The origin of new alleles

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.

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.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. Avoiding what question? Even if it were understood that these homologies are the result of HGT, it wouldn't neccesarily follow that fly genes moved to humans. It might have been the reverse; or more likely, a gene moved from one species to several others, including flies and humans. And what? It just ignores a trillion other somatic cells in favor of a sperm?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. Maybe I'm just being trite, and I appreciate that others have offered more in-depth resources - and I'll take advantage of those resources as I'm able to unearth them.Consider it the skepticism of someone who is genuinely ignorant of the evidence. No, and I apologize for not being clear. I understand as well as my schooling allows the biochemical mechanisms that would allow one of these sequences to insert itself into a eukaryotic genome. That's no biggie, with me.It's just, before that - how does the DNA get to the cell? 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?That's what I'm having a problem with, 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. All the opinions I can find on this suggest that these are contentious ideas at best, so I'm not willing to just roll over and agree that this is all super-reasonable and likely on the basis of some hand-waving, especially when HGT advocates seem to be overstating their claims as a matter of course.

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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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It should be added that it holds approximately for multifactorial characters in an effectively random breeding population if selective differences between leading alleles are constant and all of lower order than the recombination rates of the loci

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Genic and Organismic Selection
Sewall Wright
Evolution, Vol. 34, No. 5 (Sep., 1980), pp. 825-843

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Is the thread discussing the transitivity to a place on a leader allele ledger or the creation of the ledger account itself? If the latter it may matter whether it is constructed probabilistically (and in connection with EvC discussin of ID or not) or based on a similar multiplicative math but with "Zero" added.

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Evolution and the Genetics of Populations Volume 2 by Sewall Wright p177-78

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Edited by Brad McFall, : quote referenceEdited by Brad McFall, : deleted extra words

I appreciate your responses, by the way. You've offered argumentation of a consistently high caliber and you're starting to change my mind. Consider me going from "skeptical" to "open-minded but not convinced", if you will. To me, I guess it matters a little more, because we're talking about organisms that have evolved in ways that seem to be a defense against this very phenomenon - for instance, the whole idea of reproduction being a specialized bodily function.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.But I guess I don't have anything else. You put forth interesting and compelling argumentation, so I guess the only thing I can do now is do my homework and see for myself. Thanks, Hawks, for a great discussion.

Now you're fussing. You obviously don't know what "corroborating evidence" is. What is your hypothesis for how those tsetse fly genes got into your bloodstream? And don't tell me that you don't have any, cuz you do. We all do. There are all sorts of wild digital codes circulating through our veins and homologies. Humans share a lot genes with other animals. We're not detached from nature, you know.”Hoot

Maybe Crash is confused because you use nonsense sentences like this that give the impression you don't have the first clue what you are talking about.TTFN,WK

Are you sure you do? Because you certainly haven't provided any. Hrm, we dealt with this, but I guess you weren't paying attention. You seem to do that a lot. You've just got no idea what you're saying, do you? "Endosymbionic", indeed. "Through our homologies"? Um, no shit, Sherlock. But we didn't evolve from tsetse flies, and radically improbable HGT between multicellular organisms is definitely not the most parsimonious explanation when we find these unexpected homologies.Man. How did I ever get the impression I had been wrong about you, and you did actually know what you were talking about? Thanks for opening your mouth and removing my misapprehension.

Tedious, pedantic, tautological, picayune. You are more interested in barbs and put downs than you are in discussing the matter intelligently.”Hoot Mon

"Nonesense sentences"? There are 201 references cited by PubMed that address animal transposons in humans. Here’s one from C.Feschotte, Departments of Plant Biology and Genetics, The University of Georgia, Athens, GA, USA.

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Several new families of DNA transposons were identified by computer-assisted searches in a wide range of animal species that includes nematodes, flat worms, mosquitoes, sea squirt, zebrafish, and humans. Many of these elements have coding capacity for transposases, which are related to each other and to those encoded by the IS1016 group of bacterial insertion sequences. Although these transposases display a motif similar to the DDE motif found in many transposases and integrases, they cannot be directly allied to any of the previously described eukaryotic transposases. Other common features of the new eukaryotic and bacterial transposons include similarities in their terminal inverted repeats and 8-bp or 9-bp target-site duplications. Together, these data indicate that these elements belong to a new superfamily of DNA transposons, called Merlin/IS1016, which is common in many eubacterial and animal genomes. We also present evidence that these transposons have been recently active in several animal species. This evidence is particularly strong in the parasitic blood fluke Schistosoma mansoni, in which Merlin is also the first described DNA transposon family.

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”Hoot

And where in that abstract was there any mention of 'wild digital codes circulating through our veins and homologies'?It doesn't help your case to use something completely unrelated to your nonsense sentence as some sort of support for its not being nonsense.Indeed that paper only addresses 'animal transposons in humans' in as much as human are animals. If these sequences were derived from horizontal gene transmission this paper sugests it was at least prior to the divergence of man and chimps if not sooner.TTFN,WK

Oh, sorry. I didn't know this forum was a peer review for screening Nobel Prize candidates. Lighten up.

Intelligent discussion requires that both participants know what they're talking about.Someone who asserts that "digital codes circulate in our homologies" clearly doesn't. It's not pedantic to point out that when you invent your own private "scientific" terminology, you become completely unintelligable.Edited by crashfrog, : No reason given.

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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.

I notice that you and a few others here are very keen on your what you perceive to be the correct usage of terms that pertain to genetics and biological evolution. You in particular, crashfrog, are “correct” to the extreme, or otherwise pedantic about common editing mistakes. Once, upthread Message 35, I meant to write “endosymbiotic” but wrote “endosymbionic” instead, and you have pestered me over this typo on several different threads now (for just a single-letter slipup!). On another occasion Message 33, you flailed at me for using the term “mariner genes” when I meant to say “mariner elements,” which geneticists often associate with “jumping genes.” These are simple cases of typos and misspellings. How would you like it if I scanned over your posts and found misspellings and typos to make a big fuss over? You’re grasping at triviality and it doesn't help your case.Then there is this matter of “digital codes circulating through our veins and homologies” Message 66, which you claim to be nonsense. Others have joined you in this claim; even AdminNosy got involved and closed a thread over it. But I’m here to tell you (et al.) that my comment about “digital codes circulating through our veins and homologies” is NOT nonsense. Maybe it offends your youthful orthodoxies somehow, but this tells me you haven’t read enough literature on the subjects of genetics and evolutionary biology to lighten up a little (this forum is NOT a refereed journal, you know). S. J. Gould is one who used the terms “homology” and “homolgies” to refer to lineages of inheritance”applicable to discussions about “homoplasy” and “convergence,” which are alternative explanations for microevolution.Furthermore, genes ARE digital codes, according to Richard Dawkins. We’re talking here about the movement in space and time of digital codes”those mobile alleles”which do indeed circulate in our bloodstreams and through your homologies.I am sincere about discussing all aspects of allelic movement and their athletic leaps across space and time. And I’m sure I’ll hear demands from you for proof that alleles are “athletic.” You will probably scream bloody murder. But I wonder if any of Archie Manning’s athletic alleles ever found their way into Peyton and Eli. If so, that might have something to do with Archie’s digital codes, circulating through his veins and homologies.Now let’s get on with this discussion about alleles and their origins.”Hoot Mon