Writing an abstract and introduction

My supervisor provided me with some handy advice on how to structure an abstract and an introduction for a paper. I’m placing it on here, partly for myself, but also for others who may benefit from it. I find having these sentence headings really helps in the planning stage.

Abstract

1. Why this general topic really matters in the big picture.

2. Why is this study novel?

3. Previous hypothesis – What was known before?

4. Three main conclusions – Your key points.

5. Wrap up conclusion sentence.

Introduction

1. Strong first sentence to capture reader’s attention.

2. Why the topic matters generally (expand on abstract).

3. What specific questions are being addressed here, and why they matter.

4. Why the study is novel (expand a little on abstract).

5. Expand on relevent details of prior knowledge, split into paragraphs.

Background / Experimental Setup

Rest of the paper…

Research Engagement – A week in Milton Keynes

A head’s up, this will be quite a comprehensive outline and review of the week’s activities, mostly for those who are interested in attending the course (or need some convincing) so they have an idea of what to expect. If you want to know whether or not I would recommend the course  without having to read the content; I would absolutely recommend this course to anyone, career scientist or not. The skills you learn have a range of applications, but you’ll have to read on to find out more.

Alright, so I’ve spent the past week at a NERC-funded training course in Milton Keynes, run by Richard Holliman and Clare Warren. We were joined by Janet Sumner, seen often in television shows such as Bang Goes the Theory and Life, and Gerard Giorgi-Coll who works behind the scenes on shows such as ‘The Fugitive’ and ‘Cannibals and Carpet Fitters’.

Particularly in online modernity, knowing how to effectively utilise various media outlets and engage the public in front-line research is increasingly becoming pivotal to securing funding, and more importantly it plays a part in the success and advancement of your scientific field.

Before we got to Milton Keynes we had to write a short description of our research as well as identify some end-users of our research, which was certainly needed for the course.

The week was packed full of activities including:

• An introduction to Pathways to Impact (P2I).
• Interviews about our research.
• Delivering a piece to camera.
• To produce and star in a short 10-minute informative movie.
• Engage in the behind-camera work involved in recording.
• Cutting and editing the movie into a finished piece.

Aside from being very hands-on, there was a big emphasis on team work, reflecting on who the end-users of our research are, and coming up with creative ways to communicate our work to the public.

From day 1 we were working together, filming interviews with the people we had just met, which proved an effective ice-breaker. We learned about the methods behind filming an interview such as the kinds of ‘shot’ involved to create a visually interesting interview segment. We used our prepared research summaries to answer interview questions which was daunting to start with. We all soon relaxed into it as we were filming and supporting each other through the process.

We went on to each produce a piece to camera (PTC) in which we were filmed alone, explaining some aspect of our research while either walking along with the camera or by using props to help us to explain. For example, I explained briefly how we monitor turbidity currents by carving a canyon into a Victoria Sponge and I made instruments out of toothpicks, whitetac and string (a photo would help but I was a little distracted to remember to do that!). There was some real scope to exercise creativity which was a welcome change from hardcore science or, well, scientific writing.

We were then split into teams of five, with people studying similar fields, and we had to come up with a short 10-minute film. Storyboarding, scripting, filming and acting were just some of the activities we had to complete in just a day! It was intense but both teams went all-out and made the whole ordeal into something of a friendly competition.

We quickly established our priorities and decided on the content of our film (burrowing invasive Crayfish, turbidity currents, hard river engineering and soft river engineering), the format of each scene (piece to camera/interview etc), and the locations we wanted to film. One of our scenes needed to be filmed at night (Crayfish are nocturnal…) so we went to work that same night. The next day we filmed the rest of the shots, utilising all of the shots and scene types we had learned.

The final job was, of course, to edit the footage into the finished product. The end result was pretty funny and we all had a lot of fun shooting the footage and pulling it all together. The other team also did a wonderful job with their highly informative, creative, yet hilarious short movie. You can’t beat a movie about Crayfish, rivers and turbidity currents though, can you?

Richard and Clare might want a star rating for the course… So, totally not under duress (I promise), I would give this course a 5/5 from all aspects. Organisation, content, accommodation and support. I’ve never laughed so much in a week and 5 hours after the course finished, my face still hurts.

Second Year Blues

Addiction rears it’s ugly head.

I’ve found myself back in a state of gaming addiction with the dawn of the latest World of Warcraft expansion; World of Warcraft: Legion. I find myself here again because I felt the possibility of being a (gaming) success nibbling at my fingertips. This is contrary to how I feel about my Ph.D at the mid-point of my post-graduate period. At the start of any expansion, everyone is on a level playing field. I was determined to get ahead of people and master my class unlike anyone else. To some extent I have achieved that goal, but the truth is that I have been using gaming to escape what feels like a difficult post-graduate degree. The result being that I am falling behind with my work and I am neglecting friendships.

Online life is a stark contrast to reality.

When I’m playing I feel like I am doing something that I am good at. I feel focused. Successful. I am good at playing the game. I am better at playing my class than most of the people I come into contact with in the game. This may be, partly at least, due to the amount of time I spend on the game. When I come out on top of everyone else in terms of performance, I feel a sense of elation that I do not find in the doldrums of day-to-day life. Being told that you’re one of the best players someone has seen is an ego boost that you seldom receive in real life. Perhaps if I spent more time perfecting my abilities in real life, I would receive such compliments…

My character. Rather intimidating.

Life isn’t face-paced.

