Explainable Artificial Intelligence

I am currently in my eighth week of my internship in the School of Computer Science. My supervisor Aaron is the head of the St Andrews Computer Human Interaction (SACHI) Research Group. It is great to be part of SACHI and to be surrounded by cutting edge research in the field. My research project is aiming to create a visualisation to explain an algorithm widely used in artificial intelligence.

Explainable Artificial Intelligence (XAI) is a new field of research within artificial intelligence (AI). The main idea is to try and create models of AI that are understandable and can therefore be trusted in the decisions they make. Currently, most systems that have an AI component can be described as “black box systems”. This means that users of the system can see the input and output of the system, but do not understand how the system processes the input to generate the output. For example, a self driving car might brake when there is no obvious reason to stop. The input to this system is coming from all the cameras and sensors in the car and the output is the car braking, however it is often difficult to tell why the algorithms are deciding what to do. Using an XAI system, it should be simpler to understand why the algorithms decide what they do. Now that AI is being integrated into more and more systems, it is becoming essential to explain vital decisions. Imagine an AI system that decides whether or not to operate on a patient in a hospital. The decisions of the system will have to be backed up and explained whether that is to the patient’s family or in front of court.

The first few weeks of my project were spent trying to read up on papers that are very difficult to find at the moment. The term XAI has only just started to be explored and therefore a quick search in Google Scholar is not enough to bring up a long list of relevant results. However, after searching various digital libraries it turns out that there has recently been research into a specific area of AI. These techniques are trying to explain neural networks (in particular deep learning) and the decisions these systems make. An example can be seen in figure 1 below. Here the AI system “explains” its decision by highlighting an area of the picture that contributed highly to that decision. In figure 2 below,the AI system “explains” its bird classification in form of a sentence.


Figure 1: Using a heat map to explain decisions [1]

Figure 2: Explaining decisions by generating text explanations [2]

I decided to base my project on previous work that had left a perfect gap for XAI – RadarCat. The RadarCat system classifies and detects objects that are placed upon it using a small radar sensor (Google Soli). The system works by training a specific machine learning classifier on the radar data. (Machine learning is a small subcategory of AI.) Although we could classify all these objects, it is not easy to explain RadarCat’s decisions. Because most of the XAI methods that have been researched to date use visual techniques, I decided to create a visualisation that would dynamically adapt to the classifier used in the RadarCat system.

With just over two weeks remaining, my focus is on running a user study to gather feedback on the effectiveness of the visualisation. Never having run a user study, this will be an interesting and challenging new experience. Furthermore, I will be trying to summarise my findings in a project report and poster.

References:
[1] Grad-CAM: Why did you say that?; Selvaraju, R. et al.; 11/2016
[2] Generating Visual Explanations; Hendricks, L. et al.; 03/2016

Forgotten Children in North Korea

I have a friend who escaped North Korea with his sister about 10 years ago. He is not particularly fond of sharing his experiences in North Korea. He has no good stories about it, and he does not want to be looked as a North Korean. One of the stories he shared was about the flower swallow, North Korean street orphans. When I heard about it for the first time, I could not fathom what they are going through. However, as I researched more about them, it became clear to me that they have become disposable, forgotten not only by their own country but also by the international community.

My research project is controversial and sensitive. It is about the most vulnerable, unknown group in North Korea. Because of this reason, unraveling the mystery of their stories is not an easy process. First, there are not many published materials about the flower swallow. Especially, there is a dearth of the published materials in English. This means that it has not been fully researched by academia. Also, most of the materials heavily rely on the testimonies from North Korean defectors. Therefore, I needed to pay extra attention to the reliability of the sources that I found.

Initially, I wanted to interview from 10 to 15 North Korean defectors. However, due to the current escalating tension between North and South Korea, most of the defectors refused to be interviewed. They are trying to keep on a low profile in order for their families in both sides of Korea to be protected. However, I was able to meet a few people to hear their stories. Some of them cried and got upset while unfolding their stories. From time to time, they talked about things that left me utterly speechless. I have heard that North Korean people are suffering, but I did not know that it was this much.

