The Ship Canal Bridge

I recently started a new job, and in its novelty, it feels somehow quite familiar. Once again, I find myself in a building named after my field, wierdly literally; once again, I find myself on the top floor; and once again, I have a view over a body of water.

And once again, I have a view over a bridge that humans have built across said body of water.

The inspiration: William Topaz McGonagall and the Tay Bridge

7 years ago, I wrote about the Tay Bridge, and how the poet William Topaz McGonagall–no relation to Minerva, obviously, who is fictional–seemed quite obsessed with that bridge. In August 1877, he wrote an ode to the Beautiful Railway Bridge of the Silv’ry Tay, in which he praised its arches and pillars, and prayed that no accident would ever befall the passengers crossing the bridge by train, for that would be most awful to be seen.

But alas, with the very writing of his poem about the majestic bridge, it seems he had unintentionally caused it doom. Two years later, in December 1879, the bridge collapsed during a storm causing a passenger train to fall into the river Tay and inspiring McGonagall to write what would become his most famous bad poem: The Tay Bridge Disaster.

I’m not here today to talk about McGonagall, actually, except to point out that he has inspired me to write my own poem, of a bridge that I now have the joy of seeing every day (weekdays from 9 to 5).

Depending how much time you have, and before you judge my incredible poetry skills (it is, as I said, a tribute to William Topaz McGonagall who is generally considered to be the worst poet to have ever lived), I recommend you check out some of his poems, especially those related to the Tay Bridge, in order of appearance:

The result: An Ode to the Ship Canal Bridge

And now, I share with you, an ode to the Ship Canal Bridge in Seattle:

Ship Canal Bridge by Mark Yashinsky is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 United States License.

In the year 1962, on the 18th day of December
A bridge opened up that was sure to be remembered
A largest of it’s kind in the beautiful Northwest
And dare I say, by some considered the best
Bridges as majestic, there are few
Like the one connecting down town to district-U

It’s here the interstate of the number five
Uses steel upon which cars can drive
For the full 4,429 feet that it is long
All cars belong
182 feet high, they often stand in queue
Making their way downtown from the district of U

Spanning across Portage Bay
It’s double-deck steel will never lead you astray
The upper deck goes both ways
Even on the most rainy of days
And down below, express lanes take you
Southbound in the morning, and in the afternoon to the U

It’s truly a magnificent sight to see
Whether from the high buildings of the university
Or from a boat floating on Union Lake
The Ship Canal Bridge is sure to withstand any quake
For truly, dare I say, bridges as majestic, there are few
Like the one connecting down town to district-U

You can find the full known collection of the misunderstood genius of William Topaz McGonagall on:

Plane Food

Plane food is known to taste – well – not so good. The bad news is that researchers have found out why that is and there’s not much we can do about it. The good news is that researchers how found out why that is and now plane companies can prepare foods that have tastes that are more compatible with plane flight.

And then charge us an arm and a leg for it.

Nevertheless, let’s take a closer look at that science, shall we?

Taste or flavor?

When we say something “tastes” good, we typically are talking about its flavor. Flavor is our general sensory perception of something we put into our mouth (phrasing?). It’s the combination of our other senses, mostly taste – what is perceived by our taste buds on our tongue and in our mouth – and smell – what is perceived by receptors in our nose.

Wait, there’s more.

Part of flavor depends on psychological factors, and hence from other senses. Have you ever eaten an apple that – while it may have tasted okay – had a grainy feel? Would you have said that the apple was “flavorful”? I wouldn’t. And food that just looks unappealing will have to work a lot harder to make our brain thinks it’s tasty.

Finally, it turns out that sound influences the way we perceive flavor. And that’s where planes come in.

Sight, Hearing, Smell and Taste all contribute to flavor
And also highly contributes to the uncanny valley.

Quiet in the cabin, please

Research suggests that one of the main reasons for plane food tasting so bad – apart from maybe mediocre cooking and aluminum food trays – is because loud noise environments significantly influence our sense of taste.

