Wasteful waiting

from xkcd

Sometimes doing research involves quite a lot of waiting. I’ve made a little graph to illustrate:

There is absolutely no point to the Torosaurus, except that it's adorable.
There is absolutely no point to the Torosaurus, except that it’s adorable.

The trick is to find productive (no, not office chair sword fights) things to do. Seeping could be useful, especially for overnight protocol steps. Or reading papers. Or doing other experiments. Or having inspiring coffee meetings. Or doing a little morning stretch.

Waiting time is not necessarily a waste of time. The French sculptor Auguste Rodin once said:

Nothing is a waste of time if you use the experience wisely.”

Yes, I did just find that through searching google for a “waste of time quote”, but nevertheless, take advantage of down time. Rest, think, talk, dream, experiment, blog (meta). Do anything, except waste it.

Cheap is good, almost free is better!

Working in a research environment definitely changes your perspective on the meaning of “cheap” and “expensive”. If paying £194 to go to a festival seems like a lot of money, then consider that you need to pay at least half more to buy an antibody. “Cheap” purchases include most things under, say, £200. And I don’t even want to think about how much money gets spent on consumables like pipets and petridishes. If you want to really do something, you need to buy equipment like microscopes or PCR meters and you can probably buy a car with the same amount of money. Or a jet. Needless to say then, that conducting scientific research is quite an expensive endeavour and it’s no bit surprise that a lot of time goes into applying for grants.

Does it really have to be this expensive though?

The simple answer is: probably.

The fun answer, however, is NO!

I’ll give you an example (and let’s pretend to ignore the fact that I’m too lazy to find another example): easy-to-make, affordable, microscopy lenses. It is quite similar to the water drop hack, which is even cheaper than the method I am going to purpose, but not quite as versatile. I am talking about a lens made out of PDMS.

Bear with me, I am going to explain.

The idea was published last year. It makes use of polydimethylsiloxane (also known as PDMS), which is a elastomer used commonly for making microfluidic devices. The elastomer is made by mixing to reagents together and exposed to heat to allow it to polymerise and form a stable, flexible, clear, rubbery bit of stuff.

An example of a microfluidic device made of PDMS (as a result of a quick google search).

As it is clear and has a high refractive index, making a droplet-shaped bit of this PDMS might very well be used as a lens in combination with a smartphone. And it is cheap, a 1.1 kg bottle of this PDMS might cost a little bit (around £100, but I have already that this is cheap in scientific consumables terms), but you can make so many lenses out of this, it results in about £0,05 per lens. Cheap huh.

So yesterday evening, we spent some time trying to make some of these lenses, which worked quite well. It is very easy to make (we are going to try this as an outreach workshop) and it is also absolutely cool. From just a few hours of messing around – and it is quite a sticky substance to work with – with cover slips, the PDMS, a syringe and a lamp to provide the heat, we made quite some lenses and took quite some pictures.

Wait, I’ll give you another example (it isn’t really though): so using these lenses, you can make a simple (and cheap!) optical trap. An optical trap uses a laser to trap, for example, a bead*. This can be used to measure the viscosity of fluids, measure forces involved in cellular processes (protein folding, motor proteins, adhesion, cytosol viscosity, motility forces, …) or to play a game of tetris. It’s quite a cool technique, and now you can save on costs by making your own lens! (I’m sure the paper will be accessible soon.)

Anyway, this is just to say that research doesn’t always have to be expensive. And obviously it was already fun, but it can be even more fun (who knew)?

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The result of mucking around. Top left: a PDMS drip lens. Top right and bottom left: pixels from some text on a paper. Bottom right: some of my finger print lines.
Another example: the fabric of my watch. Left is taken in macro mode without the lens (even a bit out of focus), right is with the PDMS lens.
Another example: the fabric of my watch. Left is taken in macro mode without the lens (even a bit out of focus), right is with the PDMS lens.

We live in exciting times. Nostalgia-drenched movies are out now or being released soon. Our childhood hero is returning in the form of theatre. Certain fantasy characters might have actually existed**. Advances that we could only dream of (or write Sci-Fi novels about) seem within reach. And new awesome ways are being developed to make science cheap and accessible for anyone.

Finally, I’ll end with a teaser:

We are currently setting up an outreach project bringing these things together:

I-Heard-The-Cutest-Conversations-Between-Everydays-Objects43__605
But I enjoy the far away things too! (source)

And it’s already been so much fun! Learn more on twitter or wait until I dedicate a post on the subject (sometime I will!)

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*Yes, this is in no way an adequate explanation of optical trapping. I could say it uses “magic” to trap beads, though I’m sure you won’t believe me.

** Yes, I just rushed over multiple topics that I not-so-secretly wanted to mention in one way or another.

Remember why you became a scientist?

