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From Environmental Science to Earth Observation

November 11, 2015

The last year since I moved back to Plymouth(yes it’s already been a year!) has been very nostalgic on the whole. I’m now living in Peverell where I spent most of my undergraduate years, and my walk to work and town takes me right through Plymouth University campus, and past all the buildings I used to have lectures in.

The nostalgia continued last week when I was invited to attend a careers event for the same BSc (hons) Environmental Science course that I attended at Plymouth uni between 2005 and 2008. I was very excited to do this, I found the small bit of student mentoring I did in South Africa to be incredibly rewarding and here was the opportunity to talk to people who were literally where I was 10 years ago. Back when I started university I don’t think I had much of an idea about where my career would take me. I certainly didn’t consider myself capable of being one of the people giving my lectures, or one of the people whose papers I read for my assignments. I ended up in research thanks to people who told me it was an option for me. It seemed time to pass on that favour.

Taking a bunch of PML promotional material, I set up a little stand amongst other environmental science related businesses. The diversity of the work conducted by the organisations present is credit to the many different career paths that a degree in environmental science offers. It was also a great chance to catch up with some of my old lecturers, who made me feel very welcome.


The day involved a series of short talks amongst networking sessions. I had many students come and chat to me about the work PML does and about my personal work and career path. They were well prepared with questions thanks to an earlier session where they had discussed how to make the most of these sort of networking opportunities.

It was a thoroughly weird experience standing up and presenting in a lecture theatre where I had previously been part of the audience for so many lectures – from economics to ecology, and even including one given by the incredible James Lovelock. I felt the talk went well and I really enjoyed reflecting on my experiences to identify advice I could offer to the students.


Several people who were unable to attend the talk asked to see my powerpoint. As with most of my work, it’s mostly pictures, so I thought I’d summarise the main points I made here:

What do I do?

My current job title is “Marine Earth Observation Scientist”. I showed the students some of the incredible images that I spend most of my days staring at. Beyond being beautiful, these images represent vast amounts of information about the marine environment, which we can use to address the various challenges we face in both using and preserving this diverse environment. Marine science is a microcosm of environmental science itself. Whilst we largely focus on just one sphere of the Earth system, we use the same interdisciplinary approach incorporating physics, chemistry, biology and social sciences. We also use many techniques to study the marine environment, from field work for sample collection, surveys and measurements, to laboratory experiments, remote sensing using satellite data and autonomous vehicles, and modelling. I personally use satellite ocean colour data (for an explanation of that, see here) on a variety of projects covering coastal water quality, ocean heat content, ocean carbon content, model validation and integration with socioeconomics. This involves attending international meetings and conferences, giving presentations, writing reports and scientific papers, and writing funding applications. The work done by my colleagues at PML is similarly diverse – you can find out about recent work here.

How did I get here?

As is obvious from this post, I started my career journey with a BSc (hons) in Environmental Science at Plymouth University. I selected modules covering current and past climate change, and the marine environment. Crucially I selected a research project within these topics, looking at extremes of temperature and precipitation in relation to the North Atlantic Oscillation and future climate scenarios. This choice proved to be vital as it was my supervisor for this dissertation (Dr Maeve Lohan) who encouraged me to apply for an MSc in Oceanography and begin my path towards a research career. At Southampton, for my MSc, I again opted to pursue climate related modules, in addition to some on remote sensing and physical oceanography. My research project using ocean colour data was my first experience in the field that would ultimately become the topic of my Phd in South Africa. Between MSc and PhD were some tough times. I travelled a bit. And then I applied to some jobs, which in the middle of the economic crisis of the late 00’s were pretty rare. I had decided to put off a PhD for a while, but then decided that if I chose the right one, it would be a great way to get some much needed work experience and a variety of skills. Going to South Africa, rather than accepting a PhD I was offered in the UK, was overwhelmingly the right decision. The skills I acquired, the opportunities I had, the connections I made, and the confidence all this gave me, has been invaluable. After handing in my PhD, I ended up getting an interview at PML and started my new job whilst finishing off my corrections – more on that part of the story here.

My best advice for my sector – marine science research

  • Learn to programme (open source) and handle large data sets. Lots of growth and opportunity in “big data” and can add value to many types of work. Massive Open Online Courses (MOOCs) are available for this.
  • Taught masters can be very useful for transitioning to a slightly different/more specific field.
  • Be willing to travel. There is a global marketplace for environmental science skills. Overcoming my fear of flying was one of the biggest challenges I’ve faced.
  • PhDs aren’t just for academics. Independent research can provide lots of skills. Look at it as 3-4 years job experience. Pick a subject that supports growth of skills you want.

