I only started programming during my MSc. It’s actually one of my biggest regrets, that I didn’t start learning at least the basic concepts of programming, data manipulation and modelling a bit earlier. This is mostly because you just cannot do the sort of science I want to do without being at least a relatively competent programmer. The data I work with is huge. It physically doesn’t fit in excel. There are some pieces of software for manipulating satellite data, and creating simple ocean models of various types, but to advance the use of these techniques, learning some sort of code language is unavoidable. Learning to code also makes your methods repeatable. This is particularly useful, allowing for calculations to be repeated over similar data sets from different regions or to repeatedly make and alter figures, even with smaller amounts of data.
Benefits and necessity aside though, learning to code has not been easy for me. For students, I understand why they may avoid learning to code. Like maths, there seems to be something about programming that just turns some people away. Programming is another marmite (FYI, I definitely am not a maths person, though I do love marmite). People who love maths and coding – this post is probably not for you, but if you’re a newish oceanography student/programmer working with Earth system data, hopefully some of my experiences might be useful to you. Learning to code is a significant outlay of time, and an integral part of maximising the efficiency of many scientists work flows. So, whether you are a student, or an established scientist, deciding to learn a language, which one to start with, or whether to learn a new one, is not a decision that can be made lightly.
A large number of oceanographers, mostly those who have come through specific degrees in oceanography, use MATLAB to help them work with data. MATLAB was my first experience with programming. Many don’t consider MATLAB to be a programming language as such, and, contrary to many other languages, it is commonly used with a development environment or Graphical User Interface (GUI). This provides a soft landing for someone new to programming, allowing you to click on things, physically see some of the data, manually manipulate plots etc, and crucially, to write and run scripts through a single interface. MATLAB was a great tool for me during my masters research, and I learnt many more uses for it over the course of my PhD. However, there are a number of limitations to using MATLAB that started becoming apparent to me during this time.
The first thing I realised, was how dependent I was on the user interface. This happened while attending a course on linux systems and Python programming early in my PhD. The course required using a command line interface. For anyone not familiar with computers beyond GUIs, this basically means typing instructions to the computer, to navigate through the file system and execute any programmes you want to use. I was stuck at the first hurdle here. Although you can navigate through file systems in MATLAB in largely the same way as you do through a command line, I never had, I’d always clicked and navigated around my computers structure the same way I would before my programming days. I was also completely baffled by the concept of writing a script in a text editor and then calling it through the command line. Again, you can run MATLAB like this, but I had always done it through the GUI. By this point in the course I was so confused, that I totally failed to engage with the lectures and practicals on Python programming.
I eventually unlearned my fear of the command line (working with Unix/Linux systems definitely helped there), but I still stayed with MATLAB, because who wants to give up precious research time to learn a new programming language when there’s so much PhD to do? Towards the end of my PhD though, another problem became apparent. MATLAB is not open source, i.e. you have to pay for it. This made teaching with it at Universities that couldn’t afford a licence, or recommending it to students I was trying to help, difficult or even impossible. It also meant that I couldn’t use it on high performance computing facilities which also didn’t have licences. Python on the other hand, is open source and free to use. So, I made the pretty tough decision, 6 months before the end of my PhD, to learn Python, to complete the last part of my data processing. Still, I continued to use MATLAB, because a lot of my code for figures etc was already written, until the end of my PhD.
A fresh start at my new job at PML, combined with the fact that some project work had already begun, allowed me to completely transition to Python as my main language. I thought this would slow me down quite badly in my first few months, not being as fluent with Python as I was with MATLAB. I remembered the slow pace of learning to do even basic things in MATLAB. However this has not been the case, I’m really pleased to have picked up Python so quickly, despite not considering myself a natural programmer. It could be that I’ve also had to contend with learning some Fortran in this time…which does make Python seem much easier by comparison!
So I would say, if you are worried about the time it would take to transition to a new language, it might not be as big a hurdle as you think. Choosing timing carefully obviously helps – a new position is a good opportunity for this. But if you can run and ideally work with some scripts in another language before you totally transition, I think it softens the blow.
