What is the ‘Smell of Science’?

Two students have just walked into the building, probably not chemistry, physics, astrophysics or forensic science students. They were discussing the smell of the building and claimed it ‘smells like science’. I’m guessing I’m pretty much immune to the building’s normal odour, far more likely to pick up strongly scented deviations (yes I do want to know who’s using the stuff that smells like skunk – they need to take more care).
We’ve got chemistry, astro/physics, forensic science labs in the building, research and teaching for chemistry. Anyone know what the ‘smell of science’ is?

Impractically Impossibly Imperfect

This is post 2 on laboratory practicals, sparked by discussion on Twitter of A-level science reforms to replace practical assessment with an endorsement. In post 1, I considered that the only way to assess practical work directly is to observe students doing practical work. In this post I’m aiming to consider the impact that prior experience of practical work has on 1st year chemistry students.

We overtly assume little when it comes to the practical skills of our incoming students. Take an group of students and they will have sufficiently diverse backgrounds that make assumptions very dangerous. Our lab course is designed to build up the basic skills in the first semester. That’s not to say we go slow, and that’s not to say that good prior experience doesn’t help, but we go at a reasonable pace and knowing your way around a lab is an advantage.  We do, however, unconsciously assume a great deal about the practical skills of our incoming students, but this is practical skills in a far broader context.

Firstly, we assume that students can follow instructions to carry out practical procedures and that it goes without saying that this involves gathering equipment, planning an efficient way to do work, working in an organised and tidy manner, and cleaning up effectively.  I think this is a fair assumption to a point. These skills rely on extensive experience of lessons in all subjects that aren’t just sitting doing worksheets. That can be anything from art to home economics, chemistry to woodwork. It can be hobbies or clubs, activities with family, friends, scouts or guides.  And yet it seems that some students struggle with this kind of thing. Being aware of the surroundings and the other people working near by is essential here as well. Not leaving drawers or cupboard doors open, moving the stool so no one trips over it, returning items promptly after use. We assume that our students are used to working in a busy environment, again something that comes from experience.

Secondly, we assume that students are practiced at critiquing practical procedures and knowing when something isn’t right. I’m not talking about the mythical powers of any demonstrator to identify a product waved in their face and answer the ‘does this look right?’ question. I’m talking about the ability to use an ice bath so that the flask doesn’t tip, or recognise whether something is boiling or not.  There are sometimes logic gaps in how people work in a lab that come down to a lack of experience of doing stuff.

Essentially, how can we hope to teach students to transfer air sensitive materials via syringe (even after 2 semesters of lab) if they are unaccustomed to translating written instructions into physical actions, incorporating verbal suggestions, finding equipment and performing basic tasks? Less practical work in any context is bad news for the first year lab class.




REPOST: All the pretty colours…

One of the most spectacular chemistry experiments is flame tests. I think it’s a particularly elegant experiment, and also one that can easily be done in high schools. I remember doing it when I was about 14 or 15, as part of standard grade chemistry. It is very simple; you take some wire, clean it in concentrated acid, dip the wire in acidic solutions of various metal salts and then put the wire in a blue Bunsen flame. It has some of the key components of a good chemistry experiment – acids, Bunsen burners and pretty colours. In a similar manner to fireworks, different metals burn with different coloured flames. I’m sure that my standard grade chemistry teacher had a sense of humour when she suggested to us that we leave sodium until last for it was hard to see. Yes, the bright and vivid orange colour was quite surprising coming after potassium’s pale lilac, strontium’s red and copper’s blue green.

I was thinking about this during a lab session last week when we were looking at exothermic reactions. OK, we were looking at some really great demonstration type experiments including thermite and the potassium dichromate volcano. More about them another time. We were also doing the screaming jelly baby experiment, also known as the jelly baby rocket or rocket to the moon. Simply, this involves taking a boiling tube, clamping it at a 45 degree angle, filling it with some potassium chlorate. The potassium chlorate is melted with a Bunsen burner and the whole thing is done in a fume hood. Once molten, half a jelly baby is dropped into the boiling tube and a rapid and spectacular reaction ensues as the sugar reacts creating flames, sparks, sometimes a roaring noise and lots and lots of smoke (one good reason for the fume hood). We noticed that the Bunsen flame, still set to blue, turned lilac due to the quantity of potassium ions in the smoky atmosphere. It was pretty impressive really, and despite watching 5 or 6 groups of student perform the experiment, never lost its magic.
There are lots of simple, elegant and impressive chemistry demonstrations like this, often used to bribe potential students at university visit days and enchant more disruptive classes at school. They are also the things that people remember most strongly about high school chemistry.

