Chemical harpoon proteins

Image

Over the course of this summer I looked at bacterial adhesion proteins of Gram-positive bacteria. These adhesins, proteins found on the surface of bacteria, mediate binding to host tissues which is the first step in an infection process (Figure 1). Given the rise in antibiotic resistance, adhesins are an interesting new target for drugs that combat bacterial infections because unlike antibiotics, which kill bacteria and thereby create a strong selective pressure to develop resistance, targeting adhesins does not target bacterial viability.


Figure 1. Adhesion of Lactococcus lactis to the protein fibrin which is involved in blood clotting (Photo taken by Professor Manfred Rhode, Helmholtz Center for Infection Research Braunschweig).

My research focussed on thioester domain proteins (TEDs) of vancomycin-resistant Enterococci and Clostridium difficile, two pathogens of particular interest because of the hospital acquired infections they cause and their resistance to a vast number of antibiotics. TEDs were termed ‘chemical harpoon proteins’ because of the strong covalent bonds they form to a target (this is outlined by Dr. Schwarz-Linek in a video where he explains the the chemical harpoon mechanism  https://www.st-andrews.ac.uk/stories/2017/breaking-bonds).

The first step in my project was getting from a DNA sequence, encoding the TED, to a purified protein for use in structural studies, which as it turned out required a lot of work and optimization. Purifying the VRE-TED took up the first four weeks of the project because the VRE protein turned out to not be stable in solution. This meant that crystallization trials could not be performed and as a result one of my aims, solving the structure of the VRE-TED using X-ray crystallography, suddenly became unreachable. By the time I had designed a new construct and was ready to start over from the beginning I had run out of time. Luckily, some information could be gained from the first construct, revealing which exact amino acid forms the thioester bond about the VRE-TED.

Contrarily to the VRE-TED, cloning, transformation, expression and purification of the second TED went incredibly well. Normally a lot of optimization, for example finding the optimal pH, temperature or buffer for protein expression, is required until a pure, stable protein is obtained and can be used in structural studies. The most exciting moment of the whole project was obtaining a photo of a crystal of the C. difficile TED after weeks of work leading up to this result (Figure 2).


Figure 2. Crystals of purified CdTIE-B-TED were used in X-ray crystallography to obtain diffraction images.

Another aspect of my research was looking at binding of TEDs to six different cell lines, for example to colon cells and fibroblasts. I used two C. difficile TEDs that had been engineered to contain a tag which allows detection by fluorescence. No binding was detected for any of the cell lines which made the cell binding experiments rather frustrating. Luckily my supervisor has a very pessimistic, some might say realistic, view on outcomes of experiments and reminded me that whatever experiment I was doing, it would very likely not work. This lowered my expectations and made me appreciate any results and made accepting that once again after a long day of carrying out a cell binding experiment none of the TEDs had bound to any cells more bearable.

Looking back at the eight weeks spent in the Schwarz-Linek Group has made me realise and appreciate how much I have learned. One of the most beneficial aspects was the environment I was in. Being surrounded by Master and PhD students allowed me to discuss the challenges of scientific research I experienced while carrying out my own project. It has also given me a more realistic view of the life of a PhD student and has thereby changed my expectations towards a PhD.

This experience has opened my eyes to the world of actual scientific research and made me value the few, sometimes unexpected, results which in my opinion make research worth it. I am very thankful that the Laidlaw Undergraduate Internship in Research and Leadership Programme 2017 funded this project and gave me this incredible opportunity and for the amazing supervision and guidance of Dr. Schwarz-Linek and Ona Miller.

Which meteorites built the Earth? – Constraints from the Cu isotope signal of plate tectonics

Cover image: artists impression of the Hadean Earth (copyright Ron Miller)

I have spent my summer thinking about some of the biggest questions in Earth & Planetary Science:

Which materials built the Earth?

How has the process of plate tectonics served to mix as well as segregate layers of the Earth in terms of their composition?

Does does the answer to the second question inform the first?

It’s been great fun, and whilst big advances in science are hard to come by I certainly value this unique opportunity to spend my time grappling with such topics – it’s certainly given me a taste of what a career in academia would bring. Aiding my quest was my supervisor, the St Andrews Isotope Geochemistry Lab (STAiG) and my own wits.

My supervisor, Dr Paul Savage, is a specialist in non-traditional stable isotope geochemistry. This means that he is a world-leading expert in the science of using mass variants of a given element (in this case, copper or ‘Cu’) to trace magmatic, metamorphic and metasomatic (high temperature fluid) processes. His work has already yielded insights into the formation of Earth’s core, a process that separated metal and highly siderophile (literally ‘metal-loving’) from lithophile (oxygen-loving) elements on a vast scale around 4.5 billion years ago.

