What do pseudogenes teach us about intelligent design?

The human genome has about 14,000 pseudogenes that are derived from protein-coding genes and an unknown number derived from genes that specify functional noncoding RNAs. There is abundant evidence that the vast majority of these pseudogenes are nonfunctional by all measurable criteria.

• Different kinds of pseudogenes - are they really pseudogenes?
• Different kinds of pseudogenes: Processed pseudogenes
• Different kinds of pseudgogenes: Duplicated pseudogenes
• Different kinds of pseudogenes: Unitary pseudogenes
• Different kinds of pseudogenes: Polymorphic pseudogenes

It would be perverse to deny the existence of pseudogenes. Almost all of them are junk DNA with no known function. Anyone who claims otherwise can be dismissed as a kook and it's not worth debating those people.

The presence of a single well-characterized pseudogene at the same locus in the genomes of different species is powerful evidence of common descent. For example, Ken Miller has long argued that the existence of common pseudogenes in chimpanzees and humans is solid evidence that the two species share a common ancestor. He uses the β-globin pseudogene and the gene for making vitamin C as examples in Only a Theory: Evolution and the Battle for America's Soul.

As we did for vitamin C, we might now ask how a designer cold have allowed this to happen. And our ID friends wold answer in the same way they did before; Our genome was originally designed with six working copies of the beta-globin genes, and therefore the loss of one of them from such molecular errors is no big deal. Therefore, all humans alive today are descended from individuals in which those mistakes first cropped up. Fair enough. But guess what: We're not the only organisms with a set of beta-globin genes, and we're not the only ones with a pseudogene right in the middle of that set.

Gorillas and chimpanzees have them, too, and they are arranged in exactly the same way—five working copies surrounding a single pseudogene, just as in humans—but here's where life gets truly interesting. The gorilla and chimpanzee pseudogenes have exactly the same set of molecular errors. Just like the two kids in my class, they have matching mistakes. [proving plagiarism] The student papers had a common source (the original essay), as do these two pseudgogenes—the original version of the pseudogene in the ancestor of all three species.

There's no escaping the implication of these matching mistakes, and there's no point in arguing that six identical mistakes could have turned up independently in the three unrelated species. The only sensible interpretation is tht the original errors developed at random in a single common ancestor of these three species. In a court of genetic copyright law, any motion that a designer could claim originality for the human genome would be tossed out in a flash. Our genome is a copy, an altered one to be sure, but a copy, nonetheless, of earlier genomes that preserve even the mistakes that our ancestors made in duplicating their DNA.
(p. 101-103)

Similar arguments have been made by Francis Collins, Richard Dawkins, and a host of other scientists. The details may vary, and some of the details may even be wrong, but the big picture is certainly correct. There are hundreds of pseudogenes shared by chimpanzees and humans and the only reasonable explanation is that chimps and humans share a common ancestor. This is just a tiny bit of the evidence for the history of life. It is so overwhelmingly supported by evidence that we consider it to be a scientific fact that humans and chimpanzees descend from a common ancestor. If you meet someone who denies this fact then it's probably not worth your time to debate with them about other issues concerning evolution and intelligent design. They are on a different planet.

The reason why shared pseudogenes are important is because they refute the idea of convergence and the idea of direct intelligent design. There's no reasonable way to explain common pseudogenes by invoking convergence on a common function and there's no reasonable way to advocate an intelligent designer that created chimpanzees and humans separately and stuck broken genes into their genome.

So, the evidence of pseudoegenes is not compatible with special creation and we can understand why Young Earth Creationists are upset. But we don't care about them. They are so wrong about so many things that their views can be dismissed out-of-hand except to point out, from time to time, that their ridiculous ideas are incompatible with science (and the real world).

But why are other ID proponents so bothered by pseudogenes? Many of them, like Michael Behe and Michael Denton, are perfectly comfortable with common descent. They aren't bothered in the least by the pseudogene argument advanced by Ken Miller. Their concern is to demonstrate evidence of guided evolution meaning that sometimes the gods tweak the results of evolution by introducing specific mutations in a background of random mutations.

Here's how Michael Behe deals with pseudogenes in The Edge of Evolution.

