Would I eat that?

It’s something I rarely talk about, but this year is my 10th anniversary of being vegetarian. I don’t know exactly when, because it was a very gradual process. I started slowly phasing out meat from my diet in the late nineties, but lapsed in early 2001, when I was staying in Quebec for four months. Soon after I got back to Holland, though, foot-and-mouth disease hit Europe.
During the 2001 foot-and-mouth disease epidemic, hundreds of thousands of cows were killed in Holland alone. The news showed images of piles of dead cows lying on barricaded farms. Many of them were healthy cows, who were just killed to stop the spread of the disease.
I wasn’t the only one to give up meat entirely that year. After foot-and-mouth disease, followed by an outbreak of swine fever that same year, the sale of meat replacements in Holland increased dramatically. That was probably the only positive economic effect. A large number of farming families lost their business after being forced to have their animals killed, and across Europe the epidemic cost billions.
I stopped eating meat because seeing piles of dead cows on the news made me realize how they are not treated like animals, but like objects. I do still eat fish once in a while, because they don’t have the same “aww” factor and because they are swimming freely until they’re caught, and not squished in the tiniest possible spaces. Other vegetarians have other reasons for not eating meat. Some think it’s healthier, others are concerned about greenhouse gasses, and a few just don’t like meat.
But I love the smell of barbecue.
Contrary to what some people believe about vegetarians, I don’t dislike meat. I love it. The crispy skin on a chicken leg, the juicy inside of a steak that’s just right. Bacon. I just choose to not eat any of those things anymore, because I don’t agree with the way chickens, cows, and pigs are kept and killed just so we can enjoy their meat.
That moral decision will once in a while bring up the hypothetical question whether I would eat test tube meat. I don’t know. Would I? Ethically, yes. None of my arguments for denying myself meat apply to test tube meat. Okay, there is a source animal somewhere from which the starting cells have to be taken, but that is no different from the many cell biology experiments I did in the lab. If I can do tissue culture work – and I have done a lot of that – then I can eat test tube meat.
But test tubes and petri dishes make me think of research, not of food. I am picturing meat soaked in DMEM. Would I eat that? I don’t know.
Until very recently, it didn’t matter. It was just a hypothetical question, but now test tube meat has become a reality. Mark Post of the University of Maastricht has been optimizing the process of growing meat in the lab, and he will unveil the first lab-grown burger later this year.
Meat in a petri dish. (Image: Mark Post, Maastricht University.)
The research leading up to it has cost about £200,000, reports the Guardian, and was funded by an anonymous individual donor. It’s a lot for a burger, as the newspaper rightly points out, but it’s a reasonable amount of money for a research project. And if you compare it to the billions that foot-and-mouth disease cost, it’s a bargain.
“If lab-grown meat mimics farmed meat perfectly – and Post admits it may not – the meat could become a premium product just as free range and organic items have.
He said that in conversations with the Dutch Society of Vegetarians, the chairman estimated half its members would start to eat meat if he could guarantee that it cost fewer animal lives.”
Half would, half wouldn’t, and I’m still on the fence. Would I eat lab-grown meat? Would you?


Earlier this month, I joined a table of fellow geeks (including NN’s own Lou) to craft hovercrafts at Drink Shop & Do. The event was run by Science London (the London branch of the British Science Association), who regularly host science craft nights. Dan had been before, and encouraged us all to go.
I forgot my camera and my phone battery died, but Dave and Dan had non-dead phones so they took all the following pictures:
To make the hovercraft, we each got a styrofoam tray (think supermarket meat) and a paper cup. That’s all you need for the basic model. Cut a hole in the middle of the tray, cut a big ring out of the cup, put the ring in the tray, and it’s a hovercraft! If you blow in the cup/hole, the air will lift the tray and it properly hovers above the table.
To make it more crafty, we also got decorations, and to make it more scientific there was a quiz about hovercrafts. Did you know, for example, that one of the prototypes of a working type of hovercraft was made from a coffee can and a cat food can?
Ours were made from paper and styrofoam, and feathers, and coloured paper, and glitter, and glue….
(Here’s mine)
And finally, click this to see a photo of all of us, racing the hovercrafts on the table.

Make history, not vitamin C

(This post was previously hosted on my old blog at http://blogs.nature.com/eva and is published in print in The Best Science Writing Online 2012)

“Does the Flap of a Butterfly’s Wings in Brazil Set Off a Tornado in Texas?”
- Edward Lorenz

This is a story about a tiny molecular shift affecting war, politics, disease, agriculture and international corporations. Like all good stories, it also contains a healthy dose of biochemistry and genetics, some pirates and a few rodents of unusual size. The very start – the event that set everything in motion – is a genetic mutation that happened millions of years ago, but we’ll get to that. First, let’s meet the pirates.

