How to write a highly cited paper

Originally posted on 31 Oct 2014

This week on 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:
Note saying: To my friends, My work is done, why wait?
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:
Very old digital camera with a blue camera bit and a box for the electronics
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… 😉
The Empire State Building as seen from the top of the rock at night
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:

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 ( 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” (