Any undertaking in real life can be a little lackluster. It takes time to master something or for a project to come into fruition. Each endeavour can be met with setbacks that can be disheartening. My Ph.D for example takes at least 3 years to finish. Each paper can take months or years to complete. Each draft submission is met with criticism from my peers, which often means I have to return to the drawing board. Likewise I took up teaching myself to play the piano only to falter following slow progress. My piano sits by the metaphorical wayside, gathering dust. Gaming is contrastingly fast-paced, any obstructions can either be avoided or take a few minutes to overcome. Alternatives exist in gaming which allow you to proceed in other ways, unlike the rigidity that life sometimes presents you with. You have to persevere and push forwards.

The result

To start with you don’t spend a lot of time playing, but this increases. Eventually you become aware of how much time you’re spending on the game and how much you’re not spending time on things you should be spending time on. The things that really matter to your life. This can leave one in a state of depression. Due to the never-ending style of the game and the relatively slow-paced nature of life, life feels empty. I find that I can’t focus on anything that isn’t the game. Despite my successes in the game, the game is never finished, which brings with it a feeling of anxiety to reach the furthest I can in terms of in-game progress. Even if I reached the pinnacle of in-game progress, the nature of the game means that it would not be long before an additional milestone was set before me.

When compared to the fast-paced nature of online gaming, life can seem somewhat lacking albeit frustrating. The result is that I find myself questioning my life choices. Am I addicted because I don’t find my life interesting enough? The answer is probably ‘no’. The game is designed to be addictive, to keep you playing and bringing money in for the game company. It’s an effective business model and an effective distraction from real life priorities. Unfortunately it is a destructive hobby and it needs to stop.

Next steps.

For now I’ve deleted the game and I have an appointment with counselling services for depression, during which time I will bring up my addiction. This state of mind occurs in cycles and either results from or is the cause of video game addiction. Games are an escape from the challenges of reality and I need to face them and in order to end these cycles. I think. I hope.

ArcGIS Tips – DEM Edition

So you find yourself in a position where you have to make DEMs, but, like me, it’s been a while since you had to make one and are now sweatting as you peruse through the seemingly infinite menus and submenus of ArcGIS.

Displaying DEM data (bathymetry, elevation, georeferenced data points, etc.) on ArcGIS from a text file.

You have exported your georeferenced (yeah?) elevation (yeah?) data from that super simple program (ha) and now you’re at a loss for what to do with it in GIS. Here’s what you do:

To start with, DEM data generally comes in the ‘.txt’ format which is delimited (separated) using commas, and without spaces between the values (unless it is delimited using spaces). At the top you have a row of text which serve as column headers, which allow you to select that column of values within Arc.

1. Import data using the ‘Add data’ function.
2. Right click the imported file, select ‘Display XY Data’.
3. If you have the appropriate headers in the text file you should be able to input your X, Y and Z fields (Easting, Northing, Depth etc.).
4. Right click the new layer, select ‘Export Data’.
5. This should be exported as a ‘.shp’ file.
6. If this doesn’t work, select ‘Display XY Data’ again with the ‘Events’ file output from the previous steps.
7. Follow steps 3 and 4, this should now work.
8. After this, you can convert feature to raster.

If you want to use the bathymetry later, you can export to a TIFF (georeferenced, often called a GEOTIFF) using the export function (right click the raster layer you just made and export, select TIFF as the output filetype if not already selected).

Making a super professional hill-shaded bathymetry

1. Complete the ‘Displaying DEM data’ section, click and drag the TIFF into ArcGIS.
2. Select the ‘Jet’ colour scheme (or which ever colour scheme you desire) for the bathymetry
3. Make a hillshade of the bathymetry (3D Analyst > Raster Surface > Hillshade).
4. You can leave the ‘Azimuth’ and ‘Elevation’ values as they are, you can alter the ‘Z’ factor to increase the vertical exaggeration of the hillshade. I usually set that to 3.
5. Right click the hillshade, select properties.
6. In the ‘Display’ tab, you can change the transparency of the hillshade. I like to use 30% but you can play around with it if you wish.

Displaying XY data by category

Sometimes you may have the XY locations of different types of variable (i.e. waypoint, sampling location, mooring location, etc.). If you add a column into the header row of the text file named ‘Types’, for example, you can add the ‘waypoint, sampling location, decent pubs, etc.’ labels to each row and this will be the categories which you sort the XY points into within Arc.

1. You can import all of the XY coordinates into Arc and convert to shape files using the above method.
2. Right click the layer of XY coordinates and select the ‘Symbology’ tab, in there you can select the ‘Categories > Unique Values’, or ‘Unique Values, many fields’ if you have different variables. Using this you can add in each of the categories you put into the text file.
3. Be sure to choose an appropriate symbol for each category by double clicking each of the ‘point’ symbols and scrolling through the symbols until you find the desired symbol.

 

Converting elevation to depth

You just made a sweet bathymetry output from Caris or Fledermaus or whatever and oh no(!), the values imply elevation (+ive) rather than depth (-ive). Here’s a sneaky tip for getting around that without having to export your data again.

 

1. Import your elevation data using the above method.
2. Convert to depth using the raster calculator (Spatial analyst > Raster Algebra (?) > Raster Calculator).
3. Double click, or drag, your elevation layer so it appears in the box below the layer list.
4. Using the calculator function to the right, multiply the elevation layer by -1.
5. This method can be used to convert depth to elevation also.

