#RealTimeChem week: New chemistry circumstances

This post is written for the #RealTimeChem week blog carnival, themed “New elements in chemistry” in celebration of the naming of elements 113, 115, 117 and 118. 

At the time of writing, I’ve been back to research for two solid months, following an interruption to my studies due to Chronic Fatigue Syndrome (CFS). I have previously written about my experience with this illness – a tale of woe that began over a year ago already. How time flies when you’re desperate not to waste a moment of your precious PhD scholarship!

I digress. In my previous post, I wrote about my experience with CFS and its impact on the quality of my life. It is one thing, however, to live with a chronic condition, and another entirely to return to research while still battling it. I’ve been steering clear of this blog out of the desire to conserve my energy reserves, but the #RealTimeChem week blog carnival theme is just too perfectly suited to my situation to ignore. “Are you adapting to a new life situation that’s affecting your chemistry?” asks the prompt. Yes! Yes I am!

There is a fundamental disconnect between the approach to chronic illness and to research. When doing research, your work and thoughts are rarely focused on the short-term, but instead looking into the future: at the big picture you will paint using your individual pieces of data. More practically, there are always more people who want to use an analytical instrument than there are time for in one day, so early sample preparation and pre-booking your time slot is important. On the other hand, the best-laid plans of mice and people with CFS often go awry. You can’t control when the illness raises its ugly head, so you can’t plan any days you might need to take off. You need to take things day by day, listening to the demands of your body. Moreover, as I talked about in my previous post, I have had a slew of neurological symptoms related to CFS that have tangibly impaired my ability to plan ahead. It’s an unfortunate double-whammy of short-sightedness. Thankfully, my supervisor has lost none of his foresight and from the moment of my return, suggested weekly meetings to discuss my progress. I take notes at these meetings so that plans or ideas we’ve had don’t go forgotten, even when my brain is at its worst. Additionally, I have taken to occasionally taking some time off simply to sit down, think about the experiments I’m running that day or week, and really ask myself why I’m doing them.

I do have days when I’m so confused about what I’m supposed to be doing and what I’m trying to achieve that I feel like bursting into helpless tears. Amusingly, it has become difficult to draw a line between “I’m doing research and I have no idea what I’m doing” and “my brain is foggy from CFS and I have no idea what I’m doing.” As the latter kind of confusion is alleviated by my recovery, the former grows; when CFS fogs up my mind, I don’t have the foresight to worry about the future of my project. In some ways, too, these new circumstances feel very familiar. This research-related helpless confusion is one I have felt, without fail, at the beginning of each research project in the past.

The second major limitation of chronic illness is also related to time, but in a more physical sense. As soon as I returned from sick leave, I successfully applied to change my candidature from full-time to part-time. Even so, I am only gradually becoming capable of meeting these reduced contact hours. In a positive aside, through sheer desensitisation, I’m learning to let go of the guilt that I used to feel on sick days. If I need to take a day off, I need to take a day off. Besides, guilt is an incredibly energy-consuming process, and I have come to accept that there is nothing to be achieved by maintaining it.

From my reduced working hours arises another ugly feeling that feels so much like deja-vu: frustration. Research chemistry is slow and labour-intensive. This is best summarised by words that aren’t mine:


Borrowed with love from   slideshare.net/freerudite

This is, of course, an entirely universal experience in research. I’m simply feeling it more strongly now, perhaps, that I can feel weeks slipping by so quickly without much to show for them at all. The rate of trials has been reduced, so the errors simply feel more prevalent. This frustration is managed best by the company of my favourite coworkers, a glass of wine and sunny weekend days spent far from the lab.

On some days, I already feel like my old self: juggling obligations, pondering on ideas and constructing elaborate plans. I wake up tired, but it doesn’t feel like a life-sapping exhaustion, but more like a tiredness can be cured by some cups of coffee. I still regularly have to remind myself to slow down, because I’m prone to enthusiasm resulting in great bursts of effort that can burn through my energy reserves in a few measly hours. As a whole, I’m learning to manage my situation as it slowly, but surely improves.

At this point, I can cautiously permit myself this: I think I’m going to be alright.

As always, I thank the gorgeous community on Twitter for their support. If you haven’t found me yet, I tweet as @Lady_Beaker. I can also be reached via the comments, or by e-mail at chemistryintersection@gmail.com.


