Sep 262004

Part 1
Part 2

We’ve established that thermodynamics is based on two fundamental empirical laws: the first law (conservation of energy) and the second law (the entropy law). Any systematic scheme for the description of a physical process (equilibrium or non-equilibrium, discrete or continuous) must also be built upon these two laws. Here we employ a simplified but instructive model of probability that captures our reasoning without overwhelming us with details.

Eustace, our thermodynamic system, hops off the turnip truck with $100 and walks into a casino. The simplest and cheapest games are played downstairs. The complexity and stakes of the games increase with each floor but in order to play, a guest must have the minimum ante.

The proprietor leads Eustace to a small table in the basement and offers him the following proposition. He flips a coin. For every heads, Eustace wins a dollar. For every tails, Eustace loses a dollar. If Eustace accumulates $200, he gets to go upstairs and play a more sophisticated game, like blackjack. If he goes broke he’s back out in the street.

How do we book his chances? Depends on the coin, of course. If it’s fair, then the probability of winning a single trial, p, is .5. And the probability of winning the $100, P, also turns out to be .5, or 50%. Which is just what you’d expect.

But in Las Vegas the coins aren’t usually fair. Suppose the probability of heads is .495, or .49, or .47? What then? James Bernoulli, of the Flying Bernoulli Brothers (and fathers and sons), solved this problem, in the general case, more than three hundred years ago, and his result might save you money.

One round

Chance to win $100

Average # rounds

Unreal. A lousy half a percent bias reduces your chances of winning by a factor of 4. And if the bias is 3%, as it is in many real bets in Vegas, such as black or red on the roulette wheel, you may as well just hand the croupier your money. There is a famous Las Vegas story of a British earl who walked into a casino with half a million dollars, changed it for chips, went to the roulette wheel, bet it all on black, won, and cashed out, never to be seen in town again. This apocryphal earl had an excellent intuitive grasp of probability. He was approximately 80,000 times as likely to win half a million that way as he would have been by betting, say, $5,000 at a time.

Bernoulli trials, the mathematical abstraction of coin tossing, are one of the simplest yet most important random processes in probability. Such a sequence is an indefinitely repeatable series of events each with the same probability (p). More formally, it satisfies the following conditions:

  • Each trial has two possible outcomes, generically called success and failure.
  • The trials are independent. The outcome of one trial does not influence the outcome of the next.
  • On each trial, the probability of success is p and the probability of failure is 1 – p.

Now, what this has to do with α theory is, in a word, everything: Eustace’s thermodynamic state changes can be modeled as a series of Bernoulli trials. Instead of tracking Eustace’s monetary wealth, we’ll track his alpha wealth. And instead of following him through increasingly luxurious levels of the casino, we’ll follow him through increasing levels of complexity, stability and chemical kinetics.

Inside Eustace molecules whiz about. Occasionally there is a transforming collision. We know that for each such collision there are thermodynamic consequences that allow us to calculate alpha. When the alpha of a system increases, its complexity and stability also increase. The probability of success, p, is the chance that a given reaction occurs.

Each successful reaction may create products that have the ability to enable other reactions, in a positive feedback loop, because complex molecules have more ways to interact chemically than simple ones. It takes alpha to make alpha, just as it takes money to make money.

At each floor of the casino, the game begins anew but with greater wealth and a different p. Enzymes, for example, which catalyze reactions, often by many orders of magnitude, can be thought of simply as extreme Bernoulli biases, or increases in p.

If you’ve ever wondered how life sprang from the primordial soup, well, this is how. Remember that Eustace is any arbitrary volume of space through which energy can flow. Untold numbers of Eustaces begin in the basement — an elite few eventually reach the penthouse suite.

Richard Dawkins, in The Blind Watchmaker, describes the process well, if a bit circuitously, since he spares the math. Tiny changes in p produce very large changes in ultimate outcomes, provided you engage in enough trials. And we are talking about a whole lot of trials here. Imagine trillions upon trillions of Eustaces, each hosting trillions of Bernoulli trials, and suddenly the emergence of complexity seems a lot less mysterious. You don’t have to be anywhere near as lucky as you think. Of course simplicity can emerge from complexity too. No matter how high you rise in Casino Alpha, you can always still lose the game.

Alpha theory asserts that the choreographed arrangements we observe today in living systems are a consequence of myriad telescoping layers of alphatropic interactions; that the difference between such systems and elementary Eustaces is merely a matter of degree. Chemists have understood this for a long time. Two hundred years ago they believed that compounds such as sugar, urea, starch, and wax required a mysterious “vital force” to create them. Their very terminology reflected this. Organic, as distinct from inorganic, chemistry was the study of compounds possessing this vital force. In 1828 Friedrich Wohler converted ammonia and cyanate into urea simply by heating the reactants in the absence of oxygen:

NH4 + OCN –> CO(NH2)2

Urea had always come from living organisms, it was presumed to contain the vital force, and yet its precursors proved to be inorganic. Some skeptics claimed that a trace of vital force from Wohler’s hands must have contaminated the reaction, but most scientists recognized the possibility of synthesizing organic compounds from simpler inorganic precursors. More complicated syntheses were carried out and vitalism was eventually discarded.