Airline cabins are notoriously loud. Noise is often over 85 dB, which is louder than that annoying open office you work in. During take-off and landing, noise can even up to 105 dB, but as your trays must be in the upright position – you’ll not be eating at that time anyway.

Here’s how your taste perception changes: sweet tastes are suppressed, while umami is enhanced.

That means that sugary drinks don’t taste as sugary and actually might explain how I – a non-soft-drink-drinker – can bear drinking a can of coke. A mini can of coke, obviously, that’s all you’ll get. You might have also noticed that the cookies you get on the plane taste suspiciously sweet off the plane (if you are like me and just put everything you get in your bag for a future snack).

On the other hand, umami gets a bit of a boost. Umami is the savory taste you find in foods with high levels of the amino acid glutamate, such as tomato juice, mushrooms, miso, and parmesan cheese.

Some airlines are very aware of this savory fact. The German airline Lufthansa started working with chefs to make more savory meals after they had observed that their passengers were drinking the same quantities of tomato juice as beer!

Left: tall person in a plane struggling to find space for his legs. Right: Person in front of the tall person declining his seat.
As if I don’t have enough problems on the plane. From

Where do we go from here?

Other airlines could pay attention and change their recipes to take advantage of that enhanced-umami effect. Or hand out earplugs for during meals (I’m not sure there has been research on how earplugs might help).

Or – as we do in our family – you bring your own food. Just knowing you made it yourself makes it taste better; let’s be honest, airplane food just always looks a bit mushy. So make an omelet sandwich!

Bone App The Teeth!

Original paper: Yan KS, Dando R. A crossmodal role for audition in taste perception. J Exp Psychol Hum Percept Perform. 2015 Jun;41(3):590-6. doi: 10.1037/xhp0000044.

Definitely not the snowiest city…

(Note: I drafted this post on Tuesday, February 5 so it is slightly outdated.)

It has snowed in Seattle and the whole city has shut down. For the last two days, the schools and universities have been officially closed, the busses have been on their “snow route” and people (including me) have been penguin-waddling along the ice-ridden sidewalks.

Walking on snow with boots.
Thank you, shoes, for having a grip on snow, ice, and reality.

So while the extreme colds of the Polar Vortex in the Midwest of the US seem to have passed, and the snow in Seattle is slowly starting to melt, I thought I’d check in on the snowiest and coldest places. I told you some time ago that Seattle is not the rainiest city in the US. Nor is it the snowiest, or the coldest. But which city is?

The "W" from the University of Washington.
The “UDub” entrance was a prime position for your snowy Instagram pic. (People omitted)

The top three snowiest (major) cities in the US, based on data from 1981 to 2010,* are Rochester (NY), Buffalo (NY), and Cleveland (OH) respectively with 252.7, 240.5 and 173.0 cm of yearly snowfall on average. You don’t get that in inches, sorry you imperials. Seattle averages on a meager 17.3 cm.** However, US cities get practically no snow at all compared to Aomori City in Japan, where an average of 8 meters of snow falls every year (presumably based on data from 1953 to 2016).

If we take a look at coldest cities in the US, Fairbanks (AL, as you’d never have guessed), Grand Forks (ND) and Williston (also ND) make up the top three with -27.2, -19.5 and -17.7°C respectively. In fact, this morning my colleague walked in on high heels, on which I commented: “How do you do that in the ice?” Her reply was simply that she was from North Dakota, she’s used to it.

By the way, Fargo (ND) comes in on number four, deserving an honorable mention because of the awesome movie. And series. Well, I’ve only seen season one, but that was great.

The coldest inhabited place on Earth is considered to be Oymyakon, Russia (-50°C on average, a temperature I can’t even fathom). On Antartica, the coldest ever temperature to be measured was -92°C (even less fathomable).

And apparently, the coldest place in our solar system might not even that far away. The permanently shadowed craters at the moon’s south pole have shown a minimum temperature of -238.3°C, colder than some of the temperatures measured on the surface of Pluto. However, we have yet to measure temperatures at the polar, always shadowy regions of other planets, so it is possible that the Dark Side of the Moon is not the coldest place in our corner of the universe after all.

