To the horizon, and beyond!

Both of my subscription magazines – *I’m so sophisticated* – had articles about the advances in space exploration last week (though by now it’s more two weeks ago). It’s been a while since I read so much of my subscription magazines, I usually leaf through most of it – *gone sophistication* – because I’m stuck in the illusion that I don’t have any time.

Which is ridiculous, check my Netflix record.

But nothing better to bring me back into good reading habits than some good ol’ articles about space. And nothing better to get me back to blogging about science subjects again as well. Because let’s be honest, it’s quite difficult to get me to shut up about space.

It had been quiet for a while, in the space news column of your daily/weekly/monthly newspaper. Apart from some back-and-forth travel to and from ISS and the occasional news blast when a countryman was sent up (for me this was Frank De Winne and more recently Tim Peake). But in the last few months, the interest for space has rekindled. Whether it is due to the recent abundance of space movies (Interstellar, Gravity, The Martian), astronomy breakthroughs (LIGA) or NASA’s call for astronauts last year (18400 applicants!), I do not know, but astrosciences has been back in the press.

The most recent exciting news has probably been the discovery of Proxima Centauri b (from now on referred to as PCb). PCb orbit’s the sun’s nearest neighbour, Proxima Centauri, making it close enough to have a very laggy conversation with potential inhabitants of the planet. The possibilities scream to the imagination. It might have an atmosphere. It might have water. It is only 4 light years away. It orbits the Goldilocks zone of Proxima Centauri; 7 million km from it (which is about 1/20 of earth’s to its sun) . It has an estimated weight of 1.3 to 3 that of earth. It is  presumed to be rocky. It has an orbit of 11 days, making me 875 orbits of age. (Read more about PCb in the original article.)

Okay, I realise, and so does the research community, that we barely know anything about PCb. But that’s not really the issue. The possibilities are the issue. It’s closeness, it’s “just right”-ness and its promise of potential life forms are enough to get us all excited. And excitement is quite an understatement, you can be sure of that.

Luckily for us, a new form of space exploration has taken place. A first change is the commercialisation of space travel. It’s no longer just for governments to prove their superiority by making it to a certain satellite first. Several visionaries who happen to be billionaires are investing in space travel. For industry and the commercial sector, such as telecommunication, but also towards tourism. This helps to lower the cost of space travel, making “a trip to orbit” more than a very vivid dream.

Luckily for us, we have an Elon Musk, who dreams of a self-sufficient colony on Mars. Luckily for us, we have a Richard Branson, who wants to make space tourism reality. Luckily for us, we have a Jeff Bezos, who thinks that eventually there will be thousands of satellites in orbit employing millions of people. This idea of “great inversion” could allow us to change the earth into one giant nature reserve.

Luckily for us, the billionaires of the world – or at least some of them – are not only driven by profit but also by curiosity.

Elon Musk all packed up for his move to Mars. (The Simpsons, in case you hadn’t guessed.)

On the other hand, minaturisation is driving a new way of space exploration. We wouldn’t necessarily need to send enormous, fuel-consuming, costly rockets off to the planets and comets and space we’d like to explore. They can be tiny. Made out of components that are already mass produced. Relatively cheap to make. Of course, I love the idea of still sending humans to space, and I’m quite sure they will continue to do so, but the amount of data and knowledge we can gain from small satellites, such as Planet’s “Doves”, is extremely exciting on its own.

So let’s keep exploring. There is so much out there for us to learn about, and we are making the tools to do it.


Meet disco-mouse and Roboctopus


They could be characters from a Cartoon Network show, but they are just some of the amazing outputs of recent science.


A novel technique called ultimate DISCO (uDISCO) removes pigments and lipids, allowing researchers to image through dead animals. uDISCO also causes shrinkage – and consequentially perhaps odd organ proportions – and prepares the mouse for the ultimate rave.

More info: Nature Methods


This octopus-shaped robot (named octobot by the researchers, but I prefer roboctopus because it’s more reminiscent of a certain cyborg) consists entirely of soft materials and is controlled by a fluidic system and a chemical reaction. It also glows in the dark, apparently.