More recently, scientists grappled with how such reactions that sometimes require extreme conditions can take place in a cell. In 1961, Peter Mitchell proposed that the synthesis of ATP occurred due to a coupling of the chemical reaction with a proton gradient across a membrane. This hypothesis was quickly verified by experiment, and he received a Nobel prize for his work.

I claimed in Part 2 that changes in α can be measured in theory. Thanks to chemical kinetics and probability, they can be pretty well approximated in practice too. Soon, very soon, we will come to assessing the α consequences of actual systems, and these tools will prove their mettle.

One more bit of preamble, in which it will be shown that all randomness is not equally random, and we will begin to infringe philosophy’s sacred turf.

  39 Responses to “The Disconsolation of Philosophy, Part 3: Eustace Goes to Vegas”

  1. Aaron,

    I sorry, but I am lost on what you are talking about.

  2. I understand it just fine, but I have no idea how Mr. Man is going to get us from the alpha to the ought.

  3. I’m too waiting the promised transition from these isses to the oughts the moral philosophy usually consists of.

  4. Can’t wait, boss! But can alpha as such really explain any biological activity, much less human behavior? Just one item thereof?

  5. It already has explained a biological activity – how a very simple organism or chemical entity can become a complex one. This in fact explains how life can begin from the simplest of constituents. I would say that is an impressive example. It explains " how life sprang from the primordial soup".

  6. The mathematics of probability have a nasty habit of evading intuition. Be careful about rushing to a conclusion or an application just yet. The more urgent question is whether the material presented thus far is sound.

    Consider what has been presented. The events (defined as thermodynamic interactions) taking place in Eustace result in one of three calculable outcomes: increase, decrease or no change in alpha.

    Alpha is itself a flux, presented as a ratio of changes in bond energies (enthalpy) and organization (negative entropy) divided by dissipation and decay (positive entropy).

    In the casino, if Eustace is losing money faster than he is earning it, he will eventually crap out. Similarly, if any complex system is configured in a manner that is decaying faster than it is organizing and storing available free energy, its sustainability will diminish.

  7. "Eustace is any arbitrary volume of space through which energy can flow."

    Then why can’t Eustice be a one liter volume of space one kilometer North of a nuclear explosion? Are some arbitrary quantities not acceptable?

  8. Now I am lost.
    Mr. Hill: what is that you think has been taken for granted thus far in the presentation of alpha? Or was your comment of general nature?

    Mr. Kaplan: I am not following. As I understand it, we could place Eustace one mile north of a nuclear explosion and then we will get a different set of results in calculating the relevant thermodynamic and alpha properties than if we had placed it elsewhere. What do you mean by acceptable? they are different, again as far as I understand it, but I don’t see how one qualifies as more or less acceptable. Acceptable to/for what?

  9. CT:

    No, it has explained how complexity as such will emerge over time. It has not "explained" a single biological activity. "Getting complex" is not even something necessarily unique to biology.

  10. We are particularly well tuned to recognize complexity but making our intuition precise has proven to be very difficult.

    It may be instructive to consider the relative strengths and weaknesses of alternative, quantifiable measures of complexity exist along with their underlying assumptions.

  11. You appear to be advancing toward a disproof of ‘intelligent design,’ whether or not that is your intent. Congratulations.

  12. Alan: Sure, along the way, but intelligent design has already been refuted decisively in the biological literature. No one believes in it unless he really really wants to.

    I’m hunting much bigger game.

  13. Aaron,

    Bigger game than whether there is a God? Doubtful. BTW, simultaneous development in intelligent design theory is an unrefuted conundrum in my book.

  14. My money is on a Zeus and Odin tag-team. That would rock so hard; how could it be otherwise?

    I bet they even have the same birthday. Now what are the odds of that?

  15. Yes, but do Zeus and Odin play dice with the universe?

  16. I don’t think Zeus and Odin can count that high.

    "Bully a kid long enough and he’ll say he started the Chicago fire."

    It’s a testament to the power of childhood indoctrination (and a deficient math and science education) that we can live among so much internally consistent knowledge and continue to hold on to pixie dust.

    It would be peachy if we could keep our psychological deformities in check focus on topics that don’t use robes and candles as counterargument.

    Dude, like, you never know…

  17. Intelligent design comes in two flavors:

    1) Life started someplace else and come to earth from space.

