Podcast 4 - transcript

TRANSCRIPT

This is MadeAtUCL: The Podcast. Bringing you closer to the UCL research answerings life’s big questions. From engineering to art, healthcare to space exploration, ancient artifacts to the technology of the future.
Episode four: Maps

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Hello! I’m Suzie, welcome to our show, or welcome back to our regular listeners. As usual, we’ve got an episode full of stories from all corners of the university and for this episode they’re all connected through maps! 
Until my second year of university, I’d always seen maps as pretty boring. I associated them with rather sad geography lessons at school, just lines of countries I’d never been to, waiting to be coloured in and labelled. But since then, I’ve come to realise that maps can represent all sorts of information. And that all sorts of interesting things happen when you start trying to pin a real, physical thing down on paper. Even parts of the body.

Mark Emberton: The prostate is like a fingerprint. It's different in every body. 

Suzie McCarthy: This is Mark Emberton, surgeon, urologist and the Dean of Medical sciences at UCL.

Mark: So you can actually identify a man by his prostate because each prostate is unique, and that does make diagnosis difficult because in diagnosis, you're trying to tell the abnormal from the normal, if the normal shifts and is different and everybody it's very hard to make that distinction. 

Suzie: For the past 40 years, If you were a man with symptoms suggesting prostate cancer you’d go for blood tests. If these suggested the presence of a tumor, surgeons would insert a needle into the prostate to try to take a sample. But because your prostate was unique, inserting the needle in the right place was  almost a process of trial and error. your surgeon wouldn’t know exactly where the tumour was. 
 
Mark: What that meant is that we often missed tumors. And so we told people they were clear when they were not. Or we misdiagnosed tumors. In other words, we caught the edge of a tumor because we didn't know where it was, and therefore told the patient that it was lower risk than it really was. 

Suzie: Not only this, but not knowing the location of the tumor meant that treatments were less effective.

Mark: All our treatments for prostate cancer have been directed at the organ, not the cancer, which again is very unusual. If you think of somebody with a liver cancer. You don't remove the whole liver, the patient would die. You remove the cancer plus a margin but for prostate for the last hundred is it's been radiotherapy or surgery to the whole gland, because we didn't know where the tumor was. What we  knew is that there was cancer or no cancer. If you had cancer, you had your prostate removed or  iradiated. If you didn't have cancer, you didn't. So we weren't very good at that. And because we did n't know where the cancer was, we had to treat the whole organ.

Suzie: If you were a patient, this often meant stopping the prostate from doing it’s job, but also caused side effects because of the role of the structures that surround the prostate.

Mark: Yes, no, the prostate makes semen. By the time most men are diagnosed, they're past their reproductive age. So that's not a huge issue. Most of the harms of treatment come from damaging surrounding structures, vessels, nerves, rectum, bladder, sphincter, that helps you control your urine flow and keeps you dry. And and the nerves that mediate erections run down the back of the prostate, very close to the rectum. Recent studies show that incontinence can result in 10 to 20% of men. And that 70% of men, after surgery, for instance, will lose their capacity for erections.

Suzie: So how can we treat prostate cancer and avoid these undesirable effects?

Mark: If you change your treatment from directing your attention to the whole gland, and your attention is instead directed to the tumor, all the structures that I've just listed, remain intact. We can virtually guarantee continence in individuals We can give men a 90 to 95% chance of keeping erection sufficient for penetration.

Suzie: This is where advances in MRI techniques, partly developed at UCL have come in. MRI being that donut shaped scanner where you lie down and it works around you. 
A UCL study called Promise showed that for the old test…

Mark: 52% of men had their clinically significantly disease either missed or misdiagnosed.

Suzie: Whereas MRI…

Mark: Was 100% better than the standard of care.

Suzie: The use of MRI has been the first step in the improvement of treatment. It has  lead to the NHS guidelines being changed so now MRI is the first line of investigation for all suspected prostate cancer. And it means that now many men don’t have to have a biopsy at all. But for those that do, MRI on it’s own still wasn’t enough. 

MRI gives a high definition image of the tumour and where it is in the prostate. But  you can’t use metal in an MRI machine. This matters because  when it comes to sampling a tumor, you need to use a metal needle. So when taking a biopsy, surgeons only had a the more general map of the prostate gland given by the ultrasound to guide them. 

Mark: The ultrasound looks very fuzzy, it looks very vague. 

Suzie: When it can to the exact location of the tumour, they were still stabbing in the dark. (Forgive the analogy) 

But a new technology called Smart Target, developed by Dr Dean Barratt at UCL reconstructs the MRI image of the tumour and this...

