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Fosdick  Suspended Member (Idle past 5530 days) Posts: 1793 From: Upper Slobovia Joined: |
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Author | Topic: What about those jumping genes? | |||||||||||||||||||||||
Fosdick  Suspended Member (Idle past 5530 days) Posts: 1793 From: Upper Slobovia Joined: |
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.
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
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crashfrog Member (Idle past 1497 days) Posts: 19762 From: Silver Spring, MD Joined: |
Otherwise, I don't know if anyone has ever brought up the possibility of "horizontal genome transfer" before. 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.
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Fosdick  Suspended Member (Idle past 5530 days) Posts: 1793 From: Upper Slobovia Joined: |
crashfrog wrote:
I don't know what you mean by "horizontal genome transfer"... 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:
quote:Dyson replies: quote: This exchange reminds me of other arguments waged here on EvC. ”HM
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crashfrog Member (Idle past 1497 days) Posts: 19762 From: Silver Spring, MD Joined: |
Well, the OP article speaks to horizontal genome transfer, doesn't it? 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.
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molbiogirl Member (Idle past 2672 days) Posts: 1909 From: MO Joined: |
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. 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.
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Buzsaw Inactive Member |
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. BUZSAW B 4 U 2 C Y BUZ SAW. The immeasurable present is forever consuming the eternal future and extending the infinite past.
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crashfrog Member (Idle past 1497 days) Posts: 19762 From: Silver Spring, MD Joined: |
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. 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.
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crashfrog Member (Idle past 1497 days) Posts: 19762 From: Silver Spring, MD Joined: |
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.
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Buzsaw Inactive Member |
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. BUZSAW B 4 U 2 C Y BUZ SAW. The immeasurable present is forever consuming the eternal future and extending the infinite past.
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crashfrog Member (Idle past 1497 days) Posts: 19762 From: Silver Spring, MD Joined: |
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?
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molbiogirl Member (Idle past 2672 days) Posts: 1909 From: MO Joined: |
Crash writes: 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. The Tree of Life: Adaptationomics Award #1 - Wolbachia DNA sneaking into host genomes
phylogenomics writes: Basically, in their study (led by a past colleague of mine from TIGR, the brilliant up and coming Julie Dunning Hotopp) they showed that there have been multiple lateral transfers of DNA from Wolbachia (which are intracellular parasites that can infect germ cells) into invertebrates. Furthermore they showed that that the DNA transfered to the host genome is not completely transient and that in many cases it is passed on to future generations. wiki writes: Wolbachia is notable for significantly altering the reproductive capabilities of its hosts. These bacteria can infect many different types of organs, but are most notable for the infections of the testes and ovaries of their hosts. Wolbachia are known to cause four different phenotypes: * Male killing (death of infected males). This allows related infected females to be more likely to survive and reproduce.* Feminization (infected males develop as females or infertile pseudo-females) * Parthenogenesis (reproduction of infected females without males) * Cytoplasmic incompatibility (the inability of Wolbachia-infected males to successfully reproduce with uninfected females or females infected with another Wolbachia strain). This has the advantage of making the Wolbachia strain more likely to become prevalent as opposed to other strains of Wolbachia. This can have the additional result of making Wolbachia more common as a whole. Wolbachia are present in mature eggs, but not mature sperm. Only infected females pass the infection on to their offspring. It is thought that the phenotypes caused by Wolbachia, especially cytoplasmic incompatibility, may be important in promoting speciation. [1][2] Wolbachia can also cause misleading results in molecular cladistical analyses (Johnstone & Hurst 1996). Not Found, Error 404&
Zimmer writes: Wolbachia spread so quickly, researchers realized, because they take control of their hosts' reproduction. And in the past decade, they've discovered that cytoplasmic incompatibility is only one of many tricks the bacteria use to do so. In some species of wasps, for example, Wolbachia completely alter the host's sex life, manipulating the host to give birth only to females which then no longer need to mate with males to reproduce. In other species, they allow males to be born but alter their hormones to feminize them and make them produce eggs. A fourth way Wolbachia can boost their reproductive success is to destroy their male hosts (and, paradoxically, themselves in the process). In a number of hosts, Wolbachia kill all of the male eggs that they infect. When the female hosts hatch, they don't have to compete with their brothers for food--in fact, their brothers are their food. By cannibalizing the male eggs, the Wolbachia-infected females increase their chances of survival. With so many of their brethren killed off, the few males that remain can enjoy remarkable reproductive success. A species that might normally be split 50-50 between males and females may become permanently skewed to females, as in the case of the Ugandan butterfly Jiggins studies. 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.
Zimmer writes: But this sexist microbe may be the most common infectious bacterium on Earth. Although no vertebrates (humans included) are known to carry Wolbachia, infection is rampant in the invertebrate world, showing up in everything from fruit flies to shrimp, spiders, and even parasitic worms. Am I missing something? It looks like HGT is not only possible, but commonplace (in invertebrates, at least).
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crashfrog Member (Idle past 1497 days) Posts: 19762 From: Silver Spring, MD Joined: |
It looks like Wolbachia infects germ cells. And it looks like Wolbachia gets passed on. 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.
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molbiogirl Member (Idle past 2672 days) Posts: 1909 From: MO Joined: |
So maybe this supports the findings of insect genes in the human genome. Fill me in a little bit. What insect? (A link would be nice.)
Do you think jumping genes could have played a significant role in the course of either biological or social evolution? "Social" evolution?
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Fosdick  Suspended Member (Idle past 5530 days) Posts: 1793 From: Upper Slobovia Joined: |
molbiogirl responded to my statement:
So maybe this supports the findings of insect genes in the human genome.
Fill me in a little bit. What insect? (A link would be nice.) 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:
quote:This always evokes a memory of the spiny hairs growing out of Jeff Goldblum's back in the movie The Fly. Social evolution?
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.
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Fosdick  Suspended Member (Idle past 5530 days) Posts: 1793 From: Upper Slobovia Joined: |
crash wrote:
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 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
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