    In its mildest form this may be true. Organic molecules (including the most recent discovery, simple sugars) and water are found in outer space and arrive on earth via meteorites. These may have been part of the stimulus for the evolution of life. In its wildest form; spores, microorganisms and, who knows, little green men arrived here in flying saucers, this is undoubtedly wrong, but we know that because it is a natural explanation susceptible to scientific analysis.

    2) Evolution was guided by a supernatural intelligence.

    Like all supernatural explanations, science can tell us nothing about this hypothesis. (I don’t know how you go about investigating supernatural claims. Perhaps you read other’s revelations or have a revelation yourself.)

  18. The mild form strikes me more as xenogenesis than intelligent design. I don’t think anyone will argue that stellar debris falls to Earth. How does that qualify as intelligence?

    Supernatural explanations are not explanations. It is not a matter of science as much as it is scholarship. Even in the study of literature or history, a critic is not free to assert a position based purely on received wisdom or revelation.

    Such madness is the special province of religion.

  19. And even more mad is the circular argument that somehow science can be an explanation for the supernatural, which seems to be closer to the core of the attachment that proponents of intelligent design, at least those I know personally, feel toward the subject. Once they are convinced, or raised into the idea (which often requires misinformation concerning the assertions of evolutionary theory which hardly preclude the existence of a nebulous super-being) their faith keeps the universe a closed system.
    As Mr. Bourbaki states more succinctly, only the religious are capable of taking a position based on supernatural inspiration that can only be experienced by the religious.

  20. Charles,

    How is #1 a flavor of intelligent design? There is no designer.

    Simultaneous development of different biological structures, each required to make one larger structure work, is in my book an unanswered question.

  21. Bill,

    Don’t you suppose that complex life would have to have used the "different biological structures" that already existed, whatever those were? So long as the parts all evolved in a way that makes sense, the fact that they then started to work together is hardly surprising. Complex life-processes "look" to us like smooth biological harmony, but isn’t the cell doing its best with what it happens to have? It’s far from flawless, so… And not ALL of those simpler structures were used by more complex life, either, for example, to make us, right? (Observe that many viruses and microbes have qualities not found/"used" in the cells of larger beasties.) Sexual reproduction and viral infection both show how the genetic material of one thing can hijack that of another (sometimes to create a third, new and different thing from both.) Once integrated, the relatively "anti-survival" aspects of each of the former parts can drop-off (or, more accurately, be turned-off with a new genetic instruction) through evolution. You are talking about the parts of the cell, right, and not the parts of the body? I think that that one has long been put to bed, right?

  22. That’s the problem with randomness. It never seems random. When it comes to non-linear dynamics, our intuition sucks but it’s "hard work" to overcome it.

    Ever since Darwin, biologists have assumed that living things tend toward order. But now they’re discovering that life at the molecular level is fraught with chaos and chance.

  23. Mr. Valliant’s description of the cell’s life is agreement with the picture painted by modern biology using the tools described by Mr. Vaillant.

    From the article:
    But biologists are now discovering that the appearance of order is an illusion. Our molecular worldlife at its most basic levelis messy. Inside our cells, shards and scraps of protein float around aimlessly, waiting to interact. There is no guiding hand, no guarantee of exactness. Our atomic stochasticity percolates upward, infecting and influ-encing all aspects of life. Far from being an exemption from the second law of thermodynamics, we are actually its most intricate example. Randomness is writ into our fabric.

    Mr. Valliant and Mr. Vaillant providing complementary sides of the same argument?

    Some please explain that one!

  24. Jim and Bourbaki,

    My problem with evolutionary theory at bottom is not that I don’t believe it, but rather that I do. It fills the interstices where evidence fails. We see two structures and, lacking evidence, we patch together a story using a logical thesis. Well, logical theses have a nasty way of being proved wrong. I object to the way Darwinism and evolutionary theory generally fill evidentiary holes. It has become rational salt water taffy plugging holes in the dike replacing as satisfactory explanation real evidence.

  25. Mr. Kaplan,

    Correct me if I’m wrong but the problem with the way you present your position (and how this position is presented generally) is that it sells short the expectations for deliberate and measured evidence with the call for idealized omniscience and infallibility.

    Unfortunately, we are often taught science separately from the history of science so something as clean and elegant as Maxwell’s equations seem to jump off the page as if they were a flash of received wisdom. Any non-trivial theory takes time to elucidate.

    We miss out on the numerous (and sometimes silly) mistakes made along the way and, more often than not, the answers that lead to new questions. Nevertheless, the track record of intellectual achievement based on open discourse and scholarship speaks for itself.

    I have met my share of deluded Darwinists but assigning a vague pop interpretation of a very broad concept to the work of thousands of scientists is a bit naive. Is there a particular paper or result with which you disagree that is not open to debate by the whole of the life sciences community?

    I would suspect that someone has taken an opposing position to just about any questionable position in biology–so long as it is not simply rhetoric or special pleading based on received wisdom, revelation or pre-indoor-plumbing standards of legitimacy.

