A while ago I wrote a blog post about a molecule I was particularly fond of as part of a chemistry meme (May 2010 http://www.possibilitiesendless.com/?p=186). I will not name the molecule for reasons that will become clear later. About 7 months later I noticed that my blog was getting a number of hits from people searching for the formula of the molecule in question, the synthesis and characterisation of which formed part of my laboratory course in spectroscopy. More to the point, those queries, coming from my university for the most part, were framed exactly like the questions that I’d written in the pre-laboratory exercise for the experiment.
OK, so what’s the big deal? Student use search engines to look up information for assignments.
Well, actually that is a big deal. Firstly the assignments in question were not about information retrieval from the internet, they were about using basic chemical skills and information that most students should know. Secondly, the information the students were seeking online was, at best trivial, at worst, demonstrating an alarming lack of effort or understanding on their part. It seemed to me as if I had set a question that was unreasonably difficult or that the students lacked the knowledge to answer it.
That sound fair enough though, doesn’t it? People should be allowed to look hard stuff up online.
Yes generally, but in this case the students had been supplied with a picture of the molecule (coloured ball and stick, with key to decipher the colours). The question was simply to write down its molecular formula. All that was required was to count the number of pink, purple, black, grey and blue balls in the picture and write them in the standard form.
I decided to take some action. I searched for the name of the compound and realised that my original blog post was the number 1 hit. I created another blog post (October 2010: http://www.possibilitiesendless.com/?p=400) and gave some instructions on how to complete the task: “You have a picture of the molecule in your lab manuals, and also in colour on the [electronic] version of the lab manual. It may be old fashioned, but I suggest you try counting the atoms to try and figure out the formula”.
This year has seen a massive increase in the number of hits to my blog searching for this compound and the range of queries has broadened from the one above to include almost all aspects of synthesising and characterising this material. I’m a little intrigued by the motivation of the students who do this. Are they simply looking for reassurances that their answers or interpretations of data are ‘correct’? Are they too lazy to think for themselves and looking for a source of information to reword as needed? Do they not understand aspects of the tasks and so need additional support? Is the lab manual unclear as to the requirements? Is it easier to search for data than to interpret it themselves? These questions form two broad categories, one in which the terms of the assignment are deficient, and one in which the deficit lies with the abilities and/or attitudes of the students.
I should probably note at this point that I’m not seeking to criticise the students for using the internet to help with assignments, more to understand what motivates them to use it and to try to correct which ever deficit exists. If I could work out where the deficit lies, then I’ll be happy to start criticising.
More broadly however, the chances of me noticing this kind of behaviour are quite slim. It is only because this experiment is not widely carried out in undergraduate laboratories that I even noticed the hits. My reasoning for this is simple: search for ‘synthesis of aspirin’ and have a look at the information available. No thinking required what so ever to produce a write up of that experiment, and it is even possible to download completed lab reports on the topic for modification. If we assume the behaviour I have observed is normal for our students and happens for most lab assignments then we should seriously consider the nature of those assignments. The key question should be: what percentage of lab marks in any given assignment can be achieved by sourcing information from the internet and regurgitating it into the report? What percentage of marks can be gained by simply recognising that a diagram or webpage contains the answer to the question and reformatting it? And if we want marks to be awarded for thinking and demonstrating understanding of the techniques and procedures involved, how do we encourage students to do so without help from the internet?
It is clearly unnecessary for students to memorise vast quantities of facts in order to graduate. Information handling (retrieval, processing, whatever!) is a vital skill and one that graduates should be able to do, but not as a shortcut to avoid thinking or asking for appropriate help. I want to say something like ‘good students don’t google’ but I have no evidence to support the statement – I don’t know which students are doing it. For now I shall content myself with the notion that my lab assignment is not the synthesis of aspirin, that the quantity of information available on the internet is incredibly small for this particular experiment, and I shall bare this experience firmly in mind as I develop a couple of new experiments for next semester. I will be googling the questions as I set them and working out what percentage of marks will be available to reward that behaviour. It will be as low a percentage as I can possibly make it.
University of Great Britian, Faculty of Physical Sciences: Course Proposal Form
Proposed Title: FFS-101 Future for Scientists: Prognostication
Purpose and Reason for Introduction: The purpose of this course is to equip students with the ability to predict the future using a variety of techniques and to appreciate the inherent error in such methods. This course has been introduced in response to requirements for academics to assess the National Importance of research work over a 10 – 50 year time span when applying for research grants from certain funding bodies. The course team realise that the existing physical sciences course lacks adequate training in prognostication and this course is therefore compulsory for all students wishing to pursue a career in academia.
