Feb 262008
I recently read Arieh Ben-Naim’s book Entropy Demystified, a book I feel would have benefitted greatly from being more somewhat more focused on the task of explaining entropy than it actually was. While Ben-Naim, as promised, does a good job of reducing the second law of thermodynamics to “plain common sense”, he makes confusing decisions to include arguments better meant for experts and diatribes that serve nobody. As a result I feel the book, though largely useful, may ill-serve the lay audience for which it is apparently intended, especially as regards the areas where non-scientists are most likely to encounter the concept of entropy.

In my view, the purpose of a popular book on a scientific subject is twofold. First, it should provide readers with enough good science to understand the subject as it appears (if it appears) in their lives. Second, it should provide the lay reader with a framework that allows him to interpret the words of experts. That is, the reader should come away with an understanding of what scientists mean by (in this case) entropy. Thus, popular books on any subject are not a reasonable platform to argue for paradigm shifts. First of all, you’re not talking to your target audience (i.e. experts) when you do this. Second of all, the lay readers that agree with you will now be thinking of the subject in a very different way than most of the scientists they will encounter. So not only do you fail at what you’re intending to do in terms of serving your new paradigm, you also fail at one basic task of the popular science book. The unfortunate thing with Ben-Naim’s book is that it fails at the second task and ends up with mixed results on the first, for no real reason. He could have done just as good a job explaining entropy without introducing the new paradigm at all.

Entropy, despite its importance, is not a topic that lay people encounter very often. The transfer of heat from warmer to cooler bodies is a common example, as is the diffusion of dye in a liquid, or the mixing of two liquids or gases. Ben-Naim does an excellent job of explaining the role of entropy in these processes, building up from relatively simple dice games to complex discussions about temperature and gaseous mixtures. However, he does not do any job at all of explaining the role of entropy in reactions. Consequently, he fails to explain how apparent counteractions to entropy occur. A layman reading this book will understand why a gas expands, but not why it was possible to compress it in the first place. Also, Ben-Naim’s approach and focus on mixtures and the like will also leave the reader utterly unprepared to encounter discussions of entropy in connection to the hydrophobic effect. Could the framework here introduced be extended to explain micelle formation and protein folding? I don’t doubt that this is so, but Ben-Naim doesn’t do it, to the detriment of the book and its readers.

What’s Ben-Naim doing with all this space that he’s not using on talking about the role of entropy in chemical reactions? Well, he’s arguing for a view of entropy based on information, specifically defining entropy in terms of “missing information”. Although this position has some merits, this book is an entirely inappropriate place to make the case for it. Why? The most pervasive popular misuse of the second law of thermodynamics is in creationist canards about the thermodynamic impossibility of evolution. These misinterpretations often rest on ideas related to information (as colloquially used) or distortions of information theory. Although Ben-Naim repeatedly states (correctly) that information has a precise scientific meaning, he never graces his readers with it. I fear this leaves them more vulnerable to creationist distortions than before they started reading. That Ben-Naim says little to emphasize the meaning of “closed system” or the other parts of thermodynamics exacerbates the problem. The discussion of information was not strictly necessary to his overall point—his excellent introduction of probability would have sufficed—and it is easily misread and misused. In my opinion, he should have held his tongue here and allowed his book targeted at the academic audience (A Farewell to Entropy: Statistical Thermodynamics Based on Information) to make the case.

Ben-Naim also devotes pages and pages to complaints about other authors’ (Atkins particularly comes in for criticism) presentations of entropy. These sections contain a few good ideas, but on the whole read like petulant complaints about more popular writers. That these pages serve any real purpose at all is debatable; that they weaken Ben-Naim’s case is certain. No matter how much he disagrees with these authors it would be better for him to disregard them and focus on constructing his own case than deconstructing their books. I agree with him that science writers are too eager to portray entropy as mysterious, but clearing up the mystery is sufficient. His detailed rebuttals of their language are unnecessary.

