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McQuinn
The Leonardo
Salt Lake City

Registered: Oct 2004
Posts: 17

biological computation

What about life processes and computation? The transcription of DNA to make proteins seems to me computational, with the “program” encoded in the geometry of chemical structures and their interaction. (Somewhere Wolfram undoubtedly says as much but I haven’t gotten far enough in NKS to cite it.)

For example, an enzyme needn’t consult any external instruction set; its shape and charge distribution constitute both software and hardware. From cell to organism to population, every component simply “knows” what to do. Natural selection over evolutionary time has filtered what works from what does not, serving more as quality assurance than as programmer. This seems to resemble NKS much more than it resembles Von Newman architecture.

While studying bacteriophage as an amateur, I started wondering whether phage and their bacterial hosts could constitute a computer, either engineered or discovered. If we ask the question, can phage and bacteria do computation, then what criteria for computation do we establish in order to design the investigation and evaluate the results? For a computer as we customarily conceive of the concept, we want it to add and subtract, etc. etc. In other words, the evaluation is defined in terms of input-output. At a more fundamental level, we could establish the essential Von Neumann markers for computation and ask, “Do phage demonstrate that they have those capacities?” If they do, then perhaps we could make a simple computer in a Petri dish. But this is trivial, for we would be imposing the performance standard on the system under examination, rather like training a dog to articulate simple one-syllable words.

A much more challenging question is this: how would we recognize computation already conducted by a phage and host population system? By studying NKS I’m hoping to gain some insight into how to ask such a question with more specificity. Bayesian network architecture may be relevant, also. (Not having much of the formal preparation required to readily understand such material, it seems absurd that I’m even interested.)

The quest is really for architectures where the consequences are implicit in the structure, that map well to the biology of phage-host interactions.

If none of this makes sense, my shortcoming. If any of it makes sense, my good luck.

SMcQ

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Old Post 02-07-2005 04:34 AM
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Roger Pingleton
Indiana University
Indianapolis, IN

Registered: Jan 2005
Posts: 2

Computing without a computer

Let me add aditional focus to this discussion.

There has been a lot of great discussion, and a lot of great thoughts to ponder, which I am pondering and will continue to ponder. Thank you to everyone who has posted.

But what I want to get back to is, that if we trace back the creation of everything (and this includes the creation of time itself which is part of the universe), we come to a point where everything is made out of a rule (which is what Wolfram postulates).

How does this work given that the rule has nothing to interact with? It is an idea. It is a design, but a design is just a blue print. It needs a medium to work with.

And what's more, as someone has also pointed out, since time is a feature of the universe, how can the rule follow it's course without time?

This is a very bizzarre area of thought. We start with a rule that interacts without a medium (perhaps with itself) and without time and this "rule" creates a world that then has a medium (the building blocks of the universe - sub atomic particals and the like), and it creates a universe that has time.

Does any of this make sense. I find it incredibly thought provoking and hard to fathom.

Perhaps there is a medium already for this rule to work with. Perhaps there is some bizarre notion of time apart from our own that simply alows a rule like this to work, but then, where did those two things come from? What explains them?

Could the universe be recursive? Could it depend on itself; it's own definitions to create a definition of itself?

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Old Post 02-09-2005 03:43 PM
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McQuinn
The Leonardo
Salt Lake City

Registered: Oct 2004
Posts: 17

Roger,

There are two customary perspectives on your question, each very different in process and in outcome. There is also an ideosyncratic perspective, which I will get to at the end of this essay.

The psychological perspective (philosophical, if you will) is constrained by how the human mind/brain evolved to conceptualize the world so that we could survive within it. This skill set is fixed and hermetic, with learned responses serving as correction factors to keep our intuition from going astray. Within the psychological domain the questions you raise can only be “answered” through storytelling. Tools like NKS will always function in the psychological arena by analogy, allegory, anecdote and association. You can make up anything you like, whether it’s science fiction or religion or a philosophical code of conduct.

The analytical perspective creates a world apart where problems are tractable using mathematics. Analysis results in constructs that are tested for their “validity” in the “real” world by how well they account for data already observed or data yet to be discovered. The most elaborate analytical construct yet devised is probably string theory, though it has not produced any testable predictions. NKS seems a better candidate for the “theory of everything,” though that remains to be seen.

We have this choice between psychological and analytical modes only if we constantly remind ourselves to keep them distinct. You asked, “How do programs run without a computer?” It seems framed as a psychological query, the concepts of program and computer defined by everyday association. An analytical response to your question can only be evaluated analytically. Nevertheless, we are all free to pick up analytical threads and weave them into stories, like spring robins building nests out of found objects.

