"Design' is a sterile hypothesis. 'Design' is a dead end, because it discourages research into the possible natural mechanisms that could have produced design-like features."

So says Gert Korthof on his web page critical of Mike Behe. Yet Korthof is not alone, as perhaps the most common complaint against ID (and most damaging if true) is that it is a scientifically useless concept that is incapable of generating research. But is it?

Those who loudly proclaim that ID is useless often share one defining trait that is common among all, namely, they all have no experience in trying to seriously employ ID to better understand the world. Thus, their accusation is based entirely on ignorance and their inability to think of ways to employ ID becomes confused with the notion that ID cannot be used to guide research. Dawkins' has his "argument from personal incredulity," so I will follow his lead and call this the "argument from personal bafflement." The Argument from Personal Bafflement states that "since I can not think of a way to employ ID in a useful fashion, ID must therefore be useless." Of course, since those who employ the Argument from Personal Bafflement typically have no experience of ever seriously having tried to employ ID, it's an empty argument. It would be like someone who never bothered to learn to read asserting that books are useless.

I have previously shown that ID has indeed been useful in the history of science (see my posting on Teleology and Science). But let me share an experience which settles the issue firmly for me where ID is indeed quite useful.

Earlier I posted an article about proofreading. The information flow that occurs within a cell happens at several points. DNA is used to make DNA; DNA is used to make RNA; and RNA is used to make proteins. So goes the classic formulation of the Central Dogma of molecular biology. With information flow comes the issue of fidelity - how faithful is the information transferred? Scientists have long known that proofreading mechanisms exist during DNA replication where nucleotides that are misincorporated during replication are typically removed and replaced with the correct one. Similar proofreading also occurs at the two crucial points of information flow during protein synthesis: the charging of tRNAs and the anticodon-codon interactions of mRNA and tRNA. My recent posting discusses these two forms of proofreading.

After writing up that article for another board, I was thinking about proofreading and it occurred to me that an important step of information flow appeared to lack proofreading, that of transcription (where DNA is used to synthesize RNA). Now, I know a few things about transcription, but I could not recall ever hearing about proofreading being associated with RNA polymerase activity (the protein complexes that synthesize RNA). It struck me that this was a great opportunity to use ID. Here was my logic.

Imagine you need to translate a book from English into German and then German into Chinese. If it was important that this translation was as accurate as possible, you would employ proofreaders at both stages. For example, it would not make much rational sense to employ proofreaders to ensure the German text was accurately translated into Chinese without also using proofreaders during the first step (the English to German translation). It defeats the purpose of carefully scrutinizing the second translation if your first is sloppy.

Thus, using this logic, I predicted that proofreading should exist during transcription (since I strongly suspect cells, much as they are today, were originally designed by a rational agent(s)). Also, given that the degree of proofreading at the level of protein synthesis was so sophisticated, it would not make sense for a rational agent to not also ensure high fidelity at the level of RNA synthesis.

With this hypothesis in hand, I could thus go into the lab and design experiments to determine if indeed proofreading occurs during transcription. What if I did this? Well, my prediction would have born out. As it happens, I did a literature search after coming up with this hypothesis and indeed discovered there is some good evidence of proofreading during transcription. Consider just one example:

Jeon C, Agarwal K. 1996. Fidelity of RNA polymerase II transcription controlled by elongation factor TFIIS. Proc Natl Acad Sci U S A ;93(24):13677-82

Fidelity of DNA and protein synthesis is regulated by a proofreading mechanism but function of a similar mechanism during RNA synthesis has not been demonstrated. Analysis of transcriptional fidelity and its control has been hampered by the necessity to employ complex DNA templates requiring either a promoter and initiation factors or 3'-extended templates. To circumvent this difficulty, we have created an RNA-DNA dumbbell template that can be recognized as a template-primer and extended by RNA polymerase II. By employing this system, we demonstrate that RNA polymerase II can misincorporate a nucleotide and carry out template-dependent elongation at the mispaired end. The transcripts containing misincorporated residues can be cleaved by the very slow 3'-->5' ribonuclease activity of the RNA polymerase II, but enhancement of this activity by the elongation factor TFIIS generates RNA with a high degree of fidelity. This enhanced preferential cleavage of misincorporated transcripts suggests an important role for TFIIS in maintaining transcriptional fidelity.

