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I did this kind of work in a community college biotech program (literally biotech 102, we used E. Coli just to learn the technique). They are not engineering a

I did this kind of work in a community college biotech program (literally biotech 102, we used E. Coli just to learn the technique). They are not engineering a new, deadlier strain of bacteria, they are using antibiotic resistance to solve a very simple problem: genetic modification is a probabilistic process, you have Gene A and need to get it into bacteria, but Gene A doesn't make the bacteria different externally in any easily detectable way. So, after the process of inserting Gene A into a batch of bacteria you need to figure out which of the bacteria actually picked up Gene A so you can proceed to the next step of your experiment. So, what you do is you pair Gene A with Gene B, which is a very light resistance to a very specific antibiotic. Now, after you perform the electroporation, you plate the bacteria on agarose gel, let colonies start to develop, and then lightly dose the gel with the antibiotic. The surviving bacterial colonies are those which have incorporated both Gene A and Gene B (because they are paired). It's just a way of filtering bacteria after electroporation so you can do further work. It's not dangerous to people because A) this antibiotic resistance was already found in nature, B) it's a resistance to a very specific antibiotic, not all antibiotics, and C) you're doing this in a protected lab. This is an incredibly standard process, to the point where - again - I did this in a Biotech 102 program at community college. You could sign up for a classes where you learn to do this, right now.

duskwuff 1y ago
Seconding this. I think my high school AP Biology class did a similar exercise in the early 2000s.
mrheosuper 1y ago
Interesting. I have a question, why not pair Gene A with something still detectable but less "dangerous", like a gene that change body color, or emit different color under UV light. Sorry i am totally noob here
- fabian2k 1y ago
  Because the antibiotic automatically selects the successful clones. The others that didn't incorporate the plasmid don't grow into colonies. Without antibiotics your plate will be entirely full of bacteria, you can't pick individual clones from that. And you want clones, so all identical bacteria derived from a single successful integration of your plasmid into a bacterium. You don't want a mixture of bacteria with different DNA. This process isn't perfect and you need to screen out cases where your DNA sequence is not correct. And by far the easiest way to do that is to grow on plates with antibiotics, and an amount of bacteria that results in a few individual colonies, with each clone being full of genetically identical bacteria. You generally want antibiotics in your media anyway, working without antibiotics makes it much more difficult. You don't have 100% perfectly sterile conditions, with antibiotics you have a much larger margin here.
- solid_fuel 1y ago
  Just to elaborate a bit more, the problem is that even a colony which, for example, glows under a blue light, will have some members that didn't uptake the genes. So you need a more proactive filtering method. There's also the fact that bacteria tend to lose non-adaptive traits pretty quickly once the selection pressure is gone, so having the antibiotic resistance attached to your gene of interest makes it much more likely to stick around for the duration. Additionally, as others have said, this particular antibiotic (from the post) isn't even used for human treatment so it's not really particularly more "dangerous", we just tend to get nervous around anything "antibiotic resistant" because we jump to thinking about like, MRSA.
- sjducb 1y ago
  Best case you’re transforming 10^6 cells and you expect 20 of them to take up the DNA. Worse case it could be 10^11 cells for a strain of bacteria that doesn’t transform well. You would have to look at a lot of colonies to find the one that transformed.
gwd 1y ago
> A) this antibiotic resistance was already found in nature, B) it's a resistance to a very specific antibiotic, not all antibiotics These are reasonable, but... > C) you're doing this in a protected lab. ...this one is problematic. It's not taking the concerns of the people you're talking to seriously; namely, that no lab can be protected enough, that there's always a chance of leaking, and that the more GoF research is done the higher chance something is going to leak. If nothing else, not registering that you even understand someone's concern is a sure-fire way to get them to ignore everything else you say. And, I'm not sure exactly what your attitude is, but at least the way you put it here does sound overconfident. Sure, protocols should be safe if they're all followed; but the protocols are followed by people, and people make mistakes. Just take a look at all the nuclear accidents that have happened in spite of protocols. Your best bet, I think, would be to lean on A and B: "There are strict protocols in place around labs to keep things from leaking; but even in the very unlikely event that something like this does leak, it won't really have any impact: as I said, the antibiotic resistance is a mutation that evolved by itself in the wild already; it won't make things worse than they already are." EDIT: Or, at least, to say: "Look, I know it sounds really scary, but if you'd seen the protocols, you see how basically impossible they are to screw up. <brief descripiton of why it's unlikely to leak even if implemented by lazy or incompetent people.>" The point is to let people know that you hear and understand their concern, and then to educate them about why their concern is unfounded. EDIT2: This comment seems to be controversial; it's had at least 3 upvotes and 2 downvotes, which surprises me. Any downvoters care to explain?
- actionfromafar 1y ago
  You know some labs with active bioreactors which aren't protected at all? And the waste just dumped into nature... Pigs and cows fed antiobiotics.
  - gwd 1y ago
    I mean, yeah, add that in there. Listen, I'm not trying to argue that the containment protocols aren't safe; I don't know what they are. What I am trying to argue is 1. That these fears are reasonable, and deserve to be treated with respect. 2. Even if you don't agree with #1, in a democracy, just insulting and ignoring people with those fears is going to be counterproductive.