There are, of course, other options to consider beyond MATLAB and Python. Many of my colleagues use R, which has the benefit of being open source like Python, and has some quite powerful statistics packages. It tends to be quite popular amongst biologists and statisticians. However, I found R less intuitive compared to Python, and Python more suited to the matrix manipulation etc that I was used to with MATLAB. Similarly there’s IDL, which seems to be quite commonly used by those who work in remote sensing, but again it’s not entirely free to use. I have to say that I found IDL easier to work with in terms of syntax, than R, but that’s probably just based on my background.
In an ideal world, I’d want to teach new oceanographers in Python. I’ve not yet found any downsides from the perspective of my work. It seems to be a continually asked for skill in the current job market and has many applications beyond Earth sciences. However, I’m aware that we tend to inherit our programming skills from those who teach us, which is why I began working in MATLAB. Leaving MATLAB was then hard, because few people around me were working in Python. That is changing now, and the online community support for Python is excellent. There are very few problems I haven’t been able to solve with google.
I generally don’t post lots about programming on my blog, since really, there are far better people out there doing this than me. There are great basic tutorials for Python online – including Pythons own beginner guides, and the learn Python tutorials. I found the basic tutorials can be a bit overwhelming though, and get you a bit caught up in some of the details of Python which, while useful and often incredibly powerful, you may not need to use extensively. I found getting some examples of things you would typically do in MATLAB/would like to do with your data, to be the most helpful. Think file reading, selection of parts of matrices of data, basic maths and stats, plotting etc. With regards to oceanography specifically, sites you may want to check out include OceanPython, these links from RSMAS Miami, and many others – just google ‘Python Oceanography’.
I think the best and worst thing about programming, especially with open source languages and as data becomes bigger and more complex, is that your skills must continually evolve. This used to be frustrating to me, as I felt like I was never really improving, until I realised I was actually just pursuing harder and harder tasks. Now I’m enjoying the challenge more. With that said, I’d love to hear from anyone who has any recommendations for great resources on how to make the best of Python – particularly for plotting and satellite data processing.
As a marine scientist I am compelled to be interested in the sustainability of seafood. The various activities I took part in with WWF SASSI (multiple links!) were some of the highlights of my time in South Africa. I’ve been keen to keep my enthusiasm for sustainable seafood alive since returning to the UK. Theoretically this should be easy, there’s a lot of seafood here. But I’ve found that understanding which fish I can buy and from where can be a little confusing. I’m pretty dedicated to figuring it out, but then I am a marine scientist with a fair amount of free time who loves to cook. I appreciate that not everyone else has the time needed to figure out what to buy, from where, and then how to cook it, in today’s fast paced world. Sometimes I don’t either!
So I’ve come up with the idea of a #sea2shop2supper series of recipes where I will discuss what sort of fish I’ve bought, where from, and how to use it in a recipe. Hopefully this will allow me to build up a series of sustainable seafood recipes for me and others to use. I’m kicking this off by showing how I can continue to make one of my favourite dishes I made in South Africa, here in Plymouth.
Thai Hake Curry from #sea2shop2supper
The fishy subject of this dish is Hake. I ate a lot of hake in South Africa, as a readily available cod substitute. I’ve also seen it a lot here in restaurants since I got back and thought “Hooray! A fish I know a lot of recipes for that’s sustainable!”. However, if you look at the Marine Conservation Society guidelines, there’s two main types of hake available here, with different levels of sustainability. I learn’t just how much fishing and management methods can matter from WWF SASSI in South Africa. There, the Cape Hake fishery is green, orange and red listed depending on the method of fishing. Similarly, there are more and less sustainable fisheries for European Hake, and you can often get imported Cape Hake in the UK too – see the details here.