More info: Nature News & Views and Nature article
If you like cephalopods you might also enjoy my friend’s recent blog about cuttlefish; they apparently have amazing crazy eyes.

I already have a few plot ideas to turn this into a show, in case Cartoon Network is interested…


# Trust Me I’m An Engineer

Some time ago, on my usually waste-of-time website, I found a post about the first female engineer. As a female engineer – let’s not go into whether that’s self-proclaimed or not – , I naturally wanted to find out more.

First, it seemed necessary to find a definition for “engineering”.

As so many other words, engineering is derived from Latin. It can have originated from either – or perhaps both – ingenium or – and – ingeniare. As the word ingenious might hint, the first means something in the lines of cleverness, though I’ve also seen it translated as talent; the latter means to devise (according to wikipedia, I had more trouble finding the word through other sources). The stem of the word seems to resemble ingenerare (to implant) and ingenere (to instill by birth). Therefore it seems that the word initially meant something along the lines of having a natural talent for something but slowly evolved to coming up with clever tricks or solutions to solve a certain problem.

Nowadays, the current official definition of “engineering” is (according to Engineers’ Council for Professional Development):

The creative application of scientific principles to design or develop structures, machines, apparatus, or manufacturing processes, or works utilising them singly or in combination; or to construct or operate the same with full cognisance of their design; or to forecast their behaviour under specific operating conditions; all as respects an intended function, economics of operation or safety to life and property.

Hmmm, that’s one of those sentences that I still haven’t completely grasped after reading it three times and then I usually just give up. Let’s give that definition another try then. According to my understanding (and self-proclaimed experience), engineers aim to design (or invent, or optimise, or improve) something by the application of scientific and mathematical principles. This something can range from materials, instruments, software, living systems, you name it; basically anything that you can imagine inventing or improving on.

It differs from science mostly due to the fact that sciences aim to build on knowledge starting from predicions and hypothesis about the universe (or, anything).

If this not making much sense… Well, probably this comic by Saturday Morning Breakfast Cereal does a better job on describing the essence of engineering:

So, I guess you can say that engineers are more interested in applying scientific knowledge to whatever they are working, while scientists are more aimed at acquiring said knowledge. In my opinion (and again, “experience”) the distinction between the two is not always very straight cut, and a lot of people are more somewhere in between, say applied scientist, or scientific engineers, or engineering scientist (though that last one sounds more like someone trying to create a race of super-scientists through genetic engineering). I also think it’s quite obvious that both (or all people on that spectrum) need each other to achieve progress.

Nevertheless, my post was going to be about the first female engineer. Because which ever way you look at it, woman are still underrepresented in these fields, even if the situation is already much more balanced than it used to be. It also strongly depends on the type of engineering. For example, while there are about 50% females studying bio-engineering or architectural engineering at my formal school, only 15% of engineering (that later specialises into mechanical, civil, chemical, biomedical, computer, and mathematical engineering) consists of female students. Perhaps “us girls” just need some role models?

The first candidate-rolemodel, and the “first female engineer” according to that post I mentioned, is Elisa Leonida Zamfirescu.

Elisa Leonida Zamfirescu

Elisa was born in 1887 in Romania, in a quite engineery – yes that is a word, stop it red squiggly line – family.  Her grandfather, on her mother’s side, was an engineer and so was her older brother Dimitrie. I imagine her as a child inventor, a bit like Violet Baudelaire, who did not give up after being rejected from engineering school (School of Bridges and Roads in Bucharest). No, she just applied to other schools, and in 1909, she was accepted at the Royal Academy of Technology Berlin. Three years later, she graduated, and started her career in geology laboratories back in Romania. She passed the war years (World War I) in the Red Cross, around which time she met her husband, Constantin Zamfirescu, a chemist.  She spent her engineering career leading several geology labs in the Geological Institute in Romania and teaching physics and chemistry. Her contributions include her role in identifying new resources of coal, natural gas and copper. She worked until she was 75, and died in 1973.