Chemistry picture of the year: Burden

The Ring

This replica One Ring I’ve been carrying around for a better part of this year is symbolic of two things: the first is my undying love for the works of Tolkien, and the second is the different kind of burden I’ve been carrying. The fact that this is genuinely symbolic for me is, in itself, emblematic of my geekiness, but that’s beside the point.

Those of you who follow me on Twitter will know what this post is about, while those of you who have been following my blog since last year will be feeling a sense of déjà vu. I’m frustrated to report that these two periods of absence are related. Let me start at the beginning.

Following my confirmation in late February, I was preparing to present a colloquium (a short talk on a topic unrelated to my own research) to the School of Chemistry at the University of Melbourne. I also picked up a social media management job at the Royal Australian Chemical Institute, the role of president at a newly established cross-institution Young Chemists’ Group, increased my ballet dancing to two classes a week and adopted a cat. This seems like a lot to have had on my plate at once, but after recovering from my intense bout of glandular fever last year, I felt superhuman. My energy levels were through the roof, and I was determined to make up for those months spent juggling illness and PhD studies last year.

Perhaps it’s no surprise that I started slipping. At first, I started spending my weekends mostly asleep. I’d sleep 12-14 hours a night and often have up to a 3-hour nap during the day. I’d complain to my mother, a former nurse, about how I felt sick without having “any real symptoms.” I often felt disoriented during the day, and began struggling with word recollection — I even had trouble remembering names of people I’d encounter several times a week. I stopped dismissing these as side-effects of simple tiredness when, during a ballet class, I had to sway off the dance floor and lie down to avoid fainting. I went to see a doctor. Blood tests came back negative. He said to come back if I started feeling worse.

It became obvious to everyone that I was ill. I couldn’t go to the university on consecutive days: one day I would work, then sleep for two. I started feeling more lethargic, more confused, more dizzy. I stopped attending ballet, relinquished my presidency and had to return the cat to his foster carer. I missed meetings and appointments. I saw two other doctors. More blood tests and a chest X-ray came back negative. By this point, it was late April. My “diagnosis of exclusion,” as the third doctor put it, was chronic fatigue syndrome (CFS). It’s common for it to follow from a viral infection like glandular fever, he said, but uncommon for it to skip a couple of months like mine did. My symptoms fit all the diagnostic criteria.

My extremely supportive supervisor and I decided that the best course of action for me would be to take sick leave from June to August, inclusive. I was prepared to live on my savings, but to my delight, the scholarship department approved paid sick leave for almost the entire duration. I’d like to use this space to thank the University of Melbourne for its support of the sufferer of a still poorly-understood condition.

Recovery has been frustratingly slow, not the least because there is no medication or readily available treatment. I’m not a patient person by nature, but this illness has forced patience upon me. CFS, in my experience, isn’t something you can fight; it fights back. You try to push through it, to expand your limits, and you suffer the payback — if not immediately, then the following day. Really, this illness feels almost like it was crafted to make me do the absolute opposite of what I instinctively want to do. It’s the anti-me.

This is accurate also because my experience of CFS is primarily neurological. I still maintain that I have never felt exhaustion like I did during my bout of glandular fever last year, and yet, I am now less equipped to deal with the lethargy that I do feel. I often feel defeated by my illness. I need someone to tear me out of bed in the morning, or I will sleep until I’m good and ready. I’m often irrationally emotional and disoriented. My writing might feel different to read because of my difficulty to concentrate and access my mental faculties; my word recollection is still impaired, alongside my general memory. I struggle to keep on top of plans for more than a day in advance.

I’ve caught myself wishing that instead of CFS, I had an “actual physical illness.” I would wish that there was a pill I could take, or a treatment I could attend. And then I’d just feel guilty, because I can’t imagine how many people would wish what they had was as relatively benign as CFS. I’d feel guilty, because my father, a stage 4 bowel cancer survivor (in remission for over four years), would pity me and tell me that he understands how chronic illness feels. He also seems to believe that I will be better and stronger for this experience.

I have not yet had and aren’t convinced I will have some sort of illness-related epiphany. I do acknowledge that thanks to CFS, for the first time since basically the beginning of high school, I’ve been able to focus solely on what I and my body need. I’ve been able to remember how much I love spending time outside, instead of simply using that space beyond my front door as a gateway from where I am to where I need to go. I remember that research is attractive to me because I love doing things with my hands, from knitting to gardening. I get to enjoy the numerous wonderful doggies that people in my area take out on walks in the afternoon and I am occasionally privileged enough to get to pet. Currently, I don’t view these things as an equal exchange for my suffering, but my perspective may change with time. I don’t know if I’ll now magically become a better-adjusted person with a more balanced view of work and life. I’m skeptical, but I guess we’ll see.