Sneaky sneaky!

 

Taking repeat elevation (or depth) profiles from the same point.

This assumes that you have a repeat elevation or bathymetry survey ongoing.

 

1. First you must make a line shape file (See Previous Post on how to make a shape file) and position the line in the spot you want, usually across or along the axis of a channel.
2. Stack Profile > Right click > Batch process.
3. It will output everything into a single table, but you can export this to an excel or text file to use in Matlab or something.
4. I will make an additional post explaining how to code for that when I get around to figuring it out

 

Georeferencing an elevation/bathymetry

 So you received a new bathymetric survey, you go to import it into Arc and you discover that the survey has an obscure, unique georeferencing system that you can’t get a hold of. Or you have an aerial photograph that you want to georeference. What ever your issue, here’s how to fix it.

 

1. There is a tool called ‘Georeference’.
2. I’ve not used this tool much but I’m just letting you know it exists.

 

General tips:

If you can’t find a function, click on the search bar and type in a function name. It could be there! E.g. I needed to flip a bathymetry so I typed in ‘flip’ and both ‘flip’ and ‘mirror’ functions came up in the results. They weren’t useful for what I wanted but sometimes, life gives you digital lemons.

 

Always make sure the coordinate systems (e.g. WGS84) match up. Sometimes you have to convert the coordinate system, which is a bit of a headache, but there are websites online that can do this for you (e.g. http://www.earthpoint.us/Convert.aspx).

Basic ArcGIS for the amnesia-stricken student

As I’ve been moving through my Ph.D, the use of GIS systems has become increasingly important to process the data I have been collecting or have been given. Unfortunately for myself, it has been a while since I had to use GIS tools to their full effect with my undergraduate degree teaching me very briefly how to create a polygon in ArcGIS in my first and second year. That was 4 years ago. Since then I have barely used ArcGIS, and thus have forgotten the basics. In my frustration I turned to Google, that all-knowing tool of wisdom, to help me through my state of amnesia but was left feeling more frustrated than when I started. The lack of illustrated guides became apparent, even on Youtube, as I sifted through the seemingly endless buttons and sub-menus that ArcGIS had to offer.

So, to save time for others who may have indeed forgotten how to create a polygon, I have put together a short guide on how to not only create a polygon, but also how to cut or clip the data within that polygon. Ideally at this point you will know how to import your basemap and/or generate a difference map (Search for Map Algebra for generating difference maps, you literally subtract one map from the other). If not, let me know, and I can direct you to an appropriate guide or even write another illustrated guide myself.

How to draw polygons in ArcMap

• In Arc Catalog, select an appropriate folder in which to work. Make sure the basemap or difference map and the polygon are in the same folder.
• Right click on your chosen work folder and select “New > Shapefile > Polygon” and give it a sensible name (Below).

 

 

• Open the Editor toolbar if it is not already open and click “Start Editing”. On the right-hand side of the Editor toolbar is a “Create Features” button (Below).

• When you click it, it opens a window that allows you to select the feature you wish to draw onto your map (Below).

 

 

 

 

 

 

 

 

 

 

• Then it is simply a case of tracing the outer edge of the feature you wish to retain. In this case, a turbidity current event on a difference map. Once you are done, double click to finish the polygon. The edge of the polygon will turn blue to indicate that this was successful.

 

 

 

 

 

 

 

 

 

 

 

• Now to clip the data so that you’re left with the turbidity current event, and not the whole difference map. In Arc Toolbox you need to find Datamanagement Tools > Raster > Raster Processing > Clip (Below).

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

• In this menu you will have to select the input raster (the difference map or base map that you’re using) and the output extent, which is the polygon you just created. Check the “Use Input Features for Clipping Geometry” and “Maintain Clipping Extent” boxes and click “Ok”.

 

 

 

 

 

 

 

 

 

• Once this is done, you will be left with the clipped difference/base map which you can export as a TIFF for use in Matlab, or carry on working on in ArcGIS. Good job!

 

 

 

If you have any questions at all, please do not hesitate to leave a comment or conact me.

Waxing and Waning of an Anxious Gaming Addiction

Disclaimer: Don’t get me wrong with this post, I do actively enjoy playing video games. There comes a point though where you aren’t playing games because you enjoy them, but are using them as an excuse to avoid responsibilities or avoid seeing people, and that is what I am highlighting here. Careful management of what goes on in your mind is important and games are great if you aren’t abusing them, and yourself, in this way.

This post will be a bit of a side-step to previous ones. I am writing this partly as a confession, but also in the hopes that others may be able to see that other high-functioning individuals are not alone in combatting anxiety disorders and addictions (in my case video games). Part of the key to success is identifying that you have a problem and letting people in on the fact that you have a problem so that they can support you. This certainly may not be the case for everyone, but a little nudge now and then to say “hey, you’re sliding a little” is all you need to stay on track.

I had been introduced to gaming at a very young age, I was just three years old when we got a NES in the house. Super Mario Bros 3 and Double Dragon were a great boredom killer when I was a kid. As I got older I went through the Megadrive, the Gameboy and the Playstation, so I’d been accustomed to games since I started developing memories near enough. When I was coming to the end of secondary school back in ’04, I started playing Runescape which has you collecting items and gaining ‘skill points’ in order to improve your character and its abilities. Of course, as your character improves, the idea is that your ability to play the game improves along with that and you progress further in that game. This reward system is highly addictive, each time you gain a reward in a game (such as gain a skill point, find a rare item or murder your opponent) it triggers a release of dopamine. This was the hook for me, particularly on games which had no exact ending to them.