Intended Learning Outcomes:
1. Gain an appreciation for and describe a range of prognostication techniques available including, but not limited to: tarot card reading, astrology, hepatomancy (reading entrails), Mayan prophecy.
2. Understand, describe and explain the limitations of prognostication in the current research climate, and sources of major and minor errors such as climate change, changes in policy, and changes in Government.
3. Describe and explain the results of a prognostication activity with a specific research goal in mind in a written report of suitable format for inclusion into a research grant application. (Formative Assessment)
4. Successfully complete the outcomes of a practical course involving hands on experience of a variety of techniques* taught by academic staff and guest lecturers.
Assessment:
Formative Assessment: As per learning outcome 3. Students will receive feedback from staff 2 weeks in advance of the deadline for this assignment.
Summative Assessment: 50 % final exam; 50% written report based on students own prediction of module grade using one or more of the techniques in the practical course.
*Please note that the hepatomancy class will be held in the afternoon, however due to the nature of the specimens under study, students are advised to avoid lunch, particularly processed meat products.
“Launch of the Chancellor’s Circle
The Circle has been established to recognise the generosity of alumni and friends who have remembered the University of St Andrews in their will. All members of the Circle will receive donor communications and an invitation to special Chancellor’s Circle events. The launch, presided over by Chancellor Sir Menzies Campbell as the President of the Circle, took place in London in early November.”
From ‘St Andrews in the News’ November 2011, University of St Andrews Alumni Email.
Hmmm, something about the wording above isn’t quite correct…
When it comes to life after a degree, some of the most common questions I’m asked revolve around PhDs. Most undergraduate students have no idea what doing a PhD involves, let alone the standard of work required to get one, and yet it seems to be an appealing option for career planning. How do you know you want to do something when you don’t know what it involves?
On one hand I can understand – you’re surrounded by people working towards, or with PhDs during your undergraduate degree, so perhaps you want to be like them. On the other hand I have no idea why someone would want to do something that requires so much hard work without knowing what they are getting themselves into.
I struggle to give advice on PhDs. I can give reasonable advice on where to look for one, good questions to ask potential supervisors and the time of year to be looking. I can give some information on likely entry requirements but will not give my opinion on whether someone is capable of doing a PhD. It is simply not for me to judge someone else’s motivation and answer in a way that cuts down their dreams. And I think motivation is key in doing a PhD. I can explain the mechanics of doing a research degree, the requirements for a thesis and give examples of the struggles that students generally face along the way. I can state clearly that I believe a PhD is an means to an end, to a career or something, rather than an end in itself. But I struggle to really convey what is required.
Fundamentally ‘doing a PhD’ is about creating new knowledge. This is best demonstrated through the learning outcomes for the appropriate level of the UK National Qualifications Framework (http://www.direct.gov.uk/en/EducationAndLearning/QualificationsExplained/DG_10039017)
“Doctorates are awarded to students who have demonstrated:
i the creation and interpretation of new knowledge, through original research, or other advanced scholarship, of a quality to satisfy peer review, extend the forefront of the discipline, and merit publication;
ii a systematic acquisition and understanding of a substantial body of knowledge which is at the forefront of an academic discipline or area of professional practice;
iii the general ability to conceptualise, design and implement a project for the generation of new knowledge, applications or understanding at the forefront of the discipline, and to adjust the project design in the light of unforeseen problems;
iv a detailed understanding of applicable techniques for research and advanced academic enquiry”
(emphasis added, Quote taken from Keele’s code of practice for research degrees, page 35, http://www.keele.ac.uk/media/keeleuniversity/graduateschool/PGR%20CoP%20April%202011.pdf)
At first it seems strange to see something as tenuous as research as a series of learning outcomes, but after some thought and consideration of some of the things a lot of doctoral students are told by their supervisors, it makes sense. For example, a lot of students are told that in their PhD viva, they will be the world expert on the (fairly focussed and narrow) topic of their thesis. The literature review chapter of the thesis is the way of demonstrating ii, and the methodology sections demonstrate iii and iv. Are these easy for a final year undergraduate student to grasp? Perhaps not, because it isn’t immediately clear how doing research in a final year project differs from doing research towards a PhD. Superficially they are the same but at some point during the first year of the PhD, the student has to take ownership of the project and move from working for the PhD supervisor to working in collaboration with them, using their advice and knowledge to improve on their own ideas. In many cases that’s a matter of survival for the student – very few supervisors have the time or inclination to be intimately involved with every experiment designed, every set of data generated. But you can bet your life on the fact that they know a well designed study when they see one, and good data when shown it. The student is the one doing the reading, with the time and incentive to carry out a full search of all available literature (and not just those items easily accessible via electronic journals!), and has to take responsibility for the project.
