Thursday, November 03, 2005

Comments on Saul Griffith's Growing Machines

The following are some notes on Saul Griffith's MIT thesis: Growing Machines

“An analogous construction is developed in three dimensions. It is similarly shown that right angled tetrahedrons, when folded from an edge-connected string, can generate any three dimensional structure where the primitive pixel (or voxel) is a rhombic hexahedron. This construction suggests a concept of 3D completeness.”

He needs to explain this further with a diagram or draw it out a bit more.
I was also a little puzzled by the definition of self assembly by Whitesides on page 8: “the autonomous organization into patterns or structures without human intervention.” This is followed by his corollary definition:

"Self-assembly reflects information coded (as shape, surface properties, charge, polarizability, magnetic dipole, mass, etc.) in individual components; these characteristics determine the interactions among them. The design of components that organize themselves into desired patterns and functions is the key to applications of self-assembly."

The design of components that organize themselves into desired patterns is human intervention, so I am not quite sure Whitesides’ first definition makes logical sense in the context of the second definition. I know what the definition is trying to describe it but would seem that the moment an observer intervenes in the process by even observing the patterns of shape, surface properties, charge, polarizability, magnetic dipole, mass, etc., and calculating probabilities based on probable interactions, you no longer have something that is truly autonomous, or stochastic but more guided. Indeed, you say as much elsewhere after discussing the categories of self assembly:

By the end of this work I shall demonstrate that a fifth category is useful, that of logic-regulated self assembly – self assembling systems where the assembly proceeds according to logic embedded in the sub-components.

My point, is that all self assembly would seem to proceed according to some “logic embedded in the components,” even if extremely tenuous, as in your example of the random aggregation of cheerios in a bowl of milk.

This leads me to something much more interesting to me personally, which is to some extent not directly related to the thesis but more on the far fringes of metaphysical speculation. These are simply some things that that your work sparked in me while reading the text. Please do not take them as critical commentary on your experiments (I am not qualified for that) or as a direct criticism. (I will admit, however, to propagating an undercurrent of disbelief in the stochastic process.)

Everyone is familiar with the notion of reverse engineering but if you apply this concept to matter and life, something rather startling emerges. I am not saying it is true, only that it is both startling and interesting. The ancient philosophers were, in my estimation, attempting with very few tools, to reverse engineer creation with their hylomorphic philosophies of matter and form—they were hacking God! What is a Platonic form or Aristotelian essence but by analogy, a non-local logic buried in subcomponents? Aristotle, for example, defines a soul as: “the first act of a body having life potential” meaning that once matter reaches a certain critical mass, it has life potential and a self-assembling inner activity (presumably non-local) starts to organize the matter hierarchically. I hear Arnold Schwarzenegger’s dead-pan tones regarding the self awareness of the defense computer system in the Terminator movies. “At 11:05 PM on….it became conscious… it realized we were trying to destroy it and so it launched the missiles.” I often wonder if we were able to create sufficiently complex molecular computing systems that some ancient principal of non-local self organization might be able to actualize by utilizing those complex components to its own end and the machine would in fact become conscious or manifest some entity’s consciousness. One has visions of demons materializing in machines, conscious and physically present at last, or even the dead spontaneously resurrecting under circumstances that would undeniably piss them off. The future may hold some rather terrifying things in this regard for humanity. I have probably read too much science fiction to be realistic here, but as a sketch, I find it all intriguing.

The ancients didn’t have our detailed knowledge of the quantum continuum but they at least had the big picture with their notion of the atomos. They of course didn’t realize that there were much smaller particles than their hypothesis predicted but they had the notion that there had to be a pattern, which ruled or might govern the aggregations of all those tiny particles, so that one can say from the Unmoved Mover on down, the Greeks were fascinated with the notion of reverse engineering matter, conceptually, from the atomos all the way back to the source. Analogously speaking, if I look at the images on a television screen, I know that they are composed of thousands of pixels but I do not seek to understand the composition in terms of random aggregation, or self assembly, I look to the intent of the producer for the design of the patterns that appear before me. I also know that the reason and source of the images is not to be found in the television set but rather in the broadcast source. This is why I find the Aristotelian notions of material, efficient, formal and final causality so very interesting—they get at the production of patterns as both designed and purposeful, and broadcast. The efficient cause of a self-assembling unit may be air blowing across a table or the movement of particles in a liquid medium but the formal cause is the individual who recognizes and organizes the a-priori properties of surfaces and puts self-assembling units into a specific medium in the first place. Needless to say, the four causes is a primitive way of looking at causality but it is useful in categorizing distinctions in regards to the organizational capabilities of matter. Clearly, the self organizational capabilities of matter are far more complex than the ancients imagined, nonetheless for the purposes of reverse engineering matter (at least to the philosopher) they would seem to be invaluable.

I find it extremely interesting and also very exciting to think that in attempting to create self-replicating structures, scientists such as yourself, will ultimately have to create something that will move from surface molecular coding to a process that at a higher level may look very much like a form or essence using media that we can only begin to imagine. We have, of course, an analogy to the process with computing. Hardware is guided by software and absolutely none of it is stochastic. What sort of software/guideware would work at the molecular level in order to direct nano structures non-stochastically into various patterns of self replication? What molecular language or trans-molecular language would one use? How would one code molecular surfaces to operate like the locking patterns of RNA or DNA? Are there even higher non-local structures that could be manipulated? Super string theory comes to mind, which even Wheeler described as being so far advanced that it should not, in all probability, have been discovered in this century at all.

It would seem to me that there is a level of complexity to most quantum processes that occurs in more than four dimensions. Just as the dimension of height tends to clarify the meaning of length and width, other dimensions such as time give us the room to manipulate or understand better, the lower dimensions. Is it possible that the Aristotelian notion of form is simply an ancient pointer to a five or six dimensional construct of non-local energy? We only discovered cellular structure within the past three hundred years, galactic structure and subatomic structure in the past 100 years. Are there higher, non-local dimensional constructs that guide the interactions of quantum processes waiting to be discovered by those who can use the cues of the ancient philosophers? If there are, one can only imagine that they will be used in the manufacture of things that we can barely conceive of today.

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