To start with the level of gaming wasn’t so bad, for a start most games had a distinct ending, and I was just a kid so my mum was highly regulatory in how much I could play. Just like any parent would, right? The unfortunate side effect was the growing resentment I felt when she would evict me from the computer on which I was gaming, particularly when I was playing games such as Runescape with no distinct ending. When I got to sixth form in ’05 I was introduced to World of Warcraft by some people I met at school. World of Warcraft is famed for its addictive playstyle the world over, with some people taking the game to extremes in the past. Listverse lists 10 extreme cases of video game addiction, only a few of which I am guilty, but are nontheless potentially damaging to an individual.

1. I skipped school, my ultimate downfall during my A-Levels which lead to my failure of the exams.

2. I once played World of Warcraft for 18 hours in a single day. Listverse lists someone playing for 50 hours in a single stint.

3. One time didn’t leave the house for two weeks because I was gaming. Ultimately I put on quite a bit of weight over the years as a result of the lifestyle I was leading.

4. A social side effect of a gaming addiction is that you neglect those around you, your friends and family drift away and you just let it happen. Not to mention relationships.

The severe introversion and addiction went on from 2005 to 2009, I’ve spent in excess of 300 (7200+ hours) consecutive days (cumulatively) playing this one game. The money spent on the game is in excess of £1000, from purchasing game time and expansions to moving characters between servers and renaming them. It all adds up. Anxiety and depression kicked in, I was out-of-touch with the outside world, glued to the computer and tv screen while I gamed my life away. It got to the point where I got anxious about going into town on my own, or even answering the phone. The thought of going out there would claw at my mind and give me bouts of crippling physical pain which left me unable to sleep, all because of the anxiety I felt. I had a real low point one day where I felt that no one would notice if I were to die because I hardly left my bedroom anyway. This was the kick in the backside for me. After a surprisingly brief ‘tough-love’ talk with a friend, she asked me what I would want to do if I had that chance. She ended up telling me to “grab life by the proverbial balls and take what I wanted from it”. So I did. That night I applied to go back to college, with the aim of wanting study to get into university.

Not wanting to relapse into the pit I once found myself in, I walked into college with a renewed enthusiasm for education. I adapted my gaming addiction and used the reward system of education, grades, to fuel this new-found enthusiasm for the institution. I left college with almost straight distinctions and gained access into Hull University to study Geography and Archaeology. On occasion I would slide and disappear from the social scene for a week or so. I let those around me know of my past struggle and they were able to point out to me when I was retreating into my bedroom for too long to play games. My gaming never affected my studying again. Needless to say I did pretty well at university, graduating with a First in my Master of Physical Geography degree (switched degree programmes in second year) and two awards.

Now I’m doing a Ph.D, the main impact that gaming has on my life is the social aspect, and partly due to some lingering anxieties which mean that some days I just don’t wish to interact with people who are, or could be friends. I use gaming as a way of enabling my anxiety for being around people who could otherwise actively occupy my time. Recently Team Fortress 2 has been my go-to, having played 35 hours over the past two weeks (129 hours total), and it has been pointed out to me that I have been playing a lot recently. Not to say that I’m not actively involved in Ph.D life; I’ve been to the USA, Canada, Vienna, Belgium and The Netherlands for both research and recreation. I go on training trips across the country with few problems at all and I have little problem with conversing with the person next to me on the plane or train. A few years ago I couldn’t pick the phone up, let alone talk to someone in the street. Despite some hiccoughs, progress has still been made and will continue to be made. The rewards I get from my Ph.D may not be as plentiful as with my undergraduate degree, but they are there. For example, it’s rewarding when you make even a bit of progress with coding or learn how to use a new bit of equipment, and it’s great when people like your work and tell you that you’ve done a good job. As with any job right? You make progress with your work or abilities and people like what you’re doing, it feels good. There is plenty of reward to be had in a Ph.D which may sometimes seem few and far between, but you just have to be aware of it. Focus on the good.

In summary, even if you find yourself failing school when you’re young it may still be possible to pick up where you left off and give things another go. See what’s going on around you at your local college, you can do that from your computer. It will take some of your time, but addiction is not sustainable. You have to get out there. A little cliché, but the first step to overcoming a problem is admitting that you have one. Getting support from some good people will really help as you endeavour to achieve what you want to in life, but to do that you have to let them in. Just know that it is possible to overcome the issues you may face. You just have to take the first step. Thank you for taking the time to read this post.

The Future of Global Energy

I have been doing some thinking while exposed to discussions on the future of the oil and gas industry, renewable energy as well as the politics of it all.

At first I felt anxious about it all, I didn’t see a solution to the problem and felt that arguing about it was futile. Because what can we do to halt the use of hydrocarbons in our modern world? Further into the discussions however, I came to realise that the way forward is not going to be an instant change, but a gradual incorporation of new technologies which allow us to step back from hydrocarbons and move towards a renewable future.

The world is addicted to hydrocarbons, and we need to move away from these. That is a fact. Making use of hydrocarbons (through burning and using plastics) is bad for the global environment, it has been shown to cause global warming, ocean acidification and as a result change weather patterns and detrimentally affect organisms across the globe. In response to global warming and climate change as a whole, renewable energies are coming into play and ways to capture and store carbon (CCS) are being developed in order to combat the warming of the globe. This is excellent, it is the way forward and should continue to be so.