It’s a pity, because Ben-Naim really does pack in some useful and important concepts. Strip away the unnecessary information theory, and his book does an excellent job of reducing the law of entropy to common sense. Entropy Demystified explains what entropy actually means for certain physical systems, and excels at building this picture up from very simple games that anyone can intuitively understand and model. That said, Ben-Naim does not tie entropy into real processes nearly as well as he could, and his insistence on representing entropy in a way that has not yet gained mainstream acceptance may mitigate his readers’ ability to apprehend what scientists are saying about the subject. Moreover, the fact that this alternative presentation is “entropy as missing information” is more likely to perpetuate misunderstandings about entropy (especially with regard to evolution) among the lay audience than to clear those misunderstandings up. As such, I cannot recommend this book, despite its virtues.

Nov 302007
There’s another point, one that I skirted around in my last post, that I feel is worth coming back to briefly. Remember that Paul Davies’ argument asserts that science relies on an assumption, and that therefore science is based on faith. I admitted that I have faith in the assumption, but not the same sort of faith that a person has in a God. What I didn’t address was the unspoken leg of Davies’ argument, namely that operating on an assumption is equivalent to operating on faith. This is not true, and it’s important to highlight this because it shines some light on the difference between science and religion.

Let’s imagine for a moment that we are engaged in a debate on some topic that is neither religious nor scientific. For instance, we are debating whether Hitler’s attack on the U.S.S.R. was a sound strategic move. I say, “Assuming Hitler hadn’t attacked Russia, he would have had more capacity to defend Europe.” You agree to this assumption, for the sake of argument, and we continue the discussion from there. Would you say you have faith in the proposition that Hitler did not attack the U.S.S.R.? Surely you know it to be counterfactual, so you do not even believe it. So assuming a proposition doesn’t necessarily mean you have faith in that proposition.

Of course, this may not be perfectly analogous—after all, the proposition about Hitler is clearly unhistorical. So suppose we were dealing with an uncertain proposition. For instance, two detectives might be attempting to solve a murder with two suspects. One way to go about it would be to assume that one of the suspects is guilty and examine the evidence to see if any of it is inconsistent with that proposition. Again, nobody would agree that the detectives have faith in a particular proposition of guilt as they are reasoning. The assumption is merely a stipulation, a point from which to begin thinking.

All right, so it’s pretty clear that making an assumption doesn’t require an act of faith, not even the modest, empirical kind of faith I was writing about yesterday. Of course, it might seem strange for a scientist to perform experiments on the assumption that the universe can be accurately described by natural laws when he does not in fact believe that it is so. It is important to realize, however, that a scientist’s actual state of belief towards the natural law assumption is irrelevant to the process of science. Science proceeds on the basis of that assumption, and I have faith in that assumption, but I do not design or perform experiments because I have faith in the assumption. Rather, I have faith in the assumption because the results of my research have always proven to be consistent with it. But even if I did not believe the assumption—for instance, if I believe that God occasionally usurps natural laws to make “miracles” occur—I could still perform science, so long as my experiments were predicated on the assumption of universal natural laws.

This is a sticky point, for religious believers and atheist scientists alike. A researcher must stipulate the truthfulness of the natural law assumption to interpret an experiment, but it is not necessary for the researcher to actually believe the natural law assumption is true, just as it is not necessary for our historical debaters to believe that Hitler did not attack the USSR, or our detectives to believe that a given suspect committed the murder. Making an assumption is not an act of belief, or of faith.

This is a significant difference between science and religion. Religious activities depend not only on the assumption of their legitimacy, but also an actual belief or faith in their central propositions. One can conduct meaningful scientific activities without believing the natural law assumption, but one cannot perform meaningful religious activities without believing the religious assumption. One can, of course, go through the motions of ritual without believing, but then the activity ceases to be religious in nature and becomes purely social or political. It is a problem in a religion, perhaps even a mortal sin, to be a hypocrite, but for science, hypocrisy (in the sense of using the natural law assumption without actually believing it) is just a personality quirk.

