Bay 12 Games Forum

Derp.

Post this on imdb. It is vital information that must be spread like a wonderful, wonderful plague of thought. I want to see this put on HBO.

Quote from: ChairmanPoo on September 23, 2010, 10:54:40 am

Quote

in order to use a protein from bacteria, etc, you have to add these introns,

you do? (sauce?)

I thought it was the other way around? To make prokaryotes produce eukaryotic proteins you have to remove the introns?

It's both, or sometimes only the cap. The cap and tail in mRNA is there so that the mRNA molecules can be 'capped' for identification as mRNA by the Eukaryote ribosome (and for protection from RNases), and 'tailed' to prevent damaged RNA from being coded into proteins. Introns code for their placement, and the capping/tailing happens after being converted from DNA, before transcription into proteins.

In eukaryotes, mRNA that doesn't have a cap or tail are quickly recycled. mRNA from eukaryotes, or really any mRNA with the poly(A) tail introduced into bacteria, actually promotes degradation of mRNA. poly(A) tails shorten over time in Eukaryotes (at least), sort of acting as a counter for their termination (or in some cases storage).

Since there are some bacteria that actually use poly(A) terminators in their mRNA to signal the cell to make sure it's degraded faster, you would probably have to carefully consider what the effects of either omission or removal of poly(A) introns may be. So yeah, the situation is a little more complicated than "add this to make in goldfish", but in general there has to be a minimal amount of modification for it to work.

I give up. You're tossing up straw men everywhere. I'll only comment on what you've said so far and then go my own way.

Quote from: ChairmanPoo on September 22, 2010, 04:45:08 pm

burden of proof = you.

AKA: have you got any evidence proving that insterting sequence A (which works fine in animal A) verbatim into animal B will somehow result in proteins that behave like prions?

I haven't said that it will definitely produce prions, but Eagleton is asserting that there is "no danger of creating prions" without anything at all to back that up.  This seems like no more than blind faith to me.

If the only difference between a prion and the protein it affects is the way the prion is folded then you might not even need to have a transcription error, I would think that a difference in the machinery that assembles proteins might result in a different folding.  And the machinery that assembles the proteins is different between animal A and animal B, I think.

Wrong. Here is an overview of the process, in video form, from BBC. Every living creature that uses DNA uses this machinery to create proteins, from bacteria to plants to human beings. Eukaryotes have different ribosomes from bacteria, etc, but they do not differ within the domains as far as I'm aware. It's methodical, predictable, and only fails in extreme circumstances, usually with catastrophic results to the host organism.

In any case prions are just an example I'm giving for something that could go wrong with this.  There simply isn't any basis for portraying the possible consequences of this form of genetic engineering as insignificant.

So give more examples? What basis do you have that the possible consequences of this form of genetic engineering are significant? If this isn't an area you're comfortable with delving into with any certainty, why are you arguing against it? I can assure you there have been plenty of people with a stronger handle on it than me that have examined the issues as well. Yet scientific consensus is that the risks are confined to some well established issues, and peer-review makes sure they're taken into consideration. Otherwise there would have been no FDA investigation. Believe it or not, food companies don't want their customers dying horrible deaths from their products. That's bad business.

So you're recanting your claim that prions are so complex that they can't accidentally be created, right?

No, I maintain it. Prions are simple compared to many other proteins, but still very complex. One example contains 209 amino acids, from 21 possible selections. Are you claiming that there's a reasonably large chance that we could come up with a combination like that on our own? It's just ridiculous to worry about when there's so much else going on around you that could kill you.

Then you're also recanting your claim that there can't be any problems because we could only be making proteins found in other animals consumed by humans.

That approach would only detect a mistake in the insertion of the sequences, not a problem occurring during gene expression as I mentioned above.

So even the people doing the genetic engineering say that unexpected protein sequences could be created by this process.

You left out this part

These concerns have been evaluated through the functional and molecular-genetic  characterization of the EO-1α locus with respect  to its multi-generational heritability and stability, and detailed nucleotide sequence in F2- and F4-generation AquAdvantage Salmon.

No evidence of interruption of endogenous genes has been identified, lowering the risk of  unanticipated phenotypic effects in the GE fish.  No such effects have been observed in  seven generations cultured over the last 15 years, as discussed in §2.4.

This means that the gene was not found in any other place than where they wanted it. They undoubtedly selected the transcription site by locating a place where the protein could be expressed properly. Any deviation would have shown up in their sequencing and been discarded. The only possible health risk here would be to the fish, with a foreign protein doing gods know what to its organ system. That's why this isn't done in humans - you don't want heart muscle floating around in your foot. It doesn't mean your foot isn't edible and delicious to a salmon - we process all kinds of protein through our digestive tracts every day, and it's a rare beast that actually affects us more than being dissolved into its component parts. The specific protein we've added, as has been stated, is used in ice cream FFS.

