People often ask me if I miss working at the bench. The answer is a resounding “no, not even a little bit”.
It’s not that I hated it at the time – there are much, much worse ways to spend a day, after all, and I’ve experienced some of them during a variety of soul-crushing summer jobs. The routine and repetition of doing 24 minipreps (a full rotor) for the fourth time in a week did get to me on occasion, and I always hated resuspending pellets and pHing solutions, but good labmates and music would offset the worst of it. And I had decent hands, it’s not like I was bad at it.
Well, not usually.
Everyone has off-days, and in fact a recent conversation in the pub turned to mistakes that everyone is entitled to make ONCE in their lab career without (too much) ridicule from their colleagues. We came up with the following:
- retrophoresis (running a gel backwards)
- using the wrong secondary antibody for your primary
- discarding the supernatant and keeping the pellet when you meant to do the reverse
- labeling the tube caps instead of the tubes and getting them mixed up
- setting a gel without the comb in
The last one made me laugh as I remembered a particularly ridiculous day in Glasgow…
There were (of course) mitigating circumstances. My doctor had told me to stop taking my usual antihistamines due to the risk of cardiac side effects (there’s a long history of serious heart problems in my family, although my heart apparently sounds just fine through a stethoscope). It being Spring, my next ride into work (by the river, then the canal, then through the woods) left me with very watery eyes and a sniffly, itchy nose. I popped one of my new pills (Zyrtec, just say no) and got my restriction digest running. I then got on with the easy, basic, routine task of setting up an agarose gel.
It was the smell from the microwave that alerted me to the failure of my first attempt. And then the opacity of what was supposed to be a clear solution. And then the fact that the tub of powder from which I’d (kinda) carefully measured out my “agarose powder” was actually marked “powdered milk”.
Oh well, easy mistake to make, they’re kept, um, nowhere near each other on the alphabetically ordered chemicals shelf. And in different coloured tubs.
Yawning in confusion, I threw away the milk and grabbed the right tub and a clean beaker. Double checking at every stage, I made up my 0.8% agarose solution, taped up my gel rig, and poured in the cooling gloop.
Coming back upstairs after an increasingly necessary coffee,
Why am I so tired? I actually had an early night and a decent sleep last night, for once. Hmmmmm.
I stared in disbelief at the solid slab of gel, with no wells for my digested plasmids to be loaded into.
This is not good. I am so confused.
Swaying gently, I started again.
Agarose powder, check. TAE, check. Tape, check. Comb, check. (Yaaaaaaawn). OK, looks good.
After reading the same sentence of a new paper approximately 756 times, I wandered vacantly back into the lab and stared in complete bafflement at the results of my third attempt.
I’d set the gel to cool with one of the legs of the rig hanging off the end of the bench, so that the damn thing had set in a wedge shape, with the comb in the unusably thin end.
At this point I did what I should have done after the first attempt, and went home to bed. Yes, at 11.30 am. I have no idea how I managed to cycle home without killing myself; all I know is that I woke up at noon the next day with no memory of the journey, but with my helmet on the bedroom floor and my bike safely locked up in the back yard.
My doctor said to go back to the original antihistamines, my heart would probably be fine.
I certainly don’t miss lab work in the least. My current position requires me to know (and recall at the blink of an eye!) far more research and general science than any lab person has to, which I find both challenging and extremely fun (I work my brain hard!). I had good lab hands, and good enough that they let me work in the level 3 biocontainment facility for my MSc, and I didn’t kill myself once (or poke myself with any sharps like that poor German lady who poked herself in an Ebola lab). I used to always joke that a bad day in my lab would actually kill me – which it would have. I have never been so alert since the days I worked in that lab.
Regardless, I had my fair share of misfortune when I was learning. My first, and messiest situation was when I was radioactively labelling a protein in vitro, doing affinity chromatography with it, and then running a beautiful SDS-PAGE gel. Worked wonderfully, clearly showed that the protein was binding to what we thought it. Went to repeat it, and 1/2 hour after loading the gel, I wondered why the dye front wasn’t going down the SDS-PAGE gel. Well, I had loaded it. And then I reversed the electrodes (which I THOUGHT was impossible with the Invitrogen SureLock system, which it is, but apparently those gel casettes are not made for idiots! I then spent the next 4 hours decontaminanting everything that the gel and buffer touched for 35 S methionine. I have never, ever, ever, ever ran a gel wrong since then.
