better grasp it (one of the fundamental realizations Einstein had in developing the theory of relativity, i.e., relativity is all *within* the system = universe).

As for visual space being non-Euclidean or not, I called into question many years ago the interpretation of the data upon which all theories of the geometry of visual space are based, because the “alley experiments” never took into account changes of projection on the retinae as a function of eye movement, i.e., the angles of objects projected on the retina are constantly changing as the eyes move. This has never been modeled mathematically, but it should be. Just look at the point where a wall meets the ceiling an run your eyes along its length, back and forth. You will notice that the angle of the line changes as you move your eyes along it.

Yes, the space and homunculus are an inseparable pair IMO–just look at Wheeler’s symbolic representation of the observer-participant universe (the eye looking at the U).”

Bill Rosar: “I should hasten to emend my remarks above by stating that when we speak of “eyes” and “brains” such objects are only known to us by perception. So like any physical object, we cannot presuppose their existence as such separate from our perception of them–except by an act of a kind of faith (belief), much as we believe that the sun will rise every morning. Therefore talking about their “function” etc. is still all resting upon perceptions, without which we would have no knowledge of anything, ergo, something like Aristotle’s dictum “There is nothing in the mind that was not first in the senses.” Are there eyes and brains that exist independently of perceptions of them?”

Me: “Dear Bill, thank you for the interesting comments! I have several of my own (please feel free to edit the post if it is too long, boring or otherwise repellent for the readers of this blog):

1. It looks to me we agree more than my faulty style of exposition shows: one cannot base an explanation of how the space is “re-constructed” in the brain on the structure of the physical space, point. It may be that what we call structure of physical space is formed by features selected as significant by our brain, in the same way as a wind pipe extracts a fundamental note from random noise (thank you Neal Stephenson).

2. We both agree (as well as Koenderink, see his “Brain a geometry engine”) that, as you write, “the senses are part of the reality-making “mechanism,” and that vision has more the character of a resolving mechanism than a picture-making one”.

3. Concerning “computing”, is just a word. In the sense that “computing” is defined as something which could be done by Turing machines, or expressed in lambda calculus, etc, I believe too that the brain is not computing in this sense. With efforts and a lot of dissipation, it seems that the brain is able to compute in this sense, but naturally it does not. (It would be an interesting project to experimentally “measure” this dissipation, starting for example from a paper by Mark Changizi “Harnessing vision for computation”, here is the link to a pdf.

4. But if we enlarge the meaning of the word “computing” then it may as well turn out that the brain does compute. The interesting question for a mathematician is: find a definition of “computation in enlarged sense” which fits with what the brain does in relation to vision. This is a project dear to me, I don’t want to bother you with this (unless you are interested), which might have eventual real world applications. I started it with the paper “Computing with space, a tangle formalism for chora and difference” and I reached the goal of connecting this (as a matter of proof of principle, not because I believe that the brain really computes in the classical sense of the word) with lambda calculus in the paper “Local and global moves on locally planar trivalent graphs, lambda calculus and lambda-Scale“.
(By the way, I cannot solve the problem of where to submit a paper like “Computing with space…”)

5. Concerning “hallucination”, as previously, is just a word. What I think is likely to be true is that, even if the brain does not have direct access to the physical space, it may learn a language of primitives of this space, by some bayesian or other, unknown, procedure, which is akin to say that we may explain why we see (suppose, for the sake of the discussion) an euclidean 3d space not by using as hypothesis the fact that the physical space has this structure, but because our brains learn a family of primitives of such a structure and then lay in front of our eyes a “hallucination” which is constructed by the consistent use of those primitives.”

Bill Rosar: “Thanks for these stimulating thoughts and ideas, Marius. Not to worry about the length of your blog postings. Mine are often (too) long, too. My remarks will be in two parts. This is part I.

When John Smythies and I started this blog (which was really intended to be a “think tank” rather than a blog), we agreed that, following the lead of Einstein, it may be necessary to re-examine fundamental concepts of space and geometry (not to mention time), thus John’s very first posting about Jean Nicod’s work in this regard, and a number of mine which followed.

One of these fundamental concepts that calls for closer scrutiny is space itself, or, to be more precise, the nature of *spatial extension,* both of which are abstractions, especially in mathematics (in this regard see Graham Nerlich’s excellent monograph, “The Shape of Space”).

We need to better understand the basis of those two abstractions–space and extension–IMO if we are to make progress on the nature of visual space, or the other sensory modalities that occupy perceptual space as a whole (auditory, tactile, olfactory, gustatory). Abstractions reflect both what they omit and what they assume, and it is the assumptions that we especially need to examine here. While clearly visual space is extended, what about smell? Are smells extended in space?

