So, Alu elements are mobile DNA modules that can exert diverse influences on genomes and the organisms harboring them. They can affect genome function in constructive ways, by altering gene expression or supporting chromosome structure. And they can be damaging, even deadly. There are more than a million of them in the human genome, and we don't know what each one does. But, as I explained in the first post in this series, we do know that they can play both helpful and harmful roles, in the same way that other kinds of parasites can be good, bad, or indifferent.
Alu elements and other genome-wide repeats are a big problem for intelligent design (ID) theorists of some stripes. Any ID proponent who claims that genomes are carefully-designed, well-optimized systems must deal with the reality of the enormous numbers of mobile elements in (for example) the human genome. Now, I can think of various ways such an ID theorist might discuss Alu elements. She could propose that all of their characteristics (including their mobility) are part of their design, such that they can bring new design features quickly into being; she could propose that their mobility is a "bug" rather than a "feature," and perhaps speculate on how things went wrong; she could postulate that the damage caused by their expression and their mobility is being misattributed to the genome when it is instead caused by some other external process. (Or she could say, "We're still working on that one.")
Well, sadly, there's one other option for an ID apologist. She could tell only part of the story, claiming that Alu elements are one of God's gifts to humankind, while omitting the most important facts about them.
Consider what we know about Alu elements. Here is a list of what we might call their "positive" attributes:
- They can participate in the control of gene expression.
- They can participate in structural functions in the genome.
- They can be converted into functional genes.
- They can cause harmful mutations by hopping into the middle of essential genes.
- They can destabilize the genome by facilitating damaging large-scale physical interactions.
- They can generate toxic RNA molecules that must be controlled by other cellular systems.