Of course, someone could argue that these researchers did not need ID. But that response would miss the point. The question of the utility of ID is different from the necessity of ID. Something can be useful without being needed. That I have paper clips on my desk does not render my stapler useless.

This experience clearly shows me that Korthof is plain wrong - ID is not a sterile hypothesis. ID could have indeed led me to discover proofreading during transcription. It led Harvey to figure out how the circulatory system works. ID is a useful tool. The only reason critics deny this is because they never pick it up, which of course, renders it of no use to them. Yet just because they don't want to use it is no reason why someone else can't pick it up and see how it works.

Addendum (excerpts from a discussion of the above essay)

Someone else: After all, what is the primary reason for a "rational agent" to employ proofreading? What is this specificity for?

I suspect it is for life itself. That is, without such high fidelity, autonomous cellular life might not be able to exist (or if it can, it would quickly go extinct). I think proofreading at every important step in information transfer simply underscores the importance of specificity in life processes. If transcription/translation are not proofread, this not only means you increase the likelihood of plugging non-functional cogs into the machine, but you'll might also overwhelm or overtax the chaperone/folding and proteasome/degradative systems.

Furthermore, the need for such proof-reading might be a reflection of the wide-spread nature of irreducible complexity (IC) in the core biotic processes. If much of this machinery is IC, then a simple transcriptional mistake in one cog can be amplified tremendously as one non-functioning cog might be expected to have a quasi-dominant negative effect. In other words, say the electron transport chain is IC (a reasonable speculation). If a bunch of bad cytochrome c's are synthesized and incorporated, you might have seriously compromised or shut down aerobic respiration, even if everything else in the chain is functional. The cell not only can't respire for the time these faulty proteins remain, but it has also wasted a bunch of energy synthesizing all the other respiration machinery that now provides no return. If IC is common, that is all the more reason to need proofreading.

However, the significant point in my mind is that I was able to infer the existence of proof-reading by using the logic of ID. I don't claim ID was needed to make such an inference, but it was demonstrably capable of making a fairly specific inference about the workings of the cell. Recall that I was reacting to the claim that ID is a 'sterile hypothesis' and 'dead end.' I think my simple example refutes that common accusation.

[snip]

Let me repost the actual reasoning I employed to infer such proofreading. This is not an after the fact rationalization, but was indeed the very logic I used to predict something about life.

"After writing up that article for another board, I was thinking about proofreading and it occurred to me that an important step of information flow appeared to lack proofreading, that of transcription (where DNA is used to synthesize RNA). Now, I know a few things about transcription, but I could not recall ever hearing about proofreading being associated with RNA polymerase activity (the protein complexes that synthesize RNA). It struck me that this was a great opportunity to use ID. Here was my logic.
Imagine you need to translate a book from English into German and then German into Chinese. If it was important that this translation was as accurate as possible, you would employ proofreaders at both stages. For example, it would not make much rational sense to employ proofreaders to ensure the German text was accurately translated into Chinese without also using proofreaders during the first step (the English to German translation). It defeats the purpose of carefully scrutinizing the second translation if your first is sloppy.

Thus, using this logic, I predicted that proofreading should exist during transcription (since I strongly suspect cells, much as they are today, were originally designed by a rational agent(s)). Also, given that the degree of proofreading at the level of protein synthesis was so sophisticated, it would not make sense for a rational agent to not also ensure high fidelity at the level of RNA synthesis. "

Was this repackaged 'selectionist thinking.' No. In fact, I think much of selectionist thinking is really repackaged ID thinking.

