The scientific evidence for evolution is a fascinating topic, from Darwin and others' researches in the 19th century to 20th and 21st century discoveries. Here's a brief summary:
What is evolution in the first place? When an animal such as a horse, whale, dog, chicken, shark or beetle is born (or hatched, as the case may be) it becomes a member of one more generation in a long sequence of generations reaching back into the far distant past. What did those ancestors of long-ago generations look like? How are the different living things you see around you related?
Take the example of the horse or whale or other mammal. The first fossil evidence of mammals is from the Triassic Period, when the reptiles still ruled. The early mammals were small (often described by paleontologists as "shrew-like" or "mouse-like" animals) and certainly far different from the horses, whales, elephants and other mammals we see today. So we have evolutionary change over many generations. The most important evidence for evolution is the simplest: go from point A, an ancestor, to point B, a creature living today of much different form than that ancestor.
What do Creationists think happened to get from point A to point B? Millions and millions of miracles, over millions and millions of years, creating new forms of life in the precise order that matches the fossil record and the DNA evolutionary tree? Why weren't whales created at the same time as fish? Surely if they were created ex nihilo, it would be strange to create all those land mammals first, then create the forms with vestigial limbs, then finally the fully aquatic forms . . . exactly in the order of their evolution.
There is more evidence for evolution in the simple fact that we see it happening all the time, all around us. It seems unlikely that God would use miracles to create new species in the distant past, but nowadays allow species to evolve naturally, not bothering with miracles anymore. For examples, we have:
Do a web search on "examples of observed speciation" to find more examples, if you like.
Then there is the distribution of life forms on Earth. Of course, one would expect polar bears and penguins in cold climates, camels and cacti in hot climates. But why do we find penguins only in Antarctica and other regions in the southern hemisphere, but not in the north? Why should there be no camels in the deserts of North America? Alfred Russell Wallace typically gets second billing to Darwin, because of the fame of Origin of Species, but he is justly famous in his own right. Among other things, he studied the geographic ranges that species inhabited. The Creationist idea that different species were created especially for particular climates and environments was shown to be incorrect when Wallace observed that mountains and rivers marked the boundaries of the ranges of many species. He discovered that there were regions that were similar, but inhabited by very different animals.
Then there are the "evolutionary leftovers" that indicate the living creatures we see around us weren't created totally new, but instead bear evidence of change from earlier forms. The "panda's thumb" is a popular example. Notice that these are NOT imperfections (the argument with Creationists - if any - who believe that all of the created life forms are without blemish is a different argument) but traces of ancestry remaining in the body of the organism. The most glaring example, of course, is the eyes of blind cave fish. Why would they have been "created" by God with vestigial eyes? There are many other examples: the laryngeal nerve, the appendix, whale hip bones and vestigial leg bones, goose bumps and human body hair, kiwi bird vestigial wings, vestigial crab tails, vestigial koala caruncles, etc.
Then we have evidence from DNA. Chromosome #2 in humans is the most famous example: fused from two chromosomes that are separate in chimpanzee DNA, showing a common ancestor of humans and chimps.
There are other more subtle DNA traces showing common ancestry. Some of our genetic material is "pseudo-genes," genes that no longer code for a protein because of a mutation, and so are "inactive" bits of the DNA code. Consider DNA as instructions for assembling complex machines, because that's what DNA is: instructions for the chemical reactions of a developing organism. If two similar machines have similar instruction manuals, then they might have just got nearly the same wording because the machines have similar functions. But suppose the instruction manuals have the same typographical or grammar errors? Then we would expect the manuals to come from a common source. In the analogy, this would represent a common ancestor in the case of living creatures. A concrete example is the gene for synthesizing vitamin C. We need to consume vitamin C because our gene is inactive. Mapping such genes shows the common descent of humans and other primates, but demonstrates that other mammals (the guinea pig is one example) are further away on the evolutionary tree. The same pseudogene is present in humans and primates, but the guinea pig has a different pseudogene. "Intelligent Design" might argue for similarities in the active DNA code between humans and chimps, and dissimilarities between human and guinea pigs, but the inactive part of the DNA indicates the branching of the evolutionary tree.
quote: Endogenous retroviruses are the remnant DNA of a past viral infection. Retroviruses (like the AIDS virus or HTLV1, which causes a form of leukemia) make a copy of their own viral DNA and insert it into their host's DNA. This is how they take over the cellular machinery of a cell and use it to manufacture new copies of the virus.
