Exploring the Value of Species

The extinction of species is generally regarded as a bad thing. We campaign to save the whales, protect the pandas and so on. In my project, I considered these assumptions, whether they can be justified, and what this might mean for conservation debates. The first major question to answer was one I didn’t expect to find great difficulty with: if we are concerned with the death of species, what is a species? Prior to beginning my research, this seemed like an important question, but not one that would be terribly hard to tackle. Biologists surely had a thorough species definition. In fact, defining species is a contentious issue, at the center of many debates within the Philosophy of Biology. It became apparent at the beginning of my project that this issue would become a sizeable portion of my work in this internship.


Many people are familiar with the folk-definition of species; two animals are members of the same species if they can produce fertile offspring. (What we mean to say, of course, is two animals are part of the same species if their respective populations can, in general, produce fertile offspring.) This way of defining species is, however, hugely problematic. For one thing, many species – indeed, the majority of the species on earth – do not reproduce sexually, so the definition is meaningless. Even for sexually reproducing species, this account fails to draw the lines we would want to. Most notably, we have cases of ‘ring species’, a collection of species such that the first may breed with the second, which may breed with the third on so on. However, the final species may not breed with the first. This would mean “is the same species as” is intransitive: we may have that A is the same species as B and B is the same species as C, yet A and C are different species. Clearly, this is unacceptable.


It became clear, having delved into the literature on this topic, that most accounts of species fall into one of two approaches: they emphasize either the similarities between the members of a species or the relations between them. We must consider whether two organisms are members of the same species because they are alike, or because they have shared ancestry. Any answer to this question is plagued by problems, but emphasizing similarity has particular shortfalls in the context of projects such as mine, in that it undermines much of the meaning of extinction. Extinction is generally understood to be the end of a species, it’s death. However, if species are united by similarity, then it seems species behave like classes, rather than individuals. Chemical elements are an example of classes: an atom is ‘gold’ if it has the requisite structure. Gold cannot go extinct. True, every instance of gold could, conceivably, cease to exist. But if an atom appears later with the requisite atomic structure, then this atom is Gold. The intervening period with no gold atoms is not relevant. If species behave like this, then extinction is not a permanent event; the elephants going extinct simply means “there is nothing currently alive that is like an elephant”. Equally, if the elephants were to go extinct but millennia later hippos had evolved to a point where their descendants were indistinguishable from elephants, we would have to conclude that the elephants were back. For these reasons, I adopted the approach that species are not groups defined by likeness, but lineages.

A crude Cladogram of the “tree of life” mapping the development of the kingdoms.

I was then able to turn to what had been my main question initially; if species extinctions are bad, how should we understand this value? The way species value is typically understood, it is not a value we can ‘maximise’. In general, we would think if a thing is good then more is better, but some values create odd implications if we claim this. This idea can create many issues when we consider species value. Suppose we are very concerned about the prospect of the white rhinos going extinct. If it is the valuable things individual white rhinos themselves, then perhaps we wish to maximise the number of white rhinos. However, this would remain true long after they are saved from extinction; even once white rhinos had reached a large, stable population size, we would still want more of them. Perhaps we should set up white rhino colonies in the western isles and America, just to make sure there as many possible. The same would be true for any other animal’s extinction we are concerned with. This is plainly absurd. Suppose instead, we are concerned with the total number of species; again, the more the better. This does give us reason to be concerned with extinctions, but not with the overall number of the members of the species. So far, so good. But it also suggests a symmetry between prevent species extinctions and developing new species. If I’m faced with the choice between saving one species or creating three new species using genetic engineering then I should choose the latter. Yet, this does not seem to track most people’s intuitions. The kind of problems reappeared throughout the project; finding a solution to one problem, only to find it’s conclusions were more bizarre than the problem it was solving. Ultimately, I managed to construct a thesis which, I believe, manages to capture the common intuitions about extinction, without succumbing to common unappealing conclusions. I also considered what these theses mean for the recent debate surrounding whether we ought to ‘bring back’ extinct species via de-extinct species and, indeed, whether we can.


