Here are a few comments on the section that attempts to refute evolution.
Myth 1. Mutations provide the raw materials needed to create new species.
Mutant fruit flies, though malformed, are still fruit fliesThis is a stupid semantic argument. Does calling them fruit flies make them the same species? Suppose I choose to call one of these differently looking organisms something else, like "Østman fly", then have we learned anything at all, or are we just playing a semantic game?
The Drosophila fruit flies (there are other fruit flies, btw), such as the famous Drosophila melanogaster, are species members of the genus Drosophila. Thus, if we observe speciation (which we have) within Drosophila, it would be most appropriate to classify that new species within the same genus, thereby still making it a fruit fly. For actual, observed speciation in Drosophila, see this article in the TalkOrigins Archive (e.g., 5.3.5 Sympatric Speciation in Drosophila melanogaster).
Are Great Danes and Chihuahuas the same species? They are still dogs, right? But no matter what we do, we can always just say "they are still dogs". The point is that in a relative short period of time (insanely short, actually), both flies and dogs have evolved enough variation to argue that we have observed speciation. Just imagine what could happen to them if the different variants or flies and dogs were separated and allowed to evolve independently for another 100,000 years or more. If 200 years of changes in dogs can produce such differently looking dogs, imagine what 500 times more of that could produce.
If you can't imagine, let me do it for you: Suppose you had been living in Australia all your life, and suppose no dogs had been seen there for as long as you had lived. Then one day you have the chance to sail to sea with some friends in on a large raft (this is clearly after our present civilization has collapsed), and after getting into a storm, you end up somewhere in Indonesia. There you find two different species of four-legged furry carnivores. One is about a foot in length with really long hair, and the other is tall enough to lick your face without standing on its hind legs. They eat different things, live apart from each other, and do not mate whenever they come into contact with each other. You have absolutely no reason to think that they are the same species, but just to be sure you forcefully mate them with each other, but this never amounts to anything, as they are just too different genetically to impregnate each other, just like humans and chimps. They are different species. However, what you don't know is that only about 115,000 years before they both descended from the same species of wolves.
Mutations can introduce changes in plants—such as this mutant with large flowers—but only within limitsHow do they know that it can only produce changes within limits? That is an unverified claim that at most rests on the shallow observation that "plants are still plants". In fact, speciation has been observed numerous times in plants. The "only within limits" argument is pulled out of a creationist's hat. The reason why we observe that evolution only produces new species "within limits" is that the time we are here to observe these events is limited. We simply do not expect that a dog or a hibiscus evolves into something that we would never recognize as dog or hibiscus in our comparatively short lifespans. Mechanistically there is absolutely nothing to prevent organisms to evolve beyond their "kind", except in the minds of humans. The only border between microevolution and macroevolution is time, which is what we as humans do not have enough of.
So, can mutations cause one species to evolve into a completely new kind of creature? The evidence answers no! Lönnig’s research has led him to the conclusion that “properly defined species have real boundaries that cannot be abolished or transgressed by accidental mutations.”
Consider the implications of the above facts. If highly trained scientists are unable to produce new species by artificially inducing and selecting favorable mutations, is it likely that an unintelligent process would do a better job? If research shows that mutations cannot transform an original species into an entirely new one, then how, exactly, was macroevolution supposed to have taken place?Lönnig is saying this without any evidence whatsoever - contrary to evidence, actually. The reason why he is saying it simply that creationists do not want evolution to work because it contradicts the Biblical account of creation. The real lesson to take from the quote above is that the unintelligent processes are actually better at producing new species than humans. Neglecting those processes is not learning, but ignorance.
Myth 2. Natural selection led to the creation of new species.
Indeed, Darwin’s finches are not becoming “anything new.” They are still finches.And you are still using the same fallacious semantic argument. The point is that natural selection can drive organisms in different directions, and with sustained environmentally driven divergence they can become different species. So in the case of the finches, that selection pressure reversed back, but this again ignores that these processes can take a long time. However, they don't always. One group of a lizard in Crotia, Podarcis sicula, underwent amazing changes in just 30 generations on an isolated island, adapting to a new environment (i.e., different selective pressure). More examples of speciation.
Myth 3. The fossil record documents macroevolutionary changes.
To date, scientists worldwide have unearthed and cataloged some 200 million large fossils and billions of small fossils. Many researchers agree that this vast and detailed record shows that all the major groups of animals appeared suddenly and remained virtually unchanged, with many species disappearing as suddenly as they arrived.Eeerh, no... Not very many researchers agree that the fossil record shows that all the major clades appeared suddenly. The Cambrian explosion took 70-80 million years! It may well be that species sometimes do change abruptly on geological time-scales, but the more fossils are analyzed, the clearer it becomes that evolution is a gradual process.
Many scientists refuse even to consider the possibility of an intelligent Designer because, as Lewontin writes, “we cannot allow a Divine Foot in the door.”Lewontin can speak for himself. There are many scientists who can consider the possibility of a designer, myself included, but there is just no evidence for it. None. It is the difference between a conclusion from the evidence vs. a foregone conclusion that comes from a book that some people cannot allow being wrong.
In this regard, sociologist Rodney Stark is quoted in Scientific American as saying: “There’s been 200 years of marketing that if you want to be a scientific person you’ve got to keep your mind free of the fetters of religion.” He further notes that in research universities, “the religious people keep their mouths shut.”No, the religious do not keep their mouthes shut. The religious do great science, but they do not mix science and religion, because religion has no say in the matter. Ask Kenneth Miller.
Really, belief in evolution is an act of “faith.”Really, it isn't. Belief in evolution is based solely on the available evidence. Nothing more. Empty your mind of any preconceived notion about the natural world, and just look at the evidence, and the best minds have nearly unanimously come to the conclusion that life evolved. Life appeared and evolves by natural processes, and there is no need to hypothesize that any intelligent being ever interfered. Even scientists who are religious believe in evolution (of course). Just take a look at the Clergy Letter Project.
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I know, I know, I know that the reason creationists can't allow themselves to accept evolution is that it directly contradicts what scripture teaches about our origins. But you cannot refute evolutionary theory if you do not understand it. You cannot refute evolutionary theory by quote-mining scientists. Evolutionary theory is one of the very best supported scientific theories - comparable to the theory of relativity - based on fossil evidence, field observations, laboratory experiments, computer experiments, and a thorough theoretical understanding. And the evidence keeps coming in with new scientific papers published every week. A person can either read scripture and believe it is the infallible word of God, or they can join the rest of the growing amount of people who understand that religion has no place in science.