I didn't come from no monkey, updated

I was looking over the Discovery Institute's Evolution News and Views site, prior to forgetting about it. I mentioned that I am forced to revamp my email handling and was going to be blocking a lot of noise from my work address, and as I was reviewing what domains I needed to allow through, I noticed that boy-howdy, I get a lot of crappy spam from the Discovery Institute (all of which is now getting blocked). So I actually bothered to go through one of their links and see what they're babbling about now.

General impression: the Discovery Institute is really obsessed with Cosmos: A Spacetime Odyssey. They're flailing about angrily about how it's just bad and awful and a serious threat. Good work, Neil deGrasse Tyson, you're obviously doing something right!

The other thing that has them worked up, though, surprised me a little bit: they're kind of peeved that scientists keep pointing to this evidence that humans and chimpanzees are close relatives, and they throw around a lot of sciencey words trying to cast doubt on the idea that we're related. They don't come out and openly deny it, exactly — but it's still the stupid old yokel's denial that they didn't come from no monkey, stated a little more ornately to make it sound less stupid. They failed; it still sounds stupid. But have no fear, they've put their Top Man and Chief Scienceologist, Casey Luskin, on the job.

Oh, wait. That makes it even stupider.

It should be pointed out first that ID does not have an "official" position on common descent. Guided common descent would be compatible with intelligent design. However, many ID theorists do question the evidence offered for universal shared ancestry.

Scratch an ID theorist, and what do you find? Just another dumb evolution denier. Common descent, and in particular the close relationship between humans and other apes, is not in question at all, but the Discovery Institute can't even muster an official position on it. Other basic science questions the Discovery Institute will not say a word about: the age of the earth, whether the human race was reduced to an 8 person bottleneck by a big flood 4,000 years ago, Jesus: magic man or genetic engineer?, and just how ignorant is Casey Luskin, anyway?

The way Luskin questions the shared ancestry of humans and chimpanzees is to simply dump, with virtually no explanation, lists of legitimate scientific papers that show various common genetic properties. Codon frequency can affect transcription rates, so synonymous changes in nucleotides of a sequence may have phenotypic effects; yes, this is true. Position effects can also affect phenotype; this is also true -- translocations, movement of a chunk of DNA from one location to a different one, can modify gene expression. Pseudogenes aren't always free from selectional constraints, and sometimes also modulate the expression of other genes -- yeppers. These are also all basic facts that we've known for decades, that have been worked out by scientists, not creationists, and that have absolutely no relevance to the question of whether chimpanzees and humans are closely related. They say that there are many complicated ways in which variation can arise in a lineage, that it's difficult to reduce the degree of difference between two species to a single number, but everyone who does any bioinformatics at all already knows that.

For instance, here are two sequences. How different are they from one another? Can you give me a simple number that summarizes the variation?

1-2-3-4-5-6-7-8-9-10-A-B-C-D-E-F-G-H-I-J

1-2-3-4-A-B-C-D-E-F-G-H-5-6-7-8-9-10-I-J

Biologists are already intimately familiar with the difficulty of describing the variation in sequence between species. If it were just a matter of a string of DNA accumulating point mutations, it would be relatively easy, and we could simply measure how many positions had acquired a novel nucleotide, but mutations can be all kinds of other things, like translocations or inversions or deletions or duplications. So Casey Luskin high-handedly informing us that measuring variation is more difficult than just enumerating a linear series of nucleotide changes is absolutely nothing new, and telling us that pairwise comparisons are complex, therefore we should doubt the relationship between two primates, is utterly bogus and logically fallacious.

The question should be, "if we compare the differences between chimpanzee and human genomes, messy and complicated as they are, are they less different from one another than, say, the human and gorilla genomes? Or the human and mouse genomes? Or the human and fly genomes?" Just comparing any two species can only tell you that they have differences and similarities; you need to do multiple comparisons between different species and an outgroup to get a feel for the relative magnitude of differences.

Luskin's only approach, carried to an excruciating degree, is to simply say there sure are a lot of differences between humans and chimpanzees (six million years of divergence will do that), therefore it is reasonable to question their relatedness. Yeah, and my brother is a few inches taller than I am and has red hair, therefore we can't possibly be related.