Throughout my research, I found that the life of the flower swallows is worse than I expected. There are about 800,000 street orphans in North Korea. There are records that the government imprisons them as they are detrimental to the utopian image of communism. Of course, they are not treated well inside the concentration camp. Corporal punishment is rampant, and no one knows whether they are living in a decent environment. Outside the camp, children are still suffering. One defector told me that she saw a pile of dead children starved to death in a train station. The staff could not get rid of all the bodies, so he stacked them in the corner. Often time, they cross the border to find food or job. This make them vulnerable and exposed to the risk of human trafficking. Even though the situation is horrendous, the flower swallow rarely gets attention.

I strongly believe that we can only understand North Korea when looking at different aspects of North Korea. Without taking people into consideration, the country cannot be fully expounded, and the policies that we create to deter the country will be ineffective. For example, most of the defectors whom I interviewed were strongly against another economic sanctions against North Korea on the grounds that they will only kill innocent people. This shows that the actual North Korean citizens need to be incorporated in the policy-making process. However, this cannot be done without understanding them. 

I am very thankful for the Laidlaw Internship Program which offered me an opportunity to research about the flower swallow. Also, I am thankful for Dr Ali Watson’s guidance and support. I am very excited to go to America in October for the meeting organized by Clinton Foundation to present my research.

A subway station near the place where I interviewed one defector.

Geology rocks! An insight into the formation of sediment-hosted stratiform copper

My Laidlaw research project has been a long and rewarding experience so far. My research focuses on a major deposit type, sediment-hosted stratiform copper (SSC), specifically one of the world’s largest deposits in White Pine, Michigan. While there is a general knowledge of how SSC deposits form, the energy source for driving fluid migration and the copper precipitation mechanisms are still uncertain. One model that has been devised is the Thermal Lid Model. In this model, black shales act as thermal lids, trapping heat and inhibiting fluid flow. My research aims to test this hypothesis using samples from White Pine.

You may be wondering why I have decided to dedicate 8 weeks of my summer vacation to researching copper, and this is due to the fact that copper ore is fundamental to the global economy. Copper exists in every device that uses or transports electricity. So, you can thank geologists like me for your ability to read this blog post on a computer!

Now, I understand most people have not studied Geology before, which means some of the words I mentioned in my first paragraph may mean nothing to you. I will go through the general idea of my research, and hopefully by the end of this post you will have a new appreciation for rocks and the ground you walk on every day!

My research begins with understanding how the area of White Pine, Michigan formed in the first place. The Lake Superior region of North America is a portion of a failed intracratonic rift (imagine the USA being ripped apart, but not fully, with a big crack running through the middle of it). This crack then gets filled with a sequence volcanic and sedimentary rocks (think of magma, volcanoes, and the erosion of land and mountains).

The best way to think about these sediments is like a layered cake. At the bottom there are the volcanic rocks, which in this case are flood basalts.  On top of this is a layer called the Copper Harbor Conglomerate, which as its name states, is a sedimentary conglomerate rock. Then on top of this layer is the Nonesuch formation, which consists of black shales. These sediments are heavily researched due to their wealth of economic mineral deposits, including the copper deposit that I am looking at in my research. The copper in these sediments formed when cupriferous fluids flowed up through the Copper Harbor Conglomerate, and into the bottom of the Nonesuch Formation. In the model I am testing, the Nonesuch Formation (shales) acts as a thermal lid, trapping both heat and the mineralizing fluids in the system, causing copper to form.

The way I am testing this model is by determining the maximum temperature of metamorphism that the Nonesuch Formation reached. I am doing this using three different methods: X-ray diffraction and Illite Crystallinity, Hyperspectral Reflectance, and Raman Spectroscopy. I am currently in the data interpretation phase of my research, so unfortunately I cannot say at this point what my results are. From what I have looked at so far, I seem to have mixed results in terms of the temperatures I am seeing, which may mean that I will not get to answer the question I originally posed for my research. This point leads me to the final point I will make in this blog post, which is the difficulties of scientific research!

