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
.

Posted in lab mahem | 5 Comments

Bottom Lines and Reproducibility

I have a thing about reproducibility. I’m not the only one as this post on In The Pipeline shows.  Nothing annoys me more than someone spending their time and someone else’s money to carry out an experiment then not taking the care and attention necessary to record the details in a manner that allows another to reproduce the result obtain. People who don’t interpret their spectra properly and by default never prove the outcome of their reactions either way come a close second in annoyance.

I’m afraid I fall in to the skeptical camp when it comes to scientific literature. I feel I’ve written about this quite a lot in the past (http://www.possibilitiesendless.com/2013/08/frustrations-of-reproducibility/ for one). I’m sure that a lot of what is published is reproducible by the person who did it in the first place. But I’m also sure that that researcher probably had a good number of habits that probably weren’t recorded as part of the procedure and I think sometimes that will affect the outcome.  Some chemists use argon atmospheres by default but may refer to it more generically. Other details, modes of addition, method of cleaning glassware (or the impurities left in the glassware!)…the little things sometimes matter. I’ve also had a few procedures where doing the ‘established technique’ results in disaster. For example, I have one reaction where the product has to crash out as the reflux cools. Generally people would remove the solvent under reduced pressure if the product failed to crash out but in this instance that produces goo, not the desired (selectively insoluble) product.

As quoted in the post below, I’ve tried to reproduce really really interesting results and haven’t been able to. This has been likely due to some key details being missed from the records kept.  It makes me quite cross on a single-student-single-result basis, but fortunately that result didn’t get published because it was not reproducible. I suppose the question I should be asking is to what lengths should we go to ensure work is reproducible? The ultimate solution is to have someone verify the work independently, but the resources required to do so are ridiculous.  After that it comes down to the scruples of the researchers involved, they’ll probably record the minimum level of detail required by their supervisor. It isn’t reasonable to expect research groups to duplicate each and every result, but it is reasonable to expect research groups to produce original data to support their results. So my stop-gap measure would be to keep really good records, and make sure you have a filing system to support retrieval of the raw data (instrument native format) if requested.

Posted in Academia Nuts, Chemistry, reactions, Teaching | 2 Comments

On Final Year Projects

After a week of meeting with new project students, and answering many of the same questions several times, I’ve been scouting back through the archives looking for what I’ve said previously on the subject of surviving a final year project.

May 2011: On Third Year Projects

Final year research projects are very much what the students make of them, provided the academic is willing to allow sufficient leeway.  Even in a fairly prescriptive project it is very obvious when a student is participating in the decision making, reading around the topic and building up good, independent knowledge of the research field in question.  It is similarly obvious when a student has largely done what was asked of them, with little curiosity about the wider research topic.

and

Some of the most common errors with regard to projects, and probably with regard to any kind of investigative/research type activity hinge on insufficient verification of results.

 

November 2013: Project Survival Guide

Thirdly, you are conducting research which may be published. It is imperative that you conduct that research with the utmost honesty and integrity. If you forget to write down a mass or volume of reagent added, record that in your book. While your supervisor may frown at the unreproducible procedure because you didn’t make a note, it’s nothing compared to what they will feel if you make up the value and the procedure doesn’t work for the next student.

I see last November my obsession with reproducibility was firmly in place! It came to ahead in August 2013 with an unreproducible but ‘fascinating if true result in a dissertation.

August 2013: Frustrations of Reproducibility

A few weeks ago I finally found the wherewithal to head off into the lab to try and replicate a very interesting result one of last years crop of project students had obtained. They had been investigating a potentially new catalyst system and had obtained a rather intriguing and somewhat unexpected result by NMR.  The reaction conditions were tantalizingly simple and mild, the result rather nifty and well worth further investigation. And I had the left over catalyst and reagents necessary to conduct the simple test.

Nothing. After the required time stirring away (and at a warmer time of year for ‘room temperature’ than the student’s attempt was), no change in the NMR at all.

With all that I’ve said previously, I’m wondering what I have to add to these posts on the subject of 3rd year projects. As I sat thinking about writing a blog post on the topic, I was framing things quite negatively and quite fancied writing a ‘most common mistakes students make’ post. I think though, these linked posts probably cover what I had in mind in a slightly more positive way, but with a new crop of students, it’s always worth saying again!

