#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.


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 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.

Advice for new PhD students

Do not contract glandular fever in your first year. It’ll put a real damper on your studies.

I never really got any better after those few illnesses I complained about earlier this year. I was really sick about every second week, and when I wasn’t actively bedridden, I had only just enough energy to push myself through the daily grind. Extra things like seeing my friends or writing on this blog and other hobbies just had to drop.

Even after finishing a demanding Bachelor’s degree and a hectic Honours year, I can say that I have never felt that exhausted in my life. I saw a doctor several times. When things still weren’t getting better after I “recovered” from one of my endless colds, I had some blood tests done. Everything came back negative. I cried at the doctor in frustration. I felt horrible, and I didn’t know why.

With this persistent exhaustion and illness came crippling self-doubt. Maybe there is really nothing wrong with me, maybe I’m just not cut out to do a PhD. All my co-workers are putting in more hours than me, working harder than me, and they’re not as tired as I am. Maybe I made the wrong choice. Maybe I should quit.

I finally took two solid weeks off on advice from that doctor who still didn’t know what was wrong with me but probably thought some rest wouldn’t hurt. Asking for that time off, I cried at my supervisor. Thankfully, he was extremely kind and understanding — the second week was actually his idea, I originally only asked for one.

When I returned from my time off, I saw a different doctor to fill a prescription, and although I felt much better at the time, I filled her in on the situation. She thought to test for glandular fever. I just received the results today, and the diagnosis is that I have had it. Although it has been obvious to me that I’m now better, given my higher energy levels and lack of very recent illness, somehow I feel better for having that diagnosis. I guess I feel validated for all that time I had to take off to be a pathetic lump in bed or on the couch. It wasn’t just in my head.

I definitely feel like things are going to pick up from here. My research is doing very well; I think I am getting useful results almost every day now. That sort of thing is possible when you crack the synthesis of a material — I’m now in the process of testing it for all the different sorts of things it can do. Hopefully my personal life will also lift back up again and I can get back to regular posting. I am certainly going to try.

If you wish to talk, you can find me in the comments, via e-mail at chemistryintersection@gmail.com or on Twitter as @Lady_Beaker.

An apology

Dear readers,

I’m very sorry about my sudden and unexplained absence for the last two weeks. Mid-August saw me suddenly and persistently ill, meaning my activities between the 16th and 23rd of August are handily summed up in this picture:


The location of my person for an entire week

The week after my halting recovery — last week — was spent frantically running around in the lab, guiltily trying to catch up on all the things I should have been doing when I was lying around at home. It has taken me a while to get back up to speed with all of my research-related responsibilities, as well as getting my body to respond to my demands as diligently as usual. I am definitely now better (unless this cold that my partner is carrying around gets the best of me next), and will do my best to resume regular posting.

As a coincidental treat, I have been working on a guest post for #RealTimeChem’s #RealTimeChemInFocus series. It is a wordy monster about the day to day happenings in a week of my life — last week, in fact. It is just about ready to be sent off, and once it is published (unless deemed horribly inappropriate or something), I will edit this post to provide a link to it. I will most definitely also post about it on Twitter. Keep an eye out!

EDITED: Here is the link to the guest blog post. Hope you like it!

Thank you for your patience.

As always, I am available in the comments, at chemistryintersection@gmail.com or on Twitter as @Lady_Beaker.

Demonstrator’s vow

For those not in the know, or for those whose universities operate differently to those in Australia, chemistry postgraduate students here from Honours to PhD get the chance to teach undergraduates in a small capacity. During a chemistry major, alongside lectures and tutorials, undergraduates undergo a certain amount of lab work in small groups (15-20 students) supervised by a postgraduate student. This postgraduate student is called the “demonstrator,” because their role is primarily to demonstrate proper laboratory technique and etiquette. For the postgraduate student, this usually gives a small income stream to supplement our scholarships and also gives us teaching experience, crucial for those seeking to further themselves in academia.

At this point, I have demonstrated for two classes, one in each semester of my Honours year last year. It is the beginning of second semester here at the University of Melbourne now, and I have been assigned my first first year class at this university. As I prepare, I reflect back on my successes and failures last year. To my shame, I have to admit that there are more of the latter than there are of the former. Especially as my Honours year drew to a close, I let my stress and exhaustion bleed into the teaching labs and I’m afraid I wasn’t as good of a teacher as I could have been. To right this, and to honour all the amazing chemistry teachers I have had in school and in university, I wanted to devise a sort of code of honour — a vow — to guide myself and other potential demonstrators in the coming semester.