So, with 7 options for hake available according to the MCS guidelines, where do you start? Of course you can hope you have a knowledgeable fishmonger at your local market or supermarket, who will be able to tell you the fishery location and method…but if you’ve tried this I’m sure you’ll agree you can have limited success in getting the information you need. This is not to say we shouldn’t ask these questions to encourage greater uptake of information around sustainability, particularly in our supermarkets, we really should! But if you are having a particularly busy day and don’t have much time to look around, I have a readily available option for you, for this dish. Case in point – yesterday I was feeling quite ill, and Ben had asked for this thai fish curry dish for dinner. A short walk from my current flat, is Marks and Spencers, who sell fresh (not frozen) Cape Hake that is MSC certified. The Marine Stewardship Council (MSC), not to be confused with the Marine Conservation Society (MCS) who produce the lists I mentioned, provides certification for sustainable fish, and is probably the best guarantee you can get as a consumer. The symbol is a little blue and white tick/fish logo – see here. I’m pleased to have seen this logo in nearly all the supermarkets I’ve visited in the UK, ensuring there are more options, particularly for busy consumers. There is also cod that meets these standards, which would also work well in this dish, though the hake is still my favourite. At £2 a fillet (£4 for two), it’s not cheap, but M&S do offer it as part of a 2 for £7/3 for £10 deal. I’d also recommend trying to keep an eye out for when reduced items typically appear – the M&S in Plymouth City Centre had lots of reduced products available yesterday – including lots of nice fruit, veg and meat. I tend to buy these reduced items and freeze them to extend their best before/use by date, or cook them up in to bulk meals to freeze for later. This can be a great way to cook on a budget, eat more exciting ingredients you wouldn’t typically justify buying for (I bought a lot of duck yesterday!) or just save a little extra cash.
The basic recipe for this delicious Thai inspired curry can be found here. However, this is a nice and flexible dish which you can quite easily adapt. Last night for example, I simply poached the hake in the coconut milk, with two teaspoons of M&S thai green curry paste (it’s actually quite authentic and delicious, though I do try to make my own), and then served it with rice, peanuts and a quick veggie stir fry I’d got in a reduced section in M&S for 70p.
I’m excited to continue this series, so if you know of a good place to buy sustainable seafood – particularly from local suppliers, I’d love to hear about it!
***UPDATE*** Cornish Hake has since received MSC certification! So you can now do this dish with a sustainable local fish if you are in the UK 🙂
The novelty of being back in Plymouth is wearing off slightly, and I’m settling in to the rhythms of my job. This, it seems, is the worst time for suddenly being struck by second-home-sickness. The most ridiculous things will set me off (really, who cries when they hear Kurt Darren, except in despair for the state of music these days). It’s been an up and down few weeks, but I’m trying to be proactive about dealing with the downs.
I tend to use cooking as stress relief. I find the focus required to create an interesting dinner a really good form of distraction from whatever is bothering me. Particularly if I’m working with new ingredients or inspiration from cuisines I’m not familiar with. The last few weeks I’ve been looking in to the history of Persian and related regional cuisines. I bought a beautiful book called Persiana by Sabrina Ghayour and have been using my fantastic flavour thesaurus by Niki Sugent to explore typical flavour combinations.
Lamb is a frequent feature of many recipes I looked at, but I don’t tend to be one to go shopping for specific ingredients for recipes. This makes Persian style cooking a little challenging in that I don’t tend to keep things like pomegranates around and I’m still rebuilding my spice collection, so saffron is out. But I did have a big pack of lamb mince to work with.
Two dishes arose, inspired by my reading. First, a cardamom and lemon lamb meatball dish, with roasted cauliflower, cashews, carrot pickle and tahini sauce. Then a lamb and pistachio meatball and fig tagine with mojardara.
The first dish was rich and delicious and perfect for our current preference for eating few processed and white carbs (less bread, rice, pasta, potatoes etc). I personally find this keeps my energy levels more constant throughout the day, and reduces the portion sizes I tend to eat.
This to serve two.
Half a pack of lamb mince (250g)
3 cardamom pods
1 tsp of Ras El Hanout
1 small cauliflower/half a large one
A handful of cashew nuts
A splash of white wine vinegar
2 tablespoons of tahini
1 clove minced garlic
Parsley to garnish
Olive oil/coconut oil
First, make the meatballs. Mix the lamb mince with the zest of the lemon. Crush the cardamom pods to get the interior seeds, crush these and add to the lamb mix. Form in to meatballs of desired size.
