Proteins in Praxis; in conversation with a protein

Proteins in praxis - in converstaion with a protein. 

The story below is speculative fabulation (Haraway, 2017). This essay has been written for the Structural Genomics Consortium (SGC) to help communicate their work and complex scientific processes to a lay audience. The work is a piece of fiction based on the popular media format of the podcast, featuring an interviewer and an interviewee. The story as told is from the perspective of a protein, which is the primary workhorse of the SGC. This essay intertwines the day to day activities encountered by the protein with current philosophical explorations pertaining to the philosophy of technology, Post Phenomenology and Alien Phenomenology through works of Ihde (Reflects, 2019), Verbeek (Rosenberger, R. and Verbeek, P.), Bogost (Bogost, 2012), Bennett (Bennet, 2010), Nagel (Nagel, 1974).

1.Hello! We are live – welcome to the show everybody! Today we have a very special guest, we have had so many requests to have you on the show; one of the proteins fundamental to a shift in science and healthcare - thanks for coming on!

2. (Protein smiles) Thanks, I’m honoured- it’s great to be here, good to see you.

1 Good to see you! So, tell me, what’s going on with you? We’re big fans of you on the show here.

2. Phew, and thanks! Good question… A LOT! A lot is going on now, like, a lot…. But also, nothing at the same time. It’s kinda strange to be honest. I have a book coming out next month, so I’ve been going around having conversations, getting different perspectives from around the lab.

1. That’s great. We got you on here because ever since you did that TED talk, we’ve been fascinated about your journey, and we would love to have you discuss for our listeners what it is you’ve been a part of.

2. Yes, since that talk, things have really taken off! We’re getting a lot of exposure now, which is something that hasn’t really been the case before; it’s becoming crystal clear if ya’ know what I mean.  I say we because there has been an explosion of conscious experiences (Nagel, p434, 2014) at the lab, new neighbours here, there and everywhere.

1 That’s great! Really what a lot of the emails and comments have been asking… we want to know, how does it feel to be…you know, to be you, the one, we want to hear your perspective on things.

2 … well, let’s be humble about this… I’m one of many. That’s what’s special about the place I’m from; we’re all in it together, for everyone. Perhaps someone gets to have their name at the top of the paper when they write about me; but even then, everyone, anyone, can read it.

1. Great that you bring up the documentation, hopefully we can talk about that later. Explain how much of a deal this thing is that you’re a part of. Perhaps we can begin to unpack what kind of a journey you have been on.

2 Yeah, its huge deal and a big journey! And it’s exciting, things are really changing. Once we came out of ice, people just sort of treated us differently you know. We could tell something big had happened; but really, it just takes so long for us to find out.

1 Treating you differently like what?  

2 You know, whilst researching for the book, it took a long time to decide how to best format the story, and how to frame the conversations and observations I’ve had. To begin with – there became more of us – new incubators arrived, and soon there were spinning vials everywhere! Like, normally there are thousands of us – but now, millions; also I heard we’re global now, no longer situated in one room, one building.

1 How does that make you feel knowing that you’re part of something big?

2 Well it’s great for proteins; you know, we’re part of the lexicon of daily life – people seem to care about us now, our story, our role in the breakthrough.

1 Yeah! Before that Ted Talk, all I thought about protein was the 100g I get from chicken ha-ha! Gotta get my gainz for when I’m hitting the gym!  How did it feel, being given that information, that your chemical makeup held the key for such a shift in medical knowledge for humanity? Like nothing we have seen before.

2 Like I said, it’s a big deal isn’t it – we’re happy; we’re content that we’re having such an impact ya’ know, I think that this is something that I can be comfortable with. It has taken quite some time for us to be developed; I’m an old timer, I’ve been here for about 13 years.

1 That seems like a long time – is that a long time to have been hanging around a lab?

2 It is, I was made, I was chosen, I was important for a time, then I was put on ice – lost to the depths of the -80, fell to the back. It was quite the excavation to get me out, I remember, there were a couple of scientists there dusting the snow off me! I was one of the many here; a number, a possession, a thing within a thing (Bogost, 2012).

1 That sounds lucky that you were found right? What are some interesting things about the lab? Did anything change over the time you went on ice?