Anyway, I’m not complaining about living in a mild climate (at least not at this very moment), because it allows me to go on some really nice walks even in February. Last weekend, I walked on the apparently iconic Seattle viaduct, which is going to be demolished. I’m not attached enough, nor a proper Seattelite, to have an opinion on the demolition, but it was pretty cool to walk through the new tunnel (that opened two days later), the old tunnel (that will be filled in) and the viaduct.

New tunnel with light indicators saying "Last Chance"
Last chance to walk in the new tunnel because soon it will be filled with traffic jams.
View on Seattle
Okay, the view was pretty nice.
View of the Seattle docs and ferris wheel
Exhibit B.

* So I should point out that this might have shifted a little in the last 9 years.

** From Seattle’s Wikipedia page, it’s unclear over which time range this was measured.

I was at the Friggin’ Fringe

Almost three years ago, I mentioned – in a passing comment – the Edinburgh Fringe (“a ridiculously elaborate comedy festival that is held in Edinburgh every August, for almost a whole month”). Specifically, I talked about how much “Nerd Comedy” there was at the Fringe. This year was no different.
Well, I guess the difference was that, instead of going to the Fringe for a day or two, I was at the Fringe for a whole week. In fact, I was part of a show.

I still can barely believe it.

And of course, I was in a nerdy show.

Anyway, it was absolutely amazing. We had a total of 162 people come to our show over the course of 5 days, which was an absolute amazing turnout. We got a lot of laughs. We sometimes lost our track (or the chords) but that was just part of the charm. We made a lot of silly faces. Well, I did.

Some of Valerie’s many faces (I actually look worried a lot of the time)

For me, it was mostly a lot of adrenaline. I know this barely constitutes as a proper blog post about doing a Fringe show, but I just wanted to have mentioned it. While I’m at it, let me thank Matt, Coren, and Yana for being such amazing co-stars; Valentina for the amazing organization; and MCAA for putting me on a stage.

There will be a video for those that unfortunately had to miss it, at some point in the pretty near future. So if you were like *damn, can’t believe I missed that,* there’s no need to worry!


Note: wow, that is a lot of pictures of me, it’s quite unsetteling. I’m so sorry.

The devil’s in the details

One of the “hallmarks” of cancer is the ability of cancer cells to spread to other parts of the body, settle themselves in this new environment and give rise to a new tumor. This process of spreading is known as metastasis and is something that typically aggressive cancers are known to do. In almost all cancers, cells can only spread within one organism. Almost all. There are a few – so far 4 that we know of – types of cancer that can spread to another body. In other words, there are types of cancer that are contagious, or transmissible, and that’s kind of creepy.

A transmissible cancer is a cancer where the cells themselves can spread to another organism and cause tumor growth in that organism. This is not the case for virus-born cancer. For example, in the Human Pappiloma Virus (HPV) is a virus that can be sexually transmitted and some types of the virus can cause a whole range of different cancers.  In other words, the virus is transmitted and the virus gives rise to cancer development.

But in the case of transmissible cancers, it is the cancer cells that spread to another organism. Most types of transmissible cancers are sexually transmitted; these types are found in snails and dogs. There is one type of transmissible cancer that is a bit of the odd one out: devil facial tumor disease or DFTD. Sounds kind of satanic, no?

DFTD is a very aggressive non-viral transmissible cancer that affects Tasmanian devils, you know, that Looney Tunes character that creates little tornadoes when it moves…

Why you so aggressive, Taz? Credit: Looney Tunes (Warner Brothers)

Okay, not really.

DFTD is a mouth cancer that looks really bad (don’t google it, or do, whatever, I’m not your boss) and is spread because Taz devils bite each other a lot. I guess, it kind of is an STI because they also bite each other during mating.

And because Taz devils are pretty isolated (they all live on the one island), and the cancer is very aggressive (spreads easily and is very lethal), and Taz devils are pretty aggressive animals (they bite each other a lot), it is a bit of a problem. DFTD has been observed since 1996 and has now spread to most parts of the island. It is feared that DFTD may cause the extinction of Taz devils.