As a demonstrator, I vow that:

  • I will convey my love and enthusiasm for chemistry in every move I make in the teaching laboratories. I will endeavour to make the students’ experience a positive one so they may be encouraged to return in later years.
  • I will prepare well for the lesson beforehand and know all the material front, back and sideways. Confidence in the material should instil the students’ confidence in me.
  • I will try to provide a broader context for all practicals, especially the boring, repetitive ones. I will emphasise that chemistry is still primarily an experimental science and learning practical skills is learning chemistry.
  • I will be an unyielding enforcer of safety rules in the laboratory.
  • I will dig deep for a fountain of patience, remembering how nervous I was in my first year practicals. I will not be visibly annoyed at repetitive questions or silly mistakes. Although it goes against everything I stand for on this Earth, I will make a mighty effort to resist the constant urge to snark.
  • I will guide my students to the correct answers — without spoon-feeding them — by encouraging them to think like chemists.
  • I will mark reports fairly but stick to my guns if students question my marking. I will try to provide positive feedback and help my students grow. I will not shame them for their mistakes, even in writing.
  • I will be patient with my unpaid free time, which will inevitably be consumed in the duties of demonstrating, like class preparation, report marking and slow students finishing in the lab. Demonstrating takes up so little of the year — there will be other weeks for other things.

If any veteran demonstrators have wisdom to add to this list, I would be more than happy to hear about it. Perhaps even more importantly, if you are a current undergraduate and either love or hate something your demonstrator does, let me — us — know; we’re still learning, too.

You can contact me at chemistryintersection@gmail.com, in the comments or find me on Twitter as @Lady_Beaker, tweeting about my chemistry life.

Choosing chemistry

There are several reasons people choose to do certain things with their lives, I think. Reasons, such as enjoying the company of people who also do this thing. Being naturally talented at that thing, or being gifted at several skills suitable to that particular course in life, are popular reasons to choose one thing over another. Enjoyment, an excellent motivator for choice, often follows naturally from success due to one’s talents, but may follow from any number of human experiences. A more difficult to grasp incentive is the feeling of fulfilment over one’s life choices. For science in particular, some people may be driven by a desire to discover, a profound curiosity in the world around us, or a simple need to understand. A love for problem-solving is certainly a great motivator for the pursuit of science.

For me, choosing chemistry was a mixture of many of the reasons above. Raised by two scientists, my curiosity in the world was encouraged and liberally fed through my childhood. Talented at school, I was spurred on by the praise of teachers and sparkling grades. My chemistry teachers were uniformly excellent throughout my school years — talented at teaching and earnestly enthusiastic about their subject matter. In high school, my delight at solving the puzzle-like problems in chemistry class was what really kept me enjoying the subject. High school was where love for chemistry truly took root in my heart, I think. Those last years were when my teacher first began talking about chemistry in more than abstract terms. I learnt how to draw molecules, paving way to an ability to visualise chemicals. I learnt how to count molecules, mathematically, through a concept known as the “mole.” Through these relatively simple concepts, and many others, chemistry became a tangible thing in the world around me. And I was in love.
A chemistry still life_01

Some chemists like to call chemistry the “central science,” with respect to the three well-established scientific fields of biology, chemistry and physics. Physics deals with energy, and biology deals with life. Chemistry deals with matter, which is everything that is physical, tangible — real, if you will. As a science of matter, chemistry bridges physics and biology, and, because matter is ubiquitous, is arguably important to the study of both. I will leave antimatter to the physicists, though.

I take great delight in looking around me, knowing that everything I see is made of atoms and molecules. Everything around me is chemistry. Everything “natural,” like grass and trees and people, and everything synthetic, like my phone, computer, my eyeglasses — they are all a part of chemistry. As I learn more about chemistry, I learn more about the building blocks of everything around me. To me, that is infinitely exciting, fulfilling and beautiful. Learning and doing chemistry makes me feel somehow more deeply connected to the world around me. It is a feeling which keeps me passionate and excited about chemistry — and more than that, it makes me want to share that feeling.

It is heartbreaking to me how negative the current public image of chemistry is. Consider how even the term “chemical” is perceived. It evokes an instant vision of smoking chimneys, car exhausts and bottles of poisonous cleaning agents. While I wish to dispel this misconception of chemicals, at the very core of it, I want to show you, the reader, something beautiful and exciting. I am writing this to spread the joy of chemistry.

Welcome to Chemistry Intersection.

If you wish to contact me, e-mail me at chemistryintersection@gmail.com. Follow my twitter account @Lady_Beaker for tweets in the daily life of a PhD student in chemistry.