Craigies Ballyhook Flyer 2012

This has been lying in the fridge for a few weeks, waiting for me to get around to drinking it.  The Craigies Ballyhook Flyer smells like actual apples, appley apples rather than fermented apples.  It’s dark and cloudy and smells even more appley when it’s in the glass.  It’s a very dry cider, not as sweet as it smells, but it’s very drinkable (now it’s aaaaaaall gone).

If you like dry cider, you’ll love it. If you like sweet cider, you won’t. If like me, you prefer medium dry, you’ll just have to try it, and have it at the right time when you’re in the mood for it. I’d love to cook with it, I’d say it’d be lovely for casseroling sausages in. Sadly I’ll have to go seek out a bottle in town and I can be lazy at times.

Bought from: Celtic Whiskey Shop

How much: Somewhere between €4 and €5 (Irish cider isn’t particularly cheap but seems to stay under a fiver in off licences)

Ate with: The memory of Chinese takeaway, eaten earlier in the evening

ABV: 5.8%

Buy again? Maybe if I come across it. I imagine it’d be amazing for cooking pork or ham in…

craigies ballyhook flyer

It’s gone now, but it was delicious and not-see-through

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.
Continue reading

Tempted? Summer Sweet

Tempted? are a cidery based in Northern Ireland who have a range of Irish craft ciders, and bring out the odd seasonal batch of something new.  This summer’s offering is Summer Sweet, and it is so very sweet.

Unfortunately, despite my fondness for sugar, it was a bit too sweet. It’s a cloudy cider, with a strong oakey taste as well. A few ciders do the woody-taste well, but with the extreme sweetness, it just didn’t work out.  I’ll stick to the other ciders in Tempted?’s core range, and wait to see what appears next year instead.

Bought from: Martins of Fairview

How much: Just under €4.50

Ate with: Sweet Chilli Pistachios (these are AWESOME)

ABV: 5%

Buy again? Not this one, but probably other Tempted? ciders

It is indeed sweet

It is indeed sweet


Mac’s Armagh Cider (Lyte)

This evening, after a long day, I opened a bottle of Mac’s Armagh Cider. Only the lyte though, as at 3%, it shouldn’t do too much damage to tomorrow morning.

It’s a good medium cider, and remarkably dry for a low(ish) alcohol cider (it’s not dry, but far from the sweetness of pure apple juice). It’s very tasty and appley, a solid cider.

The label is a bit plain, and has a link to a broken website ( and an email address I’ve emailed about said broken site.  It tells you which harvest your cider came from (mine was harvest 20), and surprisingly, the calories (it say 225 but i don’t know if that’s /mL or /bottle).

Bought from: Irish Celtic Whiskey Shop

How much: Don’t remember, it was a few months ago

Ate with: Tesco Cheese Curls (don’t judge me)

Buy again? Definitely, just need to haul my ass into the city centre to do so.

Lovely cider

A lovely pint of cider, with an offputtng blue backlight

sCider is Delicious

I’m going to start keeping a list of tasting notes for various ciders (mostly Irish, all craft) on the blog. I’m not sure whether to keep it as part of the main site or try to make a subblog, but wordpress isn’t making the latter very straight forward. They will be gathered here for those of you who are interested.
It’s not quite science, but it is VERY delicious (usually), so it should fit for the most part. Will have to start having my fancy camera on hand when I have the odd pint from now on 🙂

Modifying the lemon drizzle cake, a little

I love lemon drizzle cake. It’s really wonderful, and not so hard to make, and in my experience, (almost) everyone loves lemony cake. As I make this cake often enough, I made some adjustments to it, to see if the people who like it a lot could find it in them to like it even more!

Inspired by my labmate’s love of lemon and poppyseed cake from the canteen (I’m impressed, they didn’t mess up the cake), I threw a teaspoon of poppy seeds into the cake batter and baked like normal. The seeds give a gentle bite to the cake, it’s really wonderful.