In addition to what I have learned during my project about the philosophy of biology and the literature on conservation, this internship has been a valuable insight into academic research. One of the most valuable aspects of this experience was seeing how – despite feeling I had a clear idea of my project and theory at the outset – elements of the project which seemed unimportant at first swell to become large portions of the final product. Equally, parts I was sure would be significant often became almost trivial. In completing this project, and especially through discussing my problems with other interns, it became clear that not only is this a common problem, it isn’t really a problem at all. Many elements of the project which felt at first like I was failing were, in fact, natural parts of the research process. There are certainly things I would do slightly differently next time. However, had I known the complete structure of my final output at the start of the project, the project would have been pointless to complete. Likewise, it was often disheartening when threads turned out to be dead ends – but had I not taken the time to consider these threads, I would not know they were dead ends, and my work would not have been thorough. To realise that many of the things that I viewed as failures were just necessary parts of the process has been incredibly valuable. Overall, completing the Laidlaw internship has confirmed that I definitely wish to pursue research as a career path.

“So all you did was watch movies?”: A study on Lebanese Cinema and the Civil War

My summer project was most definitely a personal one, that I started from a less-than-objective point of view. Although I could not say that I have grown up watching Lebanese films about the civil war, violence and trauma not being the most suited themes for childhood movies, I remember very distinctively how marked I was by watching Ziad Doueri’s West Beirut: All of the sudden, the stories that my parents would tell me, of how cheerful they were when school was cancelled, of the curiosity about the other side of Beirut that they were not allowed to cross to, even the colourful 1970s clothes that I would see on old pictures, were animated on the screen. Watching West Beirut as a Lebanese person that was born after the end of the war, I did not understand its causes and consequences. But I felt empathy, I felt belonging and I felt like I  could grasp a little bit better what everyday life was like under the war, for a teenager the age of my mother. Hence, this project aimed to analyze the extent of cinema’s ability as a medium to talk about what the Lebanese state all but refuses to acknowledge. Furthermore, in a fragmented society that is yet to heal from the war’s wounds, can cinema bring people a sense of commemoration, and through the latter, actively work towards national reconciliation?

Tarek, Omar and May share ‘riz el banet’ in ‘West Beirut’ (1998)


Upon starting this project, I very quickly realized that most if not all of the information I held about the war and about people’s attitudes towards it stemmed from commonly agreed upon opinions amongst Lebanese people, rather than academic texts. Although these are probably very interesting from a more ethnographic perspective, they presented the problem of being source-less, somewhat mythical, and not exactly reliable: ‘All Lebanese filmmakers do is complain about the war.’ ; ‘The Christians are the ones who protected this country.’ ; ‘The youth knows nothing about the war.’ etc …  The first part of my research then consisted in confirming, disproving, and learning more about my pre-conceived ideas. David Hirst’s Beware of small states was an excellent introduction to the history of Lebanon and the Levantine region in general, and included a clear and concise explanation of the civil war, which allowed me to take a step back and make sense of what exactly was a sectarian conflict between Christians and Muslims in the war, and what was a result of external politics, and the key geographical role that the small country plays in the region. Ultimately, I believe that Lebanon’s issue does not lie in its confessional divide, but rather in its difficulty to define its identity. Religion is inherently part of Lebanese politics influences the extent to which Lebanese citizens will consider themselves Arabs or Phoenicians, socially liberal or more conservative, but also on what community can get the upper hand in government, or how their leaders can build power and influence in the country, and within the region. This means that although Lebanese people can indeed be patriotic, their Lebanese identity does not stem from a loyalty to the state, but to their respective religious communities, whether Druze, Maronite, Sunni or Shi’a. Under these conditions, it is nearly impossible for Lebanon to become a fully-fledged nation, and the ideological and sectarian issues that are in part what triggered the Civil War, almost thirty years ago, remain the source of tensions in the post-war peace that according to some, was never quite achieved.