Many questions remain in this area and Cu isotopes are uniquely poised as a geoscientific tool to help us solve them. In particular, the cycling of sulphur (S) during the process of plate tectonics – the single most important aspect of terrestrial geology – must be constrained in order to understand how Cu isotope compositions have evolved over deep time. Without knowing this for certain, any models that try to match primitive meteorites (chondrites) to the Earth on the basis of their Cu will be forever doubtful (Fig. 1).

(Figure 1: the Cu isotope range of primitive meteorites and the offset between an model chondritic bulk composition for the Earth and estimates of the actual composition – processes involved in core formation may explain this discrepancy; adapted from Savage et al, 2015)

I studied an aspect of this problem by analysing Cu isotopes from rocks that sample the depths of a ‘fossil’ subduction zone. Subduction zones are places where dense oceanic crust sinks beneath a buoyant continent; this is the key distinguishing feature of terrestrial geology and acts to continually resurface the Earth, bring continents together and split them apart (the cycle of plate tectonics). When subduction beneath a given continent stops, usually due to another encroaching continental mass, a portion of the oceanic crust literally rebounds back up the subduction channel – a process known as obduction (Fig. 2).

(Figure 2: simplified illustrations of key tectonic processes – adapted from msnucleus.org)

Eventual collision of the two continents results in folding of the oceanic crust into layers far up in mountain ranges (‘ophiolites’) – such as the Zermatt-Saas ophiolite, which I visited last summer on a university-lead 4th year field excursion (Fig. 3). It’s a spectacular place and instantly fascinated me, so I jumped at the opportunity to work on samples from this area.

(Figure 3: The Matterhorn – this piece of once subducted oceanic crust now stands tall as an icon of the Western Alps)

The idea here is that, as rocks subduct down into the mantle, pressure and temperature conditions steadily rise. This often results in dehydration of the down-going slab, at which point the chemistry of those released fluids becomes important. If they are rich in S then, depending on whether we have sulphide or sulphate, Cu isotopes should be preferentially stripped from the sinking oceanic rock (as has been previously demonstrated for zinc – see Inglis et al, 2017) Overall, this would lead to an evolution of Cu isotope compositions in the deep and upper mantle (as well as the crustal rocks derived from it) over time. Our models of the initial Cu isotope composition of the Earth would therefore need to take this into account, with probable implications for which meteorites they predict to be the most likely building blocks of our world.

Using the world class clean lab and mass spectrometry set up of the STAiG lab, I set about dissolving my rocks in acid and stripping out all the unwanted elements from solution until all I had left was Cu (hopefully). This is a somewhat agonizing process that takes weeks and requires long hours in the lab, but as a geochemist at heart this was no great trouble. In the last few weeks of my internship, my supervisor and I ran the isolated Cu solutions on the Neptune mass spectrometer.

The early results are that subduction does influence Cu isotopes, although the story is complex and I am wary of making definitive statements just yet. I intend to continue working on this outside of my funded research time, compile more data and read ever deeper – hopefully by the time of the poster session later this month I will have a more complete story to share about the dynamic processes that govern our world and its origin, more than four and a half billion years ago…

References:

Inglis, E. C. et al, 2017, Geochemistry, Geophysics, Geosystems, DOI 10.1002/2016GC006735.

Savage, P. S. et al, 2015, GPL, 1, pp. 53-64, doi: 10.7185/geochemlet.1506.

msnucleus.org – accessed 10/9/17

 

Mission Creep: the unplanned twists and turns of my project.

Mission creep: ‘the tendency for a task, especially a military operation, to become unintentionally wider in scope than its initial objective’ (Collins Dictionary, 2017).

Mission Creep first surfaced in my project as the theoretical concept I would use to examine the evolution of the Libyan intervention from the initial limited aim of protecting civilians to the more grandiose aim of removing Gaddafi and enacting regime change. I applied the concept of mission creep to my analysis of language present in the media and the speeches of Obama, Cameron and Sarkozy to uncover how they managed to re-frame the mission as one to remove Colonel Gaddafi.

Protests in Libya again the foreign intervention into what was considered Libyan internal affairs.

