More Silly Science Songs

It’s time for another edition (edition 1 here) of “songs posted on twitter that I have reappropriated with stupid science lyrics“. Please enjoy/roll eyes/headdesk as appropriate. I’ve included YouTube links to the original songs this time, for those who don’t share my refined and highly sophisticated tastes in music.

 

Wuthering Heights Synchrotron Nights by Kate Bush – March 28

Out on the circley, light source floors
You diffract the x-ray beam
You had to work nights
I had jealousy
Too late, too sciencey

How could you leave me
When I wanted to
Watch BSG with you
I hated you, I loved you too

Bad dreams in the night
They told me it was just a really bright light
Leave me behind on synchrotron, synchrotron, synchrotron nights

Heathcliff, it’s me Cathy
Please come home
I’m so bored, let me watch that TV show

 

Just the Way You Are Be a Chromatographer by Billy Joel – March 25

Don’t go swagin’
To try and seal me
I’ve never sprung a leak before
I don’t imagine
You’ll lose your helium
I’d might not seal you anymore

I would not leak you
In times of trouble
We never could have flowed this far
I’ll take the noble gas, I’ll take the bad air
So you can be a chromatographer
 

Where the Streets Peaks Have No Name by U2 – May 13

I want to run I want to find
I want to identify the molecules that show up as ions
I want to reach out and touch the flame
Where the peaks have no name
I want to feel, the oven vent on my face
I see my sample disappear without a trace
I want to take shelter from the unknowns, shame
Where the peaks have no name

 

Nightswimming Titrating by REM – May 27

Titrating
Deserves a quiet lab

The standard solution in the fumehood
Made up years ago
Turned around backwards cos the label’s gone

Every titre
Reveals the indicator changes
The endpoint’s so much clearer

I forgot my labcoat at the benches edge
The burette’s low on titrand
 

You May Be Right by Billy Joel – June 10

Friday night I smashed your flasky
Saturday I said I’m sorry
Sunday came and trashed glassware again
It was just a reaction
Wasn’t hurting anyone
And we all worked through the weekend so no change

 

I’ve been stranded in the no yield zone
I walked the mass spec room alone
Even solved the NMR shifts in the rain
And you told me not to characterise
But I made the white crystalline
So you said that only proves that I’m insane

 

You may be right
I may be crazy
But it just may be the molecule I’m looking for
Turn out the lights
Turn on the UV
You may be wrong for all I know
But you may be right

 

Young and Beautiful Topical by Lana Del Rey – June 25

Will you still cite me
When I’m no longer young and topical
Will you still cite me
When I am nothing but historical
I know you will

 

Heart Nanoparticle of Gold by Neil Young – July 1

I’ve been to Stanford
I’ve been to Harvard
I’ve crossed the ocean for a nanoparticle of gold

It’s citrate stabilised
It’s such a small size
Keeps me searching for a nanoparticle of gold
And I’m getting old

 

Running on Cooking Up Ice by Billy Joel – July 10

There’s a lot of tension in my home
The cancer’s building up inside of me
I’ve got all the symptoms & the side effects
Of imminent mortality

It’s not hard to understand that
My blue crystals are superior
In a world of pregnant wife and teenage son
My motives are ulterior

So I decided to start cooking up ice
Paying the price too long
Killing and scheming cos I’m cooking up ice
Where did my life go wrong

 

 


Long Hair Lab Hack

At the end of my recent glove post I mentioned that I wear my hair down in the lab, and was admonished for doing this (and rightly so). My reason for wearing my hair down to work is pure vanity, I prefer the way I look with my hair down and I’ve also found that wearing my hair in a ponytail all the time leads to a lot of breakages where the elastic goes which makes my hair look quite yuk.

But, what I didn’t mention earlier is that when I am doing ‘wet chemistry’ type activities in the lab I usually do have my hair secured away from my face. I want to share the way that I do this in case there are any other long-haired lab lubbers out there who have the same problems as me, like:

  •          Not carrying hair ties
  •          Not wanting to use rubber bands
  •          Generic laziness
  •          Extreme vanity

OK so here goes. How to secure your hair away from your face with a pen (or pipette):

  1.        Using both hands, sweep your hair into a ponytail
  2.        Keeping the ponytail straight, twist the entire ponytail very tightly (but not so tight that it kinks back on itself) in a clockwise direction
  3.        Coil the twisted ponytail around itself, starting at the base, to form a bun and hold the end with your left hand
  4.        With your right hand, grab a pen and with the pointy end skewer the bun. Start by incorporating some of the non-bun hair (see pic) and push/weave through so you skewer both ‘sides’ of the bun ring. Using some non-bun hair is important as this will help it be weighted correctly and stay secure for longer.