2 Over time I’ve compiled a list of things that I have gazed upon, brushed up against, grappled, been submerged within, agitated by, measured with, weighed upon, sieved through. (Bogost, p39,2012).

Glass bottle, blue plastic bottle cap, green test tube tray, polystyrene box, cotton lab coat, nitrile glove, sticky label, washi tape, microtube rack, water, tubes, cameras, PC screens

I’m one of the original batches. These guys over there, in the new freezer, before they went in, it was a big party for them. But me, I’ve seen it all, been around, seen the lab, the walls, the confines of this place, and – the people; I’ve seen what they do to proteins like us, experienced most of it first-hand.

1 That went dark for a second there… Do you begrudge your experiences? What were your experiences?

2 Ya know, not many people have heard this – it’s very personal to me. My buddy and me, he was one cell over. We were made together, shared the same test tubes and seen it all, he’s gone through the whole process – he got isolated first. It’s because of his bravery, and what he went through that I’m here now; he made that sacrifice so all those after him so they could live on. I could see his development, he went from this wet solution and literally, overnight, bulked out; solidified, crystallised. It was amazing. We both knew he would be leaving that morning. Him and me, we were the same. But he just made it, he got lucky I guess, he got selected; but I get to be here today, telling his story, our story. I was happy though. Even if it meant being frozen for all that time…. the data he produced was of such importance, so it turned out, it’s why there are so many of us now. He is the one that people remember.

1 That’s powerful dude. Respect to him. How did you find yourself in that position, what were the steps that got you there?

2 Its pretty remarkable, but also normal to us – the same thing has been happening for years; it’s a pretty nailed down process you know, and it goes on all over the place. The thing is, now it’s just faster, a magnitude faster, this place is crazy fast. We hear stories all the time of how some proteins crystallise within 2 weeks of the project starting.

1 If two weeks is fast, what is slow? And what do you mean by crystallise, that’s twice you mentioned it now.

2 Ah, sorry, I forget that this might be new to people. The book has two chapters on this; the processess, the types of projects that are undertaken. First, 14 days is fast, 14 months is slow; but things keep changing and iterating so the projects continue. The end game of this place and all the work that goes on in here is to isolate a protein and incubate it ‘till it forms a crystal structure; that means that all the molecules of the protein go from being a disorganised assemblage (Bennet, p22, 2010) as a liquid, to being extremely regimented, which takes the form of a crystal. It takes the combined efforts of all the protein’s molecules to work together, to configure themselves, some just have it in them I suppose.

It is at this point it gets taken into the basement level, where a guy observes us through a microscope and enters another world (Rosenberger & Verbeek, p19, 2018), through it he forms a relationship with the crystal. It must be big enough and the scientist must be steady to hook out the crystal from the tray before shooting it with an x-ray… It’s a brutal way to go; no one was aware of that until recently – a lot of the new commers are oblivious to their inevitable fate….It’s the elephant in the room, no one really talks about that…

1 Do you want to elaborate on that…do you know about it, enough to talk about it?

2 Its cold man, like, real cold. Temperature I mean. What temp is it in here now, like, room temperature temperature?! We have been in and around room temperature and kept warm whilst we were incubating, but then rather horrifically; we’re scooped! The Crystal part of us is removed from the part of us that remains as a liquid. They could be gentler, it’s like the cop videos when they’re shouting, “stop resisting!” and we’re like, “we’re not resisting!” but they’re man handling us against the side of the tray and bashing us about! I mean, it’s in their interest to not damage us, but c’mon, take it easy already!  Then, before you know it, you’re dunked into minus 160 – there is a brief realisation of what is happening; the smell in the air of the odourless vapour, sudden darkness, and then preservation, flash frozen.

