When Science goes bad, there’s always Cake

Many of the scientists at work are talented bakers, and the rest are pro’s at eating cake. Quite a few of us have the back up plan “if the science doesn’t work out, I’ll open a bakery/café/restaurant”, after all, baking is a sort of science…

During an experiment that wasn’t going very well, I started chatting with Laura about cakes that could represent various aspects of science, whether the experiment is working or not. So here’s some of my possible science-cake suggestions, and some examples of how science can learn from disaster cakes.

The device isn’t capturing cells at all:
Super rich dense chocolate brownie, with walnuts. Served sandwiched with a very good vanilla icecream and a dark chocolate and whiskey sauce poured over the top.  In a bowl, because you’ve learned your lesson about fluids misbehaving and a plate would make a mess.

A sadly batched tray of muffins, tasty but unbeautiful

Don’t buy the cheapest gloves, don’t buy the cheapest muffin cases. Science and baking have learned many similar lessons

The perfect micrograph using all those fiddly fluorescent stains
Summer fruits tart, with a rich, chewy batter half enveloping the fruit, and a very crisp yet crumbly base. Served with whipped cream with a hint of vanilla. The juicy fruits might stain the cream but it’s all terribly beautiful and neatly presented.

Even Linus Pauling gets it wrong
An orange drizzle cake, moist and delicious, with a scoop of lemony moussey curdlike stuff. No longer full of vitamin C after baking, but hey, megadosing vitC doesn’t work anyway!

Poor melty cinnamon rolls, but they went to a good home

The rolls have leaked in the oven? Still delicious. The PBS leaked in the autoclave? Still a sterile buffer.

Have you any science-cake suggestions? Could you happilly substitute science for cake in your every day life (or vice versa)?

So you’re thinking about doing a PhD, eh?

It’s that time of year, the undergraduates are finished and wondering what to do WITH THE REST OF THEIR LIVES OH NOES! So a number of them have been directed to me, and told “ask her what it’s like, see if she’d recommend it”. I shall restate most of my advice below, for those of you who haven’t got to hear it from my face and because, apparently, it’s not bad advice.
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Why do we communicate science?

At the weekend, I had the opportunity to participate in a science communication master class as part of the Famelab competition. During it, the question of “why do we communicate science” was raised and the same sort of answers I had heard before were given: science is important to society, people need to be educated, science is entertaining and fun, people need to know what tax payers money goes on, PhD students need to tell people why they’re being paid by the tax payer without ever having contributed a penny in income tax. I had heard these before, but this weekend, I decided that the last two weren’t a good enough reason on their own.

First the PhD student and their non-tax paying ways. The PhD student might not be paying income tax or PRSI, but they do pay plenty of VAT in their day to day lives. While they might enjoy their research and are considered a student, they are still performing a job (even if it’s not defined as such). They provide teaching and demonstrating hours for undergraduate students, and by the very nature of carrying out research are doing a job for their supervisor and the greater research community. PhD students work long hours for low “pay” (it’s a stipend, not a wage, this definition matters to HR and Revenue), so it’s not as if they’re taking this tax-money and spending it on all the luxury while never seeing the inside of a lab. Is there some sort of underlying guilt for getting to study and research and be paid for it?

The point of “the tax payer needs to know what their money is being spent on” is a fair one, but I have some concerns around it being an absolute reason. Yes, I agree that information on government spending, including science, must be available to the citizens of that country. But, scientists seem disproportionately pressured to communicate with the citizens that the money being spent on science is justified. I am unaware of a similar drive for goverment accountants to justify themselves, or tax office workers, or healthcare workers. It may be that I mainly encounter scientists and keep up with science policy in particular, but it seems that it maybe some failing in the public perception of what science is that doesn’t exist with other occupations. While I have no idea how aspects of tax are handled from a government accountant’s point of view, I haven’t heard one come out and explain it for me, the lay-audience, either.

Spending public money on science can be viewed in two ways (and should probably be divided between both sides), either as a commercial venture or as a cultural undertaking. Yes, science can have commercial benefit, it advances technology on a daily basis and this can have a monetary return. Where government money is spent on such commercial science, the tax payer should see a return on their money (whether or not they do directly, much of the argument is that the return is in jobs or a reduction in cost of living). The cultural side of science is equally important. Government spending isn’t soley on commercial ventures, they fund social projects and provide healthcare, but they also fund cultural projects such as museums, libraries, public gardens and no one is about to ask the St. Stephen’s Green garden to explain why it’s there. The cultural impact of science ranges from simply contributing to our understanding of the world to imparting knowledge to the next generations of scientists (whether the knowledge is of immediate practical use or not).

I love communicating science to people, whether lay audience or people who are more knowledgeable than I am. I do it for fun, the education of others and because my work is interesting and worth shouting about. I feel the overemphasis on the taxpayer is misplaced somewhat, the media and goverment have a role in explaining science to the world as much as the researcher in the lab. Placing the burden of justifying science on the researchers alone is wrong. Science and not simply scientists have a huge role in our society.

Oh, and PhD students, don’t feel so guilty and keep on researching.