The fact is, we still need hydrocarbons. Plastics, transport, and energy consumption in general are a large part of daily life, irrespective of the full use of hydrocarbons;

Petroleum products and their relative share of total U.S. petroleum consumption in 2013 (Source here):

• Gasoline 46%
• Heating Oil/Diesel Fuel 20%
• Jet Fuel (Kerosene) 8%
• Propane/Propylene 7%
• NGL & LRG¹ 6%
• Still Gas 4%
• Petrochemical Feedstocks 2%
• Petroleum Coke 2%
• Residual/Heavy Fuel Oil 2%
• Asphalt and Road Oil 2%
• Lubricants 1%
• Miscellaneous Products/Special Naphthas 0.4%
• Other Liquids 1%
• Aviation Gasoline 0.1%
• Waxes 0.04%
• Kerosene 0.02%

The question would be; how do we fill the gap that would be left if hydrocarbons were no longer explored for? This is a difficult question. Currently there is no viable solution, both in terms of economics and in terms of technology.

Unfortunately for the industry, exploration for oil and gas is struggling to remain economic in the sense that large discoveries are becoming rarer and drilling costs are ever increasing (meaning more drilling and therefore greater costs). This means, unfortunately, in the eyes of some, that there is now interest in developing knowledge of oil and gas in terms of exploration to improve existing technology, enhance recovery and come up with innovative methodologies, in order to retain the economic potential of oil and gas, and to maintain our current way of life. This is where the CDT comes in. The oil and gas companies hope we move into industry following completion of our Ph.Ds in order to keep them afloat (excuses the pun). Sure. But this serves the purpose that energy security is maintained across the globe, both nationally and internationally. It also means that we can continue using hydrocarbons (which we NEED to do) while new ways of harnessing renewable energies and new ways to mitigate their effects come into the public domain.

So I guess the point of the discussions wasn’t to come up with a solution, it was to come up with ways to tip the balance towards breaking our addiction, while at the same time retaining our addiction and hopefully mitigating the impact of the burning of fossil fuels and production of plastics on the environment. Something of a rehabilitation programme if you will.

Until the world breaks its addiction to hydrocarbons, we will still need to explore for hydrocarbons and keep the exploration for those hydrocarbons economically viable. Renewable energies and CCS serve as a brilliant rehabilitation programme, but there is still a ways to go before we can give the boot to the use of hydrocarbons.

Edinburgh: Brilliant on so Many Levels.

I have spent the last couple of weeks in Edinburgh and I wanted to share some of the touristy things I did while I was there.

The Real Mary King’s Close – Warriston’s Close, High Street, Edinburgh.

This was a really interesting journey into the past of Edinburgh where you book, either at the booking office or online, pay the £11 and gain access into the underground of Edinburgh. It is only underground in relation to the current ground level around Edinburgh, it was once the ground level in the 1600’s. You know on Futurama where Fry gets taken into Old New York? It’s sort of like that but not as spectacular. The history is still great though. You are guided by someone acting as one of the previous tenants of the Close, and they take you through a series of rooms which were once the lodgings of entire families many years ago.

During the 1600s there was no underground sewage network to speak of, and coupled with close proximity living conditions, disease was rife. The only sewage network existed above ground with people throwing buckets of excrement out of the window twice per day. You can still smell the stench to this day. Unless it was me. I don’t know.

The bubonic and pneumonic plagues were common in these times with patients being visited by plague doctors (below).

16th Century Plague Doctor attire.

With the living conditions being so cramped (8+ people living in a single room), these diseases spread rapidly. Not a great time to be around. The underground is said to be haunted, so if you’re superstitious you may want to stay away. The history is very much worth it in my opinion.

Arthur’s Seat – You can’t miss it.

I had visited this extinct volcano during my previous visit, but found myself short of time with which to reach the summit. This time around I was determined to go to the top, so I did.

Arthur’s Seat summit. A little crowded.

The entire walk took me less than an hour with no breaks on the walk up or the walk down. I touched the cairn stone and stayed at the top a while because, you know, you get up there, you might as well enjoy the view. What a view it was. You could see the entire city of Edinburgh, including the castle and the multiple church spires, and beyond to the Pentland Hills on the outskirts of Edinburgh. You could see the island of Inchkeith on the Forth River, right across to Kirkcaldy on the other side. The climb seems a little steep from the foot of the Seat, and resulted in me not climbing to the top on my last visit as the gradient put my companions off, but it really isn’t so bad. The view at the top is more than worth it.

Even if you don’t go to reach the summit, the climb is in two stages, the first easier than the second, so you can go for the first stage and still enjoy the view and the geology. Or just the view. Or just the geology. It’s up to you. Unfortunately I didn’t take a great deal of pictures from the summit, but you can rest assured that the view is splendid.

Calton Hill – Calton Road, Edinburgh.

Calton Hill is another one of Edinburgh’s famous hills. I like to think of it as the budget version of Arthur’s seat, but a good kind of budget, not the Ibis Budget compared to the Ibis. Calton Hill is brilliant. The view is still spectacular, not quite as high as Arthur’s Seat, but it’s really nice if you don’t fancy the climb. Another difference being that you have a selection of monuments atop Calton Hill:

From left to right: Calton Hill Observatory House, Nelson Monument, Calton Hill Observatory and National Monument.