20140326_120630
I have used the (clean and disposable!) pipette here mainly to illustrate this point. It’s too long to actually be practical. I find a pen is the perfect length and it’s pretty much hidden when done correctly – see pic at the bottom.

 

Extra tips

  •          Instructions are for a rightie, if you’re a leftie do it in reverse I guess
  •          Your hair needs to be past shoulder length for this to work
  •          Make sure if you use a pen, that the tip is pointing upwards. If it’s pointing downwards you may end up drawing all over the back of your shirt (yes, I learned this the hard way).
  •          I suspect this might not work with super straight or fine hair.

 

penhair

Flawless execution of pen hair using this pen.

 

Let me know if you have any lab hair hacks!


Papes for the Peeps – Analysis of Antioxidants in Fuels

This is the latest in a series of posts where I attempt to translate my published research into a format suitable for a non-specialist audience.

My paper “Synthetic Phenolic Antioxidants in Conventional and Alternatively-Derived Middle Distillate Fuels Analysed by Gas Chromatography with Triple Quadrupole and Quadrupole Time of Flight Mass Spectrometry” was recently published in the ACS journal Energy and Fuels (paywalled).

This piece of work describes two new methods for determining antioxidant compounds in jet and diesel fuels. Antioxidants are added to some fuels to stop the fuel reacting with oxygen while in storage. When fuels react with oxygen, they can become unsuitable for use and cause engine problems. Although these antioxidants serve an important purpose, they are only permitted to exist in the fuel up to a certain concentration. Sometimes, if a fuel is suspected to be reacting with oxygen, the users might want to add antioxidant to stop the fuel from going bad – but if they don’t know how much antioxidant is in there (if any), how will they know how much to add without going over the limit?

The antioxidants are present in the fuel at very low concentrations, which makes it difficult to measure them without the bulk of the fuel interfering in the analysis. It’s possible to extract the antioxidants from the fuel, which then makes the measurement easier, but the extraction process is often long, resource intensive (uses lots of solvent) and frequently doesn’t work well enough. My laboratory recently acquired two new GC-MS (gas chromatography – mass spectrometry) instruments with advanced detection systems so I decided to see how these instruments would go at detecting antioxidants in fuels at low levels, and without any sample treatment.

SPA1

Left: generic structure of these antioxidants, where ‘R’ can represent a methyl or tertiary butyl group in 1-3 of these R positions. Right: BHT, a common antioxidant used in fuels, foods and other products, where the R group opposite the OH is a methyl and the two R groups adjacent to the OH are tertiary butyl.

 

I have posted before about how gas chromatography and mass spectrometry work, and in this study it is the mass spectrometers that play a key role in the detection of the antioxidant compounds. The two different instruments I used are able to exploit different characteristics of the target molecules, in order to detect them at low levels, without interference.

Triple Quadrupole (QQQ) MS

The QQQ achieves excellent sensitivity by fragmenting molecules in the mass spectrometer more than once. For example, using the antioxidant shown in the picture above, the spectrum for this compound is

 qqq1

Which means that ordinarily, I would use the strong signal from the ion with a mass of 205 to look for this compound. But fuels have so many other moelcules in them, that there are loads of other compounds that also generate a signal at 205 and these swamp the signal from the target compound. So I can program the QQQMS to collect the strong ions, and perform another fragmentation on it. This generates a new mass spectrum with a new set of fragment ions. In this case, the fragmentation of 205 produces a signal at 145. So I can get the QQQMS to monitor these specific fragmentations, and keep track of the transition of each ion into another ion as it is broken apart in the spectrometer. So while there may be many compounds that have a signal at 205, there is only one molecule which has a signal of 205 fragmenting to 145. By using this approach, I can be very specific in my identification and measurement of my target compounds and this specificity brings with it excellent sensitivity and low detection limits.

Quadrupole Time of Flight (QTOF) MS

The QTOF is able to detect very specific compounds because it can measure their mass very accurately. The other mass spectrometers in our lab are able to measure the weight of ions to one atomic mass unit (amu). Using the example above, the most accurate mass of the main ion we can obtain with these instruments is 205 amu. And again, there will be many other compounds with fragment ions of the same molecular weight. However, if we calculate the mass of this fragment (C14H21O) accurately, it comes out as 205.1587. Another possible ion with the same molecular weight is C13H19NO, but the accurate mass of this ion is 205.1461. This difference of 0.0127 amu is enough for the QTOF to distinguish between these two molecules, so I can program the instrument to look only for the accurate mass ion I’m interested in and discard the other closely matching, but interfering compounds.