The pirates in this story are Dutch pirates, and they were active near the end of the 16th century. During this time, the Netherlands were occupied by Spain, and after a period of repression, the Northern (protestant) provinces started to fight off the Spanish. They were most successful on water. From 1568 onward, several ships received government permission to attack and plunder Spanish ships. These “watergeuzen” dominated on sea, but in 1572 they captured the city of Brielle, marking a turning point in the Eighty Year’s War.

Meanwhile, a large part of the income for the Spanish side of the war came from trade with the East Indies. The European supply of pepper was solely provided by Portuguese fleets, and the trading post in Lisbon was no longer easily accessible to the Dutch while they were at war with Spain. Pepper was extremely valuable in those days, and the Portuguese kept their routes secret to make sure nobody else would cash in on the spice. But eventually, Dutch ships found a route to the East Indies. They sailed south, all the way around Africa, and returned with enough spices to finally make some money.

VOC ship off the coast of South Africa

Finding a trade route to the East Indies led to the formation of the East India Company (VOC) in 1602 – the first multinational corporation, and the first company to sell stocks. The company did more than buy and sell spices, though. For several years, it had a monopoly on colonial activities in Asia, and it had the power to take prisoners and establish colonies. During its existence, the VOC boosted the economy of the Netherlands to the top of the world. This period of economic growth is referred to as the “Golden Century” in Dutch history.

Money may not buy happiness, but the sudden wealth of the country certainly formed the perfect environment to nurture artistic endeavours and encourage major scientific progress. These were the century and country in which Rembrandt painted the Night Watch and Antonie Van Leeuwenhoek developed the microscopes with which he first observed single celled-organisms. The effects of the VOC trade have shaped entire fields of art and science, all because a few ships found a route to the East Indies in a time of economic need.

There was just one problem with the VOC trade route to the East Indies: It was quite long.

Scientific progress notwithstanding, there was no suitable way to keep the crew’s food, especially fresh fruit and vegetables, from going bad before they were even halfway there. This was a problem, because without fresh fruit, the crew was prone to scurvy. Scurvy was the scourge of sea travellers since the 15th century, when ships started to sail across oceans and stayed away from home – and fruit – for too long. Starting with some spots on the skin, scurvy can progress to bleeding from mucous membranes, ulcers, seeping wounds, loss of teeth, and eventually death. 15th century explorers could lose up to 80% of their crew to scurvy. The solution was known and simple: eat lots of fresh fruit.

Scurvy is caused by a lack of ascorbic acid – better known as vitamin C. Our bodies use this vitamin for many metabolic processes, such as producing collagen or repairing tissue damage. Without vitamin C, we essentially slowly start to fall apart – skin breaks open, wounds won’t heal, teeth fall out.

But we humans are one of the few animals that need to eat fruit and vegetables to keep our vitamin C levels up. Most animals are quite capable of synthesising their own vitamin C. Most, but not all. We share our need for fruit and veggies with other primates, including closely related apes, but also monkeys and tarsiers. Our inability to synthesize vitamin C is the result of a mutation that occurred more than forty million years ago in our shared primate ancestor, affecting the gene that encodes the L-gulonolactone oxidase (GULO) enzyme. Normally, this enzyme catalyses a crucial step in the formation of vitamin C. But in humans and related primates the genetic mutation produces a broken enzyme. It doesn’t work, and we can’t make our own vitamin C anymore. Luckily, it’s quite easy to compensate for the lack of GULO by simply taking in vitamin C via our diets, but this also meant that there was no selective pressure for a functional GULO, and us primates have been living with a broken version ever since.

The relative ease by which animals can compensate for no longer producing their own vitamin C is illustrated by the fact that the mutation that disabled our GULO enzyme millions of years ago was not the only mutation in the animal kingdom to shut down vitamin C biosynthesis. It happened at least three other times: bats, guinea pigs, and sparrows also have defective GULO enzymes and get vitamin C via their diets. The mutation in the guinea pig’s ancestor happened more recently than ours – possibly “only” about 20 million years ago, but that is still far enough back to also have affected another member of the caviidae family: The capybara also needs a steady diet of vitamin C to keep a hold on its title of largest living rodent on earth. Especially in captivity these R.O.U.S. (rodents of unusual size) are, like the sailors and pirates of yore, at risk of scurvy unless they eat enough fresh vegetables.


