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Author Topic:   The origin of new alleles
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 31 of 92 (380156)
01-26-2007 2:30 PM
Reply to: Message 30 by crashfrog
01-26-2007 1:32 PM


Re: The origin of new alleles
crashfrog wrote:
...(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.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.")
If you care to look it up, frog, you can find many references to mariner genes, transposons, plasmids, and neutral endosymbionts jumping around all over the place. You could start by considering this one: In an article in New Scientist (6/24/200) titled “Look Before It Leaps, Rob Edwards wrote:
An ancient mariner might help genes jump species
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. If organisms modified using this mobile element are released, there will be a risk of genes spreading to other species, the report says...
You might be interested in what kinds of plasmids and transposons are jumping inside Barbara's lab these days. Check it out.
”Hoot

This message is a reply to:
 Message 30 by crashfrog, posted 01-26-2007 1:32 PM crashfrog has replied

Replies to this message:
 Message 32 by crashfrog, posted 01-26-2007 2:36 PM Fosdick has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 32 of 92 (380158)
01-26-2007 2:36 PM
Reply to: Message 31 by Fosdick
01-26-2007 2:30 PM


Re: The origin of new alleles
If you care to look it up, frog, you can find many references to mariner genes, transposons, plasmids, and neutral endosymbionts jumping around all over the place.
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?

This message is a reply to:
 Message 31 by Fosdick, posted 01-26-2007 2:30 PM Fosdick has replied

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 Message 33 by Fosdick, posted 01-26-2007 2:49 PM crashfrog has replied

  
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 33 of 92 (380163)
01-26-2007 2:49 PM
Reply to: Message 32 by crashfrog
01-26-2007 2:36 PM


Re: The origin of new alleles
Technically, you are right. But you're splitting hairs here: "mariner elements" = "jumping genes". I should not have called them "mariner genes." My mistake, goodness sake! But what's the big deal, anyway? You've missed the entire point about endosymbionic genetic elements. Your pedantry is now evident on this tread, as well as on others.
”Hoot Mon

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 Message 32 by crashfrog, posted 01-26-2007 2:36 PM crashfrog has replied

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 Message 34 by crashfrog, posted 01-26-2007 2:54 PM Fosdick has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 34 of 92 (380165)
01-26-2007 2:54 PM
Reply to: Message 33 by Fosdick
01-26-2007 2:49 PM


Re: The origin of new alleles
My mistake, goodness sake! But what's the big deal, anyway?
It's like calling a "doctor" a "body dentist." The terminology is heirarcheal, and when you disregard that, you create confusion and betray ignorance.
You've missed the entire point about endosymbionic genetic elements.
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.

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 Message 33 by Fosdick, posted 01-26-2007 2:49 PM Fosdick has replied

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 Message 35 by Fosdick, posted 01-26-2007 3:05 PM crashfrog has replied

  
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 35 of 92 (380169)
01-26-2007 3:05 PM
Reply to: Message 34 by crashfrog
01-26-2007 2:54 PM


Re: The origin of new alleles
crashfrog wrote:
"Endosymbionic" isn't even a word.
I missed it by a single letter”an "n" for a "t"”"endosymbiotic." So, so, very sorry.
This is what I mean about your pedantry.
”Hoot

This message is a reply to:
 Message 34 by crashfrog, posted 01-26-2007 2:54 PM crashfrog has replied

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 Message 36 by crashfrog, posted 01-26-2007 4:31 PM Fosdick has not replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 36 of 92 (380188)
01-26-2007 4:31 PM
Reply to: Message 35 by Fosdick
01-26-2007 3:05 PM


Re: The origin of new alleles
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?

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 Message 35 by Fosdick, posted 01-26-2007 3:05 PM Fosdick has not replied

  
Hawks
Member (Idle past 6147 days)
Posts: 41
Joined: 08-20-2006


Message 37 of 92 (380608)
01-28-2007 2:32 AM
Reply to: Message 30 by crashfrog
01-26-2007 1:32 PM


Re: The origin of new alleles
quote:
Plasmids are circular segments of prokaryotic DNA used in bacterial conjugation.
Saccharomyces cerevisiae can harbour plasmids and Escherichia coli can even conjugate with it.
quote:
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.")
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

This message is a reply to:
 Message 30 by crashfrog, posted 01-26-2007 1:32 PM crashfrog has replied

Replies to this message:
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 Message 40 by Fosdick, posted 01-30-2007 11:45 AM Hawks has not replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 38 of 92 (380662)
01-28-2007 9:42 AM
Reply to: Message 37 by Hawks
01-28-2007 2:32 AM


Re: The origin of new alleles
I'd like to read your links but neither of them appears to work.

This message is a reply to:
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AdminAsgara
Administrator (Idle past 2302 days)
Posts: 2073
From: The Universe
Joined: 10-11-2003


Message 39 of 92 (380668)
01-28-2007 10:34 AM
Reply to: Message 38 by crashfrog
01-28-2007 9:42 AM


Fixed links
Links are fixed now.

