Since this is a tiresome canard, I shall refer to a rebuttal written by a Science Writer that goes by the pseudonym Calilasseia who has this to say (forgive the writing style, he is British, and slightly miffed at having to drag up such an inane argument) (Also, this large block of text is reproduced with permission at any location on the internet, as noted originally on the cited web page):
[27] Tiresome canards about evolution and the laws of thermodynamics.
And how tiresome these canards are. Not least because they've been debunked in the past, even without reference to relevant scientific literature, by people who pay attention to the scientific basics. Once the relevant scientific literature is consulted, these canards become visibly asinine.
I'll deal with the Second Law of Thermodynamics to start with, because that one is a creationist favourite, though when creationists parrot this specious nonsense, they merely demonstrate that they know nothing about the relevant physics, and certainly never paid attention to the actual words of Rudolf Clausius, who erected the Laws of Thermodynamics, and who was rigorous when doing so. Therefore, let us see what Clausius actually stated, shall we?
Rudolf Clausius erects this statement of the Second Law of Thermodynamics:
In an isolated system, a process can occur only if it increases the total entropy of the system.
Now Clausius defined rigorously what was meant by three different classes of thermodynamic system, and in his work, specified explicitly that the operation of the laws of thermodynamics differed subtly in each instance. The three classes of system Clausius defined were as follows:
[27a] An isolated system is a system that engages in no exchanges of energy or matter with the surroundings;
[27b] A closed system is a system that engages in exchanges of energy with the surroundings, but does not engage in exchange of matter with the surroundings;
[27c] An open system is a system that engages in exchanges of both matter and energy with the surroundings.
Now, Clausius' statement above clearly and explicitly refers to isolated systems, which, thus far, have been found to be an idealised abstraction, as no truly isolated system has ever been found. Indeed, in order to create even an approximation to an isolated system in order to perform precise calorimetric measurements, physicists have to resort to considerable ingenuity in order to minimise energy exchanges with the surroundings, particularly given the pervasive nature of heat. Even then, they cannot make the system completely isolated, because they need to have some means of obtaining measurement data from that system, which has to be conveyed to the surroundings, and this process itself requires energy. Physicists can only construct a closed system, in which, courtesy of much ingenuity, energy exchanges with the surroundings are minimised and precisely controlled, and to achieve this result in a manner that satisfies the demands of precise work is time consuming, expensive and requires a lot of prior analysis of possible sources of energy exchange that need to be minimised and controlled.
However, the Earth is manifestly an open system. It is in receipt not only of large amounts of energy from outside (here's a hint: see that big yellow thing in the sky?) but is also in receipt of about 1,000 tons of matter per year in the form of particles of meteoritic origin from outer space. Some of these 'particles' are, on occasions, large enough to leave craters in the ground, such as that nice large one in Arizona. That particular dent in the Earth's surface is 1,200 metres in diameter, 170 metres deep, and has a ridge of material around the edges that rises 45 metres above the immediate landscape, and was excavated when a meteorite impacted the Earth's surface, generating a blast equivalent to a 20 megaton nuclear bomb. Hardly a characteristic of an isolated system.
Indeed, physicists have known for a long time, that if a particular system is a net recipient of energy from outside, then that energy can be harnessed within that system to perform useful work. Which is precisely what living organisms do. Indeed, they only harness a small fraction of the available incoming energy, yet this is sufficient to power the entire diversity of the biosphere, and the development of organisms of increasing sophistication over time. Scientists have published numerous papers (twelve of which are known to me, and this is an incomplete inventory of the extant literature) in which calculations have been performed demonstrating that the utilisation of energy by the biosphere, and by evolution, is orders of magnitude too small to violate thermodynamic concerns. Relevant papers in question being:
Entropy And Evolution by Daniel F. Styer, American Journal of Physics, 78(11): 1031-1033 (November 2008) DOI: 10.1119/1.2973046
Natural Selection As A Physical Principle by Alfred J. Lotka, Proceedings of the National Academy of Sciences of the USA, 8: 151-154 (1922) full paper downloadable from here
Evolution Of Biological Complexity by Christoph Adami, Charles Ofria and Travis C. Collier, Proceedings of the National Academy of Sciences of the USA, 97(9): 4463-4468 (25th April 2000) Full paper downloadable from here
Order From Disorder: The Thermodynamics Of Complexity In Biology by Eric D. Schneider and James J. Kay, in Michael P. Murphy, Luke A.J. O'Neill (ed), What is Life: The Next Fifty Years. Reflections on the Future of Biology, Cambridge University Press, pp. 161-172 Full paper downloadable from here
Natural Selection For Least Action by Ville R. I. Kaila and Arto Annila, Proceedings of the Royal Society of London Part A, 464: 3055-3070 (22nd July 2008) Full paper downloadable from here
Evolution And The Second Law Of Thermodynamics by Emory F. Bunn, arXiv.org, 0903.4603v1 (26th March 2009) Download full paper from here
All of these peer reviewed papers establish, courtesy of rigorous empirical and theoretical work, that evolution is perfectly consistent with the Second Law of Thermodynamics. I cover several of these in detail in this post, and it should be noted here that the notion that evolution was purportedly in "violation" of the Second Law of Thermodynamics was rejected in a paper written in 1922, which means that creationists who erect this canard are ignorant of scientific literature published over eighty years ago.