Sometimes, the cell that gets infected by such a virus is an immature egg cell in the ovary of a female animal. Such cells can be stored in a state of suspended animation or dormancy for as much as 50 years before they complete meiosis and become mature egg cells ready to be fertilized. Because they are dormant, gene expression is suppressed and the infection cannot take over the cell and kill it. If that egg later matures and is fertilized, the newborn organism will have that endogenous retrovirus in every one of its cells, and so will all of its descendants.
Every viral infection is unique. The complete genome of an animal is so huge, and the insertion point of a virusâ€™s DNA is so random that it is statistically impossible for any two individuals to have the same exact endogenous retrovirus in the same exact spot on the genome unless they both inherited it from a common ancestor who had the original infection. And the infection of a germ cell is so rare that ERVs make up only somewhere between 1% and 8% of the entire human genome.
If two humans have the same identical ERV, it is proof that they are descended from a common ancestor. And if two different species have the identical ERV, it is proof that they too are descended from a common ancestor. In humans, there are about 30,000 different ERVS embedded in each person's DNA. Except for those later duplicated by a duplication mutation, all of them record unique infections of a single ancestral individual. Now here is where it gets really interesting.
There are at least seven different known instances of shared ERVs between chimps and humans... i.e. ERVs which are the identical viral DNA inserted into the identical spot of the genome. 100% of all chimps and 100% of all humans have these same ERVs. This is only possible if 100% of all chimps and all humans are descended from the single individual that had these original infections.
They are proof that humans and chimps share a common ancestor.
In a 2000 paper published in the journal Gene researchers identified ERVS shared by different primates and used them to assemble a family tree of monkeys apes and humans.
Reference: Lebedev, Y. B., Belonovitch, O. S., Zybrova, N. V, Khil, P. P., Kurdyukov, S. G., Vinogradova, T. V., Hunsmann, G., and Sverdlov, E. D. (2000) "Differences in HERV-K LTR insertions in orthologous loci of humans and great apes." Gene 247: 265-277.
Even at the level of single-celled life, there is interesting DNA evidence. Cellular structures such as mitochondria or chloroplasts have their own DNA, distinct from the DNA found in the cell nucleus. This is evidence for the evolution of the first single-celled life, cells with no nucleus or organelles, into more complex forms. Chloroplast DNA, for example, is evidence of a photosynthetic cyanobacterium that was engulfed by an early eukaryotic cell to form a larger symbiotic organism that could photosynthesize.
Then, of course, there are other interesting facts about the genetic material of living organisms, such as the chromosome count. If life were designed from some Divine blueprint, we would expect the more complex organisms to have more DNA and therefore more chromosomes. And Man, of course, at the top of the heap, according to Genesis, and made in God's image, should have the most: toolmaking skills, memory, brain, long life, the immortal soul, and, of course, a body larger and more complex than almost all of the millions of other organisms on the planet. For some organisms, this pattern does indeed hold. Myrmecia pilosula, an ant species, has only one pair of chromosomes and the individual workers, being haploid, have only one chromosome (not even a pair!) each. Small creature, small amount of genetic information. But when we look at even smaller creatures, we find, to our surprise, examples like Amoeba proteus, a microbe with more than 500 chromosomes! And so it goes. Humans have 23 chromosome pairs, one less than chimpanzees (see the example of chromosome #2 above) and a lot less than Ophioglossum reticulatum, whose 630 chromosome pairs make this lowly fern the reigning champion.
Even for structures of living organisms that don't fossilize well, such as the heart or the eye, we can see the pathways of evolutionary change in the organisms that live today. This is not to say we, with our complex four-chambered heart, are evolved from some modern species of amphibian or fish alive today, of course. Living species are all leaves on the evolutionary tree, with the branches down below showing where different forms of life diverged. But modern forms of reptile, amphibian, fish and others can show us the path evolution took along those branches.
The mammalian four chamber heart is slightly different from the reptilian three-and-a-half chamber heart, which is different from the amphibian three chamber heart, which is different from the lungfish heart, which is different from the agnathan two chamber heart, which is different from the paired contractile aorta of the amphioxis, which is different from the single contractile aorta of the hemichordates. Then there is the earthworm who does not use an actual heart; it has one or more small muscular areas capable of contracting and pushing the blood and then reabsorbing it as it filters back.
