LINEs, SINEs, and the Design Inference

Transposons are wacky little genes, and really kind of cool. You can see Wikipedia's explanation of transposons here, but I'll give you the short version. What I'm describing here are what Wikipedia calls Class II transposons.

A transposon is a sequence of DNA that can move around in your genome. It comes in long and short versions, and copies of it are found interspersed throughout the genome. The long ones (Long INterspersed Elements, or LINEs) encode one protein, a transposase. What the transposase does is it cleaves the transposon from its current location and inserts it elsewhere in the genome. And that's ALL it does. SINEs (Short INterspersed Elements) do even less. What they do is be sequences that the LINEs' transposases recognize, and therefore transpose. And that's fucking IT.

Transposons are quite possibly the wackiest things I've encountered all week. They don't DO anything. By which I mean, they have no influence on an organism's life cycle. They just hang out in your genome, moving around and taking up space.

I like things like transposons because they really drive the point home that we're just something that happened. When you're studying stuff in the natural world, especially biology, it can be really easy to start anthropomorphizing and attributing purpose without even realizing you're doing it. So much of biology is so fucking complex and often really quite good at what it does, and it's in all the language that we use, talking about what a given enzyme is "for," or "why" a given trait evolved, sometimes you can slip into thinking that we actually mean those things. And then you see something like a transposon, and it's obvious that it's not "for" anything. It has no purpose, no raison d'être. It does nothing but be there. And once you realize that it becomes obvious once again that that's equally true of us.

And for all that the design inference died 150 years ago with Darwin's work, it's crap like this that really makes it implausible to me. I mean, this is exactly the kind of random, pointless genomic drivel that one might expect to show up in a system of random changes that can get passed along, but a god designer would have to be some fucked up kind of surrealist to create something like this. I mean seriously. WHY WOULD YOU DO THAT?!? Why? It's strange and off-putting.

Well, okay. There is one thing that transposons do. Transposons can cause non-silent mutations. There are two main ways that they can do this, both at the insertion stage. The first way is, when they cut the DNA to insert themselves, they cut the different strands at different points, creating an overhang and a gap on each side. Then, while they're inserting, the gaps are filled in with sequences complementary to the overhangs (and therefore identical to the opposite overhangs), so when the process is complete you have two copies of the sequence, one on either side of the transposon. If this sequence was something your cell was using, well, now it has two of them.

The other way a transposon can have an effect is by inserting itself right into a gene (or promoter region of a gene, or whatever) that you were using, thereby breaking it. This is apparently the sort of mutation that caused hemophilia in the European royal families. A transposon inserted itself into the gene for a protein involved in blood clotting and bam! No more blood clots; sucks to be them.

But for all that that's an effect of transposons, it's only a real effect in the context of evolution. What would be the point of that in something that was designed?

Transposons are cool.