Without doubt, I’m doing much better than I was at the beginning of my sick leave. I’m starting to feel more like myself, and my endurance of physical and mental exertion is increasing. I’m optimistic that within a couple more months, I’ll be back to normal. My supervisor continues to be supportive and has approved my plan to return to my studies part-time until the end of the year. I am wary of stories that recount people with CFS relapsing as they return to their normal lives after the worst is over, so I’ll have to remain diligent about not over-exerting myself.

It’s been a rocky start to my PhD studies for sure. I’m glad I’m not particularly superstitious, because if I were, I might have already walked away. Even so, I fear there may be a limit to the hardship I’ll endure. Here is to hoping my limits aren’t tested.

Thank you for reading this post. I’d like to offer a special thanks to all of my wonderful Tweeps who have supported me this year. If you or someone you know are suffering from CFS, please feel free to contact me to exchange stories. I found sharing experiences extremely helpful, since finding medical support was such an uphill struggle. As always, I can be contacted in the comments, by e-mail at chemistryintersection@gmail.com, and on Twitter as @Lady_Beaker.

Anthropomorphic chemicals

A quick disclaimer: this post is written entirely from the perspective of a synthetic chemist. I don’t know much about the attitudes of analytical, environmental, computational or other chemists towards their work — but I would be very interested in finding out. Check in with me in the comments!

I have noticed during my years of studying chemistry that there is an almost universal tendency between chemists to anthropomorphise chemistry. One particular example I run into often is in relation to figuring out how and why a reaction works. Synthetic chemists are concerned with reaction mechanisms: exactly what happens in a reaction to transform the starting material into the product. Reaction mechanisms usually involve several steps, and several different molecules, from the starting materials to solvents and intermediates, which are somewhere between the starting material and the product. While figuring out mechanisms with colleagues, I’ve heard chemists referring to molecules as “this guy,” as in “this guy then goes on to do that, while this guy just sits around watching the whole thing happening.” In my line of work, I’ve also heard this expression when colleagues are figuring out relationships between crystal structures. “This guy” then refers to particular crystal structure. The fascinating thing about this expression is that if it were only about simplifying communication for office chatter, we could easily have adopted a slang expression like “this thing” or variant thereof. Instead, we use a very humanising term, which implies identity and agency.

Copper doesn't want to_1There is a second example of anthropomorphising chemicals that I personally am guilty of. I work in coordination chemistry, which involves organic molecules (ligands) that we try to get to bond with metal ions. Sometimes the metal ions and ligands behave in predictable ways, but sometimes they do something entirely baffling or nothing at all. In the latter two cases, I find myself talking about how the metal ion “wants” to do something in particular — that it “likes” the solvent more than the ligand, or just “doesn’t want to” bond to two different things at once. Of course, it is entirely impossible for an atom to want to do anything in the way we as humans want to, so the expression is entirely inaccurate — and we know that. So why do we do it?

I think the beginning to the answer lies in that chemistry is even now primarily an experimental science. In crystallography, for example, it has been shown that it is still very difficult for computers to predict the intricacies of crystal structures. Growing crystals, collecting data and then solving the structure is the only reliable way to go. I’m not trying to dismiss computational chemistry — but I would think that even computational chemists agree that a combination of experimental and computational chemistry produces the most meaningful results for now.

As an experimental science, then, the best (or only) way to learn chemistry is by doing it. That can seem like a baffling statement, as though I’m claiming that mixing things willy-nilly will magically transfer in-depth knowledge of chemistry into your brain. This is sadly not possible. What I mean with learning chemistry through practice is that the more practical chemistry you do, the better you become at it. To be a successful chemist, you do have to know how the theory works so that you can intelligently select your targets, building blocks and conditions. But when it’s about a particular system that you are working on and refining, or even a particular technique, working with it over a period of time begins to give you a sense  of what will and won’t work. Tangible knowledge that you can write down or impart on the next student or researcher coming to work in your field is almost never the first result of experimentation. The first result is just an abstract feeling which makes you chase one path and abandon others.

Oxygen_1Perhaps you can see the connection forming here. The relationship between an experimental chemist and their chemistry can be sort of like a relationship between people: based strongly on intuition and instinct. I am sure many of us have met a person we have either liked or disliked for a reason that isn’t entirely obvious to us from the get-go. That is the same sort of level of feeling I’m talking about in the realm of chemistry. I guess it’s no wonder, then, that many of us resort to anthropomorphising terms when describing our chemistry, when human interaction is the realm we’re used to when dealing on that cognitive level.

