I like to watch eddies that form underneath waterfalls in a cascade, the ones you see in creeks of glacial run-off rushing down the sides of mountains. The milky-green water, and everything trapped in it, seems desperate to get from point A to point B. But sometimes, the turbulence creates a moment of dithering, of pause, of milling around. If a fallen leaf, or bit of moss or bark or twig, gets swept up into the creek, it may end up in a pool, churning around with fitful energy, or sometimes even stalling in a momentarily calm center. But if you watch for a few moments longer, you will usually see the flotsam expelled from its eddy and propelled once again along its way. The forces that govern the formation and dispersal of these whirlpools are beyond me, but I can sense the mathematics flickering just underneath – present even if they are still not completely predictable or understood.
Biomedical research labs, and the departments that house them, are a lot like these pools. There’s a charged sense of purpose and activity swirling around, but for a few years, the researchers within are becalmed within a bubble of intense mental focus and scrutiny. Likewise, people are always coming and going – in any given month you’re likely to both meet a new neighbor and head off for someone else’s leaving drinks. A few colleagues carry on to bigger and better things, most carry on to do more of the same, and others sink without a trace.
I’ve been thinking a lot about lab continuity as my contract nears its completion. I’m one of several people on this corridor who’s recently had their termination meeting ahead of the end of a fellowship, and it’s time for us to start preparing for how we will pass on all the skills, knowledge, data and reagents that we have accumulated over the years. Some of us are more organized than others, needless to say.
Me, I fall somewhere between average and obsessive-compulsive. My notebooks are novelistic in detail, but my freezer space has recently become a bit dishevelled.
I've seen worse
It’s going to be a big job, but I’m determined to do it right. Because it’s no exaggeration to say that most labs harbor a lost treasure-trove of the forgotten. In my travels through the minus-eighty freezers of this world, I’ve seen rack after rack of Eppendorf tubes labelled only with the numbers one through 24; final bleeds from long-dead rabbits who gave their lives to produce an antibody that was never even properly tested; endless seas of constructs that took months to make, their tube markings smudged beyond all recognition. I’ve been bequeathed lab books full of data enough for half a paper, never to be finished by someone else for lack of documentary evidence. I’ve seen kits and arcane equipment gathering dust on shelves because the last person who knew how they worked left the lab years ago.
This untidy archive – the dirty, wasteful secret of most labs – is simply the by-product of human nature. The closer a researcher gets to the end, the less important it all seems in the grand scheme of things – especially if he won’t benefit from the work in his next stint. And the time it takes to hand everything over is often under-appreciated; you might have good intentions, but in the last mad dash to clear your bench, use up your holidays and move on, succession tasks are often deprioritized out of existence. Our lab has recently implemented a checklist for succession, covering reagents, notebooks and skills, with the recommended start time of one month prior to departure. It’s a great idea, but I’m not sure it will work for everyone. Even highly organized lists that thoughtful people leave behind often don’t make as much sense as you’d like when you actually try to use them to locate a key image or bit of DNA. Ring up that person a few months later, and even she will find herself vague about what she meant at the time.
We should all do our best to document our passages, but the reality is that most things will get swept away without a trace. The marks we leave on anything in life are fleeting. In a business where the wheel is reinvented on a daily basis, the things that are most important will probably find a way of floating to the surface eventually, with or without our assistance.
This is a problem in industry as well. There are procedural solutions like having proper lab book audits, insisting on decent monthly reports, etc etc, and there are technological solutions like LIMS and electronic lab notebook setups. I wonder how many academic labs use a LIMS or ELN? The problem with those is, you need someone with the time and inclination to be in charge of setting up and maintaining them and making sure everyone uses them, someone who won’t be gone in a couple of years themselves and isn’t under such intense pressure to get on with securing funding and/or generating and publishing results. If only there were, I dunno, say, a career structure that made space for this kind of mid-level, permanent job for highly skilled research staff…
Shhhh. I was trying to go a whole blog post without mentioning career structures. 😉
I used to have a fridge in my lab while I was doing my PhD. It had nothing of scientific value in it as far as I am aware, but it suffered from the problem you mentioned above, in that once upon a time some ex-group members had put some home brew it in, (and subsequently everyone was a bit scared to remove them) and didn’t really know what it was anymore. They could still be there, for all I know.
The problem you cite, is present in different guises in most jobs, I expect. My wife works in IT, and the problems that are created by programmers not documenting work, or producing mangled code (often in production systems), who then leave, can be quite serious. They are symptoms of the necessity to get the job done quickly by managers who have to live for the here and now, and where governance structures are often poor, or poorly enforced. I must admit I am not the best at enforcing proper hand overs myself, and have probably suffered for it.
I was going to write exactly what Tom said.
So, what Tom said, +1.
Great article Jenny! An almost poetic take on orphaned eppendorfs and vague protocols.
Thanks!
Ah, what a wonderful description. Takes me back to *shudder* *ick* *ack* [memory redacted].
I’ve probably told this story before, but my all-time favourite “freezer thing” was a tube labeled “monkey serum 1972”. When my PhD supervisor moved her lab from Toronto to Edmonton, I made darn sure it went. That was in 1996. Like David’s aging homebrew, I like to think that it’s still in a freezer somewhere, fifteen years later.