My best advice in general

  • Environmental Science is a great course for many things. To this day the things I learnt support my technical work in so many ways. In particular when it comes to communicating between the data driven, and social science driven aspects of my work.
  • Failure happens – I nearly failed A Level maths, ended up going to university through clearing and now have a PhD. Failure is an integral part of the scientific process – I went down many dead ends during my PhD research.
  • Learn to communicate confidently in many media e.g. technical/non technical writing, presenting, social media/blogs.
  • Networking is very important. Be visible. Attend events, choose advisors and mentors. Most people in science are very keen to speak to you!

I finished off my short talk with some details of MSc and PhD events coming up soon at PML.

I’m barely starting my career in marine science but I’ve learnt a lot already. I’m also putting much of this advice in to practice for myself continually – gaining better programming skills, finding mentors and networks, and learning to be a better communicator. I hope I’ve maybe made a few students aware of the options available to them and am always available to try and provide any help/advice – just contact me through the blog or on Twitter. Huge thanks to everyone at Plymouth University for making me feel so welcome.

Cornish Food Tour

June 27, 2015

Inspired by a recent Buzzfeed post describing the “18 Things Everyone Must Eat In Cornwall”, myself, Ben, my mum, her partner Jon, and princess Darcey Doodle the worlds most spoiled Dachshund, headed off to Cornwall for a tour of culinary delights.

Darcey Doodle enjoying the sun on our Cornish Food Tour looking for dog friendly places to enjoy good local food.

Darcey Doodle enjoying the sun on our Cornish Food Tour looking for dog friendly places to enjoy good local food.

First stop on our #CornishFoodTour was Strong Adolfo’s – a cafe on the Atlantic Highway just outside Wadebridge, popular with Jon and his motorbike friends. Strong Adolfo’s would be very at home amongst the trendy cafes in Cape Town. The styling is great and they serve an array of food, along with cakes, coffee and various soft drinks. I had a delicious flapjack, filled with lots of nuts, and a lovely elderflower presse. Jon – who is very particular about his coffee – loves the coffee at Strong Adolfo’s, and they do a breakfast menu, so it’s a great place to start your day.




Next door to Strong Adolfo’s is a lovely shop called The Arc. Named after the Atlantic Arc – an area encompassing the lowest economic regions around the Atlantic coast, defined by the EU. To provide support, the Arc stocks speciality local food from these regions, especially from Cornwall. This shop is a veritable treasure troves of foods I’d never seen, let alone realised they were produced right on our doorstep in Cornwall. Of particular interest to me was the number of local seaweed based products. Besides the different types of seaweed itself from the Cornish Seaweed Company, there was also a seaweed and cider salami from Cornish Charcuterie. I bought a pack of the salami, a pot of pork rillettes with sloe gin, also from Cornish Charcuterie, and a pack of brittle – a treat for mum. She was very pleased to find a variety of dukkah – a favourite treat we first tried in South Africa.






From The Arc we headed for Padstow. Conveniently there was a little food market going on in this beautiful, but very busy, seaside town. We bought a bottle of Elemental Cornish Gin to add to our spirits collection, after trying some fantastic local beers, cordial, and brownies. Padstow, as with many Cornish seaside towns, is synonymous with seafood. It’s also synonymous with one of the world’s most famous seafood chefs – Rick Stein. We decided we couldn’t really go to Padstow without having some seafood from one of his restaurants and opted to grab some takeaway food from his fish and chips shop in the harbour. I had locally caught crispy fried squid and chips, which was absolutely delicious and, although expectedly expensive, was served as a massive portion. There’s also a lovely little deli and fresh fish shop here, which is well worth a visit.


After a good walk around Padstow, we moved on to our final stop of the day – Camel Valley Vineyards. This award-winning vineyard makes a delicious bubbly which we frequently have on sunny days (and not so sunny days!) at Le Vignoble. We were excited to see the farm and try some of their other wines including several other bubblies and some white, and rosé wines. The farm is in a beautiful location, and the tasting room is very nice. The atmosphere was a little flat – possibly because it was later in the day – not something I’m used to at wine tastings. We also had to leave Darcey in the car, as dogs aren’t allowed (the only place we visited, including the clothes shops in Padstow, where she wasn’t), so this did limit the time we could spend there somewhat. Still, we thoroughly enjoyed a couple of tastings and a glass of the Annies Anniversary bubbly, which we bought a bottle of. I’d definitely recommend a visit and the Bacchus is a particularly nice white for the upcoming summer days.




