A little timeline on the second law argument, as applied to evolution (see my BioComplexity article for more detail):
1. Scientists observed that the temperature distribution in an object always tends toward more uniformity, as heat flows from hot to cold regions, and defined a quantity called “entropy” to measure this randomness, or uniformity. The first formulations of the second law of thermodynamics stated that thermal “entropy” must always increase, or at least remain constant, in an isolated system.
2. It was realized that the reason temperature tends to become more uniformly (more randomly) distributed was purely statistical: a uniform distribution is more probable than a highly non-uniform distribution. Exactly the same argument, and even the same equations, apply to the distribution of anything else, such as carbon, that diffuses. In fact, one can define a “carbon entropy” in the same way as thermal entropy, and show, using the same equations, that carbon entropy must always increase, or remain constant, in an isolated system.
3. Since the reason thermal and carbon (and chromium, etc) distributions become more uniform in an isolated system is that the laws of probability favor more random, more probable, states, some scientists generalized the second law with statements such as “In an isolated system, the direction of spontaneous change is from order to disorder.” For these more general statements, “entropy” was simply used as a synonym for “disorder” and many physics texts gave examples of irreversible “entropy” increases that had nothing to do with heat conduction or diffusion, such as tornados turning towns into rubble, explosions destroying buildings, or fires turning books into ashes.
4. Some people then said, what could be a more spectacular increase in order, or decrease in “entropy”, than civilizations arising on a once-barren planet, and said the claim that entirely natural causes could turn dust into computers was contrary to these more general statements of the second law.
5. The counter-argument offered by evolutionists was always: but the second law only says order cannot increase in an isolated system, and the Earth receives energy from the sun, so computers arising from dust here does not violate the second law, as long as the increases in order here are “compensated” by decreases outside our open system.
6. In several publications, beginning in a 2001 Mathematical Intelligencer letter, I showed that while it is true that thermal entropy can decrease in an open system, it cannot decrease faster than it is exported through the boundary, or stated in terms of “thermal order” (= the negative of thermal entropy), in an open system thermal order cannot increase faster than it is imported through the boundary, and likewise “carbon order” cannot increase faster than it is imported through the boundary, etc. (Though I was not the first to notice this, it seemed to be a very little known fact.) Then I argued that the more general statements of the second law could also be generalized to open systems, using the tautology that “if an increase in order is extremely improbable when a system is isolated, it is still extremely improbable when the system is open, unless something is entering which makes it not extremely improbable.” Thus the fact that order can increase in an open system does not mean that computers can appear on a barren planet as long as the planet receives solar energy, something must be entering which makes the appearance of computers not extremely improbable, for example: computers.
7. I’m sure that physics texts are still being written which apply the second law to tornados and explosions and fires, and still say evolution does not violate these more general statements of the second law because they only apply to isolated systems. But I have found that after reading my writings on the second law (for example, my withdrawn-at-the-last-minute Applied Mathematics Letters article) or my videos (see below) no one wants to talk about isolated and open systems, they ALL now say, the second law of thermodynamics should only be applied to thermodynamics, it is only about heat. “Entropy” never meant anything other than thermal entropy, and even when physics textbooks apply the second law to more general situations, they are really only talking about thermal entropy. Whether the second law still applies to carbon entropy, for example, where the equations are exactly the same, is not clear.
8. Of course you can still argue that the “second law of thermodynamics” should never have been generalized (by physics textbook writers; creationists were not the first to generalize it!) and so it has no relevance to evolution. But there is obviously SOME law of Nature that prevents tornados from turning rubble into houses and cars, and the same law prevents computers from arising on barren planets through unintelligent causes alone. And if it is not a generalization of the second law of thermodynamics, it is a law of Nature very closely related to the second law!
Note added later: as clearly stated in the BioComplexity article, the statements about “X-entropy”, where X = heat, carbon, chromium,…, in an isolated or open system, are assuming nothing is going on except diffusion, in which case they illustrate nicely the common sense conclusion (tautology, actually) that “if an increase in order is extremely improbable when a system is isolated, it is still extremely improbable when the system is open, unless something is entering which makes it not extremely improbable.” Thus just showing that the statements about X-entropy are not always valid in more general situations does not negate the general, common sense, conclusion, and allow you to argue that just because the Earth is an open system, civilizations can arise from dust here without violating the second law (or at least the fundamental natural principle behind the second law). At some point you are going to have to argue that energy from the sun makes the spontaneous rearrangement of atoms into computers and spaceships and iPhones not astronomically improbable, all the popular easy ways to avoid the obvious conclusion are now gone. (see Why Evolution is Different, excerpted—and somewhat updated—from Chapter 5 of my Discovery Institute Press book. )