What we find is that there is a *hierarchy* in perceptual space, one that in man is dominated by visual sensation–what has been called the “dominant visual matrix” by psychologists studying perception. Even sounds are referred to visual loci (“localized”), and I think that can be said of smells, too. But in of themselves it is not clear that even auditory sensations are extended in the same way that visual sensations are, because it is as if when a sound is gone, that part of the “soundscape” is also gone, but that which remains is visual space. In visual space an object may disappear, but the locus it occupied does not also disappear. For example, though we can point to the *visual* source of a sound we hear, we do not point to a sound–even the phrase sounds strange, and ordinary language reveals much about the nature of the perceptual world–or what the man of the street calls the “physical world.””

Bill Rosar: “Part II.

If that is so, why should we assume that physical space has all the properties of visual space and is perhaps not more like smell? Physics is making one big assumption!

I will always remember what Caltech mathematician Richard M. Wilson told me when I consulted him many years ago on ideas I had about how the geometry of visual space reflects changing perspective projections on the retinas. He said, “Keep it simple!” By that he meant being parsimonious and not jumping into fancy mathematical formulations without necessity. I am suggesting that we need to keep the mathematical apparatus here to a minimum, lest its elegance obscure the deeper truth we are seeking–just as Einstein cautioned.

So when we talk about the brain, I think we need to be mindful of what Ray Tallis says about it in his posting “The Disappearance of Appearance,” and just *how* we know about the brain, because we cannot talk about the extended world of physical space and exclude the brain itself from that as a (presumably) physically extended biophysical object. It is not that there is the physical world and there is the brain apart from it.

This ultimately becomes question-begging, because in talking about the brain, we are presupposing physical space, rather than explaining how we have arrived at the notion of physical space and extension. Certainly physical science would deny that physical space is created by the brain. Yet David Bohm would say that physics is largely based on an optical lens-like conception of the physical world, but that physical reality may be more like a hologram (now once again a popular analogy in cosmology because of Leonard Susskind’s theory).

Of course when Karl Pribram then talks about the brain being a mechanism that resolves the holonomic reality (“implicate order”) into a hologram or holographic image (“explicate order”), he forgets that the brain itself would presumably be part of the same holonomic implicate order, and would therefore be resolving itself. By what special power can it perform that trick?

So the very “picture” we have of the brain itself is no different from any other physical entity, as Ray Tallis has been at pains to show.

For now, I’m going to rest with just these rejoinders, and return to your other points later.”

# Geometry of imaginary spaces, by Koenderink

This post is about the article “Geometry of imaginary spaces“,   Journal of  Physiology – Paris, 2011, in press, by Jan Koenderink.

Let me first quote from the abstract (boldfaced  by me):

“Imaginary space” is a three-dimensional visual awareness that feels different from what you experience when you open your eyes in broad daylight. Imaginary spaces are experienced when you look “into” (as distinct from “at”) a picture for instance.

Empirical research suggests that imaginary spaces have a tight, coherent structure, that is very different from that of three-dimensional Euclidean space.

[he proposes the structure of a bundle $E^{2} \times A^{1} \rightarrow E^{2}$, with basis the euclidean plane, “the visual field” and fiber the 1-dimensional affine line, “the depth domain”,]

I focus on the topic of how, and where, the construction of such geometrical structures, that figure prominently in one’s awareness, is implemented in the brain. My overall conclusion—with notable exceptions—is that present day science has no clue.

What is remarkable in this paper? Many many things, here are just three quotes:

–  (p. 3) “in the mainstream account”, he writes, “… one starts from samples of … the retinal “image”. Then follows a sequence of image operations […] Finally there is a magic step: the set of derived images turns into a “representation of the scene in front of you”. “Magic” because image transformations convert structures into structures. Algorithms cannot convert mere structure into quality and meaning, except by magic. […] Input structure is not intrinsically meaningful, meaning needs to be imposed (magically) by some arbitrary format.”

– (p. 4) “Alternatives to the mainstream account have to […] replace inverse optics with “controlled hallucination” [related to this, see the post “The structure of visual space“]

– (p. 5) “In the mainstream account one often refers to the optical structure as “data”, or “information”. This is thoroughly misleading because to be understood in the Shannon (1948) sense of utterly meaningless information. As the brain structures transform the optical structure into a variety of structured neural activities, mainstream often uses semantic terms to describe them. This confuses facts with evidence. In the case of an “edge detector” (Canny, 1986) the very name suggests that the edge exists before being detected. This is nonsensical, the so-called edge detector is really nothing but a “first order directional derivative operator” (Koenderink and van Doorn, 1992). The latter term is to be preferred because it describes the transformation of structure into structure, whereas the former suggests some spooky operation” [related to this, see the tag archive “Map is the territory“]

Related to my  spaces with dilations, let me finally quote from the “Final remarks”:

The psychogenetic process constrains its articulations through probing the visual front end. This part of the brain is readily available for formal descriptions that are close to the neural hardware. The implementation of the group of isotropic similarities, a geometrical object that can  easily be probed through psychophysical means, remains fully in the dark though.