    Scientists are fallible just like anyone else–and they have limited resources. The blind allies and discredited theories are a mark of their openness–the whole of their enterprise is subject to challenge by you or me or anyone who cares to take a position. To keep the discourse productive, we need to offer something more (accuracy, explanatory power, capabilities) than they are currently providing. Otherwise, we’ll have geniuses like Gauss sitting on theories until they can pass arbitrary hurdles put forth by pseudo-geniuses like Kant.

    Do oblique criticisms of a theory offer up anything more than an indication that there is more work to do? I suspect scientists are already aware of this.

  26. Bourbaki,

    I agree with nearly everything you have said. Now answer me this: Do you know of any scientist worth his salt trying to disprove Darwinism? I know of none that can be taken seriously.

    In fact Darwinism has replaced religion in this important sense, it provides an explanatory theory for ordinary matters that is not susceptable of falsification.

    Do you have children Bourbaki? Well, I do and believe me their behavior is baffling. They chew on dirt, take their clothes off in the snow, demand to walk on high ledges and run across highly trafficed roads. And they ALL do these things. Would evolutionary theory say that these behaviors should have been weeded out by now? Or are we in the process of weeding them out? Our were our forebears worse and do we have fewer of these traits now than we did in the past? Or is it that evolution only wants those children to grow up who have guardians overseeing their activities? No one knows. We are left with the vacuous assertion that we have EVOLVED this way. I am sorry, but that assertion is no better or worse than that God made us this way. Either evolution or God could have made us blue too, but neither provides an explanation why.

    I also believe evolutionary theory has blinded us to facts that seem contrary to evolution. So sorry, I’m not overly impressed.

  27. Mr. Kaplan
    In fact were we blue evolution might very well be able to provide an explanation for it (principles of survivability being what they are). It could certainly offer something more plausible and *verifiable* than "God’s will".
    You offer an…interesting perspective on evolution when you invoke the scientific communities agreement on it as somehow something to be held against it. I can’t say as I have ever encountered the proposition that scientific consensus is a bad thing. So long laws of physics! We all agree on your truth and no one is trying to debunk you (*anymore*) so you must be flawed.
    What a relief. Being bound by such strictures was a real drag.

  28. Do you know of any scientist worth his salt trying to disprove Darwinism? I know of none that can be taken seriously.

    This is a curious way of framing the argument.

    Do you even bother to read the posts or the responses or are you simply following the Celestine Prophecy and, in passing, alluding to fancy scientific papers to not prove a point? Vitalism had its adherents well into the 20th century. Notice your neutered qualification: "worth his salt"; the reason that scientists are not trying to disprove the theory of evolution is simple: no one has produced a competing theory worth its salt that warrants the time and expense: increased accuracy, greater explanatory power, or new capabilities. I’m afraid that to further their careers, scientists need to offer something more compelling than ignorance and incredulity as a competitive theory.

    In fact Darwinism has replaced religion in this important sense, it provides an explanatory theory for ordinary matters that is not susceptable of falsification.

    Important sense? You need to transcend this world to convince yourself that it’s a bad idea to kill or steal? (Unless, of course, a dude in your village till’d the wrong crop–then you stone the dumb heathen.)

    Efforts to refine the theory of evolution led to the discovery of the carriers of heritable traits: the nucleic acids. But not before thousands of experiments were carried out attempting to prove that proteins, because they are so much more complex and mysterious, were the true carriers of our naked ape goodness. The nucleic acids were at best, structural and, at worst, impurities. Resolution of this conundrum led to advances that, today, practically allow us to design therapies through a web browser.

    Accuracy? Check. Explanatory power? Check. New capabilities? Check.

    Imagine somewhere, out there, someone is making progress before we’ve crystalized divine epistemic purity–perhaps you could endow an international prize for skepticism to stop this madness?

    But let’s indulge this tortuous line of reasoning because it is so…precious.

    Do you have children Bourbaki?

    Indeed, I do not. And I do not drink pina coladas and I have not made love in the rain. I haven’t seen a double rainbow over the beach at Kauai. And I’m sure one spoonful of your great grandmother’s chicken soup would be so transcendant that any doubts of the existence of divinity would dissolve the appeal of reason in the hearty, homemade stock.

    But alas, I live in a cave and eat gruel. So truth, for me, comes in bits I find wedged under my fingernails.

    As far as I know, I was an infant once. Nowhere near as promising as yours–alas, I still do that stupid stuff. All of it. And there is stupid stuff I’ve done that I can’t even bring myself to mention. So my boundless stupidity constitutes evidence that we were designed by Zeus? I think I see what you’re getting at–our parents were more ignorant than us. And their parents were even dumber. So the dumber the generation, the more credible the received wisdom. So God is the dumbest thing in the universe. I guess in physics, a photon is pretty dumb so maybe we’re arguing the same point?

