Massive brain dump – unanswered questions

1.) SciBarCamb is in two weeks. If you’d like to spend a day-and-a-half meeting interesting people and talking about science in Cambridge for only £10 – sign up .
Ideas for sessions go here
YouTube videos of demos people are bringing along are here
2.) Nature Precedings is closing. I have a manuscript in there, and the archive will stay, so it doesn’t really affect me directly, but it raises many questions that are taking up space in my head that I need for other things, so I thought I’d leave them here as questions, and will think about them later. (Or if you have thoughts, leave a comment – I can’t promise I’ll respond immediately, but I’ll read it.)
To what extent was the NPG brand contributing to people uploading their material? And the fact that it’s indexed in Google scholar? Are FigShare and F1000 Research – the two alternatives for the things that ArXiV doesn’t take – (going to be) indexed in GScholar? Why is Precedings stopping, and what does that mean for the potential for success for those other ventures? Is the fact that preprints can’t be indexed in PubMed (a first stop for searching for most) a limiting factor? Is PubMed’s indexing requirement for journals-with-regularly-published-issues hindering initiatives aimed at storing smaller units of scientific data and preprints?
2b) Following up on that last question, how are people who are used to PubMed as the source of all they need to know going to find info stored in things like FigShare? And other storage places? Should there be a central search place for all those things? How would it work? Would it be curated by researchers, by publishers, by a library or by a company? (People would most trust a library, but companies and some publishers have more money and freedom to set it up.)
3.) Apart from the search questions above – are people going to upload data without the context of a paper at all? Do they need incentives? If uploading data without a paper around it becomes something that counts toward a better chance at funding, would that not eventually lead to mass production of data without particular research questions? Would it make room for people to do research entirely by analyzing data they didn’t produce? A sort of lab-less scientists, a boom of theoretical scientists in all fields? And if, in the future, these lab-less scientists publish insights based on data collected by others, will the people who uploaded data get double the credit? (For uploading, and later for having it used in an academic paper?) And how will funding work if the people who publish the most insightful work never spend any money on experiments, and the people who need the money to sustain the experiments only upload data and never think about it academically? Will science branch out into a non-academic producing form and an academic form?
That’s it. Hope that means I can stop thinking about all this while I’m supposed to be doing other things.

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?

Poster or talk?

A few weeks ago, at a conference, I was talking about posters with some people. Not the specific posters that were at the meeting, but posters in general.
I have only ever had to present posters at department poster days, and never had anything interesting enough to warrant printing at poster-size when the poster day came around, so got stuck with the loose paneling, glue covered, home-made science-fair-style poster that nobody wants to look at.
Although, that would make it easier. It’s the fact that a few people do want to look at it – if only to mercilessly judge it – that brings me to the next problem I have with posters. When people come by your poster, they sometimes ask you to run through the whole story, but you can tell from how their eyes drift over your poster, glancing at the wrong panels, that they’re not really listening. Or, worse, they interrupt you in the middle of the important bit to ask a question that you were going to answer in exactly a sentence-and-a-half from now if only they hadn’t broken your flow. And while you’re in the middle of talking to them, new people walk up, and try to follow the conversation, but they’re completely lost, so they read the intro over other people’s heads, don’t ever catch up to the story, and walk away.

Me briefly capturing people’s attention with one of my glued-together posters for at least long enough for it to be photographed.
I much prefer giving talks, and would tick the “I would like to give a talk!” box every year. Giving a talk was considered one of the awards at poster day, and I only got it once, but it was so much better than doing the posters. Let me tell you why…
The many benefits of giving a talk instead of presenting a poster:

  • Yes, you have to make slides, but you need to do that anyway at some point, and you probably already have slides. Besides, even if you need to make new ones, you will use them again, even if they need a little modification and updating. That poster? Pretty, but old news next year.
  • You need to talk to an entire audience, but they’re gonna let you finish even though Beyonce had one of the best science presentations of all time. Or something. In any case, they’re keeping quiet until the question round, and they will only ask relevant questions, because they’ve heard the whole talk by then.
  • You only need to talk once, and not every time someone else walks up. Everyone is already there!
  • No judging! You are already a winner!
    But every time I have this conversation with people, including this time, I learn that I am in fact crazy, and that everyone prefers making a poster for days and standing next to it for hours over giving a 15-minute talk with slides you had hanging around anyway.

