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Horizontal Gene Transfer

Thread - Stealth

On  30/9/2002, Wolfie posted:

<<snip>>
for me this is not an issue, I will never accept GMOs even if they're proved safer than the spit in my own mouth.

There is nothing that will ever change my mind, ever.


Gerald Cairnes responded:

There is nothing that we can do with such profound logic so will not even try to answer you on the subject other than to make sure such views do not have an unfortunate influence on any impressionable members of the List.

All I will say is this, you have been genetically engineered, we all have, by viruses and bacteria over a very long time otherwise we couldn't survive nor would your mother's pregnancy with you have been possible without incorporation of virus genes now described as endogenous retroviruses, they make it possible for the uterus to do it's job! I would think that would be the ultimate insult to a philosophy such as yours.

Wolfie responded:

Oh yeah, I've got cane toad genes in me so dinosaurs won't eat me, what did the men in white coats put in yours?

Breeding and evolving is not genetic engineering.

You cannot get spider venom in corn because corn plants can't hump spiders and you can't get glowing monkeys or goat udders producing spider silk

How do you guys have the gall to throw that tired old phrase around that "GM is somehow natural because we've been doing it for years"

We haven't been getting sheep to hump kangaroos to produce woolly jumpers.

We have been crossing one type of cow with another, that happens... and they've always produced milk.

My argument that it's not natural doesn't seem to get past the very determined pro-religion shown very clearly by members of this list. If I am religious then fine, but don't those few of you opposing me go throwing any stones in glass houses.
Stephen Berry replied:

G'Day Wolfie,  Yes you do have genes from amphibians and spiders and plants and bacteria.  These have been delivered by virus/bacterial infections.   Every time you get an infection there is gene transfer although most of the genes thus traded are usually of no value to the organism receiving them and are never used.  It was the discovery by medical researchers that a virus or bacterium were carrying RNA/DNA into the cells they infected that lead to so call GM.   Spiders don't have to hump corn to have their genes passed to it all they have to do is be exposed to the same micro-organisms in the environment.  This is still the major method of doing GM in the lab, expose a harmless virus/bacterium to the DNA you want to transfer then expose the target organism.  We are all the result of micro-organisms carting DNA around and dumping it willy nilly in other cells.

Ray added:

Wolfie, with my beginners understanding of gene cutting let me try to explain how it is that nothing which is being done by genetic engineering is new.

Bacteria have, for well over 1 billion years, been producing enzymes which slice up the DNA of invading virus.  It is a defense mechanism.

All genetic engineers have done is discover this ability, isolate these bacterial enzymes, and cut DNA at the precise points dictated by the specific enzymes.

This skill, plagiarised from microbes, is used to isolate and to sequence DNA, and to manipulate DNA in ways like recombining one thread of nucleotide base sequences for a particular protein (e.g. silk, vitamin B, insulin..) into another genome.

No big deal.
Gerald Cairnes wrote:

It has become very clear that there is only ONE form of life on this Planet and it occurs in a wondrous array of species and varieties therefore it is the speciation which could be regarded as the departure from the basic genome. In any case we share a very large number of genes with the lowliest of organisms which makes the "shock horror" reaction of the anti GM Luddites pretty hollow. Which touches on the thread on "lies" methinks.

Of course there are issues about GM which have been and still are being discussed on this List and elsewhere and I share these concerns also. But for those who insist on driving down the wrong side of the road, unlike farming, the future is pretty clear!
Ian Musgrave responded to Wolfie's post:
>Explain to me how monkeys would come to glow in the dark or why certain
>vegetables would end up with jellyfish genes.
Horizontal gene transfer.
>this is patently NOT natural.
It is very natural, HGT occurs quite often between bacteria, more rarely between bacteria and metazoans, and more rarely still between bacteria and things like vertebrates, but it does happen and is perfectly natural. Also, there are examples of viruses incorporating gene form one organisms and transferring them to another. Again rare, but perfectly natural

An example are the RAG genes in vertebrates. These are transposases that were swapped from bacteria into sharklike fish around 200 million years ago, and they form the basis of our adaptive immune system. There are other, more recent, examples, but I particularly like that one.