Invariably, someone calls for the third way: the holistic view. Then they usually proceed to use narrative or analysis to explain what they mean. Wondering if the universe is recursive or self-defining is a holistic musing, the accepted answer depending on what mode of thought you prefer.

Now, if you don’t require explanations, but rather, you are seeking various expressions of perception, that third, holistic view can be found through Art.

SMcQ

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Old Post 02-09-2005 07:36 PM
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Philip Ronald Dutton
independent
Columbia, SC

Registered: Feb 2004
Posts: 172

Not running.

I do not think that a program (or more specifically, an algorithm) ever "runs." It just exists. Pretty simple. Computers do things specifically but they are not really executing programs. Computers utilize their own devices (atoms, electrons, maybe later quarks) to simulate the output of the algorithm for which it was programmed. Philosophically speaking, I really do not think my computer is even doing arithmetic when I run Mathematica (if i could afford it). It just is very good at simulating.

You can not prove to me that any computer executes mathematics. Computers just simulate. Why do I say this? Well, the basic arithmetic axioms (algebra or whatever system you prefer) do not even fully describe every thing... they take on a few assumptions.

The program exists and it already has an outcome no matter what the algorithm is. There exists an outcome or a state (infinite loop,etc.). If someone generates an algorithm with X amount of steps and the algorithm was generated in a random fashion such that no one in the history of the universe has ever "executed" it. Well I am sorry but the algorithm has an "answer" somewhere "out there" (in what I call the instant-answer-ether). As soon as you finish writing the last line of your algorithm on paper, the answer exists. You have to work to find it via simulation (arithmetic, computer program, logic, etc.). You have to work to extract it into our physical domain (brain/memory cells and cpu registers included in that domain).

As far as the algorithm is concerned, it never ever needs anything or anyone to perform it in order for the answer to first come into "being."

I would venture to say that a computer or any other "computation" device is only all about the business of simulation. We can't even express mathematics properly when writing out our lovely axioms so obviously these machines are just simulating computation. Mathematics is simulation by default since we have that little nasty axiom bug. A computer doing mathematics is just still doing simulation.

If you think of all the algorithms written by humans, we can easily say that they were not created by the humans but merely FOUND by the human. The algorithms exist and their answers exist without being run. But to bring the answers into our universe's domain we have to figure out how to simulate the algorithm. This discussion brings up lots of side items. My intent is just to provide another perspective on the subject.

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Last edited by Philip Ronald Dutton on 02-10-2005 at 04:54 AM

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Old Post 02-10-2005 04:35 AM
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Val Smith


Registered: Jun 2005
Posts: 39

Found something interesting

this surprising image was generated by a simple one line non-recursive function that you yourself could do on graph paper. There are a few very interesting anomalies about this:

1.None of the "Hieroglyphs" were designed by a man or a machine.
2.Restating 1: This is not a FONT.
3.This is a static map, a graph of f(x,y)
not a cellular automaton.
4.By coincidence the function has two constants, one of which is 23. 23 "appears" in the graph, but the other, 13, does not.
5. The appearance of "23" is as strange as if you dropped 23 marbles on the floor and they landed in
the form of the numerals 2 and 3.
6.The glyphs do look like a language don't they?
I see churches, houses, bridges, hearts, crosses,
and little people, as well as the numerals 2 and 3.

This and things like it can come from just a few logic gates, even directly connected to a TV!
NO Memory was required to generate this,
The "color" of any dot can be calculated
with one expression using it's coordinates.
however since it's on the internet, it had to get there through a computer.

This makes me wonder if there is a function to generate the bible, since this looks like
"information from no where", more interesting
to look at than digits of pi.

I don't remember the function except it used
Exclusive-OR, AND, and the numbers 13 and 23,
coordinates X,Y, and it was a "one-liner".

Val Smith has attached this image:

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Old Post 06-12-2005 03:25 AM
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Val Smith


Registered: Jun 2005
Posts: 39

The Hieroglyph Function

Credibility is hard to come by so I had to find it!

Notes: This is a PC-DOS QBASIC notation.

The boolean functions operate on all bits of the numbers.

First (this makes it look nicer)
LET A=X+Y:B=ABS(X-Y):REM ROTATE 45'

Then
C=(((A XOR B)MOD 23)AND((A AND B)MOD 13)AND 8)/8

C is 1 if there is a dot in a glyph at X,Y otherwise it's 0
(So graph for all positive integers x and y)

MOD means the remainder of an integer long division

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Old Post 06-12-2005 06:26 PM
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