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Tuesday, October 11, 2011

Junk & Jonathan: Part 12—Chapter 9

This is part 12 of my review of The Myth of Junk DNA. For a list of other postings on this topic see the links in Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

The title of Chapter 9 is "Summary of the Case for Functionality in Junk DNA." It is Wells' attempt to summarize the "evidence" he has presented so far.

Wells tells us that the "evidence" falls into two broad categories: (1) evidence that putative junk is probably functional, and (2) evidence that small specific bits of the genome are functional.

Within the first category there are two subdivisions: (1a) evidence that most of the genome is transcribed, and (1b) genome comparisons. Let's look at these two subcategories.

"Evidence" that Putative Junk DNA is Probably Functional

We've already discussed the evidence that most of the genome is transcribed [Junk & Jonathan: Part 6—Chapter 3]. We saw that this "evidence" is not universally accepted by workers in the field. Even if most of the genome is transcribed at some level it is generally conceded that much of the product could be rare transcripts that are nothing more than junk RNA. These are accidental transcripts that are expected at some low level due to the intrinsic properties of DNA binding proteins. Thus, even if the result is correct, it doesn't mean what Wells thinks it means and it is not very good evidence for the functionality of most of the genome.


& Junk DNA
The "genome comparisons" approach was discussed in my review of Chapter 5 under "Sequence Comparisons" [Junk & Jonathan: Part 8—Chapter 5]. The main point there was that Jonathan Wells wants to have his cake and eat it too. He doesn't believe in evolution or sequence conservation but when it suits him he's perfectly happy to use an evolutionary argument to support his cause.

Let's see how he summarizes the case in Chapter 11.
A second line of evidence in the first category comes from comparisons of DNA sequences in different organisms. According to evolutionary theory, different lineages inherit their DNA from a common ancestor. If two lineages inherit non-protein-coding DNA that is non-functional, it will be unaffected by natural selection and tend to accumulate mutations in a random manner. Many generations later, the non-protein-coding DNA in the two descendant lineages will be very different. On the other hand, if the non-protein-coding DNA is functional, natural selection will tend to weed out mutations. In evolutionary terminology, the descendant's non-protein-coding sequences will be "conserved."

Turning the logic around, evolutionary theory implies that if evolutionarily divergent organisms share similar non-protein-coding DNA sequences, those sequences are probably functional. As we have seen, many non-protein-coding DNA sequences are conserved, suggesting that they serve biological functions.
Nobody questions the fact that lots of non-protein-coding DNA has a function. Examples of functional conserved DNA includes: many genes that encode various functional RNAs; centromeres; telomeres; SARs; regulatory sequences; intron splice sites; origins of replication; and active transposons. I've explained that the sum total of these conserved regions is only a few percent of the genome. It doesn't even come close to accounting for most of the DNA that's assumed to be junk.

Let's really turn the logic around. If a sequence is NOT conserved then it's likely to be non-functional. (Although there are some exceptions.) About 90% of the genome shows no evidence of conservation in genome comparisons. Thus, according to the logic described by Wells, it's probably junk. He doesn't mention this.

"Evidence" of Specific Functions in some Putative Junk DNA

This "evidence" is described in Chapters 4-7. As I explained in those chapters, the sum total of all examples in a given species doesn't amount to a hill of beans (<1% of the genome). Wells seems undeterred by this data. He doesn't make it clear to his readers that the amount of DNA is very small. In his public lectures and writings Wells emphasizes that he's talking about "trends" and not absolute numbers. The fact that functions for some putative junk DNA have been discovered over the years suggests, according to Wells, that eventually all of the putative junk DNA will turn out to have a function. That's wishful thinking, but, just for fun, let's try and calculate when that "trend" will prove that Wells is right. We can estimate, generously, that functions for 1% of putative junk DNA have been discovered in the past twenty years (in any given species). At that rate, we only have to wait 2000 years before all of the putative junk DNA disappears. Just think of the implications. Sometime in the year 4012, our great100-grandchildren will be awarding the Nobel Prize to Jonathan Wells!

How does Wells account for the fact that many of us still think that most of our genome is junk? He closes the chapter with this teaser ....
Given the abundant and growing evidence for functionality in non-protein-coding DNA, it seems that recent defenders of the myth of junk DNA—like the authors cited in Chapter 2—are motivated by something other than scientific evidence.
Imagine that! Jonathan Wells, the Moonie IDiot, is only motivated by scientific evidence but people like me are motivated by something else. I can hardly wait to find out what that is.

1 comment :

The Other Jim said...

Hmmm... the usual suspects have nothing to say this time. Interesting...