Phospholipid bilayers made easy

Some scientists are artists, I am not one of these. Sadly, that doesn’t get me out of making diagrams to explain my work.

Some glycoproteins (proteins with sugar groups attached) sitting pretty in a phospholipid bilayer (that twin layer of pink circles with tails).

My work deals primarily in cell membranes. Glossing over the details, these can be condensed down to some proteins lodged in a phospholipid bilayer. The proteins are drawn when needed, but the bilayer occupies all the other space and its many repeating units need to be drawn to make sure the illustrated cell doesnt spill its contents into the extracellular space… (ok, that won’t actually happen, but the membrane still needs to be drawn).

Phospholipids are generally drawn the same way, circle for the phosphobit (it’s a short charged group) and a pair of long tails for the lipid part (very hydrophobic). So the phopho head points into the aqueous compartments (the cell interior or the external environment), and the lipid tails of each layer point toward each other (like oil and water, these lipid tails like to stay away from water too).

So how did I draw them I hear you say, by using the awesome free, opensource image editing software that is the GIMP (runs on any platform too, so give it a try).

First thing I did was draw a phospholipid unit with a transparent background and zealous crop so the edges of the image are tight with the drawing. Then I saved it to my images folder (as a .xcf for later use) and to my brushes folder as a .gbr (on linux it’ll be in the .gimp directory). Then when you go to the brush tool, hit the “brush” box in the tool box, then down the bottom right “open brush selection dialog” and hit refresh. Your new paint brush should be ready for use.

There are two options to consider then, the spacing between the brush images and the scale of the image. The scale is pretty easy to figure out, resize until you like the size of it. The space is measured in percent (be nice if they pointed that out more clearly), as you dont want your phosopholipid units overlapping, go for 110% or greater.

You can then draw with the phopho-brush. You can stamp it one piece at a time, or if you draw a curve, the image will be spread across it and spaced by your chosen percentage. You can also use it to stroke a curved path, which is what I ended up doing, very handy (just set the paintbrush settings before you select stroke path). I made two phospho-brush units, one pointing up and the other pointing down, then later I made brushes for each sugar unit I’d have to draw on to glycoproteins.

Don’t forget to erase some of phopholipids to make room for your proteins!

Science Hack Day and crocheted blood cells

At the beginning of the month (March 3rd and 4th to be precise), I had the pleasure of attending ScienceHackDay Dublin, which was a great big hackathon in the name of Science! A hackthon is basically a long session hacking away at your projects or your friends’ projects, think staying up stupid late to get a paper in for a deadline, except more fun and the project is of your own choosing.

The venue before the day starts

Just before science hackday starts, the network team are ready in their nest..... (Schro and VadimCK run a good network)

The event was very well organised, with food provided (including apple lattices for all!), and plenty of space to work. All internetworking sorts of things were well sorted too. After a few introductory project talks in the morning, people assembled off into groups to work on a variety of projects from programming to building hardware to visualise aurora. But wait, Tríona doesn’t do programming or building hardware, so what did she do for the 36 hour event?

A collection of crocheted cells and an antibody

Spot the phagocytosing granulocyte...

I did what I do best, and that’s Science (and crochet). So from about midday on the Saturday (I had chatting/networking to do before that) until 1am and from 10am on the Sunday till lunch, I crocheted various cells. I devised my own patterns for them, and tried very hard to document them, so I have one for the red cell and the lymphocyte, and I have half patterns for the antibody and neuron. I started the neutrophil pattern with good intentions, but X died when I went off to find jelly babies so I lost the (unsaved half-finished) pattern.

The red cell is the first pattern I did that day, and documented as I went along. I’ll put some more patterns up in the near future.

Red blood cell
dc = double crochet (that’s UK dc, a US sc)
dc2tog = double crochet 2 together, it’s a way of decreasing stitches (sc2tog for USians)
A magic circle is basically a loop you work into that can be tightened very tight to form a circle. Put two fingers together and wrap the yarn around them twice, then pick up a chain stitch as if these loops were your base stitch and work the rest of the row into the loops. When you get to the end of the first row, slipstitch to the first stitch and pull gently on the loops to work them tighter and tighter until you have no more hole, and that’s a magic disappearing circle!
Start each round with a single chain, this doesnt count as a stitch. Finish each round by slipstitching to the first dc of the round.
When you get to the end, leave at least a 30cm tail to bind off. I find I often have big gaps that a bit of darning can cover up. You’ll also have to put a stitch or two through the centre of the cell to pin the faces together in the characteristic biconcave shape.

