My old sparring partner Salvador Cordova recently posted this essay over at Uncommon Descent. Salvador describes his intent as follows:
Intelligent design will open doors to scientific exploration which Darwinism is too blind to perceive. The ID perspective allows us to find designed architectures within biology which are almost invisible to natural selection. Thus, the ID perspective is a far better framework for scientific investigation than the Darwinian perspective. What do I mean, and how will I justify my claim?
Pretty brazen, but hardly new. ID folks have been telling us precisely this for over a decade. I’m still waiting for them to open just one door, even if just a crack.
So how does Cordova back up his statement? He begins with a lengthy anecdote about airplanes:
Let me illustrate my point with some anecdotes. I was piloting a small airplane in the spring of 2002. My airplane suffered a potentially serious systems failure during the flight. In piston powered aircraft, the electrical ignition system (called a magneto system) is life-critical. Aircraft engineers consider the magneto system so crucial that they design each engine with two redundant, independent magnetos. If one magneto fails, the other seamlessly takes over. In fact, these dually redundant systems are so effective that a pilot will not even know if one of the magnetos failed in mid-flight until he’s back on the ground doing a routine inspection of his airplane!
Cordova next recounts how during a standard pre-flight check on his plane he discovered that one of the magnetos had failed, but that he had not been aware of it when he was flying because of the back-up system.
What does this have to do with biology and Darwinism? One way Darwinists conclude something is evolutionary junk, a vestigial feature, or an otherwise useless biological artifact is to apply “knock-out” experiments on an organism. If a piece of the organism is knocked out, and the organism still functions well and is otherwise “fit”, then the knocked-out piece is deemed useless, an evolutionary leftover, junk, or even bad design.
The really silly part of Cordova’s essay is still to come, but first we must comment on this remarkable paragraph. First off, “knock-out experiments” are carried out in genetics to determine the function of particular genes. The idea is to remove a particular gene from the organism’s genome and attempt to determine the effect this has on the resulting organism. They have nothing do with determining whether a structure is vestigial. The point is that the thing being knocked out is a gene, not a “piece of the organism”.
Furthermore, vestigial is not synonymous with non-functional. In fact, the term vestigial can be defined without any reference to evolutionary theory at all. Thus, the sightless eyes of cave-dwelling rodents or the pelvic bones of snakes are deemed vestigial not because we are making some assumption about evolutionary history, nor because they are non-functional. It is because they are reduced or rudimentary versions of more complex structures that exist in other organisms. They are evidence for evolution because they can be viewed as a logical consequence of organisms adapting to new ways of life. Organisms that live in perpetual darkness do better by diverting resources away from the preservation of eyes that are no longer useful for vision, for example. They are hard to explain as the products of ID. Which is why most ID folks hide behind the inscrutable motives of the designer in trying to eexplain such structures.
For much more information on this subject, click here.
Furthermore, knock-out experiments have little to do with the determination that a given stretch of DNA is junk. Rather, “junk DNA” is a term used to refer to DNA that does not code for protein. The determination that a piece of DNA is “junk” is normally based on the fact that we can determine where the DNA came from. Such DNA frequently arises from endogenous retroviruses, or from tandem repeats of other genes, among other sources. Determining that such DNA can be knocked-out or mutated without discernible effect on the organism is certainly a helpful piece of supporting evidence, but it is not the main evidence used to determine that something is junk.
We should also point out that the conclusion that much of an organism’s genome is junk is also suggested by the fact that closely related organisms frequently have wildly different quantities of DNA in their genomes. More information on this can be found here. ID folks, of course, have no explanation for why these genome sizes differ as much as they do.
Let us continue. Cordova now links to this article about new research into the size of the minimal genome required for a living bacterium. He presents the following quote from the article:
“Previous attempts to work out the minimal genome have relied on deleting individual genes in order to infer which genes are essential for maintaining life,” said Professor Laurence Hurst from the Department of Biology and Biochemistry at the University of Bath.
“This knock out approach misses the fact that there are alternative genetic routes, or pathways, to the production of the same cellular product.
When you knock out one gene, the genome can compensate by using an alternative gene.
But when you repeat the knock out experiment by deleting the alternative, the genome can revert to the original gene instead.
Using the knock-out approach you could infer that both genes are expendable from the genome because there appears to be no deleterious effect in both experiments.” (Cordova’s Emphasis)
From here Cordova continues:
Knockout experiments have also been used to argue “junk DNA” is junk. This is out rightly bad science, but it persists because of Darwinist’s eagerness to close their eyes to design and paint various artifacts in biology a the product of a clumsy blind watchmaker rather than an intelligent designer.
The strategy of using several different means to achieve a particular goal where each of the individual means is sufficient by itself to achieve the goal is used in many engineered systems to ensure that the goal will be achieved, even if one or more of the means fail. For example, the space shuttle’s on-board inertial guidance system, consists of five redundant computers!