That’s not to say that I didn’t pour a gel wrong. My first job in university, I was setting up agarose gels for another researcher who was running chromatin preps. We’d gone over this in the lab course before…but apparently not enough because instead of making a 0.8% gel, i tried to dissolve and pour an 8% gel! I couldn’t figure out why the microwave just wasn’t getting it to dissolve. I even brought the PI in, and he just started laughing at me while gathering up all the gel pouring apparatus we could find. We eventually poured ~10 gels, which thankfully could sit in TAE until needed.
Again, I always check my calculations now, which is a handy thing in my current position 🙂
I’ve also made a wedge-shaped gel (I didn’t seal one end of the tray fully and it oozed out oddly so it was as curious as it was frustrating).
I was doing a protein prep using the Ni-NTA matrix. After the wash buffers, you had to elute the protein, instead I just added the elution buffer and I let it wash through as the wash step and later realized, OMG, thats gone the two days work in wash.No way I could get the protein back rather I started a new prep.
then there was post-grad supervisor who decided to “help out” in the lab one day, and ran 4x very expensive (then) precast gradient gels with all of my precious FPLC fractions… and didn’t know you had to peel off the tape on the bottom before running. Grrr.
zerophoresis?
I largely managed to avoid that sort of lab work – I did it for a couple of months and was so good I could get PCR products from my negative controls.
My PhD supervisor liked to dabble in the lab occasionally. He was once setting up an agarose gel and was heard to ask “Do I use agar-agar, or bacto-agar?”.
What great tales. Completely foreign to the bone-botherer, of course. I do have one tale of a one-time mistake, though. During my graduate years I sepnt a lot of time at the Natural History Museum in London, and had to have access to the fossil cabinets and other places, which meant I needed a bunch of keys, which I duttifully signed out when I arrived at the Museum each morning and signed back in when I went home (this is Civil Service property, don’t’cha know). Except for the one day I went home with them. I wasn’t actually arrested, but next day when i came in the curator attached the keys to a new fob – half a broomhandle slathered in ‘biohazard’ tape.
I’ve known a few people to make up gels with water rather than buffer – and then wonder why their samples failed to separate!
I like learning from mistakes (when I don’t repeat them ten times). It’s very reassuring for future trainees who do them all again. Off the top of my head:
pouring a gel on an incline (the famous wedge-shaped gel which allows you to deposit in lovely wells and have your samples come out into the buffer on a slant)
keeping the wrong phase with phenol-chloroform extractions
collecting tissue sections on unsubbed Superfrost rather than Superfrost Plus charged slides
no Taq in the PCR (no forward primer, you name it…)
putting anything wrapped in Parafilm in a 70 degree oven
non-alkaline pH of the buffer when revealing a chromogenic reaction of alkaline phosphatase
absence of blocking levamisole for reaction, idem.
miscalculating what 30 hours’ chicken egg incubation implies as far as when the incubator should be timed to start heating
pipetting the chloroform with tissue culture pipettes and into polystyrene or polycarbonate rather than polypropylene centrifuge tubes
microdissection tools in the wet autoclave rather than the dry oven for sterilization
There’s more where that comes from. Lots.
I missed lab work so much I left a cushy permanent position in a nice office. There are a few things I dislike, but by and large I take pleasure in even the most mundane molecular tasks.
Kyrsten, I had decent hands, but not good enough hands for level 3 work! “Alert” sounds like a wee bit of an understatement…
I’ve had to deal with 32 P contaminated buffer before (EMSA assays where I had to run the free probe off the end to get better resolution of the DNA binding complexes). The Glasgow lab had a dedicated (and little used) hot room, so I claimed an older gel rig, covered it in radiation warning tape, ran the gels in the sink, and only cleaned the rig at the end of a set of experiments.