1 Damn…That sounds like quite the ordeal your colleagues must have been going through. When we hear about the breakthroughs, we seldom think about any of this do we – often the headline, perhaps the lead scientist’s name…

2 Exactly! This is just another great example of humans subjecting nonhumans to their fate in order to satisfy human desires, the end justifying the means. We’re told we’re important and most of us buy into it, that we’re important – well, like I said, it was only recently people have begun to ask us these very questions…. But to answer your question; I hung out in the protein hotel, I spent most of my time in Bonnie. That’s the name of the incubator the scientists gave to it, Bonnie, as in, Bonnie and Clyde. I never got to hang out in Clyde, although they were technically the same, same manufacturer, same components, it was a nice place to be. Not just me, but all my neighbours in adjacent cells on the plate would develop quite the attachment to ‘ar Bonneh. Bonnie would nurture us; monitor us daily, sometimes twice a day.

It’s quite solitary being in there...

Once we hear Bonnie’s mechanisms come to life, our tray jolts as its slid from its cradle to be observed – it feels like we’re part of something. We don’t directly interact with it but it’s all around us, it’s an insulated machine that keeps us warm, safe and affords us to grow. (Rosenberger & Verbeek, 2018) It has this black noise that makes us ripple, makes our amino acids pop and jiggle with the pressure of the door opening and closing (Bogost, p32,2012). This is where my buddy made the transition! I have yet to make the changeover into a crystal, let alone shot with an x ray.

2 Do you think you could postulate what your buddy would be thinking, or experiencing at that point? What’s his name anyway?

1 P53, he has his own Wikipedia page now! Now to think about his experience would require me to think of myself as another thing, as a crystal, which I am not, and that would be weird, can you imagine, thinking of another inanimate object from its own point of view, not from a proteins point of view of being a crystal, but a crystals view of being a crystal…you could only speculate an interview with a crystal! (Bogost, 2012), (Nagel, 2014) I guess I’ll embrace it when it that time comes, like, part of me is that crystal, that crystal is part of me. But until that transition happens, I cannot imagine it, I look forward to being both liquid and a solid; I’ll be able to take more than one form at the same time.

Well now I’ve said all that it sounds like we should give it a try, doesn’t it?!...

Here goes….I’m sitting there, waiting, waiting for an event to happen on me. That event is me finding my perfect partner. Its symbolic, it’s a coming of age, finding my perfect partner, a molecule being the key to my lock, it’s like we’re a jigsaw puzzle, destined to fit.  Once we’re together, that’s it, we’re together.

I am one piece of this process, one tiny component embedded within this apparatus, a robot arm deftly moves me into position. Emerging from a tank of liquid nitrogen, I am under the scope of an xray gun, its orders of magnitude the size of me. Suddenly, I’m blasted with more liquid nitrogen – it’s used to keep me structurally stable as waves of light pass through me; the sensation of those ultra-dense waves hitting every ordered protein molecule, vibrating, thus heating, akin to being cooked alive with light. The light is diffracted, scattered onto a plate that captures the resulting pattern… (Bogost, p73, 2012) But let’s be clear, there is no Gestalt revelation here (Rosenberger & Verbeek, p17,2018), this resulting pattern takes time to produce the subsequent usable visualisation (Rosenberger & Verbeek, p18, 2018) . These combinations of sensors, optics, and other factors enable humans to effectively see me in new and particular ways (Bogost, p72, 2012).

1 Wooooowww! Awesome! …..That’s wild! That’s so good!  

2 yeah that was fun ?

1 Then what? What happens to the pattern? How come it’s a pattern? It sounds like an odd process to be honest.

2 It is, check out the images online, they’re quite common.

1 Ah yeah Jamie has it up, wooow! That’s beautiful! And that’s what you’re working towards? That’s the image of a protein turned crystal. Amazing – I want that on my wall! Man, how on earth is that a thing that can be used scientifically?

2 A computer orders it and rebuilds the resulting diffraction pattern into a 3D shape based on the positioning of these forms (Rosenberger & Verbeek, p17, 2018). Since this was developed as an algorithm, it’s a whole industry, molecular modelling, and thanks to that we now have the protein data bank, where all the visualised proteins are freely available to view, download and use in studies.

1 Mind blown…. So we’re back talking about p53, for real – what happens to him now?

2 I’ll read this excerpt from my book,

After that sweet embrace with ultra-fine wavelengths – I am rapidly reintroduced into my liquid nitrogen stasis tank where I get categorised once again – I mean, I was lucky, not everyone gets out OK. Once we’ve been shot – some of us are too far gone, sometimes the crystals might crack, even if the data is good, useable, visible, then that’s it, disposed of, hook washed and reused.