And after a lengthy quote from Michael Denton Cordova seals the deal as follows:
Denton describes what I call contingency designs. It should be hopefully obvious that contingency designs are exactly the kinds of designs that are hard pressed to be created via natural selection. How does one evolve a contingency design when the primary design functions just as well? If a creature mutates a failure into a life-critical primary system, it will more likely be selectively eliminated before it can evolve a fully functioning backup system!
ID’s explanatory filter is therefore a potentially more effective tool at identifying designs which elude Darwinian style tests (such as knockout experiments) for functionality. ID’s explanatory filter looks for possible functionality by identifying specified complexity in biological artifacts which may not evidence any immediate effect on the organism if the biological artifact is knocked out.
In an attempt to keep this blog entry to a reasonable length, let me focus on Cordova’s two main claims. He argues that (1) Evolutionary thinking leads scientists to the erroneous conclusion that knock-out experiments are a sound means for detecting non-functional parts of the genome, and (2) ID avoids this pitfall.
I’m sure everyone will be shocked to learn that both of these claims are false.
We start with point number one. Knock-out experiments have nothing to do with evolutionary thinking. They are of obvious utility in genetics, because they frequently identify crucial functions performed by individual genes. The information they provide is certainly useful to evolutionary biologists, but they are neither motivated by nor central to evolutionary theory. The idea that evolutionists are so eager to view various bits of anatomy as useless junk that they cling to whatever feeble evidence they can find to make that detemrination is nothing but an ID fantasy. As should be obvious, it is essential to proper evolutionary reasoning that we have a solid understanding of the functions performed by various genes.
The error made in concluding from a single knock-out experiment that a particular gene should not be considered a member of the “minimal genome” likewise has nothing to do with evolutionary thinking. It is, instead, an error made by being unaware of certain aspects of organismal genetics. Knock-out experiments are certainly valuable for detecting genes that are essential to proper function. It is the exstrapolation from “inessential” to “should not be included in the minimal genome” that is unwarranted.
(Incidentally, let me add that I am simply accepting the characterization provided in this news brief, that geneticists really have been systematically guilty of this oversight. News briefs are frequently sensationalized in an attempt to exaggerate the importance of the work being described. But since it has no real impact on my arguent, I will accept the claims made in the brief.)
So such errors as were made were not the result of misapplied evolutoinary thinking. But how were these errors uncovered? Was it the result of ID thinking? Happily, the news brief tells us:
The researchers made this discovery after developing a new approach to genome modelling which, given the organism’s evolutionary history and knowledge of its surrounding environment, allows them to predict which genes a bacterium’s genome should contain. (Emphasis Added)
Gosh. I wonder why Salvador didn’t quote that part?
So the error that was made had nothing to with misapplied evolutionary thinking. Quite the contrary. The error was uncovered by applying evolutionary thinking to certain problems in genetics.
Taking Cordova seriously for a moment, we are led to the following question: The unwise extrpaolation described in the news brief has been going on for quite some time now. It was just recently exposed by scientists applying evolutionary thinking to the problem. But if ID provides a better framework for addressing these qustions than evolution, then why didn’t some clever ID person jump into the breach? Where were Jonathan Wells and Michael Behe and the other biology mavens on the ID side to point out this error?
Salvador can blather all he wants about how ID is a more useful framework than evolution, but the fact remains that it was evolutionists, not ID folks, who exposed this error. Scientists are still waiting, as they have been for over a decade, for ID folks to justify their assertions that ID provides a useful framework for scientific research. Instead of making good on that promise, ID folks prefer instead to waste everyone’s time with ever more bloated claims about the future time when ID will triumph. Less talk, Salvador. More action.
Which leads us to point number two. Hard as it is to believe, Salvador is actually arguing that redundancy in complex systems is what signals design. Which is amusing, since the main weapon in the ID arsenal, irreducible complexity, is based entirely on the idea that it is lack of redundnacy that signals design. A structure is said to be irreducibly complex if it has several well-matched parts, such that the removal of any one part causes the system to cease functioning. Here’s William Dembski explaining the logic:
Far from being a weakness of irreducible complexity as Miller suggests, it is a strength of the concept that one can determine whether a system is irreducibly complex without knowing the precise role that each part in the system plays (one need only knock out individual parts and see if function is preserved; knowing what exactly the individual parts do is not necessary).
But in arguing in this way, ID folks entirely ignore the possibility that a part that is essential to proper function today might have been redundant in some ancestral organism. Indeed, this is one of the primary fallacies of irreducible complexity.
In other words, a lack of awareness of the possibility of systemic redundancy is an essential part of ID’s main scientific assertion.
We might also point out that if Salvador is serious that redundancy in complex biological systems is the hallmark of design, than an awful lot of complex systems were not designed. It is a commonplace in biology to find that systems that are absolutely vital to an organism’s survival show no redundancy at the genetic level.
So I’m afraid Salvador’s argument is, as usual, ridiculous.