First Published May 19th 2009, on version 2.0!

Repost: Stinker or Smeller?

First published 04/2009 over at EP v2.0. The topic came up in conversation in the last couple of weeks so I thought I’d dig the post out! The images have disappeared but it makes sense without.

One of the advantages of resolving to ‘buy British’ (or vaguely European) is rediscovering the latest trend in culinary adventure: seasonality! With the advent of the asparagus season comes that intriguing question – why does asparagus make some people’s pee smell?

It turns out that the answer isn’t as simple as I first anticipated. I thought it would be a simple exercise in looking up the chemical responsible, reading a little around metabolic pathways and degradation products and suggesting which volatile and vile molecule is responsible. Not everyone can smell asparagus pee however, and this initially lead to the assumption that not everyone breaks down asparagus in a manner that produces the smell. Adopting the naming convention of one paper[1], those who produce asparagus pee are stinkers, and those who can smell it are smellers.

There have been a number of studies that investigate the origin of asparagus pee and range from feeding unsuspecting students various compounds that might be responsible for the smell, to making people eat asparagus every month to see if it keeps on happening. It is widely noted that the first reports of asparagus pee correlate well with the first use of sulfur containing fertilizers from the late 17th century[1]. This give a fairly decent clue (as if the smell didn’t) that sulfur compounds are to blame.
It isn’t that simple though, and the issue of stinkers versus smellers still exists. Some studies suggest that about half of the UK population are capable of producing the odour, but closer to three quarters of the American population are[2]. The sample size was small, and those results are from two different studies, also other studies contradict these findings so I’ll take those results with a pinch of salt. Another paper suggests that everyone is a stinker but not everyone is a smeller leading to the illusion that not everyone is a stinker, and also that some people may be hypersensitive, specifically sensitive to the pungent compounds[3]. Confused yet?
As far as I can tell (and as far as my journal access will let me go), the jury is still out on the precise nature of the variation between stinkers and smellers. There was one rather intriguing anecdote about women who, on becoming pregnant, started to notice asparagus pee. This could well mean that the women were smellers, but not stinkers, while the unborn children were stinkers[1]. Also, not everyone describes the smell in the same way: to some it is hideous enough to stop them eating asparagus, to others it is not unpleasant, just a bit strange.
I’ve still not answered my question though, what are the chemicals involved? Asparagusic acid  is looking like a likely culprit as subjects fed that substance produced pee smelling suspiciously asparagus like. The current thinking is that asparagusic acid is broken down into a variety of sulfur containing compounds that then go on to break down into a collection of volatile and pungent sulfur compounds in urine. These intermediates are not known, and characterising them is probably difficult due to the hazards of trying to extract them from urine without altering them chemically. The final compounds must be volatile for the odour to be detected. These include methanethiol, dimethyl sulfide and bis(methothio)methane, which is reported to be reminiscent of cheese, horseraddish, onions, garlic, truffles, with earthy and spicy notes (on the right above).
I suppose that the precise nature of asparagus pee is not a burning research question because that was about all the information I could find. Still, I think I’m mostly satisfied with a tenuous explanation involving stinkers and smellers, aparagusic acid and breakdown products. After all, asparagus is still good eating!
[1] Akers et al., Food & Foodways, 1997 (2) 131
[2] Mitchell, Drug Metabolism and Disposition, 2001, (29), 539
[3] Lison et al., British Medical Journal, 1980 (281) 1676

Crash, Flash, Splat!

This week I did two outreach activities. One was making PVA slime and alginate worms with around 50 ten and eleven year olds from a local primary school, and the other was a demo lecture as part of the Salters’ Festival of Chemistry. Keele hosts two festivals, organised by Dr Jane Essex, part of the PGCE team, Education.

The demo lecture is quite standard really, based around gases in air but each year I attempt to modify a demonstration to make it a bit different or better. Last year I modified my Elephant’s Toothpaste demonstration to make it glow in the dark [http://www.possibilitiesendless.com/2013/04/it-grows-it-glows-realtimechem/].  This year, following the advice of our excellent regional coordinator, Dr Heidi Dobbs, I modified the hydrogen balloons.