The only time that faith in the natural law assumption becomes relevant is when we move from the scientific process to the question of truth. Then we can object to Davies’ argument on the grounds that have been exhaustively described by myself and others.

Not that I expect anyone to actually listen. After all, more Americans believe in the Devil than believe in evolution.

Nov 282007
Initially, I didn’t want to make any comment on Paul Davies’ recent NYT column “Taking Science on Faith”. In fact, I didn’t even want to read it. News of its existence came to me through comments on scientific websites, and from these alone I knew that actually reading the damn thing would sadden and anger me. But, I was asked about it at work, and the internet clamor just kept rising, and I decided I might as well give it a read on the off chance that it would contain something interesting. This was a foolish gamble. Davies is a lesser man for having written such garbage, the New York Times is a lesser publication for having printed it, and I am less intelligent for having read it, because now that trash is in my brain. After the manner of Sherlock Holmes, I shall endeavor to forget it at once, but first I want to explain precisely why it is garbage so that you, at least, will have the benefit of the rebuttal.

In a strict sense, this is unnecessary: several blogs have already put up excellent posts knocking down Davies’ arguments. My own commentary is hardly fresh, then, but I don’t really write to impress the internet at large. All the same, there are a number of points that I feel haven’t been made, or haven’t been made clearly or forcefully enough. So I’ll try and handle those.

The foundation of Davies’ argument comes early on in the piece and, I’ll grant, does have a certain appeal. Davies writes “All science proceeds on the assumption that nature is ordered in a rational and intelligible way.” This is almost true, and I think it bears some elaboration. It breaks down to three ideas, which I will take up out of order.

Idea 1: Nature is ordered.

More expansively, one could say that the universe is described by laws. This is an assumption of science, but it’s important to understand that this does not mean determinism is an assumption of science. The quantum universe is probabilistic, not absolute, and though this probabilism matters most on the microscale, events at that level can have profound effects at higher levels. The scientific acceptance of randomness matters later on.

Idea 2: The order of nature is intelligible.

This is also an assumption of science. Obviously, if there were no way to identify the order of nature then there would be no reason to perform experiments.

Idea 3: The order of nature is rational.

I saved this for last because it is where Davies fundamentally goes wrong. In the most limited sense, this may be accurate: scientists resist the idea that two contradictory laws are both true. But this does not seem to be what Davies means. In fact, he’s never very clear on what this means or why it’s important, but he does seem to feel that rationality is at odds with randomness. Yet, as I’ve already pointed out, science can be perfectly comfortable with randomness, even if Paul Davies can’t. He’s not exactly in bad company: Einstein famously felt a similar discomfort with the probabilistic descriptions emerging from quantum mechanics. But the personal predilections of particular researchers do not speak to the necessary assumptions for performing science. To assemble a scientific enterprise one needs not assume anything other than that there is something to learn (idea 1) and that there is a way to learn it (idea 2). Nothing about the nature of what is learned need be assumed. Thus, we can discard idea 3 as a necessary assumption. So that leaves us with with what I’ll call for convenience the ‘natural law assumption‘:

The universe can be described by natural laws, and there exists some method whereby those laws may be learned.

It’s important to remember that the natural laws here aren’t normative, as moral laws or political laws are. A natural law is a codification of empirical observation, not a prescription of outcome. Observation of a phenomenon that violates moral or political laws results in steps being taken to alter the phenomenon, while observation of a phenomenon that violates a natural law results in steps being taken to alter the law.

