Category Archives: General

The Annual Progress Report

It’s that time of year again, when all the postgraduates get to reflect on how little or how much they’ve achieved over the past 12 months, all thanks to the university administration. I understand the reasons the university gives for the report, we need to be sure you’re not stalled in your research, we need to know you’re being supported by your supervisor, you need to pause and see what training you need to complete in the coming year, will you actually be finishing this degree? The rationale doesn’t make the report any less depressing or time consuming to complete.
For me, it seems like I have achieved little between this year’s report and last year’s. I got one or two interesting results that need further work. I got some very interesting results to go into a paper, but the reviewer wants the work repeated a lot more before acceptance for publication. I don’t have a chapter’s worth of data, but I have a number of leads. I have zero papers, and zero presentations (oral or poster) at conferences, (two minor inhouse poster presentations probably don’t count).
I learned how to use some key instruments in my lab and my collaborator’s. I taught a lot of people how to use various pieces of equipment, and just generally taught a lot of people (demonstrating for undergrad practicals and supervising final year projects). Teaching and learning aren’t counted in the metrics as outputs for my research however.
The honest feedback I received was that, while I don’t seem to have a lot done on paper, accumulating new techniques is the most important thing I can be doing in my 1st/2nd year of the PhD. The teaching is important, but I need to learn to be more selfish in the future, and limit how much helping I do for others. The internet tells me that my regular forays into the world of science communication are very useful for my CV, but the progress report doesn’t care for that, and from the looks of it, the thesis won’t care either.
I have dealt with a number of small flare-up’s of my arthritis during the past year, but it’s hard to tell if they are what are slowing my progress, or (more likely) my distraction by more interesting science going on elsewhere. Certainly when I have a lot of experiments to do, my feet get especially sore, and I get pretty tired, and I need to take a day off to sit down and try to relax. It’s hard to relax though, as I’m anxious at my apparent lack of progress compared with my colleagues and at the approaching deadlines. The annual report doesn’t help with this.
The annual report should help me plan the coming year better, but so far, I’ve found that it’s difficult to plan very far ahead. Experimental results can change what you expected to achieve, and somethings take a hell of a lot longer to optimise than you anticipated. When I see others produce Gantt charts of their project and plans for the future, I’m torn between scepticism and inadequecy, “will they really achieve that in four years?” and “should I have more done by now”.
Anyway, for now it’s time to fill in the form and get my supervisors, independant advisors, head of school, and probably half the administrative staff to sign it.

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Overwhelmed or underwhelmed

It can be hard to be constantly, permanently and eternally fascinated by your project work. I go through phases of loving it and not really being overly pushed about it. Sometimes there are far more interesting things to be doing/reading/considering. While I’ve always had an interest in sci comms and policy, reading about it and commenting is taking precedence over my work of late.

The sheer volume of work I need to complete over the next few years is pretty overwhelming when I think about it, especially when I consider how much (or how little) I have done to date. I came back from recent conferences invigorated and excited about science and what I can achieve, but that wears off. I enjoy reading about my field, I like designing experiments, and teaching people around me, but actually executing my own experiments with my hands is harder than it should be. Not due to the arthritis, but a lack of will.

At the moment, I spend a lot of time ordering supplies for the lab and doing various housekeeping chores like preparing for health & safety inspections and clearing out the remains of PhD’s who have long left the lab (seriously, how can people not archive the relevant work and discard what doesn’t need to be kept). This work keeps me occupied and useful, without necessarily progressing my PhD work. In a larger lab, these duties might be spread across more people, but in our tiny lab it’s primarily my responsibility.

So for now, things are tipping away, but I should probably see if Santa Claus will bring me focus and motivation next month…

Learning about writing

I’m collaborating with a colleague in another department, and the plan has always been to write a paper on the work we’re doing. When it started, I suppose I didn’t really think a lot about it, I just assumed I was provided a bit of labour and reagents and that most of the thinking/writing would be done by the postdoc.

Now I’m realising that the share of the work will be more equal as I have more knowledge in the area than he does, and that well, I need to learn how to do this stuff. Not only is the physical work shared, but we’ll share the writing, I’ll write on my side of the field, he’ll write on his, and we’ll share the writing on the combined work that is the project itself.