Exploiting the strengths of these two mass spectrometers has allowed me to detect and measure low levels of antioxidant compounds in very complex  fuel mixtures.


Drink milk, glow green… what?

I saw an ad for Devondale long life milk on TV recently which really bothered me. You can watch it on Devondale’s YouTube here. It features a young girl, with a fluorescent green glow going about her daily activites at home and school. At the end of the ad, we are supposed to believe that she’s somehow taken on this green glow through drinking milk which contains preservatives.

devgg

I think it’s very misleading, and it makes me uncomfortable for a number of reasons.

  1. The prevalence of glow-in-the-dark radium/phosphorus products around 100 years ago has cemented the ‘green glow = radioactivity’ myth into popular culture. In fact, radium alone does not emit the green glow, it must be mixed with phosphorus and when the radium gives off alpha particles, it stimulates the emission of light from the phosphorus atoms. ‘Radiation’ (alpha and beta particles and gamma rays) is actually invisible. Most importantly though, NONE OF THIS HAS ANYTHING TO DO WITH MILK OR PRESERVATIVES.
  2. Devondale are piling on the parental guilt in this ad with the line “what are you feeding your kids?”  As if parents don’t get enough guilt trips from the media and society already, now Devondale want to scare them off letting their kids drink milk? Of all the drinks available for kids (or anyone) to consume, milk is probably the second healthiest option after water.
  3. Milk sold in Australia, including long life varieties, DOES NOT EVEN CONTAIN PRESERVATIVES!
  • The shelf life of milk is extended by increasing the temperature at which it is pasteurised, and the environment in which it is packaged. By heating to a higher temperature, and packaging in a sterile environment, there is a huge reduction in the amount of organisms in the milk which over time contribute to its ‘going off’. Long life milk products do not contain preservative additives to extend the shelf life.
  • I’m not an expert on the food standards code but my interpretation of the relevant section is that antioxidants and preservative additives are permitted in milk, so long as they are included in the ingredients list on the container. I conducted a small survey at a local supermarket of long life milk products, and none of them listed any preservatives. Whether they are not used because they are simply not required (due to the high temperature treatment), or consciously excluded due to consumer concerns is something that can only be answered by the dairy industry.

milkcollage

I do feel for the independent dairy producers, given the ongoing pillaging of their industry by the  supermarket milk wars, but this, and the ridiculous permeate marketing ploy, is a dishonest way of advertising their product. Not cool Devondale, not cool.


When is a chemist not a chemist?

The following is a post I wrote while participating in the course Science Media SpaceThe course aims to “provide scientists with the practical knowledge needed to use social media effectively” and is certainly worth signing up for if you’d like to improve your skills in this area. This post was aimed at an Australian audience and may not make sense to you, depending on your local variant of the English language!

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My name is Renée, and I’m a chemist.

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What picture do you have in your mind about my profession? Is it a person in a lab surrounded by test tubes and beakers? Or is it a person behind a counter dispensing drugs and medical advice?

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Studies show* that 68% people associate the job title of ‘chemist’ with a person who dispenses drugs. Although the terminology varies around the world, in Australia, most people will use the word ‘chemist’ interchangeably with pharmacy or pharmacist. Indeed, in the past when it was common for pharmacists to compound and quality test their own medications, the two professions shared many similarities. Compounding pharmacists are now rare, but the shared name lives on. This can be quite frustrating for a ‘test tubes and beakers’ chemist, when you would love to talk about what you actually do for a living, rather than explain the difference between chemistry and pharmacy.

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Strategies to overcome chemist confusion
1. Be more specific when people ask what your job is. Rather than saying ‘I’m a chemist’, I prefer to say ‘I’m an analytical chemist’, or ‘I’m a fuel scientist’. This technique removes any ambiguity that comes with the word chemist. It also takes care of an annoying subset of people who know just enough about chemistry to be dangerous… The ones who when you do say ‘I’m a chemist’, smugly reply ‘organic or inorganic?’ As though the entire field can be delineated by these two outdated subdisciplines. I think I’ve gone off track a little…
2. Specifying a subfield may work for individual chemists communicating to a captive audience, but what about a collective group of chemists? Universities and professional chemist’s organisations such as the Royal Australian Chemical Institute or the American Chemical Society tend to overcome this by avoiding the use of the word ‘chemist’ in favour of ‘chemistry’ or ‘chemical’ which are not associated with pharmacy.