Davies goes on to say that making this assumption is an act of faith, which is at best misleading, and at worst outright dishonest. I can quite honestly say that I have faith in the natural law assumption, but what I mean by this is essentially the same thing I mean by saying I have faith that my car will start tomorrow, or that I have faith that the ‘pause’ button on my remote will cause the DVD to stop playing temporarily. This relates to a faith in something that is built on repeated success, not something that I preserve for its own sake. If my car fails to start tomorrow morning, I will not continue turning the key indefinitely, my faith in the inevitability of its starting intact. Rather, I will have it towed. Similarly for the remote. If natural laws failed to describe the universe, then I would give up on them, and why not? They’re not helping my goal, which is to understand the universe. In short, my “faith” in the natural law assumption is an empirical expectation that it will be fulfilled.

This attitude would be utterly alien to a believer in a religion. Indeed, almost every religion contains admonishments not to give up on belief in hard times. The power of Job and similar works derives from the strength of a person’s faith in the face of great troubles. The “Faith” of the religious is a metaphysical belief in the existence and intent of a supernatural entity.

Davies treats these meanings as equivalent, or at the very least expects his readers to conflate the two different meanings in this way. Yet Davies is clearly aware of the distinction, as the beginning of the column shows. If he has forgotten it by this point, then he is simply leading himself down the garden path with semantic sloppiness, and dragging us with him. If he remembers, then he’s being dishonest.

Davies then goes on to describe his dissatisfaction with the idea that natural laws arose randomly. I’ve already pointed out that this is a personal problem of his, not a problem generally for science. But Davies is insistent, and points out that we really should be concerned about this because it just so happens that the natural laws were perfectly tuned for life, and it seems unlikely that this would just happen by chance. This is amazing stupidity.

The natural laws of the universe are not tuned perfectly for life, and we should suspect this, if for no other reason, because there is so little life and so much universe that is utterly, relentlessly hostile to it. If some transcendental entity was sitting at the control panel at Creation, with a mission to create a universe in which life would have a really good chance of existing, then he certainly did a terrible job. Vast, cold voids of space, impossibly hot fusion engines, a universe permeated with gamma-ray bursts sufficiently strong to burn a planet’s atmosphere right off… these are not features hospitable to life. In fact, given the natural laws of our universe, life seems so cosmically unlikely that on that basis alone an entire cottage industry of science quacks makes a living arguing that life could only have arisen with the help of an omnipotent God.

“But but but,” Davies and his ilk will argue, “if you tweaked any of the constants just a tiny bit, then life couldn’t exist!” Such a statement is staggeringly unscientific—you couldn’t possibly have any direct evidence for it. I will grant that, as a thought experiment, one might effectively argue that lifeforms such as ourselves might not survive in a universe where the gravitational constant were a little higher, or the vacuum permittivity constant were lower. Yet, to conclude from this that life is impossible is just evidence that you ignored what I said above. The universe we have is incredibly inhospitable to life, and yet here we’ve got a whole damn planet covered in it. Life, even life of our kind, might make its way in even less hospitable environments. And even if it couldn’t, who knows what alternate kinds of life or intelligence might arise in vastly different universes? In such alternative existences, energy itself might be alive, and stars might recite poems to each other. We can say with confidence what existing structures of our universe would be abolished were a particular natural law to change, but how can we predict what new opportunities for life might emerge?

It’s no surprise that we would have a hard time were the physical constants and natural laws of the universe to change. It is, however, idiotic to conclude that this is because the universe was tuned for us. We were tuned for it, because it is within this universe that we came to exist.

Davies then concisely explains why the question of where natural laws come from is not a scientific question, without realizing it. Shoved in there with the multiverse mumbo-jumbo is a brief moment of clarity when he realizes that the problem is turtles all the way down. Any explanation of the origin of natural laws necessarily requires a description of the natural laws governing that origin. Which then necessitates a description of the origin of those natural laws, and the natural laws governing them, and so on and so forth through turtle after turtle until we realize there is no bottom, or we reach the layer of elephants.