 

Posted in Academia Nuts, Chemistry, Teaching | Leave a comment

Begin again

The semester is 3 days old. The new students have arrived and are progressing through welcome week. 2nd and 3rd years are walking the fine line between enjoying themselves and starting classes. Staff are wrangling teaching materials into shape and rubbing their eyes, wondering where summer went to so fast.

One thing that always occurs to me at this time of year is that it is the start of the wheel reinvention cycle again. I look for new workshop questions, better problems and exercises to elaborate key points. I battle to find new papers to set more challenging coursework, or add additional examples to existing data sets. And then I try to write my exam questions, a frustrating task that’s worse when done in advance of teaching the material.  I like the annual maintenance of teaching materials, it’s part of the ritual of getting ready to deliver sessions. What frustrates me is that there are probably several other academics out there doing the same as me. Trying to find that scrap of authentic NMR data for PF5 and a reference for it, or looking for the activation enery for Berry Pseudorotation in a series of compounds. We need to start sharing this stuff because the quantity of time being spent looking up all these old journals, or running countless simple NMR spectra, or redeveloping similar laboratory practicals.

I like the RSC’s LearnChemistry because there are resources there I can download and adapt. It’s very good for for first year teaching in places but not so much for higher levels, although many of the Chemical Vignettes are now there. And I accept the need for an element of quality control, but what would be great would be some kind of password access site where people can upload resources they are willing to, and can share, for teaching purposes. Add in a rating feature and comments boxes for queries and peer review and it could be very useful. Password protection and perhaps access for verified teaching staff only would be essential to keep model answers from easy search.

So, I’ll offer. Currently I teach 1st year spectroscopy (IR, UV-Vis, NMR), 1st year Transition Metals and p-block chemistry, 2nd year multinuclear NMR, homogeneous catalysis, bioinorganic/metals in medicine, 3rd year inorganic reaction mechanisms. I also run a 2nd year practical exam that is a 3 hour lab activity. If any of that might be useful to you, drop a comment. I’m happy to share what I can. Some of it is still a work in progress at this point in the year but it will get there. And similarly if anyone can point me in the direction of good OERs or information sources for the above list, I’d appreciate it.

 

Posted in Academia Nuts, Chemistry, Teaching | 3 Comments

Summers End

The air around Keele has been distinctly Autumnal of late, and in between heavy rain, it’s quite clear that summer is done. Hopefully we’ll get an Indian summer for those last few rays of hope before the season properly turns.

It’s been a funny summer and quite busy. I’ve had work experience students, summer students, spent a week at the Chamboree making slime, done quite a bit of other outreach and am only now heading off on holiday. What I haven’t done is made any significant dent in the teaching prep for the coming semester (or made sufficient headway into the admin to-do list). In some ways I’m not entirely sure of what I have done with my time but in other moments I recall something that took up quite a bit of it. I also got a new kitchen, went to Cornwall for about 40 hours and did other home stuff.

The end of August brings the Variety in Chemistry Education/Physics Higher Education conference (VICEPHEC). This is the 5th year I’ve come to this conference and it is a highlight of the year. I sit here in Durham, after the first day but before the conference dinner. We’ve had a fantastic and thought provoking keynote lecture from Professor Simon Lancaster on the nature of lectures, engagement and peer instruction. Dr Kristy Taylor lead an informative workshop on A-level chemistry that saw us performing A-level practical work and getting in a little bit of a snit over the value of TLC. Other talks have involved PeerWise, assessing laboratories and ways of convincing students that engaging with feedback is important. I especially enjoyed Dr Barry Ryan’s talk on information literacy – he’s using some really creative assessments that sound like they would be fun to do. He also admitted to be a magpie at conferences, collecting sparkly ideas and assimilating them into his practice – I loved that notion.

As I haven’t quite started my teaching prep yet, it’s possible that some of the ideas I’ve heard today will make it in there. Usually I’m a bit frustrated after day 1 because I’ve already sorted out the assignments and lectures and I don’t want to re-do them. Then I forget by the following year what I intended. So what two things will I take from today?

1. Time to get better engagement in lectures and encourage more learning ‘there and then’ rather than presenting stuff to be memorised at a later point.

2. The lab safety quiz should include more on lab hygiene and not just focus on procedural safety stuff.  Probably need to include more ‘read this then answer questions’ bits.

There will probably more thoughts on this as I process things from today.

 

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Units Matter Part II

With that many mushrooms, it serves 4 what?

With that many mushrooms, it serves 4 what?

Posted in Pedantry, Units | 3 Comments

Units Matter

units 1

Uhm…no.

