Google Doodle Moog

Google has a wonderful tradition of adapting its logo to current events. There is a pattern to the days that get Doodles: they are usually national holidays, human rights or environmental commemorative days, or birthdays of famous scientists, musicians, artists, or engineers.

Today the Google Doodle celebrates what would have been the 78th birthday of Robert Moog, inventor of the Moog synthesizer.

The Doodle is a Moog synth, and it’s interactive! You can change the settings, play it with your mouse or with your keyboard, and you can record up to four tracks! It’s hard to play, because it’s not very responsive, but I managed to record a 2-track intro to the Dr Who theme.

I’ve been thinking about the influence of scientific discovery on music, and most of it comes from electrical engineering. The 20th century introduction of instruments such as the Moog have even led to new styles of music. I used it to play the Dr Who theme, because to my ears it *has* to be performed electronically. (The theme was a product of the BBC Radiophonic workshop, which I’ve mentioned before.)

I don’t know if the doodle will still be functional after today, so go play with it if you haven’t yet.

Dancing scientists cure cancer

Canadian scientists are curing cancer by dancing. Well, they’re trying, at least.
Researchers of the Goodman Cancer Research Centre at McGill University in Montreal have made a YouTube video of them dancing in their labs to “Dynamite” by Taio Cruz. Their sponsor, Medicom, is donating money to their research institute based on how many views their YouTube video gets.

If charity is not enough motivation to watch it, you’re going to at least want to see the three gentlemen throw their hands in the air at 1:46. (With help of the credits at the end, I figured out that one of them is Canadian Medical Hall of Fame Laureate Phil Gold and another is former Dean of McGill’s Faculty of Medicine Richard Levin – but who’s the third?)
Montreal has a tradition of academic music videos on YouTube. Students from the city’s other university, UQAM, were responsible for the I’ve got a feeling lipdub, which has had over nine million views to date.

Are there science-themed covers of all of Lady Gaga’s songs?

I assume you’re familiar with “Bad Project”, the cover of “Bad Romance”? You must be. It’s had millions of views. Millions!

And you may also have seen the video for “Poster Face”, which debuted at last year’s Society for Neuroscience meeting:

But have you come across “Chromosome” – a parody of “Telephone”?

Or how about “Phosphorylated this way”, a song inspired by a JCB paper on cyclin-depent kinases, and set to the tune of “Born this way”?

What’s next, I wondered. Has someone covered “Alejandro” and made it about “Avogadro” yet? Yes, that has been done. There are two videos on YouTube with that theme, and both are kind of terrible, so you can look for them yourself if you really want to see them. However, I could not find “Paparazzi” covered to make it about Okazaki fragments, so that route is still open. In fact, I couldn’t find any science-themed Paparazzi covers, which seems unlikely, considering there are about a gazillion different lab-related covers of “Bad Romance”.
Hm. So it appears the answer is no – there are NOT science-themes covers of ALL of Lady Gaga’s songs. But we’re nearly there…

More cats and more macbooks

If you liked the previous post, you may also be interested in this post on Cath’s blog. It’s about the same topic, sort of. I mean, obviously it’s different, because we have totally different lives: she likes hockey and has two cats, I play violin and have just one. But you knew that, right?

The Joy of Stats

I’m going to write a blog post about my fear and avoidance of stats, but since it was partly inspired by Hans Rosling’s BBC documentary “The Joy of Stats”, you can start by watching his enthusiasm before being subjected to my post:

Technical paper: home-made mocha optimization

I made instant mocha at work and am now writing a silly blog post about it.
In this 24-hour economy, the modern workforce has little time to consume fancy beverages, yet working adults are fueled almost exclusively by caffeinated and sweet drinks. This creates an inherent dilemma: work or coffee break? When the sourcing or preparation of delicious drinks is costing the same amount of time as is won by increased working speed as a result of consuming said drinks, no net productivity is achieved.
Here, we solve this problem by developing a quicker way to produce a drink that costs 10-30 minutes (depending on distance between place of work and place of coffee procurement) to source from an external supplier.
Making the mocha
Mochas were produced by adding indicated amounts of instant hot chocolate powder (Cadbury, UK) and instant coffee (Kenco Coffee Company, UK; caffeinated) to a drinking vessel and adding 300 ml water of approximately 97-99 degrees Celcius.
Mocha 1:
The ingredients of a “mocha” are coffee and chocolate. In previous studies, we have successfully created a cup of hot chocolate by adding one big scoop (as provided by the supplier) of powder to a mug of hot water (unpublished). We have also made coffee of varying strength by adding two or three small spoonfuls of instant coffee to a similar amount of water, and adding sugar or milk to taste (personal communication, unpublished.) Our initial attempt to create the derivative drink called “mocha” focused on utilizing an equal amount of resources as the two source drinks. Therefore, in our first attempt (“Mocha 1”) we used a normal amount of water, half of the chocolate powder, and half of the coffee. (See Table 1)

