@scott_hurst posted a long tweet to @starchasr. It’s brilliant, so I’m reposting it.

The first thing I need to deal with is a couple of your very fundamental misunderstandings and seeming severe ignorance of the very basics of evolution. So, I am going to have you an entire evolution in a nutshell post and let the feed into the pharyngeal (also known as laryngeal) nerve as an example of exactly the kind of thing we find in nature that is inexplicable from a creationist point of view and to be expected, if not actually inevitable, from an evolution point of view.

Evolution has no foresight. There is no plan. There is not really such an idea as “more or less” evolved. Everything on the planet is exactly as evolved as we are, as everything shares exactly as long a genetic/evolutionary history as us. Every species alive today is at the very tips of the same “tree of life” that we are, and all come from exactly the same beginning.

A few facts of natures that are relevant:

1. The recipe (recipe is a much better analogy than blueprint) that forms our bodies is contained in the DNA of our chromosomes.
2. Our chromosomes contain segments called genes. A gene is generally the recipe for making one protein. Besides genes, there are also regions that regulate the expression of genes, there are old broken genes that no longer work and are not transcribed. Some of those broken genes were plainly inserted by retro viruses sometime in the past, as you be discovering from the ERV paper. There also seems to a good deal of garbage that seems to be not genes, not regulatory, nor even old broken genes…. We don’t know what its purpose, if any. Looking at what we find in the various broken genes can provide many thousands of pages of compelling (and fascinating) evidence for evolution on its own. We’ll probably discuss this further as some point. DNA that isn’t useful, for whatever reason, will be referred to as non-coding.
3. Through chemical action, radiation, and plain old errors during replication, DNA is sometimes changed. That is called a mutation. Sometimes the mutation can be rather large. For instance, entire genes or even groups of genes are occasionally replicated one or more times.
4. Mutations are random. Yes, random.
5. Many mutations occur in the a non-coding region. Therefore, they are without effect.
6. The vast bulk of mutations that happen to affect a coding region are bad. They are random. Random changes mostly cause problems. Often this will cause an (complex) organism to die during development. This is the cause of many spontaneous abortions in humans, btw. If it is not that severe, it will still lead to a “less fit” organism.
7. In evolutionary terms, “fitness” is only a measure of an organisms ability to spread copies of its own genes into the future. It does not mean any of the things that humans would normally associate with the term. An organism that was slower, weaker, and/or lived half as long would still be more “fit” in evolutionary terms if could produce more offspring (that also survived to have offspring of their own) than the stronger, faster, longer lived organism. This could be ANYTHING from a fungi to a cow. It doesn’t matter. (Changes the meaning of “survival of the fittest, eh?)
8. In general, being swifter of foot, stronger, sharper of vision, etc often does align being able to leave more offspring…. but that is not a requirement and is not universally true. In the end, being able to leave more surviving offspring is the final arbiter of fitness.
9. Occasionally, a mutation does make an organism more fit.
10. There are finite resources for organisms to live on. Even the slowest breeding organism (say an elephant perhaps), if left unchecked, and every offspring survived, would completely bury the planet in surprising few years. In every single species, enormously more offspring are born than can possibly survive. In nature, every organism competes with every other for the finite resources. MOST offspring do not survive to reproduce themselves. This might be the most important single thing to understand about evolution.
11. Any mutation that provides any advantage is more likely to survive this competition for resources. Organisms with “good” mutations preferentially survive. Soon most or all members of a species will carry this mutation as they will out compete their lesser cousins for survival and reproduction.
12. If any species is divided geographically or otherwise into groups, each group will obviously gather different sets of mutations. They are random, it could be no other way. When enough difference accumulate between to two group, eventually they will no longer be able to interbreed, if/when they are ever reunited. These two populations are now two separate species.
13. Let this tale play out of glacially significant periods of time and almost unlimited change can be accomplished.

Now, something that should be obvious from all of that, is that evolution is a “tinkering” kind of slow change. That is, while huge change is possible, it happens bit by bit by modifying what already exists.

This one concept gives something powerful to search for when looking at the way bodies are organized. We should expect to find man things that seem very odd if put together as a clean-slate design, but make enormous sense if they were modified bit by bit from something that that existed in an ancestor. Now, we are finally ready to look at the pharyngeal nerve.

The pharyngeal nerve is a nerve that comes directly from the brain, rather than branching from the spine. We have a few of these for various purposes, mostly to control thing on our face and head. The pharyngeal nerve is what controls the voice box in mammals and also helps in swallowing. In mammals, the path of the this nerve is rather surprising. Rather that going directly from the brain to the voice box (a pretty short trip), it goes down the neck, into the chest, loops under the aorta, and then back up the neck to the voice box. In a giraffe, this causes the nerve to be 30 feet longer than necessary. Its voice box is 15 feet up the neck from the aorta. What a puzzling “design”.

So, how does this makes sense from an evolutionary perspective? This same nerve, made by equivalent genes, and developing in a completely parallel way during embryo development in fish controls the gills. Because of the anatomy of fish and the relative location of the heart and gills, this is a very reasonable and direct route for this nerve.

Mammalian voice boxes are equivalent tissues to gills in fish. Same family of genes make it, and it develops from the same embryonic tissues as gills do in fish. Over evolutionary time, as what is now our voice boxes changed purpose and migrated… and more importantly, the heart migrated further from the head, this nerve gradually went from direct connect, to a 30 foot detour in a giraffe.

A “designer” would be foolish to come up with such a plan. But this kind strangeness is to be expected in something that was modified a tiny bit at a time over an enormous number of years.

This is just ONE especially compelling example. When you look closely at the bodies of every species, you find this kind of tinkering and jury-rigging everywhere. I can find you lists of 1000s, if not millions of examples.

Now, if the sea is FULL of competition and the land is empty of competion…. Is it any surprise that coastal fishes would eventually colonize the land?