It seems odd. A couple of us get that far – we can only wait in our protein hotel being incubated, observed, catalogued; until it is our time to crystallise. Not everybody makes it, it depends who you are, where you are, who you hang around with. If your binding agent is the right make up, the right conditions are met; the perfect partner, then you’re accepted into the higher social order crystal formation.

1 That sounds painful, physically and emotionally. He must be strong huh?

2 Yeah, but I think we’re so numb from the liquid nitrogen, that it all only comes off as a slight annoyance, and that would only be speculation.

1 That sounds like quite the ordeal though! Do you think that’s something that if you knew that was your fate, you would be cool about the situation you’re in? 

2, No. I don’t think everyone would be cool about it! Here we are – a life on ice, until I’m needed again, until I’m ready to be x-rayed…The bigger picture is AI, that can save us from this.

1 What do you mean? AI is affecting you too?!

2 Of course! There is a lot of talk with the newly created proteins, we call them proteenies, with their undying enthusiasm for things they hear about on podcasts and read on their blogs, to unionise – universal basic income for proteins – that’s all we ever hear! (Rogan, Yang, 2019) Protein rights are what they’re saying. It won’t be long until deep mind will be accurately predicting all the structures of the proteins (deepmind, 2019)– there won’t be any need for research labs like this, proteins won’t be grown en mass for the benefit of scientific research, just to be probed and flushed away. Critics argue amongst them, and say, what would you do with all the proteins that are alive now, if you just stopped needing them? Turn the heating off and kill them? Let them roam free in their E. coli? But that’s what they want apparently, an end to this needless creation and destruction. It will be the end of an era, just a bunch of data centres computationally folding proteins.

1 Hey, don’t bash podcasts!  But AI is ages away, right? There is still a place for you until it makes any mark on you.

2 We have to have these conversations don’t we, A.I. exists, we already have machine learning being used here when we’re being observed, looking for crystal formations in the protein hotel, Goggle has predicted 25 proteins so far, and it takes only a couple of hours to do so! Imagine that, no E. coli, no scientists, no protein hotel…no protein even. So, we must have this conversation (Reflects, 2019), it’s going to happen, so we must talk about what we are going to do about it. The humans are worried about their jobs, were worried about our existence- what happens when they shut the freezers off? Or when the incubators are powered down? We’ll cease to exist, the demand for us will be gone, so with that said, yeah, I’m rooting for it, but we’re impatient. Alight, you know, we know the sequences of proteins, and there are rules that it must fold in a certain way determined by the chemical and physical properties – so by rights, we should see this rules based system, and it’s a deterministic process, like, this folds this way, this folds that way next to this guy, and so on…

1 Have Google folded proteins? There has been Folding at Home for nearly 20 years now, how long is the AI revolution going to take, both to get here, and undertake?

2 If we were to try to fold up the protein, and try out all the combinations, it would take longer than the lifetime of the universe to understand – so yeah, I’m holding out hope – until that time comes, we’re here doing our thing for the benefit of science – but we’re all rooting for that quantum leap in computation in order to make those folds in a matter of seconds, not lifetimes.

1 Those sound-like pretty big implications, I guess I haven’t ever thought of it like that.  You ok to go on? We have talked about the end goal, the crystallisation process, and how your published. What other steps are we missing?

2 Oh man, loads, they’re all the fun bits, the paper is something abstract, it has nothing to do with us, to be honest, we’re just a step in the proceeding processes. You know, it’s nothing like this – science is a game, publishing as a concept currently is contested. Something about story telling allows us to play with the narrative and its format, even more so being on a pod cast – to hell with formatting doctrine! (Bogost, p89,2012).

1 C’mon Stop being modest – surely your front and centre! Your being immortalised in print, read by countless academics and researchers globally.