And I’d like to add to your list of lab artifacts those vials of cells found in the bottom of the liquid nitrogen tank, years after they were first frozen, typically with the Sharpie faded and/or the labels long fallen off. I’m sure a good archeologist could make a wonderful* project out of examining the accumulated detritus of a lab’s long lost years.
[*for “wonderful”, read “uninteresting and tedious”]
When I was a grad student I shared an office with another grad student and a (very) senior postdoc who got a job elsewhere, and the time came for him to shift the crawling chaos that was his desk. It was so bad that his wife came in and bossed him around until he did it – but that was just the start. In palaeontology, perhaps uniquely in all the life sciences, researchers borrow specimens from museums – and years, decades even – elapse before they are returned. After my colleague left I remember making a research trip of my own to study material at another institution – returning some of my ex-colleagues loans.
Surely you guys must be tempted to build a new organism with all the assorted pieces of bone left on someone’s abandoned desk. It would be a great lab party trick.
It’s been done
http://www.amazon.co.uk/Make-Your-Dinosaur-Chicken-Bones/dp/0060952261
And don’t call me ‘Shirley’.
I’ve got some eppendorfs still kicking around in my Drawer of Everything (it’s a man thing) with various plasmids in them. All dried up and gone to hell of course, but plasmid DNA is virtually indestructible, innit?
my Drawer of Everything (it’s a man thing)
I have several Drawers of Everything. This could either mean that I am more manly than you, or less organised.
If you’ve got more than one, it’s not a drawer of bloody everything, is it? Flaming paleontologists.
David,
The issue of documenting code is serious – it’s one thing I’ve written about regard computational biology / bioinformatics. (Inheriting undocumented code is a pain – been there, done that.)
More generally, to me, what Jennifer wrote about, in part, falls under—or near to—reproducibility in that you’re trying to leave things in a state that others could pick up the threads of the thing.
One of the things some (I would say most…!) of my clients don’t appreciate is the amount of ‘behind the scenes’ time involved. One of them is going back over projects as they are being completed and documenting it all for future reference, generalising code that might be re-usable, and so on. It’s a big job in it’s own right.
Great post! I love the idea of the succession checklist – if my old lab had had something similar in place, I could have saved several weeks of wasted time in the first year of my PhD.
My current department uses LIMS, and I hear nothing but bad things about it. I’ve never even looked at it myself, having been warned not to bother if I don’t absolutely have to, because it would kill many, many brain cells.
The problem is how accurately can you document anything? In the same way that it is hard in a methods section of a paper to include all the little tricks and tips you use to perform your experiments, it is hard to hand over a whole project so it can be seamlessly transferred like a relay baton to the next researcher on the production line. This I think is exacerbated these days by the sheer volume of computer data that we generate. I mean in the “old days” you can stick your blots in your lab book and it’s all in one place, but who is going to print out all their microscopy data etc and then stick it in their lab book?
In the same way it becomes difficult to label all our eppendorf tubes. There is limited room for writing, so you put a code on, then on a spreadsheet (buried on a hard drive or cd somewhere)you may have more details of what the plasmid constyruct is for example, and then you have to refer to the lab book to see exactly how it was made, and maybe that will have reference to another spreadsheet of primers and you end up on some ridiculous “paperchase” which is so difficult and inevtably somewhere dead ends before you get the information you want. Sometimes it’s just easier to start again!
@rpg – I’m beginning to think that I have a Briefcase of Everything. Feels like it, anyway.
@Cath – in my experience, people who complain about using LIMS are people who are of the lazy and disorganized type, or those that are so set in doing things “their way” that they can’t see the advantages. That said, our LIMS is something I avoid like the plague.
I just had to look up what the hell LIMS was. After reading teh Wikipedia entry on it I can’t say I’m much the wiser!
A briefcase of everything is better than a brief case of everything.
Autumnal, melancholy feel to this post – I like it!
Its amazing what you can find if you root through a fridge or freezer – ancient reagents and samples. Having a PI with a pathological fear of discarding anything doesn’t help either.
The issue of strictly audited lab books makes most scientists I know shudder. How many experimental notes never made it from the notepad to the lab book (or better still from the piece of paper towel to the notebook to the lab book).
Ah yes it’s the least of our concerns as transient entities. After all, postdocs are a lot like salmon – so freezer space takes a backseat when you’re trying to spawn. 😉
Ian, I know what you mean about the spreadsheets referencing spreadsheets referencing spreadsheets. I’m coming to think that the best way forward is to allow the person to leave with all their notebooks and files, so if any questions arise, the person who actually did stuff has all the items to hand and can probably work out what happened, even if their memory grows hazy. So the desire of lab heads to retain all the primary data can sometimes backfire.
Girlpostdoc – I hear you. Nice analogy. With some people I’ve known, there’s been a feeling of resentment: Why should I knock myself out making it easier for a place that didn’t want to keep me and had no interest in furthering my own career?
I just came out of a meeting at which a senior project manager used the following analogy about LIMS:
“It’s like one of those clothing donation bins for charities that you see on the side of the road sometimes. It’s really easy to stuff tons of stuff into it, but incredibly difficult to reach in and pull out the one thing you’re interested in”