Noise in the Machine: The Homogeneous Chaos Blues
By Jim Chaffee
For Roger Carlson
Gilbert Ryle nailed Cartesian dualism by killing the ghost in the machine. Now someone named Carl Zimmer wants to use noise in the machine to kill a straw man standing in for genetic determinism. This mushy-headed blather arises as an attempt to simulate science-talk to people inured to comic book encapsulation of the most complex ideas. Who knows what the author intended to convey, or why, but the premise demands deconstruction like Lon Cheney Junior demanded a dew claw.
I don’t know squat about Zimmer, having run across this article in a roundabout manner. A Brazilian in an Orkut community opened a topic with the heading “Fim do determinismo genético.” He posted a link to a Portuguese translation of an article appearing in a Brazilian online newspaper. 
Intrigued, I went to the link and began as I usually do, reading the opening sentence claiming that humans differ from one another in an infinity of aspects. It made me hope there had been a mistranslation. No respectable science writer would claim the existence of an actual infinity of physical anythings (though it isn’t clear aspects need be physical).
This led me to look for the original source from The New York Times, which I found online, dated April 22, 2008.  The author wrote that humans differ in too many ways to count, which is a far cry from differing in an infinity of aspects.
The original essay is entitled “Expressing Our Individuality, the Way E. Coli Do.” Catchy, no? Were it not already penned, I’d have to invent it.
If you take the time to read this short bit, the straw man pops right up into your headlights, assuming you have them on. Otherwise you might miss him, disguised as he is: Zimmer contends we put a bigger premium on nature than nurture when it comes to our individuality. I’m not sure where he gets this idea, unless its his own weltanschauung. It’s not mine.
Nor is it the view I ever run across, excepting the bizarre commercial that instructs me I get my cholesterol from my aunt. Most of the people I know believe that when they get a disease or condition it’s their own fault, usually dietary, and not that of their genes. They like to feel in control, I think. Sort of the inverse of conspiracy theory or Existentialism as substitute for God.
As you read along you find this Zimmer trying to convince you that you think bacteria like E. coli (proper name Escherichia) are machines. Which is amusing. The only human I know of who said any kind of animals (I’m loosening the notion of animal here) were machines was Rene Descartes, who Bertrand Russell claimed didn’t believe it but wanted to avoid the physical duress of the Inquisition’s enforced insistence that humans were the only souled creatures. Another kind of ghost in the not-machine, so to speak.
I personally would have been surprised if all bacteria in a colony behaved alike, or that the behavior was predictable. But that is not really the most interesting aspect of what Zimmer writes. After informing us that bacteria “are not simple machines,” he brings in the idea of noise changing the way the E. coli bacteria behave. He says that unlike transistors and wires, “E. coli molecules are floppy, twitchy and unpredictable.” This he contrasts to the deterministic behavior of electronic devices.
So right off the bat here, Zimmer misrepresents electronic devices in the way that Descartes misrepresented animals, though my guess is Zimmer did it for money and not fear of torture (he might simply be ignorant). Anyone who has worked with electronic gizmos on spacecraft will have experienced these mechanisms getting out of hand. In the early days of the GPS (Global Positioning System) when the satellites disappeared from view for a few hours, on-board atomic clocks might decide to leap in time. When they reappeared they would be so far off that the Kalman filter at the Master Control Station could be falsely persuaded by new measurements that the satellite had hopped to a lunar orbit.
Even more interesting is metastability in certain binary electronic devices known as flip-flops. With only two possible states, the device can become confused and take an indeterminate (random) time to decide whether to flip or flop.
And who is the culprit for these and too many other aspects of electronic misbehavior to count?
Noise, as it turns out. Which is in fact like a weed. That is, akin to the chicory in my garden that is currently out of hand, inedible and blooming and propagating even as I continually pull it up all summer so other plants can grow. But is it a weed? Not in the winter, when the leaves darken red and purple to become radicchio.