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Is this even a problem?
Do chemists even have a right to feel aggrieved that they happen to share one synonym of their profession with a different, albeit slightly related profession? Maybe they don’t, or maybe I’m the only one!
Is this going to cause any life or death mix ups? No.
Is this just another example of intellectual elitism? Maybe.

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*Study was conducted via twitter poll. May not be representative of population. Actual number may not be correct. All respondents mentioning ‘Breaking Bad’ were discarded.


Whitesides say ‘Analytical Chemistry’ is best chemistry!

Fellow analytical chemist and chemblogospherian Marc, recently brought this article from renowned Harvard chemist George Whitesides to my attention. Here’s my response, and there’s also an excellent post over at The Curious Wavefunction.

I don’t think this article is as bad as some people were saying, actually I don’t think it’s bad at all. Certainly he got this analytical chemist onside in the first couple of paragraphs with these choice quotes:

Measurement (or “analysis,” which arguably includes both measurement and interpretation) is the axle around which this wheel turns. So, everything in science is—in this sense—“analytical”.

Analytical chemistry […] is essential to the chemical enterprise.

So there you go. Analytical chemistry is great. End of post.

Or not.

I guess that Whitesides, in his eminence, has earned the right to pontificate on topics of his choosing and journal editors are clearly willing to grant him page upon page of column inches to do so. The article may be a little long-winded and in places quite fanciful, it’s not like he’s chucking a Breslow here guys. It’s basically a mashup of serious commentary, plugging of his own current research interests, and wild speculation. He also isn’t (as some suggested) advocating ‘black box’ analytical chemistry either, and stresses that analysis is equal parts measurement and interpretation.

Whitesides is certainly not saying that synthetic chemistry should no longer be done, or it is no longer a worthwhile pursuit. It’s undeniable that the bulk of the successes of chemistry in the last couple of centuries have been built on synthesis. Having said that, I don’t think it’s unreasonable to suggest that the emphasis could be shifted slightly away from synthetic chemistry. Currently, at my undergraduate and postgraduate institutions, synthetic chemists comprise roughly 50% and 45% respectively of faculty and I don’t think this distribution is appropriate for addressing the ‘grand challenges’ of chemistry in the future.

My personal opinion on the future of analytical chemistry as a discipline, is that it may not continue to be a useful descriptor for a subset of chemical studies. In fact, I would not be surprised, or even unhappy if in the future ‘analytical chemistry’ as we know it today ceases to exist. My reasons for saying this is aligned with what I think Whitesides is saying in this article. That is, that analytical chemistry is such an essential part of almost all of the chemical subdisciplines these days, that it will become absorbed into and assimilated with existing (or new) fields. For example, in my current role, I alternate between calling myself an analytical chemist and a fuel scientist, and the reality is that I am both. I am a fuel scientist, who uses the tools and techniques (GC, LC, MS) developed by the legacy of analytical chemists before me. And in doing so, I am not too different from the synthetic chemist who uses conducts analysis by NMR and IR, or the materials chemist who analyses with XRD and AFM. The only distinction being that I am not ashamed, indeed I am proud, to be a practitioner of metrology.\

May analysis no longer be the ugly duckling of the chemical sciences. Viva la anal. chem.!


The CERN Song

 

For Upulie, (and all of the team, friends and followers of Real Scientists).
To the tune of Tina Arena’s Burn.

 

 

 

Do you wanna be a particle, and collide?
Do you wanna be a neutrino, faster than light?
Do you wanna be a physicist, and win the Nobel?
Do you wanna meson to muon?
Do you wanna plasma, quark and gluon?
Or whoosh around the 27 k tunnel?

 

 

Be anyone you want to be
Bring to life your fantasies
But I want something in return
I want you to CERN, CERN for me baby
Like a candle in my night
Oh CERN
CERN for me
CERN for me

 

 

Are you gonna be a proton, and get smashed?
Are you gonna be a boson, and give mass?
Or go to Scotland and touch Higgs’ face?
Are you gonna be an strange, charm flavour quark ?
Are you gonna tell us, what is matter dark?
Or a test
Of supersymmetry

 

Ill lay down on your standard model
Offer up my safety goggles
But in return
I want you to CERN
CERN for me baby
Like a candle in my night
Oh CERN, CERN for me, CERN for me
Yeah
Ooh
I want you to CERN baby ooh

 

Laugh for me
Cry for me
Pray for me
Lie for me
Live for me
Die for me
I want you to CERN
CERN for me baby
Like a candle in my night
Oh CERN, CERN for me, CERN for me