  1. 12 dc into a magic circle
  2. 2 dc into each dc
  3. *2dc into next dc, 2dc into next dc, 1 dc into next dc* repeated to end of round
  4. *1dc, 1dc, 1dc, 1dc, into next four dc, 2dc into next dc* repeated to end of round
  5. dc into each dc to end of round
  6. Repeat round 4
  7. *1dc, 1dc, 1dc, 1dc, into next four dc, dc2tog in next two dc* repeated to end of round
  8. Repeat round 5
  9. Repeat round 5
  10. *dc2tog in next two dc, dc2tog in next two dc, one dc in next dc* repeated to end of round
  11. At this point stuff the cell, remember, red cells have this biconcave disc shape, where the edges are thick and the middle is thin.
  12. dc2tog until no stitches left

Things I learned today (I)

So today I got to do some Proper Lab Work, ie, mixing chemicals to make liquidy chemicals (a buffer today) for putting delicate proteins in. Buffers are solutions that provide the optimum environment for the little cells or proteins or nucleic acids that you work with, so they dont change conformation or otherwise break.

I was given the list of ingredients, and being a happy little chemist for the morning set about making the buffer. As always, I got all the tubs of powders and worked out what weight I needed of each to get the right molarity (that’s a measure of concentration). Then I proceded to add each of the powders to my glass bottle and poured most of the water I would need into it (If you’re going to be pH’ing something, don’t put in all the liquid, you might change the volume when you’re adjusting the pH with your acid or base). And then, I was utterly confused, the nice solution I was expecting to be clear was a muddy brown… sort of like when the water is turned off for a few hours and turned back on.

Panic! None of the solutions I had used for biological purposes before were this colour! So I went into the neighbouring labs and showed my bottle to the postdocs, and lo, my problem was solved (or at least identified). It turns out that manganese (being an awkward transition element) has variable oxidation states depending on the pH of its environment. So my very basic solution had caused it to turn brown. They tell me the thing to do is to add the MnCl2 after I had corrected the pH, and after redoing the solution like this, I had a lovely clear buffer. \o/ hurrah!

So all in all, beware the oxidation states of transition metals (or add them last), your local postdoc can diagnose problems by looking at a bottle of brown liquid, and that manganese poisoning can lead to a neurological disorder resembling Parkinsons disease (looking at the wikipedia article on manganese is fascinating!).

Where is the perfect review article?

So, I’m back in a lab, doing the first rotation of this structured PhD programme. The people are lovely, and the subject seems pretty fascinating, but I’ve been stumped searching through the literature.

I tend to underestimate the value of text books, but for the basic beginning of looking into a subject they’re fantastic. Naturally the most relevant books in the library have been checked out (and thanks to the clear website of the library, I dont realise this until I’m over there and the books not on the shelf). So I start looking for review papers, and here’s the problem, noone writes textbook level introductions to topics. There’s wonderful review pieces on small topics within the whole, but no crash course on families of molecules or the mechanism of glycosylation. The primary research is great, but in order to understand something in a slightly new field (or a field that you didnt study so well as an undergrad), you just can’t beat the simple introduction. The wikipedia is great for the super-superficial look at things (the science pages can be surprisingly detailed, though nowhere as impressive as the pages discussing comicbooks).

So if you’d like to write some nice detailed but not excessively dense articles on anything I could possibly be researching in the next few years, that’d be well appreciated, cheers :)

Masters are hard

So I’m finishing up my masters programme out in DCU. It’s a taught MSc. that culminates in a 12 week research project.
Semesters one and two were (to me anyway) not too hard going. The modules were interesting, some of the topics I had covered before, and most of the workshops and assignments were also … emmm interesting (for want of a thesaurus, and it’s actually the exact right word I want). The taught portion was sort of like doing final year again, except with more modules that interested you.
The research project takes place over the summer, so the masters doesnt finish up till the beginning of September. I was assigned a very interesting and challenging project that should have me doing the proof of concept of an assay my supervisor had conceived (really, not enough words in English/my head for things). The people in the lab I work with are great and really helpful, but the assay itself didn’t want to comply. With a number of hurdles including being sick a lot, contamination, and reagents that suddenly didnt want to work, I haven’t completed all the work I intended doing on the project. On top of which, again due to being unwell a lot, I haven’t got as much writing done in advance as I’d have liked. The deadline is in two weeks (probably shouldnt be writing this post) and a fair assessment might be “I’m bolloxed”. The project component of the masters is designed to give you a good taste of research and an understanding of techniques in the laboratory, it is fair to say I have gotten a good dose of both.
That said, I really enjoyed the masters programme (DC727), and would happilly recommend it to anyone interested in diagnostics. Just get started on writing up your research project earlier than I did….

The PhD hunt

So further to my IRCSET application, I was turned down.  Which was pretty crushing at the time, given how much effort I had poured into it.  I’m still waiting to get feedback on my application, so that should be pretty interesting.  When that arrives, the IRCSET chapter should be closed (until I need to look for more funding in the future).

 

In the meantime I had applied for the BioAT programme.  It’s a multi-disciplinary programme that combines research with addtional relevant taught modules.  The idea is to give the student a better range of skills and exposure to more than one research lab.

Happilly I was granted an interview, just before Easter.  At the time I wasn’t sure how well it went (I waffled on quite a bit about science).  I think my enthusiasm didn’t put the panel off however, as I was offered a place on the tenth of May.  Naturally I am over the moon!  Taking up the place means I can stop hunting for funding and that I have a rough plan for my next four years.  While I don’t have an exact project, it will hopefully be in diagnostics or a closely allied field.