Mark: allows us to superimpose on that vague gray weather mappy looking screen, a bright red mark, which usually is oval around or sausage shaped.

Suzie: Mark can then guide his needle into that sausage shaped target, to get a good sample of the tumour.

Mark: So this is a kind of augmented reality. We see a reconstruction of the cancer that was generated on the MRI scan, and that we can see in real time. Even more cleverly, the engineers that we've been working with have managed to manipulate that image so that when we squeeze the prostate with ultrasound, and change the shape of the contour of that prostate, the cancer moves within it in what looks like a very realistic way when you're doing the biopsy. 

Suzie: It’s also really useful in training new surgeons.

Mark: It gets a non expert, up to expert level straight away. I'm regarded as an expert (laughs), largely because I've been doing this a long time. And smart target is as good as me. So the worrying thing is it's going to make people like me very redundant. 

Suzie: This rang a few alarm bells for me. Partly because I didn’t realise how much of medicine is already being assisted by technology. I guess also for people like me, who can be a bit slow to understand how computers and tech works, it can seem a bit scary that a machine can replace an expert like Mark says. Particularly when things are advancing so rapidly.

Mark: No, it's fascinating. So there's nothing I do, that I was taught to do as a trainee. So all the operations that I was taught to do as training are now obsolete. And that's, you know, that's, that's in 15 to 20 years, huge advances, I mean, huge advances in in, in the way that we treat patients.

If you use a robot between you and the patient, that’s pretty standard now in most surgeries. I treat virtual postates not real prostates. And I do that on a screen and I fire energy at the cancer to destroy it in a selective manner.  Which obviously requires SmartTarget to give me location 

And so if I know where the tumour is, I can destroy that tissue using soundwaves,  I can use laser, I can use electricity, I can generate heat from radiofrequency. And that's work again that has been led by UCL. 
If we make the diagnosis early, and we find a cancer, it's not too difficult for us to treat it. And the beauty for the patient is they come in in the morning, we do their treatment, and they go home in the afternoon. And so it's all done in a day. It's painless, and they have little or no side effects. It's not magic, we still have to destroy tissue. But the side effects are really, very minimal in the majority of patients.

Suzie: Smart Target is being rolled out in hospitals in the UK and USA, and the teams at UCL are continuing to find better and better ways of diagnosing and  treating prostate cancer.

***

From mapping prostates, we’re going to change it up a bit. From the contours of the body to crinkles and creases of the past. 

Phillipa Smith: I'm Philipa Smith. I'm head of collections at London Metropolitan archives

Suzie McCarthy: London Metropolitan archives, or LMA is home to a whole collection of documents all about London. It’s open to everyone, and is owned and managed by the City of London Corporation.
Philipa has been involved in work to reconstruct an important historical document.

Phillipa: Known as The Great Parchment Book, which is also colloquially known as the doomsday book of the plantation. And that's the plantation of Ulster or Northern Ireland.

Suzie: In the 16th century tudors wanted to make Ireland part of Britain and so they took land from gaelic lords particularly in Northern Ireland. English, Scottish and Welsh settlers were sent to take over the land, creating plantations . And in 1639 The Great Parchment Book of the Honorable Irish Society was written. It documents the plantations and contains lists of the various owners and administrators who lived and worked on the land, what their  rights and obligations were  and what they produced.

Phillipa: So it's a it's a snapshot of the society in Ulster at that time, so it's really significant, but it also has resonances that that lead right up to the present day as well.

Suzie: The way Derry Londonderry looks today is largely due to the changes made during the time of these plantations. And also many of us were British or Irish ancestry may well find their own family stories at least partially told within the pages of the great parchment book. It is especially significant because there has been relatively little historical documents that provide such in-depth information about the colonisation of Ulster.

The plantations were managed by various companies set up by the City of London, who became the guardians of the Great Parchment Book. But there was just one problem.

Phillipa: Unfortunately, there was a fire. A lot of the irish society’s archive was either destroyed or badly damaged and some of the city of London's own archives were destroyed as well. So the Great Parchment Book, which was a volume, was damaged by fire, and it shrunk and became distorted. It became known as the poppadom book to people in recent times because it just looked like a pile of poppadoms and nobody could access the information contained within it.

Suzie: And that's where Tim came in.

Tim Weyrich: My name is Tim Weyrich. I'm Professor of visual computing at the Department of Computer Science at UCL.