One of the students who started the same day as me once spilled radioactive buffer, then trod in it, and tracked it around the lab. He was found by the radiation safety guy with a Geiger, following the trail, then looking up and saying “I should have known it would be you”. This student was a great scientist, but had also blinded himself with UV light, poured agar plates without any agar in them, and had various other mishaps. Darren knows who I’m talking about 😉
Sarbjit, I’m so glad I’m not the only one who’s poured a wedge-shaped gel! No-one in my old lab had ever even heard of that one before.
Srisathiyanarayanan, the only time I ever had to do anything like that (purifying an antibody from extremely precious serum), I double and triple checked every single stage, and kept all column flow through from every wash! It’s so easy to mess that stuff up.
Darren, how frustrating! (And I like zerophoresis). My PI had excellent hands (he was so good we’d bring him in to troubleshoot for us, and he could invariably get something working within a few days when it had flummoxed the rest of the lab for weeks). And he sometimes got the urge to do some lab work. One Saturday he happened to come into the lab while I was alone and practically begged for something to do. All I was doing was a digest and gel to extract a band for subcloning, but he said that would be fine, he’d do that for me and I could go and get started on my conference poster instead. He came into the office a couple of hours later saying “erm, do you have any more of that plasmid?” Yeah, he’d run the band off the end. I gave him the rest of the plasmid, and, yet again, he ran the band off the end. He apologised profusely and explained that he was writing a grant and getting distracted. I had to go back to my bacterial stock and reinnoculate, and then come in on Sunday to do the prep, digest and gel again. Luckily I only lost a day, and he did buy me some chocolate.
Bob, I do believe I’ve managed to amplify DNA from water controls too. I hope you let your PI run a bacto-agar gel, that would be fun.
Henry, that sounds like a very effective solution to the problem!
Dorothy, I’ve seen people do that too. Or forget to dilute their 10X buffer stock. Very artistic gels though. My favourite was the postdoc who asked for my help in troubleshooting her EMSAs. Turned out she’d ignored the gel recipe I’d given her and was using her standard Western blot recipe instead – complete with SDS. And then she wondered why none of her proteins were binding what they were supposed to bind. That’s in a different category though, ignorance rather than lack of attention – I had it drilled into me very early on that I should know exactly why I was including every single ingredient.
Heather, great additions to the list! And another wedge, yay! I’ve melted plastic with chloroform before too, it’s quite spectacularly messy.
Jenny, the great thing about science is the diversity of niches that suit different people. I’m glad you’ve found yours! But don’t you miss the comfy office chairs?
I am completely with Cath on this. I don’t miss pipetting at all. Science, though, I do kind of miss a bit – I do some (of the data analysis bent), but wouldn’t mind doing a bit more. But no wet-lab stuff, thankee.
A Physics professor of mine once told the tale of when he was a brand-new graduate student, working on (as I recall) interference patterns between surfaces. He said that he had two glass plates specially machined and smoothed, so that when placed very close to each other, they would form a very uniform, very thin gap.
Guess what he did?
Yes, he put them just a teency bit too close together. Glass is fluid, remember? (I’m not getting into that whole “it’s a liquid, no it isn’t, yes it is” thing here, so don’t bother. Thanks.).
Of course they stuck together, forming one continuous piece of very expensive glass. His supervisor, he related, was not amused.
Me? Oh, I’m sure I’ve done the no-buffer (hm, when I first typed that, it came out as “bugger”) gel before. I’ve also managed to boil 20% SDS over onto a hotplate (hint: good way of clearing out the lab), and blown the fuse on an electroporator by hooking it up wrong (ok, failing to see that someone else had hooked it up in a different way – my fault anyway).
But – the best story I have is a summer student who was preparing concentrated ethidium bromide stock. He got the dilution wrong by, wait for it, 100x. When fully diluted, he would have made something like 10 litres of EtBr solution (remembering that you use something like 5 *micro*litres per gel.
We hardly gave him a hard time about that, at all1. Next time I see him, I may have to remind him of that incident. 😉
1. Not true
Wow, what did you do with all that EtBr?!