So basically, I need to be writing right now (and probably not this blog post). Happily, he’s a great help, and has been assigning me the writing in chunks, so that the final paper should slot together in a sensible fashion. He’s given me some of the guidelines for the journal he reckons we should aim for (aim high, if at first you get rejected, you can improve and have another go, in fact, that’s science).

He’s talking about assigning authorship appropriately, and plans to raise this with his supervisor to make sure I’m given all appropriate credit. During his PhD, his own postdoc helped him greatly with writing his first papers, and made sure he was put as first author when his contribution was at least equal to that of the postdoc leading the project. In fact, he wants to raise the possibility of pushing me to first rather than second author on the paper, or at least joint first, but he’ll have to see what his paymaster says about it.

All in all, these carrots are certainly encouraging me to do a lot more thinking about the project, and it’s applications (all nice bits for the paper). I need to do a lot more reading, but I enjoy that part. Pulling the words out of my head to put on the page, now that’s a whole other challenge…

Post Script: I think I need to find new words for write/writing/written, but I think “crafting a paper” would be a bit much, this is one of the things I shall ponder for the next few days…

One experiment a week…

At the moment, I seem to be averaging one full experiment a week. The sort of thing you set up the night before, spend ALL the next day working on it, and head home an hour late with a file full of results.

Naturally, as a fresh-in-the-door first year PhD student, surrounded by people much further on in their research, this doesn’t appear like a lot to me. Some of my colleagues think this is a grand amount of work, others seem to imply I should be doing more. My supervisors seem to be thrilled with progress to date (I really do mean thrilled, whether I’m doing well or they’re not used to feedback, I haven’t quite figured out).

While the experiment only takes a day to carryout, planning the work and then figuring out the collected data takes a whole chunk of time too (about a day or so of analysis including writing the mini-report). The supporters of my one experiment a week method applaud my planning, and how I control for as many factors as is reasonable.

A large part of why I spend so much time planning my experiments, is that physically preparing the work can be very tiring. A poorly designed experiment, doesn’t just waste my time and reagents, but adds to how much tiredness I have to deal with in the long run. This is clearly not cool.

At this rate I should have about 150 experiments complete by the time I come to write up in three years time. Presumably all these won’t go into the final thesis, but none of them should be work that had to be repeated for being ill-thought out…

Starting labwork proper

So for the last few weeks I’ve not been doing proper work, I really only arrived in the lab in June so I spent a lot of time settling in. I still don’t know who we order paper towel off or where the acrylamide lives. I still don’t own a set of pipettes (I’m sure you’ve been following that ongoing saga…) and there aren’t spare ones in the lab (which is very strange, seems to be a mix of them getting broken or nicked).

Today, I set up my first proper experiment of the project, and, as always, was far less prepared that I’d like to be. It seems the buffers I made a few weeks ago are growing (hate that) and so in the middle of it all, I had to make up a few buffers (thank god for PBS tablets). Even though I find setting up and doing experiments can be pretty stressful, it still feels good to get a start on things. It’s just a preliminary investigation and I still don’t have a way to book the flow cytometer, but I still reckon it’ll work out just fine! (well, who knows how the data will be, but I’ll survive the adventure anyway)

Searching for help – the University Disability Office

So I had dropped into the disability office on campus at the very beginning of my PhD, but due to getting moved from lab to lab for the first few months, I didn’t have an opportunity to drop back in until today.

The office is far quieter after the exam boards have met, as their undergraduate wards have completed their exams (at least until autumn!). I went in trying to see what information I could get on e-pipettes (still looking), and other “adaptive technologies” for the lab.

The woman responsible for postgrads was very helpful, but admitted that her background isn’t in science so she couldn’t advise me directly about lab equipment. However she’s going to contact other disability officers in other Universities around the UK and Ireland to see how they cope with arthritic biologists. Hopefully (surely!) I’m not the only postgrad biologist in this boat, so I look forward to seeing how other people get around in the lab.