Noise is a random process, a not well-defined thingy in the real world from what I can gather. Random processes do have precise mathematical meaning, however fraught with difficulties in the quotidian world swept under the rug of operational definition. If you doubt the difficulties, read chapters two and four of Leo Breiman’s classic text Probability. Or at least the discussion at the end of the chapters, though the discourse on conditional probability is particularly mind-bending.
Here is the real deal. It seems the “real world” we live in is a world of aggregates: averages of random stuff at the microscopic level. At least that seems to be the world according to quantum theory. Or statistical mechanics. So to say that electronic or mechanical or electro-mechanical devices behave at the atomic level like machines, that is mechanistically, is specious.
The examples cited above (and numerous others) provide counterexamples to Zimmer’s quasi-example, at least as represented. E. coli behaves oddly at the macroscopic level because it is not predictable at the microscopic level, even given identical genes and identical situations. Well, there is a problem with that identical situation bit, since it is not clear there is ever any identical situation. But just as E. coli get trapped in various deviant feedback loops and other aberrant behavior, so can electronic devices. And not predictably, though one might try to replicate a situation exactly.
In fact with noise the idea of replication is fraught with difficulty. In a computer simulation it is possible to use a pseudo-random number generator and begin it with the same seed, getting the exact same pseudo-random sequence of numbers (which is why it is not a random number generator). However, the simulation is not the device itself. This point has been well demonstrated by John Searle in regards to the problem of consciousness in strong artificial intelligence, wherein he points out that the idea of a machine that simulates consciousness is not equivalent to the machine being conscious. Consciousness, argues the materialist Searle, is a physical process akin to digestion, and simulating digestion is not digesting (but consider for argument sake Wim Delvoye’s Cloaca). And pseudo-random noise in a software-controlled machine is not random noise in a software-controlled machine.
The mathematical idea of random process is not likely what an engineer might imagine in any case. The idea is that the manifestation is not itself random, but is in fact determined. What is random is the picking of that particular manifestation. As if some infinite dice roll hands us the result. Of course, not being privy to the outcome beforehand, we must contend with the manifestation as if it itself unfolded randomly in time.
So where are we? Starting with an attempt to befuddle us by claiming we confuse phenotype with genotype, we end up with the claim that bacteria are different from machines because of noise. More sleight of hand, it seems, illustrated in the essay’s conclusion: "Living things are more than just programs run by genetic software."
And yet electronic machines run by software can become confused as to whether an input is yes or no. (There was a time when engineers believed such behavior from a digital device to be impossible, causing all manner of difficulty in searching for a non-existent software bug, another kind of ghost in the machine.) And noise is the culprit.
The classical feedback-loop known as the phase-locked loop, essential for tracking signals in all sorts of radios and myriad other electronic devices, can suffer all manner of unspeakably unpredictable behavior with noise, from the audible clicks of cycle-slips in FM radio to false lock. More complex types of software feedback loops like the extended Kalman filter can become so confused they eventually insist on the spurious, divergence sometimes termed instability, driving the machines they control to irrational behavior. (The honest-to-God Kalman filter under certain circumstance cannot (in the long run) tell a lie, a condition known as stability.) What is more, the phase-locked loop has been taken as a model for the behavior of living cells.
The real issue, it seems, is not machine versus living thing, but determinism versus randomness.
It brings to mind (the word only a metaphor, but for what?) a conversation with an engineer some years ago. Not a unique conversation, to be sure, because the idea she expressed is common. She said that nothing was ever random. If you knew all the initial conditions and all the forces in a coin toss, for example, you would be able to tell exactly how the coin would land. I replied that was a metaphysical assumption and could not be demonstrated experimentally. Much of the discussion above goes to the heart of showing that such an argument is metaphysical, not physical. It is a metaphysical ideology known as determinism.