To my surprise, I soon began to realise that the concept of mission creep was becoming so much more than just a small area of my analysis. As the first few weeks passed I began to see the real life applications of this concept. I started the project with the belief that I would first analyse the concepts of white and western supremacy, before moving on to researching the 2011 Libya intervention, in which I would examine the role of oil interests in Libya, and the role of the media and western leaders in enacting mission creep. This would then be neatly tied up into a poster and report within ten weeks.

How wrong I was.

Slowly, almost without my notice, my own mission began to creep. My good intentions meant that my mission had started out well defined in my mind, set out in manageable chunks week by week. I envisioned a smooth 10-week programme, in which I would have no problems focusing on the research questions at hand. However, my mission slowly expanded every day. Daily I would come across another concept that I found interesting, or another instance of western supremacy in Libya, and I would set out down that rabbit hole of research. I was finding it very difficult to establish the parameters of my research project. This resulted in frustration when I realised that I couldn’t possibly cover every single aspect of the study due to practical reasons, such as time limits.

Fortunately, being the practical soul that I am, I sought advice from my ever-patient supervisor, Dr Hazel Cameron. She reminded me that there was only so much I could achieve within the ten weeks allocated to this project, and to refocus on what really mattered- the crux of the project which was the foundational concept of western supremacy. Although it might seem somewhat simplistic, reminding myself every now and then to ‘think back to the question’ as it were, helped immensely in keeping my ambitions in check. She helped me to see how to break my project down in manageable chunks, and once I had compiled a document with a more in-depth week-to-week outline, and the points of study for my project, everything suddenly came back into focus.

In retrospect, it is somewhat good to see evidence of ‘mission creep’ in our projects. It is a reminder that we have chosen incredibly interesting topics to study, topics which we are passionate about and can see a future for. Finding yourself researching an avenue you had never expected is simply evidence of your interest in your chosen topic, and your dedication to the project.  I am thankful to have had the opportunity to pursue this project, especially since I found so many different aspects of the study that I would never have been aware of before this. My main takeaway from this is that mission creep- unless intervening in another state- is not always a bad thing!

I would like to take this opportunity to thank Lord Laidlaw, and the Laidlaw Undergraduate Programme for Research and Leadership 2017 for the opportunity to undertake this research. It has been immensely valuable for me to explore the world of research projects, and I cannot thank everyone involved enough for this.

References

1. ‘Hands off Libya’, Al Jazeera.

 

 

From Aleppo to Aldi; Reflections on Conducting Ethnographic Fieldwork with Resettled Refugees.

We are all accustomed to the gruesome details of the Syrian civil war; the chemical weapons, political upheaval and mass displacement of populations sprawling over borders throughout the Middle-East and into Central Europe. The perpetual media coverage and echo chambers of Facebook paint lucid pictures in our minds of desperate refugees huddled in boats, clinging to life in cross-continental escapes, waiting for a glimpse of life in a new country. Political turmoil in the West has appropriated this ‘humanitarian’ crisis for the purpose of votes, fuelling the toxic ‘us and them’ narrative perpetuated by so many during recent political campaigns.

My research aimed to boil down these sweeping discourses into a humanist worldview that points to the ways in which issues of displacement transcend refugee experience, investigating the facets of resettlement that at one time or another any human on planet earth may face. In conducting the research I negotiated many obstacles concerning methodology and ethics, this brief blog posts aims to reflect on some of these experiences to assist future interns who are conducting fieldwork. I do not claim to have any authority; these are merely my experiences but they may offer some small insight into some of the ways in which fieldwork and its methodological accoutrements may be conducted.

To illustrate the ways in which issues of displacement transcend refugee experience I focussed my investigation on actors involved in the process of relocation who situated themselves at a grassroots level. Most prevalent of these groups was the work of volunteers who provided multiple services to newly resettled refugees; teaching English, providing social support, and engaging individuals in community during the preliminary stages of relocation.

By becoming a volunteer with an organisation offering support to refugees I was able to offer my services and conduct my research in an ethically sound manner while immersing myself in the quotidian experiences of those at the forefront of my investigation. Ethnographic inquiry is a relational process, as researchers we should strive for emotional reflexivity and situate ourselves within the field, these methodological choices will ultimately influence the depth of analysis we afford ourselves at the end of fieldwork. As Shore recognises ‘fieldwork is an emotional encounter as well as an intellectual exercise…’ (1999: 27-29). Thus, one piece of advice would be to situate yourself as close to your subject of study as possible, this allows the above to flourish and makes fieldwork less of a chore while giving you the opportunity to experience your research in a holistic sense, removed from books and journal articles.