More compelling evidence for the shared ancestry of humans and other primates comes from their hemoglobin—not just their working hemoglobin, but a broken hemoglobin gene, too. In one region of our genomes humans have five genes for proteins that act at various stages of development (from embryo through adult) as the second (betalike) chain of hemoglobin. ... In that region between the two gamma genes and a gene that works after birth, human DNA contains a broken gene (called a "pseudogene") that closely resembles a working gene for a beta chain, but has features in its sequence that preclude it from coding successfully for a protein.

Chimp DNA has a very similar pseudogene at the same position. The beginning of the human pseudogene has two particular changes in two nucleotide letters that seem to deactivate the gene. The chimp pseudogene has the exact same changes. A bit further down in the human pseudogene is a deletion mutation, where one particular letter is missing. For technical reasons, the deletion irrevocably messes up the gene's coding. The very same letter is missing in the chimp gene. Toward the end of the human pseudogene another letter is missing. The chimp pseudogene is missing it, too.

The same mistakes in the same gene in the same positions of both human and chimp DNA. If a common ancestor first sustained the mutational mistakes and subsequently gave rise to those two modern species, that would very readily account for why both species have them now. It's hard to imagine how there could be stronger evidence for the common ancestry of chimps and humans.

That strong evidence from the pseudogene points well beyond the ancestry of humans. Despite the remaining puzzles, there's no reason to doubt that Darwin had this point right, that all creatures on earth are biological relatives.

The bottom line is this. Common descent is true; yet the explanation of common descent—even the common descent of humans and chimps—although fascinating, is in a profound sense trivial. It says merely that commonalities were there from the start, present in a common ancestor. It does not even begin to explain where those commonalities came from, or how humans subsequently acquired remarkable differences. Something that is nonrandom must account for the common descent of life.
(pp. 72-73)

This clear statement by Micheal Behe is a way of separating the kooks from the serious ID proponents. It's my new benchmark for debating them. If they reject Behe's argument for common descent then they are kooks and I'm not going to debate them.

But there's a problem. The ID proponents who remain upset about the pseudogene argument and common descent are often very coy about why it bothers them so much. They won't "come out" as kooks. For example, Casey Luskin doesn't like it at all and he's eager to jump on any evidence that a pseudogene isn't a pseudogene. Sometimes the irony of his argument is astonishing; like when he claims that the β-globin pseudogene isn't a pseudogene because a bit of the pseudogene in chimps and humans looks more conserved than they should be [Dover Revisited: With Beta-Globin Pseudogene Now Found to Be Functional, an Icon of the "Junk DNA" Argument Bites the Dust].

Casey Luskin loves the results of a recent paper that examined the evolution of the β-pseudogene in the chimpanzee and human genomes. The paper appeared in Genome Biology and Evolution (Moleirinho et al., 2013). The authors looked at diversity in the β-globin locus (1092 human genomes) and found lower than expected diversity in the pseudogene using standard evolutionary models and complex calculations based on modern evolutionary theory. They conclude that there might be a regulatory site within the pseudogene that determines chromatin structure for the entire locus. Presumably it arose after the pseudogene was created when that sequence became available for the evolution of a SAR. (Assuming the result is correct.)

The irony is that Casey Luskin has to rely on evolution and common descent to provide the evidence that some of the DNA in the β-globin pseudogene might have a function. But he's quite happy to use that evidence to challenge common descent and "Darwinism."

I don't know what goes on in the minds of Intelligent Design Creationists who oppose the idea of pseudogenes unless they're kooks who reject common descent. They desperately want to prove that pseudogenes are functional. Presumably they have in mind a scenario where the gods decide to break a functional gene and then create a new function from the broken gene. Who knows? It's impossible to get the ID proponents to explain anything.

You'll often come across ID proponents who claim that the common descent argument of Ken Miller et al. is the main argument for junk DNA. This is not correct. They may not be kooks—they may simply be confused. It's clear that pseudogenes are junk, if they are nonfunctional, so the argument takes that as a given. The reason for using pseudogenes to convince creationists isn't to prove junk DNA—that much is obvious—it's to show the absurdity of postulating an intelligent designer who would design species with common pseudogenes at the same location in their genomes. Micheal Behe gets it.

