The origin of new alleles

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Plasmids are circular segments of prokaryotic DNA used in bacterial conjugation.

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Saccharomyces cerevisiae can harbour plasmids and Escherichia coli can even conjugate with it.

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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.")

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It actually appears as if T. cruzi DNA can insert in the host DNA. But Hoot Mon's claim that WE carry around tsetse-fly genes seems of the mark.Edited by AdminAsgara, : quotes are not needed for dBCode URL links

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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."

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I fail to see why that would be a difference. Although the horizontal fluidity of genes makes it difficult to define exactly where a gene comes from, I think it would be fair to say that if a gene has been transferred from organism x to organism y, then organism y now carries a gene from organism x. The problem, of course, is that the gene might originally have come from organism a, b, c... etc. and spread independently to both x and y. But in the end both x and y carry the same gene, so I'm not sure why your objection would matter.

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...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.

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Bacteria can reproduce inside eukaryotic cells and bacterial DNA can migrate into the nucleus. I don't find it too implausible that a gene from a fly was transferred to an invasive bacterium that later invaded a human cell that subsequently took up some bacterial DNA, especially if the gene/s were on a horizontally mobile element (again, the DNA might have originated in another organism and then spread independently to both tse-tse's and humans). Of course, for this to be heritable in a sexually reproducing organism, this would have to occur in either a gamete or in the cells that produce the gametes.So, Hoot Mon's link and claim that DNA has been transferred between humans and tse-tse's doesn't seem all too farfetched.Now I just have to try to figure out why this is actually important for this thread.

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1) We're not talking about functional sequences that are crucial to tsetse flies.
2) They're not specific to tsetse flies or humans.

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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.

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You claimed earlier :"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.". So it was a given that a piece of DNA got from a fly into humans. Whether or not this DNA was crucial to the fly is irrelevant.The non-specificity of the genes to humans and flies might, as I also pointed out in an earlier post, be relevant. BUT it was already a given that the DNA had transferred from a fly into a human - and so, in this instance, it is irrelevant.

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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.

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Mariner elements do contain genes. These were at least (well probably anyway) functional at the time of transposition.

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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.

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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.

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I very much doubt that it would be a common occurrence. But there are no absolute barriers against it either. As I already stated, DNA can migrate into the nucleus of a eukaryotic cell. Free DNA can be longlived inside a human - mothers can carry around their childrens DNA in themselves for years after birth (it probably crossed the placenta). Bacteria and viruses can aid in the transport of DNA into/out of eukaryotic cells. Transposons such as the mariner elements mentioned are "likely" to integrate into a genome (in that they contain the gene to do it and that the gene is not dependent on host-factors), should the find themselves in the right spot. I suppose that lack of direct observation might be called hand-waving but there are mechanisms that can do it.

I wrote the following off-line and I just noticed that Wounded Kind and Hoot Mon has discussed parts of what I've already written. I did not change this post because of this, so parts of it might be a bit redundant.

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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.

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Er, YOU stated: "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". While I agree that it is debatable whether or not there has been horizontal gene transfer between flies and humans (as I've already stated), that is not what I have an issue with in this instance. The issue is that GIVEN that it HAS happened, should we consider that "humans carry around tsetse fly genes"? My answer is yes. Your answer is that there has been no transfer in the first place - i.e. you're avoiding the question.

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These were at least (well probably anyway) functional at the time of transposition

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This is the sort of hand-waving I'm talking about when it comes to horizontal gene transfer between extremely complex, disparate organisms.

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Transposons are very good at cutting themselves out of and into other DNA sequences. We could argue that some other mechanism brought them to the place where they currently reside, but that is not very parsimonious.

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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?

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Bacteria can get to all sorts of places where they "shouldn't" be. Inside our epithelial cells, across the blood-brain barrier, and yes, inside out gonads After all, people do get gonadal infections. Bacterial infections can occur all along the way from the point of sperm production through to the point where fertilization takes place. Moreover, naked DNA can reside in blood (for long amounts of time) without being enclosed in any membranes, so a bacterium isn't even an absolute requirement.

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I'm still waiting to hear what those are.(mechanisms)

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If you are looking for a system in eukaryotes that actively promotes this, then I doubt that there is any. If you are looking for biochemical mechanisms for how it could happen, then I would say that you are demanding too much detail. Given that DNA can be inserted into human DNA by microorganisms and given that microorganisms can be found in the vicinity of gametes (not to mention that there is an absolute requirement for them in the first place) and given that transposons are good at jumping from one piece of DNA to another, you can easily create a hypothetical scenario where genes could jump from flies to humans. The probability that it will happen at any one instance will be low but there will be loads of opportunities for it to occur whenever there are interactions between the two species over long periods of time. I'm sure either of us could comb through the literature and find specific mechanisms for how each step takes place, but why bother. Each step is plausible in that it in no doubt has happened/happens.

