What about those jumping genes?

It's interesting, but I'm not entirely convinced that this isn't just contamination. Wolbachia is nearly universal throughout insect species, and while they say that their samples were from insects that were Wolbachia-free, they don't say how they ensured that. So far, though, your example goes the wrong way. Insertion of bacterial or viral genes into a metazoan host is considerably removed from HGT between two metazoan organisms.

What? You mean, what's the difference between finding bacterial sequences in your sample because they were in the genome of your sample by HGT, and finding them in your sample because some Wolbachia got in while you were homogenizing the tissue in preparation for extraction?You really can't imagine what the difference is, there?You really have no idea what you're talking about, do you?

How could it? That's what I don't understand from the article.In my lab, it's irrelevant, since we're using primers to selectively amplify individual genes. (I say "we" because I do some of it, but I'm just the lab tech, not really a researcher.) We're not sequencing whole nuclear genomes, so contamination is only a problem when its contamination between samples. We don't worry about bacteria that might settle in from the air (or the Wolbachia that reside in their gut.)But it's not at all clear how you would definitively exclude Wolbachia - a nearly universal insect pest - from your sample. And once you homogenize and extract, it's all mixed up anyway. And if you're amplifying the whole nuclear genome, then you wind up amplifying not only your insect sample but any bacteria that were in there with them. And it's hard to imagine how you could sterilize the inside and outside of an insect without destroying its own DNA. I'm open to suggestion, but then, my lab isn't working with the whole nuclear genome. So it's not an issue for us.The problem is that the article gives no indication on how they were able to accomplish this unlikely feat. Suggestion: post less, fuck around with your boat more. What the hell are you doing on the internet with hot babes and boats all around you? You must be some kind of idiot.

Yes, HM, that's my point. Are you paying attention? Can you focus for a minute? Allow me to repeat myself:Contamination of Wolbachia in the extraction isn't an issue when you're targeting your amplification at specific genes (genes that bacteria don't have), because the unamplified bacterial genome just falls into the background noise.Contamination of Wolbachia in the extraction becomes a big issue when you're amplifying the entire genome, because the primers you have to use will amplify all genetic sequences, including the sequences in whatever bacteria were living on the surface of your sample. The researchers here claim that there was no Wolbachia in the sample, but I don't understand how they ensured that, so I'm reticent to take their claim on face value.Obviously, if you had Wolbachia in your sample, it would look just the same as if there were Wolbachia genes in your sample's genome. The only way to tell the difference is to run a sample with no Wolbachia in it, but I can't imagine how they actually found a way to do that.Try to keep up, ok? I know it's hard with a boat full of bird shit.

I don't know what you mean by "horizontal genome transfer", and it's certainly not an issue I raised.Are you sure you're paying attention, here? Maybe you can go back and re-read when Jennefer is, um, done.

It does, I guess, which makes me suspect contamination all the more. You find one or two genes, sure, that could be HGT. You find the whole thing? That's almost certainly contamination.Incidentally I had the pleasure, a number of times, to meet and converse with Mr. Dyson when he held an honorary chair at my college. A more genial, intelligent man I've never met. Though I don't think much of his biology, nor his bizzare stance on global warming. Well, nobody's perfect.Edited by crashfrog, : No reason given.

I actually think the reverse is true. If horizontal gene transfer is commonplace, we'd have to rewrite all our assumptions about molecular genetics. HGT might very well undermine the molecular techniques we use to construct phylogenies. At the very least, it introduces great confusion as to whether or not the same sequence in two different species represents common descent or HGT between two unrelated species.I just think that the likelihood of "naked" HGT is very, very low. I guess I shouldn't be surprised to see one or two examples of it known throughout the entire living kingdom. Retroviruses do the same thing, and given the evolutionary pressure on a virus to be as simple as possible, it's not unreasonable to consider a retrovirus the simplest possible molecular structure that can reliably insert its genome into the chromosomes of another cell.Naked DNA? It's unstable outside the cell. It has none of the markers or proteins necessary to penetrate a cell membrane reliably, so it just sort of has to wander in at random. Cells don't just incorporate random DNA that they stumble across, so the segment has to meander it's way into the nucleus, and just be in the right place at the right time when some portion of the DNA just so happens to be randomly ligated. And, of course, this all has to have happened in one of the germline cells, which are protected by many layers of immune and caretaker cells, and then that gamete has to be the one that fertilizes or is fertilized to form a new organism.Mutations are common enough - hundreds every cell replication - that they're easily the source of more than enough diversity. (All organisms, living and extinct, account for less than one thousandth of one percent of all the diversity mutations are capable of.) But the idea of finding HGT's in genomic sequences without a mechanism that makes it a lot more likely seems astronomical to me.Compared to the likelhood of contamination? I work in a genetics lab, so I know how easy that can be, especially when you're amplifying whole genome sequences.Still though, Buz, I think you have it backwards. The classical models of molecular phylogeny don't have much room for HGT.Edited by crashfrog, : No reason given.

Other than that, Buz, I'd like to thank you for your kind words, and I hope you continue to enjoy the discussion.I think science is at its best when people are disagreeing, and I don't think evolution has anything to fear from the issues we're raising here.

I don't think it has anything to do with creationism, Buz. Creationism isn't based on any physical evidence, but rather the strength of its adherents' religious beliefs.So quite frankly I don't see how any scientific discovery could have any effect on creationism. Creationism is a position that has no connection to any evidence whatsoever. How could it be affected by a scientific discovery?

I didn't realize it was that small (despite living with entomologists.) Everybody I know who talks about it described it as a gut parasite, akin to E. coli, not actually an intracellular organism.That does change it somewhat, for me. Instead of jumping genes and naked DNA locking on to sperm cells, it's a lot more like less efficient, larger retroviruses. See, that's a little more reasonable, if Wolbachia is living right there in the cell.Thanks for the info. Really clears it up for me. Incidentally, the discussion HM and I had those months ago was about the prospect of nuclear DNA ligating itself right out of the nucleus of something like the tsetse fly, floating through the human bloodstream, and somehow locking on to a human gonad cell and inserting itself into that nucleus. That's what I found so ridiculous.But endosymbiotic Wolbachia inserting genes into their host? That makes a lot more sense know that I know that about Wolbachia. Given endosymbiosis, it's a lot more reasonable. After all, even in our own genome, we have genetic sequences that, at one time, must have belonged to the endosymbiotic organisms that have become our mitochondria.

Back to the same problems with naked DNA wandering around an organism's body. If a retrovirus is the simplest possible chemical structure that can get DNA from one cell to another reliably, the idea of naked DNA doing it seems unfeasible. Yeah, I do, too. For right now I think the problem is that HGT, if it's found to be common, is going to cast a lot of doubt on constructed phylogenies. Possibly a lot more doubt than is justified. No reason to stop looking for HGT, of course, but it's a good reason to refrain from a conclusion of HGT until one is very, very sure.

I'm afraid I don't.

Seconded. A fascinatingly informative series of posts. Kudos!