Suzie: Tim’s specialism has all sorts of applications. At first, I think of gaming and films,  but it turns out this expertise can be useful in solving the rather common problem of reconstructing damaged historical documents.

Tim: It's actually not an unusual state for a parchment to be in, you know, people documented many things on parchments and kept them in light in libraries that were lit with candles. Many, many archives have documents in similar state and in the past, conservation attempts often started by humidifying departments and then trying to stretch them back into shape. But the problem is that parchment is animal hide. It does the same as hair does if it gets close to a candle. It starts shriveling, and distorting in very unpredictable ways.

Suzie: These unpredictable distortions mean that it’s not just a job of flattening out the page. After all, it’s not a flat object we’re after, it’s one we can read. Once the parchment has become so distorted and shrivelled, flattening it risks ironing in the creases and further obscuring the words under the folds. 

So, to prepare the document, the conservations did the opposite of what they would usually do, and push   ed out those cracks and crevices to make the parchment …

Phillipa: even more lumpy bumpy than it was originally, because we were trying to push out the creases, expose the text. 

Suzie: After this transformation,  it was time for the computer scientists to work their magic.

Tim: It's not unlike the problem of a mapmaker's. Mapmakers have a shape which is the shape of the earth’s, sphere, mountains and so on, and they have to depict it in on a two dimensional map. Mapmakers also were often faced with this problem that as you try to flatten something, you introduce distortions whether you want it or not. In modern days, we all use two interfaces such as Google Earth that sidestep this problem by just introducing a camera that flies over the shape of the earth, that is textured with the appearance. 

Suzie: So the plan was to make an interactive program that modelled the 3D shape of the parchment.

Tim: And so you can navigate along the lines as the lines travel across the distorted shapes, and it turned out to be quite readable.

Suzie: So there was now a 3d model of the great parchment book, which uncovered hidden histories by revealing text written 200 years ago. But this was a world which could only be traversed through the wizardry of computer software. So the researchers decided to go further. And to try and digitally flatten the pages back into a 2d image. 

At first, this felt like an impossible problem to solve, because the distortions were so unpredictable, and computers struggle when there isn’t a clear pattern to the puzzles they’re trying to solve.

But Tim and his colleagues realised there WERE parts of the document that would have originally been very regular.

Tim: It’s lines of text, that were written very straight

Suzie: For administrative documents like this, scribes would literally rule lines on the page to make sure they didn’t veer off course.

On top of this…

Philippa: Because hand writing at that time was very uniform

Suzie: They could also use certain letters that were originally all the same size and shape

Tim: such as lowercase E, lowercase A

Suzie: Which gave the computer enough information to unshrivel the parchment.

But it wasn’t just computers responsible for the final reconstruction of the document. 

Phillipa: We did have a transcriber, a historian with expertise in reading 17th century handwriting who did do the transcription of the text. Because of her experience, and because documents like that are often quite formulaic in parts, even where there was text missing, she could sometimes work out what was going on as well. So there was another sort of reconstruction going on at the same time. She did work with the person doing the the digitization. So I think that collaboration was really, really important,

Tim: It's not a computer solving all the problems. It is not the human expert doing everything, there needs to be symbiosis between technology and a human. 

Suzie: From the initial stages of making the poppadom book more lumpy and bumpy, through the digital imaging and the flying cameras,  all the way to the final transcription, it was really important that the conservator and computer science teams worked closely together. And that’s what allowed this brand new method of reconstruction to be created. 

Tim: And to me, this is also where research becomes interesting, computer science research.

Suzie: This is what Tim wants computer scientists to do more of in the future. He wants them to branch out to see how they can support other disciplines such as history and conservation, but also to focus on how they can listen to experts in other fields when designing their software. He is continuing work on the particular software used to reconstruct the great parchment book to make it more accessible for those without specific training in digital imaging. And in the meantime, the great parchment work is open and available for researchers of all kinds to investigate the history of Ulster.

Phillipa: We've now got this website that has the digitally flattened images, it's got the transcription as well. It's a really valuable resource for research. I know students at the University of Ulster are using it. Conservation students are using it across across the world. On all sorts of levels, it's being used in research. It's it's of continuing interest of people. In 2016, it was added to the UNESCO UK Memory of the World. And it was the first document from Northern Ireland to be added to that register.

Suzie: This says a lot about the significance of The Great Parchment book, and why Tim’s work was so important in uncovering previously hidden histories. It’s also offered a way forward for other fire damaged documents, so that conservators can continue to reveal secrets of the past.

So this new method offers a way forward for other fire damaged documents, so that many previously hidden histories can be revealed And for LMA, having such great result has given them the bug for scientific conservation methods.

