Chemistry Blog

May 19

A tale of a tired lecture course. Flip it.

It dawned on me that no one cared. The proteins that I found so fascinating just didn’t seem to intrigue them as much as they did me. I thought the video of water molecules flipping as they passed through the channel of aquaporin was marvellous. But it hardly gleaned a reaction from the sea of faces staring blankly out at me. 

Screen Shot 2015-05-19 at 14.42.33

I left the lecture theatre and trudged back to my office. Wondering what was to be done with the course I’d tinkered with for years and never been happy with. Maybe it was time to just stop tinkering, throw it all away and start afresh?

The thought drifted away as I flicked through the, not insignificant, pile of emails that had dropped into my mail box during my brief absence from my desk. Top of the list was request to review a grant proposal.

And then inspiration struck, I could get my students to write grant proposals! That way they could explore the ideas and material that they are interested in without having my predilection for Major Intrinsic Proteins foisted on them.

So I set about a total revamping of the course.

  • The lectures slides went in the bin.

Well actually they got turned into screencasts. But they might as well have gone in the bin, because the students don’t watch them.

  • I gave the students examples of grant proposals that I’d written (ones that had got good reviews, even if they hadn’t been funded :-( ).
  • I supplied them with a load of references to papers that contained neat ideas.
  • And I gave a lecture with avenues of research that I thought were intriguing.
  • Then I provided them with a slightly altered version of a research council’s form and told them to complete it i.e they had to write a case for support, lay summary, justification for resources etc.
  • They worked in groups of 6-7 and set about their tasks.
  • The rest of the lectures I turned up to check on how things were going, guide the projects, tell them what I thought might work or not etc.
  • And come the end of the course I marked the proposals based on genuine research council criteria AND each group peer reviewed 3 other proposals using the same criteria. Group members also gave an effort mark to each other (so free loaders didn’t get an easy ride). And the final mark was made up from an amalgamation of my mark, the peer review and the inter-group mark.

The results were great. Some really fabulous ideas sprung up. I’ve had students ask me if they can actually work on their research projects during their final year dissertations, and I bet some of proposals would have made the quality cut off in real funding rounds.

Right, enough from me, I’ve just come across a great idea for a project I need to get into the next funding round. ;-)

May 08

Campaign for Clear Code starts here!

I’m concerned about the software that’s installed on my electronic devices.

You should be worried as well.

Have you really considered what you are opening yourself up to every time you download a new app or install an upgrade?

Have you thought about what all those faceless software giants are doing with the code that they are busy sneaking onto your phone?

Do you have any idea what they are slipping directly into your pocket? It certainly isn’t good for you. After all its not you they care about. All that really concerns them is profit, pure and simple. They want you coming back for more, why else would they make those damn games so additive?

Screen Shot 2015-05-08 at 21.26.12

And has that code even been tested properly? They claim it has, but why then does big software continually release patches and updates?

Just stop for a minute and ask yourself this. Do you really know what you are putting on your computer when you downloaded Candy Crush? Have you ever seen the code?

Take a look at this.

if(tic[f][z]==’ ‘)
goto x;

Understand it?

No, me neither.

Want to know where that snippet of code came from? Its just a small part of a computer program for tic-tac-toe. And if a game as simple as that has stuff like that in it then imagine what’s in Candy Crush, Angry Birds or even Powerpoint?

And it gets worse. Because some computer programer, in the pay of cooperate giants, writes this sort of thing before processing it into something that might not even contain recognisable words! The software companies call this ‘compiling’ and afterwards its bears no resemblance what-so-ever to the natural code.

I, for one, won’t stand for this sort of thing being foisted on me by big-software any longer.

Now is the time to take a stand.

I call for a campaign for clear code.

Basically, if a 10 year old child can’t code it then it has no place on my devices.

From this point onwards I’m reverting back to simple code that anyone can understand. I’m using nothing more than Scratch running on a nice wholesome Pi. I urge you to do the same.

And don’t even get me started on anti-virus software. Much better to share infected USB sticks around.

May 05

What has Chemistry got to say?

The XKCD comics have been keeping me entertained and informed for years.

But sadly, in the latest comic, Chemistry seems rather quiet.

So how about some suggestions for the next panel, where Chemistry finds a voice?


