I spent another day behind a microscope.

2D MDCK layer
Image taken on a Zeiss 710 Confocal microscope at the University of Dundee.
MDCK spheroid and 2D layer
Image taken on a Zeiss 710 Confocal microscope at the University of Dundee.
3D MDCK spheroids
Image taken on a Zeiss 710 Confocal microscope at the University of Dundee.
Glowing edges filter
Image taken on a Zeiss 710 Confocal microscope at the University of Dundee, but then put through a filter.

The last images are put though the very professional “Glowing edges” filter found in Microsoft Office Powerpoint.

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.

 Twitter screenshot: "One step closer to understanding the mechanics of the gut, one step closer to curing cancer! #ShareMyThesis"

 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;

A 3D rendering of a sample that looks like floating specs in a dark universe
Image taken on the OCT system at IMSaT (UoD).

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

A 3D rendering of a sample that shows a heart-shaped area
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.”


A Sunrise over the university campus in Dundee
Sunrises (and probably sunsets as well) are particularly beautiful on this part of the world lately. Maybe it has to do with the fact that I live in the “sunniest city in Scotland” (and here I was thinking that was a silly thing to say) or it’s just the time of year…
In any case, I’ve been enjoying my walks to work lately, they seem to be perfectly times with the sun rising over the Tay river.
The wonderful colours during sunrises and sunsets due to the fact that sunlight has to travel much longer through the atmosphere than during midday. As sunlight travels, more blue and violet light is scattered out of the beam that eventually reachers our eye (this is called Rayleigh scattering, i.e. differential scattering depending on the wavelength – or colour – of the light), causing the sky to appear more red for the morning or evening observer.
When clouds are added into all this, sunsets become even more awe-inspiring. Clouds reflect the first rays of light (in the case of sunrises) back to the surface. With their interesting shapes, the result is fantastic.
So why are there so many wonderful sunrise views here? I have a few theories:

  1. Scotland is pretty Northern (at least compared to what I’m used to). That means the sun stays relatively low to the ground this time a year, prolonging the “best light” duration. Sunrises and sunsets do take a while here.
  2. Weather in Scotland can best be described as “temperamental”. Quite often we get all seasons in one day. The day can start out wonderfully, but end up in pouring rain. In any case, the chances of having the combination of sun and quite some clouds is probably quite high compared to some other places I’ve lived.
  3. I’m easily impressed.

Probably, the reality is a combination of all three. In any case, waking up and walking to work in this light often makes my day. It makes the lack of mountains all around – something that made me love my time in Grenoble, in the French Alps – completely bearable.
So before I head home for Christmas, let this be my present to you. The view from my flat followed by the room in my office. If I plan things right, that’s how my day starts (though in the summer I doubt I’ll be getting up at 4AM just for the view).
Sunrise views from the university building towards the river Tay

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.)

Image of crystallized salt after drying a hydrogel
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.

Top left: lego blocks in a petridish. Top right: a bit of agar molded by lego. Bottom: a 6 well plates with molded lego-wells
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)

MDCK cyst (hollow clump of cells) with nuclei in blue and actin in green
Image taken on a Zeiss 710 Confocal microscope at the University of Dundee.
MDCK cyst (hollow clump of cells) with nuclei in blue and actin in green
Image taken on a Zeiss 710 Confocal microscope at the University of Dundee.

More/nicer to come soon!

How to write a highly cited paper

Originally posted on 31 Oct 2014

This week on Nature.com: an overview of the 100 top cited papers, according to Thompson Reuters’ web of science database. Surprisingly, publications on nobel-prize winning findings aren’t at the top.
Most of the top 100 most cited papers, are actually methods papers.
Which leads to the conclusion, that if you want to write an amazing paper that will send your author index skyrocketing, you should find a new, efficient and ground-breaking protocol that will be used by everybody in your field. And don’t work in a small niche field, that won’t help you one bit.
So, invent a new methodology everybody will just have to use, wait a few decades, and bam, you might get yourself a first-author spot on the honour list of top-cited papers in the world. Wouldn’t that be great?
Next post, how to win a Nobel Prize, or something else on the long list of things that I haven’t achieved and never will.
Rephrase: Next post, how to win a Nobel Prize, or something else on the long list of things that I haven’t achieved yet.
On a side note, I recently came across a bunch of “how to” articles titled “10 simple rules“, most of them written by Philip E. Bourne. Quite an entertaining read for during your coffee

Colorectal Cancer

Originally posted on 18 Sept 2014

Today is “Dag tegen Kanker” (this is Dutch for: day against cancer). They have set up a inflatable walk-through sized intestine to show people how intestinal cancer develops. Unfortunately, the video is in Dutch, but it shows the walk-through bit in the beginning.
As my PhD project is on the mechanics of gut tissue in health and disease (the latter being cancer), I thought this was relevant.
Colorectal cancer is the 2nd most common cancer for women and 3rd most common for men. A lot of people don’t realise they have it, until it is too late.
So, research in the topic, leading to more understanding of onset of cancer, the pathways involved and novel diagnostic methods (for earlier detection) are of great importance. No, I’m not saying that because it involves my own research.
But that probably is why I’m sharing it.

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:

4-panel image of a 3D printer printing a blue cylinder
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.)

two-panel image with a very oldschool drying oven on the left and a very oldschool TEM on the right
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.

Pretty Pictures

Originally posted on 29 Aug 2014

After two weeks of a semi-intensive microscopy workshop, I have learned several interesting things. Additionally, I have also learned some valuable life lessons.

  1. You’re never too old to be a crazy scientist. I know this because putting dry ice into a glass of lemonade is completely irrelevant but totally cool. Never grow up.
  2. The whole point of microscopy is to make pretty pictures². There are multiple ways of achieving this – obviously I am now an expert after this course – but if you want to be published, the end result just has to look amazing.

Exhibit A:

Light sheet microscopy image of a baby octopus (purple and blue in color)
Octopus bimaculoides. Light Sheet Fluorescence Microscopy with a Zeiss light sheet microscope (www.zeiss.com/lightsheet). Image courtesy of Eric Edsinger & Daniel S. Rokhsar, Okinawa Institute of Science and Technology.

This looks absolutely incredible, right? It is a tiny embryo octopus, but don’t you just want to own it and train it and use it to be the very best? Of course you do!
Exhibit B:

Scanning Electron Microscopy image of protein-inorganic material hybrids that look like flowers
Image published in Nature Nanotechnology. “Protein-inorganic hybrid nanoflowers”, J. Ge, J. Lei and R.N. Zare. DOI: 10.1038/NNANO.2012.80

Sometimes not only the imaging technique, but the whole point of creating a structure is just to have something pretty, like this nanoflower. I’ve got to admit, giving me that on a first date would definitely work in your favour.
However, at this very moment; all I’m able to image are things like this:

Image of a MDCK 3D culture that looks like a peace-sign
Image taken on a Nikon eclipse TS100 at the University of Dundee.

Just look at those phase rings! And the bad resolution! Awful!
But at least this collection of cells looks pretty peaceful, so that’s something.
² Footnote (it is number two because of simplicity, ² is on my keyboard): this obviously isn’t true. The point is to make images that have the right quality to show what you want to know. It’s just more fun if they turn out to be pretty (and) awesome.

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).
Grey-scale image after a so-called explosion of a microbead leaving a fractal pattern
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!

Harry Potter and the Hopefully Benign Colon Polyp

From “Middle Aged Harry Potter Books” (https://www.someecards.com/)