What about those jumping genes?

Good response. Write a letter to Nature and complain about this. They might print it. Otherwise, I don't know if anyone has ever brought up the possibility of "horizontal genome transfer" before. I find it quite remarkable, but what do I know with all these annoying distractions...(Jennefer, please, not now!)”HM

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.

crashfrog wrote: Well, the OP article speaks to horizontal genome transfer, doesn't it?Re: HGT, an interesting a relevant exchange occurred recently in The Edge between Richard Dawkins (via John Brockman) and Freeman Dyson, concerning these two remarks made by Dyson:"By Darwinian evolution he [Woese] means evolution as Darwin understood it, based on the competition for survival of noninterbreeding species.""With rare exceptions, Darwinian evolution requires established species to become extinct so that new species can replace them."Dawkins comments:

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These two quotations from Dyson constitute a classic schoolboy howler, a catastrophic misunderstanding of Darwinian evolution. Darwinian evolution, both as Darwin understood it, and as we understand it today in rather different language, is NOT based on the competition for survival of species. It is based on competition for survival WITHIN species. Darwin would have said competition between individuals within every species. I would say competition between genes within gene pools. The difference between those two ways of putting it is small compared with Dyson's howler (shared by most laymen: it is the howler that I wrote The Selfish Gene partly to dispel, and I thought I had pretty much succeeded, but Dyson obviously hasn't read it!) that natural selection is about the differential survival or extinction of species. Of course the extinction of species is extremely important in the history of life, and there may very well be non-random aspects of it (some species are more likely to go extinct than others) but, although this may in some superficial sense resemble Darwinian selection, it is NOT the selection process that has driven evolution. Moreover, arms races between species constitute an important part of the competitive climate that drives Darwinian evolution. But in, for example, the arms race between predators and prey, or parasites and hosts, the competition that drives evolution is all going on within species. Individual foxes don't compete with rabbits, they compete with other individual foxes within their own species to be the ones that catch the rabbits (I would prefer to rephrase it as competition between genes within the fox gene pool).

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The rest of Dyson's piece is interesting, as you'd expect, and there really is an interesting sense in which there is an interlude between two periods of horizontal transfer (and we mustn't forget that bacteria still practise horizontal transfer and have done throughout the time when eucaryotes have been in the 'Interlude'). But the interlude in the middle is not the Darwinian Interlude, it is the Meiosis / Sex / Gene-Pool / Species Interlude. Darwinian selection between genes still goes on during eras of horizontal transfer, just as it does during the Interlude. What happened during the 3-billion-year Interlude is that genes were confined to gene pools and limited to competing with other genes within the same species. Previously (and still in bacteria) they were free to compete with other genes more widely (there was no such thing as a species outside the 'Interlude'). If a new period of horizontal transfer is indeed now dawning through technology, genes may become free to compete with other genes more widely yet again.

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As I said, there are fascinating ideas in Freeman Dyson's piece. But it is a huge pity it is marred by such an elementary mistake at the heart of it.

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Dyson replies:

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Thank you for the E-mail that you sent to John Brockman, saying that I had made a "school-boy howler" when I said that Darwinian evolution was a competition between species rather than between individuals. You also said I obviously had not read The Selfish Gene. In fact I did read your book and disagreed with it for the following reasons.

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Here are two replies to your E-mail. The first was a verbal response made immediately when Brockman read your E-mail aloud at a meeting of biologists at his farm. The second was written the following day after thinking more carefully about the question.

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First response. What I wrote is not a howler and Dawkins is wrong. Species once established evolve very little, and the big steps in evolution mostly occur at speciation events when new species appear with new adaptations. The reason for this is that the rate of evolution of a population is roughly proportional to the inverse square root of the population size. So big steps are most likely when populations are small, giving rise to the "punctuated equilibrium'' that is seen in the fossil record. The competition is between the new species with a small population adapting fast to new conditions and the old species with a big population adapting slowly.

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Second response. It is absurd to think that group selection is less important than individual selection. Consider for example Dodo A and Dodo B, competing for mates and progeny in the dodo population on Mauritius. Dodo A competes much better and”has greater fitness, as measured by individual selection. Dodo A mates more often and has many more grandchildren than Dodo B. A hundred years later, the species is extinct and the fitness of A and B are both reduced to zero. Selection operating at the species level trumps selection at the individual level. Selection at the species level wiped out both A and B because the species neglected to maintain the ability to fly, which was essential to survival when human predators appeared on the island. This situation is not peculiar to dodos. It arises throughout the course of evolution, whenever environmental changes cause species to become extinct.

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In my opinion, both these responses are valid, but the second one goes more directly to the issue that divides us.

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This exchange reminds me of other arguments waged here on EvC.”HM

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've been trying to find the article ... I can get to Nature, but news@nature is a "premium" and MU doesn't have a "premium" subscription apparently ... I found this summary, tho: Page Not Found This fellow seems to think it isn't contamination.

I.E. Hootmon for authoring the thread and Crashfrog for arguing the minority view regardless of whether it is supportive of evolutionism or not. (That is not to imply that CF's viewpoint is the correct one. It appears that nobody knows for sure at this point. That's for each of us to evaluate in our own minds as the thread progresses.)Likely others unapprised in the subject to whatever degree find this fascinating topic as interesting and informative as I do. So far as how this debate relates to the big EvC debate, the possibility of HGT appears more supportive to evolution whereas contamination would be the more supportive of the traditional ID version of creationism.So far I think I am understanding something about what HGT is about and perhaps the significance of the debate. NOTE: I was thinking of posting this in POM but decided I'd better aire it here in the thread in case I am mistaken in something I'm stating. Perhaps if I find it acceptable I may decide to link this message with a short introduction in POM.

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BUZSAW B 4 U 2 C Y BUZ SAW.
The immeasurable present is forever consuming the eternal future and extending the infinite past.

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.

Thanks for the detailed explanation. I had to look up some words which aided in comprehending what you posted as to why contamination may not be counter to ToE.I'm still wondering why it would be the opposite as you say in which case contamination would undermine the traditional ID version of creationism.

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BUZSAW B 4 U 2 C Y BUZ SAW.
The immeasurable present is forever consuming the eternal future and extending the infinite past.

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?

The Tree of Life: Adaptationomics Award #1 - Wolbachia DNA sneaking into host genomes Not Found, Error 404& Crash, walk me thru this one.It looks like Wolbachia infects germ cells. And it looks like Wolbachia gets passed on.And big chunks of the genome have been found in lots of species. Am I missing something? It looks like HGT is not only possible, but commonplace (in invertebrates, at least).

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.

Fill me in a little bit. What insect? (A link would be nice.) "Social" evolution?

molbiogirl responded to my statement: In 2000, New Scientist published an article titled Look before it leaps, reporting that tsetse-fly genes have "jumped," by way of mariner elements, into the human genome:

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A "JUMPING GENE" being used to genetically engineer organisms has crossed the species barrier at least seven times in evolutionary history, in one instance between flies and humans, according to a study commissioned by the British government.

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This always evokes a memory of the spiny hairs growing out of Jeff Goldblum's back in the movie The Fly. Well, maybe it's possible for a social-insect gene to turn a human being into a party animal. Paris Hilton come to mind.”HM
Edited by Hoot Mon, : No reason given.

crash wrote: I agree. Why does Creationism need a cause-effect mechanism to be validated? I always thought Creationism was above all that. Why would any logical explanation serve the needs of Creationism, or even ID? This harps back to the old question: Why does religion need to justify itself scientifically? I don't ever see science trying to justify itself religiously.”HM