A few days ago we passed a poster on a door that said: “Remember why you became a scientist?” It was a poster promoting outreach activities, such as promoting STEM (Science, Technology, Engineering and Mathematics) in primary schools. However, it had a slightly different effect on us. A simultaneous groan was uttered. You must know that this happened in the middle of the week, a quite stressful week for most of us. I also had a hard time remembering. PhD’s tend to go in ups and downs, a fact that is sometimes cleverly used for a whole range of webcomics. And at that moment, even though I’m only 6 months – no wait, 7 months – into my PhD so I can hardly complain, it was a bit of a down. So running into a poster asking if I remember why I wanted to be a scientist caused me to slip into a tiny existential crisis.

Luckily it didn’t take to much remembering.

In the good old days of sending around questionnaires (“How well do you know me?“) by email, a friend filled in the following:

Q: What will I be when I grow up?
A: an inventor

It all fit. When we were kids, that friend and I had made plans to build a “test-car”, where we could interchange the engine to test different alternative fuels, not-so-loosely based on the grasmobile. It never got past the plans, but nevertheless, we had the ambition to better the world and help the environment. We wrote poems about time travel. My personal heroes were not movie stars or superheroes, but the quirky old professors in the comics I read, like Professor Barabas, Professor Gobelijn or even Professor Zonnebloem (Professor Calculus). All bonkers (especially the latter) but amazing geniuses. I played with a microscope, collecting leaves and dirt to look at. I had plans to solve global warming and cure cancer.

I became a bit more realistic when I got older, but still, I got into engineering and research. I still want to discover the world, make an impact and make the world an ever so slightly better place.

 2015-02-06 10.05.48

 Beside that, I simply like science. I find pleasure talking about it with friends, reading about new new findings, in short, simply geeking out. Science is awesome. We scientists just loose sight of that sometimes.

And if I have a hard time remembering, I have results to remind us. Even if things don’t turn out exactly the way I predicted or hoped, interesting thins happen: A 3D OCT* scan that looks like a galaxy;

Screen Shot 2015-02-06 at 09.44.09
Image taken on the OCT system at IMSaT (UoD). 

or a result just simply asking me to be its valentine…

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Image taken on the OCT system at IMSaT (UoD). 

So there is still hope for me!

* Optical Coherence Tomography (OCT) uses the interference patterns of backscattered light to form an image, or in other words: as light travels through a sample, it is scattered back differentially by different objects in the samples. By looking at the light coming back and comparing it to your initial light beam, you can deduct structural information of your sample. The “stars” in the image, the bright dots, are hopefully spheroids of cells. The brightest spot in the middle is strong reflection from the liquid surface (because it’s not flat). Another way to think about OCT is “Ultrasound with light.”

You know you’ve worked too long in a lab when…

Today I came across this list of signs that you have been working too long in a lab. I would even say it applies to working too long in a certain branch of science, or doing research for too long.

But, slightly plagiarising inspired by that list, here are some things that I have noticed are indications that you are working in a lab, any research lab, but mostly a biology/biochemical lab. Well, let’s just say that they’re indications of me at the moment.

You know you’re doing PhD research in Life Sciences when…

  • … you sometimes have to run from social activities, such as lunch, because you’re busy with a protocol.
  • … you’re no longer scared of rodents.
  • … no one of your family or non-work friends can really explain what you do. And face it, most of your work friends can’t either. Can you, come to think of it?
  • … you can’t watch CSI/The Big Bang Theory/Any SciFi movie/… without cursing at at least one scientific inaccuracy.
  • … you use acronyms for everything and never stop to explain what they mean. Do you even still know?
    (APC… Adenomatous Polysomethingamajingy?)
  • … you sometimes have a headache at the end of the day from looking down a microscope/at a computer screen for too long.
  • … you slightly disappointed that you don’t have to wear your safety equipment all the time. You actually think a lab coat and safety goggles look cool.
  • … while choosing an outfit to where in the morning, you make sure the skirt/dress is long enough so it won’t look like you’re wearing nothing/just tights under your lab coat.
  • … you want dry ice or liquid nitrogen at home to do silly experiments with.
  • … you want parafilm at home because it’s obviously really useful.
  • … you nudging friends to do “Friday afternoon experiments” with you. (Oh, that’s how you win a Noble Prize, by the way.)
  • … you try to make the best out of failed experiments.
  • … you find a way to use LEGO for science, so you can go shopping on Pick a Brick.
  • … you feel slightly exhilarated travelling on public transportation with some samples, even though they in no way can start a epidemic ever.
  • … you’ve been in the lab so long that you’re afraid to ask what people are talking about when they say HET or Min (and eventually realise they’re really obvious things).
  • … you start a blog about it. (Wow, meta…)

Just to illustrate a few of these points:

Sometimes a failed experiment can result in something beautiful.
(It’s just crystallised salts. No biggie.)

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Image taken on a Nikon eclipse TS100 at the University of Dundee.

How Lego had the perfect dimensions for exactly what I wanted to do.

I love my job!

But I was like this before I started this PhD…

My first confocal image

Originally posted on 17 Nov 2014

It might not be much.

It might not be particularly good.

It might not show anything significant.

But nevertheless… I have run my first confocal image sequence. And I have proof!

I present to you: a Phalloidin/Hoechst stained MDCK cyst!