duskwuff 1y ago

Seconding this. I think my high school AP Biology class did a similar exercise in the early 2000s.

mrheosuper 1y ago

Interesting. I have a question, why not pair Gene A with something still detectable but less "dangerous", like a gene that change body color, or emit different color under UV light. Sorry i am totally noob here

fabian2k 1y ago
Because the antibiotic automatically selects the successful clones. The others that didn't incorporate the plasmid don't grow into colonies. Without antibiotics your plate will be entirely full of bacteria, you can't pick individual clones from that. And you want clones, so all identical bacteria derived from a single successful integration of your plasmid into a bacterium. You don't want a mixture of bacteria with different DNA. This process isn't perfect and you need to screen out cases where your DNA sequence is not correct. And by far the easiest way to do that is to grow on plates with antibiotics, and an amount of bacteria that results in a few individual colonies, with each clone being full of genetically identical bacteria. You generally want antibiotics in your media anyway, working without antibiotics makes it much more difficult. You don't have 100% perfectly sterile conditions, with antibiotics you have a much larger margin here.
solid_fuel 1y ago
Just to elaborate a bit more, the problem is that even a colony which, for example, glows under a blue light, will have some members that didn't uptake the genes. So you need a more proactive filtering method. There's also the fact that bacteria tend to lose non-adaptive traits pretty quickly once the selection pressure is gone, so having the antibiotic resistance attached to your gene of interest makes it much more likely to stick around for the duration. Additionally, as others have said, this particular antibiotic (from the post) isn't even used for human treatment so it's not really particularly more "dangerous", we just tend to get nervous around anything "antibiotic resistant" because we jump to thinking about like, MRSA.
sjducb 1y ago
Best case you’re transforming 10^6 cells and you expect 20 of them to take up the DNA. Worse case it could be 10^11 cells for a strain of bacteria that doesn’t transform well. You would have to look at a lot of colonies to find the one that transformed.

gwd 1y ago

> A) this antibiotic resistance was already found in nature, B) it's a resistance to a very specific antibiotic, not all antibiotics These are reasonable, but... > C) you're doing this in a protected lab. ...this one is problematic. It's not taking the concerns of the people you're talking to seriously; namely, that no lab can be protected enough, that there's always a chance of leaking, and that the more GoF research is done the higher chance something is going to leak. If nothing else, not registering that you even understand someone's concern is a sure-fire way to get them to ignore everything else you say. And, I'm not sure exactly what your attitude is, but at least the way you put it here does sound overconfident. Sure, protocols should be safe if they're all followed; but the protocols are followed by people, and people make mistakes. Just take a look at all the nuclear accidents that have happened in spite of protocols. Your best bet, I think, would be to lean on A and B: "There are strict protocols in place around labs to keep things from leaking; but even in the very unlikely event that something like this does leak, it won't really have any impact: as I said, the antibiotic resistance is a mutation that evolved by itself in the wild already; it won't make things worse than they already are." EDIT: Or, at least, to say: "Look, I know it sounds really scary, but if you'd seen the protocols, you see how basically impossible they are to screw up. <brief descripiton of why it's unlikely to leak even if implemented by lazy or incompetent people.>" The point is to let people know that you hear and understand their concern, and then to educate them about why their concern is unfounded. EDIT2: This comment seems to be controversial; it's had at least 3 upvotes and 2 downvotes, which surprises me. Any downvoters care to explain?

actionfromafar 1y ago
You know some labs with active bioreactors which aren't protected at all? And the waste just dumped into nature... Pigs and cows fed antiobiotics.
- gwd 1y ago
  I mean, yeah, add that in there. Listen, I'm not trying to argue that the containment protocols aren't safe; I don't know what they are. What I am trying to argue is 1. That these fears are reasonable, and deserve to be treated with respect. 2. Even if you don't agree with #1, in a democracy, just insulting and ignoring people with those fears is going to be counterproductive.