    But the chief cause of our natural unwillingness to admit that one species has given birth to other and distinct species, is that we are always slow in admitting any great change of which we do not see the intermediate steps. The difficulty is the same as that felt by so many geologists, when Lyell first insisted that long lines of inland cliffs had been formed, and great valleys excavated, by the slow action of the coast-waves. The mind cannot possibly grasp the full meaning of the term of a hundred million years; it cannot add up and perceive the full effects of many slight variations, accumulated during an almost infinite number of generations.

    –Charles Darwin
    On the Origin of Species by Means of Natural Selection

    I also believe evolutionary theory has blinded us to facts that seem contrary to evolution. So sorry, I’m not overly impressed.

    This sounds like the arguments against free markets because they let us "squander" our money. Or against democracy, because "stupid people" can vote. If you can provide a theory that accommodates these facts to which we are all blinded more accurately, go for it.

    Might I recommend that before you trot out papers by John Bell and Sin-Itiro Tomonaga (QED, by the way, introduced undetectable "virtual photons" to avoid violating conservation laws), or any other high fallutin papers, that you cut off a more manageable morsel so that it’s easier to discriminate the true origin of this "blindness". The road might be longer but I bet the ride won’t be as bumpy.

  29. Bourbaki,

    So much to slog through. Which I will do in time. But one thing strikes me — You believe stupid people should be able to vote?

  30. Mr. Kaplan,

    If your comments weren’t so generic, we would not need to turn up so much soil. And if you are up to defending religion, slogging should be second nature.

    We naked apes are a rich mosaic; stupid comes in so many flavors, each proudly handed down for generations not through open discourse but through egocentric fallacies and fantasies directed primarily at children.

    But having parents who spiked your world view shouldn’t curtail your rights. So, if by stupid you mean religious, then, yes, even stupid people should be given a say in how they are governed.

  31. Let us suppose, Bourbaki,that anthropologists discover a fossil of a complex organism that is carbon dated to a time when we currently believe only single- celled organisms existed. Will evolutionary theory itself be questioned or merely the calendar for evolutionary advance? What evidence frays the theory?

    Relativity is being questioned daily as quantum tunneling and entanglement stretch the rate of information transfer past the speed of light. Reimann questioned the foundations of geometry and surpassed Euclid. What could cause the demise of Darwinism? If you say, "Nothing", I have a problem. If you say, "Finding fossils of the type you describe" then I have no problem with Darwinism.

    Do you remember when Communists used to advance as evidence of Marx’s farsightedness the fact that his predictions had not come true yet? Well, that is what Darwinism does.

  32. Yes Mr. Kaplan that is the scientific method; new evidence discredits existing theory, new theory is writ to accomodate this evidence (provided that it is sound evidence). It is this openness that allows for scientific progress. Your comparision to Marxism is wildly off the mark.
    So now that we have established that you "have no problem with Darwinism" I suppose we can move on to more interesting material.

  33. Mr. Kaplan,

    I guess the explanations about "competing theory" and its comparables (accuracy, explanatory power, new capabilities) might be too "jargony" so let’s put the issue in terms that the voters can understand.

    If you can offer a story that offers more straight up dope than Darwin and provides more cool tricks for us to use, I will personally fund your research–liberal media be damned. Super powers would be excellent capabilities if you can provide them–I’ve always found Darwin lacking in that department. And I don’t think we should wait for those fat cats in the Vatican to give them to us.

    I have no doubt that you are excited by your discovery that there exists a divide between science and this hot new field, "omni science". I assure you that you are not the first to notice it but if I know my Bunsen burners, I suspect scientists everywhere are conspiring to silence you.

    Further, if you could share your general relativity crib sheets for getting satellites into orbit (since Newton was ‘overturned’) it would save me some major computing resources–Ricci tensors are such a pain! I really hate it when scientific fashionistas throw out old theories and force us to upgrade every few years. I was just getting my head around F=ma, now I’m going to have to learn a whole new system after relativity is ‘overturned’? Some days I don’t know why I bother.

    And what ever happend to Gauss, Bolyai and Lobachevsky? I thought they had some passing involvement in geometry–you know, asking questions and such. Perhaps they gave up the whole thinking game and put unquestioning faith in Marx? Or was it Kant? Idiots, they should have known there is but one place to put faith–Zeus!

    We’ve gone from

    "The limitations of your science suggests that my God exists"


    "My ignorance of your science suggests that my God exists"

    I think I’m beginning the see the light! A photon is stupid. God is light. God is stupid. I should be stupid, too.

    I believe I’m really going to like this new "omni science".

  34. CT:

    Yes that is the scientific method, but I do not believe it works when discussing Darwinism. The scientific establishment will talk about one flavor or other of Darwinism, but not whether the theory itself is valid. It is assumed true even in the face of paltry evidence, like scant fossil evidence.