Despite her contributions to the world of engineering, Elisa was not technically the first engineer. Alice Jacqueline Perry, an Irish cailín born in 1885, graduated a few years before. Her family sounds very well educated; her father was co-founder of the Galway Electric Light Company as well as county surveyor for the County Council and her uncle invented the navigational gyroscope (two of her sisters also continued into higher education, by the way), Alice was quite a mathlete, or would have been if they had those in the 1900s.

Alice Jacqueline Perry

She received a scholarship to study at the Queen’s College in Galway in 1902, where she pursued a degree in engineering. She graduated in 1906, with first class honours. Alice was the first female engineering graduate in Ireland, the UK, and in my understanding the world. A month after her graduation, her father’s death caused her to take up his position temporarily for County Council, making her the only woman to have been a County Surveyor – basically a Council Engineer – in Ireland. She moved to London in 1908, starting a job as a Lady Factory Inspector. She moved to Glasgow in 1915 (and seemed to have continued an inspector job there as well). In 1921 she grew bored of engineering, an started writing poetry (eventually publishing seven books of poetry). She was heavily involved in the Christian Science movement, and moved to Boston headquarters in 1923, where she worked until her death in 1969, about a month after the moon landing.

These may seem like quite ordinary lives, but I can only imagine the challenges Elisa and Alice might have faced as female engineers in those days, just as female scientists or female doctors had a whole stream of male criticism and prejudice to swim up against.

I assume that there were some female engineers before 1900, though perhaps not with an official engineering degree; after all, inventors have been around forever and it is no great leap of imagination that some of those inventors were woman. And you might argue that we don’t really know any famous female engineers because they haven’t contributed anything major, but I will argue back that a lot of progress happens in little bits and every little contribution has been necessary to get to those major leaps. (Come to think of it, I don’t think I can name any great engineers off the top of my head.)

As there are quite some great female scientists, there are some great female engineers, and naming the first ones is only the start of a long list, that I am positive will grow longer in the future. Perhaps one day, I’ll find my name on that list. (I doubt it, but it can’t hurt to be ambitious, eh.)

More than Sci-Fi

We live in exciting times. Technology, that novelists and script writers could only dream of, now exists without us being amazed about it every single day. We have computers, that make immensely complicated calculations and simulations for us all the time. We send people into space and leave them there for months. We can talk to someone on the other side of the world with a simple click on a green phone logo, we can even see them if we want. We use the touch of our finger on a screen to control our devices. We ask our phone questions and it talk backs to give us the answers. We are able to step into virtual reality without getting nauseous. We send out cars that can drive themselves to map our streets. We are able to manipulate single genes, single molecules, single atoms.

Seriously, how are we not amazed every single day?

With all that has been achieved up to now, I can’t help but wonder: “What’s next?” Which crazy science fiction technology will we turn into reality tomorrow? Will humans soon be inhabiting another planet? Will some one create a working lightsaber?

Will we ever be able to travel through time?

I’ve dreamed about this. Not literally –  though maybe I have, I just never remember my dreams so there’s no way to tell – but conceptually. I love reading about it. I love watching movies about it. I love having discussions about the paradoxes it could create. But in the same way that I know the dinosaurs in Jurassic park aren’t realistic, I know it cannot and probably never will be real.

See how I said probably? Did you notice that spark of hope?

To start with, there’s the way my friend (oh wow, his last post is also about SciFi!) states that he’s travelling through time and space at a constant forwards speed, as we all are. So in that sense, we’re all travelling through time, slowly. More interestingly, by travelling through space at a high speed, one would be passing through time at a different speed than others, because the space traveller would have aged less than anyone who had stayed on earth. This idea is called the twin paradox (recently used to explain how Luke ends up being younger than Leia, even though they’re twins) and is due to time dilation, an aspect of special relativity where time slows down when moving at near light-speed speeds. (If you ever have the chance to ask Lieven Scheire to explain special relativity to you, don’t miss it, it’s genious.) So we are able to travel through time at different speeds, and essentially travelling little bits into the future, and renders me hopeful that more sophisticated time travel could be possible.