Gerald Cairnes replied:

I think that people generally do not appreciate the fact that there is only one form of life on the planet and all the forms are but individual expressions of the basis for Life e.g. DNA/RNA. Each life form Homo included is but a subset of a much larger relatively invisible process and while we may feel like independent individuals we are all linked to this common "thread". Therefore it should be no surprise that genes transfer readily from one organism to another.

The rate at which this occurs between bacteria for instance on a minute by minute basis on a World scale would be a stupendous number. Most of these transfers will be unsuccessful or in some cases fatal but a small number will be successful and transfer advantages to the recipient which will likely become dominant. Evolution proceeds not only by  slow incremental steps but also by large leaps when the conditions are right. These effects would I think absolutely dwarf anything which we do at this time but we do need to know more and in most cases this is being considered. I does no commercial organisation any good at all to release a GM organism that is going to do wholesale damage to people the results would be catastrophic commercially.

I won't deny there are some cowboys around and we have seen some of them in recent time paid off with millions of dollars but Times are a Changing and this situation will improve. Since the Poseidon, Bond, Pyramid, Worldcom, Enron ................... etc. the picture is becoming clear and I doubt that the community will continue to tolerate this sort of behaviour much longer. I have been complaining about this for nigh on 40 years and ostracised on occasions as a "Leftie" or "Pinko" the usual character assassination these people use to discredit anyone who draws attention to their lousy performance and frankly malfeasance. But there always have been cowboys and as far as GM is concerned their influences will merge into the background but what is important is how they seduce politicians to force their particular desires on the community. That is the issue being mixed up with the GM which is at a lower level but gene transfer is a very robust system.

The next time you get the "flu" consider yourself genetically modified but this is likely to be short lived as your immune system deals with it. Much more important are the many "silent" infections which occur without our awareness but which leave behind fragments which can be either beneficial or harmful. Here again even if the immune system does not zap these fragments or the cells containing them the greatest probability is that any effects they have are likely to be terminal for the cell concerned. there is a great levelling characteristic in the operating system. In any case moist changes need to be small ones to be successful. Up until 1974 I rarely needed to use a handkerchief or was bothered by allergies then I caught one mother of a dose of the "Dreaded Lurgie" and ever since I have had significant food and respiratory allergies. Question is what fragments got left behind which are deleterious but not enough to kill the cells yet rendering them highly sensitive to allergens?

There are always risks with anything we do and it behoves us to be diligent in our GM manipulation but I would see the risks of a catastrophe from such a source as being remote. Most of drive cars and there is a significant risk in that. We live in a World of constant change and like Canute we can't hold back the tide although we stand a reasonable chance of moderating it's influences. There is a very good chance that Wolfie is not the same man he was last year! :-)

Ian Musgrave posted:

> > >this is patently NOT natural.
> > It is very natural, HGT occurs quite often between bacteria, more rarely
> > between bacteria and metazoans, and more rarely still between bacteria and
> > things like vertebrates, but it does happen and is perfectly natural. Also,
> > there are examples of viruses incorporating gene form one organisms and
> > transferring them to another. Again rare, but perfectly natural
>germs... bacteria [bah!]

They are the dominant form of life on this planet (by species diversity, habitat diversity and sheer biomass), with rather sophisticated biochemical systems, so don't knock them. Never disparage things that can live in boiling acid.
>I'm talking about well developed organisms. [mammals, vegetables, fruit
>trees]
RAG genes were transferred to mammals, and by some accounts 0.5% of the human genome is horizontally transferred genes, this is probably an overestimate, but even so, a substantial part of our genome comes from other organisms via HGT.

In plants, for at least Arabidopsus, something like an astounding 10% of its genome comes from HGT (mostly from cyanobacteria). Some plants have a form of haemoglobin they got via horizontal gene transfer. There is a beetle with a large chunk of its X chromosome composed of HGT'd bacterial genome.