It was an excellent day out, but I feel we only scratched the surface of the culinary adventures that Cornwall has to offer! We’ll be back soon!

Bringing the Braai to Britain

May 31, 2015

Growing up, a BBQ was a rare summer evening activity, keeping fingers crossed for sunny weather, and usually involving a disposable foil contraption and some combination of plain sausages and burgers. Living in South Africa however outdoor cooking on a fire was a totally different experience. There’s no escaping “braai” culture in SA. Coming from the Afrikaans word “braaivleis” for grilled meat, the term braai is now used across cultures in SA and has become a firm part of my vocabulary. And this is not just because of the many fond memories I have braai-ing in SA. To call a braai a BBQ has been (to me) to equate the skill of cooking and diversity of food I’ve seen created in SA, with those overcooked sausages of my childhood. Thankfully, the UK has apparently gone mad for the BBQ in recent times – evidenced by National BBQ week and an array of facebook groups and twitter accounts of BBQ enthusiasts.

My first ever braai.

My first ever braai.

Potjie bread in Botswana

Potjie bread in Botswana

Braai-ing in Swaziland

Braai-ing in Swaziland

We loved braai-ing in SA so much that our weber, grids, jaffle irons, potjie pot and favourite spatula took pride of place amongst the small shipment of belongings we brought back to the UK with us. Once the shipment arrived we were itching to get cooking again and the recent run of good weather, and National BBQ week were all the reasons we needed.

Braai master Hobbit happy to have his weber and guitar spatula back!

Braai master Hobbit happy to have his weber and guitar spatula back!

Our last few braais have been a great chance to mix the best of local food from the UK with some of the things we learnt from the braaimasters of SA. I’ve also been very pleased to find so many of my favourite SA braai foods available here. From the Good Food market, held every first sunday of the month at the Royal William Yard, I managed to buy boerewors (a delicious type of sausage common at SA braais), and chakalaka – a vegetable relish. From our local Tesco, I also bought 3 types of Mrs Balls chutney (original, peach and hot) and Karoo ostrich fillets. In terms of local meat, British beef has been fantastic – with rib eye proving a particular favourite. There’s also lots of high quality pork sausages here (we love the free-range Gloucester old spot sausages from M&S), and a great selection of venison available at both markets and many supermarkets. Fish wise – we’ve been experimenting with mackerel and seabream – see a followup #sea2shop2supper post on these. Not forgetting the sides, there’s also great seasonal vegetables in the UK – jersey royal potatoes and asparagus make for some delicious salads. Drinkswise – we’re absolutely spoiled here for great beers and ciders – Dartmoor Brewery’s Jail Ale, St Austell’s Tribute and Korev lager, Brewdogs IPA’s and Healey’s Rattler cider are just a few favourites. We’ve also been able to source a surprising amount of South African wine, including Villiera MCC from M&S, Springfield’s Chardonnay from Le Vignoble, Rustenberg’s Rousanne from Majestic and the Klein Zalze chenin and red blends from Waitrose.



Ostrich and chakalaka

Ostrich and chakalaka

Local jersey royal and other potato varieties make a great potato salad, dressed simply with olive oil and some chopped spring onions.

Local jersey royal and other potato varieties make a great potato salad, dressed simply with olive oil and some chopped spring onions.

Springfields wild yeast chardonnay.

Springfields wild yeast chardonnay.

For me, braai-ing in SA was always about long afternoons spent with lots of friends. Since moving back to the UK, it’s been great to share these experiences with our families.

Braai-ing with my mum for South Africa's heritage day.

Braai-ing with my mum for South Africa’s heritage day.

Family and friends have been really excited to try some of the braai recipes we brought home with us, so here’s a few of those and some other things we’ve been grilling up lately.

Fig and blue cheese burgers

Makes 4 big burgers, or 6 smaller ones


500g beef mince – I use the highest fat, roughly ground mince I can find.

1 red onion, chopped finely

150g blue cheese

Fig jam or chutney – I use the one from Ticklemore, available in Waitrose.

Some nice crunchy bread rolls – I bought cheddar and smoked paprika buns from M&S.


Caramelise the onions in lots of butter until really soft and delicious.

Mix these onions with the mince and loosely form in to patties.

Grill on the braai as you like – we like slightly rare.

Place in buns and top with a big spoonful of the fig chutney and lots of crumbled blue cheese.

Cheddar and pepperdew braaibroodjies

These are a type of toasted cheese sandwich made on the braai. As with toasted cheese sandwiches, you can fill these with almost any combination of fillings. I often use cheddar cheese (the UK has so many good options for this, Cornish Tickler is one of my favourites) and pepperdews. These are easiest done with a grid so they can all be flipped together.