As this is my first time doing research, I was not sure what to expect in terms of how smoothly it would go, or whether I would get any results that I wanted. My project was originally supposed to look at rock samples from both the Zambian Copperbelt along with rock samples from White Pine, Michigan. Unfortunately, my rock samples that had been collected in Zambia were stopped by customs and still have yet to arrive (yikes!)! While I found it really disappointing that I was not going to get the opportunity to study these rocks, I have been working with wonderful samples from the mine in Michigan which I am very lucky to be studying. As mentioned above, another difficulty I am having with my research is with my results that I have received. Although I have not fully interpreted them yet, they do not appear to have the consistency which each other that I had hoped for. While I may not be able to answer my original research question, my results still tell me very interesting things about this area, and are useful for gaining general knowledge about this deposit type.

I still have three weeks left of my research, and I am looking forward to learning what my results have in store for me. I have a lot of interpretation to do and my research is proving to be incredibly intellectually challenging which is everything I had hoped for! What I am researching is not covered in the Geology curriculum here at St Andrews, and I am incredibly thankful that I have had the opportunity to be exposed to different topics through the help of the Laidlaw Internship.

A jazzy photograph of me working with the Raman Spectroscopy gun!

Cancer cells, Biophotonic and Chopsticks

Hello everyone, I hope everyone is doing well on their projects.

Laidlaw internship so far has been a fantastic journey for me. Meeting new friends, exchanging new ideas during CAPOD’s events and most importantly submerging myself into daunting tasks are priceless experience.

As this is the final week of my project I will summarise my process in this blog by starting with some background knowledge.

My project is a part of a bigger project which develops biophotonic tools to study biological processes. The concepts of the project came from many everyday life phenomena. One of them is the Doppler Effect which describes the shift in frequency when there is relative movement between a wave source and a detector. We see this effect regularly whenever an ambulance approaches us, its pitch will rise up and then drop down during its recession.

Simulation of Doppler Effect.
Photo Credit: The Physics Classroom. Access on 4 August 2017. http://www.physicsclassroom.com/class/waves/Lesson-3/The-Doppler-Effect

Within biological cells, there are waves and vibrations which are characterised by stiffness. As we fire a laser beam at the cells, the laser frequency will be shifted with the same concept similar to that of the ambulance. This method is called Brillouin microscopy.

This is how Brillouin microscopy works [1].

Another concept I have learned and used is thin layer interference, where light (consist of many wavelengths) is reflected from a surface and causes wave interference. This interference constructively strengthens the intensity of some wavelengths and destructively suppresses other, which explains why we see rainbow patterns on soap bubbles.

Thin layer interference in soap bubble
Photo credit: zacktionman via Foter.com / CC BY-NC. Access on 4 August 2017

The cells will be put on a thin layer and as they exert forces, the thickness of layer which is measured by light will change. From the change in thickness, the forces can be calculated. This technique is called Elastic Resonator Interference Stress Microscopy (ERISM).

This is how ERISM works [2]

These two methods will provide us a robust and sensitive mechanical picture of cells. The mechanical properties are very crucial as they can be used to study calcification of heart problem, delivery of drug and especially invasion of cancer cells. The cancer cells have an interesting feature, they have sensors or “feet” that try to probe the weakest points on human membrane to invade. My supervisor’s group has planned to study these processes using the two methods combined, in hopes of understanding and further combating cancer.

Now, let me describe my experience of the past nine weeks using a famous Asian folklore that I learnt when I was eight years old as an analogy. One day, an old man gathered all his sons and daughters and gave them a challenge. The challenge involved breaking a bunch of chopsticks. Even though his children are strong and healthy farmers, none of them can fulfil the challenge due to the toughness of the bundled chopsticks.

An old man setting a challenge with chopsticks for his children
Photo Credit: truyencotich.vn. Access on 4 August 2017

On my first few weeks of my Laidlaw internship, my task was to get the software of Brillouin microscopy working, using the guide lines from previous PhD students and other teams’ software’s notes. Once this part is done, it will be combined with the ERISM software. The software will reduce manual effort significantly and give researchers much more data in a shorter time. The task looked impossible at first glance, I did not even know what most of the elements of the previous software were. With only twelve hours of experience with the programming language, LabVIEW, that was used to program this software from my third-year lab sessions, the whole situation was best described using the pictures below.

