We’ve been in the weeds a bit lately and got some detail on just what’s going on.
First, let me reiterate that I personally don’t think that ‘microevolution’ and ‘macroevolution’ are appropriate in a scientific sense. They are useful for describing large scale, gross changes vs. small scale allelic changes, but there is no line that can be drawn that says “This is macroevolution.” (more commentary on that here and here)
That being said, we can’t see all the intermediates from the fossil record, so we have to assume that those intermediates existed. This is a perfectly valid assumption and probably correct (remember science can never prove something true). We know it’s probably correct because we see organisms today and we see the intermediates (teacup chihuahua all the way to Russian wolfhounds).
With all of that out of the way, let’s look at the evidence we have that supports the idea of these large scale (beyond the species level) changes. There are a lot, so this may be a long post.
Genetic and Molecular Evidence
1) Every living thing on the Earth uses the same genetic code. This shouldn’t be in dispute, but it goes farther than you may think. In fact, it’s not even just DNA and RNA. It’s how the DNA and RNA strands are interpreted.
Without getting into too much detail, three RNA nucleotides in a row are called a codon. That codon tells the ribosome to insert one and only one very specific amino acid. Now, what’s fascinating is that in every organism so far discovered on Earth, the same codon codes for the same amino acid. CUG codes for leucine in humans, fish, and bacteria.
Supporting evidence for this is simply the fact that insulin, a major component in the ability of humans to regulate blood sugar is almost exactly the same in a variety of organisms. We’ll talk a bit more about that in a minute. But what is really impressive, is according to the International Diabetes Foundation, 70% of all insulin used in the world comes from biogenic sources. That is, either bacteria (E. coli) or yeasts, have the human insulin gene inserted into their genome and those organisms make human insulin for us. (Note that the possibility of allergic reactions has nothing to do with the chemical structure of the insulin molecule itself. It is human insulin.)
Similarity in Important Compounds’ Molecular Structure
As we talked about above, humans can use insulin from pigs and from cows. The structure of these insulin molecules is slightly different than from human insulin. This is true of many important molecular compounds within organisms. Opsins are light sensitive compounds found in vertebrate eyes, worms, molluscs, the brains of insects, etc. Cytochrome c is another important compound that is found in almost every eukaryotic organism.
What’s truly interesting about the similarities in these types of compounds (there are many), is that if you compare them, the ones most similar to humans are organisms that would otherwise be considered most closely related to humans. The more differences, the more likely the organism is to distantly related to humans.
This is NOT circular reasoning. We are not saying that organisms are closely related and then using the similarity in these compounds to show this. We are using this as a second check, if you will, of what we think.
We are saying that, if these organisms are closely related, then one piece of evidence that would support that is a very close similarity of molecular structures. If we found a modern insect, with exactly the same opsin gene as a human, that would actually be detrimental to the concept of common descent. Insects are not at all closely related to humans so their opsins should be similarly not very closely related. Likewise, if we found that chimpanzees had wildly different versions of these compounds, that would also not be supportive of common descent.
But, what we do find supports common descent quite well.
I will not pretend to know much about Endogeneous Retroviruses. Here’s what I do know.
Some viruses actually insert themselves into the genome of their target organism and wait. These viruses will activate later and cause whatever destruction they do… except when they don’t.
Sometimes, these viruses insert themselves into the host DNA and ‘forget’ to come out. They just stay there, generation after generation, remaining in the host DNA as a forgotten remnant of something. Now, there is all kind of research being done on ERVs, what they do, what they can do, etc.
But, for our purposes, they do show one important thing. If two organisms have the exact same ERV in the exact same place in the genome, then those two organisms are related. It’s a marker. It would be extremely improbable for the same virus (out of thousands of possible ERVs) to be inserted into the exact same place (out the nearly infinite number of possible location in a genome) in two different species.
Both humans and chimpanzees have the same ERVs, they are in the same place, and the ones that are active are active in both species. This is evidence that humans and chimps descended from a common ancestor that had these ERVs.
Further examples include the Felidae family, in which all small cats have a particular ERV while no large cats have it, indicating that the ERV occurred after the split between the Felis and Panthera genuses.
These are simple non-coding regions of DNA. However, they display the same effects that ERVs do. If two organisms display the exact same change (to render a gene no long usable), in exactly the same place, then it is much likely that these organisms are very closely related.
Of all mammals, only one suborder of primate cannot manufacture vitamin C.** The non-tarsier prosimians. Scientists worked out a pretty good relationship between the various primate species (including humans) before we knew about vitamin C, so this is a good test of the principle of common descent.
None of primates that scientists thought are in the non-tarsier prosimians can make vitamin C. This includes humans, chimpanzees, gorillas of all kinds, orangs, etc. All of the primates related to tarsier prosimians can make vitamin C. Further, every non-tarsier prosimian has exactly the same mutation that inactivates the genes needed to manufacture vitamin C.
What are the odds that several hundred species and well over 7 billion individual organisms all have exactly the same mutation that inactivates the same gene in the same place?
Common descent suggests that it is only required to happen once and that mistake is passed down to all subsequent offspring. Of course, this is but one example of an entire family of examples. A very large percentage of our DNA is pseudogenes.