This sort of gene shuffling leaves Bt cotton in the dust, and it is all natural.
On Wednesday 02 October 2002 23:39, Wolfie! wrote:
> So spontaneously overnight, corn decides that it should be luminous
> or goats start producing silk. yes I suppose things can evolve like
> that.
Zero Sum replied:

Quite correct, Wolfie.  It is called "expression".
> perhaps the corn wants to be pollinated by night flying bugs...
> perhaps the goats want to spin webs with their udders to eat the
> bugs.
You might be trying to annoy your opponents with those "wants" but you are going to antagonise your "supporters" too.
> perhaps pigs might grow wings when I wake up one morning after a
> visit from the easter bunny and the tooth fairy who leaves me a note
> to say that in a cute pink fluffy world, GM really is natural.
Wolfie.  I worry about GM for what I consider very good reasons.  But unnatural?  No more so than heterosexuality...

and in a further post:

<<snip>>

And I'll throw in a joker for you.  You can consider that I have been "genetically modified".  Thirty years ago by the blood bank.  They wanted grouping serum and injected me (a volunteer) with a substance from pigs to raise the level of antibodies to foreign blood in my system.  The idea was to raise the antibody count to between 100-400,
but mine hit 2,000 (IIRC) and any transfusion mis-match (of even some of the rarer factors) would probably kill me instantly.  It was suggested that I was no longer a suitable recipient for a blood donation.

So there you are Wolfie, you are corresponding with a GMO.  My blood is no longer entirely human.  Doesn't that send shivers down your spine?

Ian Musgrave  responded to the same post:
>So spontaneously overnight, corn decides that it should be luminous or
>goats start producing silk.
Or sharks decide they want an adaptive immune system. As I mentioned before, and you have ignored, our adaptive immune system is due to HGT of the RAG transposonases. Up to 0.5% of the human genome is horizontally transferred genes.
>yes I suppose things can evolve like that.
In evolution, _want_ is irrelevant. The peppered moth didn't _want_ to be black, one moth had a random mutation that made it black, and the mutation was selected for. Sharks didn't _want_ RAG transponase, they got them in a HGT even, and fortuitously they made a survival difference that evolution could select for.
>perhaps the corn wants to be pollinated by night flying bugs...
>perhaps the goats want to spin webs with their udders to eat the bugs.
The beetles didn't want most of their X chromosome to be Wolbacia genome, but they got it any way, thanks to HGT. Evolution has no interest in _want_.
>perhaps pigs might grow wings when I wake up one morning after a visit
>from the easter bunny and the tooth fairy who leaves me a note to say
>that in a cute pink fluffy world, GM really is natural.
Why do you keep on keep on ignoring the evidence that GM like events _are_ natural. Do you think spider silk proteins are more privileged than RAG transposase, or 2on2 haemoglobin, or metabolic enzymes. Do you think goats producing spider silk protein is more strange than plants producing natural HGT 2on2 haemoglobin?

It seems that your real objection to GM is that it violates your sense of  _scala_natura_. Unfortunately, biology ignores _scala_natura_ as well.

Cheers! Ian (who notes that while HGT may be natural, this does not automatically make it good)

>Ray wrote:
> >
> > >>I'm talking about well developed organisms. [mammals, vegetables, fruit
> > trees]
> >
> > Okay Wolfie, may I remind you that were it not for the transfer of your
> > father's genetic material you could not be male.  In fact you could not BE.

Ahh, ray, that's not HGT.
>he made me with his penis, it's natural...
>that genetic material was mine to have, I'm not part butterfly.
Around 0.5% of you _is_ non-vertebrate.

I'm pretty sure now that your problem stems for an essentialist view of nature, ie that organisms have certain essential properties or descriptions, and to go outside those properties is to be non-natural (and in some way, deeply offensive, as this violates what it is to be an organism). Transferring, for example, a haemoglobin gene to a plant defies the essential nature of a plant and is hence non-natural.

Yet nature is _not_ essentialist (and this was one of the lessons Charles Darwin taught us), and haemoglobin has been transferred to plants by natural means. Organisms are sloppy, ill defined (species problem anyone?)
and carry genes from things that are wildly different from themselves, and nature cares not a jot.

On Monday 07 October 2002 16:00, Wolfie! wrote:
> If the two cannot mate, then it is unnatural and cannot happen.
> it requires "mad nerds in labs" to join the DNA manually and
> make something out of that... an un-natural, but obviously
> functional process.
Zero Sum replied:
No, because the "mad nerds in labs" are doing the same thing that viruses are doing all the time anyway.  Viruses do it at random and they do it with purpose.  That is the only difference.

Annihilating all "the mad nerds labs" wouldn't stop it happening as there are plenty of viruses around.
> So all this huffing about it being natural was pointless, I'm right.
No, you are wrong.  Genes get interchanged all the time.  Cross breeding is a separate issue.

