Briefing Chat: The Bunsen burner myth that turns out to be just hot air

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1:27Welcome to the Briefing Chat podcast, the Friday show where we talk about a couple of papers that have been highlighted in the Nature Briefing. Nature's daily email roundup of the latest science news. And this week I have with me the wonderful Sharmini Bundel. Sharmini, what have you been reading about this week? So Nick, Nick, you know how genetics is really complicated? I am aware of this, yes. like really complicated we got all these genes in our body and some of them make proteins and some of them influence the making of the proteins and some of them are like what what are you doing stretch of dna why are you there we don't know they're all these doing these different things well google deep mind have just released an atlas a sort of database of predicted effects of 9 billion genetic mutations.

2:19Whoa. So 9 billion different mutations and the possible predicted effects that each of them could maybe have with the caveat that genetics is very complicated. I was going to say, as you mentioned, genetics really complicate. A lot of things interact with other things. Sometimes genes, you know, go in different ways. They get spliced differently. There's all sorts of ways. Genetics is really complicated. so uh how have they i guess done this with nine billion mutations so i was reading this article in nature and this work is building on previous deep mind work which is an alpha genome ai model and that's the thing that's actually doing the predictions right so what this alpha genome atlas is doing is basically they've pre-computed the nine billion answers so that researchers like have it available immediately rather than having to go and ask the ai hey can you calculate this and that which can be a bit complicated can be a bit slower so this ai model has basically taken loads and loads of data from publicly available databases of experiments this is both human and mouse cell experiments and then using what you know the humans have already been doing it makes predictions based on things that haven't been done yet and again there's lots of sort of caveats to this but what it essentially does is for any given dna base pair you know you've got all your letters you've got your gtca take one swap it out for each of the three alternatives that it could be and then the ai model sort of looks at all of the potential impacts of that and then predicts what the actual outcome would be in terms of function but you know i think a lot of people would be aware that AIs can sometimes be wrong so how accurate are these predictions do we have any sense they're not in a way they're not intended to be accurate so the idea here isn't like oh I wonder what this genetic change will do I know I'll just ask the AI the idea is that and this is particularly for sort of think about rare diseases that's the sort of case study that they've given it so far is you know very occasionally you might get a really obscure disease that has arisen from a random mutation in one person and sometimes that could be a single base pair mutation although it's often not but it could be and what they've done in their early access trial is given some rare disease researchers access to this atlas and all the predictions that it has.

5:01And they've used it to hunt down a particular mutation that they think could be responsible for the symptoms that a particular patient was experiencing. Okay, so the AI is like guiding them towards the right answer, I guess. Yeah, so it's kind of like the AI saying like, hey, have you thought of this? Which they hadn't. No, it's, you know, it's some obscure little letter in some obscure little gene. But then they can go off and start experimenting with that which they did and they looked at what it did and said yeah actually i think this is probably a pathogenic mutation that we didn't know about before that can cause problems but it was only in the brain and therefore it wasn't being detected in the blood so they they had struggled to find it so is this tool now like out and people can use it in the labs it is it's free for non-commercial use if you're commercial you're gonna have to wait for their licensing conditions which they haven't determined yet but yeah basically any researcher can go and access this in a browser and query, you know, yeah, just this huge amount of information to guide you towards maybe where you should be looking for your next piece of research.

6:08So one of the things that it does is it gives you like a number, which is called the AVI score, the Alpha Genome Variant Impact Score. And it's basically like a really rough summary of how, almost how important a change is. I like, is this change going to do much? Because some changes are fine. Like nothing's going to happen. You can have that mutation. I'm sure we're all full of mutations and it's all fine. But occasionally some of them will have this really big sort of downstream impact. And this AVI number is supposed to, again, estimate, guess the likelihood of any particular one mutation having a big impact, being important.