Slice the cauliflower in to 1 cm slices or florets depending on how you would prefer for presentation, I like slices. Drizzle with some oil (I mostly use coconut or a light olive oil) and sprinkle with ras el hanout.
Put the meatballs and the cauliflower on to a tray and bake in a medium (180 or so) oven until they are nice and brown and the cauliflower have softened (time will depend on size).
To make the tahini sauce, mix the juice of the lemon with the tahini and a dash of olive oil and season with some ground pepper.
Grate the carrot and dress with the white wine vinegar.
To serve, stack the meat balls on top of the cauliflower, drizzle with tahini sauce and garnish with parsley, crushed cashews and the pickled carrot on the side.
Inspired by the success of the first dish I decided to use the rest of the lamb mince for the other dish, fancying something with maybe a sweeter and more tomato based sauce.
This also to serve two.
Half a pack of lamb mince (250g)
1 yellow pepper
1 red onion
1 tin of tomatoes
A handful of pistachio nuts
6 dried figs, quartered.
1 tsp ras el hanout
1 white onion
2 tsp cumin seeds
2 tsp yellow mustard seeds
1 tsp ground coriander
1/2 tsp ground cinnamon
1 tsp turmeric
Oil for frying (I used rapeseed oil)
Mint and parsley for garnish.
First make the meat balls by mixing the lamb with the pistachios (chopped finely). Lightly brown these in a frying pan. In another pan (saucepan or frying pan, see next point), fry the red onion (roughly chopped) until soft. At this point you can use a proper tagine pot (mine is on a ship somewhere mid-Atlantic) or continue in a saucepan. Add the yellow pepper (chopped in to sizeable chunks), the tomatoes, the figs, the ras el hanout and the browned meatballs. Bake in the tagine or simmer until the sauce has thicken beautifully.
Meanwhile make the mojardara (rice and lentils). This recipe is a mix between the one in Persiana and from the Cranks Bible by Nadine Abensur – also an excellent book. Cook the rice and lentils separately (tinned lentils will speed this up). While these are cooking add a decent amount of oil to the meat ball pan. Slice the white onion thinly and fry until crisp. Put these aside, add the cumin, mustard seeds, coriander, cinnamon and turmeric to the pan. Fry lightly until aromatic. Add the rice and lentils and combine, before mixing the crispy onions through,
Serve the tagine on top of the mojardara and garnish with mini and parsley. It would probably also be nice with a little yoghurt or feta, though I didn’t have and and it was still delicious. We had ours with a bottle of the Fire Flower Shiraz Mourvèdre from South Africa – bought at Waitrose.
I highly recommend making extra mojardara. It lasts in the fridge, makes a great lunch or breakfast (top it with a fried egg) and the combination of rice and lentils is much better than just having the rice.
I was pleased with both these dishes, but I’ve got lots more ideas to experiment with yet. These dishes can take a little bit of time, which is often fine for me, but not everyone, so my next challenge may well be some simpler dishes for busier days.
Whilst discussing the end of my PhD and the recent move I’ve made to start a new job in Plymouth, I spoke a lot about the many worries a young scientist may have while trying to build a career. I should have noted then that these worries are not limited to those of us beginning a career, and a whole set of new worries may face my more senior colleagues. Stress, I’m sure most people will agree, is an ever present part of work, and managing this can be difficult when faced with what seem like never ending and ever increasing pressures. In science this can include long hours, pressure to gain funding, publish papers, etc, in addition to the stresses of any work environment and balancing life in general. Luckily for me, my new workplace is supportive and proactive and recently offered us the opportunity to undertake personal resilience training to help cope with this sort of stress.
You can find lots about personal resilience training online, and we completed a questionnaire to help assess our current approaches to resilience which is available here. Some of the other stuff I looked at online sounds a little “fluffy” (though I’m particularly sceptical in general I will admit), and there are certainly some criticisms of resilience as an alternative/distraction from addressing systemic problems. But the more I’ve read, and since attending the course, I’ve realised that there are definitely aspects of resilience that I’ve already found useful in my life (particularly for coping with my somewhat infamous fear of flying) and can develop further to support my progress in my scientific career.