Look, you seen people mention HGT ( *Horizontal* Gene Transfer), well the reason it is called *horizontal* is that sexual reproduction is *Vertical* Gene Transfer.  Genes go down the generations vertically and viruses and genetic modification pass genes horizontally.

And Ian Musgrave also responded :

<<snip>>
Virus infects organism 1
Virus progeny accidently copies host gene
Virus progeny infects entirely different organism
Virus integrates gene from organism 1 into completely different organism 2
Organism 2 has gene it can possibly get via sex with organism 1.
That's HGT the natural way, that's why you have about 0.5% non-vertebrate genes in your body, sticking your fingers in your ears and going "LaLaLa I can't hear you" won't make them go away.

That's why plants have 2on2 haemoglobins
That's why certain beetles have most of their X chromosome from bacteria (actually, this may not have been virus mediated).
Perfectly natural transfer of genes between wildly unrelated organisms
>They're all telling me how easily genes cross the species barrier.
Yes, via HGT. Not sex. We have stressed this many times
>but after the horse x human post, they're saying "oh that's sperm
>incompatibility and can't be done" riiighhhtt...
Almost certainly won't work for humans and horse, but does work for whales and dolphins (different genra) and ferns (entirely different families). Is family level a big enough taxonomic difference for you? Even then this is
beside the point. Sex is vertical gene transmission. We are talking about horizontal gene transmission (which is the natural analog of genetic engineering, where a virus is used to transport a foreign gene into a completely different organism).
>So you've got a cow and a bull in a pasture together and they stand
>there and vibrate certain ch'i energies so that the reproduction
>fairies will appear from their seventh dimensional space and interweave
>their DNA in a totally natural fashion.
Sticking you fingers in your ears and going "LaLaLa I can't hear you" doesn't become you.
>If an animal needs to reproduce in a natural fashion, sperm and ova are required.
Sure, and if a virus wants to deposit an alien gene in you, only the virus is required.
>When I mentioned my horror about, say, corn and spider venom,
>"they who know" said that it was all perfectly fine and acceptable
>for this to occur in nature anyway.
Sure, though why you think that having the gene for phospholipase A incorporated into corn is more horrifying than having the gene for 2on2 haemoglobin incorporated into plants (which happened) or RAG transposases
incorporated into humans (it happened).
>even though we have a certain problem where pollen and spider semen
>are incredibly... wildly... incompatible with each other.
And plants are incredibly, wildly incompatible with things that have haemoglobin, that didn't bother the virus that transported the haemoglobin gene into plants (where it is doing quite well thank you). Humans are wildly incompatible with the organisms that host the RAG transposases (or any of the non-vertebrate genes we carry), but that didn't bother the viruses that transported them too us.
>If the two cannot mate, then it is unnatural and cannot happen.
>it requires "mad nerds in labs" to join the DNA manually and
>make something out of that... an un-natural, but obviously functional
>process.

Or viruses, viruses, they are sooooo unnatural aren't they? Did you even _bother_ to read our posts were we talked about horizontal gene transfer?
>So all this huffing about it being natural was pointless, I'm right.
You are wrong.
>them: "oh yes all natural"
>me: "what about the sperm?"
>them: "oh that cant happen due to incompatibility"
In some species, genera and families, but not in others (pace Wolpins, Cammas and _really_ weird plants)
>me: "but animals can't breed without sperm."
>them: "that's beside the point"
In HGT genes get transferred to organisms via viruses (or other more esoteric DNA uptake mecanisms that bypass sex entirely).
>me: "you can't have it both ways"
>them: "oh yes we can".
Certainly, the human genome is littered with bits of virus and genes the viruses bought with them (can you say "processed pseudo gene"). Sex is not the only way to get new genetic material, viral gene incorporation is real,
and something like 0.5% of our genome is DNA from non-vertebrates shuttled over into us via viruses (or rather 0.5% is complete genes that work, there quite a bit more broken genes about).
>me: "fine, go and play in your padded cell"
them: "Please learn some biology instead of sticking your fingers in your ears and going "LaLaLa I can't hear you""
At 06:01  7/10/02 +1000, Ray wrote:
>At the level required to produce antibodies in the blood, Wolfie you can be
>glad that genetic transfer DOES exist.
Yes, but not in the way you appear to think. Rather, because the RAG transposase that is responsible for shuffling the antibody genes into new configurations, and making adaptive immunity possible, were incorporated
into vertebrates from bacteria via horizontal gene transfer.
>I am not sure that the auto-production of chemical antibodies is directly
>connected to DNA and RNA, but I feel pretty confident to suggest that it is
>indirectly connected. (I guess I can stand being shot)
Ray, I _know_ you have textbooks with this stuff in it, why don't you try something radical like actually opening up a text book and reading it before typing something.