To be sure, all evidence of which I am aware is contrary to determinism. No matter how careful a calculation is made, for example, the implementation always misses the mark. Approximate cause and effect seems the nub of perceived determinism. But let’s see why causality is probably (in what sense here this word?) not demonstrable.
If I smash a plate with a hammer, I demonstrate a cause and its effect. Determinism at work: the hammer smashes the plate. Right? But what if I hit exactly the same plate, with exactly the same hammer, in exactly the same way again? Would the plate break into the same exact pieces? No one can say. There’s the rub. If this cannot be repeated, then it cannot be predicted, and thus is not what could be called deterministic. Hence not really cause and effect except via the fog of imprecision; that is, so long as one doesn’t look too closely.
In order to ascertain if this particular event is truly determined, in the sense that given the precise initial conditions one can exactly predict the outcome at whatever level one examines, one might decide to repeat the experiment. If we cannot ever know all the initial conditions, we ought still be able, by repeating the precise experiment, to get precisely the same outcome in a deterministic world.
But how can we repeat this experiment?
Suppose I build a machine to precisely smash a plate placed in precise position, a plate made of precisely the same materials in precisely the same way as its predecessor.
You could argue, This is not the same experiment. What are pieces exactly the same? At what level? Molecular? Atomic? Subatomic? Is it possible to use the same exact hammer again, given that it had already smashed a plate? Is it possible to construct the exact same plate? In fact, would that original plate be the same exact plate a fractional step later? That is, if I smashed the plate a picosecond later would I be smashing the same plate that had existed a picosecond earlier? On a macro enough level, certainly. But do the micro properties make a difference even in this temporally loaded case?
This argument is along the lines of the famous saying of Heraclitus to the effect that one cannot step into the same river twice. Nothing new here. (Actually, we stand before a crossroad with a branch leading to questions of dependence on initial conditions, stability, and chaos theory, but we forgo the fork since it would take us too far afield. Suffice it to say the chaos of chaos theory is not random behavior, though it might appear so to the untrained eye. But look to Smale’s horseshoe!)
The question I am putting is, if it were possible to exactly replicate the experiment, would the results be the same?
I see no reason to believe so. I foresee noise fucking things up, changing the outcome ever so slightly. Perhaps only detectable at microscopic level, but still and all different.
So what the hell is deterministic, anyway? Well, it isn’t the opposite of random, that’s for damned sure.
Deterministic is if you start at some place with specified conditions, you will without fail end up at a place at a later time that can be precisely predicted without deviation. You follow a trajectory, if you will, not in the sense of bogus-speak  as demonstrated by Petraeus and Crocker, but a trajectory in the sense of mechanics. Traditionally, determinism is behavior obtained from differential equations, be they ordinary or partial. The idea is that starting from some initial conditions, like the position and velocity of my hammer, the outcome is completely known once the differential equation describing the hammer blow is known.
As parenthetically hinted above, there is oversimplification here due in part to my own desire to avoid the complication of chaos and the confusion of chaotic bopping for randomness. The little book Chaotic Evolution and Strange Attractors by David Ruelle is a lovely side excursion if you have the time and fuel for it, with a mathematical description of a chaotic information-creating machine. (Akin to an information Cloaca?) However, for our purposes let’s pretend to be happy Taoists following the trajectory of the wise man, avoiding struggle as we go with the flow, so to speak (flow in the precise sense).
Noise is a random process, and randomness is not the opposite of determinism. Already we’ve alluded to as much above, discussing noise at the micro level averaging up to what we experience at the macro level, the quasi-regularity engineers love to extrapolate to determinism fucked by imperfect information. This seems to be perhaps Ruelle’s viewpoint, though I am not certain. (There are those who attempt to explain away noise by equating it with chaotic behavior and lack of information as part and parcel of the metaphysical assumption of determinism.) But random behavior is controlled by laws that allow predictions in the long run; of course, as Keynes noted, in the long run we’re all dead.