Posted by PvM on April 22, 2007 05:47 PM

On UcD, Salvador Cordova, makes the common and fallacious argument that ID somehow predicted function in ‘junk DNA’. In fact, there is no logical foundation for this claim as ID lacks predictive power beyond ‘Darwinism does not explain X’. At most Sal can claim that people who are also proponents of ID have ‘predicted’ function for Junk DNA. But as such they are not much different from scientists who have predicted function for Junk DNA as well. Where they differ is in what motivated them to reach such a conclusion.

Cordova wrote:

ID theory has provided positive inspiration toward scientific inquiry and participating in the reversal of “the greatest mistake in the history molecular biology“, a mistake inspired by Darwinist dogma.

ID has contributed little either in predicting or establishing function in ‘Junk DNA’ but it also seems to be basing its claims on further ignorance about the origin and evolution of the term Junk DNA (which originated from the ideas of proponents of neutral evolution and was originally limited to refer to pseudogenes). While it should not come as a surprise that ID attempts to ride on the coat tails of real science, such an attempt can be quickly countered.

Nevertheless, even in his enthusiasm, Sal seems to have downgraded ID’s contribution to ‘positive inspiration’. Even ID proponents seem to shy away from making claims that ID is scientifically fertile and are willing to settle for ‘inspirational’.

Already in 1998 Should Scientists Scrap the Notion of Junk DNA? Bob Kuska describes how science had come to realize the many treasures in ‘junk DNA”.

(Journal of the National Cancer Institute, Volume 90, Number 14 Pp. 1032-1033)

and Bring in Da Noise, Bring in Da Junk–the Semantics of Junk DNA

The term ‘Junk DNA’ is somehow unfortunately chosen as it has led quite a few creationists like Sal astray into believing that ‘Junk DNA’ cannot have function or that it was inspired by Darwinian dogma.

Let’s explore this in some more detail. More generally, the term junk DNA refers to ‘non coding’ DNA, that is DNA which is not directly expressed as proteins. In other words, Junk DNA denotes parts of the DNA for which no function has (yet) been identified. Since science has established that there exist strongly conserved regions of DNA with no identifiable function, it has concluded that this may point to a yet unknown function of Junk DNA.

The term Junk DNA can be traced back to an article by Ohno titled “, “So Much ‘Junk’ DNA in Our Genome.”, published in 1972. What many have forgotten is that Ohno was commenting on a particular form of ‘junk’ namely pseudogenes and the term “Junk DNA” slowly took on a different meaning to include all non-coding sequences (sequences that do not produce proteins).

See for instance: B. Kuska, Should Scientists Scrap the Notion of Junk DNA? JNCI Journal of the National Cancer Institute 1998 90(14):1032-1033

Recent findings by scientists have shown that the use of the term Junk to describe non-coding DNA has been unfortunate as evidence has been found that shows that some of the non-coding DNA indeed has function (as many had already suspected based on Darwinian arguments). For instance, there are regulatory elements which regulate the actually gene expression, which reside in non-coding parts of the genome.

The literature seems to understand that Junk DNA does not mean ‘without function’.

Note that the term “junk DNA” is not a term of art. It may simply mean DNA whilst they have a function - do not code for protein at all. It may also mean DNA sequences that appear to have no function at all.

Source: An Introduction to Genetic Engineering, Life Sciences and the Law By George Wei 2002 SUP

At Genomicron, T Ryan Gregory provides us with an exquisite overview of Junk DNA

T Ryan Gregory wrote:

To satisfy this expectation, creationist authors (borrowing, of course, from the work of molecular biologists, as they do no such research themselves) simply equivocate the various types of non-coding DNA, and mistakenly suggest that functions discovered for a few examples of some types of non-coding sequences indicate functions for all (see Max 2002 for a cogent rebuttal to these creationist confusions).

Now remember that ID can at most observe that there exists DNA for which no function has been found and allow our ignorance to lead to a design conclusion. However, ID lacks the predictive capability to make a claim that Junk DNA has a function. On the other hands, science, facing the hard tasks of reducing our ignorance through research, hypothesis building has reduced our ignorance about Junk DNA by finding how some ‘Junk DNA’ serves a function after all.

Wikipedia identifies much research in this area and despite the claims by some ID proponents that ID somehow inspired or predicted Junk DNA, the ‘shocking’ reality is that ID was mostly absent from the scene.

Why ID is scientifically without much value

So why is ID doomed to remain scientifically irrelevant? For the simple reason that it cannot compete with ‘we don’t know’. In other words, at best, ID can be ‘we don’t know’, at worst it becomes a gap theory where our ignorance is replaced with a term ‘intelligent design’.

That this is the case is not hard to understand. ID is based on the observation or at least argument that a particular feature cannot (yet) be explained by science. Since ID however does not provide any independent hypothesis to explain the feature, it cannot compete with the ‘we don’t know’ hypothesis. In other words, at best, ID is an argument from ignorance: We don’t know, thus designed. ID proponents tend to shroud this by using unnecessary terminology such as complexity (which basically means the same as ‘we don’t know’) and specification (which basically means nothing more that ‘it has a function’). Worse, once science has identified an explanation for the system, and ‘design’ quickly disappears.