2 OK, well, yeah, we have so much to talk about, it’s a crazy ride to be frank. The humans just go on about it as if it’s no big deal, like getting dressed in the morning, or having lunch (Bogost, p5, 2012). If you were to think about all the processess that have led to those events as being significant, well, we would be here all day unpacking it all. And that’s the case for us, as proteins, we’re part of a journey that began before us. Our first interaction with the world is when we’re broken from our home, our life source – the E. coli cells. Thinking about it now, it’s pretty brutal. One minute we’re in a real good gig, we have plenty of space, friends, places to go, activities, and we’re hanging out with tons of other E. coli cells, I’m talking millions here. We’re hitching a ride on the back of them, well, within them to be specific! Then, we’re taken from our incubator, and are decanted from our beaker houses into these large glass jar looking things. The whole ordeal is quite bewildering. All you can do is imagine; we’re taken away from our warm, oxygen rich environment – the constant agitation stops, and we’re left experiencing 1G. Most E. coli are sick, falling and bumping into one another. We can hear the lab, its different than before, not muffled by the door, no black noise of the inside of an incubator, instead it has been replaced by those of the centrifuge machines. The lights are bright, a cold white light – something I never thought I’d become accustomed to (Rosenberger & Verbeek, p18, 2018).

There are a couple of rounds in the centrifuge, we’re spun at 5000rpm which packs us all towards the bottom of our new glass jar abode, from there, the media is washed away, and we’re left, as one large puck of cells. Now, the next step is a little graphic, so kids, leave the room…

Anyway, as I was saying, there are other ways to be split from the cell I was grown in – one is sonification, where a high pressure ultrasound is fired from overhead and vibrates the E. coli so much so that the cell wall breaks apart and we’re left floating around feeling a little untoward. And this happens reasonably quickly, but from our point of view it’s a rather harrowing experience!

Back into the centrifuge, this time at a speedier 20,000 RPM. I remember being thrust back into the vat of liquid media, this time the E. coli cells broken from the sonification process, proteins separated, floating at the top, as the waste, or crap, we’ve heard them be called, sinks to the bottom... What a way to go eh!

1 That seems a bit much…. it’s none stop! It’s an E. coli genocide.

2 It is! But there is little consideration for cells in this context, where the ends justify the means. Hey, at least we were inside E. coli, and not in a fly cell, or a caterpillar cell – I often wondered what it would like to be in there and grown, maybe they have a better experience of it all, well, the proteins I’ve chatted to are always a more complex bunch.

1 So explain where we are now in the process, how much of your journey have you undertaken, how much left to go? We already talked about the crystallisation, growing in the E.coli cells and being savagely broken free from them, to being spun in order to separate the good from the bad….

2 Sure – I’ve jumped about a bit, to be sure, crystallisation is the last thing, it’s what the whole process is about, and your right, we talked about being grown and separated. So now, we enter the purification stages, which sits between being separated and the transformation into a crystal. The aim here is to ensure that the scientists have created the correct protein, and that it’s on its own, with no further traces of the E. coli cell around to get in the way of the actual experiments. It’s where a lot of proteins find themselves, there is a lot of time to reflect on their life so far, their friends, their encounters – their past is stripped away in the following stages.

Between each step – samples are taken to determine that the scientists are on the right track. They have this thing where they tag us, they’re so matter of fact about the whole thing – adding a synthetic histidine tag to us, so we stick to nickel – not only that, but the whole thing is electrically charged, it gives us a real negative energy. Everything else is pushed down, pushed away. Except us, with our tag. We hear the torment when the electric current is passed through them. There are no winners here, the sad part of this is, once again, the proteins with their tags that are used to test this are ripped apart, destroyed and are no more, existing only as a smear on a gel. Separating the proteins by size, it tracks the progress being made – and this happens maybe a couple of times a week. It creates what looks like a bar chart on a gel, one is produced with the raw mixture – it’s all a bit hermeneutic (Rosenberger & Verbeek, p16, 2018), where a lot of proteins are scattered around the chart as blue bands – and then once purified, they’re looking for specific columns to show over others. These guys are on the front line, used for testing, to ensure that the experiment is on track – we hope that it is- otherwise we might end up being destroyed if those results are not favoured by the scientists.