Phillipa: For example, DNA testing of parchment, also using x rays to read parchment volumes that have become completely fused into a block so you cannot read anything inside them.

Suzie: It's like sci fi historians! [laughs]

If you’d like to take a look at the Great Parchment Book yourself, and maybe do a little historical sleuthing of your own, you can find the links on our website. We also have a full list of all the sponsors and partnerships of this project, without them, it wouldn’t have been possible!

***

We’re now stepping out of the library and mountains of parchment, to the very literal forests of Central Africa.

Jerome Lewis: Hi, I'm Jerome Lewis. I'm an anthropologist at University College London. I've been doing a lot of applied work with two research groups one called the Center for the anthropology of sustainability and another called the extreme citizen science research group.

Suzie McCarthy: The extreme citizen science research group covers all sorts of disciplines and projects at UCL. It supports communities around the world  to do their own scientific research so that they may find ways to deal with issues that are concerning them. 
It started with work that Jerome did in the early 2000s.

Jerome: In Congo, where I did my main field research as an anthropologist,. I spent three years living in the forest with the Mbenejele., the hunter gatherers there.

*SPEAKS MBENJELE* 

So I said, I speak Mbenjele, it's a nice language but you don't understand it.

Suzie: In fact, a lack of understanding is what lead to this citizen science project with the Mbenjele. 

A logging company was looking to fell timber from the forests where the Mbenejele live. They wanted to gain a Forest Stewardship Council certificate, to give a green label to their forestry. But...

Jerome: they didn't have any idea how to deal with local people. FSE principle three requires that loggers respects forest users and indigenous people in particular, and that mustn't be any conflicts between what the forest is doing what the indigenous people require from the forest. But the foresters has had no idea how to address this and we had hours and hours of discussions with the bosses and I translating for my Mbenjele friends and there was just... it was like a dialogue of the death. Nobody understood anything anyone was saying. And it was very difficult for the Mbenjele because they live out in the forest. They don't know about door handles and opening doors, closing doors and all the basic protocols and practices that are expected of people in meetings, formal meetings with agendas and all this kind of stuff. So it was very tiresome. 

Suzie: One of the trees in the forest is the Sapelli tree 

Jerome: which is African mahogany. They’re used in lots of firedoors in the UK, in London for instance.

Suzie: This is a popular and beautiful wood, and is also used  for furniture because of its shine and natural strength. 

Jerome: Anyway, finally I suggested that look, what you need to do is actually start recording what things they use and then see if there are any problems with what you want to use.

Suzie: And this began an approach that reoriented the focus to begin with an understanding of the forest through Mbenejele’s eyes.  Because for them, the Sapelli tree is not important for it’s wood, but they...

Jerome:  Collect caterpillars from them, which are a really important food source, every year. And they’re extremely valued on local markets so they have a very high cash value.

Suzie: So it was clear the Mbenjele and the logging company had very different ideas about the uses of the Sapelli tree.

Jerome: We had some quite amusing exchanges with the logging director who’d say, "Well, I better start doing caterpillars then and stop this logging business."

Suzie: Jerome and the Mbenjele got out of the tiresome meeting rooms and into the forest to start mapping the Sapelli trees. The hunter-gatherers explained that they didn’t need to preserve all the trees, because it’s only the tallest ones that rise above the canopy of the forest. And that means the butterflies find them as they fly over, lay their eggs, which soon turn into caterpillars. 

Jerome: So those emergent trees that poke out through the top of the canopy are the key ones, so we went out and we started mapping them. And then I asked the Mbenjele, what else are you upset about the loggers damaging? They said, Well, we don't like them damaging our cemeteries. We don't like them damaging springs where you get clear water coming out of the ground and various other things. medicinal trees, sacred areas and so on. So we said, well, let's map all these places.

Suzie: I said at the start of this episode that it’s only recently that I’ve understood just how important maps can be in shaping the world around us. Maps are not just neutral objects that show us where things are. In many legal and political systems around the world, they can be really powerful documents.

Jerome: By showing you know exactly where different resources that you exploit are, you make a very strong claim to being someone who uses those resources. And in many legal systems, use is evidence of rights.
Often there are overlapping uses, so we’ve tended to shy away from boundaries, because for many indigenous groups, having rigid, strict boundaries is not actually a big deal. You know, there’s a general understanding that if you stray a little bit into our area it’s not a problem and if you stray a little bit into our area that’s not a problem either. We  avoid boundaries, but we make sure resources are mapped so people can see the use patterns of an area.