If we consider that all films are political, Lebanese films, whether they deal with the subject of war or not, then inevitably take on importance beyond that of a work of art or entertainment. When interviewing Lebanese filmmakers, I couldn’t help but notice that they were a little bit defensive, if not exasperated, by the suggestion that the work they were doing was explicitly activist. Cinema is not pedagogical, its is not

An ex-militiaman explains his reasons for fighting in ‘Alone with the War’ (2001)

educational, it does not aim to replace the work of historians or politicians. Films were not made to achieve national reconciliation or to shed light on its unspoken aspect, but rather as a consequence of the lack of commemoration, and the lack of collective understanding of it. On the subject, the filmmaker Vatche Boulghourjian told me “This trauma is going to stay with you. And the same goes for a country. We experienced it collectively and individually […] My professional work has been focused on searching for what exactly happened at that time. It’s a human desire no matter where you live to seek out what exactly happened to you and to your loved ones.” Through introspective and personal work, Lebanese cinema nonetheless did its part in providing for people like me and across Lebanon imperfect images of the war, and stories that humanize and victimize all participants of a war that still impacts Lebanese society today. Reconciliation may still not be achieved, but through the construction of symbols that are fundamentally Lebanese rather than sectarian, it is possible for the country’s present and next generations to truly form a nation.

Finally, I’d like to thank Lord Laidlaw and everybody involved with the Research and Leadership program for this opportunity. This has been an amazing opportunity to work on what may have been a little too unconventional for an essay, to grow as a person and feel more comfortable in a position of leadership, and yes, to watch a lot of films!


“I know it’s morally wrong, but so what?” On the possibility of amoralists.

In my Laidlaw project I have been looking at the connection between moral judgements — judgements like ‘it’s morally wrong to eat meat’ or ‘it’s morally good to help strangers in need’ — and moral motivation, often called the practical aspect or force of moral judgements. A large part of my project has been dedicated to evaluating whether it’s possible to genuinely judge something to be right or wrong while also being left completely unmoved by that judgement. If it’s possible to make genuine moral judgements while remaining unmoved by them, that allows for the possibility of amoralists. Amoralists are people who recognise or make moral judgements but also lack the motivational aspect that so many of us are (hopefully) familiar with.

In the debate on the connection between moral judgements and motivation, there are two broad, rival philosophical camps: motivational internalism and motivational externalism. These two camps are separated by whether they consider the motivation that follows from moral judgements to be necessary and internal to the judgements or contingent and external to the judgements (hence the names). Part of the debate between internalists and externalists centres on the possibility of amoralists. The amoralist’s attitude can be captured by statements such as ‘I know I ought to do it, but why should I care?’ or ‘I know it’s morally wrong, but so what?’ The amoralist appears to make or recognise moral judgements as well as any other person, but remains unmoved by those judgements.

For internalists it would not be possible to make genuine moral judgements without being at least partly moved by them, because they hold that moral judgements are by definition motivational. There is a necessary and conceptual connection between making a moral judgement and being moved by that judgement, so on their view amoralists are conceptually impossible. Externalists, on the other hand, often appeal to the intuitive possibility of amoralists. They use the amoralist to try to show that there is only a contingent connection between moral judgements and moral motivation. They do this by separating the motivational aspect from the moral judgements by, for example, taking moral judgements to be beliefs and taking the Humean theory of motivation to be correct; the view that only desires can motivate action. So, moral beliefs are not motivating by themselves, but may be accompanied by some desire to be good, and that’s where the external and contingent motivation of moral judgements comes from. This means that, for externalists, it is possible to make genuine moral judgements while also remaining unmoved by them, and thus the amoralist is not conceptually impossible.

Internalists often respond by arguing that what we actually imagine when imagining the amoralist is someone making “moral judgements” — “inverted comma moral judgements”. Michael Smith (1994) compares these “moral judgements” to the (inverted comma) “colour judgements” of someone who has been blind from birth but who manages to perfectly distinguish coloured objects by means of touch. Smith thinks it would be strange to say that the blind person actually possesses colour terms, just like it would be strange to say that the amoralist possesses moral terms if she is completely unmoved by them.