Drink Amount of hot water Amount of coffee Amount of chocolate
Coffee 300ml 2-3 little spoons
Chocolate 300ml 1 scoop
Mocha 1 300ml 1.5 little spoons 0.5 scoop
Mocha 2 300ml 2 little spoons 1 pouch

Table 1: ingredients of source drinks and derivative drinks.
As previously published in a brief publication of preliminary data, a taste test of Mocha 1 (non-blinded, N=1) revealed that the flavour did not resemble that of commercial drinks of a similar nature. Taste was described as “watery” and “not very good at all”. The objective qualifier “watery” was utilized to optimize the production of the beverage, as described below.
Mocha 2:
A classic method to make a drink less watery is to add less water, but a less conventional approach is to increase the amount of solute and solid particles. We used this second experimental method to create the optimized derivative beverage “Mocha 2”. In producing Mocha 2, we made use of a premade pouch containing the exact amount of chocolate powder needed to make one cup of hot chocolate. We added to this 2 little spoons of instant coffee, and the amount of water needed for one cup (see Table 1). Despite the excess amount of solid matter in the cup, emulsification and solubility were not notably affected (Figure 1).
Figure 1: Visible spectrum optical analysis of Mocha 2 indicates no apparent deviation in solubility compared to control beverages (not pictured)
Taste tests (N=1, non-blinded) described Mocha 2 as “just like hot chocolate”, “oh, wait, now I taste the coffee”, and “this is pretty good, actually”.
In both cases (Mocha 1 and Mocha 2) total production time did not exceed 5 minutes, including boiling of water using an electrical kettle.
We describe herein the rapid production of a beverage similar in flavour and basic ingredients as commercial products that may prove far more time consuming to source. Although we have yet to perform a full financial analysis, our own budget calculations (not shown) indicate that long-term adoption of this drink may also be more economically desirable. Together, our data suggest that Mocha 2 may increase productivity by offering a similar nutritional value as commercial beverages, while being less demanding on both time and monetary resources.
Conflict of interest:
The authors declare no conflict of interest, but would welcome Cadbury donations.

BRCA2 cycle path

There’s a cycle path in Cambridge that has the code for the breast cancer gene BRCA2 painted on it, with each nucleotide a colour. If this sounds familiar, you probably read about it, and the geeky attempts to decode it, on Jenny’s blog year. (I just re-read it and was again really proud of my math abilities while soaked in rain.)
Today I finally went to check out the cycle path.
Now, when I said “in Cambridge”, I actually mean “in the middle of a field just outside Cambridge”, but I’ve noticed that that is pretty much true for everything in Cambridge. I mean in the middle of fields. This weekend, for example, is also the annual outdoor film screening in Cambridge. It is also in the middle of a field outside Cambridge. I was all excited about it (films! outside!) until I figured out that part. So instead of going to that field, I went to another field to look for the cycle path.
I knew the cycle path ran between Addenbrooke’s hospital and Great Shelford, and found a cycle path on the map that corresponded with that route. It took me a while to find out how to get from the hospital grounds to the cycle path, so I went inside the hospital to buy a drink and take a break before I even started. (I worked in a hospital for almost all of my PhD, so now find hospitals a totally normal place to buy some refreshments on the weekend. Why? Where do other people buy their lemonade?) With help of my iPhone I found the cycle path, but… it looked normal.
[Not pictured: normal looking cycle path. I guess you can kind of imagine it. Just some asphalt in a field.]
The BRCA gene art doesn’t actually start at the hospital, where people could visit it and admire it, but a few minutes of cycling further down the path and, yes, in the middle of a field:

It was about ten minutes or less to pedal to the furthest end of the path, and from this point on the gene sequence was there the whole way. Here are seven seconds of the cycling journey along the BRCA2 path. (Cycling in the middle of the path for artistic reasons for the video. I otherwise kept left like a proper safe cyclist.)

