What is it made of: Carrot

The carrot, in all of its ordinariness, must be my favourite vegetable. I love its fresh crispiness when uncooked, and its sweet juiciness when cooked. Despite its unassuming looks and ubiquitous presence in our supermarkets, the composition of a carrot is anything but simple. Nature has this wonderful way of taking bushels of molecules, stirring them up and then spitting out something so perfect and whole as a carrot. As scientists, we struggle a little to take that apart to identify all the small constituents of this complex aggregate — especially since it isn’t as simple as pulling out one molecule at a time to identify it. This difficulty of analysis is true for almost anything that is found “naturally” in the world — that is, over the formation of which we have no direct control. Further, even if thorough analysis was possible, making sweeping conclusions about all carrots based on the analysis of a single carrot would simply not be possible, since nature loves variation. With this in mind, I will still give a fair run-down of the important components of my beloved, ordinary vegetable, the carrot.

A carrot is composed of — like many fruits, vegetables and living organisms in general — primarily water. This ubiquitous, tiny molecule makes up about 85% of the carrot. Slightly less than 10% is made up of carbohydrates — or, between friends, “carbs.” For the uninitiated, carbohydrates are a class of molecules that consist of carbon, hydrogen and oxygen. In its most basic form, the formula of a carbohydrate is one carbon atom per one water molecule. This is where the term carbohydrate comes from: they are the “hydrates (i.e. water) of carbon.” Carbohydrates come in the “simple” variety of glucose, sucroce and fructose, as well as complex carbohydrates, which are natural macromolecules: large molecules consisting of several repeating units.

The next 1-2% of a carrot is composed of “dietary fibre.” This rather vague term refers to some carbohydrates that are not easily digestible, unlike the carbohydrates mentioned above. An example of such a carbohydrate is cellulose, which is the primary structural component of many plants. Cellulose is the main dietary fibre present in carrots.

Approximately 1% of a carrot is composed of proteins, another type of natural macromolecule. Proteins are huge, extremely complex molecules made of an array of repeating units called amino acids. Similarly to carbohydrates, they are also made up of carbon, hydrogen and oxygen — where they differ from carbohydrates is the added presence of nitrogen.

A simplified view of a protein. The molecule is so large the chemical structure cannot easily be drawn. Image source: http://www.topsan.org/

0.5% of a carrot is made up of fat, a third kind of natural macromolecule. Alike proteins and carbohydrates, fats are made mostly from carbon, hydrogen and oxygen. The repeating unit in a fat is called a fatty acid.

An additional 1% is accounted for by ash. This term accounts for everything that could not be lumped into any of the other categories analysed for. Ash is residue left over after analysis — random stuff lumped into the carrot by nature.

Although they do not make up an appreciable percentage of the carrot’s composition, metals such as calcium, sodium, potassium and magnesium are present in a carrot in trace amounts. Even small amounts are significant, because these metals are very important for the normal functioning of our bodies. Iron and calcium deficiencies, for example, are or at least lead to known and common medical conditions. Vitamin C and various other small molecules are present in carrots, too, in sub-percentage quantities.

Beta-carotene is one such small molecule. This is arguably one of the most important small molecules to the carrot, since it is what gives the vegetable its distinctive orange colour. This molecule is a hydrocarbon, which means it is composed of only carbon and hydrogen. Its structure (pictured below) contains several double bonds between carbon atoms. This leads to the conjugation of electron density — that is, freedom for the electrons in the bonds to move around the molecule. In hydrocarbons like beta-carotene, this often leads to intense colours like the orange of a carrot.

Skeletal formula

The structure of beta-carotene. Image source: https://en.wikipedia.org/wiki/Beta-Carotene

What I have accounted for in this post is not even nearly the entire story about what carrots are made of – but it is a fair approximation. Perhaps knowledge of the multitude of complex components that make up a carrot will make the bite into the sweet, juicy vegetable all the more satisfying.

The information in this post was sourced primarily from Chemical composition, functional properties and processing of a carrot – a review by Sharma, K. D. et al., J. Food Sci. Technol. 2012, 49(1) 22-32.

You can contact me in the comments, via e-mail at chemistryintersection@gmail.com. I tweet about the daily life of a chemistry PhD student on Twitter as @Lady_Beaker.