I have no idea. That lab has since moved from Toronto to Edmonton, and might be shut down by now (my PhD supervisor being now past retirement age, not that that stops anybody, usually).
Given the things I discovered when helping them pack up to move, I suspect they’ve still got it. My favourite was a tube labeled “Monkey Serum, 1972”. The lab moved in 1997.
I tried a very alternative career path for a while following my PhD. After a few months completely detached from any kind of science, I found myself sitting in the very salubrious public library in Vail browsing through Nature… that told me something.
What about the 2 undergrad students in my old lab who spent 2 hours in front of a laminar flow hood doing bacterial culture work… with the UV light switched on the whole time (to avoid contaminating their work obviously). Once their corneal/retinal inflammation went away, they had fantastic suntans for a few weeks (even for Aussies).
Almost as funny as the time my friend came into work after having a nuclear med scan… ran up to the radiation safety officer with a screaming Geiger counter pointing at himself and shouting “help, I spilled it everywhere”. She eventually (and I mean eventually) saw the funny side of it.
@ Cath… you wouldn’t be talking about my good friend Dr Timpson would you?!
Cath, I’m loving this 🙂
On one of the Antarctic research cruises I did during my PhD – completely sleep deprived, miserably cold, and basically on auto-pilot – I labeled two sets of sediment samples I had painstakingly sliced* and formalin-pickled completely the same. Same station number, sample number, same depth in sediment. Same colour labeling tape.
I did not notice this until I received the shipment of boxes back in Southampton two months later and started putting everything on shelves. Yes, couldn’t use any of them (you wouldn’t know what’s what) and had to throw it all away.
I’m not telling you the other story, you’d start crying…
*they come up in a sort of ‘tube’ and you literally slice them into thin layers
Richard, lab freezers are scary things. My favourite was the rack of genomic DNA samples labelled by species – we had a bunch of different primates plus mouse, rat, rabbit, dog, cow etc. But the cat DNA was labelled with the name of the actual cat it came from – the PI’s pet, whose spleen was helpfully preserved by the vet, and who was in the acknowledgements of every resulting paper!
Darren, great story with the Geiger! Our radiation safety guy would have had a fit… how long is “eventually”?
And yes, I was talking about Dr Timpson – I wasn’t going to out him, but hey, you started it!
(Classic “science is a small world” story – I worked with Dr T in Glasgow, Darren worked with him in Australia, and now Darren and I work together in Canada).
Steffi, that’s a very sad story. I bet field work has all kinds of opportunity for expensive and frustrating lapses in concentration. I hope you had other samples from that trip that you could analyse.
Good grief, of course I had other samples – and it was kind of hilarious, once I got over the frustration (‘but now I have less!’)…
Ah well, you see, us pure lab rats have very little concept of field work1, so “couldn’t use any of them” and “had to throw it all away” maybe sounded worse than it was 😉
1 When people talk about Antarctic research and sediment samples, does anyone else think of The Thing and its derivative episode of the X-Files? No? Just me?
I know someone (not me) who actually licked the inside of a -80C freezer because he didn’t believe “the hype” about how your tongue sticks.
Scientists! Tsk
I’ve done zerophoresis & retrophoresis a couple of times. As well as every imaginable variant of un-PCR (no primer, two sets of the same primer, no DNA, wrong DNA, wrong enzyme, wrong/too much dNTPs etc.).
Excellent post 🙂
In fact, I think the only thing I didn’t break/screw up/explode at some point was my electrophysiology rig. Knowing you were using $50,000 of gear was a great mind-leveler. Now, my idiot labmate…how many times and in how many different ways can you flood a $30,000 microscope with salt solution? And not clean up after yourself!??!?!!!
Don’t forget “wrong extension time”.
Cath: no, it was just the two sets of subsamples that were labeled the same – not all the samples I had. But don’t ask about the stats for that particular sample.
And of course watching The Thing is a must on the stations. But The Virus is the real killer when you’re at Palmer Station…
Oooooooh (eyes light up) The Virus sounds like my cup of tea. I can’t believe I’ve never heard of it!