In the interests of full disclosure, I really don’t like loud bangs and prefer not to set them off. I usually ensure I have a handy volunteer so I can cower at the other side of the room. I’m not going to debate the virtues of flash-bang lectures in the context of outreach either. Of course, modifying this experiment meant that I had to practice the day before.

A similar modification is detailed in Education in Chemistry, essentially using metal salts to colour the hydrogen flame [http://www.rsc.org/Education/EiC/issues/2010Jan/ExhibitionChemistry.asp]. On Heidi’s advice, we put a tiny quantity of grease on the outside of the inflated balloon shortly before the lecture started, then sprinkled on copper acetate. It must be tiny quantities of grease and metal salt otherwise the balloon sinks. While this turns things into high comedy, not many school managers appreciate their lecture theatre benches being scorched from a low flying copper yielding hydrogen balloon!

The practice runs worked and on the day we did copper acetate and strontium oxide. With more preparation, I’d get a series of the chlorides probably. The grease method worked well so I can’t comment on the injection version.

It went down well anyway so I’d recommend it to anyone who generally does a flash bang lecture.

Amazon as a chemical supplier

Once upon a time I lived in North America and was always amazed at the range of (what I considered to be lab only) chemicals on sale in drug stores (pharmacies) and home depot (DIY store). Cans of toluene and acetone would keep place along side the more familiar meths, and hydrogen peroxide would nestle with the cotton wool. And it didn’t seem quite right because in the UK, many of those substances were not on obvious display. I couldn’t comment on whether they were for sale having never tried to buy them.

Flash forward to last week when I was looking for some super absorbant polymer. Best supplier: Amazon. And the range of chemical stuff on sale through the Amazon UK site gives me pause really. Who knew that the general public needed stuff like potassium iodide (laboratory grade) or that oxalic acid was a useful rust remover. Or that sulfuric and hydrochloric acids worked along side potassium permanganate and potassium chlorate. I did establish that it would be quite possible to buy a nice selection of stuff for home made fireworks.

Sadly there were few product reviews for me to determine the purpose to which these purchases were being put.

More intriguing was the range of lab ware type products, and I get some of this is for home science and schools. Not so sure about the test tubes for shot glasses though. More curious was that much of the plastic labware is cheaper through Amazon than through one of our approved suppliers.  Great for science outreach budgets that don’t go through ‘official channels’ (i.e. cheque deposited into bank account), a little curious in the context of value for money for tax payer funded science.

So perhaps the world has now reached a stage where Amazon is all you need.

Discipline Disciple

I had another attack of paper inspired frustration last week. One of the project students had made a product that I was expecting to be an oil, but instead had a rather beautiful looking solid so I went in search of a melting point or confirmation that it was in fact solid. Our standard mode of doing this is running a search in Reaxys as we have limited access to Chem Abs or SciFinder so I was reasonably pleased to find a couple of hits for a series of similar compounds, and then the holy grail: a published account of the compound itself.

Now, if we’d been trying to make new stuff, we’d have been disappointed at this result but it’s a third year project and doing verification characterisation rather than brand-spanking –new product characterisation allows us to focus on the reason we wanted to make the molecule rather than grabbing a full set of data. Efficiencies have to be made in a Dual Honours system for projects. So, initially enthusiastic, I acquired a copy of the paper, noting fairly contentedly that it was in a high impact chemistry journal.

Well it all goes to show that nothing in the lab is ever as it seems, and nothing is ever easy. After 6 weeks of indoctrinating the new first years with ‘keep good records in your laboratory notebook’, and the second years with ‘fully interpret all spectral data otherwise you don’t know what you’ve made’, it was down with a bump to find a paper that offered absolutely no characterisation of the pivotal organic compounds made. Yes, a very nice applications paper, lovely results, but not a shred of verification that they made what they said they made. And no, it isn’t in the experimental section, nor is there a reference for the procedure/synthesis to point us in the right direction. As far as I can tell (and I appreciate that our literature search is incomplete), there is no previous report of this molecule.

I did verify that it should be a solid however, by way of the line “the solid was used directly” in the experimental section.


I’m aware that different disciplines have different standards in the reporting of experimental data. I’m aware that the expectations of different disciplines vary wildly, but to me the heart of the issue will always be that if you cannot prove something was made properly, every single experiment from that point, using that substance, is a waste of time, money and effort. And on that I’m somewhat uncompromising.