Of course, this is not a necessary consequence of assuming the existence of natural laws. Rather, it is a consequence of assuming causality. But quantum mechanics appears to be quite at home with uncaused events, and there is no special reason to believe that natural laws must be caused. Davies seems to believe this, but at this point I hope you are at least a little skeptical of his judgment in the matter.

Davies then concludes that religion and science are both founded on faith. I’ve already pointed out that the truth of this statement relies on the conflation of two totally different meanings of ‘faith’. But even if Davies is correct, this is hardly a catastrophic failing. The world abounds in demonstrations that faith in a benevolent, all-powerful God is ill-placed—the faithful of all religions suffer death, disease, and horrible agony, even in their moments of worship. The wicked are everywhere rewarded, the virtuous everywhere trampled upon, and their prayers go unanswered. Oh sure, the jock on TV thanks God for the opportunity he was given, but what about those other 100 million kids who never made it to the NFL? Didn’t they pray, too? Did God love those boys less than he loved Pacman Jones, or did he just have nothing to do with it?

The natural law assumption, by contrast, has proved to be phenomenally successful. In fact, it may be the single most successful idea in the entire history of mankind. Virtually everything that surrounds you as you read this—the clothes you wear, the treated air you breathe, the chair you sit in, the materials in your building, the computer you are looking at—is the fruit of this amazing idea. Even if we are dealing with equivalent kinds of faith, then it certainly seems you have substantially more reason to place your faith in the existence of natural laws than in the existence of God.

Davies then goes on to make much of the fact that the concept of natural law emerged from the concept of a deity. While this is quite true, it doesn’t say anything essential about science. Science existed before the first codifications of “natural laws” and has advanced substantially since. The clockwork universe of the Enlightenment died with the Heisenberg Uncertainty Principle, and on the theological side, the watchmaker God has faded as well. So Davies is technically correct here, but he’s babbling on about irrelevancies.

Until, that is, he comes to the end of the paragraph and says:

physicists think of their laws as inhabiting an abstract transcendent realm of perfect mathematical relationships.

I certainly hope he does not believe what he is writing here. Natural laws cannot ‘inhabit’ any ‘realm’ because they do not exist. They are not things. The representations of natural laws exist, as patterns of ink on paper, patterns of electrons on magnetic media, patterns of neural connections in human brains. But there is no thing you can point to and say “That is a natural law” any more than there is a thing you can point to and say “That is a ‘That wall is brown'”. Natural laws as we discuss them are ideas without physical existence—they are nothing more than shared descriptions of observations. Natural laws as they appear in nature are just properties of the universe—they are not separate from the matter and energy we presume them to govern. John Wilkins has a really good explication of this reification fallacy.

Once you see the mistake that Davies is making, the next paragraph evaporates, leaving a faintly unpleasant smell. His analogy is not appropriate because whereas religion imparts reality to its God, science does no such thing for its laws. Certainly the laws have no reality apart from the universe (as God supposedly does), and to claim that there is something analogous between the theological relation of God to the universe and the scientific relation of natural laws to the universe is to either completely misunderstand what natural laws are, or to engage in a willful deception.

Davies’ closing to the article tumbles out of his assumptions, and follows them into the same black pit of shame. The whole article is an embarrassment—to Davies, to his “Beyond” institute, and to Arizona State University. What I find most infuriating about it is that I will now be forced to endure endless rehashes of this sloppy, misleading mess at the hands of creationists, flat-earthers, and alterna-quacks. “Science is faith!” they’ll cry, “A scientist said so!” and then I’ll have to remember the conflations and fallacies and patiently explain them, over and over again, until the day I die. So damn you, Paul Davies! Damn you to the abstract transcendent realm of perfect mathematical relationships!

Aug 282007
While reading Jane Stemwedel’s musings on the missing gray zone in animal-research discussions, it occurred to me that when taken as a philosophical position, rather than an emotional appeal, the animal-rights people are really demanding that all bioscience be ended. I don’t mean to make the old slippery-slope argument here; rather, I mean to say that when viewed in the light of cold reason, rather than sloppy anthropomorphism, the demand to eliminate animal suffering boils down to a demand to end bioscience research. Although we biochemists investigate life, our tool is death, and we use it constantly.