Of course, some projects vary from this model. Industrial projects may be more prescriptive due to the demands of the funding. There may be less room for the student’s creativity to develop the research in new directions and more requirements for them to complete tasks on time and to a satisfactory standard. There’s still room for developing all of the skills because if there isn’t, they are no more than laboratory technicians and cannot fulfil the above criteria.
How do you convey all of that to a wannabe PhD student? It’s like your final year project but much harder and you’ll have a lot of responsibility. Treat it like a job, not like being a student. You’ll have to work harder than you think, and often harder than you want to. You will hate it at times, you will love it at times and a lot of the time what you are doing probably won’t work for a variety of reasons. Your success will be so reliant on your ability to find and process relevant information from the published literature, attain mastery of the various techniques needed and design good, robust scientific experiments that produce publishable results, that most failures will feel intensely personal. And you have to do all of that in three years, probably on a budget of some description (money, access to equipment, hours in the day). There is no time to do rough work with the aim of repeating it properly at some point in the future. Think of the hardest assignment you’ve ever had at university and a PhD studentship will be, and should be much harder. Still interested?
Below I’ve listed the key elements found in a common item as mass percentages. See if you can guess what this is! If no one gets it within 24 hours, I will post a clue. If you guess on Twitter (@kjhaxton), please DM your guess so others can play.
Oxygen 65 Carbon 18 Hydrogen 10 Nitrogen 3 Calcium 1.4 Phosphorus 1.1 Potassium 0.25 Sulfur 0.25 Sodium 0.15 Chlorine 0.15 Magnesium 0.05 Iron 0.006 Fluorine 0.0037 Silicon 0.002 Rubidium 0.00046 Strontium 0.00046 bromine 0.00029 Lead 0.00017 Copper 0.0001 Aluminium 0.000087 Cadmium 0.000072 Cerium 0.000057 Barium 0.000031 Tin 0.000024 Iodine 0.000016 Titanium 0.000013 Boron 0.000069 Selenium 0.000019 Nickel 0.000014 10 Chromium 0.0000024 Manganese 0.000017 Arsenic 0.000026 Lithium 0.0000031Caesium 0.0000021 6e-6 1.0e-7 7e18 No Molybdenum 0.000013 Germanium 0.000005 Antimony 0.000011 Silver 0.000001 Niobium 0.00016 Zirconium 0.0006 Lanthanum 8e-7 Tellurium 0.000012 Gallium 7e-7 Yttrium 6e-7 Bismuth 5e-7 Thallium 5e-7 Indium 4e-7 Gold 0.000014 Scandium 2e-7 Tantalum 2e-7 Vanadium 0.000026 Thorium 1e-7 Uranium 1.3e-7 Samarium 5.0e-8 Tungsten 2.0e-8 Beryllium 5e-9 Radium 1e-17
Below I’ve listed the key chemicals or elements found in a commonly available product, which may (or may not) be slightly UK-centric. All chemicals drawn below are part of the same product. I’ve drawn the chemical structures of principal components where simple and appropriate; given the E number or CAS number (however tempting Sigma-Aldrich catalogue numbers would be) if no simple chemical structure exists for an additive; and given the chemical formulae or name if neither of the above make sense. See if you can guess what this is! If no one gets it within 24 hours, I will post a clue. If you guess on Twitter (@kjhaxton), please DM your guess so others can play.
A few years ago while living in Vancouver we returned to our basement apartment from a day’s shopping. After about 5 minutes we felt our throats were very scratchy and our eyes were burning and we couldn’t really work out why. There was no obvious odour in the apartment although it was perhaps colder than usual. We opened the outside door and all the windows and ventilated the place for an hour or so. A few hours later, our neighbour came back. Both apartments shared the same outside door and hallway. He looked a bit sheepish as he explained that he’d been camping and while unpacking his backpack had let off a can of bear spray.