How would this work? It’s amazing to think that when we look into space, we’re actually looking back in time. Could it ever be possible to travel back in time as well? (I would think that if we’d like send people to travel through space beyond our solar system, travelling through time could be a prerequisite, that is if we want to actually have the same people coming back to tell us what they’ve seen.) Extrapolating from time dilation, we could imagine that travelling at a speed faster than light would allow time reversal. Unfortunately, we don’t even have the technology to travel as speeds close to the speed of light. And that’s not even mentioning that “faster than the speed of light” is not really a thing. (For now? <– See that spark of hope again?)

Another option would be travelling through wormholes, which is a connection between two different points in space time. Unfortunately, we’re not really sure those things exist, so that’s not really a possibility either.

Or perhaps we could build an infinite improbability drive, or a ship that moves time and space around us while remaining stationary. Or have a space ship that’s actually a living creature that propels us through the wibbly wobbly timey wimey thing. Or, I don’t know, a time travelling car?

But if it was up to me, I would tackle time travel differently. I would use a bath tub to travel through time, and incidentally space. (And a friend and myself came up with this idea before that movie about the hot tub time machine came out!)

Screen Shot 2015-08-12 at 13.38.45
See? Proof!

I guess for now I’ll just have to stick to fiction and keep on dreaming…

Never say biologists don’t have a sense of humour!

Sometimes, when reading a biology paper, I have to refrain myself from bursting out laughing. Biologists, and more specifically geneticist, come up with the most ridiculous names for genes. Not that I’m complaining, it brightens up even the most boring of papers (though sadly not all names are funny). Here’s a (very!) small selection as an example of biologists’ sense of humour:

  • Really Interesting New Gene (RING)
    The lack of inspiration for naming this gene is in itself quite funny.
  • Sonic Hedgehog
    This was the first funny one I’d come in contact with; at first I just thought I misunderstood the speaker. But it’s a real gene, that when mutated causes fly embryos to be covered with spike-like structures, and thus look like a hedgehog. It also gives the fly supersonic powers.
  • Don Juan
    A gene present in sperm cells of male fruit flies. It makes them extremely sexy.
  • Dissatisfaction
    A gene involved in many aspects of sexual behaviour, apparently not the very useful ones.
  • I’m not dead yet (Indy)
    In reference to a scene in Monty Python and the Holy Grail, when mutated this gene causes an increase in the lifespan of fruit flies. The flies live forever unless swatted.
  • Van Gogh
    In zebrafish, a mutation of Van Gogh results in tiny ears – wait, fish have ears? In fruit flies, a mutation of this gene causes the wings to develop a wing pattern that apparently looks like Starry Night.
  • Tinman
    A mutation in Tinman in mouse embryo results in no heart and the desire to feel love.
  • Casanova
    The result of this gene mutation in zebrafish is that they are born with two hearts, making it a incorrigible womanizer.
  • Spock
    So zebrafish really do have ears, though with a mutation in the Spock gene they end up being pear-shaped. And possibly slightly pointy. It is unsure if the mutated fish are also confused by human emotions, though it is reasonable to believe that most fish probably are.
  • Callipyge
    Sir Mix-a-lot would just love this one. A mutation in this gene results in sheep developing very large hind ends, or “beautiful buttocks” (callipyge in greek), and increased twerking abilities. You got buns, hun!
  • Dracula
    When zebrafish with this mutation are exposed to light, the fish die due to their blood cells bursting (yuck). You probably can kill them by running a wooden stake (or toothpick) through their heart as well.
  • Brainiac
    Fruit flies with this mutation have increased development of brain cells, causing them to realise that a closed window is not an exit.
  • Cheap date
    Give a few drops of alcohol to flies with this mutation and they’ll appear drunk. I’m not sure how many drops it takes to get a wild type fly drunk, but apparently Cheap Date flies are more sensitive to alcohol. They’ll probably be okay with eating some cheap garbage left overs as well, further reducing costs of a date.
  • Ken and Barbie
    Flies with this mutation lack external genitalia. They also have unreasonably small waists and plastic hair dos.
  • Halloween Genes (including disembodied, spook, spookier, shadow, shade, shroud and phantom)
    Mutations in Halloween genes cause flies to grow scary, abnormal exoskeletons, giving them instant status as spiderman nemeses.