Setting up a fieldsite and ultimately playing a role within an organisation is a daunting thought at the start of research. Through emails and phone calls I found I built up a confidence in relaying the aims of my research and distilling the objectives into bite size abstracts that could be understood by anyone I spoke to. This was also incredibly beneficial for me personally as it allowed me constantly hone in on what it actually was I aimed to find out –  a problem all students share throughout the process of research. These skills were particularly important as I was denied access for my initial fieldsite and had to find a new site that was consistent with my research proposal; focusing more thoroughly on one of my research aims allowed a much more interesting discussion to form from the rubble of my first attempt.

As my research progressed I identified a number of individuals who would become my key informants and through time would influence and inform my project to a large degree. These individuals were people I had built up a relationship with or had offered their help as they found out about the work I was doing. After gaining ethical approval from the organisation and the individuals themselves I begun to formulate questions stemming from ideas I had about the research. Conducting semi-structured open-ended interviews with volunteers was conducive to the informant-led approach to ethnography my research pertained to. As Malinowksi stated, the goal of ethnography is ‘to grasp the native’s point of view, his relation to life, to realize his vision of his world’ (1922:25). Although native is a bit strong in today’s ‘culturally sensitive’ Anthropology the point still holds firm; let the interviewee talk and do more listening than anything else, it is their story that you are there to capture.

By recording interviews on my phone, I was able to let the interviewee lead the conversation and move from topic to topic in an organic form, allowing pauses and un-related thoughts to pepper the interview was a great mechanism that put the individual at ease and also afforded supplementary information to be gained from the interviews. Recording also allowed me to reflect heavily on the interviews while spending a large amount of time transcribing, this is one thing to keep in mind – every 15 minutes of recording takes around 1 hour to transcribe.

Ethics play a crucial role within ethnographic field work; consent is the operative word. While conducting my research I found it natural to write down notes left, right and centre, believing that all these ideas and overheard conversations would fill my write up with intimate knowledge or never-before-heard insights into my subject area. However, it is crucial to bear in mind that much of the events and conversations you experience while conducting research will // should not make it into the final write up because the people you are quoting are unaware of your identity as a researcher. As a whole, covert research is deceptive and ethically un-sound, it does not give your informants the respect they deserve. Furthermore, it may undermine your whole project and blow any chances of re-visiting the fieldsite in the future. As arduous and mind-numbing it can be, to conduct research in a credible manner ethics applications must be observed and full consent given from your informants. If you respect this you will find, as I found, that people open up and trust you more fully knowing that the intentions behind the research are for the purpose of furthering knowledge and not pulling skeletons out the the closet. With my ethics cleared and consent forms signed I found it fulfilling to talk to people knowing that the data I gathered was solid and could be used in the write-up, while maintaining the relationships I had fostered in the field.

As this discussion illustrates ethnographic inquiry is messy work and involves a lot of flexibility, re-drawing of plans, and constant negotiations. However, at this late stage in the internship with my final piece and poster nearly finished, it is fulfilling to reflect on the journey I have been through. The skills I have learned on the ground – conducting interviews, writing notes, observing events with an analytical eye – and the confidence I have gained in the logistics of planning research – emails, phone calls and meetings – are things I would never have developed making coffee for corporate parrots in an office somewhere. I have also met a great bunch of individuals who are working hard to help some of the world’s most vulnerable people integrate into life in Scotland. While the personal relationships I formed with Syrians over the past few months are not temporary, they will last far beyond this internship. All in all, it’s been a privilege.

 

Lasering rocks in Norway

Rocks won’t come to you, so you’ll have to go to them: one of my reaons for studying Geology! My Laidlaw project concerns an area in Norway, so I spent ten days studying the rocks over there. This involved lasering them with a novel spectrometer, which formed the crux of my project.

When continents collide, the immense resulting forces thrust rock bodies onto each other. These rock slivers, ‘nappes’, can get stacked into huge ‘imbricates’ (figure 1). The creation of such intricate structures is often linked to the presence of a weak layer, e.g. a muddy horizon that acts as a “grease”.For my Laidlaw project, I studied such an area, the Porsa Imbricate Stack in Northern Norway, where stacking seems to be enabled by the abundant graphitic slates.

fig. 1 – cross-section of the Porsa Imbricate Stack, note all the tiny slivers on the left!