This is what I have studied during my lab sessions. Photo Credit: resources.hwb.wales.gov.uk. Access on 7 August 2017

This was how the project seemed to look like. Photo Credit: https://tulipgarden9.blogspot.co.uk/2013/09/cot-ien-chang-chit-day-ro-o-ha-noi-xuat.html. Access on 4 August 2017

After the initial three weeks without producing any codes or ideas, I started looking for help from people around me. All the suggestions converge into one point: breaking up the task into smaller pieces. I tried to look at the bigger picture to understand the concept and find the point where I can start. With that correct methodology, I was able to control the first simple piece of hardware (the stage that moves the sample) in the fourth week. The most important camera was tackled two weeks later and I could finish up our initial plan by the seventh week of my internship. Looking at the process of the first part again, everything seems like an uphill battle for me. Finishing up the first part opened up many routes, acting as a stepping stone for me to delve further in the project. I am now working on combining two software together.

At that point, I suddenly realised the final part of the story from my childhood: After all of the children gave up, the old man showed them how to solve the challenge. The solution is amazingly simple by taking each individual chopstick and break them up one by one. The link between my obstacle and the story struck me strongly. This idea, though very simple, at the right context had further enlightened me. “This is what the cancer cells were trying to do as well” , I thought.

Since then, I can see how beautiful nature is, especially how such a message from a simple folklore is common between different objects. Next time, if anyone challenges me to break a “gigantic bunch of chopsticks”, I would tell them: ”Piece of cake!”.

Bunch of chopsticks
Photo Credit: cafekubua.com. Access on 4 August 2017

To sum up, I would like to acknowledge all of my supporters:
– To Lord Laidlaw, I am deeply grateful for giving us an opportunity to pursuit our passion and your vision on developing future leaders.
– To my supervisor Professor. Malte Gather, people of Gather Lab and especially Andrew Meek for listening to my problems and answering every single question. I will miss breakfasts and group meetings with lots of cutting-edge Physics on Monday mornings. Sorry to all who had to spend time to share the experimental set-up with me.
– To Cat and Harris, thank you for all of your efforts on creating such good events that inspired me, especially the Networking event and Leadership sessions. I found Action Learning Set (ALS) extremely useful and enjoyable. My ALS group (Billy, Patrick, Erin, Rachel and Veronica) filled me up with joys, discussions and ideas. I would like to thank them as well.
– To all of my friends who have helped me since I started my application and throughout my project: Thanks CD for proofreading my application and encouraging me to express more ideas on it even if it was during our terrific exam revision time; Jason and SinNee for sharing their individual experiences that helped developing my initial idea in a freezing cold evening at Tesco; Ryan Moodie for showing me where to focus and emphasize in my project and Dr. Aly Gilles for immediate support whenever I need help with basic LabVIEW knowledge or bugs.
– To Dr. Chuong Tran for the accommodation and lots of Maths discussions; all of my Vietnamese friends in St. Andrews. The meals we had together helped relieve my stress and strengthen my insight on my project.
– Finally, I deeply appreciate the support provided from my family, friends, Angus, Fiona, Judy and the St Andrews’s Bible study group who are always by my side and shaped who I am today.
Reference:
[1] Scarcelli, G. & Yun, S.H. Nat. Photonics 2, 39–43 (2008)
[2] Kronenberg, N. M. et al, Nature Cell Biology 19, 864–872 (2017)

My frustrating (but ultimately hugely rewarding!) experience of studying International Refugee Law

As I head into the final week of my Laidlaw research project, I can’t help but look back. I realise now that I was naïve to think that I had everything figured out, but that I am also incredibly proud of how far I have come. At the start of my 10 weeks I had, what I thought, was a pretty solid plan and a pretty clear idea of where my project was going to go. I even had what seemed like a pretty solid idea of what conclusions I would be able to draw from my research. Boy was I wrong! The seemingly simple task of looking at the discrepancies between state refugee laws and international refugee law turned out to be much more complex than I thought.

