The origin of new alleles

I'm not sure which organisms you're talking about (or which planet, for that matter) where plasmids enter the genomes of sexually-reproducing eukaryotes.Edited by crashfrog, : No reason given.

Transposable elements? Yeah, I'm familiar with them; in fact, I worked in the very department where Barbara McClintock discovered them back in the 20's; I used to walk right past her greenhouse a couple of times every month. Hell of a lady. No, they're not. (I've never heard of them being called "mariner genes." "Jumping genes" is the common term.) They're genetic sequences that move from chromosome to chromosome within a cell. A lot of them are the result of viruses (retrotransposons), and about 45% of our genome is comprised of them and their remnants.Plasmids are circular segments of prokaryotic DNA used in bacterial conjugation. How would they get into eukaryotic cells? How would they integrate themselves into the genome? Viruses do that because they've specifically adapted to reproduce that way (and only that way), but most bacteria are too large to penetrate a cell, and the cellular organelles of eukaryotes are radically different than the cellular biochemistry of the prokayote cell. Are you maybe just making things up? Why would we have tsetse fly genes? Insects aren't viruses; they don't inject their DNA into hosts. (The worst thing they do is inject the parasitic Trypanosoma protozoan into the host's bloodstream, causing the much-feared "sleeping sickness.")

There's no such thing as a "mariner gene". This usage as synonymous with "transposon" is unique to you.They're talking about mariner, a specific family of transposons.Transposons aren't plasmids, HM. Read your own article! They simply spliced them into the plasmids of E. coli - a standard technique in genetics research.You really need to be reading closer, HM. Your quick skim of this article was clearly not sufficient to accurately grasp its content. When are you going to admit you were in error to assert that transposons are plasmids?

It's like calling a "doctor" a "body dentist." The terminology is heirarcheal, and when you disregard that, you create confusion and betray ignorance. What was your point? That tsetse flies infect us with their DNA? The article doesn't even come close to saying that; it's completely wrong.Was your point that transposons are plasmids? No, they're not; you're wrong about that."Endosymbionic" isn't even a word.You see, because you didn't know what the hell you were talking about, you completely failed to get across whatever point you thought was so important. You wouldn't think you'd have to tell someone how proper use of technical terminology was important to clear communication, but honestly, some people...Edited by crashfrog, : No reason given.

It's not pedantic. These are technical subjects which require technical language to communicate complex concepts.When you just make up your own terminology and usage, nobody knows what the fuck you're talking about. Doesn't being understood mean something to you? How can we give your point consideration if we don't understand what it is?

I'd like to read your links but neither of them appears to work.

I don't see where it says "Humans have tsetse fly genes" in the article. What your earlier article does say is this:

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Over the past few years we and others have examined in some detail several apparent examples of recent horizontal transfers of mariners across large host phylogenetic distances. I believe that these extraordinary claims require extraordinary evidence to support them and hence have felt it worthwhile to carry out three such studies. We are currently completing and writing up the last two of these studies.

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In other words - "we can't prove it yet." I'm willing to give them the benefit of the doubt that they're actually preparing these studies, but neither one of your two articles proposes a mechanism of horizontal gene transfer between insects and humans, and several entomologists that I spoke to thought this was a tenuous possibility at best.Moreover - the fact that some endogenous retrotransposon jumped from tsetse flies to humans (or vice-versa) is not the same as saying "humans carry around tsetse fly genes." Once again your... idiomatic language seems to have led you to a conclusion you can't support with evidence.We don't have tsetse fly genes. These sequences are as functionless and degraded in tsetse flies as they are in humans, as they are in every species that shares them.

Sure, in single-celled organisms. In complex, multicellular life? I don't see how it's any more than the biology version of "spooky action at a distance."I'm amenable to learning, of course. If you can explain them to me, hit me with it. In my genetics classes we covered the mechanisms in prokaryotes. I'd love to know how it works, say, between insects and humans. I don't see how it works in sexual metazoans.For instance, a biting fly pierces my skin and begins to feed off my blood. How does any of it's genes get from the cells of its digestive tract (the only cells currently in contact with my body) all the way down to the protected gametes in my genitals? And I'm male. How would it work in my wife, who at birth had already generated all the gametes she'll ever have? Meiosis is over by the time she could possibly be exposed to these parasites.