This led me to investigate topics in philosophy of language and philosophy of mind on concept possession and mental content (the contents of attitudes like beliefs and desires). The freedom given to us in this internship has been particularly rewarding for this reason. I have been interested in exploring a more holistic approach to doing philosophy where I can and need to move between different branches of philosophy and look at connections between them, and this summer project has given me the liberty to do just this.

David Hume looking fabulously smug due to his sweet hat and his lasting impact on metaethics.

In the end I’d like to thank Dr Justin Snedegar for supervising me and for the support over the summer, especially when I was frustrated because of dead ends in my research. Thanks to CAPOD for giving us valuable networking sessions and leadership talks over the summer. Finally, thanks to Lord Laidlaw for giving me the opportunity to explore and research a topic of my own interest so early in my academic career. This has been an incredible experience and a massive boost of motivation to continue with academic research.

Brink, D. Moral Realism and the Foundations of Ethics, Cambridge University Press, 1989.
Pigden, C. Hume on Motivation and Virtue, Palgrave Macmillan, 2009.
Smith, M. The Moral Problem, Blackwell, 1994. 


Uncovering Austen

“It is a truth universally acknowledged that” this may be the most overused opening to Austen criticism in the world. I should know. I’ve spent the last 8 weeks researching the publication, and critical, history of Jane Austen’s works. From hagiography and misogyny to Colin Firth, sopping wet, wading through a lake, I’ve been exploring the changes in perception of Austen over the past 200 years.

Something which has been highlighted by my research is the importance of researching and restoring old books. Unless you’re insanely protective of your book collection like me, you don’t give a second thought as you pull a book off of its shelf and crack open its spine. It’s meant to be opened. That’s its sole purpose: to be read. What we don’t think about is the long-term damage caused by these seemingly innocuous actions. Like most things, books are worn down by each use and, eventually, will begin to fall apart. The top of the spine will be the first thing to go. Years of being pulled off of a shelf by its most accessible end, slowly weakening it, day by day. A book’s spine is much like the human spine, without it, we’re screwed. Once that weakens, the bind begins to deteriorate leading to loose pages and, in some cases, complete disintegration. I am not exaggerating. Some precious books must now be kept in unopened cases as the books will literally disintegrate if a page is turned.

A severely damaged copy of “La Belle Assemblée” from 1815.

Thankfully, this hasn’t yet happened to my collection, but I am regularly asked why I don’t just invest in a Kindle and get rid of my books.  It’s simple. Curling up on the sofa with a cup of tea and a piece of plastic just doesn’t appeal to me. Personally, nothing will ever compare to a physical book; the feel and smell of which is comforting to me. A Kindle, eventually, just hurts my eyes. Or needs charged. I quite like not having to be tethered to a wall to enjoy my favourite novels. Furthermore, if we give up on physical books and accept their eventual death, we could easily lose a large part of history.

As part of my research I have had the good fortune to be able to meet with book conservationists and observe their work. It’s a tough job, and an expensive one. It is often the case that, due to a lack of financial stability, some books just cannot be saved; the cost simply outweighs the benefits. When it comes to Austen materials, there are books that are missing covers or have been rebound, that are missing illustrations or title pages, or they are missing original dedications and inscriptions. With each lost page, we lose a small piece of Austen’s history. It has even gotten to the stage that places, such as Chawton House Library, run an “Adopt A Book” scheme in an attempt to preserve the history of early women’s writings.

A stunning copy of “Pride and Prejudice” which has been preserved.

So, what is the solution? Do we simply resign ourselves to that fact that eventually our books are going to end up in the bin? Do we continually replace our old books? Do we create adverts of books falling apart to sombre music while asking for donations? Or do we begin to rely more heavily on technology?

I, for one, hope that people begin to invest more in conservation work and help save the many beautiful books out there before it’s too late. Until then, I will settle for curling up and reading as many as I can.

Some wonderful, and accommodating, conservationists.