You act as though all possible problems can be evaluated and accurately assessed for risk by someone casually reading about this stuff and that simply isn't true.  These genome alterations and the ways in which they interact with other biological systems are not something to be taken lightly.

And here lies the problem. You want to imply that GM is harmful, and yet you refuse to do any amount of research on why it might be so. No one is taking this lightly but you.

None of your proofs that there's nothing to be worried about hold up to even the mildest scrutiny.

As far as I can tell, you haven't given my 'proofs' any kind of scrutiny at all, besides trying to find logical and grammatical mistakes and omissions and outright denying any reason I try to give you.

Bleh.

So... you didn't actually answer my question there.  What makes you think that only complex proteins can re-fold other proteins?

I don't. The issue with prions is that they re-fold other proteins into themselves. Hence the source of their name - proteinaceous infectious particle.

And now you're also claiming that the alterations of the genome only reproduce with 100% accuracy proteins that are found in other animals?  Do you have a source on that one?

Do you have a source saying that it doesn't? Anyway, no, I never claimed that. It's not 100% accurate yet. Discounting the unlikelihood that a mistake in sequence insertion might possibly create a protein harmful to humans, prion or not, there are means to determine if the modification has occurred in an undesirable place. Essentially, they've inserted the modifications into a very specific place, and the sequence they've used is straight-forward to identify.
From http://www.fda.gov/downloads/AdvisoryCommittees/CommitteesMeetingMaterials/VeterinaryMedicineAdvisoryCommittee/UCM224760.pdf If you're saying that after 15 years of evaluation, there's still a significant chance that a harmful protein could have developed spontaneously somewhere in the fish's genome and is waiting to give you cancer or something 20 years down the line, I really don't know what to tell you. Good luck with the lottery.

I didn't say anything about the salmon escaping, so I'm unsure of what you're responding to here.

This is the only risk with this case, as far as I can tell, so that's the risk I responded to

Okay, how exactly do you know all of this stuff about the probabilities of accidentally doing something that has never been done accidentally or intentionally before?  Are you a molecular biologist or something?  I don't even see how scientists could know what you're claiming to know; we didn't even know that prions existed until recently.  You appear to me to be pulling stuff out of your ass in a desperate attempt to assert your point by any means whatsoever, truthful or not.

Because prions have very specific, complex (however simple compared to other proteins) structures that would be prohibitively difficult to create intentionally without copying existing structures, let alone accidentally by altering non-prion proteins. The very fact that prions are poorly understood is prohibitive to their accidental creation - we're at the stage where we're transplating the encoding of proteins into the genomes of other creatures, not producing new proteins reliably, and no one is doing so in commercial products yet. I know about these things by reading about them. I'm not a molecular biologist, but I do have a brain. It's just not a risk.

I.. Was that aimed at me, in any way? I'm not sure how it relates to anything I said.

Nah, sorry if it seemed that way. I was saying that people don't generally use that as reasoning for opposing GMO, as evidenced by the poll results. I mean there were probably people that voted yes for other reasons than those stated, but half?

I eye-rolled forever at 'frankenfish'.

The problem is more about people making the world their playground. Some people believe that life (and "natural" wildlife) is worth something in itself, apart from it's economical value.

Look at the poll results.
27%
Yes. The FDA has already said that genetically altered salmon is as safe to eat as the traditional kind.
50%
No. Altered fish has never been eaten before -- we don't know what it could do to us.
23%
I'll wait and see. If it hits the market and there are no problems, I may try it.

We know exactly what it can do to us. We eat chinook salmon. We eat ocean pout. The article itself brings up 'new allergies' as a concern - do you know anyone that's only allergic to ocean pout? I'll just assume you don't, msnbc, because fish allergies are caused by a specific protein, parvalbumin, present in most fish.

The environmental concern is real, and when I saw this it spooked me a little. But it's addressed adequately by their measures. They're breeding female salmon with hormone-altered female salmon, meaning they're all female. The triploid method is statistically reliable and established as producing fish that are extremely unlikely to survive - At absolute most, you'd have 5% of fish (almost certainly less) fighting against the odds that the 95% other fish are escaping instead, trying to fight their way through chlorine kill-zones, heat exchangers, nets, several hydroelectic plants down-stream, etc. etc. Then -those- have to compete against native salmon, which statistically easily outcompete triploid salmon in mating. Take a look at this, which is a lot more informative than nbc's article. The tactic for news agencies that want to boil up some fear over this is the standard 'scientists don't know what they're doing and neither do you'. Well, there you go msnbc. Get reading, poll-takers, or shut up and let the grownups put food on your plates

Regarding patents, I actually see it as somewhat beneficial (if troubling) in GM foods specifically. Simply because it makes companies less likely to slip in some "trade secret" alterations to their products, which might alter any number of factors. If they're required to publish the sequenced genome of their product as a part of their patent, it's straight-forward for a regulatory body to check it against what's on the shelf.