The first shock came when I realized how difficult it was to navigate the complexities of international law. Whilst I thought I knew what the key document, the 1951 Refugee Convention and the 1967 Protocol stated and meant thanks to my Human Rights module, I was unaware of the sheer amount of debate that surrounded the interpretation and scope of this regime. This was daunting, and honestly scared me quite a bit, as I soon learnt that I still had a lot to learn before I could even begin to look at the national level. However, once I eventually wrapped my head around the different interpretations and some of the literature on this, I learned to view these academic debates as incredibly interesting and something I could end up contributing to.

The next reality check came in trying to navigate the complex state policies and immigration law for each of the individual states I was studying. There were a couple of reasons for the difficulties. Firstly, I do not have any law experience, so reading law documents for each of the four states I was surveying was extremely difficult. I helped myself out by reading explanations of the laws instead of the laws themselves and then using the laws only to double check my understanding. Secondly, government websites presenting these laws turned out to be horrendously difficult to navigate. This turned what was supposed to be a relatively simple task of finding various refugee policies into a test of my patience and determination. Surprisingly, the Swedish government website was the easiest website to navigate (despite the potential for the language barrier to be an issue) and the British government was the most difficult. I ended up just having to power through and adjust my original research schedule.

The final major difficulty came in trying to remain positive when reading about the harrowing treatment of refugees by states. As I was examining the tensions between national state immigration law and the rights refugees are afforded under international law, I became aware of the importance of my research. This part of my project could be framed as a constant struggle between the sovereign right of states to decide their own national refugee and immigration laws, and the supposedly inalienable rights afforded to refugees under international law. Many refugees lack the ability to demand these rights for themselves and end up having to fight against the governments of the states that are meant to provide them with a safe haven. However, it is important that these struggles are brought to light. This is increasingly important in the face of justifications from politicians that are framed in such a way that seems to protect refugees whilst simultaneously taking away their ability to claim particular rights.

My usual set up in the Main Library, where I did most of my research

All in all, this has been an amazingly rewarding summer. Whilst my motivation and confidence have definitely fluctuated constantly (and it was definitely hard to spend time in the library on the rare days that St Andrews became sunny and warm), I am incredibly thankful for the experience. I have learnt that research doesn’t always go perfectly to plan, but that this is okay. Finally, I have also learnt to trust myself and trust that it will all work out in the end. A huge thank you to my supervisor, Professor Patrick Hayden, for the helpful guidance and reassurance. A further huge thank you to Lord Laidlaw and the University of St Andrews for providing me with the opportunity to pursue this opportunity, I can’t wait to see where it takes me in the future.

Of Cosmopolitanism, Patriotism, and Academic Freedom

My Laidlaw research project was supposed to focus on human rights theory – on the puzzles that refugees generate for human rights theory. But, since my Laidlaw internship started in July, I had a bit of time in June to do some reflection on the exact questions and direction I wanted to pursue with my research. I realised I was a lot more interested in a broader question: what is the ethical significance of nationality when it comes to global justice?

At the heart of this question is what Kok-Chor Tan calls the tension between patriotism and cosmopolitan justice. The idea behind cosmopolitan justice is a simple one: people should matter equally purely in virtue of being human. It’s also common sense: we don’t think we should give greater consideration to people of a specific gender, ethnicity, religion, etc. On the other hand, for many of us, patriotism – the love for one’s country – requires that we show greater concern for one’s compatriots. For example, as Charles Beitz notes, it’s fairly uncontroversial to think that a government should prioritize the domestic poor over the foreign poor when redistributing income to improve welfare – even if the foreign poor are a lot worse off than the domestic poor. In short, cosmopolitan justice tells us that everyone is entitled to equal consideration, while patriotism tells us that compatriots are entitled to greater consideration. My research investigates the possibility of reconciling this tension.