While covering this topic, it's also necessary to deal with the canard that entropy equals 'disorder'. This is a non-rigorous view of entropy that scientists engaged in precise work discarded some time ago. Not least because there are documented examples of systems that have a precisely calculated entropy increase after spontaneously self-organising into well-defined structures. Phospholipids are the classic example of such a system - a suspension of phospholipids in aqueous solution will spontaneously self-assemble into structures such as micelles, bilayer sheets and liposomes upon receiving an energy input consisting of nothing more than gentle agitation. In other words, just shake the bottle. Moreover, the following scientific paper discusses in some detail the fact that entropy can increase when a system becomes more ordered, a paper that was published in 1998, and hence, has been in circulation for over a decade now:
Gentle Force Of Entropy Bridges Disciplines by David Kestenbaum, Science, 279: 1849 (20th March 1998)
Kestenbaum, 1998 wrote:Normally, entropy is a force of disorder rather than organization. But physicists have recently explored the ways in which an increase in entropy in one part of a system can force another part into greater order. The findings have rekindled speculation that living cells might take advantage of this little-known trick of physics.
Entropy, as rigorously defined, has units of Joules per Kelvin, and is therefore a function of energy versus thermodynamic temperature. The simple fact of the matter is that if the thermodynamic temperature increases, then the total entropy of a given system decreases if no additional energy was input into the system in order to provide the increase in thermodynamic temperature. Star formation is an excellent example of this, because the thermodynamic temperature at the core of a gas cloud increases as the cloud coalesces under gravity. All that is required to increase the core temperature to the point where nuclear fusion is initiated is sufficient mass. No external energy is added to the system. Consequently, the entropy at the core decreases due to the influence of gravity driving up the thermodynamic temperature. Yet the highly compressed gas in the core is hardly "ordered".
STOP PRESS: as if to reinforce this point, my attention has just been drawn to this scientific paper:
Disordered, Quasicrystalline And Crystalline Phases Of Densely Packed Tetrahedra by Amir Haji-Akbari, Michael Engel, Aaron S. Keys, Xiaoyu Zheng, Rolfe G. Petschek, Peter Palffy-Muhoray and Sharon C. Glotzer, Nature, 462: 773-777 (10th December 2009)
The abstract is suitably informative here:
Haji-Akbari, 2009 wrote: All hard, convex shapes are conjectured by Ulam to pack more densely than spheres1, which have a maximum packing fraction of φ = π/∫18 ≈ 0.7405. Simple lattice packings of many shapes easily surpass this packing fraction2, 3. For regular tetrahedra, this conjecture was shown to be true only very recently; an ordered arrangement was obtained via geometric construction with φ = 0.7786 (ref. 4), which was subsequently compressed numerically to φ = 0.7820 (ref. 5), while compressing with different initial conditions led to φ = 0.8230 (ref. 6). Here we show that tetrahedra pack even more densely, and in a completely unexpected way. Following a conceptually different approach, using thermodynamic computer simulations that allow the system to evolve naturally towards high-density states, we observe that a fluid of hard tetrahedra undergoes a first-order phase transition to a dodecagonal quasicrystal7, 8, 9, 10, which can be compressed to a packing fraction of φ = 0.8324. By compressing a crystalline approximant of the quasicrystal, the highest packing fraction we obtain is φ = 0.8503. If quasicrystal formation is suppressed, the system remains disordered, jams and compresses to φ = 0.7858. Jamming and crystallization are both preceded by an entropy-driven transition from a simple fluid of independent tetrahedra to a complex fluid characterized by tetrahedra arranged in densely packed local motifs of pentagonal dipyramids that form a percolating network at the transition. The quasicrystal that we report represents the first example of a quasicrystal formed from hard or non-spherical particles. Our results demonstrate that particle shape and entropy can produce highly complex, ordered structures.
So as if the Kestenbaum paper on entropy driving ordered systems, and the empirical evidence from phospholipids were not enough, we now have this. Consequently, the message to creationists is simple: don't bother wasting your time posting the "evolution violates the Second Law of Thermodynamics" canard, because it is now well and truly busted.
Some creationists, however, erect a related, and in some respects, even more asinine canard, that evolution somehow violates the First Law of Thermodynamics. Guess who provided us with rigorous statements about this law? That's right, Rudolf Clausius again. Let's see what he actually stated with respect to this, shall we? The Clausius formulation of the First Law of Thermodynamics is this:
The increase in the internal energy of a system is equal to the amount of energy input into the system via heating, minus the energy lost as a result of the work done by the system upon its surroundings.
The mathematical expression of which is:
dU = δQ - δW
If the process is reversible, then this can be recast in terms of exact differentials by noting that δW is equal to PdV, where P is the internal pressure, and V the volume occupied, and that δQ is equal to TdS, where T is the thermodynamic temperature and S is the entropy of the system. Therefore this becomes dU = TdS - PdV.
Oh look. Clausius explicitly framed the First Law of Thermodynamics in terms of energy exchanges within a system. He did NOT assume constancy thereof. Indeed, the rigorous framing of the First Law of Thermodynamics explicitly takes into account the possibility of a system being a recipient of energy that can be used to perform useful work. Therefore creationist canards erected about the First Law of Thermodynamics are null and void for the same reasons as those erected about the Second Law of Thermodynamics - said canards not only ignore completely Clausius' original and rigorous formulations of those laws, and ignore completely that Clausius framed his formulations around energy exchanges between a system and its surroundings, but rely upon outright misrepresentations of those laws.
Indeed, Clausius had energy exchanges in mind with respect to the Second Law of Thermodynamics as well, which is why the statement on entropy was framed in terms of an isolated system, which engages in no such exchanges with the surroundings. When energy exchanges are taking place, the operation of the Second law of Thermodynamics within such systems is subtly different.
I also wanted to add a bit about your silly assertion that it's only a theory... Trust me, it's a fact, and is rejection of reality on a wholesecale level to assert anything but. The mechanisms by which evolution happen are also quite well understood, but there are fine points that are still being worked out. Evolution is a theory in the same way gravity is a theory, only that we actually know a great deal more about evolution than we do gravity.
THAT is a logical process that seems to escape people who deny evolution. Again, 