Finally, consider the timeline of life on Earth. The simplest living things, the primitive unicellular organisms of billions of years ago, took the longest to develop! Why would that be? If a supernatural force were involved, why would it take so many hundreds of millions of years to develop the earliest single-celled life forms, while far more complex organisms, like Archaeopteryx, Australopithecus, Rhynia gwynne-vaughanii, Miohippus, Ichthyostega, Hylonomus, or cynodonts were "created" in the blink (on the geological time scale) of an eye? Seen as a natural process, however, the timeline of change is easy to understand: it takes a long time for nonliving chemicals to develop into living organisms, and it takes a long time for single-celled organisms to make the great leap to combine into multicellular life, if there is no supernatural intervention prodding them along.
Is the Origin of Species miraculous? In the sense that the birth of a child is miraculous, yes. Complex and marvelous, it is true, but also natural, following natural principles of the universe. "Speak to the earth and it shall teach thee."
When you write "the best evidence for evolution comes from the definition of evolution" you capture the gist of it. If there were no evolution, then all the new creatures born (or hatched, etc.) would not be different, so over the billions of years of life on earth there would have to have been endless instances of creation of new life forms - in exactly the same order as that of evolutionary change!
When you say, "the millions of years attached to the geological column are ridiculous ... No millions of years involved, a few thousand is the biblical time period" are you implying that the Earth's history doesn't go back billions of years, but rather only a few thousand?
Consider the sedimentary layers on the floor of the Atlantic Ocean. The way they are arranged doesn't make any sense from a diluvian perspective, but rather from the perspective of gradual accretion over a long period:
In the case of the Atlantic Ocean, the sediment varies in thickness. The thinnest sediment is near the Mid-Atlantic Ridge where new sea floor is currently being generated. That is to say, sediment thickness there is zero. The thickest sediment hugs the continental margins, which certainly have more than a few thousand years of accumulation. Try around 150 million year's worth! Funny, that the measured rate of sea floor spreading, when extrapolated backwards in time, gives the same age for the Atlantic sea floor as does radiometric dating. Funny, how the sediment gets thicker and thicker as one moves away from the sea floor spreading zone! That is, the farther we get from the Mid-Atlantic ridge the thicker the sediment tends to get; that thickness correlates with increased age of the sea floor as determined by radiometric dating as well as the known rate at which the Atlantic is widening. ...
What are the odds of such a triple "coincidence" occurring? It's easy to see why scientists "bet" on an old earth. And what about those magnetic stripes on the Atlantic sea floor? If that ocean floor is indeed spreading, then the thickness of those stripes and their distance from the Mid-Atlantic Ridge preserve a chronological record of magnetic field reversals. When those distances and widths are divided by the sea floor spreading rate, do we get a match with the magnetic reversal chronology based on the radiometric dating of continental rocks? Yes, we do!
It's not just biology you're up against. What about astronomy? If you can see the star V762 Cas in the constellation of Cassiopeia you're looking at light that left the star 16,000 years ago, long before the Bible says the stars were created (if you follow the Young Earth Creation Hypothesis). Not to mention the galaxies visible billions of light years away. What about physics and chemistry? Radioactive dating has the same implications for the YECH.
Saying "I usually answer the astronomy question by saying that time is a completely different thing at that level" is an interesting approach. And time does get affected by astronomical objects: black holes and so forth. But arranging the black holes so that the photons from stars tens of thousands of light years away and galaxies millions of light years away all manage to get here in hundreds of years is a pretty contorted cosmology!
It's not just Egypt! What about Sumer and Agade and the Yangshao "painted pottery" culture of China? Were all of those somehow mis-dated?
If you want to peg the universe at six thousand years old (the "subjective guesswork" of adherents of the young earth creation hypothesis using multicentenarian biblical patriarch ages and similar "science"...) with a flood reducing the earth to a tabula rasa a millennium or two later you get a very dubious chronology indeed.
And let's not forget the fish. If you dump all that fresh water in the oceans and let it swirl around for more than a month all the fish that have to have salt water to survive will find life difficult!
Even if you postulate that Pangaea took only a few thousand years to split up, you can't possibly be saying that koalas (and penguins and Micrixalus and bison and Anami rabbit and snow leopards...) lived close enough to Noah's apartment to (A) get there in time to board the ship and (B) make their way back home after the Flood.
And what did the koalas live on during their journey back home (which was a slow journey, as you can see from all those cute videos of koalas), considering that the eucalyptus trees had all been wiped out by the flood?
Hey, wait a minute, what did the koalas live on during their journey (very slow, hand over hand along the branches of the eucalyptus) through all that territory where eucalyptus trees don't grow on the way to the Ark in the first place?