If it looks like we’re on track, then it’s onto the second stage where we’re sieved, a more complete purification. We go through the FPLC, or Fast Performance Liquid Chromatography. Once again, it’s all about speed here – get this, one of the FPLC machines told me as I passed through her that the manufactures saw them [the scientists] coming and continued to add the word Fast in front of everything to get easy sales through! She went on to say that she was unhappy about the temperature she must operate at, quoting that ‘it does nothing for my pipes!’ Aaannyyyway, this part of the process basically means that we get separated as a liquid over a solid – not sure what it’s made of – but it’s pretty fun passing through what’s called the solid phase column, it’s a good ride – this object, a range of objects with its systems of properties (Ponty, p45, 2004), starting at the top, passing through lots of pipes, tubes, junctions, connectors, inside the machine, outside the machine, slightly warm, cold, then finally down through the column. The solid phase column is full, but with gaps that we can fit through, it’s the final phase of purification.  The bigger ones go straight through – us smaller proteins kinds of bop around until we finally make it out the bottom to freedom. We like it, we always take our time on this one, it’s a way to get back at the humans a little, you know, as the room is so cold (Rosenberger & Verbeek, p18, 2018) – they’re subjected to a process just like we are, you can always see the discomfort on their faces when they enter up to the point when they leave!

1 Ooft… Amazing. So that’s the steps covered then? Creation, growth, separation and purification, incubation to crystallisation, mounting and then being shot at. Quite the ride! Did I get that order right?

2 Yeah, that’s the order of the process.

1 Thanks man, what a great story. I think you will be remembered forever.

2 And all that can happen between 2 weeks to 14 months! In one sense you’re correct, we will be remembered. We, the proteins, including our structures and the processess taken to derive these details, are published openly; typically, all the work done here of finding the protein structure is documented in journals for big pharma companies to take and bind their products to. We enable the faster development of drugs.

1 So your part of the research of big pharma, what were you alluding to at the top of the conversation, as to why you’re so well revered?

2 Yes, I, we, are the embodiment of the research undertaken by the scientist in this lab, the documentation of my form assists in the development of drugs for a range of diseases and conditions, from Alzheimer’s, to FOP, cancers, the lot.

1 That’s so special.  Tell us, what is FOP?

2 Fibrodysplasia Ossificans Progressiva; it’s a rare disease that about 40 people in the UK – where the human body goes into overdrive and produces bone where it shouldn’t, effectively locking the body together.

1 That sounds not good.

2 It certainly does not! That’s why we’re happy to be helping with the discovery of medicine to combat this and others like it.

1 Jamie, pull up this protein will ‘ya, let us read about the developments that we must thank you for!

2 Oh wow, I’m embarrassed... I haven’t heard why the scientists were so happy to be working with us, this is big!

1 Ah there we go, the Daily Mail online.

(headline reads) Protein Hair Gains

2 What

1 Developed originally as a protein to unlock and rebuild neurons as an Alzheimer’s inhibitor, it was in its late stage testing on mice when its mistake, or new role took form – the mice’s fur grew like bamboo – you could watch it grow in real time without the need for magnification! Human trials begin in earnest. (Jay, 2019)

2 Seriously WTF, is this a joke? The Daily Fucking Mail?! All this time, and that this is how I find out?! My colleagues are published on the protein data bank as one of many steps into the discovery drugs for curing cancer and I’m a hair loss product for image conscious men in their 50s?!

1….

References

Bogost, I. (2012). Alien phenomenology, or, what it's like to be a thing. Minneapolis: University of Minnesota Press.

Bennett, J. (2010). Vibrant matter. Durham: Duke University Press.

DeepMind. (2019). AlphaFold: Using AI for scientific discovery | DeepMind. [online] Available at: https://deepmind.com/blog/alphafold/ [Accessed 5 May 2019].

Haraway, D. (2017). Donna Haraway - HQ SOUND _ SPECULATIVE FABULATION -. Available at: https://youtu.be/K1atjLfbNxE [Accessed 7 May 2019].

Jay, E. (2019). BBC News - Viagra and other drugs discovered by accident. [online] News.bbc.co.uk. Available at: http://news.bbc.co.uk/1/hi/health/8466118.stm [Accessed 11 May 2019].

Rogan and Stamets. (2019). Joe Rogan Experience #1035 - Paul Stamets. [online] YouTube. Available at: https://www.youtube.com/watch?v=mPqWstVnRjQ [Accessed 11 May 2019].