Apr 30

Reagent pencils, turning chemistry into child’s play

If you’ve ever sat opposite a doctor and wondered what she was scribbling on her notepad, the answer may soon not only be medical notes on your condition, but real-time chemical preparations for an instant diagnostic test.

Thanks to the work of a team of researchers from California Polytechnic State University, recently published in the journal Lab on a Chip, chemicals formed into pencils can be made to react with one another by simply drawing with them on paper. The team may have taken inspiration from colouring books for their take on a chemical toolkit, but their approach could make carrying out simple but common diagnostic tests based on chemical reactions – for example diabetes, HIV, or tests for environmental pollutants – much easier.

The project started with an established technique called paper-based microfluidics. This uses the capillary effect of paper to carefully mix together what are called reagents – those chemicals mixed to form a reaction, or to measure the presence or absence of a substance. The capillary effect in action is easily seen by dropping two inks of different colours onto a piece of tissue paper. As the liquid is absorbed by the paper the colour drops spread out until they merge with one another and form a colour blend. In the same way two or more reagents can be mixed with water on a strip of paper.

Colouring-in chemistry.
Lab on a Chip/RSC

In this case, the difference is that the reagents aren’t added to the paper via droplets. Instead they’re applied via pencils, meaning that without specialist equipment anyone can set about creating chemical reactions by simply using them on the paper.

The team made the reagent pencils by pulverising a mixture of graphite (just as you’d find in normal pencils), test reagents and polyethylene glycol, which helps to keep the reagent dispersed throughout the mixture, as is used for the same reason in toothpaste. They compressed the mixture into pellets and mounted them into mechanical pencil holders bought from the high street stores.

The reaction paper pad was created by using a waxy ink to print small connected enclosures onto filter paper. The reagent pencils could be used to colour in these areas within the enclosures – when water was added to the paper, the reagents dissolved and, confined by the waxy ink, were forced to diffuse towards one another and react.

Real world uses for real world problems

The team demonstrated a potential use of the reagent pencil technique by using it in place of a common test used by diabetics to check their blood glucose levels, which involves reacting a pinprick blood sample with a chemical solution and examining the result.

One pencil was constructed with a mixture of enzymes, one called horseradish peroxidase (HRP) and the other glucose oxidase (GOx). A second pencil contained a reagent called ABTS. When combined in the presence of glucose these react together to give a blue-coloured product. Comparing the results from their pencils on the pad with the more traditional dropper method used by diabetics the team found the results were identical.

An example of how chemical reactions using pencils can provide instant results.
Lab on a Chip/RSC

The image shows, on the left, the reagents applied via droplets of solution. On the right, the reagent pencils were used. The top row shows the paper at the beginning of the test, the bottom row the result. Applied to the left enclosure, the sample solution carries the two reagents together which react. The coloured product produced is, as shown on the graph, identical between the two methods.

This is of course extremely easy to set up. Traditional diagnostic tests require training, while this pad and pencil system requires no more than skill than required to colour within the lines. The reagents are extremely stable once made into pencils – usually they would degrade in a matter of days as liquids, limiting how and where the tests can be made. However the reagent pencils showed no sign of degrading after two months.

So this pencil tool kit has obvious advantages: a kit of reagent pencils, much like a box of colouring pencils, is easily transported, without the chemicals degrading. Kits could be designed with particular tests in mind – and the reaction mix can be adjusted by applying more or less, without the need or equipment to make-up complex solutions. There’s scope to monitor environmental pollutants, carry out diagnostic tests in remote locations – not to mention teach chemistry in primary schools.

The Conversation

This article was originally published on The Conversation.
Read the original article.

Apr 29

The Food Babe quiz. Can you tell Vani Hari quotes from other irrational nonsense?

By now I’m sure you’ve all seen the ravings of Vani Hari a.k.a. Food Babe. Her one women campaign to spread fear through nonsense has netted her (in)fame, fortune and influence. Not to mention a pretty strong back lash from the rational side of the internet.

So to test if you’ve been paying attention I thought I’d set a little quiz.

All you have to do is identify, in the list below, genuine Food Babe musings mixed with other random nonsense.

Answers at the bottom of the page.

So here goes, with a nice game of …

Food Babe or Not Food Babe.

1) There is just no acceptable level of any chemical to ingest, ever.

2) Chlorophyll is the first product of light and, therefore, contains more light energy than any other element.