There is a pitfall here: with anthropomorphising your work, you risk developing affection for it. The problem with that is the possible development of confirmation bias — you want your chemistry to work out, so you are more likely to interpret ambiguous data as a success rather than a failure. That is a whole can of ethics-related worms, though, and in the interest of brevity, I’ll leave it for another time.

My thoughts on the tendency to anthropomorphise aspects of our work is that it reflects the way chemists may think about chemistry. Although we are scientists who require hard data to support our claims, I feel that is rarely our first point of call in practical chemistry. The instinct comes first, and the data to support or debunk it comes after — which then feeds back into the subconscious knowledge of your work.

If you have feelings about this blog post, you can reach me in the comments, via e-mail at chemistryintersection@gmail.com or on Twitter, where I tweet as @Lady_Beaker.


Chemistry picture of the week: Filtering


In Australia, apart from the final talk of a PhD and obviously thesis submission, the most important event of one’s postgraduate degree is the first year confirmation. The confirmation occurs at the end of your first year, and is essentially a review of your work by your supervisor and a panel of other academics in the school. The academics’ job is to decide whether you’re suitable to be confirmed as a PhD candidate and to continue your research at the university. At the university I completed my undergraduate and honours, this was largely a formality — even the laziest of students always passed their confirmations and were allowed to continue. At the University of Melbourne, I have heard of students failing and having to resubmit. At the start of 2015, I saw two of my co-workers stressing out over their confirmations. Their nervousness was obvious — I even caught them practicing their talks in an isolated instrument room at the back of the lab. And this year, it’s my turn.

I’m a fairly fast writer once I get on a roll, so I’m not too concerned about the 30-odd pages we’re supposed to produce as the written report. I think if I leave that for the month of February, I’ll still have plenty of time — especially as I try to be organised with my data as I’ve talked about before. What I am currently concerned with is amassing as much hard data for my report as I can — so when I make a statement about my chemistry, I can refer to an experiment or measurement I’ve conducted to try to qualify or quantify that statement. As such, the last couple of weeks of December and the first weeks of 2016 have been largely spent avoiding attempts to synthesise new materials, instead repeating old reactions to yield plenty of material to conduct measurements and further experiments on. That means that my last month or so of work has consisted of a lot of filtering.

Most chemical reactions synthetic chemists perform are done in a solvent, which is a liquid such as water or ethanol that dissolves other chemicals. In many cases, the desired product is a solid, which means that you require a method to separate the solid from the remaining liquid. Enter filtering. Filtering may be familiar from filter coffee, which is made by passing boiling water through a filter paper holding coffee grounds. The end result is the extract of coffee without the solid coffee beans. Filtering works in the reverse: you start with a mixture of solid and liquid, and pass the mixture through a filter paper which catches the solid and deposits the liquid. To speed up the process, we use vacuum filtering, which pulls the liquid through much faster and also dries the remaining solid.

Here’s a secret, though: it’s deathly boring, particularly when you’re filtering tiny amounts and are trying to make sure you don’t lose any of your product. When it’s small crystals, you want to drop as much solid at a time onto the filter paper and always drop it on the same, small spot so that the solid can catch more solid. It’s a slow, painstaking process when you have vials and vials and vials to empty using this method. Afterward, I do get to look at my beautiful shiny crystals under the microscope to note the appearance of the bulk product, which does give a bit of satisfaction to the whole process. In the worst case scenario (which happens frustratingly often given how science tends to require a lot of trial and error), I end up wasting this little bit of product on an experiment that gives me no useful results, and I have to remake the material — which means filtering time is again upon me.

Amassing useful results for my confirmation report is difficult work, but it is immensely rewarding to watch the troves of data gathering and forming the beginnings of an interesting “story.” Every little piece gives me more insight into how my system works, and I really do love that. That sense of satisfaction is what makes it worth doing the repetitive, sometimes frustrating tasks it takes to get there.

For comments or queries, you can reach me at chemistryintersection@gmail.com, in the comments or on Twitter as @Lady_Beaker, where I tweet about the everyday happenings of my PhD.

Chemistry PhD resolution for 2016

As the year is starting up, I — like most everyone — reflect back on the past year and consider my hopes and expectations for the future.