Bear spray is an aerosol form of Oleoresin Capsicum which is an oily residue from chili peppers, preferably hot ones. It contains compounds like capsaicin, the substance in chili peppers that burns. Bear spray affects the bears in much the same way we were affected but hopefully to greater effect if sprayed into the face. Pepper sprays are similar in nature using oleoresin capsicum and may be called OC sprays. They are supposedly non-lethal weapons and may be used in crowd control in some countries but are illegal in others. They are related to tear gasses which make use of lachrymators (chemicals that cause tearing). OC spray may cause tearing amongst other effects. All are technically chemical weapons so consider that the next time you need bear spray for a camping trip.
What Am I this week was indeed a form of pepper spray – bear or OC spray, take your pick. The large organic molecules are capsaicin and derivatives, propylene glycol as an emulsifier and water as a base.
Capsaicin has other uses and may be used medically as a topical ointment. For example some of the LaKota products use capsaicin. These products may be used for relief of pain from arthritis and other conditions. Not bad going for a substance that is usually a major irritation to people preparing chilli peppers for dinner.
Below I’ve listed the key chemicals or elements found in a commonly available product, which may (or may not) be slightly UK-centric. All chemicals drawn below are part of the same product. I’ve drawn the chemical structures of principal components where simple and appropriate; given the E number or CAS number (however tempting Sigma-Aldrich catalogue numbers would be) if no simple chemical structure exists for an additive; and given the chemical formulae or name if neither of the above make sense. See if you can guess what this is! If no one gets it within 24 hours, I will post a clue. If you guess on Twitter (@kjhaxton), please DM your guess so others can play.
This is the end of week 2 of the semester. The first week was not a proper ‘freshers week’ per se, but a week of induction talks, meeting with personal tutees, new project students (all 5 of them!!) and laboratory safety talks. I ended up doing the 1st year lab safety talk and the 3rd year project lab safety and lab rules talks. I’ve postponed the 2nd year lab safety reminder talk for a few weeks, until they’re just about to start lab work again. I’ll start working on it on Monday.
One thing that struck me was how different the 1st year and 3rd year talks were. The 1st years are hitting the lab for the first time with us and we’re not making too many assumptions about prior lab experience – it’s easier to include everything. I also feel with the 1st years that safety is more about going through the motions and following a set of rules, than evaluating risks effectively. For example we’re asking all of our first years to fill out COSHH/Risk assessment forms for the first 5 experiments. Last year we gave them the forms and asked them to read them, but in any case, the lab manual contains good information on safety and the lab briefing will emphasise it. The experiments should also be fully assessed by the lab staff so we’re leaving little to chance. That’s how it should be while students learn to evaluate risk.
The 3rd year talk was a bit different. As the majority are doing synthetic research projects and are involved in planning reactions for the first time, this talk focussed more on the types of risks that need to be thought about. It isn’t quite the level of safety talk you’d give to research students who could be completing far more hazardous procedures (quenching stills comes to mind), but it’s getting on for it. A lot involves emphasising good and courteous laboratory practice, as well as how to recognise and minimise hazards. And so much more involves common sense like clean up if you spill a substance on a balance, wash up and if you’re using stinky chemicals, don’t subject others to the stench. Common sense does seem to be a little less common than I’d like, particularly when it comes to cleaning up small spills.
The 2nd year talk? No ideas as yet, it is the difficult stage where they think they recall last years well so don’t want to be told stuff again, but need to develop their sense of risk awareness and hazard management. I’ll probably briefly remind them of the lab ‘rules’, and show them how to use the new COSHH form properly.
One thing that does occur to me is that reading MSDS can be a health risk in itself. While there is no doubt that they contain valuable information on how to deal with incidents, storage and chemical incompatibility, much of the safety information is abstract and difficult to put into a relevant context. For example, an LD50 value is a difficult concept to translate from MSDS to hazard management for some of our students. There’s also risk blindness (similar to black note fever experienced by musicians when confronted with a page of very dense music manuscript) – the list of potential harmful effects often overrides the rational part of the brain and translates into ‘very very dangerous stuff, be very very afraid’. At that point nothing else goes in other than the ‘your kids will have gils, and you’ll probably die because of measuring out 20 mg of this stuff’. Seriously though, there are chemicals for which the hazard is very extreme and needs to be very carefully managed. And then there is the majority of chemicals encountered in a synthetic laboratory. I’m not trying to belittle risks, but respect is always better than fear, confidence better than nerves. Chemophobia is too pervasive within the chemistry community as well as the wider world and it gets in the way of getting good work done. If you want to put things into some perspective (but not to instill a sense of over confidence and marginal risk), look up the MSDS for some of the compounds in shampoo, or synthetic vanilla flavour, capsaicin, or the like. They make interesting reading, and certainally serve as a good reminder that common and accepted compounds* carry risk in sufficient quantity.
