Towards new horizons: sequencing Lil Bub’s genome through crowdfunding

Update 15/04/2105: Crowdfunding just went live! If you’d like to donate, go to our experiment.com site!

If you’re a regular reader of this blog, you might have noticed a lack of posts over the last couple of months. This was largely because I’ve been busy setting up a new project with two friends (and former collaborators) of mine: to sequence the genome of Lil Bub, an internet celebrity cat – with the help of crowdfunding. We’ve christened the project the LilBubome, and after many months of preparation we’ve finally launched our blog, our twitter and our facebook page. The crowdfunding will start in 4 days.

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Marching on the capital

– a personal take on the French #SciencesEnMarche movement

Amélie and the garden gnome

Amélie and the garden gnome

Before I moved to Lyon, my view of France was based primarily on popular media. Looking back at my expectations, I can now report a disappointing lack of obsession with garden gnomes, whereas the myth of exorbitant amounts of dog poo on French streets has proven true. I can’t comment on the quantity and quality of late night porn on national television (supposedly a lot and explicit) since I don’t own a TV. As for endless strikes and protests, after a lackluster year with no major demonstrations, finally something big is happening! Researchers in France are – as someone said on twitter – “doing what the French do best: protesting”. In a movement called Sciences En Marche, scientists from all over the country are cycling, hiking and kayaking towards Paris, protesting against the government’s neglect of science. Reports of the demonstration and the demands have been reported elsewhere (amongst others a detailed write-up in the LabTimes, and also in Science and Nature). So today, having seen Sciences En Marche in action, as the “protests” arrived in Lyon, I’ll share my personal view of things.

SciencesEnMarche in Lyon. The flag of the movement is attached to a Velov bike, an iconic symbol of the city, as Lyon was one of the first towns to adopt a bikesharing system.

Sciences En Marche in Lyon. The flag of the movement is attached to a Vélo’v bike, an iconic symbol of the city, as local scientists join the demonstrators on their way to the city center.

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And so they fail again? The EC’s Science 2.0 consultation

The European Commission (EC) has a complicated relationship with media campaigns. Two years ago, its #sciencegirlthing campaign and the accompanying ridiculous video earned it some pretty heavy criticism.


While it was generally agreed that intentions were good, when considering the practical realisation, the phrase a miss is as good as a mile sprung to mind (see here, here and here). After such an epic failure, you’d think the EC learnt its lesson when it comes to media campaigns. Alas, it is not so. Last week, they launched a public consultation on “Science 2.0” (#science20). Initially, I was thrilled: finally, decision makers wanted to hear my opinion on the topic. However, as I went through their website my heart sank: once again, they’ve got it all wrong, bunching together different aspects of Science 2.0, not differentiating sufficiently between different groups of respondents, and generally not quite getting the point why researchers are using online tools. Continue reading

Outreach and politics

or When politics hit close to home

Everything is a matter of perspective.

Without the "Sz" and an accent on the a, my home village, Szirák tuned into a country ravaged by war and insurgency.

Without the “Sz” and an accent on the a, my home village, Szirák transformed into a country ravaged by war and insurgency.

On a hot summers night back in 2013 some – to my knowledge still unknown – hooligans committed crime. They thieved and vandalized public property. Alternatively, one might say they made a statement. By stealing two letters and an accent they turned my small Hungarian home village, unknown to the majority of the global population, into a country suffering from poverty and war and violence: they changed Szirák into Irak (the Hungarian spelling of Iraq). And while, obviously, my village does not have to deal with insurgency and fighting, by many other criteria one might see the likeness: Szirák is a tiny village with less than 2000 inhabitants in a poor rural area of Hungary. Unemployment rates are incredibly high (60% in 2011) and the roads leading to and from the village are so bad you don’t drive there, you slalom your way around ankle-deep potholes. While there’s clean water, electricity, telephone and internet, a centralized sewage system is only now being introduced in the area. The village has seen its share of senseless vandalism and violence, the roma (gypsy) and non-roma population are at constant odds with each other, and there are large social differences: standing proudly next to half-built houses and dilapidated ruins is a 4-star wellness hotel in an old chateau, where well-off tourists can book a “classic package” for 55.000Forints/person – that’s about half of what most villagers, working for minimal wages, earn. So, by and large, things are pretty grim. Continue reading

Museum Magic

Poster for the 2014 Young Natural History Scientists' Meeting by xxxx.

Poster for the 2014 Young Natural History Scientists’ Meeting by Sophie Fernandez (MNHN).

Every museum has its moment of magic. In New York and Washington, exhibits came to life thanks to an ancient Egyptian tablet. In London, the mummy of Imhotep was resurrected in the halls of the British Museum. But next month in Paris, you will not need ancient sorcery to get under the spell of science: the Association for Students and Young Researchers (BDEM) at the French Museum of Natural History is organizing its 1st Young Natural History Scientists’ Meeting (12-14th February 2014)!