Ryan Nichols, author of “ The Vacuity of Intelligent Design Theory” noticed how ID proponents are often unaware of the limited thesis proposed by Dembski:

Ryan Nichols wrote:

Before I proceed, however, I note that Dembski makes an important concession to his critics. He refuses to make the second assumption noted above. When the EF implies that certain systems are intelligently designed, Dembski does not think it follows that there is some intelligent designer or other. He says that, “even though in practice inferring design is the first step in identifying an intelligent agent, taken by itself design does not require that such an agent be posited. The notion of design that emerges from the design inference must not be confused with intelligent agency” (TDI, 227, my emphasis).

Source: Ryan Nichols, Scientific content, testability, and the vacuity of Intelligent Design theory, The American Catholic Philosophical Quarterly, 2003 ,vol. 77 ,no 4 ,pp. 591 - 611

Nichols continues to describe why ID is also doomed to remain scientifically vacuous.

Proponents of Intelligent Design theory seek to ground a scientific research program that appeals to teleology within the context of biological explanation. As such, Intelligent Design theory must contain principles to guide researchers. I argue for a disjunction: either Dembski’s ID theory lacks content, or it succumbs to the methodological problems associated with creation science-problems that Dembski explicitly attempts to avoid. The only concept of a designer permitted by Dembski’s Explanatory Filter is too weak to give the sorts of explanations which we are entitled to expect from those sciences, such as archeology, that use effect-to-cause reasoning. The new spin put upon ID theory-that it is best construed as a ‘metascientific hypothesis’-fails for roughly the same reason.

See also one of my earlier postings showing why ID is doomed to remain scientifically irrelevant.

The reason ID fails is simple, it lacks any predictive power beyond ‘X cannot be explained by Y’. In case of Junk DNA, there is simply no logical foundation for ID’s claim that ‘Junk DNA’ needs to have function, unless one presumes capabilities, or aspects of the designer. But ID is clear that it is unable to address these issues and that these issues are separate from ID.

Now, historically, the reason why ID can claim that it made successful predictions is because contrary to its claims, it did make presumptions about its designer and argued that God would not be wasteful. So now ID is faced with an interesting conundrum, either it admits that it was the assumptions about their God not being wasteful which lead to this ‘prediction’, or accept that it lacks any scientific foundation for its claims. Of course, either way, there is no good scientific reason to presume that God would not be wasteful, or God would surely not have created antelopes and cheetash :-)

So how did ID make this ‘prediction’ ? For this we need to understand the history of this prediction, which, to noone’s surprise, can be found in creationist arguments.

See ‘Junk’ DNA: evolutionary discards or God’s tools?

It’s time to put to rest yet another “confusion by design”

As I pointed out elsewhere almost a year ago:

The idea that Junk DNA has function has no roots in ID unless it relies on the premise of a Christian God and even then the argument has no predictive value since creationists argue on one hand that God designed all life and that thus design was initially perfect, leading to the conclusion of no ‘junk DNA’ or Junk DNA will have function. Or they argue that Junk DNA can be explained by the Fall, leading to a deterioration of the genome.
Since ID provides no logical link between its scientific premises and its prediction about Junk DNA, the conclusion is inescapable, its prediction is guided by theology not science.

In other words ID cannot make predictions about “Junk DNA” which follow from their premise. All it can do is detect complex specified information and since junk DNA has no specified function yet, it cannot make any such predictions. Unless there is another premise which guides ID such as the efficiency of the Designer or the Designer’s Creation being perfect in the sense of no superfluous systems or DNA which has no function.
So either ID is vacuous scientifically or it makes predictions which follow from particular assumptions about the Designer. The latter one is contrary to ID’s approach and thus has to be rejected, unless one links ID to its historical and metaphysical roots.

Source

On UcD Campana observes in response to Dembski fishing for evidence that Junk DNA was inspired by Darwinism (how hard is it to do the necessary research I wonder?)

Dembski wrote:

I suspect that the “junk DNA” hypothesis was originally made on explicitly Darwinian grounds. Can someone provide chapter and verse? Clearly, in the absence of the Darwinian interpretation, the default assumption would have been that repetitive nucleotide sequences must have some unknown function.

Campana wrote:

I just got my hands on Ohno’s paper. It seems like the link provided by Pellionisz pretty well summarizes what is going on here. Ohno was looking for function, and the paper does seem something like a lament. However, this only appears to negate Bill’s postulate that “the ‘junk DNA’ hypothesis was originally made on explicitly Darwinian grounds.”

By using the term “junk DNA”, Ohno was offering terminology to summarize one proposal for the role of repetitive DNA.

The Ohno paper is one of a number of papers in a collection, and another interesting paper in the anthology, by R.J. Britten, offers an overview of early 70’s perspectives on the origin/purpose of the repetitive DNA. Britten reveals that, “Whether the repeated DNA in its now widely interspersed state is simply spacer between genes or carries out an active role is the subject of intensive current investigation.” On the next page, Britten offers 9 possible roles of repetitive DNA, including only one the possibility that it was “2. CARRIED ALONG (Parasitic or garbage).” By using the term “junk DNA”, Ohno was offering terminology to summarize the “CARRIED ALONG” proposal for the role of repetitive DNA.

Based on this Britten quote above, and a brief review of all of the hits on PubMed for “junk dna,” it seems that scientists have been looking for functions in the “junk” all along. As Bill suspected, the default scientific position has been to look for function, as well it should.

So will ID and Dembski continue to repeat its claims? We shall see. If history is a predictor of the future then we may expect more…

My thanks go out to my dear friend and YEC’er Salvador “Darwinian TE (Theistic Evolution) just doesn’t cut it scientifically” Cordova and Uncle William “Bill” Dembski without whom this useful tutorial would not have been possible.