Held by human being, 5'8" for scale.

Held by human being, 5’8″ for scale.

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#RealTimeChemCarnival

Yesterday we were at the RAF Cosford Museum to run activities as part of the Chemistry at Work event for schools. We’ve been before and it remains a spectacular venue for outreach.cosford chem at work 1

Set up and ready to go!

Again we took our ‘Is Faster Better?’ activity, looking at catalysis through the catalysed decomposition of hydrogen peroxide. We introduced a new catalyst that introduced a degree of unpredictability to the whole experiment.

cosford chem at work 2

Keeping the test tubes at arms length!

We adapted this prep to use iron trichloride powder and 0.1M solution. During testing, the tiny quantities of powder and drops of solution created a fairly satisfactory result, compared to solid/aqueous KI and yeast. But ‘in reality’ both were fairly unpredictable. Clearly better catalysts provided your aim was good and the bulk of the stuff got into the peroxide-soap mixture, but if not, quite bizarre and unreliable. The good thing about comparing a microspatula tip of solid with three drops of 0.1 M FeCl3 (or 2M KI) is you can discuss quantity and dissolution as factors. You do have to be adaptable however when one set of reagents does something different every time!

cosford chem at work 3

Richard with a school group

The museum is still a wonderful place to do science outreach of any sort, surrounded by the planes, tanks, cars and missiles!

Posted in Chemistry, Travels, Uncategorized | Leave a comment

The Reciprocal Space of Social Media

In a bit of end of semester navel gazing last week I was contemplating the usefulness or otherwise of blogging. The first website I ever ‘ran’ was back in 1997 and it’s creation coincided with having reliable access to a computer and the internet on starting university. While it is long gone (I do still have printouts!), it was what would now be classed as a blog. Then came a series of blog-like websites with photos and tales of travels and then I discovered blogging ‘proper’ in 2006. That’s a long journey but not as long as the journey from then to here. In total, probably 7 or 8 websites/blogs, some still active, some long gone (beyond even the reach of the way back machine). It’s strange to consider the various versions of me that has inhabited online spaces.

I was jolted from this brief reverie by a tweet from a colleague:

I suggest that all new (UK) academic appointments should be encouraged to engage with social media! Comments?

@Robajackson, Twitter, 8:02 PM – 23 Jun 2014

My first response (although not one I tweeted, for 15 years on the internet will teach you a thing or two about off the cuff responses*) was ‘oh dear goodness me no, the last thing the world needs is a whole bunch of self-centred young academics running around on social media’. I’m aware that this is a highly uncharitable view and my second response (again not one I tweeted) was ‘when on earth would they find the time, doesn’t @robajackson appreciate just how. much. there. is. to. do. these days as a new academic? My third response was a more refined version of my first response: ‘yes, OK, I suppose it has its benefits but please someone teach them that it is about reciprocity and community.

Back in the ‘old days’ of blogging, before RSS readers became de rigueur, keeping up with the chemistry/academic blogosphere took effort. I remember countless hours spent hopping from blog roll to blog roll and I’m pretty sure I had a pre-defined route around my little neighbourhood on the net. I commented significantly more, I engaged with my own comments significantly more, I discovered new blogs at a far greater rate (I have no evidence to suggest rate of creation of blogs is now lower but it is harder to find new blogs), and I payed more heed to the diversity of those blogs in appearance, form and style. Now they all appear through an RSS reader and they all look the same, form and style being dictated by the RSS reader of the day.  Feedly’s recent outage prompted me to return to the old ways and I realised that I’d missed it. Blogs felt a bit more of a community back then, more conversation orientated and with a heap of carnivals and like minded people taking on issues collectively, there was always a strong sense of inhabiting some sort of reciprocal space. I can still name the person (pseudonym) that left the first ever comment on my blog and I can still remember the incredulity that someone had found and read it.

Why does that matter and how does it relate to the tweet? Well social media is now more diverse and there are a lot of forms to keep track of. There are a lot of utilities out there to help stream the social media and homogenise it. And those utilities make the broadcast aspects of social media ever easier. Type something, and one click later it is on multiple sites. But that’s not the strength of social media and anyone who thinks it is an excellent opportunity for self-promotion is missing out on about 80% of the point. Social media was, is, and should be a reciprocal space where it is possible to forge and maintain relationships in a different way to personal interactions. But it is about relationships and reciprocity. Without that, we might as well give every young academic a megaphone and permit them to yell about their achievements once per hour.  That would be…tiresome!