So, which do you prefer – poster or talk?

Stovetop underwater volcano

A few days ago, my friend Karen shared a video of something she discovered in her kitchen:
A funnel in a pot of near-boiling water creates an underwater volcano when the water inside the funnel starts boiling much sooner than the rest of the water. Does anyone have an explanation?
The videos are below. The first video shows the submerging of the little funnel, and the second is the boiling water coming out of the spout. (It’s a bit dark, sorry about that.)

How does this work?

The thing with the plunger?

You know those multi-pipettors? Not the one with the eight rows of tips, but the one where you fill it up and go chnk-chnk-chnk a few times in a row? Do you know what the disposable/washable part of that is called?
I just discovered the answer yesterday, in “Active Surplus” – a Toronto store that sells all kinds of bits and bobs that you can’t buy on their own anywhere else. They sell buttons, dials, wires, sheets of paper, bits of glass, overstock knickknacks, and a whole aisle of labware odds and ends, including this:

Ahhh, that’s got to be the official name of it then.

That survey again

If you haven’t yet clicked it, because maybe you were on vacation or heading a revolution or otherwise incapable of ticking boxes for a few seconds, here is the survey again in which I try to find out how people find my blog. It is for a purpose, which I will reveal when I show the results later this week. It’s interesting, though. And I look forward to making Venn diagrams. (That was not the sole purpose of doing the survey, but a perk nonetheless. Venn diagrams!)

I’m curious

Who are you people? I’ve thought of a handful of reasons why you could possibly be reading this. Please take a moment to click on this one-question survey and select the ones that apply to you.
You can also leave a long anecdotal comment here, but I thought I’d do it so you can also tell me if you’re just randomly passing through.

Squishier – the poll

(Read this post first)
Now with a poll that may or may not work! Vote for the new cow’s name:

What should Squishy Cow’s new friend be called?

View Results
Create a Poll

For reference, that’s Squishy on the left and the new cow on the right.


My bloggy friend Fiona has had a very strange recurring problem: she keeps finding ants on toothbrushes. Only Colgate toothbrushes of a particular type are affected, and it doesn’t matter if the brushes are used or new. Ants seem to love the rubber on these. They’re ant magnets!

Being a rational creature, Fiona has been trying to find out why these ants love the rubber on the brushes so much. She recently ruled out Colgate’s (already shaky) explanation that it was related to toothpaste residue when she found the ants on a bunch of unused brushes. So if that’s not it, then what ? Anyone have any scientific explanations? Read both original posts and their comments for more info.

Knowledge for sale?

I was just reading the “Cambridge News & Crier” – a free door to door paper about all the weekly goings-on in Cambridge. Kittens need loving homes, Area Man grows giant pumpkin – that kind of thing. There was an article in this week’s issue about 40 people being laid off with the closing of a local Astra Zeneca branch. (Thousands are being laid off worldwide.) The article had a human interest angle about how the company was trying to help the laid-off staff members, and a brief paragraph about the type of research they were doing there: developing cancer drugs based on DNA-damage sensing.
Reading those two paragraphs so close together suddenly made me wonder: what happens with the knowledge when a commercial lab closes? In academia, the results can be quickly published if a lab is closing, as peer-reviewed paper or in a student’s thesis, or a former lab member takes the project with them to their new lab, but in industry everything is confidential. What happens with the progress they made? Are their patents and plasmids and notebooks being sold to another company? Or has it all been a waste of time, and will another lab need to start at square one to develop similar drugs from scratch?
To put it more dramatically: are more lives at stake than those of the employees and their families when a medical research facility closes its doors?