Out of view of the above photograph is the Dugald Stewart Monument which has a large urn (looks a bit like a trophy) in the centre, surrounded by columns. It commemorates the life of  Dugald Stewart, a professor of philosophy at the University of Edinburgh in the 18th century.

The Museum of Scotland & Game Master’s exhibition – Chambers Street, Edinburgh.

A brilliant museum, with free entry might I add, that includes pieces from all periods of Scottish history from neolithic arrowheads to the claymore of William Wallace (a.k.a. Braveheart) to more recent history. The collections rival many of those that I have seen, both in terms of completeness and in terms of personal interest. Personally, I preferred the Museum of Scotland to the Natural History and Science Museums of London (I still need to visit the British Museum). If you want to learn about Scottish history, the Museum of Scotland is the place to go.

The Game Master’s exhibition was pretty neat, giving visitors the opportunity to play games, both retro and new, from the original arcade games (but no Mortal Kombat sadly) before home consoles to the early Mario games on the NES, Donkey Kong, to more recent games such as Warcraft III: The Frozen Throne. Console, handheld console and PC games were all represented which I thought was nice, but perhaps missed a few games out that I would’ve liked to have seen. Crash Bandicoot, Mortal Kombat and something from the Burnout series for example. I’m not sure if I could say it was worth the £7.20 to gain entry either as I still own a number of the games that were on display. If you want a blast from the past and some nostalgia, then go for it. If, like me, you look after your consoles and games and they still all work, then you might be left feeling a bit disappointed.

The Hanging Bat craft beers – Lothian Road, Edinburgh.

I’m not sure I can say much about this place as I’m not really an expert on beer or ale, but it was certainly interesting. When you go in you have the option of buying pints of beer or buying a flight of beers (£12.50 for 5 x 2/3rds of a pint per flight) where you can sample different beers. I recommend the latter. You might not like them all, but once you get through four or so flights with some friends you will be left feeling a little tipsy and have a better knowledge of what different beers taste like (assuming little to no prior knowledge, like myself). There were all kinds of beers with all kinds of quirky names, light beers which resembled cider to very dark beers which resembled Guinness, and everything in between. I didn’t have a resounding favourite because I’m not a huge fan of beer, but went for the one I preferred the taste of with each flight. Even if you’re not a fan I would recommend it, it’s an experience to say the least.

Scottish food – The Castle Arms (Haggis, Neeps & Tatties), Johnston Terrace, (behind the Castle).

‘When in Rome…’ Or in this case, ‘When in Scotland…’ I decided to try quite a bit of traditional Scottish food on this visit. I had haggis spring rolls which were a good introduction to haggis, but didn’t give you a full sense of what haggis is like as there is only so much haggis you can fit into a spring roll. Scallops are apparently traditional Scottish cuisine too. I had no idea. I hadn’t actually had them before either so I gave them a go and I wasn’t disappointed. In a pub I saw ‘Haggis Neeps and Tatties’ advertised on the menu so, naturally, I opted for that. Actual haggis, in this recipe at least, was quite spicy. I think they put quite a bit of peppercorn in there, but isn’t a required ingredient (according to the Wikipedia), so my hunt for the perfect haggis continues. I really like the texture, it reminds me a bit of black pudding, and the flavour is generally quite nice and meaty, other than the burning sensation that accompanies peppercorns. Last of all I had Cranachan, a traditional Scottish dessert. I imagined it to be a little bit like Eton Mess, but I was very wrong. It’s fruit (I think it was raspberries) and cream, essentially. I did like the contrast between the bitterness of the berries and the sweetness of the cream. Not my favourite dessert ever, but certainly worth a try.

Ghost Bus Tour – Chambers Street, Edinburgh.

Arguably the most entertaining section of the trip to Edinburgh (no offense to those who gave presentations!). The tour involved going around the city in a refurbished Routemaster bus from the 1960’s, touring parts of Edinburgh with a spooky past.

Location of Ghost Bus pickup.

I would tell you which parts but my memory is actually terrible so I have forgotten (it was a week ago, give me a break), and it would also ruin the fun of the trip. You learn about murders, people driven mad, other supernatural beings and cases. The gent giving the tour was the best. He was in character the whole time, had a brilliant accent for the job, even had a sweet mustache. Describing the trip will not pay it enough credit, but if you do anything in Edinburgh and you want a good laugh and a bit of a fright, then I recommend this.

St. Giles Cathedral – High St, Edinburgh.

Not that I am a church goer these days by any means, I decided to step into the St. Giles Cathedral to see the architecture and the stained glass within. I was not disappointed. The Cathedral is open for worship and is used for services throughout the week (see the website), but when it is not being used for services it is open to the public. Free entry. If you like Gothic style architecture, you will love the Cathedral. Despite receiving many alterations since its construction in 1385, following a fire which destroyed the original, it remains a marvel to the eye.

The interior of St. Giles Cathedral showing its arches and stained glass.

I didn’t really go for the history, just to appreciate the architecture, but there is plenty of information on the website that I linked above if you are interested in French hermits (St. Giles). There is a beautiful chapel with a decorative ceiling and many carved busts and the like. The level of detail is astonishing. I would post more pictures, but you really need to go and look. You will not be disappointed.

The CDT: The Currently Demanding Timesink.