(both a single slice as a multiple intensity projection of the z-stack)

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Image taken on a Zeiss 710 Confocal microscope at the University of Dundee.
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Image taken on a Zeiss 710 Confocal microscope at the University of Dundee.

More/nicer to come soon!

There’s no school like the old school

Originally posted on 5 Sept 2014

New isn’t always better.

I had this conversation a few days ago with a fellow researcher: The engineers in his lab had just set up a new oscilloscope, an instrument that can be used to measure an ultrasound signal. (Edit: This is not really true, but for the purposes of this rant, it will do such fine.) This new marvel of an oscilloscope had a whole bunch of fancy features and elaborate knobs. Unfortunately, just setting up a simple experiment was now immensely complicated, while it was really easy to do on the old system.

While he was complaining about this, the only – very philosophical if I have to say so myself – answer I could give him was: “Well, new isn’t always better.”

If you ignore the painful cliche, there seems to be some truth in my statement. Why change something if it is working perfectly well for what you want it to do? That’s the problem with engineers, there’s always an extremely cool way to do things. It might be slightly more complicated, and redundant, but if you can do make something awesome, why settle for the boring, easy method?

(There is actually a smbc-comic that describes this wonderfully.)

But I have to admit , I tend to do the same. Then again I am some sort of an engineer. Today I 3D printed a small cylinder, while the ink tube of a fountain pen probably could have served the same purpose. Why did I 3D print it then, you might ask? Because I could! 3D printing is awesome!

I mean, come on, look at this machine making it happen:

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Ultimaker 3D printer at the University of Dundee.

I’m diverging. Another thing I wanted to point out, is that old stuff can be extremely robust and do the job just at well. A few examples (straight out of my university) are an oven that looks as if you can mount in on your head and walk on the bottom of the ocean, and an electron microscope that looks as if it was stolen from a space ship on a 70’s sci-fi movie set. (The EM microscope photo isn’t actually the one in my building but a picture I found through googling “old electron microscope”. It looks very similar to the one they have downstairs.)

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Oven (University of Dundee) and Transmission Electron Microscope (google search).

Granted, it might not provide the same resolution. But for a quick check and for certain applications, it’s good enough. And it looks absolutely antique. I guess you can compare it with having a record player, there are much easier and better sounding ways of playing music nowadays, but maybe you enjoy the crackle to the sound and the extra work of having to wind it up.

So, the moral of my story is, there’s no school like the old school. Depending on the application, that is. As a geeky and slightly hipster engineer, I seem to alternate between the two. I like to use wonderfully antique equipment sometime, and slightly too elaborate novel methods other times.

On a side note, I came across an this article: a Scottish Distillery has sent a batch of whiskey to space to see how zero-gravity conditions influence the interaction between their whiskey and some charred oak. It seems a bit far-fetched to me, why would you even want to know how things react without gravity? Why would you spend all that money to send things to space. Because you can, obviously.

As quoted from the director of the distillery in question: “This is one small step for man but one giant leap for whisky.

I’m sure it is.

New insights on Scientific Research

Originally posted on 15 Aug 2014

One month into my PhD, that’s to become a “Doctor of Philosophy” even though it has nothing to do with philosophy, or being a doctor for that matter. At least not the kind that would step forward in a crowded restaurant after some random guy gets a heart attack and the bystanders yell out “Is there a doctor here?” On the other hand I do know CPR thanks to my extensive first aid training (i.e. 1 course).

Back to the point: One month into my PhD, I have learned a great lot about science, and how to do science, and why I wanted to be a researcher in the first place. First of all, it comes with a whole range of transferable skill, who knew I would learn different test tube shaking techniques? If this doesn’t work out, I can always become a cocktail waitress (it’s somewhere down the list after working as a card dealer at a casino). There’s also some nail polish-expertise to be gained, surprisingly, and not just for the girls.

Aside from that, there’s a lot of cleaning and setting up and waiting and doing the dishes. Which all sounds pretty boring – and granted it isn’t extremely exciting – but I haven’t gotten to the good part yet.

Here it comes… ~

You can make things explode. Yes, explode. The wonderfully geeky thing about science, is that sometimes things don’t react the way you thing they will. Sometimes they don’t do anything at all (not very exciting). Sometimes they explode (very exciting). And sometimes explosions lead to beautiful patterns (extremely exciting).

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I’ve always known that there’s a certain amount of serendipity to science, just look at the discovery of penicillin or graphene. It turns out it has just the right amount to keep it interesting. For example: “I’ll just try this and see what happens” and end up with fascinating fractal patterns. Or when you decide to send that person you found through google search an e-mail and end up talking about possible collaborations. Not to mention the extended coffee breaks that leave you with a whole lot more questions but more importantly countless new ideas. It’s about that first month where there’s a lot of reading, a lot of e-mails, an occasional dozing off, but mostly a lot of new friends and possibilities.

Don’t worry Harry Potter. I will find a cure for your little middle-aged problem. Not directly, because that’s science for you. And I’ll have to take care not to make anything explode. But I will make it happen, I have three wonderful years ahead of me!

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