Casey Luskin isn't the only IDiot on staff at IDiot Central. They also have Ann Gauger. She does exactly the same thing, citing a Science article that discusses the difficulties of quantifying the differences between genomes. It also points out that the subtle differences can be immensely significant, which Gauger makes much of.

Here are some large-scale differences that get overlooked in the drive to assert our similarity. Our physiology differs from that of chimps. We do not get the same diseases, our brain development is different, even our reproductive processes are different. Our musculoskeletal systems are different, permitting us to run, to throw, to hold our heads erect. We have many more muscles in our hands and tongues that permit refined tool making and speech.

Golly, yes. We're different from chimpanzees. We do things they don't, and they do things we don't. My brother has red hair, and mine is brown. None of this is controversial, or in any way challenges the idea of relatedness or degree of relatedness. To do that, you have to compare multiple lineages and quantify all these variations -- we go beyond simple nucleotide counts, for instance, to ask how many duplications? How many regulatory changes? How many deletions? And when we measure those, doing more than just asking how many bases are different between two different genes, we also get measures of relatedness. And they line up!

Gauger notably fails to refer to the figure in the article she cites.

Throughout evolution, the gain (+) in the number of copies of some genes and the loss (–) of others have contributed to human- chimp differences.

Why, Ann, why? Because it actually demolishes your whole argument by demonstrating degrees of similarity between different species using a different index, the number of gene duplications and deletions? If you want to question chimp/human propinquity, you don't get to simply ignore the data we use to justify that.

But of course, Gauger wants to argue that the unique attributes of humans are somehow especially special and deserve special consideration -- that they completely set us apart from other animals.

Going beyond the physical, we have language and culture. We are capable of sonnets and symphonies. We engage in scientific study and paint portraits. No chimp or dolphin or elephant does these things. Humans are a quantum leap beyond even the highest of animals. Some evolutionary biologists acknowledge this, though they differ in their explanations for how it happened.

You know, I would agree that we carry out certain things to a greater degree than other animals -- we do have more elaborate language, more intricate technologies, much more complex art. But other animals exhibit curiosity, playfulness, exploration, communication, and we can look at a chimpanzee, for instance, and see attributes that we've amplified and expanded. The roots of our humanity are patent in other species, and we are not qualitatively unique. Furthermore, other species have abilities we don't. Can you sing under water and have your music transmitted over hundreds of miles of ocean? Can you wash your car with your nose? Aren't you a little bit embarrassed by the puniness of your teeth?

But Gauger is oblivious to the astounding beauty of other organisms -- it's all about us.

In truth, though, we are a unique, valuable, and surprising species with the power to influence our own futures by the choices we make. If we imagine ourselves to be nothing more than animals, then we will descend to the level of animalism. It is by exercising our intellects, and our capacity for generosity, foresight, and innovation, all faculties that animals lack, that we can face the challenges of modern life.

Generosity? Has Ann Gauger never had a dog?

As for innovation, yeah, I agree. Humans do have some novelties. Here's a paper about the de novo origin of human protein-coding genes, that compared those chimpanzee and human genomes looking for just the unique genes in the human lineage (this is only one measure of difference, of course; they are not looking at location or sequence comparisons, just what genes are brand spankin' new and not shared at all with chimps). They found a few.

Many new genes, generated by diverse mechanisms including gene duplication, chimeric origin, retrotransposition, and de novo origin, are specifically expressed or function in the testes. Henrik Kaessmann hypothesized that the testis is a catalyst and crucible for the birth of new genes in animals. First, the testes is the most rapidly evolving organ due in part to its roles in sperm competition, sexual conflict, and reproductive isolation. Second, Henrik Kaessmann speculated that the chromatin state in spermatocytes and spermatids should facilitate the initial transcription of newly arisen genes. The reason for this is that there is widespread demethylation of CpG enriched promoter sequences and the presence of modified histones in spermatocytes and spermatids, causing an elevation of the levels of components of the transcriptional machinery, permitting promiscuous transcription of nonfunctional sequences, including de novo originated genes.

Behold my ball sack, noble repository of all that is precious and special and extraordinary and exceptional in mankind. How come the creationists never have time to praise the mighty testicle, and are always going on and on about sonnets and symphonies and such?

I am quite comfortable with my status as an animal. I have a lot of respect for other organisms, and I can also recognize traits that are particularly human. Why this puts creationists on edge is a mystery: I just blame it on their ignorance.