A few more honourable mentions: Armadillo, Bagpipe, Bag or marbles, Grunge and Teashirt (fly), Jelly Belly, Seven up, Snafu, Wishful Thinking, Slamdance, Slowpoke, Smaug, Stardust, Grim and Reaper, Shaven Baby, Kryptonite and Superman, and Swiss cheese. If I ever discover a gene (very slim chance), I will do my best to come up with something original, but with all that out there, it will be a challenge.

Extra note: Not only biologists have a sense of humour. There is a theory in physics called “The Hairy Ball Theorem”. Don’t worry, it’s about not being able to brush coconuts (What?). And I’m sure there are more examples out there.

On Growth and Form

Before I start, a short comment on personal growth:

After a quite frustrating day yesterday, I decided to get up bright and early, go for a run and then head to work today. It’s actually a national holiday here (ascension), but as I have to take my holidays explicitly, and “I’m here for work and not for fun (except for weekends)”, that was my plan. So I was up and ready to leave for my jog, when my flatmate just entered the front door, after a night out. Made me think.

I guess I’m a “real grown-up” now…

But now, On Growth and Form.

I have discovered that Dundee has had quite an interesting inhabitant. His name is D’Arcy Wentworth Thompson. I had never heard of him until sometime last year when we went out to dinner in a restaurant called The D’Arcy Thompson. A plaque on the wall informed us he was a biology professor in Dundee (at the time the university was still part of the University of St. Andrews) around 1900.

Sometime later, I went to a talk about penguins, more specifically about the two penguins that Dundonian Arctic explorers had brought back from their trip south. The penguins had gone through quite a bit, one even was the official mascot of a student faculty club, but they are now on display in the D’Arcy Thompson Zoology Museum on the campus of the University of Dundee. We went to go see the museum after the talk, it’s a room stuffed with, well, stuffed animals. Quite an impressive collection, including a giant crab. (Giant means more than a meter across. Imagine running into a wild one!)

The penguin before it went missing. (ca. 1900)

But it wasn’t until last week that I realised how interesting Mister D’Arcy really was – and I just realised that sounds like a sentence from Pride and Prejudice. A research letter in Nature Physics on the combined mechanics of cells in tissues mentions the following:

In 1917, D’Arcy Thomson published a treatise On Growth and Form in which he suggested that morphogenesis could be explained by forces and motion – in other words by mechanics.

You might recall that my PhD is about the mechanics of gut cancer. And I didn’t know about D’Arcy, shame on me! In the meantime I’ve tried to get my hands on the book, not too difficult because there are some on line pdfs circulating with the whole thing. Unfortunately, I’m the worst at reading from a computer screen, so I haven’t gotten very far*, but it seems that Mister D’Arcy was quite interesting indeed. His 1136-paged book reads a bit a philosophy book (or it does in the first 304 pages). He tells the story – for it’s written like a story – of how the mechanics in biology is quite similar to the mechanics of inanimate bodies, and that growth and morphology can essentially be explained by physics. He gives a whole list of examples, where he makes analogies between biological systems and physical systems. He admits that this will not explain every detail of biology, but that it is possible to explain certain simpler phenomena of organic growth and form using mathematical and physical descriptions. His studies on fractal patterns and linear transformations (rotation, translation, shearing) have been important for image analysis, architecture, mathematics and probably many other fields.

Mathematical transformations of homologous features in fish.

Then how had I never heard of Mister D’Arcy (I realise it should be Mister Thompson but that just doesn’t have that ring to it)? Luckily I’ve figured my lack of knowledge on time and can rectify that mistake. D’Arcy had innovative ideas, that have been pushed to the sidelines by molecular and genetic research in morphogenesis. Nevertheless, is book is merely descriptive, so there is still much to be learned. Which is where projects like mine come in.

Hurray, I have a purpose!

Thank you Mister D’Arcy!

*If anyone knows where I can get my hands on a good hard copy, please let me know! Amazon only cells “bad quality and incomplete” versions, so it’s proving quite difficult.

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

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.