Last year, I went to a talk by Elizabeth Murchison, who studies transmissible cancers, and it turns out that DFTD is actually quite interesting. In her talk, she explained that her team used genome reconstruction to track the origin and evolution of DFTD, and this led to the discovery that there are two independent types of DFTD (if I remember correctly, one of the cancers originated in a female Tax devil while the other originated in a male and that’s how they knew it had to be two separate types of DFTD).

Why would I care? Well, first of all, it is a unique situation to have a transmissible cancer that is isolated to one island, which – scientifically – is a unique opportunity to study how cancer evolves and spreads. Moreover, it is pretty strange that there are two types of a rare cancer (transmissible cancers are very uncommon) that have originated within one species. The two types of cancer started in similar tissue types, and have similar mutation patterns, which implies that Taz devils may be particularly susceptible to transmissible cancers.

But then the question is: why now? Taz devils have been around for ages, why have they now, within what seems to be only decades, developed two different diseases that are very similar to each other and that may lead to their extinction? Is it due to human influence, or perhaps climate change*? Has this happened to other species before, but we just didn’t know because we weren’t around or we didn’t know about cancers yet?

And, can we save the Taz devil? There are efforts to set up Taz devil sanctuaries on smaller islands off the coast of Tasmania to avoid these cancers spreading to the whole population. But if this type of cancer can spontaneously originate, how do we avoid this happening a third time?
Unfortunately, I haven’t made it to Tasmania yet (did I mention I traveled to the other side of the world recently), but I did see a Taz devil in the zoo. Can we save Taz, so he may roam around and make weird tornado thingies?

Tazzie spotted in Taronga Zoo (Sydney)… Okay, they’re kind of cute in a giant rodent-looking type of way.

* Okay, technically speaking that means that it is still indirectly due to human influence.

Penguins Are Awesome

Let me tell you about my favourite molecule. It is completely useless, but awesome nevertheless. Its name is penguinone, simply named that way because its molecular structure looks like a penguin.

The resemblance is uncanny

The full scientific chemistry-nerd name for penguinone is 3,4,4,5-tetramethylcyclohexa-2,5-dienone, but why would we bother with such a mouthfull?

So far, there hasn’t been a use for penguinone, but in the last few years, my friends and I have started a bit of a running joke around penguins, including putting penguin easter eggs in our presentations and reports, using penguinone to explain certain phenomena (specifically Raman spectroscopy), and spreading random origami penguins in random places.

And then, a very talented friend of mine made a crochet penguinone and all hell broke loose. Well, not really, it just prompted a twitter account which Pengiunone now uses to post narcissistic travel pics and random penguin pictures. Because: #PenguinsAreAwesome.
This included episodes like when Penguinone was looking for a new place to live:

was on vacation in mostly very sunny and warm places:

doing arts and crafts:

and participating in the March for Science:

So there’s no point in telling you all this. I just randomly remembered that some time ago (okay, a long time ago), I wrote a bit about geneticists having fun with names, but as it turns out, chemists are pretty punny too.

EduTourism (II)

I had just submitted my PhD thesis for review (*mini-applause for myself*) and decided that the two months I had before my PhD viva (or PhD defence) would probably drive me half-insane and maybe I needed an extended break somewhere very far away.

So I went very far away: I booked a trip to Australia. However, still being me (as in: a science communication addict?) and considering my previous experience as an edutourist, I emailed a few universities to let them know I would be around and willing to volunteer at any scicomm event they might have. One university replied. I also signed up to an Australian mailing list and answered a call for volunteers.

So, in between my actual travels, I ended up doing some public outreach slash science communication down under. And boy, it was fun.

The university that replied to my spontaneous volunteering was LaTrobe University in Melbourne, where I had the opportunity to talk to a year 9 class (which are, I’m guessing, 14-year-olds?) about my research and my experience as a PhD student. I slightly changed a previous talk of mine (mostly left out the singing; oh yes, I went to a conference and brought my ukulele once, it was marvellous) and spoke to a class of maybe 30 students about the Physics of Cancer in general, and how my research sort of fits into that field. The students seemed very interested and asked some questions about what it’s like to do a PhD and if all that travelling isn’t very tiring. As thanks, I received a gift card which was super useful because I used it to buy a raincoat. Apparently, it does rain in Australia.