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The Inventory

or: The Afterlife of Lab Equipment

3 cell culture hoods (2 without key)
2 centrifuges
2 tables (drawers missing)
1 chair
2 shelves
4 incubators (rusty, but clean, all shelves washed and autoclaved)
2 water baths (encrusted with limescale, even after a week of acetic acid treatment)
2 chests of drawers
1 microscope (without bulb)
1 vacuum pump (NEW!!! :))
1 fridge
1 freezer

This inventory sums up my last month’s worth of work. It may not seem impressive, but there it is. For me, every one of those items represents a small victory. You see, for my postdoc, I got my very own, private cell culture room, but unfortunately no budget for equipment… However, as a resourceful scientist with an empty room and no money I decided to negotiate and scavenge, two expertise I had exquisitely mastered during my PhD. Negotiating got me a decent vacuum pump. Scavenging got me the rest. Continue reading

Woman, know thy place!

Generally, I try not get (too) involved in the whole gender bias, glass ceiling, women having to chose between family and career, etc debate, mainly because I think it’s too complex an issue to briefly discuss in a blog post. But a new Hungarian ad for a fair for women has made my blood boil, and calls for commentary. Continue reading

Is more really better?

As long as I can remember, I’ve heard teachers, professors and politicians say that we should encourage more high-school and university students to pursue a career in science. And I used to be a believer. After all, the people who said this, were the ones at the top, the ones with a proper oversight of things. However, today, I’m not so sure anymore. In fact, I’m becoming more and more convinced that encouraging people to pursue a career in science (or at least research) may just be a way for universities to generate competition and thus obtain a source of cheap labor.

conspiracy-theory-alert_display_imageSounds like a conspiracy theory? Maybe. But here’s why:

As I grow older, more and more of my friends, who used to work in research (and who really liked doing so) drop out. They move towards alternative careers, such as science communication, industry, teaching etc. And they generally list the same reasons for doing so:

1. Early-career researchers get little reward for their work: this primarily means that they consider themselves being underpaid and overworked. Money matters.

2. There’s too much insecurity, pressure and competition as you move up the ranks: there are many, many good scientists with great publication records, who’d all like to have a junior group leader or tenure track position. Obviously, the more people you feed into the system at the lower ranks, the more will compete for the jobs at the top. But there are increasingly less long-term contracts handed out . Security matters. Moreover…

3. … science is becoming less of a vocation and more like a job: It seems to be less crucial nowadays how good or creative you are, and increasingly important how well you can manage and advertise yourself. Your ideas and hands-on experience seem to matter less than what your CV looks like, in what labs you’ve worked and how well you’ve published. And since the results of your first five to ten years of research may therefore define your later career options, this discourages “outiside-the-box-thinking” and taking on risky projects. Often this also means, that science-related non-research activities are undervalued: I’ve filled in fellowship applications where there is no option to include teaching or the organization of science events as an asset.This is extremely frustrating, if you consider that much of science knowledge is actually passed through the grapevine: by great teachers and lecturers who transmit their love of science as well as up-to-date knowledge, and by experienced lab staff who show you the do’s and do not’s of experimental design and lab techniques.

Motivated teachers matter!

Motivated teachers matter!
from “Piled Higher and Deeper” by Jorge Cham http://www.phdcomics.com

So, all in all, my interpretation of the data: thanks to increasing numbers of PhD students and postdocs, there’s plenty of “raw material” to chose from. Therefore PIs and legislators can get away with providing low job security, as well as relatively low salaries. Also, having more early-career researchers also requires less personal touch and more standardized metrics.  And keeping it this way means a cheap workforce, which is why people at the top encourage more students to pursue a career in research. And thus the vicious circle continues…

Still think it’s a conspiracy theory? Maybe. Maybe also have a look at Paula Stephan’s book, How Economics Shapes Science. It provides a much broader and nuanced overview of the interplay between economics and science, including a detailed analysis of supply and demand in research.

But please keep this rant in mind, next time someone tells you we need to recruit more students into science!

The guinea pigs that weren’t

You may have heard: Michael Bloomberg, the mayor of New York City, is worried about the health of his citizens. More specifically, he’s worried about obesity. So, a couple of months ago, in a rather drastic measure, he decided to introduce the NYC soda ban: to limit the sale of certain sugary soda drinks larger than 16 ounces (approx 0.5 l) in certain businesses overseen by the Department of Health and Mental Hygiene. However, back in March, one day before it was supposed to take effect, the ban was ruled unconstitutional by a State Supreme Court. Yesterday, the state’s Appeals Court decided that this previous ruling should be upheld.

Shame.

Not that I am personally particularly worried about the caloric consumption or the health of NY citizens. No. I was, however, looking forward to one of the largest health experiments ever, with all those people roped in as unwilling experimental guinea pigs.

Guinea what? Why? How?

Guinea what? Why? How?

For one, it would have been a great behavioural experiment: would people have maintained the same volume of soda consumption, drinking a larger quantity of smaller volumes?

But more importantly – assuming that people would have reduced their soda consumption – would it really have made a difference? I mean, soda often comes up as a “culprit” in association studies between obesity and environmental factors, but these are mainly associations. And generally, the population with the highest soda consumption is also the one with highest consumption of unhealthy, high-calory food, partaking in less physical activities etc. So, there has been much to-and-fro about true causation and a possible fix. Therefore, I would have been extremely curious about the outcome of such a large-scale, long-term experiment, where this single variable is modified. I mean, clearly, it wouldn’t have been a perfect experiment (where’s the control group?), but from a scientific point of view, it could have been an interesting one…