Graphite (e.g. your pencil lead) is essentially organic matter that became crystalline under exposure to high temperatures, deep in the Earth. This process, graphitisation, is gradual and irreversible, which makes graphitisation an indicator of the maximum temperature a rock experienced (fig 2)

fig. 2 – diagram of graphitisation (2)

This is were the laser gun comes in. By measuring the ‘Raman’ backscattering of the laser hitting the rock, you get a spectrum that tells you the rock’s graphitisation grade (fig 3). Normally, one would have to collect many samples and analyse the rocks at home, but this new handheld device allows you to measure the spectra right in the field.

fig 3. example of an Raman spectrum. The area & height ratios of the peaks will change, depending on the temperature the rock was exposed to.

However, this involves having software that quickly analyses the spectra for you. This, I came to realise over the latter course of my project, is far from a wee two-week task! Especially obtaining an accurate spectrum-temperature correlation turned to out to be difficult. Each Raman set-up gives a different “signature” to the theoretical spectra, which makes it impossible to take a correlation from another paper (that uses different equipment) without incurring some level of error (1). I did manage to create a functioning, accurate fitter, but until we manage to obtain calibration data on our samples, the data can only interpreted as relative, not absolute temperatures. Sadly though, I won’t be able to obtain those constraints before the end of the summer: the lab technician is on holiday, the convential laser in the chemistry building is about to move away and my supervisor left to the States for fieldwork…

Thus, whilst I’m currently trying to finish the report and poster, it will be another while before our laser gun is completely fit for work. I’m very keen to keep working on this though; hopefully fourth year will leave me at least a bit of time for that. Research projects like this often make little impact, but I’m excited that this project might just slightly contribute to enhancing our “old-fashioned” field trip equipment (hammer, hand lens, compass) with compact analytical devices as this one.

Overall, the Laidlaw internship has been very rewarding and enjoyable, but there also were harder moments every now and then. Especially after a month of dissertation field work in June, keeping myself motivated in Norway sometimes was difficult. The overall research question, furthermore, is becoming larger and more difficult, the more I look into it; it’s quite a challenge to keep the report’s synthesis neatly framed.

Part of the excitement of Laidlaw lied in that somebody apparently deemed you ready to do academic research! Whilst of course I still feel pretty unknowledgeable compared to my supervisor and all the other staff in the department, I do feel I gained confidence throughout my internship. I really enjoyed completely submerging myself into my research topic and learning more and more about it, something I’ll definitely look for when planning out my future.

Lastly, I’d like to express my gratitude towards my supervisor Tim Raub for his time, patience, guidance and sharing his inspiring thoughts, Catriona and Eilidh for organising such thought-provoking, inspiring events and Lord Laidlaw for offering me this invaluable opportunity.

the “office” in Norway, bathing in the midnight sun

The field area on a sunny day

A nicely folded volcanic rock in the mapping area.

Example of the graphitic slates in the mapping area, with some quartz veins running through them.

References:
1: Kjøll, H.J. (2015) Structural Evolution of the Porsa Imbricate Stack (Finnmark, Northern Norway) [master’s thesis: NTNU]
2: Gao, Fengge. (2002). The future prospect of polymer nanocomposites in reinforcement application. e-Polymer. 2. T_004.

Genetic Modifications, Memories and the Smell of Mice

Have you ever had something on your mind and suddenly forgot what it was? The way our brains function, and sometimes don’t, is fascinating. During my project I have been working with genetically modified mice and looking at the ways memories are coded in the brain. Half of the mice had a special gene inserted which resulted in a termination of the function of the layer II of lateral entorhinal cortex (LEC), one of two major inputs to the hippocampus, an area of the brain that is crucial for episodic memory. The aim of my experiment was to examine the role of layer II of LEC in episodic memory formation.

In combination with the lab work, Laidlaw events and action learning sets, the first weeks of my internship passed very quickly. At the beginning, I was handling mice and habituating them to a box in which the testing took place in the following weeks. This was happening in a clean unit where people need to have a special access or be on good terms with lab technicians to let them in. I had to wear overalls on top of my clothes and also shoe covers. Even though the clothing prevents contaminating the unit, it does not protect researchers from acquiring animal smells. If you guessed that I started smelling like a mouse, you were right (subsequent apology to the people who sat near me at networking lunches).

Testing consisted of four behavioural tasks, each running for a single week. These tasks involved combinations of objects, places and contexts that were presented to the mice. Every trial was recorded on a video and I subsequently measured how much each mice was exploring the objects in particular settings. It was hypothesized that the exploration times in relation to novel and familiar configurations of objects, places and contexts would differ between control and experimental mice. This part of my internship was rather lengthy and initially it was difficult for me to estimate how much time it would take. It has taught me the lesson that in science everything lasts much longer than one initially estimates. The internship has given me invaluable experience to successfully designing my future research projects.

