If I had a million dollars…what I’d do!

£50,000 is an interesting sum for UK academics – it’s just about enough for a PhD studentship funded at RCUK rates and some consumables (potential issue with fees but not a major one). It’s probably about enough for a 1-year postdoctoral researcher or 18 months of a graduate research assistant. It might well be sufficient for teaching buy-out for a year’s sabbatical and expenses. It could also be a large number of summer studentships, all or part of a shiny bit of kit, or a means of accessing facilities at another institution.

So what would I do? A postdoc or research assistant would be more use to me really than a PhD studentship. A 12-18 month position to get some initial data on a couple of projects that would allow for initial publications and future funding applications. I’d shy away from a PhD studentship because despite the longer term benefits of training someone, I’d rather  focus on the research. I have a few project ideas brewing and it would be really nice to get a dedicated person to tackle them rather than the piecemeal effort I make, balancing everything else.

 

 

Posted in Academia Nuts, grant hell | 1 Comment

If I had a Million dollars….

Thought experiment for academics:

If someone handed you £50,000 (approx 65,000 euros and $80,000 US), what would you do with it?

Would you use it for work related purposes? Perhaps a sabbatical, pump priming a pet project or funding a research worker. Assume no constraints and no ‘overheads’ can be taken from the money.

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Chemical Shortcuts

I was writing some lecture notes this morning when it occurred to me that I’d probably never told my students of some shortcuts that are really useful. I was trying to draw structures for a synthetic route towards paclitaxel…trying is the operative word unless you are aware of what a SMILES string is and the fact that you can copy-paste that through paste-special in ChemDraw and other programmes and the structure will be drawn for you. In the case of paclitaxel derivatives, that’s hours of pain reduced to seconds of smugness.

The best source of SMILES or InChI strings is ChemSpider (www.chemspider.com) that has all kinds of useful information as well as that bit. What I didn’t know before writing this post was that SMILES (apart from creating a great many smiles at the sheer simplicity of complex structures) stands for Simplified molecular-input line-entry system, and InChI, International Chemical Identifier.

Another simple trick when looking for scientific journals (or making quick references in work ahead of proper referencing) is to copy-paste the DOI of the article rather than the reference. Digital Object Identifiers (http://www.doi.org/) are found on most reputable articles (and probably most disreputable ones as well, but hey) and can be a very quick and easy way to keep tabs on references electronically. They are found on most journal articles, their websites on the publishers site, and are readily googled to find the full text.  Of course, they do not replace the proper reference in the desired format but they do make wrangling a reference collection in early drafts much easier.

I can’t think of any more at the moment – any suggestions?

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

REPOST:The Ritualistic Nature of Literature Searching

I’m reposting this today as I’ve got a session with our 2nd years on information literacy this afternoon. We’ll be covering Web of Science searches along with other hints and tips for wrangling the scientific literature.

First published February 9th, 2009 on v2.0…

It has just gone 8.30am and on this snowy Monday morning I have reached my desk, set my shoes to dry on the office radiator and booted the computer. Before I make my first cup of tea of the day, I’m blogging. Procrastination? Actually, no, let’s call it a plea for help.
The first thing I do on Monday mornings is log into Web of Knowledge and search for ‘dendrimer’ with Latest(current)week setting. I know, you’re thinking that there is nothing unusual about this. Perhaps you’ve seen my profile and noticed that part of my research is to do with these dendrimer things. It is only natural that I’d search for recent papers published that may be relevant. No, the problem is that I do this every Monday morning that I’m at a desk with a computer, and I have done this ever Monday morning (except for holidays and brief unemployment) since the turn of the millennium.
It has never occurred to me to automate this search in any way, shape or form. It has, if I may suggest such a thing, become a research related ritual. The difference this morning is that it struck me as odd.
As keyword searches go, it is pretty lousy. One lonely keyword spanning a whole subfield of chemistry. No specification for biomedical applications, or environmental metal stuff, no acknowledgment that other keywords may yield relevant results (for example: polymer, hyperbranched polymer etc), and that combinations of them may be quite efficient.
It doesn’t work, yet I do it weekly. One task for today: find a better way! Will update later…

Posted in Academia Nuts, Chemistry, Publications | 14 Comments

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!