    I have little doubt that in the question I posed regarding the timing of multi-celled organisms, only the calendar would change and not the working assumptions of evolution. A better example of this is Wolfram’s argument against Stephen Jay Gould’s doctoral thesis on the natural selection of shells. In his thesis, Gould argued that there are millions of possible types of shells, but only six distinct types exist. Accordingly, he views that fact as evidence that natural selection has pruned the evolutionary tree.

    The mad but brilliant Wolfram turned the argument around. He analyzed shells into only six mathematical types, all of which exist. Where then was the action of natural selection on shell type?

    While I believe neither argument says anything about Darwinism, it is interesting we have heard little of the Wolfram argument.

    My view, which is derived from the application of Popper’s principles, is that Darwinism is not a scientific theory but what I call a meta-theory. A scientific theory will postulate a thesis which is falsifiable. A meta-theory postulates how a scientific theory must be constructed in order to be considered valid.

    At bottom, Darwinism is an extended tautology. In a statistical sense, when only the fittest survive, those that survive will have been the fittest for the particular conditions. We can’t predict who will win and who will lose under any set of conditions. In any explanation of who won, we ASSUME the Darwinist position and argue as if the winners won because they were fittest. Thus Darwinism suffers from the same ills that Aaron complains befalls philosophy–it doesn’t predict and it only explains things by setting the conditions for the explanation ahead of of time. Now it is fine to explain using only one method. But that method must be susceptable of being wrong.

  35. Popper emphasized the role of refutability but, as with much philosophy, the lure of idealism led to gross oversimplification. There is a very real divide between theory and practice yet Mr. Kaplan is seeking modus tollens for a comprehensive scientific theory.

    Rarely are things so simple in practice. There have been many "counterexamples" to the hypothesis that there are no alien abductions. Every alleged ‘victim’ is one. Yet most scientists continue to believe that little green men are a fantasy. It is evident that not all supposed counterexamples have enough credibility to refute an otherwise consistent hypothesis.

    Hypotheses on the edges of current knowledge, like the theory of evolution, can often only be tested in situations where many ancillary hypotheses are tested as well. These ancillary hypotheses are background assumptions about how the main hypothesis fits into the general body of knowledge; how the principles of mathematics, physics and chemistry necessary to test the hypothesis operate to confirm it.

    The integrated nature of comprehensive scientific theories rule out any arm-chair use of modus tollens. I’m afraid in actual science matter quickly become too messy and complicated for the anthropic idealism of philosophers and theists.

    Let’s consider a simple case first. Newton’s theory of gravity makes predictions about the future motion of planets. In the nineteenth century, these predictions for the orbit of Uranus were found to be slightly but consistently wrong.

    Some astronomers wondered if the discrepencies might be due to an unknown planet beyond Uranus. Once this planet (Neptune) was discovered in 1846, Newton’s theory was strenghtened. Neptune was further confirmation of the theory.

    Later, other irregularities were noted in Mecury’s orbit. Astronomers also tried to find a planet near Mercury that might account for this deviation. An amateur French astronomer, Lescarbault, reported seeing a planet within Mercury’s orbit in 1859. The planet was accepted as real and named Vulcan by Urbain Jean Leverrier, co-discoverer of Neptune. Subsequent astronomers could not find the planet–and it was soon branded a mistake.

    Mecury continued to depart from its predicted orbit. The deviations were regular and distinct from Kepler’s laws. The discrepencies were ultimately accepted as evidence that Newton’s laws did not account for all gravitational dynamics.

    The history of Neptune and Vulcan demonstrates two features of counterexamples: first, a counterexample may refute an auxilliary hypothesis rather than a main one–it is important to find out which hypotesis is truly at fault; second, when a theory is ‘thrown out’, it is in favor of a broader theory that is consistent with the corroborated predictions of its predecessor. General relativity predicts gravitational dynamics identitical to Newton’s theory in all but the most extreme gravitational fields.

    Not only must a new theory account for the successful prediction of the theory it aims to replace–it must offer something new that is beyond the reach of the its competitors.

    In Karl Popper’s own terms, a new theory must have greater empirical content.

    Biology is an extremely broad, integrated body of knowledge that is held accountable to mathematics, physics and chemistry. The theory of evolution proposed to explain how these dynamics fit together to produce the diversity of living systems without appealing to some anthropic notion of a completely unsubstantiated divine influence. Never underestimate how difficult it is to convince naked apes to abandon their magic sticks.

    That doesn’t make it a meta-theory. Despite his philosophical idealism, Popper never said that a theory had to conveniently testable.

    It’s easy to forget just how crazy it must have sounded to assert that a cockroach and Mozart are instances of the same thing. And it’s even easier to point out that there are things that we have yet to explain.

    Mr. Kaplan mentions Wolfram and his "discoveries" in applying cellular automata to explain everything. CA was the brainchild of mathematician John von Neumann who was interested in the idea of artificial life, particularly self-reproduction.