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Well, I think you're making an equivocation here. If there were horizontal gene transfer from flies to humans, could we say that we "carry fly genes"? Sure, but that's basically tautological.

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Well, not necessarily. It depends on what you would define the "home" of a gene. We could easily imagine how some gene/s originated in organism a, transferred to b, then c and... y and z. Would we say that z was carrying a y gene? Probably not. If we only know of the transfer from y to z (and we only knew of the gene in those two organisms) we could reasonably say that z now carries a y gene. But does it really? I realise that this is more of a philosophical question than a scientific one. To add to the confusion: It is very difficult to say where ANY horizontally mobile element comes from. I would like my resounding yes answer from before to be complemented to include the alternative "No. It is a horizontally mobile element. It does not come from any specific orgamism".

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Moreover, my point is that it isn't the same as saying "horizontal gene transfer occured involving flies and humans and potentially other organisms", and it isn't the same as simply noting unexpected homologies between those two species. That's what I'm getting at.

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I've been suspecting that we have just been talking past eachother. I understand what you are saying and moreover I agree with you.

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And what? It just ignores a trillion other somatic cells in favor of a sperm?

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Why? I just don't buy the idea of a magic DNA bullet, spiraling it's way unerringly to Mr. Man's gonads, guided by the hand of who-knows-what.
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Not, how does it get to a cell, any cell - how does it get to one specific kind of cell located in a very specific part of the body?

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First of all, it would not have to target a "sperm". Precursors for these exist and even females produce gametes.I also think you are being a bit too teleological here. You could ask the same question when any of our 10^13 cells are being examined for evidence of HGT. Merely claiming that it was too unlikely for THAT cell to be affected as opposed to the others isn't a very good argument (but yes, I realize that it IS less likely for a gamete to be affected than, say a skin cell.). In the end, does it even matter how the bacterium/DNA got there? People do get infections in their gonads, so it's obviously possible (and no, these people do not always become infertile).

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...and I don't think I'm the only person who sees HGT having a more limited relevance to metazoan organisms with specialized reproductive cells than to single-celled organisms.

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Agreed.

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...basis of some hand-waving, especially when HGT advocates seem to be overstating their claims as a matter of course.

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Speaking of hand-waving...

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Consider me going from "skeptical" to "open-minded but not convinced", if you will.

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That's a reasonable enough position. Talking about any one instance of a potential example of heritable HGT in eukaryotes (e.g. the fly-to-man example discussed here), I would probably take the same position. Saying that, I'm probably closer to the convinced side that is has happened/does happen - at least sometimes. I would certainly expect it to be more common in certain organisms (e.g. worms and fungi) than others.

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I mean, if we just absorbed DNA from the things we came into contact with, what a mess that would be! If I ate a tomato, I'd start to grow leaves.

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That's a movie I would like to see.

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Genes are pure information”information that can be encoded, recoded and decoded, without any degradation or change of meaning.

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Dawkins seems to be very deterministic when it comes to the phenotypic effects of a particular (expressed) DNA sequence - and because of this he is also wrong (I don't have the book available, so I'm just going with what is written here). Try to insert a eukaryotic gene containing introns into a prokaryote and you will quickly realise that the meaning of the DNA sequence will now most likely have changed. However, I will agree with the statement that as far as DNA ability to transmit it's own information goes (i.e. it's ability to act as a template for copying purposes), it is for all intents and purposes digital.

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I don't see what that has to do with being digital. Even an analogue recording can be duplicated. For instance, an LP record is made by pressing a reverse master onto the vinyl record. That's an example of an analogue "code" acting as a template for copying purposes.

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Digital codes are codes that use discreet numerical values to represent analogue signals; like the way the datastream coming off of an audio CD represents analogue signal waveforms. To assert that DNA is a "digital code" is to be making an analogy, not stating a fact. It's like digital codes, sure; but it's also like a stock market ticker, or a busy file clerk, or any number of alternate analogies could be made. And to assert that DNA is literally a digital code is as nonsensical as asserting that DNA is really a tiny little file clerk living inside our cells.

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Just like the discrete signal found on a CD, nucleotides form a similarly discrete signal. And since when do digital signals have to represent analogue ones? You ask the question if something analogue can be copied? Yes, of course. But that is not interesting, as the signal being copied is not discrete. (as a side note: given that our DNA sequencing methods are "crude", our ability to detect said sequence relies on the use of millions of DNA copies - this helps reduce the noise inherent in the signal. The signal WE receive is effectively analogue for each and every nucleotide).So when I claim that "DNA's ability to act as a template for copying purposes, is for all intents and purposes digital." I think that I am right, since it is a discrete signal that is being copied. Pretty good analogy, I would say.