Chemistry picture of the week: Knowledge

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A significant portion of a PhD in synthetic chemistry is spent in the lab, either trying to make things that nobody has ever made before, or trying to make them in a way nobody has ever used before. When something works, we aim to publish it in a scientific journal and/or put it in our theses. Most of the time, when something doesn’t work, there isn’t much you can do with the effort you have expended on it, unless you are fortunate enough to accidentally make something you didn’t actually intend to make. There is an encouraging saying that negative results are still results, but the reality is that no journal will publish an account of a scientist unsuccessfully trying to make something a hundred ways. This is unfortunate, since there is a lot of knowledge to be gained from things that don’t work. Currently, the only way to get this knowledge is through personal communication with coworkers who have worked on a project similar to yours before, and have discovered all the pitfalls before you. Another unfortunate fact is that in the scientific world at this particular point in time, one cannot succeed without a formidable publication record. It is almost more important how much you have published and in what journals than how “good of a scientist” you are.

All too often, science doesn’t quite behave the way you would want it to, and the thing that you are trying desperately to make is very elusive. We end up spending weeks, even months trying different variations of the thing to no real end. That is precious time of our scholarships essentially wasted. This makes it very difficult to weigh up the importance of synthetic lab work with the second aim of a PhD: learning. A chemistry PhD — just like a PhD in any subject anywhere — is about consolidating and refining one’s knowledge in one’s field. This is impossible to achieve by simply working in the lab day in and day out. Sure, practical skills are honed only by using them, and interpretation of your own data can teach you about how your own chemistry works, but, as I noted on Twitter a few weeks ago, the literature is often smarter than you. Furthering one’s knowledge can encompass anything from reviews of the literature relevant to one’s research topic, attending seminars, teaching, reading books and consulting peers.

I am currently struggling with balancing these two major objectives of my PhD. Every moment I spend at my desk instead of my lab feels wasted, especially since I’m one of those unfortunate cases that doesn’t have much of anything to put in my thesis as of yet. The project I’m working on is proving to be quite challenging. So, I’m finding it hard to stay out of the lab to read books and trawl the literature. And, simultaneously, as I choose to spend yet another day working in the lab rather than sitting at my desk reading, I feel guilty about that too: as though I’m choosing simply to throw things together blindly, hoping that they stick, rather than rationally planning my next step with reference to empirical evidence.

I’m hoping that once I have a bit of a base to stand on in terms of concrete positive results, I can feel more confident about what my project really is about. With that basis, perhaps I can also have a better starting point in terms of expanding my knowledge — more practically, which topics to read up on. I have this gut feeling that this might just be an empty hope, however. I think science is in many ways about constant uncertainty, and that as a young scientist, I’m going to have to deal with it outside the realm of my chemistry, too. This is crystallised in what a senior coworker said to me a couple of months ago when comforting me as I was feeling lost: “Science is a bit like that. At some point you realise that everybody is making it up as they go.”

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

What is it made of: Introduction

I think scientific curiosity boils down to two basic questions: “what is it made of?” and “how does it work?” The difference between them is the difference between a child taking something apart, and then having the ability or willingness to put it back together again. There is certainly intersection between the questions, like “how does what it’s made of influence how it works?” or “how would it work if it were made of different things?”. Their answers are also bound to have interplay. I do not believe focus on one of these fundamental questions over the other — simply as a matter of what one is interested in — is uncommon, though.

My question of choice is certainly “what is it made of?” My project is heavily focused on crystallography, a method of analysing chemicals that arguably comes closest of any analytical technique to directly imaging the structure of a compound. I spend a lot of my time looking at the structures of compounds, looking at how they behave in crystalline (ordered) solids. I also really, really like doing what I do, and get very excited when I get a new structure. I think it naturally follows that I am curious about what other things are made of, and what they look like, on a nanometre scale.

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In chemistry, your glass is always full!