Another thing that struck me as I was preparing the safety talks is how few undergrad lab safety talks there are available on the internet – do we all just hide them away in the dark recesses of our virtual learning environments? Are we scared to make them public just in case something happens that the talk didn’t cover? I would have thought that prospective students and their families, and those of current students might quite like the idea of being able to see the safety requirements set out somewhere. Just a thought. And where can we actually share best practice for undergraduate lab safety?
*I try, where possible, to use the term compound rather than chemical. Chemical is far too abused and has too many emotional connections associated with it for it to really be used in any rational context. Part of me thinks we should just give up on the chemical = mostly everything argument against the chemicals = bad people. Chemists have generally accepted alternative definitions or uses for organic, effervescent or volatile (cf personality), crystallise (cf ideas), just like other branches of sciences have accepted that their jargon has been comandeered for less than dictionary defined purposes.
As the end of summer rapidly approaches and the start of semester looms like an unassailable mountain on the horizon, I have the urge to sit down and answer the age-old back to school essay question ‘what did you do over the summer’. I shall refrain for now, and console myself by answering a different question, posted by CENews on their International Year of Chemistry Blog for a chemistry blog carnival: what is your favourite reaction?
This question is very difficult, because everyone’s favourite chemical reactions should probably be those involved in respiration, the chemistry that keeps us alive, but there are also a whole host of fascinating and beautiful reactions that serve less practical purposes. Should my favourite reaction be something frivolous like the reaction that makes a firework go? Should it be something sensible that most of my research hinges on? Should it be the chemical reaction I do most often in the lab, or the one that works best? And in that initial panic of simply not being able to chose (frankly, a similar panic to that experienced when picking dessert in a very nice restaurant), my eye falls to an undergraduate dissertation sitting on the desk next to me. On the front cover is a wonderful image, created by the student, representing the goal of what was then a brand shining new research project (and also one of the first project students I supervised). The dissertation covers those first tentative and, let’s face it, largely unsuccessful first steps that break fresh ground in a new area of research. The dissertation, however, represents hours of work by an incredibly committed student and despite things not always working, she persevered. I should pick one of those reactions.
I’m going to pick a reaction that is simple to execute, welcomingly high yielding and from which incredibly beautiful structures can be constructed with a little effort. I’ll pick the Michael addition reaction of methyl acrylate and ethylene diamine in methanol. I’m specifying the solvent because my understanding of the serendipitous discovery of poly(amidoamine) dendrimers hinges on the addition of methanol giving an unexpected reaction product (figure 1).
The reaction above, producing the branched product, seems very straightforward, and it is. Some of my past project students may be smiling at this point because it is, in many ways, deceptively straightforward. Measure out the chemicals, mix, stir, and remove the solvent. For this first step it is easy, but then things start getting bigger and bigger until we end up with something that looks like figure 2.
Out of a very simple reaction (no, I’m not getting into the method) and its opposite, the addition of ethylene diamine to the terminal methyl ester, a very beautiful and symmetrical molecule can be created. As dendrimers go, this one is small which indicates the limit of my molecule drawing patience. This chemistry tests the patience of many – despite the high yielding reactions, they are not high yielding enough and defects start to creep into the structures. The odd side reaction becomes a big deal when those reactions are carried out hundreds of time on one molecule. There aren’t many occasions in chemistry where that is the case. And those dendrimers can be fiendish to characterise, trapping reagents and solvents within their arms, trying to get a decent looking (but broadly lumpy) clean NMR spectrum is an art form. That’s part of the fun though.
We don’t make dendrimers, we make dendrons (a 1/4 of figure 2 with reactive roots), but many of the difficulties of the synthesis still occur and trip people up.
So my favourite reaction forms amide or peptide bonds, similar to Carmen Drahl over at The Haystack (as I post this, the link isn’t working, I’ll double check later, it’s probably my end).
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