The Politically Incorrect Guide to Science

I was in a bookstore today and came across the Politically Incorrect Guide to Science. Anyway, it had a section on "Darwinism" and I thought I'd address that section, so here goes:

p.202 Offers a critique of Science's methodology of Naturalism, as "No Miracles Allowed". They say that if you would never accept a miracle no matter what, of course you're going to accept evolution. Well, I'm here to correct this. The reason Science doesn't allow miracles is because you could prove practically anything if you were allowed to include unobserved supernatural phenomena as proof. Of course, science has the option of simply saying "We don't know"; and if creationism was true, I would expect that all living forms would have arisen all of a sudden by some unknown force, and this would be excellent evidecne for creation. Unfortunately, that isn't what we see. Dinosaurs didn't live with man, catfish didn't live with trilobites, and daffodils weren't around in Triassic Period.

p.204 Claims that while we do see some intermediates, we cannot possibly prove that one form is really ancestral to another. This is certainly true, but let me say this: When we find mostly fish in the Devonian Strata, and in the next Strata we find amphibians, and in between these forms is a fish who had strong limbs that could enable it to move on land, it makes you think that one of these basic forms gave rise to another over time.
"Tiktaalik" and "Panderichthys" show this transition.

p.207 "Natural Selection is a Truism"
Yes, this page the old misunderstanding that the fittest are so because they survive, and they survive because they are the fittest. Allow me to clarify: Those born with traits most favorable to survival will, on average, leave behind more offspring than those with less favorable traits. There are shifts in gene frequencies caused by this: A new mutation can become prevelant in a population due to natural selection at work.

p.216 The Evolutionist's Challenge
Colin Patterson is quoted as asking, "Can you tell me... anything about evolution that you know is true?"
I would like to answer this challenge. I know that we share a common ancestor with chimps. I know this because we have viruses in our genome that are in the exact same places in the chromosome as the chimps. I know that these viruses are inserted into the genome randomly, and such a thing could not happen by chance: Chimps and humans have a common ancestor who had these viri and that is why a virus which inserts itself at random is found in the same place in our genomes.
http://www.talkorigins.org/faqs/comdesc/section4.html#retroviruses

However, Talk Origins has an article up about Creationists frequently misquoting Patterson, and I wouldn't be surprised if this was the case here:
http://www.talkorigins.org/faqs/patterson.html

p.222 Makes the case that bats arose suddenly. They don't seem to be aware of the fact that a fragile animal like a bat wouldn't fossilize well, or that forests and caves aren't the best enviroments for fossilization. This reminds me of the old time creationist argument that their were no pre-whale fossils. Michael Behe made this claim once, and a year later one was discovered. After that, four more were discovered. It turns out that once the first one was found, paleontologists then knew where they should look, and of course they found even more "Missing links" once they began digging. Perhaps a pre-bat fossil will be discovered one day in a remote forest in Africa, and maybe even a good 3 fossil sequence will be uncovered. Anyway, it is very foolish to make such an assertion like he has made; since fossilization for bats would not only be extraordinarily rare, but also the fact that bats may have evolved in one fairly small area, so in this case absence of evidence does not equal evidence of absence.

p.226 Drags up the old tired "Lies in the Textbooks" argument about Haeckel's embryos. My opinion is that these drawings should've never been in the textbooks, but the idea that this is some sort of conspiracy and that the main evidence for evolution is false is flat out wrong. All vertebrate embryos have similarites, such as the pharyngeal pouches, and so the basic argument Haeckel was making is still correct. Here are some photos.

They also bring up another tired old case: The Peppered Moths.
It must be stressed that this is by far not the only example of Natural Selection that exists. Here are several more:
http://www.msu.edu/~sharrowr/naturalselection.html
http://www.gate.net/~rwms/EvoMutations.html

p.229-230 Darwin's Finches
This blog is now becoming very long, so I will spare you explaining this and just live you with this link.

I would also like to comment that it is amazing that this book would bother quoting Jonathan Wells, who has been shown deceptive on more than one occasion:
http://www.ncseweb.org/icons/index.htm
http://ib.berkeley.edu/courses/ib160/padian.html.old