Of course the production of antibodies is connected to DNA, where do you think the heavy chain and light chain of the Immunoglobulin molecule comes from? Their respective genes.

[oversimplified]
During infection, lymphoid stem cells proliferate into B cells, during proliferation, the RAG transposases scramble the Variable regions of the heavy and light chains of the immunoglobulin molecule, so that each B cell has a immunoglobulin gene with a unique sequence at the antibody binding site. The IgG is expressed on the surface of the B cell, and if it binds to a bacterial antigen (like a cell wall protein), then that class of B cell rapidly proliferates, producing a mass of B cells all producing the same IgG
[end oversimplifiaction]
>It is just a bit closer to HGT, I think,
No, it is nothing like HGT.
>than the idea of crossing a human
>with a guinea-pig to make a gemlin (Mogwie?), where I have been informed,
>human sperm can fertilize the ovum of a guinea pig, but the cell division
>does not start.
References to the peer-reviewed literature please.

>yeah sure... is this the abc science group or am I on heavens gate?

The science list, which is why my original post contained substantial science, which you snipped, yet again, without comment. What is it about the science that you don't comprehend? I'd provide references to the
peer-reviewed literature, if I had assurance that you would at least make an effort to read them.

Biology, like physics, contains many things that run counter to our intuition, and may be deeply disturbing. You may find the concept that viruses can pick up foreign genes and insert them into wildly different organisms disturbing, but it is real, and natural. We owe our adaptive immunity to just such an event.

I love biology, it is a passion I am lucky to have a job in. It makes me sad that people will avidly read popular books on physics, yet similar books about biology and molecular biology go unread. Hands up anyone who
has read "the 8th day of creation", now who has read "A brief history of time"?

The Eighth Day of Creation: Makers of the Revolution in Biology
by Horace Freeland Judson Cold Spring Harbor Laboratory; ISBN: 0879694785;
Expanded edition (November 1996)

At 09:23  7/10/02 +1100, Forbsy wrote:
>Would anyone who knows more than I do about genetics (e.g. Ian Musgrave,
>Chris L, Peter Mac) care to comment on the contents of the article at the
>following URL.
>
>http://www.i-sis.org/SenseNonsense.php
Ian Musgrave replied:
Large chunks of hysteria mixed in with a little bit of interesting science, no HGT is not the end of our models of evolution. In fact, I know Mike Syvanen, who the author alternately praises and excoriates. I should pass this on to him for a chuckle.

If I get time, I'll review this article properly.

Chris Lawson responded:

And this paper is even worse. It completely fudges the "central dogma" of genetics to create a strawman. No geneticist has ever believed the first "implication" that Dr Ho lists. That "implication" is:

"Genes determine characters in a straightforward, additive way: one gene-one protein, and by implication, one character. Environmental influence, if any, can be neatly separated from the genetic. "

I would defy Dr Ho (or indeed anyone) to find a single reference to support the claim that neo-Darwinists believed this tripe. I would also defy Dr Ho to present an actual logical argument linking Crick's central dogma with this statement; the two things are completely unrelated. I would finally like to point out that the central dogma has been known to be wrong for at least three decades, so making claims about the current state of biology
based on a theorem that is known to be wrong by all working biologists is further evidence of shonky thinking. You might as well try to discredit modern physics on the basis that the old ether theory was wrong.

And finally I point out Dr Ho's remarkable argument that horizontal gene transfer is natural, but not natural enough to make GM acceptable. He's trying to have it both ways. Horizontal gene transfer shows that genes have been skipping around the biosphere for billions of years. This proves that anything that is GM could immediately jump all over the place and cause ecological disaster. On the other hand, HGT in nature is very rare, which means GM technology is unnatural. In fact, Dr Ho closes his argument with what he considers to be telling evidence of the prevalence of HGT and the danger is represents in the light of GM -- all this in the same article that he claims gene transfer is unnatural and uncommon.