Cambio Ltd's Blog

So my time as Cambio blogger is up! How the time flies. I’d love to report having my lab work finished and thesis writing well underway, but the truth is that neither is true. While fairly lab fit, I seem to be running a marathon, and am beginning to ‘hit the wall’.
The parallels are actually fairly accurate – physical fatigue that isn’t relieved by periods of rest, and mental fatigue that can make you think “I can’t do this!” The problem is, I wouldn’t launch myself into a marathon with no training – but that is what’s happened with my PhD. While my university provides excellent skills training, unfortunately there is no course about how to push through the final stages of a PhD, no one to explain the equivalent of carb loading for lab work.
This all sounds very negative, but the truth is, I never read anything like this when I was starting my course. No one warned me about how tiring it can be to finish a PhD, or how to cope with it, and I could have done with knowing. There is a reason why a PhD is a respected qualification. They don’t just give them away. So as I depart I’d like to say a few things that have helped me – though I imagine hindsight will be the best teacher of all.
Talk to your lab mates
One of the most helpful things throughout my PhD – from the beginning when I didn’t know what I was doing, to the present when I’m getting exhausted – is to talk to people in my cohort. My lab buddies are a constant source of support for my frustrations, and there is no therapy quite like ‘being in it together’.
Try to keep healthy
If you’re doing your PhD straight out of uni you may be able to simply power through without your body complaining too much, but I suspect that towards the end it may begin to grumble. Ramen noodles and coffee is not going to help your plight (despite what PhD Comics may suggest). Drink water. Get enough sleep. Eat lots of veg. Walk into uni rather than driving. Look after yourself and save yourself some grief.
Take a break
Whilst some supervisors are over the moon if you’re working every hour God sends, your body won’t be. Treat it like a job. As a PhD student you will have a holiday allowance like an actual real person, so make sure you take it. Seven day weeks are a no-no.
Try to stay organised
Personally, this has been my single best way of reducing stress. You might not need to go as far as making a GANTT chart in Excel (ahem), but writing down your plans and a rough timescale does wonders for getting things off your mind. If it’s on paper, you don’t need to remember it. And if you feel you’re getting nowhere, seeing what you’ve ticked off can be brilliant motivation.
Keep the end in sight
While organisation helps stress levels, keeping an eye on my goal is what keeps me motivated, and is helping me power through the wall. Whether it’s the prospect of a well-paid job, having Dr. on your credit card or getting one qualification up on a sibling, visualising what you want at the end is excellent incentive when you get low. For me it’s a week watching my new Frasier boxset in my pyjamas with a family-size packet of Wotsits (see previous post). And then the credit card thing.
So, there are my pearls of wisdom. If there’s a cure-all for PhD stress I haven’t found it yet – please do suggest your own ideas. I am now off to try and complete my lab work by September, write a thesis and eventually regain a normal life. I seem to recall that at the end of a marathon they thrust sugary food into your hands, so I’m holding out hope on that one.

It is a truth universally acknowledged that a final year PhD student in receipt of their penultimate stipend will lament the time they wasted in their first year.
I realised last week that I am now halfway through my final year. There is no denying the fact that the end is rushing up at me. I need results, I need a thesis and I need some career plans. All three are definitely in progress, but currently in want of delivery. I am most definitely lamenting the time wasted in my first year reading endless papers and attempting the most laughable (to my present self) experiments. But hindsight is a wonderful thing.
Oddly, I’m finding that motivation is proving to be my nemesis. I know what I need to do, and I mostly know how to do it. But somehow the work is just not forthcoming. I want to work, and I definitely want to finish my PhD, but it’s like my brain is trying to trick me into believing that if I don’t go into the lab, somehow I’ll gain some more time. Procrastinate, procrastinate! Obviously I know this is rubbish, but it seems a widespread problem amongst third-years. So at least I’m not alone. I’ve found that, like the saying “The art of writing is the art of applying the seat of the pants to the seat of the chair” (Mary Heaton Vorse) the art of lab work is the art of getting one’s butt into the lab. It all seems to work from there.
The thesis is another mountain – in paper terms, quite literally. Sadly, my hopeful plans of 700 words a week have not worked out quite so ordered, but I’m certainly getting there. I’ve discovered several books which are proving a great help including How to Write a Thesis by Rowena Murray and Scientific Writing by Jean-Luc Lebrun. It sounds a bit sad, but I’m actually looking forward to a point where I can hide away in my office and focus on writing. You might want to ask me if I still feel that way come September though.
Being so near to the end of my PhD also results in two questions that I have come to dread from friends and family:
1. “How’s the PhD going?”
2. “So, what do you want to do when you’ve finished?”
I know they’re asked in good humour and with good intent, but the first generally has no good answer that I’ve found – the closest being “fine, thanks”, “I’m getting there” or, on a good day “really well, I’ve got some results!” The second generally sends me into fits of “well, I know what I want to do, but I don’t know if the job actually exists”, followed shortly by a lot of babble about science communication, sustainable farming, website design and running workshops.
To be honest, in the first instance what I’d really like is to spend a week in a darkened room watching Jeremy Kyle, wearing my PhD bonnet and eating cheesy Wotsits, though I’m aware this does not constitute a career plan. It is however a great motivator for finishing, and a good reason to get my backside into the lab.