6:46And what that kind of means is something that might be worth you, scientist, going and doing more experiments on. So, yeah, it's really it's channeling you. It's like, hey, look over here. The AI reckons this might be a thing. Go do your experiments. See if it's a thing. And you mentioned that one team of researchers have used this to look for like how a rare disease may progress recalling to a mutation. Have other researchers tried it out and what do they think of it? Well, it's only just been released now. So this hasn't been widely available yet. And yeah, these particular researchers got early access to it.

7:20And part of it was that they were sort of testing to see how effective it was in this particular case study. And they actually tested this AVI score, because they had, you know, there's this consortium that works on unexplained rare genetic disorders. And they gave it previous examples that they already knew the answer to. and basically said, what's the AVI number for the mutations that actually did turn out to be the right answer? And it says, so the AVI placed the causal variant, so put that mutation that did in fact cause the problem, in the top 50 possible candidates of mutations for that patient almost 30 % of the time, which is higher than a previously existing ranking method.

8:03Well, it sounds like an interesting case study, but I guess we'll have to wait and see whether this will be another like alpha fold moment, which was another of DeepMind's tools that really transformed biology. Yeah, it's funny you should say that. I've got a direct quote here from this article from a molecular biologist who said, this isn't an alpha fold moment. And they've said the predictive performances of genomic models like alpha genome are still far from brilliant. And these models should not yet be used alone to make clinical decisions. so yeah maybe not quite at alpha fold level yet but extremely useful well a sensible caveat to end that story on then and speaking of caveats there is a workhorse of science which may have actually had an overblown reputation i am talking about the humble bunsen burner and its ability to sterilize workplaces that may not be quite true i will not have you say a word against the wonderful the epic, the iconic Bunsen burner, which I vaguely remember from my A-levels.

9:05I don't think we're using it to sterilise things. I think it was something about different coloured flames. I don't know. But you've worked in a lab and been in the lab much more recently than me. How would they usually be used? Well, Bunsen burners can be used, like you said, to create different coloured flames. But in laboratories, especially in microbiological laboratories what they're often used for is to basically keep an area sterile the idea has been the thought has been that the flame creates convective current so it lifts air up and away from your plates and stops bacteria landing on them so there's basically a zone that is sterile around the flame and because of that you can do all sorts of different experiments with the plate sort of open for example you could streak a plate so that's where you take a little loop and you spread your bacteria across a plate and you could do that next to the Bunsen burner because that area is in theory sterile but according to this article reading in nature based on a study in microbiology spectrum that may not actually be the case and in fact maybe these Bunsen burners are sometimes making things worse oh no oh no this is gonna be I think it's gonna be bad news for a lot of microbiologists.

10:25What was their experiment? Basically, one of the researchers behind this study, Hannah Gavin, was curious as to what the actual evidence was for Bunsen burners having this idea that maybe they can make an area sterile. And... Yeah, surely people have like tested. This seems like a really easy thing to test if you're a microbiologist, right? Because there's bacteria everywhere. You're always trying to keep things sterile, keep the bacteria off your agar. It does. But actually, as it turns out, But this may just have been done on tradition alone. So there is no like evidence, experimental evidence from history.

11:00It's just there's been a long 200 year plus history of people using Bunsen burners in this way. And there's a nice quote from Hannah Gavin in the article as well that says that this information void has allowed for the propagation of all these hypothesis theories, law and mythology around the Bunsen burner. but actually there are not that many experiments so she and her colleagues went out to go and do one and what they did is they grew a strain of a bright orange bacterium called gordonia rubyperctincta and this is a bacterium that doesn't often contaminate plates so it's not something you would find by accident you know if something went wrong in their experiment and they tried to simulate all the things that could potentially uh contaminate a petri dish where you grow bacteria so things like vacuum cleaners stirring up dust or scientists sneezing or you know you know skin cells falling off them that sort of thing so they sprayed this bacteria in a liquid around the lab to sort of simulate contamination and they also like shook dry towels laced with bacteria and did other things to sort of try and contaminate on purpose their workspace and they did this in a place where there was an active Bunsen burner and the plate that they were seeing would be contaminated or not was next to the Bunsen burner and with a plate that was next to an inactive Bunsen burner and then compared them to see what grew there.

