Without easy access to our laboratories during lockdowns this year, I and other PhD students have shifted our focus towards data analysis and literature reading. But I struggled with that: I started my PhD programme in September last year and so didn’t have a lot of old data and work to catch up on.
To remain productive and get over lockdown boredom, I started reading the online manuals for various pieces of lab equipment I was planning to use, including the JPK Nanowizard 4 Bio-AFM, an atomic force microscope (AFM) that my group has customized to measure electrical forces in liquid in 3D space. I planned to use this set-up to study the electrical properties of some biosensors.
There was a lot of reading material out there: I’ve read four manuals on various aspects of the AFM set-up. I’ve also read books and articles on other equipment, and watched a few online demonstration videos.
I doubt I would have read these manuals in normal circumstances, but without hands-on, in-person training, it was the only way I was going to get to know the equipment. Many questions I had in my initial training were answered in the manual, and I picked up tips for getting the best performance out of the equipment.
For example, to measure the sensitive electrical properties of a biosensor quantitatively, as I need to do, the tools must be extremely carefully calibrated; without careful planning, it’s really easy to get incorrect results. Fortunately, this is covered extensively in the manuals of the many pieces of electrical equipment I planned to use, from the oscilloscope to lock-in amplifiers. Having read these, I will be able to optimize the measurements and avoid errors without spending too much time troubleshooting, in ‘why doesn’t my experiment work’ frustration.
Reading manuals has also helped me to improve the experimental set-ups that I plan to use. For example, the AFM has a mechanism for holding samples gently that I hadn’t noticed before. This counters external vibrations coming from the building or floor, improving the stability of the measurements.
I put this holding mechanism to the test when I returned to the lab in September. Because I knew what I was looking for, I found another source of noise that could have damaged my results: a cooling fan hooked to the optical microscope on which the AFM sits. I’m sure I wouldn’t have noticed this had it not been for my attempts to put the manual’s instructions into practice.
After reading around 500 pages of manuals during the lockdown, I needed a way to summarize them to use later: I created my own index, which I colour-coded with marker pens. Red was for crucial details, blue for good-to-know features and black for technical details explained in simple terms.
The list in red was not short, which points to the wealth of information that doesn’t reach an average user. Often, I found that detailed, step-by-step instructions in manuals could easily have been replaced with flow diagrams that could have saved readers time. Similarly, I found myself wishing for a better structure in many manuals, or for some kind of smartphone app or interactive version of a manual, rather than an old-fashioned PDF.
Knowing an instrument well can make the difference between an average and an excellent measurement. I’ve learnt that you can make up for a lack of experience by reading the manual. As a result, I’m more confident around my equipment and less anxious about breaking it. This doesn’t make up for being locked out of the lab for four months, but reading the manual has given me more of a head start than I’d have had otherwise.
So that’s one positive to take from lockdown: manuals are worth a read.