CLEARS things up

One of the things ‘going on’ this academic year is a project investigating safety in the laboratory. We’re not trying to come up with better lab rules, I think that’s one of the biggest differences. We all comment that in the chemistry lab students (and sometimes staff) do very bizarre things, but more lab rules don’t seem to make a different to the number of things like that which occur. In first year, it makes sense to have a clear set of lab rules. Following them should allow the students to work in comparative safety, learn how to complete risk assessments but also learn how to be in the lab and how to do experiments. If you include full risk assessments on top of a standard diet of first year experiments, the cognitive demand is sky high.

Rules have their place and provide adequate baseline for behaviour in a lab environment. They also aid compliance with various legislative aspects of health and safety. Rules inhibit learning to think about lab safety in a more creative and adaptable way: rules inhibit learning about safety. In most academic subjects we’ve moved away from rote learning approaches, favouring more interactive, problem based learning approaches. Why then do we think that learning and applying a set of rules largely without thought is an appropriate approach to learning about laboratory safety.

In second years, students are expected to take on a little more responsibility for working safely: the techniques they use are more advanced, the chemicals have greater risks associated with them and need more specialised precautions. We may move from a lab full of students working on one experiment to a rota system where students may be working on one of 5 experiments at a time. The experiments have still been risk assessed by staff before deployment. The students do have to be more adaptable in assessing risk, but the rules don’t generally change between first and second year.

By third year, students are embarking on independent research projects and the responsibility for completing risk assessments falls on their shoulders. They have to complete COSHH forms of some description, and often having learned in 1st and 2nd year to view COSHH forms as annoying time wasting paperwork, fail to see the benefit in the opportunity to plan their work to be efficient and safe. While we may sign COSHH forms and check them quickly, many of our project students are doing reactions we have never done ourselves and may not be as familiar with the risks as we might be (which is not to belittle the experience held by academics). There may also be an attitude that we would not ask our students to do anything ‘dangerous’ because they are students.

So what do we plan to do in this project: Chemistry Laboratory Engagement and Assessment of Risk and Safety? We want to investigate ways in which students learn to think about laboratory safety. We want answers to the eternal question of why disposable nitrile gloves bestow the students with superpowers able to resist all chemicals. We want to figure out why half the class wants to put the aqueous sodium chloride in the halogenated waste. We want to investigate the misconceptions, the chemistry misconceptions, that underpin some of the frequent safety mistakes we see in the lab. We want a safety system that encourages students to think and evaluate rather than demanding simple compliance with rules but we can’t have that until we have a better idea of what on earth goes on in the minds of students when they are lurking in the laboratory.

Spooktacular Chemistry Fun

While the internet was wringing its collective mouse cords over the spectacularly badly thought out http://gizmodo.com/5954522/how-to-use-basic-chemistry-to-scare-the-hell-out-of-your-neighbors this Hallow’een, we were out doing some fairly decent and safe science to impress local families. We had three experiments on the go: flame tests, alien blood and enzyme catalysed decomp of hydrogen peroxide. The flame tests were given a wonderfully spooky twist by naming the salt solutions ‘Vampire blood’, ‘Dead Sea Salt’ etc, and the visitors to the event tested each by way of a soaked wooden splint in a portable Bunsen burner. Our visitors were from all ages and backgrounds but the response to the beautiful blue green of copper was generally the same wide eyed wonder.

Alien blood required slightly more improvisation as one of our chemicals wasn’t quite working properly. We settled on coloured acetone dissolving polystyrene packing materials along with a liberal sprinkling of fictitious aliens using their blood to get at your Christmas presents. The thing that impressed me was the ability of young children to separate the fiction back story that made the experiment kind of fun, and the science – many were able to comprehend both and wanted to know what the alien blood ‘really was’.

The peroxide decomp…well…that was incredibly surprising in the response we got. As it was Hallow’een, we’d decided that using bits of different organs and comparing the relative rate of hydrogen peroxide decomposition was the way forward. Rates that can be measured in terms of how much green bubbly foam (add washing up liquid and green food dye to the peroxide) are pretty easy to do. I was expecting some bits of heart, lungs and liver, I wasn’t expecting 3 full sheep’s plucks (heart, lung, liver all still attached to one another and the windpipe).

We started out in ‘a bit too gross triage mode’ and decided that keeping the bulk of the organs out of site from all bar the most interested and robust visitors would be appropriate. How wrong we were. The vast majority of visitors were fascinated by the organs, and we were able to demonstrate the lungs inflating by blowing into the windpipe. The peroxide worked fairly well although we weren’t able to get a glowing splint to relight most of the time. The liver was far superior in decomposing the hydrogen peroxide, logical really, having the greater concentration of enzymes of all organs tested.