*Disclaimer: The opinions expressed on this blog are my own and do not necessarily represent the opinions held by others involved, directly or indirectly, with the CDT*

I’ll start with a definition of term(s): CDT actually stands for Centre for Doctoral Training. The purpose of this CDT, to completely plagiarise the website, is:

“The Centre aims to create a highly skilled workforce with expertise that can be used across the wider energy and environmental sectors.  It will equip industry with the skills needed to explore, sustain and reduce the environmental impact of oil and gas exploration and extraction at a time of economic challenge and pressure for responsible environmental management.” See the website for more information.

The CDT programme is sponsored by a selection of oil companies in the hopes that I, and some or all of my peers, will eventually complete our Ph.Ds and make the transition into the oil industry. The actual funding for the Ph.D itself comes from both the Natural Environmental Research Council (NERC), an non-governmental body, and each host university with a 50/50 split in the funding. The nine companies sponsoring the programme hold the hope that our fresh minds will bring new ideas to generally reduce costs brought to the industry by natural hazards, drilling in the wrong area and so forth. There is also an environmental focus serving to enhance the mitigation of oil spills as well as test the impact of spills and leaks on ocean life.

I am of course grateful for this opportunity and appreciate the collaboration going on between both academic institutions and the companies involved in funding these projects. I am also grateful for the training opportunities which are presented as a direct result of being a part of this CDT, including raising the awareness of environmental issues surrounding the oil and gas industry and the efforts the industry makes to satisfy the needs of the environments in which they explore. The courses also seek to provide us with some knowledge of how the industry explores for hydrocarbons, such as the exploration process and the extraction process. I believe it to be similar to the training offered to all entry level industry employees. We are also presented with the opportunity to make contacts within industry, which may prove vital in the future in securing employment if we do indeed choose to go into industry. It also means we are not only able to make a more informed career decision, but also have better prospects upon completion of our Ph.Ds as we will have training that other applicants may not. Awareness of how the industry operates and skills vital to the industry. The benefits are lining up here. Now for some facts.

The CDT has advertised 75 projects and will be funding 31 of those at a cost of £589,000 a year, resulting in a cumulative spend of £2,356,000 over 4 years on refining existing techniques, developing new techniques for hydrocarbon exploration, as well as protecting infrastructure and the environment. Again, to plagiarise the CDT website:

“In total, just under £8 Million has been pledged to support the scheme, £2.7 Million of which will come from NERC and a further £5.2 Million from the various (academic and affiliated) partners over the next six years.”

Plenty of cash to keep this research going from an environmental council, it’s partners and affiliates, and our host universities, with the training programmes funded by the industry purely to give us an insight into what they do in the real world. The contextualization is very nice to have.

So how are these projects split?

Well there are four themes outlined by the CDT:

• Effective production of Unconventional Hydrocarbons
• Extending the Life of Mature Basins
• Exploitation in Challenging Environments
• Environmental Impact and Regulation

Each theme is said to hold the environment at it’s heart as the environment is a concern for those contributing money to the programme, NERC and the academic world. From this perspective, this set of topic themes is great. It is clear that we still need the industry (see below), so knowing how to go about business with the environment in mind, is brilliant. The industry gets to continue producing oil and gas, and we get to find out how to do this safely.

I went through the list of projects myself and produced my own division of topics from an industrial point of view:

A very black-and-white split of the Ph.D title themes on offer through the CDT. Who doesn’t love a pie chart?

Infrastructure concerns things like pipeline protection from geohazards, environment concerns things like the impact of spills on ecology and the bacterial degradation of oil, and exploration covers everything from fracking (ooh, naughty word) to seismic interpretation to investigations into unconformities. At a glance this is skewed heavily towards the exploration side of the oil and gas industry (partly because exploration involves such a broad range of topics!), but you have to bear in mind the ultimate goal of the industry: to lose as little money as possible, be it through damage to infrastructure or through fines for environmental negligence, but to ultimately extract as much product as possible and to make a profit. Not only does a major spill produce a lot of bad press for a company, but it is also a LOT of lost product that they will not get back. They also wouldn’t want to annoy the locals with fracking, so doing it more effectively would be great for everyone. Reminds me of George Carlin talking about ‘NIMBY’ (Not In My Back Yard).

Taken from the Wood Review 2011 (originally from the BBC).

You can see from the Wood Review (completely free of bias right?) that the profit margin of the oil industry stood at around 7-10% in 2013 when the oil price was high, with the industry barely scraping by in 1997 when there were no distinguishable profits (from this figure anyway!). So you could say that during times of rising oil prices, the industry makes more, and during ‘leaner’ times when oil price is falling, the industry makes less profit. Simples. Anyway. The industry tends to prepare itself for these leaner times when prices are falling to buffer itself from a fall in profits or a rise in costs, like some kind of insurance. Pretty smart. I guess, from a business perspective it isn’t surprising that the industry would be more concerned with gaining as much product as possible in the hopes that they can make as much profit as possible. Sweeping statement alert: As the oil and gas industry underpins much of the world’s economy, why not let them take some profit for the work they do? After all, products of the industry exist in every aspect of modern life from artifical vanilla flavouring (this isn’t nuts, it’s vanilla) to clothing and all the plastics we use.Without the oil industry our lives would most definitely be altered beyond recognition. So while there is a real emphasis on FINDING more oil (high demand, increasingly difficult to find readily available oil), there is also an effort to improve the existing infrastructure and look after the environment and ultimately reduce accidents. Believe it or not, oil spills aren’t in the best interests of the industry. It’s a lot of money, quite literally, down the drain.