So do consider engaging with social media but please do not think that it is an easy route to fame or ‘impact’. The tools are powerful and with power comes responsibility.  You have a responsibility to learn to use them effectively. You have a responsibility to ensure your actions through social media do not harm others (particularly students and colleagues**) or yourself. You also have a responsibility to engage with others, to share their stuff as you would hope your own would be shared. It doesn’t work right otherwise.

But if in doubt, just don’t bother.

*I now operate a think thrice tweet once policy!

**You might as well get this straight from the start: you use social media, you will stuff up something. It will get you into some kind of bother at some point. At least be smart enough to figure out how to avoid the massive reality check moments from the start and leave the stuff ups to the realm of minor border skirmishes. You need to figure out how to handle interactions with different groups of people (students, family, friends, colleague, professional contacts) and how you will pitch your social media persona to cope with this. Sometimes social media can feel like everyone you’ve every known in any context in one room all talking to you. Think about that.

 

Posted in Academia Nuts, Blog Theory, Science and Media, social media | 4 Comments

Maths for Chemistry

I attended the HEA Developments in Mathematics Support for the Physical Sciences one day meeting at Liverpool University back in April. Various speakers described how maths was tackled in their subject at their university (I was one of them, describing Maths for Chemistry at Keele’s (r)evolution over the past 6 years, you can find the presentation on my slideshare), and a lot of good discussion was had.
So why did we need to have a maths meeting for the physical sciences and what is the problem? Most academics who spoke described the wide range of mathematics qualifications that their incoming first year students have. Keele is no exception and we require a C at GCSE. Having recently become aware of different papers sat by GCSE students, I now understand that this may not be an appropriate entry level of maths as it allows students to avoid some topics that are quite important for studying chemistry at university level. Our first year cohort has maths qualifications ranging from the C at GCSE through to acceptance on a course to study Chemistry and Mathematics. What does this mean for teaching chemistry or physics? It means that we can make few assumptions about the level of prior knowledge our students have. It also means that no matter what maths support we put in place, some students will find it straightforward, others will find it very challenging. This is for a variety of reasons.

At this point I’ll note that I’m aware a few of my students read this. I do take great care about the language I use to describe our students, and I try to make positive generalisations. I’m not keen on applying deficit models of any subset of students [I find the language of ‘women underachieving’ to be extremely annoying] so I’m trying very hard here to make general points without trying to single out any group.

Why will a group of students find maths challenging? Many don’t have confidence in their own ability to ‘do’ maths. Many have had past experiences of maths that may mean they think that they cannot ‘do’ maths, as if it is some fixed ability that they have in a fixed quantity. Many made different subject choices post-GCSE and maths wasn’t one of them so there is a little catching up to do. But I do know that I have never met a student who had a fundamental inability to ‘do’ maths. I’ve met students (both while teaching and as a student myself) who were extremely resistant to trying maths, I’ve met students who wouldn’t put time in to practice but never a student who, by virtue of some intrinsic trait, couldn’t do maths. If there’s one area of science where a defeatist attitude really holds students back, it’s maths.

I loved Peter Khan’s talk ‘Studying a physical science in the language of mathematics’ in which he described maths as a language. Like all languages he said, it is best to learn it young and it takes a lot of practice to gain fluency. I came back to his words later that day as I read a joke about differentiation by parts and my maths language skills kicked in to translate the symbols into words to explain why I was laughing to someone else (admittedly it took a fair bit of explaining…). I haven’t really used that maths skill for 3 years.

So where does that leave those of us who teach the more physical side of chemistry, or really anything that requires calculators? I think we have to split maths into two broad areas. One is scientific numeracy where students have or develop the confidence to perform tasks in the chemistry context that use maths. A yield calculation, determining the concentration of acid in a titration, working out the mass of reagent to add, the ability to put numbers into an equation and manipulate the equation to obtain the answer, drawing a straight line graph…I could go on. Sometimes I think we confuse students by pointing out the little tricks they can use to check they’ve got the right answer. As I teach spectroscopy, I often give them ‘typical values’ for spectroscopic quantities. Perhaps that muddles the issue for those who are focussing on getting an answer first. So there’s the scientific numeracy and then there is the other maths stuff, things like calculus and the like.

The only thing I’m sure of is that unless a student is willing to try when it comes to maths, and be smart enough to try at the first opportunity given, some topics will be unnecessarily difficult.

Posted in Academia Nuts, Chemistry, Travels | 1 Comment