Speaking of fresh vegetables – how were the VOC crew going to manage the journey to the East Indies, which took longer than the expiration date on their perishables? The ideal solution was to restock along the way, but the continent of Africa was not exactly a farmers market where you can just get some more fruit and veg when you need it. Well then, they would just have to make a farmers market. The VOC took several Dutch farmers, and settled them in South Africa to grow more food for the ships passing by along their trade route. The restocked ships could then sail on with a scurvy-free crew.


The VOC’s Commander of the Cape, Jan van Riebeeck, founding the first Dutch colony in South Africa on April 6, 1652.

If the VOC crew had been able to make their own vitamin C, like most animals do, they wouldn’t have had to bring farmers to South Africa. That move, guided by a mutation that happened millions of years ago, entirely shaped the more recent history of South Africa. How? Here’s a hint: The Dutch word for farmer is “boer”.

The Boer population of South Africa were the direct descendants of the farmers relocated there to supply the VOC ships with the fruit and vegetables for their voyage to and from the East Indies. After the VOC was disbanded and British colonials settled in South Africa, the Boer population moved away from the Cape. Conflicts between the Boers and the British Empire, most notably the Second Anglo-Boer War at the end of the 19th century, directly led to the formation of the Union of South Africa in 1910, which was the predecessor of the current-day Republic of South Africa.

So there you have it. In a scene set by pirates, and with R.O.U.S. lurking in the background, an entire country, with all its political and cultural complications, was formed as a result of a method to distribute fruit and vegetables to the crew of 17th and 18th century trade ships to compensate for a genetic mutation that makes humans incapable of synthesising their own vitamin C.

Our broken GULO enzyme may not have been able to make vitamin C for millions of years, but it’s made history all right.

Colin Firth’s first scientific paper

Colin FirthColin Firth is having a pretty good year. First he won an Oscar for the King’s Speech, and now he also has a paper out in Current Biology!
When guest editing Radio 4’s Today programme in December, he suggested that it could be interesting to investigate whether there were any differences in brain structures between people who lean toward the left or right of the political spectrum.
Geraint Rees of UCL ran the ensuing study, scanning the brains of 90 people to find associations between brain properties and self-reported political preference. Previous studies had found that certain characteristics matched to either liberal thinkers or more conservative minds. People who identify as politically left-leaning are more likely to prefer change, and that has been shown to correlate with increased neural activity in the anterior cingulate cortex. But Firth asked whether the brains actually looked different, and Rees now showed that indeed the progressive voters also had an increased anterior cingulate cortex compared to more conservative voters.
And how do you recognise the brain of a conservative? They have enlarged grey matter in the right amygdala, associated with an increased fear response, which is in line with previous work that showed that right-leaning voters have increased sensitivity to threatening facial expressions.
Huh. So do our brains predetermine who we vote for in the next election, and if so, why not get us all a brain scan instead of making us line up at the polling station? It’s not that simple. Or, to quote the paper:
“Although these results suggest a link between political attitudes and brain structure, it is important to note that the neural processes implicated are likely to re?ect complex processes of the formation of political attitudes rather than a direct representation of political opinions per se. The conceptualizing and reasoning associated with the expression of political opinions is not necessarily limited to structures or functions of the
regions we identi?ed but will require the involvement of more widespread brain regions implicated in abstract thoughts and reasoning”

This brings up all kinds of complicated philosophical questions about free will, but the only question I have right now is: what’s Colin Firth’s Erd?s-Bacon number?
ResearchBlogging.orgRyota Kanai, Tom Feilden, Colin Firth, Geraint Rees (2011). Political Orientations Are Correlated with Brain Structure in Young Adults Current Biology, 21 (8), 677-680 : 10.1016/j.cub.2011.03.017

The biggest petri dish in the universe

I admit, I just clicked the link on the BBC news site because it said something about “beer”, but it turned out to not be about the drink, but a town. Bill Bryson was right – English towns really do have the strangest names…
“Bacteria taken from cliffs at Beer on the South Coast have shown themselves to be hardy space travellers,” the article started. “The bugs were put on the exterior of the space station to see how they would cope in the hostile conditions that exist above the Earth’s atmosphere.”
And cope they did. A year a half in space, subject to temperature extremes and all kinds of radiation, but they made it. The bacteria now live under slightly less harsh conditions at the Open University in Milton Keynes, where researchers will poke and prod them to see which genes were involved in their survival. (My money’s on the family of heat shock proteins .)
Well, that’s nice. But I also find it a bit worrying. If space is treated as a giant petri dish – which it was for this particular experiment – shouldn’t we be more concerned about the fact that we’re contaminating the very system that’s being studied? Were the bacteria well-contained? Who says there aren’t now some British sea cliff bugs propagating on a meteorite on a collision course to Mars?
When in several years time we find our much sought after “Life on Mars”, don’t pop the champagne cork just then: I bet it will turn out to be nothing but the contamination from one of our previous space experiments….