Posted in Chemistry, lab mahem | 2 Comments

On the process of doing research.

Question: if you are the first person in the known universe to attempt a reaction, why on earth would you assume that the reaction has worked and progress to the next step without characterising your product fully?

I appreciate that undergraduate labs are often ‘illustration of concept’ labs that have been designed and further refined to work properly with only a tenuous link to experimental technique, but there seems to be a major logical gap between the idea of carrying out research and verifying that the experiments have worked. This comes up from time to time with students and it always makes me stop and wonder what’s going on. And where’s the curiosity? Where is the drive to prove that you were the first to do a reaction and here is the best possible evidence to support that? That’s probably more to do with ego than curiosity but still.

I suppose the flip side is far bleaker – when did I become more cynical that my working assumption is that a reaction has not worked ? And I assume that I need to analyse it fully to determine just how much it has failed before varying something and trying again! Perhaps the more optimistic approach is better, but then there is the disappointment…

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The role of repetitive examples: practice makes perfect?

A few months ago, I read a journal article that I have subsequently lost track of. It was on cognitive demand/overload and related to calculations. If I recall correctly, it showed that the simplest type of calculation is essentially using an equation in its presented form (e.g. speed of light = wavelength x frequency) with all quantities in their most appropriate units and giving an answer in the most straightforward units. The most complex was then using multiple equations requiring manipulation with quantities in units requiring conversion and an answer requested in different units again. If there were more subtle points to the paper (or if anyone can recall it before I get to my office and see if I printed it for the file), please let me know.

It got me thinking, as do many such papers that present something that is perfectly logical once it has been pointed out to you. Mainly I was thinking back to high school maths where new concepts would be met with multiple examples of increasing complexity before any type of context has been applied. I thought I’d give this a go this year with my 1st year spectroscopy. We do a lot of equations and there can be a good amount of additional complexity added in through unit conversions and the like. For each equation (mainly the equations of light) I came up with exercise sheets that started with using the equation in the presented format with quantities in appropriate units. The final exercises involved rearranging the equation, and generally converting the units of the starting quantities and often the answer. These were uploaded to the class blog along with the answer sheet (numerical only) and highlighted to the students that were struggling a little more with the maths. Problem sheets and exam style questions were then used in workshops and for class test preparation that put the maths into the spectroscopy context.

I can see how this approach could be really useful for more complex equations – I’d suggest that most of my students tackle the exercises for IR vibrational frequencies, particularly getting practice at calculating reduced mass (kg people!).  I’m not sure, however, how this approach translates in to less mathematical areas of chemistry. It would work really well for organic mechanisms, and balancing equations, but not so sure about other bits.

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Handling Information

We place pretty high value on developing skills in information retrieval and handling frequently conflicting information in our curricula, but we’re not the best at it ourselves sometimes! My ‘mission’ over the past few months has been to reduce the duplication of effort in information we provide to our students. For example, our library operate an excellent reading list service and there is a convenient weblink to the reading list for each module. That reading list is frequently manually duplicated in module guides and in multiple lecture notes. Another example is deadlines for assessment. We produce assessment calendars for each year group with module, short title of assessment, mode of submission (electronic vs in person), date and time. But frequently that information is duplicated into module guides and elsewhere. The problem is that this means that everyone has to remember to go into multiple documents to update something if there is a minor change. I like information in one place so that it is easily updated and easily found by students.

I get a lot of email.  I struggle to sift through it but there are a few things I do automatically – I scan then ignore a great number of emails that come through generic mail lists. Of particular note are the announcement emails sent through Blackboard to update students. We send a lot of them! And that means that students receive a lot of them. If I assume that students get as many emails as I do, it is easy to see why they frequently don’t get the message.