    Unfortunately, Wolfram regards the early work with cellular automata as rudimentary. He uses no references from the numerous people who have contributed to the science over the years, perhaps considering their work irrelevant. Obsessed with the idea that he was on to something special, he spent more than a decade in isolation, pondering the possibilities.

    Wolfram defines randomness, explains seeming randomness in financial markets, finds an exception to the second law of thermodynamics, conjectures why extraterrestrials might be communicating with us in messages we can’t perceive, elaborates on why humans appear to have free will, reconstructs the foundations of mathematics, devises a new way to perform encryption, insists that Darwinian natural selection is an overrated component in evolution.

    Wolfram’s theory doesn’t invalidate the Darwinian model but rather augments it with CA dynamics. As for the silence in the scientific community for his results, Wolfram might want to consider releasing his ideas in manageable chunks that are more portable than the Manhattan Yellow Pages.

  36. Let me add just a few comments to Bourbaki, altho once again he hardly seems to need it.

    First, I am curious as to what Mr. Kaplan regards as the evidence for evolution as he thinks it such an insignificant body. It has been corroborated. That is, insofar as is possible – we can not travel back in time and watch it happen so if that is what you require for evidence than I am afraid I will have to concede that yes the evidence gathered from our time traveling is scarce indeed. It has been confirmed in thousands of observations and with as much experimental work as any reasonable person thinks necessary.

    The thing that Mr. Kaplan laments, namely that we assume it beforehand and then construct the facts or new theories to fit it is because *it is accepted as fact*. It is no longer necessary to check everyday to see if the theory of evolution is still sound in the same way that it is no longer necessary to check to see if the laws of thermodynamics are sound. Variations and details within evolutionary theory are still open to (some) discussion, but not the principles itself.

    Again, this is not because it has not been put through its paces, but rather because it has and for that reason we can safely accept it in our investigations as a known. The progress of science, of humankind would be slow if we were not allowed to accept as true that which we have learned. Naturally if someone were to come along with, and this is the important part, a better theory – one with new capabilities, better explanatory power, more CPPD, of course the scientific community would allow for its possible truth and investigate it accordingly. If it were valid and good – so long evolution.

    In the meantime until this mystery theory emerges lets go with the one that has withstood scrutiny (intense scrutiny I might add) been proven fit after the rigors of scientific investigation and questioning and that offers us new capabilities and explanatory power. Contrary to Mr. Kaplan’s quiet conspiracy of scientitsts working to ensure evolutionary theory’s preeeminence, it has earned its place as fact of the universe as all science must before we accept it. Science and math are just plain cool that way.

  37. Bourbaki and CT:

    I am reminded of a discussion I had with the noted entomologist Bernard Greenberg (see, e.g., Entomology and the Law: Flies as Forensic Indicators). We were discussing my dissatisfaction with Darwinism, and, after satisfying himself that I was not some religious fanatic, he told me a story of the use of DDT to delouse populations in Italy toward the end of WWII. "Within six generations, all lice (I think we were talking about lice, but it might have been horseflies)were DDT resistant. If that doesn’t prove natural selection, nothing does." After a few innocuous questions, I asked, "And how many generations does it take for that trait to leave in the absence of DDT?"

    "I am not sure. Six or ten, something like that."

    "How do you explain that? There is no Darwinian explanation for losing a trait in the absense of external reasons."

    "The trait must impose some cost," he said.

    "Show me the cost."

    I don’t know if you see what I am saying, but Darwinism causes us to filter the phenomema we view. We see natural selection in immunities, but not in reversion to the ativistic state (a reversion which has become very important in the treatment of AIDs by periodically cycling drugs). We can’t explain why kids take off their clothes in the snow, but any half-baked theory will cite Darwinism and provide an explanation fitting its requirements.

    Darwinism blinds us from the phenomena, to the realities that don’t quite fit the theory.

    I recently bought a Saab. Now I see Saabs everywhere. But ya know what? There aren’t really that many Saabs–I just notice ’em. Same with natural selection.

  38. I was not some religious fanatic

    Is there any other kind? You’re either willing to fill those empty spaces with openly corroborated scholarship or you’re broken enough to substitute some private egocentric fairy tale and, worse, derive pride and identity from collective delusion. If you somehow see equivalence between those two choices, then the nature of your obstinacy is clear.

    I don’t know if you see what I am saying, but Darwinism causes us to filter the phenomema we view.

    I know exactly what you’re trying to say: the theory of evolution doesn’t explain every observed phenomenon. That the theories of Fama and Thaler don’t explain every aspect of the financial markets doesn’t lead us to believe there is some divine force guiding wealth to the deserving.

    You are making a wholly unremarkable observation yet you’ve been shining this turd for days.