To this effect, alongside my “chemistry picture of the week” series, I am planning on starting a series of posts titled “what is it made of?” In this series, I plan to pick an utterly commonplace material thing, find out what it is composed of — by web research and not by physical experiments, unfortunately, since I don’t have the facilities for that kind of thing — and report my findings. This series is a way of sating my own curiosity and that of fellow internet dwellers. It is also a potential way to combat chemophobia by the association of chemical structures and terms with common, harmless things. It also works nicely in tandem with the “picture of the week” series. With the “picture of the week”, I want to delve into the daily life of a young chemist, and expose some of the nitty-gritty that goes into doing science. In other words, I want to bring life into science. The “what is it made of” series will aim to do the opposite: bring science into life.

I repeat a sentiment from my first post: I am infinitely excited by how chemistry makes everything. I am excited by how intricate and beautiful and intelligent it must be to be able to ultimately manifest in all of the things we see around us — and by how cleverly we can manipulate it to make things nature won’t. I hope this series will help me share that enthusiasm a little.

I tweet about everyday chemistry things as @Lady_Beaker. You can also contact me via e-mail at chemistryintersection@gmail.com.

Chemistry picture of the week: Dishes

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As chemists, we need to be aware of what sorts of chemicals we are dealing with and how we can dispose of them — and clean up after them — appropriately and safely. We also need to be sure that our glassware is as clean and free of residues and chemicals we did not specifically add so that each reaction or measurement we conduct is as reproducible as possible. After all, one would not bake an apple pie in a dish that was previously used to cook chicken wings without cleaning it. A surprisingly large amount of time doing chemistry is spent doing dishes.

Pictured above is the receptacle I use to store dirty chemistry dishes in. My system is to build up a metal bowl full of dishes before I pause to do them. I find this allows me to accomplish a fair amount before I need to stop, while also not hoarding too much glassware at once. I do have lab mates who will build up entire 20 L buckets (yes, several) full of dishes before they do theirs. For those guilty of doing this, I will only say the following: hoarding glassware is a good way to make your chemistry friends disappear.

The way everybody does their dishes varies from group to group, too. In my old research group, with which I did my Honours, we would first wash most visible residue off with appropriate solvents: often one of the fantastic foursome of water, ethanol, acetone or methanol. For some glassware, this would be good enough, and after drying, the glassware would be ready to go. For glassware full of stubborn precipitates, we would dunk them in the base bath (made from mixing potassium hydroxide and isopropanol; the “recipe” for base baths also varies from group to group) overnight. Rinsing with copious amounts of water and drying would then leave the glassware good as new — except for the fact that base baths work by dissolving a layer of glass. Any glassware should not be left in the base bath for extended periods of time. Additionally, glassware susceptible to fracturing or implosion should be dealt carefully when washed in the base bath repeatedly.

The group I did undergraduate work with dealt with sensitive rare earth chemistry as opposed to the largely aqueous metallosupramolecular chemistry I did in my Honours and do now. As such, our wash-up regimen was a bit more rigorous, too. Before glassware was left in the base bath, it would be dunked in an acid bath overnight. I would tell you what it was composed of, but I realise now I never bothered to find out. I suspect it was a solution of hydrochloric acid of some concentration. The rationale was, I believe, that the acid bath would dissolve any metal residues left on the glassware, while the base bath would resolve any organic residues. The base bath was followed by a rinse with first water and then acetone, followed by drying in an oven for at least 24 h, due to the water-sensitive nature of our chemistry.

My current group has deemed the corrosive, flammable base baths an unnecessary hazard for the work we do. For thorough cleaning, we use a detergent and hot water, followed by ethanol if some residue happens not to be entirely water-soluble. To someone used to using base baths to clean stubborn glassware, I have found this method surprisingly effective and safe, comparatively. We let our glassware drip-dry overnight, and then it will be good to go again. Very occasionally, some glassware will require more rigorous cleaning — such as glass frits used for compounds insoluble in common solvents. But I would not say this is often the case.

The way we clean our dishes definitely depends on the kind of chemistry that we do. For sensitive chemistry, more rigorous regimens are required. For less sensitive chemistry, the risks and hazards of those rigorous regimens may outweigh any gain. All groups have their own tips and tricks — we could certainly learn from each other here. If you are a chemist, weigh in: how do your dishwashing procedures vary from the ones I’ve learnt?

You can reach me in the comments, by my Twitter account @Lady_Beaker or by e-mail, at chemistryintersection@gmail.com.

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.