Experimental setup: A mouse is presented with new and familiar objects.

Indeed, the Laidlaw internship programme has confirmed me in my decision to pursue research in the future. I am definitely going to apply for a PhD in neuroscience and I believe that the experience I gained by participating in this programme will help me to secure a good place. I have learned a lot during my internship not only about the brain but also about leadership. I am now designing my poster and look forward to presenting my findings at the poster event and the Northern hub conference. I am very grateful to Lord Laidlaw for this amazing opportunity. I would also like to thank Cat and Eilidh from CAPOD who have been organising for us a number of exciting events. It has been a blast!

Viewing Nature with Hopkins

Have you ever ventured out into the natural world to find yourself meeting it with a sense of rapture, of ecstasy? Gerard Manley Hopkins certainly did. Maybe the sun was shining, maybe the rain pouring. You might have been alone, with a close friend or in a crowd. Whatever the way, you found yourself looking out on the world as though it is charged with power and joy. Some might call this experience numinous, others mystical. Some might think nothing of it at all.When I first read the poetry of Gerard Manley Hopkins I knew he had a sense for the wildness of things, of nature, of birds and trees, and that he had a taste for their meaning. “The world is charged with the grandeur of God,”[1] he exclaims, and calls his readers to engage with the created world. “Look at the stars! Look, look up at the skies!” he says, look at the “May-mess” and the “march-bloom.”[2] Though Hopkins writes about far more than just nature, for him a viewer who engages fully with the natural world thereby engages with God.

But why? We begin to catch a glimpse of the answer in the sestet of Hopkins’ sonnet, already quoted, The Starlight Night. With regards the wonder of the stars, and the majesty of the march-bloom, Hopkins explains

These are indeed the barn; withindoors house
The shocks. This piece-bright paling shuts the spouse
Christ home, Christ and his mother and all his hallows.

For Hopkins, the world can barely contain the glory of God harboured within, ready to announce itself to the observant viewer, who, in rapturous response “rears wings bold and bolder/ and hurls for him [God/Christ], O half hurls earth for him off under his feet.”[3]

One of the purposes of my project was to consider how Hopkins’ view of nature fits within the wider Christian tradition. What is it rooted in and where might it lead?

To consider the first question I turned to John Duns Scotus, a Franciscan philosopher of the 13th century. Scotus’ influence on Hopkins is well documented, and even noted by Hopkins himself. Scotus’ most important innovation relates to the Christian idea of the incarnation. For most Christian theologians, the incarnation happened in response to and as a remedy for humanity’s sinfulness. Scotus, however, held the minority view that God would have become human even if humanity had not fallen into sin. Rather, the human incarnation of God was forever intended to be the glorious culmination of God’s plan of creation. Related to this idea is the notion that creation itself is a revelation of God a) because what artist can create something that does not reflect themselves? and b) because God is in the business of self-disclosure. Whilst any medieval scholastic philosopher would have agreed that the Good is self-communicative, Scotus’ vision is stronger than that because he emphasised that each thing expresses God in its own individual way, because of its individuality.

Where might this all lead us? To Thomas Merton, an avid reader of both Scotus and Hopkins. Thomas Merton was a Trappist monk who lived in the 20th century. He was a convert, a writer, a political activist, and a spiritual master for millions of Americans and people worldwide. Merton, drawing on Scotus, taught that each thing, simply by being itself, gives praise and glory to God. What’s more, such a message is central to the Merton’s understanding of Christianity; the human task is to simply be our true selves, stripped of disguise, pretence, anxiety and striving. If trees and flowers can do it, he asked, why can’t we?

Obviously these sorts of questions go deep and deeper, and can be approached from a hundred and one angles. I just know that when I go for a walk in the rain through the woods or along the Fife coastal path something in me comes alive like at no other time. Reading Hopkins I know that he had those experiences too, which is why I continue to read and enjoy him. I am grateful to Lord Laidlaw and the Laidlaw Undergraduate Internship in Research and Leadership for this opportunity to have studied Hopkins’ poetry under the magnifying glass. For now I am left with more questions than I started with but perhaps that is to be expected. Still, I look forward to further exploring the natural world, to more deeply reading Hopkins, and to pondering the big questions of life, all from somewhere within the Christian Tradition.

[1] Gerard Manley Hopkins God’s Grandeur
[2] Gerard Manley Hopkins The Starlight Night
[3] Ibid.

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.