“Google ‘panspermia’” twittered Richard , when I voiced a similar concern in far fewer characters elsewhere. I didn’t need to, because I’ve heard of the idea that life on earth resulted from outer space.The difference is: that is something that (probably) happened and which we still need to study further to be sure about. Putting bacteria on the outside of the space station is something that is being done now (fine, two years ago), on purpose, even though we’re well aware of the risk of sample contamination. Yes, we’ve been going into space for half a century, but always blindly assumed (or at least tried to convince ourselves) that we were just looking around, and not leaving traces behind. This experiment was done with the purpose of exposing bacteria to non-Earth conditions and seeing what would survive. Like a giant survival screen, in space.
So, yes, it worries me that we’re basically purposely contaminating a system of which we don’t yet know what was even in there to begin with.
Richard says: “it’s people like you wot get in the way of progress”
I say: “google ‘ethics’”

Go, internet!

Overheard at a bus stop in Cherry Hinton (near Cambridge). Two mothers talking, and one said to the other: “I did some research on Google, and apparently more people died of swine flu than of the vaccine, so I’m going to get [kid’s name] vaccinated after all.”
They were on their way to the doctor for the little boy to get his shot just then. He clearly did not know what that meant, because when his mom told him where they were going, he did not protest.
This was the first time I’d actually heard first-hand of someone changing their mind (for the better) on a vaccination issue, and thanks to the internet, so I thought that was pretty cool.

Here comes the sun

Last week, my friend Maria asked me a question that I didn’t know the answer to because it’s totally outside my field of expertise. But I knew that Dan Falk would know, and Maria knows him too, so I made her ask him instead.
It’s an interesting question, so with their permissions, here are the question and answer reproduced for everyone’s learning enjoyment.
Maria: [Looking at this table of daylight hours] “Why does sunset time start being later on December 12, 9 days before the solstice, but we still lose time of day, since sunrise is later and later. How come they are not the earliest/latest at the same time, on Dec. 21?”
Dan: “That is a very good question indeed; and although the answer is well known (to astronomers!) it remains very difficult to explain in simple terms – and I admit I have some trouble wrapping my head around it (in spite of having written a book on “time”!).
The short answer is that the discrepancy is due to the earth’s orbital axis being tilted (this is what gives us the seasons), and also to the earth’s orbit being elliptical rather than circular.
Now for a more painful analysis: The solstice, by definition, is the day on which (for us here in the northern hemisphere) the sun reaches its most southerly declination, which also gives us the shortest day of the year. If we measured time with a sundial – which gives “local solar time” – the solstice would also have the earliest sunset and the latest sunrise. But we don’t — we use “mean solar time.” (Actually UTC, but for the purposes of this discussion you can ignore the difference between this and mean solar time). (You can look up “mean solar time” in the index to my book – In Search of Time 🙂 ) Mean solar time is an average: Think of it as the time that a sundial would read, if the Earth’s axis wasn’t tilted with respect to the ecliptic, and if its orbit was a circle rather than an ellipse. But of course it is tilted, and the orbit is an ellipse. The result is that clock time differs from local time, and the difference can be quite large. The difference is called the “equation of time” (wiki-googleable), and it depends on one’s latitude as well as where one is located relative to the centre of your time zone. Anyway, as a result of these two effects, the time of sunset as read by a clock (i.e. as measured via mean solar time) is at its earliest more than a week before the solstice, and, similarly, the time of latest sunrise is more than a week after solstice. (Additional thoughts: Notice that “solstice” is unambiguous: Regardless of how we measure time, there is no ambiguity as to which day of the year is the shortest. But “latest” sunset is relative to the system of measurement! “Late” means that our clock displays a late hour. And that depends on whether we’re using a sundial, a clock, or something else.)”
Dan also left Maria with some links:
The earliest and latest sunrise and sunset – Utrecht University
Thread on ABC science online