Suzie: This has been an effective way for many indigenous peoples to take part in legal systems more on their own terms.

But there were still barriers in the way. For many, being able to read and write is less important than really knowing and understanding your land and your people’s history, which you gain through experience, not through books, documents or maps.

And the problem for Jerome and the Mbenjele was that the GPS system they were using to do the mapping needed each point to be written down manually, which was slowing everything down and causing errors to be made. 
So they needed to develop a different approach and it was Jerome’s wife who held the key

Jerome: She works in public health, and she had been developing a mobile clinic for non literate hunter gatherers. And it's quite challenging to think about how can you ensure dosages are done safely and correctly And so she developed a pictorial way of sticky labels that she stuck on the medicine bottles in order to make sure that people were safe in their use. So all was on symbols. And it was that really that gave me the idea that well, we could do this mapping on symbols too.

Suzie: This lead to the creation of Sapelli, software named after those caterpillar trees.  This is an app that can be downloaded onto a smartphone and uses icons or symbols to help identify and map important features of a particular area. But the app has been designed to use anywhere and can be adapted to the community that uses it, so that everyone knows and recognizes exactly what those icons mean.

Jerome: So what we do for instance, if we’ve drawn the symbols, which in some cases is a more efficient way of doing it, we show them to people and we ask them what does this mean? We don’t tell them. And if they get it wrong then obviously that’s not a good symbol, then we work together with them to draw it in a more appropriate way. Sometimes they’ll draw it in the dirt on the ground, sometimes they’ll take us to something and tell us ‘take a photograph of this’ and other times we’ll redraw it by hand together with them commenting as we draw or they’ll take a pencil and draw it, but the point is it has to be together, as something that you do as a collaborative process. 

And the way we know they’re right is when we hold up that piece of paper with the icon drawn on it and everybody says ‘oh that’s what it is, that’s what it is, that’s what it is’ and that’s when we know, right that’s the correct icon.

Suzie: So once again, the app and the process of mapping needs to be something that focuses on the type of knowledge and understanding that is already held within these communities. It means whether or not people can read or write, they still have the power to protect their land rights.

Jerome: And the advantage of that is that it means that those people who have the real ecological knowledge tend not to be the people who've been to school. Schooling destroys ecological knowledge. And this is a huge problem for so many indigenous communities around the world. And indeed, I think for Europe in general, from just not spending enough time in nature basically,

Suzie: And the software does not restrict the kind of indigenous and local knowledge that can be documented and shared.

Jerome: We have created a tool which is wide open to be populated in whatever way people wish it to be populated, and they can use for recording problems like poaching, recording abuses by conservation guards or recording laxity at roadblocks supposed to be checking for meat smugglers. There are a whole range of issues that people will say they want to record. 

Suzie: And people are doing this around the world. In Kenya, the Masai are documenting where their medicinal plants grow, to protect them from the expansion of tourist areas.

Jerome: they named 126 plants individually that they knew. if you're listening to this, trying to think how many names of plants you can provide in the next 30 minutes and see what your total is.

Suzie: And from Central Africa, Sapelli software has traveled as far as Southeast Asia

Jerome: It's being used in Cambodia by the Prey Lang community network. And whenever illegal loggers are heard in the forest, they all come together on their mopeds, and they zoom out to where they are. They start taking photographs of all the trees they are cutting down. They succeed in confiscating their chainsaws, take them away, they make sure that the authorities get a full reports with all the evidence provided. And they've done an extraordinary job in protecting the Prey Lang forest from further massive deforestation.

*MUSIC*

Suzie: The Prey Lang community were awarded the UN Equator Prize for their fantastic work in protecting their forest. We’ll be hearing more from Jerome in a future episode about another prize-winning project, this time in South America. So stay tuned!
In the meantime, if you want to take a look at the Sapelli software for yourself, and get to work on some citizen science, follow the links on our website.
We’d also really like to hear your thoughts on the series. You can tweet about it with the hashtag #MadeAtUCL.
Until next time.

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Made at UCL: The Podcast is made by me, Suzie McCarthy. The executive producer is Nina Garthwaite.  Mixing support from Mike Wooley. We'd like to thank all our researchers for welcoming us into their labs and offices. #MadeatUCL is a campaign that brings to life disruptive thinking from UCL. Research presented in this episode was nominated and selected because of the impact it has made on everyday life and society. This episode is brought to you from UCL Minds, events, lectures and podcasts open to everyone.

Transcribed by https://otter.ai Edited by Suzie McCarthy