Thick white bread, sliced.

Butter, softened so it’s easily spreadable.

Cheddar cheese, grated.

Pepperdews, sliced finely.


Butter the slices of bread on one side – this will be the outer side.

Fill sandwiches with grated cheese and pepperdew.

Place in grill and cook over cool fire.

Fig and blue cheese burgers, and cheddar and pepperdew braai broodjies.

Fig and blue cheese burgers, and cheddar and pepperdew braai broodjies.

Bobotie jaffles

Bobotie is one of my favourite South African dishes. Sweet curry spiced mince with baked egg custard and chutney sounds pretty odd, but South Africa’s national dish really is wonderful. I’ve made it so many times, I don’t even have a particular recipe, I tend to spice up the mince and taste it and add more spice and chutney until it tastes how I like it. Jaffles, are also a bit like toasted sandwiches, but thanks to the jaffle iron, can be filled much more than braai broodjies. For this recipe, I make a spiced mince based on the bobotie recipe, and replace the egg custard with an egg, cracked in the middle.

This recipe makes 6 or so and you will need a jaffle iron.

Braai broodjies in a grid, and jaffle irons in the coals.

Braai broodjies in a grid, and jaffle irons in the coals.


White bread, sliced.


500g mince

1 onion, finely chopped.

2 cloves garlic, finely chopped.

2 tablespoons of curry powder.

2 teaspoons of turmeric powder.

3 allspice berries and two cloves – crushed in a pestle and mortar.

3 tablespoons of spiced fruit chutney – I often use the peach or hot Mrs Balls chutney.

6 eggs (1 per jaffle)


Soften the onions and garlic in a little butter.

Brown the mince, add the spices and cook until soft.

Finally stir the chutney through.

Butter the bread, again, the buttered side will be the outside. Place one slice, butter side down, in to the jaffle iron. Make a little nest of the spiced mince on the bread, and crack an egg in to the centre. Top with another piece of bread, again with the butter side outward and close the jaffle iron.

Cook in relatively cool coals, checking regularly to make sure they don’t burn, you want them to just be crisp, so the egg is still slightly runny.

Serve with chutney.

Bobotie jaffles

Bobotie jaffles

More braai recipes to come through the summer!

#sea2shop2supper: Rainbow Trout Ravioli

April 6, 2015

One of the nicest things about finally coming back to the UK is being reunited with many of my belongings that I couldn’t take to Cape Town. Something I’m very happy to see again is my pasta machine. I have made pasta without it in the last few years, but it wasn’t as easy. Now that I’m back I have no excuse and there really is nothing that beats homemade ravioli with any one of the myriad tasty fillings that can be invented.

Continuing my #sea2shop2supper series I decided to make some simple rainbow trout ravioli.


Rainbow trout are rated as a 2 for sustainability on the MCS guidelines. They are typically farmed in freshwater so I guess not technically “sea”food but they are a great sustainable option for a special fish dinner.


I bought 4 rainbow trout fillets from my local M&S for £6 and used two for this dish.


Rainbow trout ravioli with almond butter sauce

To serve 2


300g 00 pasta flour
3 large eggs
2 trout fillets
1 lemon
2 tablespoons of blached sliced almonds
2 tablespoons of butter
2 handfuls of English spinach.
Chives to garnish
Ground black pepper


First make the pasta dough. I used Jamie Oliver’s basic egg pasta recipe here, and it worked really well. I halved it and it made more than enough dough to make enough ravioli for two, plus some extras.

While the pasta dough is resting, make a little parcel out of tin foil to cook the trout fillets in. Zest the lemon and cook the trout fillets with the lemon zest for about 10 minutes at 200 degrees. Once cooked, flake the trout in to a bowl and season well with pepper and a small squeeze of lemon juice. Pour any juices from the parcel in to a frying pan.

To make the ravioli, roll out the pasta in to sheets as thin as possible. Put teaspoons of the trout mix along the sheet, with a 3-5 cm gap in between. Brush around the edges of the mix with a little water. Lay another sheet on top and form the ravioli, making sure there’s no air left around the mix. Slice with a knife or ravioli cutter and make sure the edges are well sealed. Cook in boiling, salted water for 4 minutes.

On medium heat, add butter to the frying pan, once melted and starting to bubble, add the almonds. Once the butter is slightly browned, add a squeeze of lemon juice and remove from the heat.