Since a common stress is not having enough time for things, the course we attended was kept short – just a few hours. We started off discussing what we felt resilience entailed, and came up with a variety of sometimes conflicting answers, showing there are many individual approaches to being resilient. We then spoke about some common components of resilience from various theories – including confidence (feeling competent etc), social support (being emotionally aware and having a supportive network), adaptability (being flexible and viewing change as ok) and purposefulness (having personal values, drive and direction). We also chatted about negative self talk, which seems to me to have a lot in common with the frequently discussed “impostor syndrome” that seems to effect many scientists, myself included. The biggest aspect I took from all this was the need for self awareness and analysis – understanding how you feel, why, and stepping back to check whether you are being unduly negative and can try to think about things in a different/more positive/constructive way.
We were given some useful tools to help focus our thinking on resilience, which I have already started using. I particularly liked the idea of the circle of concern and circle of influence suggested by Covery, Simon and Schuster, 1992. The idea is simple but good for inspiring reflection on personal circumstance. The model is basically two circles, a larger one, encompassing everything you are concerned about, and an inner circle which encompasses the things you are concerned about, but that you have influence over. The model allows you to think about how you can expand that inner circle. I quickly found that there was actually very little within my circle of concern that I didn’t have some influence over, or couldn’t think of ways I could increase my influence over. A second tool was the idea of a resilience prescription from Charney 2007 – including a number of general guidelines to increase resilience:
– Find a positive role model/mentor and develop an active support network.
– Develop resilient thinking – thinking about what is positive and what you have influence over.
– Develop cognitive flexibility – reframing negative situations to look at the positives.
– Identify and focus on what provides you with a sense of purpose and nurture this.
– Recognise and develop the things you are good at but also train in multiple areas to increase confidence.
– Look after yourself physically – maintain a healthy diet and exercise.
A few tasks finished of the workshop. We were asked to think of three positive things someone had said about us recently. I think it is all too rare that we offer praise and encouragement directly to colleagues, friends etc and this is something I’m trying to do more. I had the most wonderful outpouring of support and encouragement (both personal and professional) when we left Cape Town recently and have kept all the emails from friends and colleagues to re-read on days when I’m feeling a bit lonely or having a bad science day. This forms part of my own personal “resilience prescription” – the last task we completed for the workshop. To my prescription I added that I must find a mentor and build a new group of collaborators. I had a great supervisor and wonderful group of colleagues in Cape Town, and I certainly feel their absence at the moment. I also decided to breathe new life in to my existing hobbies – writing this blog, taking part in science communication etc and to take on some new challenges, which has included learning to rock climb this week. It’s a highly personal thing, but if you are struggling with the constant ups and downs of work life, maybe take a look online at some of the information available on resilience, or see if your workplace can offer a training course.
I’ve been following The Samphire Bush restaurant on Facebook since I saw many of my Plymouth based friends and family liking the beautiful photos of their food. Seafood is the speciality of this little restaurant, situated in the increasingly popular Stonehouse area of Plymouth. Obviously seafood is a source of internal conflict for me. I love it as a cook and foodie, but I’m always concerned about sustainably as a marine scientist. I also appreciate the difficulties restaurants face in sourcing sustainable options, and incorporating these in to a profitable business model with ever picky consumers. Regardless, I had seen sustainable options advertised on The Samphire Bush Facebook page, and was really pleased to see their support and promotion of the National Lobster Hatchery, so Ben booked a table for a birthday meal for me.
We struggled to find parking near the restaurant, so I’d recommend taxi-ing or parking in the nearby Royal William Yard. We were greeted warmly on arrival by hostess Maja and offered a table in a corner of the cosy, relaxed dining room. The Samphire Bush offers both a full menu and a fantastic value set menu (£14 for 2 courses/£16 for 3 courses). On the set menu was red mullet and flounder, which are mid-list on the marine conservation society guidelines, not bad, but I had my eye on the local scallops, calamari, crab and lobster which are personal favourites of mine. I opted to have three starters I couldn’t resist, whilst Ben had the set menu including the red mullet, and a chicken dish for main. My scallop dish was beautifully served, and perfectly cooked in a unique combination with cauliflower puree and Shimeji mushrooms. This was followed by a delicious crab and lobster cocktail, fresh with beautiful flavours of apple and tomato. My final dish was the calamari with curried aioli and mango and coriander tartare – a delicious contrast of spicy and sweet flavours and soft and crispy textures. Ben’s mullet dish, with chorizo, was probably the star of the evening (though it faced strong competition from the crab and lobster cocktail) and his chicken main was a well cooked alternative to all the seafood on offer. I finished off my meal with a panna cotta, which was included on the set menu Ben had ordered. I love panna cotta and this one was very nicely done, served with tart rhubarb to cute through the sweet cream.
