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Some enzymes can be very hard to simulate since the reactions they catalyze involve quantum mechanical effects. Very hard is different from impossible, though, and enzyme/substrate interactions are studied using Density Functional Theory simulations, and
higher fidelity methods. These atomistic-scale methods run on Turing machine-like computers, or maybe someday quantum computers. </div>
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One way in which 3-d biochemical systems have functional differences from computer programs is nuanced context dependence. We write computer programs to be comprehensible to other people and so we focus attention on a small number of variables at a time.
Nature doesn't care about what humans can understand, so this is not a consideration for how biological systems work. </div>
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To me, algorithms that are friendly to human cognition as components of models of biological functional behaviors are just zeroth order hypotheses to test. Understanding that the heart's functional role is to circulate blood is different from understanding
how the electrical signaling of the heart works. </div>
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Marcus</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Friam <friam-bounces@redfish.com> on behalf of Prof David West <profwest@fastmail.fm><br>
<b>Sent:</b> Thursday, October 20, 2022 2:27 PM<br>
<b>To:</b> friam@redfish.com <friam@redfish.com><br>
<b>Subject:</b> [FRIAM] naive question</font>
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<div style="font-family:Arial">Marcus and glen (and others on occasion) have posted frequently on the "algorithmic "equivalent" of [some feature] of consciousness, human emotion, etc.<br>
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<div style="font-family:Arial">I am always confronted with the question of of "how equivalent?" I am almost certain that they are not saying anything close to absolute equivalence - i.e., that the brain/mind is executing the same algorithm albeit in, perhaps,
a different programming language. But, are their assertions meant to be "analogous to," "a metaphor for," or some other semi/pseudo equivalence? <br>
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<div style="font-family:Arial">Perhaps all that is being said is we have two black boxes into which we put the same inputs and arrive at the same outputs. Voila! We expose the contents of one black box, an algorithm executing on silicon. From that we conclude
it does not matter what is happening inside the other black box—whatever it is, our, now, white box is an 'equivalent'.<br>
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<div style="font-family:Arial">Put another way: If I have two objects, A and B, each with an (ir)regular edge. in this case the irregular edge of A is an inverse match to that of B—when put together there are no gaps between the two edges. They "fit."<br>
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<div style="font-family:Arial">Assume that A and B have some means to detect if they "fit" together. I can think of algorithms that could determine fit, a simplistic iteration across all points to see if there was a gap between it and its neighbor, to some
kind of collision detection.<br>
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<div style="font-family:Arial">Is it the case that whatever means used by A and B to detect fit, it is
<u><b><i>merely</i></b></u> the equivalent of such an algorithm?<br>
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<div style="font-family:Arial">The roots of this question go back to my first two published papers, in
<u>AI Magazine</u> (then the 'journal of record' for AI research); one critical of the computational metaphor, the second a set of alternative metaphors of mind. An excerpt relevant to the above example of fit.<br>
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<div style="font-family:Arial"><i>Tactilizing Processor<br>
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<div style="font-family:Arial"><i>Conrad draws his inspiration from the ability of an enzyme to combine with a substrate on the basis of the physical congruency of their respective shapes (topography). This is a generalized version of the lock-and-key
mechanism as the hormone-receptor matching discussed by Bergland. When the topographic shape of an enzyme (hormone) matches that of a substrate (receptor), a simple recognize- by-touch mechanism (like two pieces of a puzzle fitting
together) allows a simple decision, binary state change, or process to take place, hence the label “tactilizing processor.”</i><br>
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<div style="font-family:Arial">Hormones and enzymes, probably/possibly, lack the ability to compute (execute algorithms), so, at most, the black box equivalence might be used here.<br>
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<div style="font-family:Arial">[BTW, tactilizing processors were built, but were extremely slow (speed of chemical reactions) but had some advantages derived from parallelism. Similar 'shape matching' computation was explored in DNA computing as well.]<br>
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<div style="font-family:Arial">My interest in the issue is the (naive) question about how our understanding of mind/consciousness is fatally impeded by putting all our research eggs into the simplistic 'algorithm box'?<br>
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<div style="font-family:Arial">It seems to me that we have the CS/AI/ML equivalent of the quantum physics world where everyone is told to "shut up and compute" instead of actually trying to understand the domain and the theory.<br>
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<div style="font-family:Arial">davew<br>
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