"Fx of Junk DNA" or "Mondo hackitude-o-rama".

I do not read the intelligent design blogs, but I do read the blogs of some people who read the intelligent design blogs. Today, Afarensis points to a series of “predictions” put forward by ID proponents at the behest of William Dembski on his blog Uncommon Descent for use in an upcoming interview or something. Curious to see what ID predicts (since, as noted, I don’t read their blogs and they don’t publish in the scientific literature), I took a look.

Apparently, many ID proponents don’t know what a prediction is, or at least not what a useful, testable, scientific prediction is. For example:

“Intelligent design can predict that science will never be able to explain how this complex life arose (homochirality). This prediction has been confirmed every year for decades.”

“That after “billions and billions” of generations of any particular biological entity no new morphology will occur due to random mutations and natural selection.”

“ID predicts that many, if not all, innovative technology achievements of human kind (read agency) will have direct parallels in, or derivation from, biological systems.”

And so on.

But here is what caught my attention.

“The single most important prediction of Intelligent Design is that, although there might be the occasional degeneration of either macroscopic or microscopic structure, most structures should serve a purpose. Thus most organs should not be vestigial, and most DNA should not be “junk DNA”.”

Others concurred that 1) junk DNA won’t be junk, and 2) this is a prediction of ID, and 3) this distinguishes ID from evolutionary science.

I have been over this many times, but of course ID proponents probably don’t read my blog (or the scientific literature). Here are the salient points:

1) There is good reason to believe that non-functional DNA is common. The mechanisms of formation — primarily things like transposable element multiplications, gene duplication and pseudogenization, replication slippage, and unequal crossing over — can add DNA without any requirement that it serve a function. Actual data from genome sequences confirms that the most substantial fraction of eukaryotic DNA is transposable elements, some of which are functional, some of which cause disease, and perhaps most of which are now inactive molecular vestiges. Evolutionary biologists do not simply assume non-function out of ignorance. The default assumption for much non-coding DNA is non-function because of what we do know about how it gets there.

2) I have yet to see a convincing, or even unconvincing, argument for why ID requires that non-functional features be rare or non-existent if indeed nothing can be known about the designer. Even very sophisticated products of design by humans have their redundancies and non-functional aspects. For a fun example, consider what was discovered when parts of the source code for Windows 2000 were leaked to the internet during development. It was laced with curse words, warnings of “hacks” that had to be written in to make parts work, and just general expressions of frustration. For example:

// We are morons. We changed the IDeskTray interface between IE4″

// TERRIBLE HORRIBLE NO GOOD VERY BAD HACK

* The magnitude of this hack compares favorably with that of the national debt.”

// Mondo hackitude-o-rama.”

These are remarks that do not code for anything. You could take them all out and nothing would happen to the function of the software. Or, taking a larger view of this analogy, your computer hard drive probably has on it all sorts of redundant, partly deleted, or perhaps even malevolent bits of code, and yet it nonetheless was a designed structure.

Here is the argument I am making. Either IDists cannot say anything one way or the other about non-function, or they must provide information about the method and motive of the designer to justify the assumption.

3) One of the basic assumptions made by hardcore adaptationists is that non-coding DNA must be functional or it would have been deleted. So, this “prediction” is not exclusive, or even original, to ID — it is based firmly in the most rigid applications of Darwinian processes.

One commenter on the ID blog said this:

As already mentioned, “junk-DNA” would completely undermine ID if it turned out to really be “junk”. But, of course it isn’t.”

I disagree on both fronts. The existence of truly non-functional DNA would not automatically indicate a conclusive refutation of intelligent design, it would only be evidence against design by a divine designer. One can have design with non-function. I also note that there presently is no convincing evidence that more than a small portion of the human genome is functional, let alone the many genomes that are much larger than that of humans.

IDists can consider “all or most non-coding DNA will have some function” their “single most important prediction” if they choose, but this is meaningless because it provides no specifics, it does not actually allow a test of ID unless they acknowledge the features of the designer, and it was already made by some evolutionary biologists decades ago.




7 comments to "Fx of Junk DNA" or "Mondo hackitude-o-rama".

  • Kyle Ain

    The fact that you don’t read “intelligent design blogs” and only what “others” say about them says a lot about your objectivity. You are a person who only looks for beliefs that match your own, rather than the truth. Furthermore, did it ever occur to you that creationists writing about intelligent design are writing about what those like you say about it? Duh? What, do you think creationist can only come up with information from their own mind? Where in the world would that info come from? Or are they only repeating what the first creationist said? If so, it’s amazing that this first creationist has said so much, enough to fill a bookstore, and yet still isn’t known as the originator.

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  • scripto

    Thanks for the new way of looking at this “junk” DNA. Determining function through the process of formation seems like a better way to go about it. Determining function through a process of elimination must be very time consuming an open ended. My question is, “Do some of these non-functional elements gain function over time, can this potential be selected for and do you have any examples of formerly non-functional DNA gaining function?”

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  • TR Gregory

    There are many examples of genes derived from transposable elements.

    For example, see Jurgen Brosius’s table of genes that show evidence of being so derived.

    There are also estimates that a major portion of regulatory elements, parts of the adaptive immune system, binding sites for regulation systems, and many other functional components are exapted from former TEs. Please note, however, that there is no evidence that this applies to more than a minority of TEs.

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  • Baltrus

    Isn’t it a bit hypocritical of the ID movement to mention conservation of “junk” DNA in the genome (and therefore all evidence of the implied function of said “junk” DNA) because this data was gathered through comparative evolutionary genomics?

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  • scripto

    Thank you TR Gregory for the link. This should be more ammo in my neverending debate with an ID proponent regarding the ability of known evolutionary processes to increase information and produce novel functions. I’m just an interested amateur and a lot of this stuff is way beyond my education level. The best example I was able to find (until now) concerned the formation of the nylase enzyme. This seemed like a pretty cut and dried example of an increase in genetic information with a known mechanism for the increase resulting in a novel function. Cut and dried to me, anyway, not to him. It’s nice to know there are hundreds of other examples – with references yet!

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  • Chris Harrison

    Reviewing a recent paper on the number of human protein encoding genes, Larry Moran just posted about the finding that researchers revealed 18 instances where a functional gene evolved from a pseudogene.

    The paper is:

    Clamp et al (2007). Distinguishing protein-coding and noncoding genes in the human genome.

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  • Doppelganger

    You are a person who only looks for beliefs that match your own, rather than the truth.

    How ironic…

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