12:28So yes this bacteria it was just all around in the air so it really was about whether this whole theory of convective currents keeping the air flowing upwards would stop these particular bits of bacteria landing on the plate yes exactly and it didn't and in many cases actually there was more bacteria on the plates next to the active Bunsen burner than on the one that wasn't there was only one example where the active Bunsen burner performed better and that's when the workspace was so contaminated like orders of magnitude more contaminated than any modern lab would ever be then it did perform slightly better but on any other test that they did when they varied the conditions they changed like how things were contaminated they changed the levels of contamination they changed the amount of flame coming from the Bunsen burner on every other trial it was the same or more than the one next to the inactive Bunsen burner like like significantly more like more the more What is what's shocking me here?

13:26Do they have a proposed mechanism for why more? They do not have a proposed mechanism for why more. You can imagine that it might be that the currents are going in a different way. I'm not sure. So that may be a future experiment that they try out. But I guess the point of this was to sort of understand whether this even works and it doesn't work. So it could be the end of the era for Bunsen burners being used in this way. Now, I must say that they are a bit of an artefact of the past. I was going to say, how many labs are out there being like, you know what, if we really want this to be sterile, let's just stick a Bunsen burner next to it.

14:02It doesn't seem like it was the most thorough method to begin with. No, I mean, there are like cabinets and things that people use now that are designed to very much keep things sterile. So they have like filtered air and they have air currents that literally do keep the air from outside separate from the air inside and they get sterilised by UV. and all the rest of it but there are certain things that you do with bunsen burners that is quite useful so the flame itself can sterilize things so you can use metal tools and sterilize them on the flame and then you can touch the plate so that refers to those streak plates i was talking about often you do it with like metal things these days you can get plastic pre-sterilized tools so you could use that instead but it's a bit more wasteful but yeah the idea that there's like a sterile ring around the Bunsen flame seems not to be true and frankly I feel like I've been lied to all my life upon learning this this does feel this does feel very sad also it feels like if you were to get into it there'd be some sort of complex fluid dynamics problem about the exact where the air flows as you said like the currents going here there and everywhere I just can't believe no one's no one's tested it out or it just goes to show even in science like if your supervisor says oh oh yeah, do this.

15:18That's how everyone does it. Yeah. I mean, I literally have a memory of being in the lab during my undergraduate when I was doing a bit of microbiology and they literally took me to the Bunsen burner and told me, right, so you need to turn this on, you need to put it like this and put the plate nearby because that keeps it sterile. And apparently that is not really true and it's just something that's grown out of tradition rather than empirical evidence. I'm so reluctant to let go of this magical Bunsen burner thing. I want more evidence on this. I want like detailed flow diagrams before we fully condemn the Bunsen burner.

15:53I'm sad on its behalf. I am sad too. And I must say as well that they're not the first people to express doubts about this. I have been doubts from scientists about the efficacy of this for a while. It's just they seem to be the first team that have actually gone out of their way to properly test it and found these results. but like you many biologists and other scientists may struggle to accept this like scientists do follow the evidence but learning that something like this doesn't actually work as expected that may be hard for them to bear like if you are a microbiologist listening to us and you use a Bunsen burner routinely do let us know your thoughts but uh yeah perhaps the Bunsen burner's life in the lab is flaming out oh no oh I can't oh that's that's a tragic ending right we're gonna I have to leave it on that very sad but poetic line.

16:43Thank you, Nick. And yeah, that's the end of the Briefing Chat show for this week. But if you cannot possibly wait until next Wednesday when we'll be back with the main show, why not follow us on the social medias? They're fun places where we occasionally post. We are at Nature Podcast at various places on the internet. We are indeed. And if you can't reach us there, you can always reach us on email. We're podcast at nature.com. And as always, in the show notes, we'll put links to all the stories we discussed and where you can sign up to Nature Briefing to get more like them directly to your inbox.

17:15I'm Nick Petra. Ciao. And I'm Sharmony Bundel. Thanks for listening.

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