Learned societies are one of the mysteries associated with the academic world. In the first months of my PhD I distinctly remember my supervisors brainstorming the societies I should join during a meeting. Being unfamiliar with the concept I sat meekly by, nodding in agreement and writing things down, but I had never come across learned societies as anything more than the organisations that produced scientific journals. Why would I want to pay money to join one?
Well, there are many reasons, but the most obvious is conferences. Most societies have one of these each year, and as a member you generally get reduced registration rates. This alone is a pretty good reason to join. As a student they are a really good way of building your confidence, getting used to how they work, and meeting people who work in your field (see previous post), and normally carry the benefit of a further reduced rate for under- and post- graduate students. If you’re lucky, the society may also subsidise your transport and/or accommodation.

On this theme, a very cynical reason to join a society is grants. These are often available to students not only for conference attendance, but to support travel to another lab for research experience or to attend meetings. Do be aware though that their availability varies between organisations. Societies sometimes award prizes to promising early career scientists as well, and can often point you to other sources of funding for various activities.
Another standard benefit is the member’s magazine. I find these a really good way of finding out what’s going on in my field – both in research and events held at various venues. I also find they’re a really good way of finding out who you need to talk to about certain aspects of your research! If you’re lucky they occasionally do an issue that seems to focus entirely on your research area, or contain detailed information on how to carry out a certain technique. There is also the added bonus that you occasionally find yourself or your group mentioned, which is always good for motivation!

The last (and in my opinion the best) reason for joining has to be the opportunities available for developing your skills, which by and large are communicated by e-mail or through social media. Science fairs, courses, competitions… there is a huge range of opportunities to be had if you want to develop your CV in this way. Since joining my array of societies I have had the good fortune to attend several science communication training days and a week-long GRADschool course, contribute to monthly magazines and online blogs, record podcasts and attend some really exciting events – all subsidised by the societies. Granted these bear testimony to my passion for science communication, but there are plenty of other ways you can develop your own special abilities.

Even if your supervisor doesn’t advise you to join some societies I really recommend you do – you’ll learn a ton, and almost certainly get your money’s worth!

Whilst speaking to a final year student recently, I learned that she is soon to attend her first scientific conference. How she has managed to sneak under her supervisor’s radar this long I’m not sure, perhaps she’s even better than me at avoiding e-mails inviting abstracts for conferences.

A conversation ensued that made me realise that a) I’ve been to too many conferences and b) that this means I have acquired some useful knowledge. So I thought I would share some of it here…

1. Submitting an abstract

If this is your first conference, then the chances are you’ll either have winged it in with no responsibilities, or your supervisor has persuaded you to submit a poster. Whilst ‘submitting an abstract’ sounds intimidating, this is really a polite way of determining if your research will fit into the conference’s scope. So read the information they give you and make sure you tailor what you write to the conference’s scope, especially if it’s a slightly different audience than you normally engage with. There’s no point churning out acronyms and jargon terms to an audience unfamiliar with them!

TOP TIP? Make sure you make your research sounds interesting. If you can use the words ‘cancer’, ‘obesity’, ‘sustainability’ or ‘climate change’ so much the better.

2. The poster session

Having spent hours slaving over your poster, it will probably be hung on a numbered board. At some point in the proceedings you will be required to spend a period of time standing awkwardly by your poster attempting to persuade passers-by to read it. If you are lucky you are part of a large research consortium which means you have an audience for your poster; you may succeed in partaking in some interesting chats about your research. Otherwise you can clutch your cup of tea whilst glaring daggers at posters whose subject is more photogenic than yours or chuckling smugly at the posters whose designer clearly didn’t read the poster specifications and are thus too big/ too small/ the wrong orientation and hanging awkwardly off the sides of the board.

