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Author Topic:   What about those jumping genes?
Fosdick 
Suspended Member (Idle past 5500 days)
Posts: 1793
From: Upper Slobovia
Joined: 12-11-2006


Message 1 of 102 (419535)
09-03-2007 12:33 PM


I had an argument with crashfrog about jumping genes way back when (I can't find the thread.) It involved the discovery of tse-tse fly genes creeping around in the human genome. Well, this news from Nature is interesting and relevant to that issue. Here's a case of a fly getting its version of what happened to a human in the movie The Fly:
Bacterial genome found within a fly's
DNA transfer from bacteria to animals is more common than thought.
So maybe this supports the findings of insect genes in the human genome.
The topical question for this proposed thead is: Do you think jumping genes could have played a significant role in the course of either biological or social evolution?
”HM

Replies to this message:
 Message 3 by New Cat's Eye, posted 09-04-2007 1:07 PM Fosdick has replied
 Message 6 by crashfrog, posted 09-04-2007 3:22 PM Fosdick has replied
 Message 28 by molbiogirl, posted 09-09-2007 3:38 AM Fosdick has replied

  
AdminNosy
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From: Vancouver, BC, Canada
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Message 2 of 102 (419539)
09-03-2007 12:42 PM


Thread moved here from the Proposed New Topics forum.

  
New Cat's Eye
Inactive Member


Message 3 of 102 (419720)
09-04-2007 1:07 PM
Reply to: Message 1 by Fosdick
09-03-2007 12:33 PM


Do you think jumping genes could have played a significant role in the course of either biological or social evolution?
Could be another source for mutations.

This message is a reply to:
 Message 1 by Fosdick, posted 09-03-2007 12:33 PM Fosdick has replied

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 Message 4 by Fosdick, posted 09-04-2007 2:44 PM New Cat's Eye has replied

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


Message 4 of 102 (419740)
09-04-2007 2:44 PM
Reply to: Message 3 by New Cat's Eye
09-04-2007 1:07 PM


CS responded to the question:
Do you think jumping genes could have played a significant role in the course of either biological or social evolution?
Could be another source for mutations.
A mutation can produce an allele of a gene”the simplest example being a single nucleotide polymorhism (SNP)”but OP article speaks to whole genes from prokaryotes jumping into the genome of an insect. That is much more dramatic than a SNP, wouldn't you say?
”HM

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 Message 3 by New Cat's Eye, posted 09-04-2007 1:07 PM New Cat's Eye has replied

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 Message 5 by New Cat's Eye, posted 09-04-2007 2:51 PM Fosdick has replied

  
New Cat's Eye
Inactive Member


Message 5 of 102 (419743)
09-04-2007 2:51 PM
Reply to: Message 4 by Fosdick
09-04-2007 2:44 PM


That is much more dramatic than a SNP, wouldn't you say?
Yes, but a source for alleles none-the-less (but actually all-the-more).
Your point?

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 Message 4 by Fosdick, posted 09-04-2007 2:44 PM Fosdick has replied

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 Message 7 by Fosdick, posted 09-04-2007 8:09 PM New Cat's Eye has replied

  
crashfrog
Member (Idle past 1466 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 6 of 102 (419748)
09-04-2007 3:22 PM
Reply to: Message 1 by Fosdick
09-03-2007 12:33 PM


It's interesting, but I'm not entirely convinced that this isn't just contamination. Wolbachia is nearly universal throughout insect species, and while they say that their samples were from insects that were Wolbachia-free, they don't say how they ensured that.
So maybe this supports the findings of insect genes in the human genome.
So far, though, your example goes the wrong way. Insertion of bacterial or viral genes into a metazoan host is considerably removed from HGT between two metazoan organisms.