3) Please consider removing this additive from your diet because artificial dyes…Are man-made in a lab with chemicals derived from petroleum (a crude oil product, which also happens to be used in gasoline, diesel fuel, asphalt, and tar).

4) Your brain uses more oxygen than any another organ. If you need to concentrate it is important to keep you oxygen levels high .… Green leaves produce oxygen so if you need to study eat plenty of leafy vegetables to keep that brain well oxygenated.

5) When you look at the ingredients, if you can’t spell it or pronounce it, you probably shouldn’t eat it.

6) With a name like 8-methyl-N-vannillyl-6-nonenamide it’s bound to be a baddie. If you want more evidence of its unpleasantness then you may like to know that it is used by the police to control rioters.

7) Mass produced bread contains Potassium Bromate. Its used to help make the bread light and fluffy. Bromates have been banned as fire retardants in furniture, so how come its still used in the food we eat!?

8) Wheatgrass … is more than 70% chlorophyll which is essential for improving blood sugar problems.

9) For the experiment pictured above, microwaved water produced a similar physical structure to when the words “satan” and “hitler” were repeatedly exposed to the water.

10) You all know that we breath out carbon dioxide. But did you know that it’s an acid? … Whenever I’ve been in a crowded place I cleanse myself of the effects of all that acid breath with a good dose of Spirulina.

11) North Americans deserve to truly eat fresh – not yoga mats.

Credit: Fraud Files

How did you think you did? Here’s the answers.

1) Genuine Food Babe. An easy one to start with. You can find this little gem in her book. Don’t go out and buy it now.

2) Food babe again. Apparently wheatgrass is a miracle.

3) Food babe. Those nasty men in labs.

4) Not Food babe. Just me trying to channel Gillian McKeith.  

5) Food babe. But how are my fellow dyslexics and I going to eat?

6) Not Food babe. That one was me, with tongue firmly in cheek.

7) Not Food babe. Just random nonsense I made up, but sounds good doesn’t it?

8) Not Food babe. This gem came from the menu of the health food cafe I dinned in recently.

9) Food babe! Honesty, has she no shame? We’ll actually she might, since she’s removed offending post from her blog. But luckily the internet forgets nothing.

10) Not Food babe, I just made it up. But Vani does have some odd ideas about Spiriulina.

11) Food babe. What about fresh yoga mats? 

How did you do? Tell use you scores in the comments. And play along on twitter with #FoodbabeOrNot

Apr 18

It’s time science reclaimed health food from the quacks


IMG_0189I’m not quite sure what came over me, I’d set out in search of a beer and a burger. But somehow ended up in a juice bar wolfing down falafel, quaffing a cucumber, celery, ginger smoothie and sprinkling sweet potato chips with some strange pink salt.

And it was good. Really, really good. Tasty, satisfying and altogether wholesome.

Whilst I mopped up the last of the beetroot ketchup with my rye bread and slurped the dregs of the green juice, I flicked through the menu, idly wondering why the salt was pink. Tucked away on the back page I found the info I’d been looking for.

Apparently it was Himalayan pink salt.

What I read next pretty much ruined the whole dining experience.

Himalayan Pink Salt

This is a natural salt not like white table salt, which is a drug. Pink salt is extracted from the Himalayan mountains. It is negatively charged helping to draw positive ions out the body.

I sat paralysed. And wondered if this was due to my dinner having been laced with this strange substance that had removed all the ions essential for nerve impulses.

I regained enough movement to flick on my phone and Google the credentials of Himalayan salt. My panicked state subsided. For it is 98%, good old, sodium chloride, 2% polyhalite and a smidgen of rust (hence the pink tinge).

Once my composure had returned, I continued to flick through the menu. It was laced with plenty more pseudo-scientific claptrap.



At this point I was starting to wonder if the place was run by Food babe. I rapidly made my exit and went in search of a stiff drink.

In the pub down the road, over a nice glass of single malt I got to thinking. The food, service and atmosphere in the juice bar had been great. Their products really were healthy. There was no need for the pseudo-science. Especially since genuine science about their ingredients is actually really interesting.

So I say to you Juice bar (and I will write to them) “Why not redraft your material with real science? I’ll even help you do it.”.

And if that doesn’t work, how about someone out there starts a health food cafe which doesn’t shy away from hard science, where real evidence prevails, where they tell you why the salt is pink, what chlorophyll actually does and how to eat a healthily diet. Wouldn’t such a place be more credible?

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