The other useful thing I learned from visiting the office is that they can apply on my behalf for grants for adaptive aids, so the e-pipettes and easy open microfuge tubes would count as such. This is especially good, given the limited funding for consumables and laboratory supplies that we were assigned for research (why are biotech reagents and equipment so expensive!).

VWR e-pipette: Review

So today I got to try an electronic pipette, specifically this model. The local rep very kindly arranged a loan of a 0.5-10uL and a 10-200uL set of them (serious kudos to the rep though, he’s the only person to find me samples to actually trial).

The instruction manual I was loaned was pretty basic, covered everything you need to know, these are the buttons and this is how to set the functions. I couldn’t figure out how to set the reverse-mode for standard pipetting, but I imagine there’s more if I had gone poking through the settings.

The pipettes don’t need a fancy charging stand, you can just plug them in and bung em in a drawer. However, you can’t use them while they’re charging, which is a potential drawback.

Now for the moment of truth: are they any use at pipetting and how are they for arthritic hands…

As they were a loan of someone’s working set, I just trialed them with water and a balance (can’t be contaminating someone else’s stuff!). They pipette grand, they’re easy to programme and the various mixing/multidispense/normal modes work grand.

And for my hands? Not much use unfortunately, after about five minutes of playing with them, my wrist started to hurt and I found it difficult to get a comfortable grip on the pipette itself. The aspirate/dispense button is around the back of the main barrel of the pipette and the tip-ejector button is directly on the front. In order to operate the aspirate/dispense button with my finger, I had to hold my hand away from the pipette, which was not comfortable, essentially I could press the button OR hold the pipette comfortably. I had no problems with the tip ejector, which is good as that can be a problem for regular pipette usage (for those times when you REALLY JAM ON THE TIP).

All in all, it’s not comfortable for my hands but it seems like an ok pipette otherwise. At €380 (.ie list price) for a single pipette, it’s not overly expensive for an electronic one but you’d still want to be happy with what you’re buying. Sadly, I’m going to have to continue looking….

Window Shopping for e-pipettes

One of the most important parts of any good experiment is to have high quality equipment, stands to reason. It’s important to have the best quality equipment you can get (afford).  The big instruments that do the heavy duty analysis go out to tender and have maintenance contracts on them, so you can generally rest easy that they’ll be doing the right thing.  The smaller bits and pieces can have a bigger impact on results than you might expect.

One of the key pieces of preparatory equipment in the biology laboratory is the micro-pipette.  It’s a straightforward enough concept, you jam a disposable tip onto one end and the pipette can suck some of the volume out of the tip and thus suck up liquid.  The pipettes are callibrated so you can suck up and dispense very specific and tiny amounts of liquid.

Manual pipettes such as this on the right:

gilson pipette

A gilson manual pipette. Great pipette but terrible on arthritic thumbs.

rely on a spring to move the piston in the pipette to a “sucked up” position. So to empty the tip of air or liquid, you have to press against this spring. Then to suck up the air, you slowly release the pressure to prevent liquid getting sucked up too fast (this is a particular problem with viscous fluids like glycerol).

Working against this spring can be hell on your hands if you have arthritis (or RSI for that matter, which you’ll get from doing too much pipetting).  Electronic pipettes remove this spring problem and use something like a stepper motor instead to move the piston.

 

I’m currently on the hunt for a set of Good electronic pipettes, that cover the same range of volume dispensing as the manual ones but with a similar or better accuracy/precision.  Despite there being no electronic single channel (multichannel can take many tips and are dead handy) in any of the nearby laboratories, there are a plethora available online, so now the fun part is deciding which ones balance accuracy and precision with cost and ease of use.

A bit of background

There are many types of arthritis, juvenille, rheumatoid, osteoarthritis, psoriatic…..  Arthritis is characterised by an inflamation affecting the joints.  This can lead to pain and stiffness and can lead to long term damage and disability.

Arthritis can affect people of all ages, but predominantly tends to affect women post-puberty and post-menopausal.  You might notice that these are times of major hormonal shift, and many autoimmune diseases such as lupus and arthritis manifest about these times, in fact, many autoimmune diseases are found at a much higher incidence in women.

Knowing this background, my arthritis is relatively “normal”. I was diagnosed when I was about 26, and yes, I am female.

I am also a scientist.

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