TOP TIP? Don’t sweat it, it’ll be fine. Next year you’ll have to do a talk…

3. Socialising

Last year there was a general consensus in a lab meeting that we would all attend a particular conference, one of the larger ones in our field. I dutifully submitted an abstract and applied for a grant. I booked my train ticket and arranged for the cat to be fed while I was away. About a month beforehand I discovered that no one else had actually got round to registering, so I would be Billy no-mates for the three day duration. Sob.

As it turned out this was a complete blessing. When I got my conference pack in the post I highlighted sessions with less enthusiasm than normal, but when I arrived I found it much easier to do what I wanted without feeling swayed to stay with the collective. Having no one to chat with also forced me to mingle much more widely, and I ended up making a few very good contacts which developed into some fantastic highlights on my CV. It also meant that any fear I may have had about socialising was well and truly conquered. Being able to eat obscene volumes of prawn tempura without being judged was also a plus.

TOP TIP? Make sure you get the most out of your conference, even if it means abandoning your colleagues from time to time. Go forth and mingle!

4. Eating

This is perhaps one of my least favourite aspects of conferences. While I am a great fan of food, I am not a fan of attempting to balance a plate of mini quiches, salad and sausage rolls whilst attempting to make polite conversation with people who may potentially affect my future employment prospects. Spraying someone with crumbs or getting lettuce stuck in my teeth are very real possibilities that fill me with dread. Personally I prefer to eat whilst pretending to peruse posters before attempting potentially important conversations.

TOP TIP? If such a conversation is unavoidable avoid salad (they never cut it to mouth-sized pieces, resulting in unflattering mouth-cramming situations), and garlic (for obvious reasons) at all costs.

5. Drinking

I have yet to work this one out. On one hand, alcohol is often supplied free for the obvious purpose of persuading scientists to socialise. However, it is a fine balance between getting your money’s worth and acting like an inebriated idiot in front of potential future employers. Whilst there is every chance that they may chuckle at the foibles of PhD life, there is also the possibility of unexpectedly meeting them at an interview. Answers on a postcard please!

TOP TIP? If you’re not attending with your lab buddies, remember to make some friends during the conference. This makes liberating the leftover wine at the end much less socially awkward

Happy New Year!

So it’s the beginning of a new year and once more the department is filled with slightly dazed postgrads, harried looking lecturers and technical staff who look as if they haven’t missed a beat. The kitchen sink is once more filled with coffee grounds, and the lab fridge, cleaned before the Christmas break, is beginning to fill up with unlabelled tubes and iffy-smelling cultures. My supervisor arrives looking uncharacteristically relaxed and tells us to have a laid-back week. Facebook tells me I have graduated from the university, and I have a little cry.

I take some data over to my main supervisor who surprises me by saying that she thinks there’s a paper in it, and that she thinks I can submit my thesis in September. My response to each was a somewhat incredulous “really?” with the latter drawing the additional comment “what, this September?!” My writing up plan has suddenly undergone something of a seismic shift. Being finished in less than nine months is both thrilling and utterly terrifying. Eeek!

Sadly this means I have rapidly developed final-year syndrome, which is characterised by long days in the lab, implausible multitasking and a slightly crazed expression. The sudden realisation that after 27 months wondering wandering in the wilderness, the end is now actually in sight. By my supervisor’s calculations I can have my practical work finished by the end of April and then start writing. Needless to say I did not have a laid-back week!

I can see why my department is so keen to have PhD’s concluded within 3 years. In my previous jobs projects lasted for a set time, and then reached a natural conclusion: I submitted the report, I sent the materials to the printers, I hosted the meeting. In contrast, any scientific research has the tendency to resemble an unmeasured length of twine, and it takes experience to judge where to draw a line and publish before moving on.

As an inexperienced scientist I do not yet possess this skill and so am reliant on my supervisor’s experience to judge it for me. Having a deadline helps. It dawns on me just how important having guidance is in completing. In its absence I can see why some friends have taken 5-6 years to submit: there is always one more experiment that can be done. But does it really contribute to your research, or is it just preventing you from finishing anything?

On my official forms it says I have a minimum of 3 years and maximum of 4 years to complete my studies. I would be interested to know what the average time taken to complete a PhD is, because I know people who have had to wait for their 3 year ‘minimum’ in order to submit, and others who still have not submitted after 5 years. I am also a little dispirited by the number of academics who have said to me that you need to be extremely lucky to complete your studies within the 3 years.

For me luck has not been hugely forthcoming, owing to my PCR frustrations. However, ever the optimist, I am hopeful that I will find sufficient funding to sequence the ~1000 strains I have, and thus be well on my way to making my original scientific discovery. I am very aware that data is only part of the story though: I’ve been on enough science communication courses by now to understand that research is only useful if you can tell other people about it. A PhD is nothing without a written thesis.