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 Message 8 by Fosdick, posted 09-04-2007 8:14 PM crashfrog has replied

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


Message 7 of 102 (419792)
09-04-2007 8:09 PM
Reply to: Message 5 by New Cat's Eye
09-04-2007 2:51 PM


The long leap of the gene
That is much more dramatic than a SNP, wouldn't you say?
Yes, but a source for alleles none-the-less (but actually all-the-more).
Your point?
My point is that genes jump further than you might expect, and indeed they can survive the leap intact, suggesting again, along with Dawkins, that genes have selfish determinism.
”HM

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 Message 5 by New Cat's Eye, posted 09-04-2007 2:51 PM New Cat's Eye has replied

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 Message 10 by New Cat's Eye, posted 09-05-2007 10:36 AM Fosdick has replied

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


Message 8 of 102 (419796)
09-04-2007 8:14 PM
Reply to: Message 6 by crashfrog
09-04-2007 3:22 PM


Horizontal gene transfer
crashfrog writes:
It's interesting, but I'm not entirely convinced that this isn't just contamination.
What's the difference?
So far, though, your example goes the wrong way. Insertion of bacterial or viral genes into a metazoan host is considerably removed from HGT between two metazoan organisms.
Still seems like a real nifty HGT feat to me!
”HM

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 Message 6 by crashfrog, posted 09-04-2007 3:22 PM crashfrog has replied

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 Message 9 by crashfrog, posted 09-04-2007 9:22 PM Fosdick has replied

  
crashfrog
Member (Idle past 1466 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 9 of 102 (419808)
09-04-2007 9:22 PM
Reply to: Message 8 by Fosdick
09-04-2007 8:14 PM


Re: Horizontal gene transfer
What's the difference?
What? You mean, what's the difference between finding bacterial sequences in your sample because they were in the genome of your sample by HGT, and finding them in your sample because some Wolbachia got in while you were homogenizing the tissue in preparation for extraction?
You really can't imagine what the difference is, there?
You really have no idea what you're talking about, do you?

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 Message 8 by Fosdick, posted 09-04-2007 8:14 PM Fosdick has replied

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 Message 11 by Fosdick, posted 09-05-2007 11:37 AM crashfrog has replied

  
New Cat's Eye
Inactive Member


Message 10 of 102 (419891)
09-05-2007 10:36 AM
Reply to: Message 7 by Fosdick
09-04-2007 8:09 PM


Re: The long leap of the gene
My point is that genes jump further than you might expect, and indeed they can survive the leap intact, suggesting again, along with Dawkins, that genes have selfish determinism.
I'm sorry, I'm not catching your implication.

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


Message 11 of 102 (419896)
09-05-2007 11:37 AM
Reply to: Message 9 by crashfrog
09-04-2007 9:22 PM


Re: Horizontal gene transfer
crashfrog wrote:
What? You mean, what's the difference between finding bacterial sequences in your sample because they were in the genome of your sample by HGT, and finding them in your sample because some Wolbachia got in while you were homogenizing the tissue in preparation for extraction?
You really can't imagine what the difference is, there?
Just curious. Doesn't your sampling method differentiate between sampling contamination and HGT contamination? If not, you need to work on your lab procedures.
You really have no idea what you're talking about, do you?
Probably not. I've got young, beautiful women here distracting me while I'm trying to think. Then my investor calls and tells me to get out of the market right now. Birds are shitting on my boat. The next-door neighbor's pit bull is running loose again. Oh, and here come the grandkids to swim in my pool and mess up my kitchen...and you have the gall to ask me if I know what I am talking about?
”HM
Edited by Hoot Mon, : No reason given.