1) We're not talking about functional sequences that are crucial to tsetse flies.
2) They're not specific to tsetse flies or humans.In other words, I don't see a reason to call them "tsetse fly genes"; there may be endogenous retrotransposons that are homologous between humans and flies such as the tsetse, but that's not at all the same thing. Are we even talking about genes, though? Or just transposable elements? They're degraded beyond all functioning, and are nothing more than introns in eukaryotes, anyway. Not just any cell; a human gamete that then happened to be the one in a million sperm that impregnanted a mate.I find it physiologically implausible, I guess. There are physical barriers and protections between sperm and the rest of the body - mostly to keep the sperm protected from the male's own immune system.It doesn't have to just get into a cell; it has to get into a germline cell, and I don't see anybody saying how that happens without a lot of handwaving. I'm just skeptical, is all, that horizontal gene transfer can be that common in metazoan life.

Well, thanks for the recommendation - I don't even have a library card yet but I'll see if I can't find it.

Er, no, we don't. That's my point. There's no evidence that these are sequences from flies; only sequences homologous between these flies and humans. This is the sort of hand-waving I'm talking about when it comes to horizontal gene transfer between extremely complex, disparate organisms. I disagree. The barriers that seperate spermatozoa from the rest of the body are so tight they can screen out antibodies, which are much smaller than bacteria. How is your nomad bacterium supposed to get through that? I'm still waiting to hear what those are.

No, I'm saying that a DNA transposon that leaps into the genome of a skin cell, or a blood cell, or some other somatic cell doesn't get passed on to any other individuals.The transposon would have to leap into a gamete, and I don't see that as physiologically likely, given how protected spermatocytes are from the rest of the body. They're basically in a little isolation ward of their own, to avoid an autoimunnological response from the male's own body, which doesn't recognize haploid sperm cells as its own.Two arbitrary cells in close proximity? I don't have a problem with that. Sure, genetic sequences could easily leap between them under the proper circumstances.But what possible circumstances could result in a DNA leap between the mouth of an insect and a sperm cell that, for all intents and purposes, might as well be on the other side of the planet? This is the part that horizontal gene transfer advocates gloss over. "Eh, it just happened." It's just highly unlikely to me, is all.

And what I'm telling you is that, like in the brain, there's a barrier between spermatozoa and the rest of the body, including the bloodstream. It's such a tight barrier that it can keep out your own body's antibodies. (And an antibody is a lot smaller than a bacteria, or even a free-floating transposon.)Why is that so difficult to grasp?AbE: I shouldn't say "like in the brain", because the barrier is actually very different, but it's there to screen out an autoimmunological response from the body, and to do so it has to be capable of screening out some very small things. Smaller than a free-floating endogenous retrotransposon.Edited by crashfrog, : No reason given.

We know that when sperm come into contact with the rest of the body, it triggers an autoimmune response that tends to destroy the sperm and leave the male infertile. Ok, so it's the one in a million occurance where free-floating DNA makes it all the way to the genitals, past a trillion other cells that it ignores before it finds a sperm, and then it's the one in a million chance this happens but the male is not rendered sterile by the autoimmune response circumventing the nurse cells, and then that one sperm is the one in ten million sperm that fertilizes an ovum.At what point is the unlikelihood of this occurance greater than the total number of human males who have ever lived? And are these genes purported to be universal in the human genome? So we're talking about this having to occur fairly early in human evolutionary history, which means we're talking about it happening to a fairly small population.I'm trying really hard not to sound like a creationist, or something, but the improbabilities are really adding up; all the genetics researchers I know think this is an unlikely possibility to say the least, and horizontal gene transfer advocates have a marked propensity towards overstating their claims, calling it "a new paradigm in biology" and other phrases that look great on posters and grant proposals, but might be just a tad hyperbolic.It makes me distrustful, especially when conclusive evidence doesn't seem to be forthcoming.I offer the following paper not to dismiss the entire phenomenon nor to paint HGT's proponents as universally mendacious liars, but simply one small example of how there maybe be generally simpler and more parsimonious explanations for unexpected genetic homologies between unrelated species: No webpage found at provided URL: http://www.cbcb.umd.edu/~salzberg/docs/ScienceLateralTransfer.pdf

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The human genome was analyzed for evidence that genes had been laterally
transferred into the genome from prokaryotic organisms. Protein sequence
comparisons of the proteomes of human, fruit y, nematode worm, yeast,
mustard weed, eukaryotic parasites, and all completed prokaryote genomes
were performed, and all genes shared between human and each of the other
groups of organisms were collected. About 40 genes were found to be exclusively
shared by humans and bacteria and are candidate examples of horizontal
transfer from bacteria to vertebrates. Gene loss combined with sample size
effects and evolutionary rate variation provide an alternative, more biologically
plausible explanation.

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I'm sorry, I thought my point was abundantly clear. It's simply that when we find unexpected homologies between unrelated organisms of considerable phylogenetic separation, HGT shouldn't be the immediate conclusion without some corroborating evidence.