This is what a confused Casey Luskin says ...

Well, it's been Exhibit A—literally, offered as evidence in a court case—for critics of intelligent design who argue that our genome is full of useless, functionless junk, and therefore can't be a product of design.

Now, Casey Luskin may be skeptical about common descent (he's very coy about that) but here he's just confused. Pseudogenes make up only a tiny fraction of our genome (<1%) so they aren't ever being used as evidence that our genome is full of junk. There are other arguments that support lots of junk in our genome.

Here's another example of Casey Luskin's confusion about pseudogenes. Keep in mind that the vast majority of pseudogenes are not transcribed, according to ENCODE so there's no reason whatsoever to think they might have a function. The vast majority (>90%) are clearly junk. That makes it difficult to understand Casey Luskin's logic when he says ...

Pseudogenes serve as another good example of how Darwinian biologists have assumed that a type of non-coding DNA they didn't understand was functionless genetic junk, and thus ignored their functions. Indeed, the aforementioned paper in RNA Biology explains that one reason why evolutionists have been so slow to abandon the assumption that pseudogenes are junk is because their functions are difficult to detect. The authors observe that "almost all pseudogenes that exhibit significant biological activity are expressed in specific tissue or cell lines," meaning only specific tissues or cell lines may use a given pseudogene for some function. Additionally, it's difficult to detect function for pseudogenes because we have lacked the research tools to understand how they influence gene expression. The paper predicts that "more and more functional pseudogenes will be discovered as novel biological technologies are developed in the future," and concludes "The study of functional pseudogenes is just at the beginning." Indeed, two leading biologists writing in Annual Review of Genetics reported that "pseudogenes that have been suitably investigated often exhibit functional roles."
Problem 10: Neo-Darwinism's Long History of Inaccurate Predictions about Junk Organs and Junk DNA

No "leading biologist" would ever say that most pseudogenes have a function. Even the most vocal critics of junk DNA will admit that most pseudogenes are nonfunctional junk DNA.

ID proponents also claim that the common descent argument is used as proof of "Darwinism." But it's not. It's one bit of the evidence for common descent but there's lots and lots of other evidence. The existecne of pseudogenes just happens to pose a challenge to creationists who aren't comfortable with common descent.

Besides, in order to explain the existence of pseudogenes you have to invoke Neutral Theory and fixation by random genetic drift and those are decidedly non-Darwinian. I think this particular misunderstanding is at the heart of the objections of many ID proponents. They think that if they accept the existence of pseudogenes they will be accepting all of evolution and everything that it implies. That's why there's so much resistance.

Here's how Casey Luskin views it ...

But Ken Miller's argument for Darwinian evolution, and against ID, depends on the beta-globin pseudogene being "non-functional," implying as he does that the genetic differences between it and protein-coding beta-globin genes are errors. In light of this new evidence for the functionality of the beta-globin pseudogene, it seems that those genetic differences may not be errors at all. If so, then Miller's argument, his Exhibit A, collapses.

When I open a page of Darwin I immediately sense that I have been ushered into the presence of a great mind. ... When I read Phillip Johnson, I feel that I have been ushered into the presence of a lawyer.
Richard Dawkins, Biol. & Philos. 11:539-540. (1996)Do you see the problem? Luskin thinks that the argument of Ken Miller and Michael Behe is not just an argument for common descent, it's an argument for "Darwinian evolution." That's much more threatening, even though it's an imaginary threat as Michael Behe explained in his latest book. Luskin also thinks that the β-globin pseudogene is the only example that supports the case for common descent. The truth is that there are thousands of pseudogenes common to chimps and humans.

Casey Luskin is a lawyer and lawyers are very good at making arguments in support of their clients. Truth is not the objective when arguing for your client. Winning in a court of law is the objective. But in science truth is the only objective. If you question common descent then you have abandoned the search for truth and you are just a lawyer.

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Moleirinho, A., Seixas, S., Lopes, A.M., Bento, C., Prata, M.J., and Amorim, A. (2013) Evolutionary constraints in the β-globin cluster: the signature of purifying selection at the δ-globin (HBD) locus and its role in developmental gene regulation. Genome Biology and Evolution 5:559-571. [doi: 10.1093/gbe/evt029]