Criticism of evolution

Overview
This page relates to general criticisms of evolution that are seemingly independent of comparison to any alternate theory.

Mathematical
The evolutionary process is not a long series of random coin-tosses somehow resulting in the creation of all Earth's organisms after enough lucky hits, but rather an ongoing competition for survival. The organisms which are best at making more of themselves get to do so, over and over, for however many millions of years it takes.
 * Criticism: The odds of arriving at the exact genetic code of a viable organism by sheer chance are so vanishingly small that it cannot possibly have happened that way.
 * Details: Even Mycoplasma genitalium, the organism with the shortest-known DNA sequence, has approximately 580,000 Base pairs. Each base pair can be one of 4 possible configurations (A-T, C-G, G-C, or T-A), leading to a total of 4 possible genetic codes to try before arriving at a working Mycoplasma genitalium. 4 works out to a number with about 116 thousand zeros in it. Therefore the odds of life appearing at random, as the evolutionists claim, is about one in ten to the 116th power – or so close to zero that if you you rolled the "dice" one million times a second for 4.5 billion years (the evolutionarily-claimed age of the earth) you would bring the odds of creating the Mycoplasma genome all the way up to – wait for it! – 1 in 10!
 * Notes: This is basically an argument from incredulity which cues the listener to think "therefore, organisms must have been intelligently designed" without further examination, even though there are sound reasons to think otherwise. It is also a straw man argument, as it seriously misrepresents the evolutionary process.
 * Response:

An example: In computing, there is a technique known as genetic algorithms. A set of programs is generated randomly; each program is evaluated for how well it solves the "target problem". Programs that pass the "test" (to oversimplify the process a bit) have copies made, with random changes (mutations) made to most of the copies; programs that fail the "test" are not copied, and die out. This process eventually results in something that's not only workable, but is often better than anything anyone had been able to "intelligently design" by hand.

If you took those programs and tried to arrive at them by random coin-tosses the probability of arriving at something that would even run, much less work, much less work well, would be so close to zero that it might as well be zero. The filtering process of natural selection can, over time, build something enormously complex and "designed"-looking – and this is only simulations running rather slowly in a computer over days or weeks, not millions of years.

Semantic

 * Criticism: Evolution is just a theory.
 * Response: This attempts to confuse the scientific usage of the word "theory" with its less formal usage. Just as there is a "theory of orbital mechanics" which explains and accurately predicts the positions of the planets in the past and future, there is also a "theory of evolution" which explains how an observed phenomenon (evolution) resulted in countless aspects of the living world we see today, correctly predicting many details not known in advance and being completely in agreement with observations from other areas of science. There may be no other "theory" that is more widely accepted, despite a great deal of examination from inside and outside the scientific community.

Thermodynamics

 * Criticism: The second law of thermodynamics clearly states that disorganization always increases. So how could life arise and increase in complexity without violating the laws of physics?
 * Answer:

Primary answer: That law states that disorganization (entropy) increases within a closed system. The Earth is not a closed system; it receives vast amounts of energy from the sun. If the sun is included in the system, then that system is closed for all practical purposes (the amount of energy received from outside the solar system is miniscule), but the law still holds because the sun's entropy is constantly increasing in proportion to the energy it gives out (i.e. vastly more than the decrease in entropy on Earth).

Additional information:
 * 1) "Order from disorder is common in nonliving systems, too. Snowflakes, sand dunes, tornadoes, stalactites, graded river beds, and lightning are just a few examples of order coming from disorder in nature; none require an intelligent program to achieve that order. In any nontrivial system with lots of energy flowing through it, you are almost certain to find order arising somewhere in the system. If order from disorder is supposed to violate the 2nd law of thermodynamics, why is it ubiquitous in nature?"
 * 2) "Entropy" is not always equivalent to "disorder", though for the sake of this discussion they are probably close enough. A fully-entropized universe could seem quite "orderly", however: everything at the same temperature, no inconvenient lumps or clusters of molecules to disrupt things, etc.