Chemistry picture of the week: The baby bird

Baby bird

This week, my supervisor and I set my confirmation date for the 19th of February. After the meeting, the reality of what I needed to get done by that date really hit me, and I spent three days of the week floundering. My intention was to try to organise my results and figure out how to use them to tell a story, but in reality, I was just panicking and getting nothing productive done. Yesterday, I finally took my coworkers’ advice, put aside my own results and started working on my literature review instead. I thought that having some words on the page and flexing my technical writing muscles would only help when it came to actually writing about my work. As a result, though, I’ve had a pretty boring week, and don’t have any interesting chemistry stories to tell. Instead, I’m going to tell you about the baby bird.

The baby bird came into our lives on Wednesday in a cardboard box. One of my coworkers, a sweet soul who once rescued a stray cat and coos over just about any animal she meets on the street, walked into the office holding the box. She told us she found this little bird just outside the chemistry building. At this point, we realised that she meant she literally had the bird in the box, and crowded around it to have a peek. There it was, this little ball of feathers, huddled in a dim corner of the box. It chirped unhappily at us for shoving our faces at it. This coworker of mine asked for advice for what to do with the bird — she was convinced that its mother had abandoned it. We didn’t really have any good advice to give, apart from the obvious fact that she couldn’t keep it in the office. She reluctantly took the box outside. She tipped it over as a makeshift shelter and left the bird a little bowl of water.

We thought that would be that. The next morning, though, the baby bird was still there. My coworker took a second box outside, and told me she’d brought the bird some food. I never asked her what she’s attempting to feed the bird, but I spied a bowl in the second box that looked to be full of bird seed. Yesterday evening, as I left the building to head home, the bird was bravely exploring its new surroundings — that is, as long as I kept a reasonable distance. At this point, I began to suspect that the bird might be there to stay.

This morning proved me no different. A third box has been taken to join the other two, which are now wet from the heavy shower this morning. My caring coworker continues to look after the bird, while another is irrationally annoyed at her. I’m a softie, so while I don’t really want to meddle with the wild animal, I really hope that everything turns out alright for the little bird.

For posts about chemistry, stay tuned. In the meanwhile, you can contact me via e-mail at chemistryintersection@gmail.com or find me on Twitter, where I tweet about chemistry stuff 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

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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.