Normally I would post this kind of stuff on easternblot but I’m having huge problems with my host right now. Whenever I try to update the site, they block my IP and now I can’t reach my own site from house and from two major UofT libraries. I found out that I was being blocked by contacting the people where the traceroute timed out every single time. They were the people who actually own the servers, they rent out space to resellers, and they were very friendly and helpful but can’t unblock me without the reseller’s permission. I just paid for another year of hosting, too, and can’t get the money back if I can’t contact them (which I can’t!) so I’m thoroughly annoyed by all this. I’m looking for a new host, but since I’m out of town for two days I’ll leave it until I get back.
Meanwhile, I figured: why not post the pretty things I found for easternblot on Expression Patterns for a while. After all, Nature Network is free, and the tech support has a face and name and actually talks back when something is wrong. And NPG doesn’t block my IP address when I try to post. That’s another major advantage. Makes things a lot easier.
So after all that information that you didn’t care much about, here’s some more interesting – and prettier – information.
Information is Beautiful makes infographics from information they spend a long time looking up in far less accessible places. Here is the most recent ,“How Safe is the HPV Vaccine?”. It’s pretty big, so it’s in the extended entry. Click below to see the whole post (if you don’t yet)


Front page science: collecting controls

I found a copy of today’s Toronto Star newspaper on my coffee break, and was thrilled with the front page. All four front page articles in the print edition are about science! ALL OF THEM!
The two smallest ones are the first paragraphs of articles about a meteorite that crashed in a local town and about research in acoustic fingerprinting . The second-largest article (one column above the fold) is about Swine Flu , but it was the huge-with-photo main front page piece that really blew me away. It’s the only time I have ever seen a story about the relevance of good controls that prominently displayed anywhere.
This is the story:
For the past few days, a group of Tamil protesters have been outside the American consulate on University Avenue to demand intervention in Sri Lanka. Meanwhile, just up the street in Sick Kids hospital, a group of researchers has been desperately trying to get enough controls to prove that one of their young patients really has a genetic disorder that is making her blind so that she qualifies for genetic treatment. The girl was at risk of being pulled from the treatment group because the original controls were not taken from her ethnic group, and there was a chance that the mutation she has is common in her country of origin and not actually causing disease.
She’s Tamil, and her doctors had just a few days to find another 20 or so healthy Tamil controls…
You can see where this is going now: the researchers grabbed swab kits and consent forms, joined the protesting masses outside the US consulate, and within hours they had found enough controls.
bq. ““I think it’s a great thing they are doing – it is always great to help with scientists,” said Navaratnarajah after handing over his contribution to the team.”
With the ongoing debates about whether bloggers will replace journalists, I think journalists just made a great case there. No science blogger could ever have been at the right place and time to get this amazing story, and without good journalism it would never have been the main story in a print newspaper.
This is the week of the Sick Kids radiothon, and this edition of the paper also had an entire Sick Kids supplement, but usually that just temporarily puts patients or diseases to the foreground. To get a cheerful, serendipitous story about collecting controls to take up two-thirds of the front page, pushing down a current raging infectious disease to a mere column, is still quite something. Kudos to the Toronto Star and staff reporter Emily Mathieu!

Cause and effect

I was on Facebook today, and yesterday, and the day before, and saw that several people on there linked to the study about Facebook users getting lower grades in college. The headline of this particular article is actually quite neutral, “Facebook Users Get Worse Grades in College”, but it does tend to pave the way for “Facebook makes you stupid” comments. That’s not what the study shows, though. It can’t show cause and effect, just correlation. Several years ago, a similar study might have shown a correlation between time spent watching TV and grades, just because the people who refuse to study need to do something with all their free time.
One of the paper’s authors says a similar thing:
bq. “I’m just saying that there’s some kind of relationship there, and there’s many third variables that need to be studied,” said Aryn Karpinski, an education researcher at Ohio State University.
There are many variables.
The study also showed that students who work more hours at jobs are on Facebook less. Well, yes, they are simply away from the computer more. And students with more extracurricular activities spent more time on Facebook. Again, that’s not surprising. Many extracurricular groups congregate on Facebook and use the site to advertise events. Facebook is part of the day to day administration for many student groups. Even my non-student orchestra has a Facebook group and uses that to announce upcoming concerts.
And then there are the people who go on Facebook to fill out fifty “What Painting/Food/Author/Actor/Book/Animal are you?” quizzes in a row. If they do that instead of studying, then, yeah, that will probably affect their grades. But as someone who spends time on Facebook and has always had at least 5 simultaneous extracurricular activities all through university and STILL ended up top of my undergraduate graduating class, I don’t think Facebook causes low grades. It’s hard to prove – you’d need to find students who are not yet on Facebook, monitor their grades, force them to join the site and spend time there, and then see what happens to their grades. I say nothing.