    Are you building up to a point? Are you going to lead us somewhere, anywhere, through this thicket of snow, sea shells and Saabs that demonstrates the adverse cost of wasting our time on evolutionary theory, the discovery of nucleic acids and the development of modern genetics?

    I have no doubt that our understanding of evolution will change over time and our current model will seem crude if not outright silly. But evolution is still relatively young and its scope is incredibly vast.

    Since you’re beating the drum so hard about the toll of this Darwinian myopia, let’s turn the question around:

    Show us the cost of the theory of evolution.

    What avenue to truth have we crowded out? My offer still stands–if you’ve got a compelling alternative theory that has been lost in the wake of the HMS Beagle, I will gladly fund its development.

    But let’s not waste another moment! More tales about your biologist friend, Eddie, and his inability to balance his checkbook will only stand in the way of informing the world of this marvelous but neglected theory.

    We await its unheeded wisdom…

  39. First a technical point. What we are discussing here is not fairly nor accurately called Darwinism. It is called evolution. Darwinism in its purest form does *not* capture the breadth and depth of evolutionary theory as iterative changes to it have been made since Origin. "Evolutionary theory" or just plain evolution better fits the theory in question (shocked tho I am to be in the 21st effing century and still having to discuss it as tho it were in question).

    I think I am beginning to see the nature of your objection to it now tho Mr. Kaplan. You seem to dislike that it is used to explain things that you regard as outside its purview. I agree that this is the case from time to time in much the same way that poor ole Heisenberg has been more abused than the fat quiet kid with the thick glasses in gym class. If evolutionary theory is young, evolutionary based theories of complex human behavior and sociological evolution are positively nascent. Nevertheless they are not to be dismissed outright and much can be said in these fields even if you do not understand it or accept it.

    It (evolutionary theory) is not nor was it ever intended to explain everything about everything and many people who understand it poorly unfortunately do just this.

    That said no objection or instance that you have yet proffered is one of these instances. Putting aside your problem with it that it cannot explain certain phenomena *to you*, it can certainly explain the specifics you have brought up. The example of the DDT can in fact be explained tidily by evolutionary theory. There was some cost to immunity such that when it outweighed the benefits it was no longer a "favored" trait. I am not sure why you disregard this explanation, but whatever. Or this may not be true and there may be a host of other reasons why immunity vanished and these reasons may have nothing whatsoever to do with evolution. If this seems to be forcing the facts to conform to our theory it is ? because evolution is right. No one doubts it and therefore explanations need be given to incorporate the state of the world and discoveries to fit it and not the other way around. Just like QED was forced to invent virtual photons to avoid thermodynamic violation. If your theory is in violation of a scientific fact then your theory is either wrong or it had better be airtight and robust and open to independent confirmation. If it is we will accept it. Until then we will conform the facts to that which is known. If phenomena arise that seem to undermine our knowns we don’t simply abandon our given when they have become worthy of being called knowns.

    But let us suppose we have a theory, any theory, that to date has proved remarkably adept and useful in explaining previously mis- or not understood events and phenomena. Now let us introduce something and ask how does your theory explain…this! Suppose we cannot offer a good explanation for it right now. What choices do we have regarding our theory? We can wash our hands of the whole theory despite the good it has done us in explaining so much else. In addition we can adopt some arbitrary and completely unsubstantiated explanation in its place, say a religious or divine explanation. While this gives us answers to every question we may ever have, for those of us not indoctrinated into the cult and those of us who are reasonably curious and attentive this is as bad an idea as there is. There is no reason to accept the divine explanation and whatever shortcomings our theory might have at least it offer explanatory power, meet CPPD etc. Surely preferable to the wholly unsupportable (by all accepted methods of proof – logic, empirical confirmation) "God did it" approach.

    We can also admit that right now we can’t explain certain things that our theory should be able to explain. Simply because we have a failure to see how something works within a given framework we do not abandon that framework, one that has worked so well and been put to such testing as to have become accepted , simply because we have encountered the case that it cannot explain yet. Seems a bit rash to me. Perhaps our theory needs tweaking or perhaps we have misunderstood the question or perhaps our theory cannot explain this event as it is not designed to explain it. None of which mean our theory is wrong nor do any of these possibilities recommend ditching our proven, robust helpful theory. Were all inquiring minds to quit the first time things got rough we would be scrawling this thread on a cave wall in Mastodon blood.

    All of this said, let me reiterate that nothing you have said thus far as "how can your evolution explain this?" even remotely comes in the vicinity of the neighborhood of the zip code of being a challenge to evolution. I am sorry that you do not understand the theory very well, but I am grateful that the facts of the matter are not decided by public/popular opinion and understanding. I do not know your religious or theistic convictions but I daresay that it is you who are trying to force the world to fit your preconceptions. The difficulty you are experiencing in doing so is because the theistic interpretation is flat out wrong and so naturally there is going to be a whole bunch of ill-fitting pieces to the puzzle for you.

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