Serve the ravioli on a bed of English spinach (the heat of the pasta will wilt it) with the sauce drizzled over the top and plenty of chopped chives.


Springfield tasting at Le Vignoble

April 6, 2015

When I lived in Plymouth BCT (Before Cape Town) my wine drinking only extended as far as a reasonable Rioja from Tesco, or the occasional bottle of cava or french champagne. Living in Cape Town was a massive awakening for me, in terms of the diversity and craft of wine making.

While I was busy learning about how wine is grown and made, Plymouth saw the arrival of the most awesome wine tasting lounge – Le Vignoble. Set in the historic and beautiful Royal William Yard, Le Vig (as it has come to be known amongst my friends and family), is owned by Yannick Loué. Yannick exemplifies many aspects of my favourite winemaker and vineyard experiences in South Africa. His focus on small producers, quality and value in wine, and a personal, approachable wine tasting experience, is precisely what I loved so much about my many weekends wine tasting in the Western Cape.

I’ve been to a couple of wine tasting evenings at Le Vig before and they’ve always been really fun, entertaining and enlightening – particularly because I’ve really only tasted wine extensively, from South Africa. However, I still have a lot of unfinished business with South African wine, I’m not sure you could visit every farm there even in a whole lifetime. With my second-home sickness playing up, I was very pleased to hear that Le Vig would be hosting South Africa’s Springfield Estate for a tasting evening.

I can’t tell you how wonderful it was to hear not only a South African accent again, but all the humour, passion and heartfelt welcome I’ve come to expect from those in the South African wine industry. Jeanette Bruwer who presented our tasting, is one half of the brother-sister team who own the Springfield Estate, situated in the Western Capes beautiful Robertson wine valley. Her passion for their product was evident from the start, you cannot help but be enthused by someone who’s main reason for making good wine, is so they can enjoy drinking it!

We started our tasting by comparison two sauvignon blancs – the “Life from Stone” and “Special Cuveé”. Now, I drank a lot of sauvignon blanc in South Africa. We lived a few minutes from the Constantia wine valley – famous for it’s sauvignon blancs and had visited and tried wines from many coastal and inland wine areas throughout the Western Cape. I’ve even tried New Zealands famous Marlborough sauvignon blancs. But these two sauvignon blancs from Springfield had a character all their own.

The Life from Stone is, as indicated by the name, from vines which are grown in a high vineyard with very rocky soils. Whilst the Special Cuvée comes from a lower vineyard with sandstone based soils. The latter was my preference, more subtle with gooseberry and green pepper flavours, whilst the Life from Stone was more heavy with fruit, and some smokey flavours.

Following the Sauvignon Blancs we compared two Chardonnays from the estate. The first made with wild yeast, had a very distinctive note reminiscent of pink strawberry refreshers. That sounds gross, even to me, but it was really delicious and not at all cloying in terms of sweetness. The Methode Ancienne followed, which whilst carrying the more typically woody notes of many South African chards was much more subtle. Despite my love for this characteristic style of Chardonnay, I actually bought a bottle of the wild yeast chardonnay to take home.

Moving on to reds, we first tried the whole berry Cabernet Sauvignon. Tannins were soft and it was rich with berry flavours and I imagine will age very nicely (we tried the 2013). Following this was a blend called “work of time”. Appropriately named, given the 7-8 years it takes to get this wine to release. Cabernet Franc driven, this was a stunning and powerful blend, with very gamey flavours, making me crave a decent venison potjie. The last of the Springfield Estate reds was a Methode Ancienne Cabernet Sauvignon (2008). This was really refined and a great example of the variety.

We finished off the tasting with the “Thunderchild” (2013). This is a wine made by Springfield, using grapes from a small patch of vines planted on donated land. The profits from the wine go to the Robertson Herberg children’s home. The wine itself is very big and brash but quite delicious and it was great to see the support for an important cause. For more information about the wine and Herberg children’s home, see their Facebook pages.


I also learnt in the last few days of Springfields support for another cause close to my heart. Although we didn’t get to try it at our tasting the “Miss Lucy” wine brings attention to the overexploitation of seafood including SASSI red listed species such as the red stumpnose, after which the wine is named.

All in all it was a fantastic evening, made special due to the wonderful welcome from Jeanette, Yannick and their support. We are already booked in for another tasting this week which will feature another South African wine maker from Holden Manz in Franschoek. Check back for a review of that soon.

Moving from MATLAB to Python as an oceanographer.

March 31, 2015

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.

A new language can turn things upside down for a while ;)

A new language can turn things upside down for a while ;)


March 23, 2015

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 :)


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