The trouble with the transitional evidence argument is the fact that the fossil record is absolutely minute. Virtually no animals actually survive in the fossil record so to expect to find this complete picture is impossible. That said there are now a great variety of transitional fossils that have been discovered.

Thermodynamic argument is also not relevant. One the world is not a closed system (the sun provides energy etc) and also (perceived) order will always arise in a complex system (take snowflakes, sand dunes etc). Perceived order and disorder arise in all areas of existence without any involvement from anything.