Deepwater Horizon spill in 2010, Gulf of Mexico. Imagine just how much product was lost. Never mind the cleanup cost and bad press that BP received. It makes sense for industry companies to avoid this right? Even if no one were to be caught up in the blaze.

This brings me to my next point. I am apparently a rare breed, my Ph.D title falling into the relatively small infrastructure section of the pie chart. As a result, the training offered by the CDT may not necessarily cover the topic of my Ph.D. More benefit for me? I get to listen and learn about the rest of the oil and gas industry which I seldom encounter from my world of turbidity currents. I feel this may be a drawback for others as they may not learn enough about the vital aspect of the industry which is turbidity currents, while vital, is not as highly prized as the ability to find more of this liquid gold, and rightly so. Because of this ‘training gap’, the directors of the CDT have instructed us to produce presentations to keep each other up to date on our research, inadvertently broadening our training even more. Fantastic! Here’s hoping that ‘cup of tea’ analogies will win some people over and make them aware of the geohazards out there that can potentially create problems for the industry.

The only drawbacks to the CDT that I can possibly think of are that the training takes such a long time. 6 weeks in 6 months so far. A week per month. Roughly a quarter of our Ph.D lives so far have been spent on training. Another drawback being that, while the topics covered so far have been interesting, have not been entirely relevant to each Ph.D. The length of training sessions is not set to continue however, as we progress through our Ph.Ds, the length of the training decreases. That does leave me wondering to what extent each aspect of the industry will be covered. I suppose time will tell.

Some takeaway messages from this post would be that more environmental impact and infrastructure Ph.D topics could be brought forward, but this may stifle the efforts of those concerned with exploration. It’s also important to remember that, while spills happen, oil companies seek to prevent these as much as possible, and that without the oil industry, life wouldn’t be as we know it.

Matlab Madness and the Imposter Syndrome

Contrary to the order of the title I wish to talk about ‘Imposter Syndrome’ first.

Since I began my Ph.D journey I have encountered both elation and despair in terms of progress within the space of six months. I have been given various shards of advice so far, the most notable being “Don’t ever compare your Ph.D to someone elses, it will only chew you up”. As easy as that is to say, it is not as easy to do. You hear people around you talk about their progress and, when you’re stuck in a rut with something (such as Matlab), this can be disheartening. Some advice of my own would be to fear not, the ruts come and go, but if you keep at it you will get through it.

Meeting with and presenting to people much more experienced and educated than yourself can also leave you doubting your abilities. Not that they try to make you feel this way, but the questions fired at you when the answer escapes you can be particularly embarrassing. Luckily for me so far I have had my supervisors in the room who have pitched in and helped me with the questions. The key is to not over think too much (a common pitfall of my own) and remember that you are on your journey to becoming an expert, and that no one expects you to be one at this stage.

My undergraduate degree for example was Physical Geography which encompassed the entire physical world from atmospheric circulation, oceanic circulation, fluvial (riverine) processes to ecology (at all scales), glacier dynamics and volcanoes. Such a wide range of topics does not mean that you could possibly be an expert in any of these areas upon completion. In hindsight I wish I had done a more focused degree, but then again I wasn’t sure what I wanted to do at the start of my degree so a broad range of topics was beneficial for me.

With regards to presentations and such, you just have to bite the bullet and get it over with. The more you do it, the more comfortable with it you will be.

Over the past few months I have been making myself more familiar with Matlab, a multi-paradigm numerical computing environment offering the production of graphs, histograms, pie charts, contour plots (both filled and unfilled, 2D or 3D), application of numerical formula to every element (cell) in a matrix (worksheet), isolation and extraction of a particular section of data which may be interesting, the list goes on. Matlab is a truly wonderful program that much is certain.

Above is a plot produced in Matlab of flow in a river, the arrows highlighting the direction the water is moving, indicating cyclical nature of water around a river meander apex. I guess you could think of Matlab as a more advanced Microsoft Excel, used almost entirely through the command prompt and running scripts.

I had encountered it during my undergraduate years while writing my thesis to produce contour plots of flow data from Kluane Lake in Canada. I had never made a multi-functional script which could calculate and produce multiple calculations and plots with the single press of a button, and by changing one value would result in changing the entire sequence of calculations to produce different plots. This has been the main source of my elation and despair over the last few months. I am fortunate enough to have an office mate and a supervisor who are both incredibly proficient at using matlab, and both have been invaluable so far.

I have learned how to import data which may not necessarily be in the correct format for Matlab, I have learned how to change and manipulate the data, I have learned how to change the dataset I am working from to produce different figures, and I have learned how to plot figures, even multiple data sets on a single figure.

This video goes into detail on what a matrix or an array is, how to use or change single elements (or cells) of an array, how to use or change sections (rows/columns) of an array, and how to reshape and transpose an array. Pretty fundamental stuff.

This video goes into detail about how to use IF and ELSEIF statements  in Matlab. This is vital for writing scripts. I got the basics from my officemate, but this video gives you the basics too.

The official Mathworks forums, and unofficially, Youtube and Stackoverflow.com are great places to look if you ever get stuck. Just type your problem into Google or Youtube and away you go. It’s that simple. It takes a bit of practice, but just keep at it and you’ll get there. My biggest challenge was that using Matlab requires a different way of thinking than what I am used to, it is more step-based and logical than I would normally think in my day to day life. Like I said, practice makes perfect, keep at it and you will get over the hill which you have found yourself at the foot of.