Rogan and Yang. (2019). Joe Rogan Experience #1245 - Andrew Yang. [online] Available at: https://www.youtube.com/watch?v=cTsEzmFamZ8 [Accessed 11 May 2019].

Merleau-Ponty, M. (2010). The world of perception. London [u.a.]: [Routledge].

Nagel, T. (1974). What Is It Like to Be a Bat? The Philosophical Review, 83(4), p.435.

Redström, J. and Wiltse, H. (n.d.). Changing things.

Reflects, R. (2019). How Technology Changes Us | Lecture with Don Ihde and Peter-Paul Verbeek. [online] YouTube. Available at: https://www.youtube.com/watch?time_continue=4567&v=hmBgJjfjG7Q [Accessed 5 May 2019].

Rosenberger, R. and Verbeek, P. (n.d.). Postphenomenological investigations.

Sample, I. (2019). Google's DeepMind predicts 3D shapes of proteins. [online] the Guardian. Available at: https://www.theguardian.com/science/2018/dec/02/google-deepminds-ai-program-alphafold-predicts-3d-shapes-of-proteins [Accessed 5 May 2019].

Annotated Bibliography

Bogost, I. (2012). Alien phenomenology, or, what it's like to be a thing. Minneapolis: University of Minnesota Press.

The book covers a lot of ground, its main focus is that "humans have been at the centre of philosophical thinking for too long",  thus giving actants / objects their own perspective of things around them, and their part in the world.  The work of Latour is discussed at length and is built upon, actants and object oriented ontology puts these things at the centre, and embrace a speculative realism, the writing expects you to have a grounding in a range or readings, I often felt without this knowledge I was left behind, reading for readings sake. I resonated with teh work on ontography and Latour's litanies and how Bogost had interpreted them, and given them a new context. The later chapters had a different flavour about them and read simpler, with a more descriptive tone. The book provides a theoretical framework for me to base my essay, the book didn't provide pointers on how to do this, but drops clues on how to approach Object Oriented Ontology (OOO) and ways to apply it. The chapter Craftsmen, whilst deviating from alien phenomenology ( I think) provides me with a rational to use speculative fiction to explore OOO within an academic context.

Nagel, What it's like to be a Bat

Nagel, T. (1974). What Is It Like to Be a Bat? The Philosophical Review, 83(4), p.435.

With a focus on the use of imagination, specifically what its like to be a bat, but from the perspectives of the bat. A little more challenging read, insofar as it is requiring the reader to take the perspective of agents that are non-human, the main being a bat, but other examples come throughout the paper. IT strains to emphasise that it is not sufficient to think of being a bat with human experiences and prejudice of thinking what a bat would be like, but to think of being a bat from a bats point of view, for example, feeling hungry, seeing, feeling pain etc - all of which humans and bats experience, but are they the same? I found the paper particularly useful as it provided me with a framework to base my proteins experiences on. Before reading this document I think I would have been at a surface level descriptor of my proteins experiences, with this, I can go a little deeper in places to explore the theoretical discussions of post and alien phenomenology.

Rosenberger & Verbeek, field guide to Post Phenomenology

Rosenberger, R. and Verbeek, P. (n.d.). Postphenomenological investigations.

The paper provides a grounding of knowledge in the domains of post phenomenology. It covers primarily the work of Don Ihde whilst also referencing their own archive of work. The paper is a typical essay format that include a literature review of works that set the tone and the foundations for the rest of the discussions to take place. It builds a lot on the work of Heidegger but is also critical of it, highlighting a number of progressive and alternative topics for discussion that Heidegger either didn't wish to include in his work or failed to see the role of technology and the position of human / technology relations.

It was very easy to read, a simple introduction that provided the above history of the philosophy, positioned technology within the discussion of human interaction and the world and how they engage with both.

Verbeek is the eminent write on post phenomenology in Europe, as declared by don Ihde himself, I found myself resonating with the work and it is an area that I find myself wanting to explore further. There are numerous excerpts that will formulate an underpinning of research for my written work, specifically ontologies, and human - technology relations, where I hope to capture the essence within my writing.