“Picture of People of the Five Nations: Walking in Line” by Sadahide, 1861

Many respond to this tension by setting limits on patriotism, informed by our commitment to cosmopolitan justice. For example, Kok-Chor Tan argues that people may give greater consideration to their compatriots only when the rules and principles of the overarching institutions meet the conditions of cosmopolitan justice. Robert Goodin suggests that being patriotic is just an effective way of discharging our more general cosmopolitan duties; but, in world of great inequality, it is this commitment to cosmopolitanism that compels countries to put worse off foreigners first. Others argue for a conception of cosmopolitan justice that does not conflict with patriotism. Richard Miller, for example, argues that cosmopolitan justice means equal respect for all but not equal concern for all. On such an account, individuals are under an obligation show equal respect for non-compatriots but are under no obligation to show them equal concern, especially when it often comes at a cost to their compatriots.

One of the best things about the Laidlaw internship has been the academic freedom. I have moved seamlessly from focusing on human rights theory to the tension between cosmopolitan justice and patriotism and, more recently, to solely on patriotism. This academic freedom is unlike anything else in my undergraduate degree. I got the chance to take intellectual risks and pursue my research in the direction that most interests me, with no fear of an impending deadline for an essay or a mark to collect at the end. It’s been the best introduction to academia that I could ask for.

I want to thank my supervisors Dr Elizabeth Ashford and Dr Natasha Saunders for supporting and inspiring me, CAPOD for the incredibly helpful leadership component of the internship, and Lord Laidlaw for making all of this possible.

How one painting captured my imagination…

Although I am in the middle of my research project, I would like to start by telling you, dear reader, how it all started. My research is based around one painting, that I came across two years ago, while doing an internship at the Ministry of Culture of Republic of Moldova. I remember very clearly the very first time I stood in front of the painting. It was more than a visual encounter; it was an all-encompassing sensory experience and it is to this day, the episode I recall every time I get to talk about my project.

The Museum of Art was in reparation at the time, and only one wing was barely kept alive with a few workers and an exhibition of a Polish artist. However, I wasn’t interested in the displayed paintings, I was more curious to see more of their permanent collections, gathered under decades of Soviet rule, and stockpiled in inaccessible storage rooms. After interacting with some of the museum workers, and being guided through the unexplored corridors infused with a cold humid smell, we got to this very old door; its colour has faded with time and its corners were worn-out and flaky. A single small key opened the door to reveal tens of paintings, whose story and value was unknown. And between them, there it was, The Allegory of Fire, showing Venus and Cupid in the forge of Vulcan, in a composition that was overwhelmingly green, a green that was soft, rich and warm, with an almost velvety surface.

Although it was speculated before that the author of the painting might be Jan Brueghel the Elder, the famous Flemish artist, there was no proof of this. In fact, the documents archived in the museum told a completely different story and identified the author as Otto van Veen. I started researching similar compositions even before my internship started, and several specialists in the field have confirmed the possibility of a link between the painting and Jan Brueghel the Elder’s studio. However, it was the Laidlaw internship that gave me the opportunity to study this subject in depth, to travel to Rome and see several Brueghel originals in Galleria Doria Pamphilj, in an attempt to identify the author of the painting found in Moldova.

At this stage of my research, I have gathered over twenty paintings that are variations of the same composition – The Allegory of Fire, painted by Brueghel in early seventeenth century. I categorized the works in three groups, according to the painting style: a) the ones that were painted by Jan Brueghel the Elder, b) the ones painted by his studio; c) the ones painted by Jan Brueghel the Younger (the son of Jan Brueghel the Elder). Optimistically, this classification and a further close analysis of the works will allow me to authenticate the painting found in Republic of Moldova. It is very difficult relaying solely on visual analysis when attributing a work of art. Although modern technology – infrared reflectography, chemical analysis, X-Ray photography – offer a lot of possibilities, they are not available in Moldova. Nonetheless, I hope that my experience in painting would help me in differentiating between the styles and techniques of these three groups.

Finding such a big number of paintings that share a striking resemblance, has also opened two other topics that I would like to explore in the future. First, I am very interested in the copying practices widely employed in the seventeenth century. A lot of artists at the time used the help of their assistants to replicate successful composition. The fact that these compositions would be sometimes finished and signed by the masters, opens a question about the meaning of authorship and originality. Second, some of the paintings are mirrored compositions of each other. This is a very interesting phenomenon, and it could indicate Brueghel’s use of optical devices. As I have found no sources that discuss the use of optics in Brueghel’s studio, I would like to explore this further.