For me, last year began with great motivation and enthusiasm toward my new group and project. The year then descended into predictable frustration and self-doubt when results weren’t instant and easy. About four months in, I finally made my breakthrough, but my progress was greatly impeded by the fog of exhaustion and disorientation brought on by my extended illness. Despite this, I managed to push through and have a handful of interesting results to elaborate on. This work is not nearly finished, which is beginning to worry me — my supervisor told me halfway through the year that he would love for me to have this thesis chapter done and dusted by March-April 2016. Additionally, the self-doubt intensified by my illness still lurks at the back of my mind. For the last few months of 2015, I was not sure whether I was simply lazy or still recovering, but I never felt as though I was working the hardest I possibly could.

During the year, I have become at home in my new group — there are several group members I can now confidently call good friends. I’m slowly making myself familiar to the academic staff in the building through demonstrating, seminars, social events and such. I have joined the Royal Australian Chemical Institute (RACI) as a student member, as well as the Australian Science Communicators. I attended a few events organised by the former over the course of the year, although mostly only to catch up with co-workers from my old university.

This is where I stand. When thinking about New Year’s resolutions, I don’t like to make extensive lists. I feel as though the greater the number of goals, the greater the chance of failure — and the greater the number of failures, the easier it is to simply give up. Instead, I like to think of a few important things I would like to keep in the back of my mind as I start the new year. Habits take time to make and change, so I like to give myself some wiggle-room. On this track, I started thinking of a few things I would like to focus on in the coming year. I thought perhaps I should give myself a single goal in the categories of academia that are important to me right now: my research, networking, teaching and communicating. The more I thought about it, however, the clearer it became that all of those goals could be smushed into a single idea, which is the following:

Push your boundaries.

It is so easy to do what is comfortable and familiar. Continuing on a track of your research that is perhaps boring or bordering on stamp-collecting, but will most likely produce results. Using advice or suggestions your supervisor or co-workers have made without exploring on your own. Not attending large social events because meeting several new people in a new environment makes you feel uncomfortable. Shying away from pushing  — or even asking — for a publication with a supervisor who might be more focused on students further along in their studies than you. Neglecting to take opportunities to engage with undergraduate students because you aren’t sure you’re the best person for the job. Neglecting to take on larger challenges in addition to your research because you’re afraid of how much of your free time it’ll consume. Arriving late to work because getting out of bed in the morning is one of the hardest little things to do for an evening person.

These are just a few things where pushing myself to do the slightly uncomfortable thing will greatly benefit me. It has been a mentality I have tried to cultivate even throughout 2015, but this year, I want to push even harder. Some decisions I will regret, I am sure, but as the saying goes — what doesn’t kill you only makes you stronger.

If you’d like to share what your resolutions for 2016 are, you can find me in the comments, by e-mail at chemistryintersection@gmail.com or on Twitter as @Lady_Beaker, where I tweet about the daily life of a PhD student in chemistry.

Chemistry picture of the week: Buggy research


When I talk about bugs in my research, I wish I was talking about software or something. No, the problem we are currently experiencing in my lab is more literal than that.

A couple of weeks ago, I and coworkers in the same section of the lab noticed these black particulates accumulating on our lab bench. We shrugged it off for a week or so, but it soon became a real annoyance. Having to brush little black things off of your precious clean vials, or, worse, having to pick them out from a product you filtered the day before can be, if not detrimental, then irritating at the very least. We observed that the black things were confined to below the large air conditioning vent above our lab benches. We notified the building manager about it. He expressed concern over the situation, saying that it could mean that there is something wrong with the air conditioning. He would have someone look at it.

I turn up to work on the next day, having missed the air conditioning technician who came by earlier that morning. A coworker accosts me: “Hey, have you looked at those black things? Like… really looked at them?” His tone is mischievous and ominous and I’m really not a fan of it. The air conditioning technician had identified the black stuff as thrips — tiny insects that are killed in the air conditioning system but are too small for the filters. As a consequence, our work benches were being rained on by tiny dead insects. I don’t think I really need to qualify that declaration with a record of my reaction. I think that statement — “rain of dead insects” — is graphic enough on its own.

I have to give it to my university: they were very prompt at identifying the issue. The building manager even followed up with the information that Campus Services has agreed to upgrade the filters to stop it.

We are still dealing with the rain of dead bugs, but hopefully not for long — especially since we have recently spotted a few live ones crawling around. And I swear… They’re getting bigger.

You can reach me in the comments, by e-mail on chemistryintersection@gmail.com or on Twitter, where I tweet about daily science happenings as @Lady_Beaker.