La Trobe Institute for Molecular Science

The other event I attended was the Science and Engineering Challenge, which is a national competition organised by the University of Newcastle that challenges teams of high school students (I’m guessing 14-year-olds?) to do a range of different tasks related to engineering and science, such as building a water turbine, a suspension bridge, a catapult, creating an encrypted code or building an earthquake-proof structure. I helped out at the Sydney event for two days.

Students at the final challenge: suspension bridge. It was very suspenseful.

Apart from the fact that I wasn’t allowed to take part myself – I would have loved to build a water turbine and catapult – it was absolutely amazing. My role was to facilitate the aforementioned activities (one for each day I was there), and it was really interesting to see the creativity and competitiveness of the students. Sometimes, the more unexpected design was more efficient, sometimes the group with the most extensive and thought-out plan ran out of time and couldn’t finish their idea. It was up to me to encourage the students to think both logically and out of the box without actually really helping (or so I tried).

As with many science outreach activities, the event relied on volunteers from universities. But more unusually, there were also volunteers from the Rotary and from companies (on Thursday I was there, a bank). This made for an interesting range of ages and backgrounds, which in my opinion was a wonderful extra touch and helped bring home the message that a) one of the most important skills for STEM* is creativity, b) with a STEM degree, you don’t necessarily have to stay in STEM, you can go into a whole range of careers, and c) STEM is really awesome, considering all these people – not all them working in or studying a STEM subject – that give up their time to come help at the event.

Anyway, I went on holiday for 5 weeks all on my lonesome and having a few days of scicomming in between was really fun.

Thank you Jess from LaTrobe University for the opportunity to speak to the y9 class and the tour of the university, and Terry from Newcastle University for signing me up for the Science and Engineering Challenge.

* Science, Technology, Engineering and Mathematics


Last week, I was in New York City.

For the most part, I was on holiday.
*cue 3-line rant about how amazing it was*
I can’t stress enough how amazing it was – obviously; New York is awesome – and how much delicious food we had – lobster sandwiches and NY pizza and (no-Turkey-for-me) Thanksgiving dinner – and how sad I am about being back in the real world.
*end rant*

But alongside the fun and leisure, I also volunteered for a science education event organised by RockEdu, Rockefeller University’s educational outreach office.

Apparently, it was surprising that I would give up half a day of my holiday to volunteer at an outreach event. But to me, it was an interesting experience, an opportunity to try out my outreaching enthusiasm in a different context, make some useful connections and most of all, a whole lot of fun!

After this experience, I’d really like to pitch a new idea: EduTourism (#EduTourism, spread the word, folks): volunteering in educational programmes while on holiday. It gives a new perspective on outreach, it gives you a good excuse to visit another academic institution, and it is a perfect way to interact with locals! Also, it makes you feel that your trip was more than just a – albeit entertaining – waste of money.

What I especially liked about the RockEdu lab, was how organised everything is. Instead of the usual format of a science education team, i.e. a bunch of volunteering PhD students and PostDocs who want a break from their research and the occasional coordinating staff member, RockEdu has a team of 5 or 6 people permanently working in outreach. They write grants, create activities, set up mentoring programmes, coordinate summer projects, etcetera etcetera. Moreover, they have a lab space that is exclusively and specifically used for science education. Instead of activities carried out in some corner between labs or in an improvised table-based laboratory missing crucial equipment or sockets, these benches are meant for education! Classes can come in – for free – and participate in a science experiment tailored for their age and level.

So I spent part of the day helping a group of 16ish-year-old AP bio students through a GFP purification process, something I myself knew about but had never actually carried out. Using blue flashlights and yellow goggles, the whole process could be followed closely, which was pretty neat. We learned about proteins, fluorescence, jellyfish, what doing a Phd is all about. We ran a gel and looked at some GFP-expressing worms as an example of an in vivo application. I thought it all was pretty cool and the students also seemed to have enjoyed themselves (while learning something, of course).