I’ve gotten freezer burn on my hand from -80 deg C sample hunting. I can’t even imagine what it would be like for a tongue!
It’s interesting, I had great biochemistry lab hands. But chemistry? wow. My teacher kept doubles of all glassware, and after a while he just stopped charging me for them when I dropped them while cleaning. My chemistry lab partner learned to pull the glass front of the fume hood down when we had set up the distillation apparatus and before we turned on the water, after “my” set up managed to soak her more than once. 4th yr chemistry, we were doing an extraction with NaOH and you had to shake, release pressure, shake, etc for about 20 min. I was doing this, but the pressure built far faster than i appreciated, and spilled NaOH all over the fume hood (not much on me – just a few drops on the lab coat). But my laboratory text didn’t fare well – it literally dissolved – I had to go buy another. And then there was the time that we had to measure out our product at the end of a set of reactions…and it blew all over the fume hood.
Now in molecular biology and biochem, things fared much better, which is probably why I turned down the Chem department for their offer to give me a full scholarship for the last few yrs of undergrad (though let’s face it – chemistry paid better than microbio so I don’t know what I was thinking) I was really good at the theory, horrible with the followthrough.
I was the type of kid that when pouring a glass of milk from a 2 L tetra pak carton would SPILL IT EVERYWHERE. So when my mom found out that during my MSc I was growing upwards of 12 LITRES of a biothreat bacterium a week in culture and working with all of it without a drop even spilled in the hood, she nearly had a heartattack. And then she just plain didn’t believe me.
But in microbiol, I could get things to work that no one else could – mainly because of my crazy attention to detail. with the exception of the two incidents above, I don’t think I made any major mistakes at all. This came in particularly handy when it took me over a year to purify enough polysaccharide from our biothreat agent to use in my test vaccine (yes, I was working 6 day weeks and 10 hours a day- apparently I was cheaper than buying a big fermentor!!)
All of my experiences have helped me to troubleshoot what other people do, mainly because I’ve done them. And part of my current job is to take our products in the lab, do stupid stuff, and see what the result is so we can document what happens – sadly I don’t get to do that often. My attention to detail, partly gained from learning from my mistakes, allows me to pinpoint a cause for why a product failed faster than nearly anyone else in my department. Thankfully, I usually end up having a great relationship with the researchers that phone to ask for my help because I think on some level, we realize all scientists can have “an off-day/week/month/set of experiments” and that sometimes, it’s the little details that will kill your experiment.
Kyrsten> I am in awe. I would’ve either injected or spilled on top of me the biothreat microbe… I am so happy I am not in the BSL3. BSL2 works very well on my stress level anyway so I don’t need to think about instant death at least 😉
Cath> Thanks! I have laughed all the way down to here. The sterilization thing was a fellow phd student of mine that put a whole lot of flasks with plastic tops in the dry sterilization rather than the wet autoclave… it started to smell and fume before everyone went home for the evening.. 😉
Personally I think the first year undergrad chem class sums me up. We were warming oil in a beaker and waiting for it to reach the right temperatur. “No worries, the smart [ehh] student said, I can always just dip my finger in it and see if it is hot.” Yeah… I kind of did that awhile with water before you can see bubbles… oil is, heh, kind of different. [no, I never had the time to finish the movement since my lab mates expressed WHAT?!]
…and that stressful time when I tried to clone a fragment into a vector and it just did not work. Checked the DNA concentration in the tube and found out there was none… (I didn’t extract the DNA but got it from an old prep from “someone older than me in the lab” in the freezer… yeah, not so much anymore.)
As a PhD student I was once trying to reduce a flavin mononucleotide solution with hydrogen gas but then remembered I’d forgotten to add any catalyst. As I sprinkled some platinum on activated charcoal into the flask there was a bright orange flash and a bang. Fortunately the flask did not shatter and I still have my eyesight…
Oh, and congrats on your 100th post Cath!
100?! Yay! I had no idea, thanks Stephen!