Special thanks must go to Lord Laidlaw for this wonderful opportunity; my amazing supervisor Dr Katie Garner, who will always gush about Jane Austen with me; Cat and Eilidh for their continued support and motivation; and the incredible staff at Chawton House Library for helping me extensively on my research trip and taking me in as one of their own.

In case anyone feels the urge… https://chawtonhouse.org/get-involved/support-us/adopt-a-book/ 😉

Transverse Field in an Ising Model which exhibits a Kasteleyn transition

My Laidlaw project has been extremely rewarding in more ways than one: It is the first time I have performed original research in the context of theoretical physics; the opportunity to meet peers at the same level and support each other and; the wealth of knowledge provided to us in the numerous events which are held.

My research is a continuation of Doctor Hooley’s paper [1] which considered a particular magnetic model and showed that a special phase transition occurred.

The model is a two-dimensional Ising system with anti-ferromagnetic bonds horizontally and ferromagnetic bonds vertically and diagonally. An Ising model is a classical system which considers particles to have half-integer spin and couplings between nearest-neighbours. One can think of the particles as tiny bar magnets, with a north and south pole. Ferromagnetic couplings prefer to align spins, while anti-ferromagnetic couplings prefer to anti-align spins.  In this system, all the bonds cannot be satisfied simultaneously, hence the system is “magnetically frustrated”. There are six configurations in the elementary plaquette (a square with a spin particle at each corner) which correspond to the minimal achievable energy – the system is degenerate. The degeneracy is interesting because when the system is cooled to zero temperature, there is not a unique ground state and hence it retains a non-zero entropy density, which seems to violate the third law of thermodynamics.

Five elementary plaquettes and the couplings.

Any magnetic field in the z-direction magnetises all the spins upwards fully, as “all-up” is one of the degenerate ground states. Reiterating, the longitudinal magnetic field eliminates the degeneracy. Hooley showed that there is a phase transition line between the interplay of this magnetic field and the temperature. If the temperature increases beyond this line, the system changes into one with lines of down spins extending from the top end of the system to the bottom. These lines do not cross and never make loops, characterising a “Kasteleyn transition”.

My work this summer has been trying to explore this phase space when an additional x-direction magnetic field is applied. We expect to see the Kasteleyn transition being characterised by a choice of states that the system picks when the fields are varied.

The beginning third of my internship was background reading which was critical before I could proceed. These weeks allowed me to go over the various parts of statistical and quantum mechanics that I needed, and let me explore the more recent developments in this area. Although I felt particularly thrown in the deep end, it was paramount to my understanding. Reading all the time instead of solving problems can be frustrating but one of the great rewards of this was the night and day difference in my understanding of Hooley’s paper before- and after the reading period.

The rest of my internship has been spent working on the problem. To explore the effect of this second “transverse” field we approached the problems via various methods. One method is quantum mechanical perturbation theory, which is essentially the Taylor series applied to QM. Here, we consider one part of our Hamiltonian to have known solutions, and the other part to be a small change which gets weaker with the increasing power of some parameter. Perturbation theory was applied numerous times, with different parts of the Hamiltonian assumed to be the “original”.

The second main technique used is the quantum mechanical variational method, which tells us that the expectation value of a Hamiltonian with respect to any state is greater than or equal to the true ground state energy. This simple rule is useful as it allows us to guess a state, work out its expectation value, change the value of a parameter and then if the new expectation value is smaller then our guess gets better and better. Both methods allow us to find out which states are chosen when different strengths of longitudinal and transverse are applied.

I am incredibly grateful to be a part of the Laidlaw summer program and am thankful to Lord Laidlaw and the university. I would also like to thank CAPOD for the events and the support which they provide the students. Thank you to my peers who have kept me supported with good ideas and motivation. Last but certainly not least, a massive thank you to my supervisor, Doctor Chris Hooley who has led the direction of the research, and for his endless support and ideas.

My setup in the physics building.

[1]  C.A. Hooley, S.A. Grigera arXiv:1607.04657

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.

[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.
[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)