Overall, I’m really glad I took the time to participate in EduTourism, and totally hope that this will become an actual thing.

Screen Shot 2016-11-30 at 09.25.24.png
C. elegans with GFP. Image from @RockEdu (twitter)


Over the past two months I have collected pictures, taken with my not-always-so-smart phone, of views on the Tay Bridge from the top floor of my building. I mainly wanted to characterise the different types of suspended water particles based on how limited the resulting view was. However, in the mean time, the clouds have lifted, or at least occasionally, so I was unable to gather all the reference pictures needed for my mist-classification project. It was going to range from “I cannot even see the church tower” to “wooooow”. Instead, I was treated on some colourful sunrises. Hardly something to complain about.

Here is a mini subcollection of those pictures, including one from yesterday showing the hint of snow we have received:

So, before January ends and I sound like a complete div: Happy New Year. May it be filled with beautiful sunrises and other things people wish each other.

A tabby cat’s walk – part II

Forgive me. In my excitement of being able to make a Harry Potter reference, I did not adequately research the previous post.
It all became clear yesterday. It was a lovely day, a Sunday deserving its name. I was out for a walk, had just explored the Dundee Botanical Gardens, and was now heading towards Tesco Riverside to stock up for the upcoming week (Thanksgiving, hurray!). On my way, I passed aforementioned McGonagall’s walk.
Plaque on the ground saying "McGonagall's Walk"
Turns out, that in my previous post, I had quoted the wrong poem! Mr. William McGonagall had written another poem about the bridge, some time before the Tay Bridge Disaster. Nevertheless, I think the jest of my post still rings true: this poet was an absolute disaster.

The full poem will be at the end of this post, as to not force you read through the whole thing, but I will quote one verse here. It seems Mr. McGonagall was a bit of a fortune teller. Sadly:

Beautiful Railway Bridge of the Silvery Tay!
I hope that God will protect all passengers
By night and by day,
And that no accident will befall them while crossing
The Bridge of the Silvery Tay,
For that would be most awful to be seen
Near by Dundee and the Magdalen Green.

Before I leave you alone with the full poem (feel free to not read it), I’ll leave you with some pictures from my Sunday walk. Better use of your time to look at those, I’d say.


The Railway Bridge of the Silvery Tay – by William McGonagall

Beautiful Railway Bridge of the Silvery Tay!
With your numerous arches and pillars in so grand array
And your central girders, which seem to the eye
To be almost towering to the sky.
The greatest wonder of the day,
And a great beautification to the River Tay,
Most beautiful to be seen,
Near by Dundee and the Magdalen Green.
Beautiful Railway Bridge of the Silvery Tay!
That has caused the Emperor of Brazil to leave
His home far away, incognito in his dress,
And view thee ere he passed along en route to Inverness.
Beautiful Railway Bridge of the Silvery Tay!
The longest of the present day
That has ever crossed o’er a tidal river stream,
Most gigantic to be seen,
Near by Dundee and the Magdalen Green.
Beautiful Railway Bridge of the Silvery Tay !
Which will cause great rejoicing on the opening day
And hundreds of people will come from far away,
Also the Queen, most gorgeous to be seen,
Near by Dundee and the Magdalen Green.
Beautiful Railway Bridge of the Silvery Tay!
And prosperity to Provost Cox, who has given
Thirty thousand pounds and upwards away
In helping to erect the Bridge of the Tay,
Most handsome to be seen,
Near by Dundee and the Magdalen Green.
Beautiful Railway Bridge of the Silvery Tay!
I hope that God will protect all passengers
By night and by day,
And that no accident will befall them while crossing
The Bridge of the Silvery Tay,
For that would be most awful to be seen
Near by Dundee and the Magdalen Green.
Beautiful Railway Bridge of the Silvery Tay!
And prosperity to Messrs Bouche and Grothe,
The famous engineers of the present day,
Who have succeeded in erecting
The Railway Bridge of the Silvery Tay,
Which stands unequalled to be seen
Near by Dundee and the Magdalen Green.