At the other end was the town of Great Shelford. Here, the end/start of the path was actually close to houses, so it’s something you can visit on foot if you’re in Shelford, but the Cambridge end of things really requires a bike. (Maybe it didn’t start at the hospital because the gene was too short… but why didn’t they make the stripes bigger?!)

Both ends had an information sign as well.

The path was opened in 2007, and includes the 10,000th mile of cycle path in the UK. The nearby Sanger institute (famous for its genome sequencing) suggested to decorate the path with a gene, and BRCA2 was chosen because it also has approximately 10,000 base pairs, but also because it’s a gene that people can relate to. Genetic screens for breast cancer risk are something that people will have heard of, and this is the gene that those tests look at.
Now what we still haven’t figured out is: is the gene on the cycle path the healthy version, or a concerning mutation? If I’m ever really, really, bored, I might decode the whole path and find out.

Tissue Culture

Minor nitpick: it’s cell culture rather than tissue culture, but the joke still stands.
(Found on Twitter through Glendon Mellow )

My life as a guinea pig

I’ve experienced the other side of research recently. A number of weeks ago I spent an afternoon working with Cambridge students in their department. I wasn’t doing the research, I was the research.
I’d been a test subject before, when during my undergrad in Amsterdam I did a number of psychology experiments in exchange for bookstore vouchers. But those were all small studies, and I often didn’t feel that I knew what they were actually testing, leading me to suspect that the whole procedure was some kind of Stanley Milgram-inspired experiment. For example, on one of these occasions, I was given a fifteen minute break in which the student doing the experiment took me to the Human Movement Science department in the same building, where they were also doing experiments on human volunteers. I was asked if I wanted to do a quick 5 minute wall-climbing task within my 15 break in the other study, but it didn’t look fun enough so I declined. But what if that was the test! What if the whole “which picture is different” task I was doing ad naseum was just a ruse to discover whether people would be willing to take two steps on a climbing wall with very short notice? That was ten years ago now, and I haven’t yet seen any studies on “Spontaneous Wall Climbing” come out of Amsterdam, but you never know – these things may take years!
When I found an ad on Facebook for a study in Cambridge looking for volunteers, I was again expecting it to be a similarly mysterious black box, where they just asked volunteers to do some random tasks without saying what it was for. I understand why that is, of course: you don’t want to influence your test subjects if they know what you’re looking at. But this study was different: they were doing a genetic study of perception , and they were very open about what they were studying. (Perhaps because you can’t suddenly change your genes anyway, even if they tell you what they’re looking at.) What’s more, I even qualified! I took the online questionnaire, which did have some odd questions in it, but they were also explained when I came to the lab a few weeks later.
The test day involved a rotation through several dark computer labs, each with a computerized perception test. One of them I found very difficult, almost impossible even, as I couldn’t see what I was “supposed” to see – not even in the “easy” example I got before the test started. I felt like I was failing the test, but then remembered that there is no “fail” – I just have a phenotype! Other tests were easy for me, but probably difficult for others.
The research group updates all participants of the study’s progress, with occasional e-mails about how it’s going and which conference they will present the data. In the latest update they wrote:
“We have now tested more than 800 people and so we are nearing our planned target of 1000. We hope to complete the testing phase of the study by July 31. We are not allowing ourselves to analyse data as we go along (since there’s always the danger that we might be influenced in the way we carry out the testing) but we hope to be in a position to report preliminary results from the visual testing at the European Conference on Visual Perception, at the end of August.”
They still need a few more people in the next few weeks, so if you’re in Cambridge and have some time to spare, go check out the Pergenic site . You need to be of European descent (since that is the genetic background they’re looking at) and within a certain age group to qualify.
Research on human volunteers is quite different from what I’ve done on the other side of the bench. People are reduced to data points, and I’ve been sent a government paper in the past in which I was reduced to one datapoint in analysis of Dutch students who continue their studies abroad. But I did like that they sent me that paper, and I also like that Pergenic is updating their participants. It really puts the “human” in “human volunteer”.


I don’t have time (work, orchestra) but here is the result of the poll:

Squidgy it is!
(I don’t even have time to explain this – just look through my archives)