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.