Poppy seeded lemon drizzle cake

Lemon drizzle cake filled with poppyseeds and super tangy drizzle for my sister’s graduation

In addition, my beloved’s favourite part of the cake is the lemon drizzle part (and quite a few other people, I’ve found), so I doubled up on the lemons to make his face pucker up even more. I used the juice of two lemons for the drizzle but the same amount of sugar. The centre of the cake is the most dangerous for those of us who like moderately (rather than insanely) tangy cake, I have yet to master the art of getting the drizzle to hang around the edges. As the cake top is a bit wetter with the extra juice, only dust it with icing sugar right before you plan to show off.

The above pictured cake was dusted with icing sugar twice, once before heading to the university for my sister’s graduation (yay! she’s got a PhD now, in microbiology though, yucky), and then again when we got home and were about to eat the cake. The cake didn’t last long, but that’s ok, cause when you get a PhD, many people make cake, so there was carrot cake, caramel squares, and cheesecake too!

Graphing with the twitter archive and R : or how I tweet too much

So last weekend, @encephalartos produced a graph of his tweets as extracted from his twitter archive, and thereby tempted me to spend the rest of my weekend and some extra time beyond figuring out how he did it. Turns out he used excel to break the timestamps and R to do the rest, but I didn’t realise he used excel till I had spent hours figuring out time in R, so I present to you the entirely R way of doing it.

I like to use Rstudio for doing my R work. It’s available for Linux, Windows and Mac so you’ve no excuse. Most of my R knowledge comes from workshops that Kevin O’Brien ran in Tog. If you’re based in Dublin and want to hang with some R folk, the Dublin R group meets (ir)regularly around town.

The Twitter archive is a great excuse to practise your R skills, as (depending on how much you tweet) it’s a nice large dataset with results that will be interesting but not critical to the running of the world. You can download your archive by going to the settings page on and at the very end, there’s a button to click to request your archive. After a few minutes you get an email with a link to download the zipped archive that contains lots of delicious data. For these graphs, you only need the file tweets.csv which contains all your data as a handy flat file, where columns are separated by commas.

Getting the archive ready to graph

Importing your archive in Rstudio is really easy. Go to Tools>Import Dataset and follow the instructions (or you could look up a tutorial how to do it the proper R way, but why have an IDE if you don’t use it 🙂 ). The default settings should cover the tweets.csv but double check that it looks right in the preview pane.

The timestamps column is what’s interesting to us today. It’s formatted in ISO 8601 format, but Rstudio will have imported it as a character rather than a date, so we have to do some quick conversions.

You will also need to install/load the relevant libraries for the date handling and graphing.

#You only need to install once, but you need to load with library() every session.


Convert the timestamp to POSIXct format using as.POSIXct() and put it in a new column (I don’t like overwriting old columns).

tweets$posix_timestamp <- as.POSIXct(strptime(tweets$timestamp, '%Y-%m-%d %H:%M:%S'))

If you run data.class(posix_timestamp) it should return "POSIXct", confirming the data translation worked. Incidentally, when I looked at my new posix_timestamp column, I saw that it ended in GMT and IST depending on the time of year, it would seem IST is Irish Standard Time, which is equivalent to BST (British Summer Time). I think the conversion to IST might be due to my system settings being for Ireland.

Graphing tweets by week

Once you have the dates converted to POSIX format you're pretty much there, you just need to generate the graph!

ggplot(tweets, aes(x=posix_timestamp)) + geom_histogram(binwidth = 60*60*24*7, aes(fill = ..count..)) +scale_fill_gradient("Count", low = "skyblue", high = "blue") + xlab("Date") + ggtitle("Tríona's Twitter output by week")

The natural bins for POSIXct objects are 1 second, so to get week-long bars, you have to multiply them up. The start of the "week" is presumably the start day of the archive itself, I need to get around to figuring that out.

You can play around with the binwidth to get days or years as you fancy. Likewise you can change the colours and titles.

All my tweets since I joined twitter, graphed by week. Includes retweets and I have no idea when the start of the "weeks" are...

All my tweets since I joined twitter, graphed by week. Includes retweets and I have no idea when the start of the "weeks" are...

In Rstudio, you can export your graph by clicking on the little "export" button over where the graph appeared. I like to export and .png but you can make your own choices about your preferred image type.

