To me, a total outsider, developing antibiotic resistant strains of TB sounds at least "gain of function"-adjacent. Are there any experts here who would like to hazard a judgement?
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.
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
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.
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.
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.
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?
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.
As others have pointed out, this is a fairly routine practice that happens even in schools. It’s the nature of the experiment that makes it relatively safe. The fact that it happens in a protected lab is just icing on the cake (they’re dealing with TB bacteria, so it’s inherently non-zero danger just because of that.) You seem to be pointing to the icing and arguing that because one part of the cake might not be perfect, the whole thing is unsafe. But it’s the entire cake that the author is pointing to in their argument. And then rather than engage with the article, you’re arguing that, rather than engage on the substance, we need to engage on the level that some non-experts (who don’t understand the protocols) are scared and hence the correct standard is that we need our practices to reassure them.
But we’ll never be able to reassure terrified, scientifically under-informed people to their satisfaction, particularly when they’ve already decided that GoF is somewhat scary and maybe even partisan. So the result of this attitude is that we can’t do relatively safe but important research on diseases that might save your life or the life of someone you love.
(Also, FWIW I have an advanced degree and 10 years employment at research institutions under my belt, including 4 in medicine. Its not that I don't believe the claims in the article, its just that they are outside my field of expertise and I want to understand them)
1. You don't have to be "scientifically under-informed" to find C concerning
Listen, I don't consider myself an under-informed person. I have a PhD in computer science, I regularly watch science videos on YouTube, I click on interesting things (like this article) that show up on Hacker News. But until this thread, I had never heard that the sort of thing described at the top-level comment even went on, much less was I familiar with the containment protocols. (How could I not, if I they're taught in Biology 101? I'm pretty sure I didn't take Biology 101; only Physics and Chemistry.)
My starting assumption coming into this thread was that the protocols described here probably are perfectly safe; and that even for more dangerous GoF research, informed people have done a cost-benefits analysis, and determined that the lives potentially saved are worth the lives potentially risked.
Points A and B of the person I responded to reassured me.
But point C I personally find concerning. In computer science, only an absolute fool would ever say, "This system has absolutely no security vulnerabilities". On the contrary, you generally have to live with the fact that there almost certainly are security vulnerabilities in any system you run, and hope that they're found by the good guys before they're exploited by the bad guys; as well as structuring your system to be able to minimize the potential lost caused if not.
Now sure, maybe I'd have a different attitude if I'd taken Biology 101. But that doesn't change the fact that C, as stated, actually weakened the article towards someone like me, who is generally prone to trust the scientific establishment. How much more would it weaken the argument to someone with a more skeptical, anti-science stance?
2. In a democracy, the opinion of the "scientifically under-informed" matters
I realize it's frustrating to have to explain this to the "scientifically under-informed", many of whom are being misled by bad actors trying to profit by stoking fear. But that's the reality of the world we live in. It's not enough to know the right answer; you must convince other people of the right answer.
And I won't even say "unfortunately", because this is a fundamental feature of democracy. Like checks and balances or trial by jury, having to convince non-experts prevents the system from going wrong.
I'm not suggesting we should butt out entirely as non-experts. I'm saying we should defer to people who really understand the field. In this case, we have plenty of experts who actually know what they're talking about, some on the pro-GoF side and some on the anti-GoF side. The commonality is that I've never once heard any expert from either side express concern about techniques that induce resistance to non-human-use antibiotics. And I suspect the reason I've never heard anyone complain about this is that there isn't really much risk here at all.
So instead of getting upset about how it's scary, and then demanding researchers stop doing research to make us non-experts feel better, we should turn to a stable of people who understand what's happening to help us make these decisions, and stop demanding researchers make us feel better.
In the 90's I heard a (possibly apocryphal) story about a computer lab at my school . A student had been thrown out ass-over-kettle for 'dangerous hacking'. Their crime? Opening their mail in PINE over Telnet.
Most of the stuff Sarah Stanley was doing here are things you can technically do in your own kitchen, if you're a little careful. Just because you've never done them personally yourself, doesn't mean lots of other folks can't or haven't! (And I can totally see someone doing it to get some of the scout merit badges even [1] )
There's really no way to reassure you that I can think of though. Except maybe get you over to a (home?) lab and have you mess with some genes yourself. You'll see it's utterly mundane.
Obviously; I wouldn't quite recommend starting with TBC. That one is a wee bit more exciting. hence the protected lab. But what this research group was doing with it is/was otherwise not more dangerous beyond that.
[1] There's several stem badges for biology that include genetics, but none that are specifically molecular genetics - yet.
You do this by including antibiotic resistance genes alongside your modification. Now all modified cells are resistant to the antibiotic. Then you apply a small amount antibiotic to kill the unmodified cells. Now you only have the cells with your interesting modification.
This is the mainstay of molecular biology. Every lab biologist has done it. We even do it as college students in lab practicals.
Banning the use of antibiotic resistance genes in biological research is effectively banning all wet lab medical research.
Conveniently ignoring the fact that they're literally feeding the stuff to livestock to improve growth rates / feed efficiency [1]. Talk about dangerous gain-of-function "research". Industrial vat grown protein cannot come soon enough [2].
This specific use of antibiotics resistance is also extremely common. Pretty much every single microbiology experiment starts this way, and every time you want to genetically modify bacteria you do this. This includes every time you want to produce any protein, because you need genetically modified bacteria for that. This is a large part of all labwork in this field.
As the article notes, the antiobiotic used is one that isn't used for humans. So there is not significant additional danger due to that modification. The bacterium itself is much more dangerous than most that are handled in the lab, but that's why they're in a BSL-3 lab.