I’ve been trying not to send as many whole class emails or announcements this year and I made a conscious decision at the start of the year to ask my students to communicate with me in different ways. Firstly I set up office hours because I’m not sure students always understand what an open door policy means, but also because it must be really frustrating trying to find academics who are naturally busy and not in all the time. So far few students have taken up the offer of office hours to come and ask questions. Secondly I decided to distribute all teaching materials through the blog function on Blackboard. I felt this would allow me to attach files (lecture notes, annotated lecture notes, problem sheets, exercises and answers)* and write brief comments and posts on the teaching material. I thought this would also let me embed videos, audio and other bits if I wanted to do pre-sessional activities. I also though it would provide a useful forum for students to ask questions about the course. Like most academics, I find that I can get the same question asked multiple times so I requested that questions be asked (via an anonymous comments feature) on the blog post so that everyone can see the answer. I’ll update on this in January when I have a whole semester of blog use to evaluate its effectiveness.

At this stage I have a few comments on Blackboard blogs, features that would make this type of use a lot easier.

1. The ability to alter post dates. This could be permitted through a setting in the options when setting up the blog. I appreciate that this is problematic if the blogs are being used for assessment but it would be convenient to be able to change posts to keep a course’s postings in a reasonable chronological order. I’m working around this by using placeholder posts [e.g. ‘summary of lecture will appear hear shortly’] when I need to upload more content.

2. The ability to schedule posts. My plan was to do a post per teaching session, attaching notes and including the information that would have gone in an announcement or email about what to bring to the session. After each session my plan was to post a summary of the key points of the session, any areas where more clarification was required, annotated lecture notes and exercise sheets as appropriate.  With the exception of the annotated notes and points of clarification, it would suit the way I work better to be able to write these in advance and have them appear. Actually, if I could schedule posts, I probably wouldn’t issue PDFs of annotated notes and would just leave the powerpoint download that can be obtained in the Camtasia produced screencast of the lecture. Scheduling would also be really useful generally.

3. Tagging, keywords, categories or something like it. It would be nice to tag posts with keywords to help students find information. Specific words like ‘exercise’, ‘answers’ and terms for the course ‘NMR’, ‘IR’ etc would make the blogs a lot easier to navigate.

4. A really quick way to see if comments have been made and get to the post to reply to them easily.

I like many of the features that I can access – I find the interface easy (not dissimilar to the other blogging or CMS platforms I use), I like the easy inclusion of audio clips, and the simple upload and attachment of files. And I like having one place to put everything – otherwise it is upload this file to that folder, another file to a different place, got to the announce feature or email to make a message…

*My lecture screencasts are not uploaded to the blog. They are put in the single Blackboard folder required for my teaching.

 

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Two-thirds to go!

As my colleague Dr Rob Jackson has just reminded me by way of a blog post, the semester is 1/3 over! He has a great picture on his blog related to his Forensics Arson course. My current crop of courses simply cannot compete with that!

This is week 5 and yesterday was ‘super Tuesday’. I had 6 hours of teaching and a student staff liaison committee meeting in a row without a break. I started at 10 am with 1st year NMR for 2 hours. We looked at the basics but focussing on interpreting proton NMR through coupling and integration alone. For some reason the minute chemical shift tables appear, all the knowledge about coupling and integration fly out the window so they are banned while we learn about the basic theory. Then I had 3rd year inorganic reaction mechanisms and we went through some more things that are important when considering octahedral complexes. That was an hour and was  followed by our first Student Staff Liaison Committee of the year. After that, it was two hours of Industrial Chemistry with our Single Honours 2nd year class. We were looking at the role of Green Chemistry in synthesis and the benefits beyond environmental gain of ‘greening’ reactions. That session finished with us going through the guidelines for the Industrial Chemistry Module’s big assignment – a 2000 word essay in the style of a Chemistry World Type piece.

Today is slightly less hectic – 2nd year polymer chemistry presentations. The students had free choice of topic so it should be interesting. And there are biscuits…

 

 

[In week 11 I have ‘super Friday’]

Posted in Chemistry, Teaching | 1 Comment

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
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Posted in lab mahem | 5 Comments