** A reader has informed me that some other mammals besides the listed primates also cannot manufacture vitamin C. This list include guinea pigs, chinchillas, and all bats (Jenness, R., E. Birney, and K. Ayaz. 1980. Variation of L-gulonolactone oxidase activity in placental mammals. Comparative Biochemistry and Physiology 67B:195-204). Interestingly, the bats provide the same evidence as the primates do for common descent as they all appear to have the same mutation resulting in an inability to manufacture vitamin C.
Now we’ll move into the realm of comparative anatomy. Avatisms are simply anatomical features that don’t belong. They are easily explained by common descent as leftover features that, due to mutation, get activated in individuals.
Within each individual’s genome are a series of genes that control how the individual develops from a single cell to a giant multi-celled monstrosity that might mass up to a few kilograms at birth.
And yet, all vertebrate embryos have some similar traits. For example, all vertebrate embryos, fish, birds, reptiles, and mammals all display gill arches at some point in the fetal development. In humans, the gill arches become the pharynx. In fish, they obviously become the gills.
There are additional events like this, not just in humans (for example most birds go through a stage where the embryos have teeth, but they are reabsorbed).
These, like the avatisms, are left-overs from the genes we still have from our distant, common ancestors.
The Fossil Record
The fossil record is incomplete. As I mentioned to commenter here, the process of fossilization requires very specific conditions. There is no doubt in any paleontologist’s mind that there are millions of species that we never know about because they were never in positions to be fossilized. It’s a rare event. Then we have to take into consideration the movement of the Earth and changes wrought on rock by weathering, erosion, heat, and pressure. It’s wonder that so many fossil records are so good. But there are quite a few that are excellent.
I won’t go into details, that’s multiple posts for other times. But the fossil history of whales and their ancestors, modern horses and their ancestors, and a variety of marine molluscs shows the detail that includes those intermediates that I talked about in previous posts. [Keep in mind that these are links to wikipedia articles and one should also read and consider the peer-reviewed literature that informs many of these articles.]
Plus, fossils provide a second back-check on our conclusions. The case of Tiktaalik is a perfect example. Knowledge of the fossil records allowed Dr. Shubin to predict the age and type of rock where a transitional fossil like Tiktallik would be found. If the organism was found, then it should have certain characters based on what we know of both prior and post organisms.
Not only was Tiktaalik found exactly where predicted, the characters of the organism perfectly aligned with evolutionary based prediction.
Whenever someone says the flood was a real, historical event, one of the first things rational people ask is, “How did the koalas get to Australia?”
There are a lot of other questions that can easily be answered by evolutionary concepts like common descent and standard scientific geologic concepts.
Here’s some pieces of evidence that support the principle of common descent:
Old World Monkeys (Africa) and New World Monkeys (South America) are pretty different groups. Many traits of one are not shared by the other. Only New World monkeys have prehensile tails, and they tend to be smaller with flatter noses than Old World monkeys. The dental formula is different and the entire vision system is different (only female new world monkeys can have trichromatic vision and not all of them do).
The marsupials of Australia and New Zealand are excellent examples of this. Also, transplanted cacti in Australian deserts do very well, but only North American deserts have native cacti.
Don’t forget the very similar flightless birds of New Zealand, South America, and Africa.
All pieces to a puzzle that is easily answered by the mainstream scientific view.
Note that fossils often display patterns of distribution that only make sense when the continents were in specific alignments.
There are two major concepts that support evolutionary principles with regards to islands and the species that inhabit them.
The first is island endemism. There are several fascinating species that only live on islands. This includes a variety of extinct and extant organisms like the dwarf elephant, Komodo dragon, tuatara and Homo floresnsis.
These populations show the uniqueness that can occur in isolated habitats.
The other factor is the specialized radiation into unique niches on islands. Darwin’s work in the Galapogos emphasized this. From the various species of finch that fulfill all the bird niches (seed-eating, insect-eating, nectar-eating, etc) to the highly specialized marine iguana. Again, these populations both show the uniqueness of island biogeography and that single populations can radiate into unique species to take advantage of untapped resources.
I’ve talked about them before ad infinitum, but they remain an example of speciation in action.
Any one of these categories of evidence, when taken singly, may not mean very much. But when taken as a complete set of data, the patterns become clear. There is significant evidence to support evolutionary principles including common descent and macroevolution.
Note that I have not discussed any evidence from evolution itself. You see, the naturalists prior to Darwin already had some inkling of common descent.
Natural selection and Darwin’s work was needed to know that common descent is the most likely explanation for the diversity of life around us. What Darwin did was give us a mechanism that explained HOW species descended from a common ancestor.
Now we could talk about observed instances of speciation. We could talk about the additional evidence from artificial selection. We could talk about the mathematical principles from computational biology and artificial life.
But we don’t have to. The above represent incontrovertible evidence that all known living things on Earth are descended from common ancestors. The rest is just beating a dead horse.
Now, I have posted this elsewhere and no creationist has ever successfully argued against all of these pieces of data. The have attempted one or two, but that doesn’t help. Any creationist wishing to push ‘design’ or ‘special creation’ or ‘Young Earth Creationism’ or even ‘Old Earth Creationism’ must not only remove every single bit of data in these categories, they must give an more effective explanation for why these patterns do occur.