Graphing hours vs. weeks

Now that the time is in a POSIX friendly format from earlier, it's easy to extract parts of the date using the Lubridate package we installed.

tweets$day_of_week <- wday(tweets$posix_timestamp, label = TRUE, abbr = FALSE) tweets$hour_of_day <- hour(tweets$posix_timestamp)

We then take these new columns and convert them into a table to make them easier to graph as their frequencies will be listed. A table can't be directly graphed, so we convert it into a dataframe and we can work on from there.

daytime <- table(tweets$hour_of_day, tweets$day_of_week) dfdaytime <-

dfdaytime should be return data frame rather than table when you run data.class(dfdaytime).

R will have renamed the columns when it created the table, with hour_of_day becoming Var1 and day_of_week becoming Var2. Frequency will be in a third column called Freq

Now that we have the new dataframe made, we can plot the graph!

ggplot(dfdaytime, aes(x=Var2, y=Var1, fill=Freq)) + geom_tile() + scale_fill_gradient(low = "skyblue", high = "hotpink") + ggtitle("Heatmap of Tríona's tweets by day vs. hour") + xlab("Day of week") + ylab ("hour of day")

As before, fiddling with the colours and labels of axes and graph title are easy. Choosing a colour that makes the data clearest is the hard part...

Graph of my tweets by day vs. hour. You can see when I tweet most, and when I sleep most. As this archive has 5 years of tweets in it, the during-work-hours tweets may be from before I started the PhD proper...

Graph of my tweets by day vs. hour. You can see when I tweet most, and when I sleep most. As this archive has 5 years of tweets in it, the during-work-hours tweets may be from before I started the PhD proper...

Further rambling

ggplot2 is a pretty powerful package in R for making graphs, and thanks to this bit of twitterage, I'm that bit closer to mastering it. Part of its power comes in the piecemeal assembly of the graphs (you spotted the +'s between each chunk of graph code), so after declaring what you want in the graph and the type of graph, you can start adding on other bit to en-fancy-fy the graph further.

The graphs include retweets, so I need to figure out the easiest way to sieve them out (about 25% of my tweets are retweets). I also need to figure out how to make the bins align with the start of the week. I should probably also reproduce the heatmap for the last year, so my supervisors can see I don't spend my entire work day tweeting 😀

Peanutbutter Brownies

A number of members of my collaborator’s group are leaving for pastures new, so I have made cake as a goodbye-you’re-really-gonna-miss-it-here gift.

raw brownies

The brownies prior to baking. The peanutbutter and chocolate chunks sink into the hot brownie batter during cooking, so this method allows even distribution of filling.

The recipe is my usual brownies recipe (also found in the cheesecakebrownies recipe) with the addition of blobs of peanutbutter instead of nuts. I did have nuts, but it was a bag of hazelnuts, and would have needed roasting and skinning, but peanut butter is delicious with chocolate, so this “laziness” worked out well too.

  • 225g butter
  • 375g caster sugar
  • 3 eggs (orignal recipe called for 4 medium, but we buy ex large normally)
  • 75g cocoa powder
  • 100g self raising flour
  • 100g bar of chocolate (or “chocolate”, as I often use scotbar)
  • Peanutbutter (about 3 tablespoons, have more than enough anyway, there should always be peanutbutter in a kitchen)

Grease and/or line a cake tin (I used my 17cm tin and a small dish, the small dish is for have a small set of home brownies when the big tin is brought to work). Pre-heat the oven to 180°C (170° for fan ovens).

Melt the butter and add the sugar. Beat in the eggs one by one. Sift the cocoa and flour together, and add to the mix in three parts.

Divide between cake tin(s). Break up the chocolate bar and plop pieces around on the brownie. Get a teaspoon and a knife and plop 0.5tsp sized dollops about the surface. The chocolate and the peanutbutter will sink during cooking anyway. Put into the oven for 40 mins.

Cooked brownies

See? Allllllll sunk into the brownies. The greaseproof paper means the sunk/melted chocolate chunks wont glue the cake to the tin (trust me, voice of experience, chocolate glue is hard to get off tins without heating).

Let the brownies cool in their tin, then turn them out and cut them up. Alternatively, don’t wait for them to cool and attack them with a spoon… just mind yourself, they’re pretty hot.

spoon on a brownie

Too impatient to wait for them to cool…

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.