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Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 40 of 92 (381249)
01-30-2007 11:45 AM
Reply to: Message 37 by Hawks
01-28-2007 2:32 AM


Re: The origin of new alleles
Hawks wrote:
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 off the mark.
I didn’t make this up. An article in New Scientist titled Look before it leaps is the one mentioning tsetse fly genes in humans:
quote:
An ancient mariner might help genes jump species
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. If organisms modified using this mobile element are released, there will be a risk of genes spreading to other species, the report says.
The so-called mariner element can move around in the genome of individual species thanks to the transposase enzyme it encodes, which "cuts and pastes" it from one place in a cell's DNA to another. Such jumping genes litter most creatures' genomes. Their ability to insert themselves into chromosomes makes them attractive to genetic engineers as a means of moving genes from one species into another.
In a project for the Ministry of Agriculture, Fisheries and Food, Andy Brass and two colleagues at the University of Manchester compared the DNA of ...
I can't seem to locate the referenced British study, but here's another report that connects to the New Scientist article:
Safe Online Gambling & Casino Guide | Reliable Casino Comparison
quote:
LONDON, June 21 (Reuters) - British scientists are concerned that a jumping gene used to genetically modify organisms could spread to other species, New Scientist magazine said on Wednesday. The so-called mariner element had jumped species at least seven times in evolutionary history, according to a report commissioned by the British government. "In a project for the Ministry of Agriculture, Fisheries and Food, Andy Brass and two colleagues at the University of Manchester compared the DNA of 80,000 different organisms, using five million sequences," the weekly magazine said. "They found seven pairs of similar mariner sequences." The scientists said there was strong suggestive evidence that the gene moved between the tsetse fly and humans. They also suspect it crossed over to a mosquito, bee, beetle and a cat flea. By using it to insert genes into animals or plants the researchers fear it could spread into other species. But other scientists who are using mariner in GM organisms played down the potential risks. "We can engineer things so that the risk is acceptably small," David Finnegan, of the University of Edinburgh, told the magazine.
”Hoot Mon

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 Message 41 by crashfrog, posted 01-30-2007 12:20 PM Fosdick has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 41 of 92 (381260)
01-30-2007 12:20 PM
Reply to: Message 40 by Fosdick
01-30-2007 11:45 AM


Re: The origin of new alleles
I don't see where it says "Humans have tsetse fly genes" in the article. What your earlier article does say is this:
quote:
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.
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.

This message is a reply to:
 Message 40 by Fosdick, posted 01-30-2007 11:45 AM Fosdick has replied

Replies to this message:
 Message 42 by Fosdick, posted 01-30-2007 12:55 PM crashfrog has replied
 Message 44 by Hawks, posted 01-30-2007 5:04 PM crashfrog has replied

  
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 42 of 92 (381265)
01-30-2007 12:55 PM
Reply to: Message 41 by crashfrog
01-30-2007 12:20 PM


Re: The origin of new alleles
...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.
Perhaps you're right about this, frog. Maybe there is nothing at all to "horizontal gene transfer." But I have carefully read Frederic Bushman's Lateral DNA Transfer/Mechanisms and Consequences (2002), and he makes an awfully good case for the mechanisms you are questioning. You should check it out of the library. Pay particular attention to Chapter 10 "Lateral Transfer in Eukaryotes: Fluidity in the Human Blueprint."
Lateral genetic transfer is fascinating, and many of the mechanisms are well understood. Upthread I posted a muse of mine that crossing over in the first prophase of meiosis is also evidence of an escape mecahism used by genes to avoid their parasites. Hamilton, Williams, Dawkins et al. are proponents of genetic "strategies" that give meaning to the need for sex. So I became interested in lateral DNA transfer from that POV.
Please tell me what you think is invalid about gene flow as a means to accomplish microevolution.
”Hoot

This message is a reply to:
 Message 41 by crashfrog, posted 01-30-2007 12:20 PM crashfrog has replied

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 Message 43 by crashfrog, posted 01-30-2007 4:47 PM Fosdick has replied

  
crashfrog
Member (Idle past 1467 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 43 of 92 (381336)
01-30-2007 4:47 PM
Reply to: Message 42 by Fosdick
01-30-2007 12:55 PM


Re: The origin of new alleles
Lateral genetic transfer is fascinating, and many of the mechanisms are well understood.
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.
Please tell me what you think is invalid about gene flow as a means to accomplish microevolution.
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.

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 Message 42 by Fosdick, posted 01-30-2007 12:55 PM Fosdick has replied

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 Message 48 by Fosdick, posted 01-30-2007 7:37 PM crashfrog has replied

  
Hawks
Member (Idle past 6147 days)
Posts: 41
Joined: 08-20-2006


Message 44 of 92 (381341)
01-30-2007 5:04 PM
Reply to: Message 41 by crashfrog
01-30-2007 12:20 PM


Re: The origin of new alleles
quote:
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."
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.
quote:
...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.
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.

This message is a reply to:
 Message 41 by crashfrog, posted 01-30-2007 12:20 PM crashfrog has replied

Replies to this message:
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 Message 46 by crashfrog, posted 01-30-2007 6:19 PM Hawks has replied
 Message 47 by Fosdick, posted 01-30-2007 7:17 PM Hawks has not replied

  
NosyNed
Member
Posts: 8996
From: Canada
Joined: 04-04-2003


Message 45 of 92 (381342)
01-30-2007 5:11 PM
Reply to: Message 44 by Hawks
01-30-2007 5:04 PM


Genes or retros
I would agree that it isn't impossible (maybe not even "far-fetched") that a gene could somehow be carried across the species barriers. However, my limited understanding of the terminology makes me think that a "endogenous retrotransposon" is not a gene.
That is, it does not produce any messenger RNA or protein products. This makes it much more likely that it could be succesffully carried over.
If an actual gene was carried over and produced proteins there is, I'd guess, a pretty high probability that it could kill the receiving cell and go no further. Again,I'd agree it may not do so and the jump isn't impossible.
I guess I'd have to review the whole darned thread to figure out why that matters much.

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