An easy way to see this is that Darwinian selectionist thinking cannot lead to this inference (except in an after the fact manner). Why? Darwinian selection entails only that things "work", not that they be inherently rational or sophisticated. And since I had no reason to think cells cannot work without transcriptional proofreading (prior to finding that it existed), I had no reason to think natural selection had created it. But it goes even deeper than this.

Imagine proofreading did not exist during transcription. I think this would pose a serious problem for ID, as it would make very little logical sense to so carefully proofread messages that were generated without proofreading (go back to my translation analogy). Instead, this would look more like another example of the manner in which evolution spits out 'higgledy piggledy' things. As we know, evolution is often very messy and wasteful. It also typically builds things by jury-rigging pre-existing things in a higgledy piggledy manner. Thus, there is simply no reason to think that selection entailed the existence of transcriptional proofreading. The selectionist view easily absorbs both the existence and non-existence of transcriptional proofreading. In fact, selection has other messy solutions it could exploit, such as selecting for redundancy that would minimize transcriptional errors. And the more I think about it, its existence could only be inferred by adopting a ID perspective that can, of course, be repackaged in selectionist terms after the fact.

But the bottom line is that I did indeed use ID logic to infer this biological fact prior to knowing about this biological fact. It is an experience so significant to me that I can even recall what I was doing at the time of this inference.

So how did I come to hypothesize that proofreading was essential? It did not come from any previous knowledge about transcription. Unlike your friends, I did not infer its existence from RNA polymerase and transcription behavior. The data set I used dealt with the very different process of translation. So what would lead me to extrapolate information from translation to transcription?

Well, it certainly wasn't Darwinian logic, as nothing there would allow me to infer the existence of proofreading. It was indeed a certain logic that has been developing since taking ID seriously.

First of all, there is the overall background emphasis of specificity that comes with ID. This is in stark contrast the general emphasis on messiness that comes with Darwinian thinking. The more specified something is, the stronger the design inference. Thus, one looks for examples of extreme specificity to minimize the error of making a false design inference.

Secondly, with the general emphasis on specificity rather than messiness the background, there was also something else in the background. What ties translation and transcription? A suspicion that we're dealing with a designed system of information flow. That is, the tie is abstract and conceptual. Thus, I have been reading up on some mechanical engineering texts that outline the process of design. Not too long ago, I finished one that describes, "Function can be described in terms of the logical flow of energy, material, or information." This has significantly colored my thinking, as I have been looking for logical flows (something I would rarely expect from the blind watchmaker). In other words, if something is designed, and the two systems are linked in a more conceptual than structural manner, one expects to find a certain logic that binds them.

Now, with these twin perspectives of specificity and logical flow in mind, I encountered the various articles on some rather amazing and sophisticated means of proofreading translation. This then led to my analogical thinking, where of course, the analogy dealt with a rational and teleological reality. Confronted with some rather sophisticated and specified proofreading near the terminal stages of information flow, it seemed to me at the time most logical to expect its existence at a preceding stage (as my analogy illustrates).

Of course, you raise the issue that my analogy was flawed because "determining this is a largely empirical exercise for which not a lot of data is available." Okay, so I skipped a step and got lucky. Nevertheless, the bottom line is that the reasoning worked. That's the simple fact. If you'd rather, I could simply argue that the same ID reasoning could serve as the impetus for generating this needed data in order to reach the same inference with the same reasoning.

You also seem to misunderstand the nature of my analogy. You repeatedly focus as follows:

"Again, only if your preset conditions were true: if it was important that this translation was as accurate as possible..., would transcriptional proofreading "make sense." If not, then it wouldn't matter."

This was an analogy to highlight the relationship between specificity and logical flow among designed events. It employed "if, then" reasoning. So where did the preset "if" come from? Not from darwinian thinking, as it cannot imply these preset condition. It came from ID. If life is designed, and specificity is a common trace of design (and typically required of designed components) then conceptually, one might expect to see this theme of specificity laid out in a logical flow.

Return home.