The “Shared Error” Argumentnew evolution book co-authored by evolutionist Dennis Venema and Scot McKnight is influenced by the mythical Warfare Thesis (here and here) and makes erroneous arguments that the fossils and echolocation support evolution (here and here). We now move on to another topic: broken genes, or pseudogenes. This is a popular argument amongst evolutionists and Venema uses as his example the olfactory receptor genes. The idea here is that, in different species (such as the human and chimpanzee), the same damaging mutation can be found in the same pseudogenes. When we find the same strange spelling mistake in the homework of different students we conclude that plagiarism occurred. It is more likely that the mistake had one source, rather than occurred twice, independently. Likewise, the same mutation in different species points to a single source in a common ancestor—common descent. Furthermore, we don’t see mutations that violate the expected pattern. Clearly common descent is the obvious, most parsimonious explanation. As Venema concludes, common descent is “overwhelmingly supported.”  This is a powerful argument for evolution that has influenced many people. There’s only one problem: It fails historically, philosophically, and scientifically.
First, the olfactory system is profoundly complex. Odors entering the nose interact with finely-tuned receptor proteins (created from the olfactory receptor genes), setting off an incredible cascade of events in the cell, resulting in an electrical signal sent to the brain. Studies have found that each cell expresses only a single olfactory receptor gene, and so is sensitive to a particular odor. At the brain, the signals are grouped and organized by odor. In other words, for all the cells in the nose expressing the same olfactory receptor gene (and thus sensitive to the same odor), their signals spatially converge as they feed into the brain area.
And of course, as with all the senses, These incoming signals are providing mere electrical information. There is no odor, or light, or sound entering the brain via these nerve cells. Instead, a bunch of electrical signals are entering the brain via these nerve cells. The brain, by itself, has no way of knowing what these electrical signals mean. It must somehow be given the source and meaning of these incoming signals. It then processes and interprets these signals and the end result is that we are conscious of images reported by our eyes, sounds reported by our ears, smells reported by our nose, and so forth. All of this defies evolution, and should give us pause.
Second, the evolutionist’s contention that common descent is needed to explain those shared mutations in different species contradicts the most basic biology. Simply put, similarities across species which cannot be explained by common descent, are rampant in biology. The olfactory system is no exception. Its several fundamental components, if evolution is true, must have evolved several times independently. The level of independent origin which evolutionists must admit to (variously referred to as convergent evolution, parallel evolution, recurrent evolution, cascades of convergence, and so forth depending on the pattern) is staggering and dwarfs the levels of similarities in the olfactory receptor genes. To cast those relatively few similarities as mandates for common descent, while ignoring the volumes of similarities that violate common descent constitutes the mother of all confirmation biases.
Third, the strength of this evolution argument is lack of function, but that renders it fallacious. As lawyers know, if you can’t convict the defendant on the facts, you decry how horrifying the crime is. In this case, the entire argument hinges on the utter uselessness of the broken genes. As Venema explains, they are “damaged,” “defective,” “mess[ed] up,” “wrong,” and “ruin[ed].” Clearly, according to Venema, these genes are useless—that’s why they are called pseudogenes. This is crucial because, for evolutionists, this means they would only arise by chance (what designer would implement useless designs?).
All of this means that evolutionists have a very simple formulation: Either those crippling mutations arose once in a common ancestor, or they just happened to arise by chance, coincidentally, multiple times. Clearly the former is much more likely, and this points to common descent. It is, as Venema concludes, “overwhelmingly supported.” 
But this powerful argument comes at a cost. There is no free lunch.
The conclusion that common descent is “overwhelmingly supported” utterly depends on our knowing the pseudogenes are useless. Disutility underwrites the assumption of chance as the only alternative to common descent. And chance as the only alternative is crucial. It is why the argument is so powerful, because the chance hypothesis is so unlikely.
Restricting the problem to a contest between evolution and chance makes evolution the obvious winner, but amidst the celebration we forget the weak link. We forget that the entire edifice resides on our certainty of disutility. This, it turns out, is a very weak link.
The history of evolutionary thought, going back to the Epicureans, is full of predictions of disutility gone wrong. It is, quite literally, a theory of gaps. When gaps in our scientific knowledge leave us with ignorance about function, evolutionists routinely assume there is no function. After all, if the world arose by chance, it should be a claptrap, full of aimless, useless designs, if they could even be called that.
But as those gaps close with the inexorable march of scientific progress, it seems we inevitably learn of function. Evolutionists are consistently claiming disutility at brand new findings, only to be proved wrong, again and again. Look no further than the seemingly endless parade of “We thought it was junk, but now …” stories.
Ultimately, the long history of disutility claims are informed by the theory rather than the evidence. This is a classic example of what philosophers refer to as theory-laden observations.
None of this means there are no truly useless structures in biology. There may well be plenty of them. But it has a terrible history.
Furthermore, regardless of the history, disutility is very difficult to know. As with the proverbial “proving a negative,” proving that a pseudogene, or anything else in biology for that matter, actually is useless, is a very difficult undertaking.
From introns to transposons, initial claims of uselessness have given way to a steady stream of findings of function. And, yes, the olfactory receptor “pseudo” genes are no exception. They are now being called pseudo-pseudogenes because all those evolutionary claims of uselessness are rapidly fading. As one recent paper concluded, “such ‘pseudo-pseudogenes’ could represent a widespread phenomenon.”
This is yet another example in a long history of failed disutility predictions. Clearly, the assumption that we know that olfactory receptor pseudogenes are useless is unfounded. Even the name (pseudogenes) will serve future generations of scientists as a constant reminder of this evolutionary foible. Venema’s powerful argument was demolished before the book was even published.
The story does not end here for even if something like pseudogenes could somehow be proven useless, this would not justify the evolutionary formulation of random chance origin as the only other alternative.
Evolution fails to explain how even a single gene could evolve, let alone the entire olfactory system. In fact the presence of supposedly useless structures, such as pseudogenes, is hardly a plus for evolution. As Elliott Sober has pointed out, there is nothing about this story that provides a positivistic argument for evolution.
The argument, and all its strength, hinges entirely on the refutation of the alternative. This is a proof by the process of elimination. Hence it becomes utterly crucial that the alternatives are carefully and exhaustively considered. In particular, all possible alternatives must be known, understood, evaluated, and disproved.
Do you see a pattern here?
This powerful evolutionary argument not only crucially depends on knowing that the pseudogenes are useless, it also crucially depends on knowing that a simple random chance model is the only alternative to evolution, for their origin.
Not only is this philosophically problematic (how do we know that the random chance model is the only alternative?), historically it has a terrible track record. As Kyle Stanford has shown, the history of science is full of theories that were advocated with this type of contrastive reasoning (by disproving a perceived alternative), only later to fail because the assumed alternative was wrong.
To summarize, this highly influential, popular, argument from similar structures that appear to be useless, lies in ruins. It is a disaster. It fails historically, philosophically, and scientifically. It should never have been used in the first place, for its scientific failure was entirely predictable from both the history and philosophy of science.