I think some of the scientists responding to the True Origins site give good evidence against the arguments made regarding the second law of thermodynamics. If you 'close' the system by bringing the external source of energy into it (i.e, the sun), there is still no real problem because the second law deals with total entropy, not entropy in isolated instances. If a being/organism/group of molecules arranges itself in a way that counters our intuition regarding entropy, it is only because it used energy to do so. That energy is released as heat and dissipates outward in accordance to the laws of thermodynamics. Everyday, energy is trapped and used by complex and simple things to create order out of chaos. These things produce heat and the so called closed system of the Earth and its source of energy are not violating the laws of thermodynamics because the total level of entropy has not decreased.
As for your arguments that plate tectonics doesn't explain things, I'd like to see more. Having seen models that explain the creation of Japan, the Kurile Islands, and more recently Hawai'i from the hot spot currently under the Big Island and having compared the drift and the dating of the seabed to show a pretty much perfect scientific match up of the events, as well as countless other examples of evidence for plate tectonics, It'll take a lot to convince me that the theory is incorrect. Everything I've seen, from road cuts in the Green Mountains to the type of soil found on the Himalayas, suggests that the plate tectonic theory is correct.
As far as speciation goes, the very fact that species are vaguely bounded and that it's hard to draw sharp dividing lines sometimes is evidence that supports the idea of evolution.
Rac