A couple of weeks ago I was lucky enough to go on a GRADSchool course run by Vitae*. Towards the end of the week we did some goal setting, and gave ourselves targets towards getting where we want with our careers. Some people were going to sign up for training courses, some were going to investigate non-academic career options. Me, I was struck by our group leader’s definition of a good PhD thesis, which was simply a finished PhD thesis. With this in mind, and the end of my third year looming, I decided that the most constructive thing I can do, no matter my career choice, is to get the darned thing written. Seventy thousand words ain’t going to happen by magic!

So I’ve set myself a target to have 30,000 words written by my birthday in September, which coincides with the time my funding runs out – an extremely good motivator! This works out at about 700 words a week, and being a very visual learner I have of course set up a spreadsheet to keep me on track. I’ve also moved my working week around so that I have a day just for writing, which suits me much better than fitting it in around lab experiments. So far, so good: I have 7% of a thesis.

My only problem is that I am not a natural in the scientific lingo. Other forms of writing feel quite natural, but I am still getting my head around how scientific language works. It is a fine art, and in my experience there is a thin line between very good and very bad writing. The skill is to be technical and succinct without being grandiloquent or using too much jargon. The most helpful tip I’ve had is to write a sentence, then read the first 10 words: if you’ve not said anything useful, rewrite it. Obviously the only way to improve at anything is practice, so all the more reason to get writing now – it’s easier to play around with badly written sentences than no sentences. I’ve heard repeatedly that “writing up takes longer than you think!” – so get writing!

* Having spoken to a number of people there (being a gregarious soul) I think I may have been the only person there of my own volition rather than ‘because my supervisor wanted me to go’, but I don’t think I met anyone who felt their time had been wasted. If you are a PhD student and your supervisor suggests you go, do.

In my original project description there is a very innocuous sentence that reads “rhizobia diversity will be assessed by PCR fingerprinting with REP/ERIC/BOX PCR”.

The problem is, it won’t.

Unfortunately, neither will RP01, RP04 or RP05 RAPD primers, or NodA or GyrB primers, as 2 years of tweaks and frustration have shown me. It would seem I’m at a dead end. So with a year to go, 1000 strains and a £2,000 budget I am faced with the dilemma of how to address my project title of “Rhizobia Diversity in Farm Soils”. Hum.
One of the main problems of this is the more I delve into the topic, the more I wonder what ‘diversity’ means. A quick look in my Chambers dictionary yields the definition:

n diverˈsity state of being diverse; difference; dissimilarity; variety.

But how much difference? How much dissimilarity? How much variety?

I’m beginning to see why I will be a doctor of philosophy…

My original hope was to use banding patterns to identify my strains. My NodA assay very reliably gives me two very different banding patterns for the two bacteria I work with: Rhizobium leguminosarum bv. trifolii and Sinorhizobium meliloti. But it doesn’t give me any finer resolution, and I can already identify with some reliability to the species level because of the plant I’ve isolated them from in the first place. And I must say looking at a plant is a much quicker way of discerning that level of diversity!

So discernment to a species level is pretty easy when you’re coming at it from the direction I am. If it comes off an alfalfa plant, chances are it’s S. meliloti. No need to spend a week showing that molecularly. But my project is aimed at discerning more subtle differences that might have been responsible for crop failures in a previous project: perhaps changes in a gene that affects nodulation ability under low pH, or desiccation, or Ca deficiency. Or something that improves N-fixation ability. Or, or, or… something!
So how do I find that difference?

There are currently 92 species of ‘true’ rhizobia in 12 genera, though it sometimes seems that these classifications change on a bi-weekly basis. I think I’m right in saying that they’re based on 16S rRNA profiles: differences in sections of housekeeping genes that are similar, but whose differences merit their classification as a separate species.

This week I had my first lesson in metagenomics and phylogeny, a combination of brain-crunching pain and excitement at delving into the private lives of my bacteria. Using the 16S rRNA sequence data for 4 wild-type strains of S. meliloti, including its sister strain S. medicae, I crunched them in BioEdit and found… very little difference.

16S is clearly not the gene I will be using for this method.

There are other options though, and with the age of next-generation sequencing upon us it is much easier to analyse diversity at a very fine level using this method: it is clearly the way forward. The problem is the cost. I have almost 1000 strains, far more than I can afford to sequence. My alternative is RFLP, which is cheaper but a nightmare to analyse for that many samples, and won’t give me such fine detail. So I am left with a dilemma that must be familiar to a lot of university-based researchers: how do I squeeze the best value out of my funding? How can I get some original, publishable, rigorous results? At this point I’m considering paying for the sequencing myself!