With regards to drinks, The Samphire Bush has a broad selection of wines, I enjoyed a glass of the great value house white (an Italian wine, which varietal escapes me). I was also happy to see they were keeping things local, with my favourite Rattler cider on tap. We had a lovely chat with Maja about the wine, and she told us that they were looking at some new wines to add, offering us a delicious french red to try.
Our evening ended with a lovely chat with Maja and chef Martin about the National Lobster Hatchery and about the use of sustainable seafood options in restaurants. Their enthusiasm and passion was inspiring, and I was really pleased to see this in a restaurant that specialises in seafood. They have many awesome events planned – including special wine tasting meals, so we will definitely be visiting again soon.
To be honest I’d not need much reason to visit a restaurant with such a wonderfully quirky name as the Greedy Goose. But there was greater motivation behind booking a special dinner at this new Plymouth eatery this week. It’s the first time my mum and I have been able to celebrate our birthdays together in nearly 5 years. We were born on the 16th and 17th of February respectively and have, for many years before I moved to SA, had joint celebrations in some lovely places. A particularly wonderful birthday, was my 21st, for which mum and my dad arranged a lovely dinner for family and friends at the historic Prysten House in Plymouth, at the time home to the Tanner brothers first restaurant “Tanners”. We have a long history with Tanners and regular readers may remember the particularly excellent wine pairing dinner that mum and I shared on a visit home in 2013. So, we were understandably sad to hear that the Tanners restaurant would be closing at the end of last year, but suitably excited to find out that this beautiful location would play host to a new restaurant from former Barbican Kitchen (another Tanners restaurant) head chef – Ben Palmer and wife Francesca.
Prysten house remains ever the beautiful setting it always has been, but is now complete with a subtle but fun collection of goose themed paraphernalia – eliciting a number of squeaks of joy from myself. Service from the beginning of the evening was impeccable, and I particularly enjoyed having a pre-dinner drink from the broad wine selection. Mum and I enjoyed a very delicious but surprisingly well priced glass of prosecco, and decided to have another bottle to go with our dinner.
The Greedy Goose offers several ways to dine – including a tasting menu, with or without pairing, or the general menu, which includes a selection of dishes forming a great value set menu – 2 courses for £17 or 3 for £20. Both, mum, her partner Jon and I opted for the set menu, whilst Ben couldn’t resist a main dish of lamb. Still, after adding extra drinks and coffees, the bill at the end of the evening was really good value. Despite this, service at The Greedy Goose was definitely reflective of high end dining, with attentive staff and some lovely little touches. In particular, a lovely selection of freshly made bread and an amuse bouche of smoked fishcake, beautifully presented in a smoke filled jar, were delicious and thoughtful. Starters of parfait with pear chutney, and duck egg with venison hash were quirky and tasty, a trend that continued in the main courses. Mum particularly loved the addition of devils on horseback to her chicken dish and Bens lamb main combined typical local flavours in the lamb and buttered samphire with more eastern elements of shwarma, aubergine and cashews. Classic dishes were also given a revival and I enjoyed a delicious mushroom and truffle risotto, whilst Jon had calves liver, beautifully soft with flavours of sage and honey.
I can rarely face a big dessert after a rich dinner, so I was pleased to see the option of tiny treats to go with after dinner coffee. A great way to round off a lovely evening and I would highly recommend a visit to The Greedy Goose, already doing justice to the history of this fantastic venue, and writing a promising future of its own. We’ll definitely be back.