Kyrsten, so you’re saying that researchers like you because you know what it’s like to do dumb things occasionally?! I love it!
I too am much more clumsy and accident prone outside of the lab than in it. Something to do with severity of consequences.
Asa, I’m glad your labmates saved you from a horrible burn!
Chemistry classes are a whole other category of mishap potential. We had one of the old-school teachers who liked to impress us by making loud explosions, but he deserves his own post one of these days.
Yup, and I freely admit I made my own mistakes when I’m explaining to customers why it’s a bad idea not to repeat them. Sometimes it actually makes them stop and listen.
There was a post higher up on weird stuff found in lab freezers. When I was fresh out of undergrad, I took on a job purifying a toxin from Aeromonas. When I wasn’t running columns that were almost as tall as me, the PI asked me to catalog everything we had in the -80 deg C. It took a few weeks of going through, and while i found the normal bacterial strains, one vial was really odd. It said “Vibrio cholerae from T. Smith, 1982”. Well, I pulled it out and ran over to the PI (Dr. Smith). Turns out, it was the strain of Vibrio cholerae they isolated from him when he got nasty food poisoning from oysters! The “official line” was probably that he just wanted to keep a stock of v. cholerae in the lab because it was a similar toxin to what we were purifying…but let’s be honest – how cool/weird would that be to keep that?
Åsa, nah, it wouldn’t be instant death. The organism I worked with, Burkholderia pseudomallei (and the related one, B. mallei that we also worked with), has a reported latency of about 62 yrs so I’ve got a few more years yet! The bacterium itself is not bad if the infection is actually recognized in time. But Burkholderia mallei is rather more evil: I knew the guy they wrote this article about – and he’s actually even listed as an author on his own paper!
Kyrsten,
Watch it when you say this bacterial strains location lab so public…Let not you get in to troubles…
Oh I don’t disagree with you Srisathiyanarayanan, but the PI I mention is not Dr. Smith – that’s an anonymous name.
And for the Burkholderia lab, there are quite a few across the world who work on this – this could be any one of them. I didn’t work in the labs where those papers were published, that’s for sure!
also, the V. cholerae is long dead. We disposed of it properly according to regulation and according to all health and safety guidelines. And any Burkholderia strain are kept under intense security and there’s no one who could get access to them. Besides, you have to remember that B. pseudomallei is an environmental bacterium…
Okay Kyrsten.. Cool..
62 years?! That’s crazy! Probably not the first choice organism for an aspiring bioterrorist then.
Kyrsten> I guess that means that my BSL2 organisms are kind of more deadly then… at least it is quicker if you get an infection with G+ streptococci/staph … or influenza… Isn’t Burkholderia one of those old “pseudomonas” species that were found in the nevironment and always called P since they produced a similar toxin? (or have I mixed something up here)
The freezer stock story with Vibrio is so fun. Crazy things I tell you. there were some similar stories in my old lab 🙂
Åsa> Yes, the B pseudomallei was actually once named Pseudomonas – you are very right! And I’ll tell you, after growing Pseudomonas, this Burkholderia pseudomallei smells worse (which I didn’t think was possible!) When I was growing up multiple litres, I’d enter the level 3 lab and you could just smell it. Awful, smelled like death. I think it’s some sort of metabolite they produce during their growth. Even though i had a HEPA filter respirator (when you are growing that large a quantity of culture it’s an absolute requirement), the filter did NOT filter out the smell.
Truth be told, I LOVED BSL3 culture – totally awesome set up and I had it often to myself (nice, quiet lab). The only downside, and the one that really got to me in the end, is when you have to run experiments in the main lab and in the BSL3 lab at the same time. If you have a gel running, you have to factor in “shower and dress time” into any lab activity in the BSL3. Also, on days I’d do time courses, I’d be having multiple showers a day (the showers are NOT optional for BSL3 – being a requirement of exiting the lab and all – also most BSL3 outer doors are set not to open until you’ve been in the shower for a minimum of x minutes…). I tell you, you know nothing about cracked skin in winter until you have to take more than two showers….
And this was in a properly cold Canadian city, right?!