Thursday, June 15, 2006

Junk DNA and the anti-design hypothesis

The charge against ID is that assuming something has purpose doesn't lead to useful science.

The countercharge (from me) is that assuming something doesn't have purpose doesn't lead to useful science.

I've started a new post because these ideas are very interesting, and deserve more visibility than they would get in comments of an existing post.

Looking at this in the context of non-coding DNA...
To demonstrate [that an anti-teleological approach restricted science], you'd need to show that this approach had caused people to reject valid evidence that certain DNA had function. Otherwise, all that you'd be demonstrating was that lack of function was indeed a valid null hypothesis, which people would happily move away from in the face of evidence.
I don't think so. To demonstrate this, you have to show that having assumed that something had little or no purpose, people turned their faces away from it to areas that looked more promising. Had they assumed that it had purpose, they might have continued their investigations and discovered the purpose at an earlier stage.

I was trying to remember back to Biology of Cells Part I (1986-7). I don't recall ever being taught much about non-coding DNA, other than the fact that there was lots of it - and I'm pretty sure that the phrase "junk DNA" goes back in my mind well over a decade.

I also looked in Alberts et al ("Molecular Biology of the Cell", 1983) to find out what he said, which was:
Most Chromosomal DNA Does Not Code for Essential Proteins

...Population biologists have estimated just how much of the DNA of higher organisms actually codes for essential proteins (or is involved in the regulation of genes coding for such proteins). In outline the argument runs as follows: Mutation is an accidental process in which randomly selected nucleotides in the DNA sequence are altered at a low but finite rate. Since most such mutations will be deleterious to the organism when they occur in an essential DNA sequence, there is a limit to the number of essential genes that can be stably maintained. It has been estimated from the observed mutation rate that no more than about 1% of the mammalian genome can be involved in regulating or coding for essential proteins....

What does the rest of the DNA do in higher eucaryotic genomes? We have already suggested that some of it may have a purely structural function in the organization of chromatin. In later sections of this chapter we shall discuss more recent evidence on the nature of the noncoding DNA and some other hypotheses about its function. Whatever the answer(s), the data shown in Figure 8-33 make it clear that it is not a great handicap for a higher cell to carry along a great deal of extra DNA, which suggests that there has been little pressure to minimize DNA content to include only the essential regions.
Note "essential" - non-coding DNA is considered "non-essential". And the index, at least, gave no indication as to where any later discussion of other hypotheses could be found. There was little other mention of non-coding DNA throughout the book

Even more significant is Goodenough ("Genetics", 3rd Edition, 1984). Again there is no reference to "junk DNA", but there are two short sections that relate to non-coding DNA. Firstly, in the context of considering the chromosome of a virus visualizing the chromosome of T4 we can think of a given single strand of DNA as having long sequences of bases containing meaningful information, followed by long sequences of bases that do not code directly for protein and presumably code for nothing at all.[p.264, emphasis mine]
The only other section on "non-coding DNA" referred to in the index is in the section relating to "'Split Genes' in Eukaryotes" -
the coding oregion of most eukaryotic structural genes is interrupted by noncoding sectors, called ... introns.
A later section (9.11) talks about the "'Purpose' and Evolution of Intervening Sequences". She writes:
why do eukaryotes "bother" to have introns that they first transcribe and then excise? Several observations are compatible with the theory that introns serve no purpose .... On the other hand, there are indications that at least some introns have functional roles .... Perhaps the most interesting theory is W. Gilbert's proposal that introns might have been important in eukaryotic evolution.... the Gilbert proposal suggests that most present-day introns may be evolutionary relics[her emphasis], once important for creating new eukaryotic genes and persistent simply because cells have no way to get rid of them
As far as I can tell from a quick study, this is all the detail that Goodenough goes into regarding non-coding DNA. There is no obvious reference to the fact that the majority of DNA is "non-coding" and had no known function at the time.

So to conclude, I can't offer evidence on the basis of the information I have to hand that an anti-design hypothesis inhibited research. However, I have demonstrated that this non-coding DNA, despite its significance within a cell, was basically ignored at an undergraduate level as late as the mid-1980's. At best, this suggests that it was considered to have no biological significance; it was "not essential"; non-coding DNA was an "evolutionary relic". What would motivate people to investigate the significance of something when mainstream textbooks had dismissed it in those terms?