My objection to the animal-rights crowd hinges on their attribution of equivalent values to human and animal life, or human and animal pain and suffering. If you are willing to accept degrees, to say that a certain amount of animal suffering is tolerable in order to alleviate human suffering, then I am not arguing directly against you. I run into trouble when the crowd says that no outcome justifies animal research, because this argument implies that no research should be performed at all.

Consider the case of the laboratory mouse. On the one hand, there is an intuitive appeal to the animal-rights argument in their case. “How would you feel,” they might well ask, “if you were locked up in a cage all day and subjected to experiments?” And of course, most of us would not like it at all, but that isn’t relevant because our likes and dislikes are psychological constructs for which it is not clear mice have any equivalent. We’re relatively closely related to mice, and they have behavioral characteristics similar to our own, which leads us to empathize with them, or so it seems. But this is a false empathy; we empathize with the mouse as if it is a human being with human traits and psychology, but this is manifestly not the case. The human mother, even a fecund one, mourns over her dead infant; the mouse mother eats hers. A human behaving as the mouse does would be called depraved, but we do not call the mouse depraved because we recognize that it does not think or feel as a human does. The similarity of responses to stressful stimuli owes more to a coincidence of behavioral evolution than matched psyches. Arguments against research on the basis of perceived empathy are therefore largely empty.

Given that anthropomorphic empathy is a dead end, the next line on animals is that they have intrinsic rights, especially that no animal individual should be used in research that does not help that individual. This implies something else, namely that an animal must consent to be researched upon. As it is impossible for the animal to give consent, we must imagine conditions under which it might give consent and stipulate those as a precondition to research. But on what basis to we attribute these rights? What virtue of a living creature endows it with the right to self-determination?

The most natural response to this question is that a creature gains the right for self-determination by having the ability to weigh the consequences of its actions and choose wisely. Indeed, this is the attribution by which we typically operate, and why we allow children and the mentally infirm only limited degrees of self-determination. However, this is clearly not the attribution the animal-rights activists are using — a mouse does not even have the ability to conceive of the possible consequences of research, much less weigh them. For the animal-rights activist, the simple fact of being alive gives rise to the right to self-determination.

But why then should we stop with mice? Untold millions of drosophila have been bred and destroyed in the name of genetic research, not to mention everything that’s been done with nematodes. Sure, it’s more difficult to relate their behavior to ours, but these creatures live and die in captivity, and exhibit stress responses during certain experiments. What property of a mouse means that it has self-determination and the flies and worms don’t?

And we’re still being biased even if we let them in. After all, what’s so special about multicellular organisms? Why should they be the only ones with a right to self-determination? If all it takes to require consent is being alive, then E. coli, of which I have personally raised and destroyed billions in the pursuit of NMR dynamics data, qualify too. In fact, their tale is really gruesome when you think about it. They’re subjected to extreme temperatures and such rapid changes in them that they ingest large chunks of foreign DNA (themselves the product of enormous bacterial slaughter). I feed them a starvation diet loaded with strange chemicals, get them so high on IPTG they start to produce one protein almost exclusively, and then once they’re done I murder them by repeatedly freezing and thawing them before I shatter their bodies with sound waves or crush them to death.

So there we are — bacteria have rights, too, at least if you accept the reasoning of the most extreme (philosophically) animal rights supporters. I could go on to make a case for cultured cell lines as an independent life form, but really I’ve already gutted molecular biology, any cell biology involving DNA manipulation or foreign proteins (think how many bacteria died to bring you that Pfu turbo), and all of biochemistry and structural biology. If we grant that animals have the right to self-determination, none of the biosciences can possibly survive the scrutiny. That’s what animal-rights activists are demanding, whether they know it or not.