Other displays at the event, run at Keele’s Sustainability Hub, included bats, lizards and snakes (I got to hold a python which made my week), dry ice, non-Newtonian fluids, making smoothies with the ultimate dynamo bicycle, face paints, pumpkin carving, the Make-it-Molecular crew were there and much more that I didn’t get a chance to see. It was a pretty amazing half-term event for families and good fun for all those who volunteered. Makes me look forward to the next outreach/science comms event in December…which reminds me, I need to order the chemicals!

With thanks to L Mills for the photographs.


Chemical Treasure Hunt Part II

I have written previously about our work identifying the contents of Blists Hill Victorian Pharmacy Jars (http://www.possibilitiesendless.com/?p=931), and we’ve pretty much solved the riddle of the jars. Briefly this Victorian Pharmacy exhibit has many jars filled with either the original and sometimes labelled contents, but possibly also poorly documented replacements made by well-meaning curators over the years. The last post described some rather Victorian chemistry to confirm the presence of mercury in a sample.

Since that work in January, we’ve largely finished off the riddle of the jars, my colleague Jane Essex and various volunteers (undergrads, ChemNet students, local school students) did amazing work a few weeks ago figuring it all out. Some surprising contents included cochineal beetles (identified when someone accidentally squished one and saw the characteristic colour), modern indigestion tablets, and a lot of food dyes – you’ve got to have the coloured solutions if it’s chemistry, right?

How do you go  about identifying a complete unknown? Well the first step is usually to figure out if there’s anything likely to give a flame test result in it. Flame tests are straightforward to carry out, don’t use a large quantity of material and pretty much confirm the presence of metal ions by characteristic colours. Sometimes the name on the jar gives a clue – it might be an old name for something readily identifiable, it might be exactly what it says on the tin or it might not be. In any case, it’s a starting point and that’s better than nothing. After flame tests (and you can often figure out things like sugars by the way they burn as well), the next tests really depend on where you think it’s going. If it is a brightly coloured solution with no flame test results, chances are you’ve got a food dye and you’re heading for UV/Vis analysis. If it’s a white powder and you’ve got a flame test result, the hunt for the counter ion begins. Suspected sugars are also easy enough to test for. The real challenge comes in those clear, colourless liquids that may, at some point, have contained some extract in water or water-ethanol mix. So maybe you dry the sample down and analyse the residues, perhaps you go high tech with NMR or IR.

The real joy of this work, and the reason that it will be appearing in our undergraduate laboratories this coming year, is that it is genuinely open-ended problem solving. One common comment on feedback from participation in our analysis days is that they would have liked it if someone could have told them they were correct or not. You can’t just give up on this chemical puzzle, and satisfaction with the answer is intrinsically linked to your own ingenuity in figuring out what tests to try next. This is not the sort of problem based learning where the students can slack off and wait for the answers (or if it’s one of those open educational resources, simply google the answers). The plan for our undergrads is to get them to identify some unknowns in the laboratory. We’ll be kind and give them a recipe book of possible tests but points will be awarded for identification in the fewest number of tests. I may not be kind to the demonstrators however – I don’t want the students to be told the answer, or be given hints. It’s quite possible that I may get a colleague to make up the unknowns and keep the identity key hidden from all of us. No peaking, no prompting, proper problem solving.

The second type of activity that will hit the undergrad lab, this time in the form of group projects, will be analysis of ‘proprietary’ mixtures. These were often created by pharmacists and designed to treat anything (and likely nothing). We did one a few weeks ago that was essentially oil in water/ethanol. These require a little more sophistication than  a handful of tests from the recipe book – they often have organic components and water soluble components that need to be identified. A simple example would be a herbal extract (something like eugenol) in an oil-water emulsion. Identifying all the components could be quite a challenge. So I get to do some research into these proprietary mixtures this week and make a few up for the students to get their teeth into.

If anyone’s wondering why we’re making up samples rather than just finding another pharmacy that wants some analysis done, I feel it’s fairer for assessment for there to be a defined if undisclosed answer. There’s also the pressing issue of risk assessment, we can have enough demonstrators around for an analysis day, it’s a bit harder during term time. We’ll call this a pilot study year to see how these activities work in the lab class and look to develop it further next year.