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 Message 9 by crashfrog, posted 09-04-2007 9:22 PM crashfrog has replied

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 Message 13 by crashfrog, posted 09-05-2007 12:13 PM Fosdick has replied

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


Message 12 of 102 (419902)
09-05-2007 11:50 AM
Reply to: Message 10 by New Cat's Eye
09-05-2007 10:36 AM


Re: The long leap of the gene
CS wrote:
My point is that genes jump further than you might expect, and indeed they can survive the leap intact, suggesting again, along with Dawkins, that genes have selfish determinism.
I'm sorry, I'm not catching your implication.
CS, if "selfish genetic determinism" doesn't get your attention, then I don't know what will. I'm taking Dawkins' and Hamilton's side in this consideration of jumping genes and their roles in evolution. I would like to know just how deterministically they jump. And, since genes are purely digital information, I wonder if that is somehow beneficial to their jumping. (Maybe the air is thinner up there in the digital world.)
”HM

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crashfrog
Member (Idle past 1466 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 13 of 102 (419905)
09-05-2007 12:13 PM
Reply to: Message 11 by Fosdick
09-05-2007 11:37 AM


Re: Horizontal gene transfer
Doesn't your sampling method differentiate between sampling contamination and HGT contamination?
How could it? That's what I don't understand from the article.
In my lab, it's irrelevant, since we're using primers to selectively amplify individual genes. (I say "we" because I do some of it, but I'm just the lab tech, not really a researcher.) We're not sequencing whole nuclear genomes, so contamination is only a problem when its contamination between samples. We don't worry about bacteria that might settle in from the air (or the Wolbachia that reside in their gut.)
But it's not at all clear how you would definitively exclude Wolbachia - a nearly universal insect pest - from your sample. And once you homogenize and extract, it's all mixed up anyway. And if you're amplifying the whole nuclear genome, then you wind up amplifying not only your insect sample but any bacteria that were in there with them. And it's hard to imagine how you could sterilize the inside and outside of an insect without destroying its own DNA.
If not, you need to work on your lab procedures.
I'm open to suggestion, but then, my lab isn't working with the whole nuclear genome. So it's not an issue for us.
The problem is that the article gives no indication on how they were able to accomplish this unlikely feat.
you have the gall to ask me if I know what I am talking about?
Suggestion: post less, fuck around with your boat more. What the hell are you doing on the internet with hot babes and boats all around you? You must be some kind of idiot.

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 Message 11 by Fosdick, posted 09-05-2007 11:37 AM Fosdick has replied

Replies to this message:
 Message 14 by Fosdick, posted 09-05-2007 12:23 PM crashfrog has replied

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


Message 14 of 102 (419907)
09-05-2007 12:23 PM
Reply to: Message 13 by crashfrog
09-05-2007 12:13 PM


Horizontal genome transfer?
crash, the OP article is talking about a whole genome, you know.
ADDED: Oops, sorry, I see that you have acknowledged this in your post.
”HM
Edited by Hoot Mon, : No reason given.

This message is a reply to:
 Message 13 by crashfrog, posted 09-05-2007 12:13 PM crashfrog has replied

Replies to this message:
 Message 15 by crashfrog, posted 09-05-2007 12:31 PM Fosdick has replied

  
crashfrog
Member (Idle past 1466 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 15 of 102 (419910)
09-05-2007 12:31 PM
Reply to: Message 14 by Fosdick
09-05-2007 12:23 PM


Re: Horizontal genome transfer?
crash, the OP article is talking about a whole genome, you know.
Yes, HM, that's my point. Are you paying attention? Can you focus for a minute? Allow me to repeat myself:
Contamination of Wolbachia in the extraction isn't an issue when you're targeting your amplification at specific genes (genes that bacteria don't have), because the unamplified bacterial genome just falls into the background noise.
Contamination of Wolbachia in the extraction becomes a big issue when you're amplifying the entire genome, because the primers you have to use will amplify all genetic sequences, including the sequences in whatever bacteria were living on the surface of your sample. The researchers here claim that there was no Wolbachia in the sample, but I don't understand how they ensured that, so I'm reticent to take their claim on face value.
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.
Try to keep up, ok? I know it's hard with a boat full of bird shit.

This message is a reply to:
 Message 14 by Fosdick, posted 09-05-2007 12:23 PM Fosdick has replied

Replies to this message:
 Message 16 by Fosdick, posted 09-05-2007 12:52 PM crashfrog has replied

  
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