Sunrises

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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).

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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!

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

I want to wake up in the city that never sleeps…

Originally posted on 2 Oct 2014

I went to New York last week.

Before I went to the City, I went to Rochester. Apparently, Rochester has quite some optics going on, with the Institute of optics, a few university spin offs and small companies, giving me the opportunity to turn a personal trip into something slightly more professional. I didn’t though.

I did go to the George Eastman house. George Eastman was a rather peculiar and impressive person. He founded the Eastman Kodak Company about 20 years after he dropped out of school. He chose the name “Kodak” because it sounded good in every language and has the same letters to start and begin with. He was known to throw legendary parties in his big mansion. He used his fortune to establish a number of schools and academies. He loved art and music and hunting, there were a lot of paintings and dead stuffed animal parts and even an organ in his house. I’m pretty sure he needed a whole list of adjectives to adequately describe him.

Then, at the age of 77 years, he wrote this note:

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and shot himself in the heart.

Strange man.

Unfortunately, Eastman Kodak Company (also known as Kodak), is not doing too well lately. Even though Kodak engineer Steven Sasson invented the first digital still camera. It was bit and bulky and looked like this:

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but I’m sure it was innovative. You would think the invention of digital camera technology would put you right up there with the big shots. But it might have been one of those bad predictions. “There’s no real market for digital photography.” Right.

Anyway, if you’re ever in Rochester, the George Eastman house is definitely worth a visit!

On another note, I learned the other day that Rockefeller centre in NYC has science going on in it. If only I’d known, I just went up to the roof and enjoyed a magnificent almost-midnight view of the city… 😉

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Pictures cannot do it justice.

By the end of the week, I’d decided that I love New York and that I want to live there someday. I’m pretty sure I’m the very first person ever to have that dream.

 

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:

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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.