In conclusion, I would like to thank again for the possibility of undertaking this internship. What I found most impressive about it, was the possibility of contacting through my supervisor, Dr. Julian Luxford, the most prominent specialists on Brueghel, who offered their insight on my project. I also gained more understanding of how complex and at times unpredictable the process of authentication is. With the help of my supervisor, I also learned how to address official letters to imposing establishments, like the Ministry of Culture of Moldova. The ability to communicate with experts in the field and various institutions is inspiring and it motivates me to want to explore more topics and ask further questions.

No Need to Cry a River

Entering my final week of the Laidlaw project it’s hard to believe how fast the time has gone. Just ten weeks ago I was facing the daunting task of climbing the Mourne Mountains and collecting jars upon jars of samples from the River Shimna by myself. It was a lot more exercise than I anticipated and a lot more falling into the river than I wanted (big shout out to various family members who accompanied me to make sure I didn’t drown) but mostly this project has been a lot of fun and because of that I am so grateful to the Laidlaw committee and Lord Laidlaw for giving me the opportunity to carry it out.

My project is centred on investigating the pollutive effects a dam can have upon a river. Fofanny Dam and Reservoir was built along the River Shimna below the Trassey walk and has been the cause of three serious hot water spills in the past decade. The Northern Irish Environmental Agency (NIEA) provided figures from pollution tests further downstream where there was evidence that the river has recovered from any effects of the dam, however minimal testing had been carried out around the actual reservoir. My aim was to establish the water quality above and below the dam and investigate if there was any difference that could potentially be caused by pollutive effects.

After collecting samples of macro-invertebrates from sites above, alongside and below the dam they were transported back to St Andrews. A couple weeks spent squinting down a microscope and some much appreciated guidance from my supervisor and I managed to classify everything down to family level on the taxonomy index. This allowed me to use biological indicators and scores to compare water quality between sites and I have produced some very interesting results. Both above and below the dam had relatively poor water quality, meanwhile two of the sites right above/alongside the dam had moderate to good water quality- a completely different set of results than I had predicted!

The positive outcome from these results is that the spills from the dam and reduced flow rate are not having a significant pollutive effect on the river. Therefore I do not need to recommend any mitigation procedures to the NIEA to improve the river quality. It does however mean that there may be other aspects of the surrounding environment which could be preventing the river reaching its full ecological potential which should be investigated. For the remainder of my project time I now have to write the report and poster to explain the other causes of pollution around the river. So keep a look out for me at the poster presentation in October if you’re interested in what else could be happening to our rivers!

 

^ A picture of me at the final sampling site feeling very proud!

Big Questions:

With fewer than two weeks to go, the completion of my Laidlaw summer research project is fast-approaching, and the more than slightly daunting task of drawing conclusions from the past 8 weeks of research is now upon me. Thankfully in that time I have amassed a fair quantity of notes, all hand-written as I somehow never lost the habit, and somewhere in there I hope to find the interesting and original insights that will make my efforts, and the Laidlaw programmes generous support, all worthwhile.

Attempting to understand the complex relationship of France’s far-right political party the Front National, to the country’s intrinsic, foundational, and undeniably unique conception of secularism or laïcité, has been interesting, and at times involved tackling many more questions than those I originally sought to deal with. Beyond the shocking headlines and video clips of French police forcing Muslim women to remove their veil on sunny southern beaches, and of town mayors (not exclusively from the Front National) defending such actions, there are actually far-deeper issues at play which elude the simple labels of racism and discrimination, albeit that such intolerance exists in France as much as it does elsewhere.

Perhaps unsurprisingly, the most rewarding and academically fruitful aspect of my summer research project was undoubtedly the two weeks I spent conducting interviews in France at the end of June. I spoke to a broad range of people, Front National party members, and elected politicians of course, but also representatives of activist groups and government officials. While I did hear views I personally would describe as racist and Islamophobic, what I heard a lot more of was a sense of apprehension about the future, and a legitimate opposition to globalisation, multiculturalism, and a direction of modernity which many saw as threatening to their identity.

