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are the two main sources of evidence that Alu elements are mobile genetic elements.

1. We've seen them jump, and we know a bit about how they do it. Simply put, Alu elements areknown to move, and they move by using known mechanisms. In fact, biologists have estimated thelikelihood that a new "jumping" event will occur in a newly-conceived human embryo to be about5%, meaning that roughly one in twenty persons are born with a new Alu element insertion

somewhere in her/his genome. The process by which Alu elements move is very similar to theprocesses used by other mobile elements.

2. They're highly conserved, meaning that one Alu element looks a whole lot like all the others.(There are five or six subtypes of Alu elements; the similarity is even more pronounced within thosegroups.) So we're not talking about a vague category of things that look sort of like a jumping gene.

We're talking about a family of DNA elements with very specific features. Remember that they'realso called "repeats," because even in the early days of genomic analysis (before we had the actualsequences of whole genomes) biologists knew that huge stretches of the human genome were madeof chunks of DNA that were highly similar often identical and repeated over and over and over.

Taken together, then, in the Alu elements we have a huge family of closely-related DNA elements

with structural features that are known to mediate movement within the genome. If all that soundsa little too technical, don't worry; what matters is that you grasp the basic notion (human genomesharbor so-called "jumping genes" that can move about within those genomes) and its magnitude(Alu elements are just one type of mobile element, and they alone make up more than 10% of thehuman genome).

So, do these things have a "function"? That's a tricky question. (Just the kind of question preferredby ID propagandists.) Alu elements and their kin are currently viewed by biologists as parasites,and if you know anything about parasitism then you know it's a bit too simplistic to ask whether aparasite is "good" or "bad" for its host. In many parasitic relationships, the host organism incurssome cost (or risk) by hosting the parasite, but also enjoys some benefit. You might think of the

bacteria in your gut in this way; they're good to have around, but they can cause problems if they

get out of bounds. It's like they've been domesticated: they're still potentially harmful, but if kept incontrol they're useful. Or at least, if they obey the rules, they're not too big a burden.

Considered in this way, Alu elements make sense. They can be useful. For one thing, their sheerbulk enlarges the genome, and genome size affects things like cell size. Alu elements can introducenew genetic diversity into a species, far more quickly than other kinds of mutation, and so they can

be drivers of evolutionary change, by altering the genetic landscape literally overnight. Some Aluelements are known toinfluence the expression of genes (i.e., when those genes are on or off). And,notably, Alu elements can sometimes be converted into useful genes. In other words, likeconventional biological parasites, they can be good to have around.

But, like conventional biological parasites, they can be dangerous. Alu elements can destroy criticalgenes by hopping into them. (The Alu element is about 300 DNA "letters" in length, and if thoseletters are added to the protein-coding part of a gene, the nearly-certain outcome is the conversionof the gene to gibberish.) Such events are known to underlie instancesof devastating humangenetic diseases. Because the Alu elements are so numerous and because the various types all lookalmost completely alike, theyfoster damaging interactions between parts of the genome andthereby facilitate large-scale genetic damage. And so humans (and other animals) pay a significantprice for hosting mobile genetic elements, and the risks are exactly what we would expect from"jumping genes" that move without regard to the potential harm their relocations can cause.

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http://dx.doi.org/10.1038/ng1223http://genome.cshlp.org/content/19/9/1516.fullhttp://genome.cshlp.org/content/19/9/1516.fullhttp://dx.doi.org/10.1016/j.cell.2008.09.022http://en.wikipedia.org/wiki/Human_florahttp://onlinelibrary.wiley.com/doi/10.1111/j.1469-185X.2000.tb00059.x/abstracthttp://onlinelibrary.wiley.com/doi/10.1111/j.1469-185X.2000.tb00059.x/abstracthttp://www.pnas.org/content/107/46/19945.abstracthttp://nar.oxfordjournals.org/content/34/19/5491.longhttp://nar.oxfordjournals.org/content/34/19/5491.longhttp://dx.doi.org/10.1073/pnas.0601161103http://www.nature.com/gene/journal/v3/n1s/full/6363864a.htmlhttp://www.nature.com/gene/journal/v3/n1s/full/6363864a.htmlhttp://dx.doi.org/10.1006/mgme.1999.2864http://dx.doi.org/10.1006/mgme.1999.2864http://www.biomedcentral.com/1471-2164/12/157http://www.biomedcentral.com/1471-2164/12/157http://dx.doi.org/10.1038/ng1223http://genome.cshlp.org/content/19/9/1516.fullhttp://genome.cshlp.org/content/19/9/1516.fullhttp://dx.doi.org/10.1016/j.cell.2008.09.022http://en.wikipedia.org/wiki/Human_florahttp://onlinelibrary.wiley.com/doi/10.1111/j.1469-185X.2000.tb00059.x/abstracthttp://www.pnas.org/content/107/46/19945.abstracthttp://nar.oxfordjournals.org/content/34/19/5491.longhttp://dx.doi.org/10.1073/pnas.0601161103http://www.nature.com/gene/journal/v3/n1s/full/6363864a.htmlhttp://www.nature.com/gene/journal/v3/n1s/full/6363864a.htmlhttp://dx.doi.org/10.1006/mgme.1999.2864http://www.biomedcentral.com/1471-2164/12/157

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Those facts alone should lead us to predict that humans (and other animals) wouldemploydefenses against these parasites, if not to eradicate them then at least to keep them fromoverrunning the place. And these facts should make readers of most ID writing on this topic think alot differently about ID claims. For one thing, we should be suspicious of any argument tackling thestraw man of whether or not Alu elements are "functional elements" as opposed to "junk DNA."

But look again at the risks that I discussed. I mentioned two big ones: the risk that an Alu elementwould hop into a gene and thereby damage the gene, and the related risk that Alu elements wouldcause other structural damage to genomes. But can these elements be damaging in other ways? Ifthey function as parasites, and if they insist on making RNA in hopes of hopping to anothergenomic neighborhood, mightn't they pose risks more immediate than mutation?We now knowthat they do, and we know a little about how humans and other mammals fight back. That's for PartII.

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http://dx.doi.org/10.1016/j.cell.2008.09.022http://dx.doi.org/10.1016/j.cell.2008.09.022http://dx.doi.org/10.1016/j.cell.2008.09.022http://www.nature.com/nature/journal/v471/n7338/abs/nature09830.htmlhttp://www.nature.com/nature/journal/v471/n7338/abs/nature09830.htmlhttp://www.nature.com/nature/journal/v471/n7338/abs/nature09830.htmlhttp://dx.doi.org/10.1016/j.cell.2008.09.022http://dx.doi.org/10.1016/j.cell.2008.09.022http://www.nature.com/nature/journal/v471/n7338/abs/nature09830.htmlhttp://www.nature.com/nature/journal/v471/n7338/abs/nature09830.html