One interview in particular stands out in my head. On the 19th of June, I spoke to a farmer turned FN regional councillor in the small village of Châteaurenard, not too far from Marseille, who had joined the Front National after a proposed free trade deal with Morocco which would see his produce being undercut by agricultural imports from North-Africa. He saw globalisation as threatening to his livelihood, and the Front National as the only party which would defend local interests against global market forces. While many of us may question how he chose to fight his campaign, few would fail to understand his concerns.

As such, in the debate around the Front National, and laïcité, globalisation inevitably emerges, as does immigration, integration, terrorism, colonial history, political history, and a range of contemporary social issues. I would say that attempting to chart a course through this complex web of often very sensitive subjects, and while taking their relevance into account, remaining focused on the question at hand, has been a particular challenge of my project. Deciding which avenues of research to pursue, and which to leave aside as an inevitable consequence of the time constraints of a ten-week project has thus been an important learning curve from my time as a Laidlaw intern, and will no doubt be important experience for any time-sensitive projects I may undertake in the future.

A grey day in Paris

Cryo Electron Microscopy: continuously challenging technique from start to finish

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Looking back to the past weeks of working in a laboratory, I cannot believe how much my supervisor managed to train me and guide me through my project. I have learned so many different and most advanced techniques used in cell biology research directly from him and this made Laidlaw summer internship more precious than I have ever expected. One of the most challenging technique of all I have learned was to perform Cryo-Electron Microscopic imaging.

The elements that are involved in Cryo EM starts from culturing the cells properly. Once you defrost the cells that were kept in the liquid nitrogen tank, you must take care of them by regularly changing the media (liquid with nutrients and growth factors that help the cells grow and multiply in numbers), checking that they don’t have fungal infection or dividing them into flasks for more space to grow. For my experiment, I had to treat appropriate chemicals to my cultured cells to differentiate them into a more mature form of neuronal cells. This added up extra bits of care and procedures to be done before actually running any experiments on them.

Once you fix the cells after the experiment, you would scrape them off the dish they were growing on, and spin them down in a centrifuge to make a palette of cells which will be as small as a grain of rice. And this is where things get more challenging. The next step is to load the palette on a metal stub. This sounds quite simple, but you are expected to deal with a very small, slippery and fragile palette of cells and load them in a shape of a mountain on a stub that is barely 2mm wide. This has to be done within approximately 30 seconds, otherwise, the palette will crumble and become like a jam (which cannot be sectioned and thus will be disposed). Once you shaped the palette on the stub correctly, this is to be frozen instantly by going into liquid nitrogen.

If the techniques mentioned above do not sound challenging to you, here comes nanometer level of samples and thousand pounds worth of diamond knives to deal with. The tiny frozen cell palettes are now ready to be sectioned into 70nm thickness. The machine that you will be handling (a cryostat) has two very small diamond knives (one for trimming to make blocks, and the other for actual sectioning). They are so delicate, needless to say, you should never touch the tip of the knives, but you use a stick with an eyelash attached at the tip to handle the sectioned samples. I would have to say I still feel nervous after handling them for weeks. Once you finally start sectioning the blocks, you will have to fight the static, delicacy of the 70nm thickness, the condition of the knives, temperature setting, weather of the day and all sorts of factors that can change the quality of the section. I usually take about 1 to 2 hours to find a perfect combination for the day that would actually lead to proper sectioning. After all this, you need to pick up the section with a small metal loop with less than 10 microliters of liquid blob. By very gently touching the sectioned sample, it will attach to the blob which will then be moved to 2mm diameter copper grid.

The copper grids with sectioned cells on it are then to be washed, labeled with antibody and gold particles, stained and dried. This takes about three hours to complete as long as you do not lose the grids in between each step. Prepared grids are to be imaged in an electron microscope, which the machine itself takes up a whole room and is also, very delicate to control.

Starting from growing cells to finally imaging the results take nearly two weeks for each cycle, and I personally found it slightly stressful that not a single step during the two weeks are any less delicate and challenging than the other. Nonetheless, it is unbelievably satisfying when you image the grids and finally get to see the result of your experiment with your own eyes.