Roger Hyam

Roger Hyam

I'm the Digital Information Development Officer at The Royal Botanic Garden Edinburgh

Mar 212017
 

Thanks to the tireless work by Wikileaks an interesting letter has come to light addressed to the Devil himself from one of his advocates in our world. It reads:

Your Most Gruesome Majesty,

I write of a great triumph in spreading fear, mistrust and uncertainty in the world. I hope that this will contribute to solving our overcrowding issue. The day will soon come when the earth is so much like hell humans no longer need to go to hell to suffer. I hear of minor progress on the temperature front by my fellow daemons in the energy sector but I’m sure you will see my triumph as eclipsing theirs when you are considering the next round of promotions.

I’ve managed to get good people in developed countries to think they don’t have enough to eat – even whilst they are getting fat! By making them insecure I’ve got them thinking they have to somehow make it on their own. In the past we have sold a lot of guns and 4×4’s to people who don’t need them on the basis of a survivalist/security motivation but now I’m managing to subvert peaceful city dwellers into lusting after a garden they will never use and being finicky about perfectly good food. You’ll be so pleased with how bad they are all feeling. The eat local and grow your own campaigns I have manipulated into place will, for example, get Scots terribly upset at not being able to source locally produced, organic bananas. This should keep them nicely diverted from what we are really up to.

I’d like to share some of my calculations so you can see how much fun we are having up here and because I know the devil is in the detail!

Humans need to eat about 2,200 kcal a day on average and they have many crops that will provide them with this energy. Take the potato. There are 770 kcals in a kilogram of potatoes so 3kg will feed a person for a day and roughly 1 tonne for a year. There are 5.3 million people in Scotland and potato productivity is about 44 tonnes per hectare so to feed the whole population would take about 125,000 hectares of arable land. That may sound a lot but it is only 22% of the arable land in Scotland and only 2% of the total agricultural land. Most of it has dumb beasts on. OK – so it would be hell to live off just potatoes (that might actually be an idea … ) but from the human perspective the principle is clear. The population could be fed on a small proportion of the land available if they ate a diet based on what grows well here. They start from an incredibly secure base before they begin trading with others who have far more productive lands in warmer climates that can provide a varied diet and yet Scots are still worried about their security.

What is so great about my achievement is that by getting people to think they must eat locally produced food they can start to feel they are an island unto themselves – which in the long run we can exploit into hating others who might take it away. This can happen so long as the humans never think too hard about what they are actually eating and what might be best for them and the planet. For example they all love to eat tomatoes (another South American plant) but growing tomatoes in Scotland is incredibly inefficient. Far better to grow them in a warmer climate and ship them North – preferable dried. But if I work at it I’ll get them putting up plastic tunnels and heating them because dogma is our ally in all matters. Better local than anything else! (I must insist that I get credit for such an initiative and not those lazy daemons in the energy department.)

I think my favourite part is the cognitive dissonance that prevents the humans joining the dots and keeps them heading our way.

Recently they were chatting about the Tsimane people in Bolivia (there is definitely a South American theme developing here). The Tsimane don’t get heart disease because they just eat potatoes whilst the Scots, who could easily live off potatoes but don’t, are riddled with the disease. OK that is an exaggeration but if a daemon can’t exaggerate who can?

In the Tsimane diet 72% of calories come from carbohydrate, 14% from protein and 14% from fat. A pure potato diet would give 88% carbohydrate, 12% protein and 0% fat which isn’t far off a diet for the “healthiest hearts in the world”. Maybe if the potatoes were fried in a little rape seed oil occasionally they would be nearer to it and rape seed oil is easily produced in Scotland – but we should keep quiet about that.

When the humans talked about the Tsimane diet on the radio they were so preoccupied with the meat coming from a rodent (capybara) they didn’t even notice that the diet was actually close to something they already had available in Scotland. If, instead of being obsessed with the provenance of food they just switched to a high starch, low meat, plant based diet they’d benefit themselves and the planet with very little bother.  Agriculture would just adapt to supply it. They forget that most of the plants they grow go to animal feed and alcohol production – both industries you will be familiar with from your other projects. Instead they worry about how far their broccoli has travelled (and with 2,000 hectares of broccoli grown in Scotland last year  a lot of it is local anyhow). I have made them unhappy and competitive about a perfectly innocent plate of vegetables. I’m sure you will recognise my achievement.

Another bonus for us is the humans think that by growing their own veg or buying it from someone with a small holding rather than a regular farmer they are somehow helping people in far off countries who really do have food security problems. If they wanted to help global food security they could simply emit a little less carbon. But keep them driving their 4x4s to the allotment then jetting off to the sun that’s what I say!

The only real worry I have is with the pesky scientists. If they do their job right and start counting and measuring everything before opening their mouths then they will soon work out the best way to foil our plans. Fortunately scientists are often as gullible as the other humans and can be easily swayed on to the latest trends.

Your cringing servant,

Belphegor


Kudos to C.S. Lewis, Screwtape and Wormwood


 

Feb 282017
 

Happy to see our paper on the use of internet technologies to mobilise specimen data finally in “print”. We are hoping this will add traction to the adoption of this approach to sharing data as the more institutions who adopt it the more useful it will become and the more kinds of research it will enable. At the moment the project is a model of European cooperation with the author list reading: Germany, UK, Germany, France, Belgium, Belgium, The Netherlands, Slovakia, Finland, Czech Republic, UK, UK, Germany. We have had interest from North America so hopefully this will go global in the next couple of years.

Abstract

With biodiversity research activities being increasingly shifted to the web, the need for a system of persistent and stable identifiers for physical collection objects becomes increasingly pressing. The Consortium of European Taxonomic Facilities agreed on a common system of HTTP-URI-based stable identifiers which is now rolled out to its member organizations. The system follows Linked Open Data principles and implements redirection mechanisms to human-readable and machine-readable representations of specimens facilitating seamless integration into the growing semantic web. The implementation of stable identifiers across collection organizations is supported with open source provider software scripts, best practices documentations and recommendations for RDF metadata elements facilitating harmonized access to collection information in web portals.

Download

Jan 272017
 

I’ve spent the last few days working on the data pipeline I first mentioned in The Cloud Lottery that is Scottish satellite imagery. This pipeline consists of a series of R scripts that will place an order for Landsat 8 surface reflectance data and vegetation indices from the United States Geological Service, download the products as they become available then strip out the layers I’m interested in analysing, removing any areas of cloud or high atmospheric aerosols as they go. The hope is I’ll be able to leave this running and build a continuously updated dataset covering areas of interest that I can then query for data analysis purposes.

The Open Street Map of Edinburgh with Enhanced Vegetation Index (EVI) overlay. A particularly clear day on 25th October of 2016

When working on a job like this it is easy to get buried in the detail and lose sight of the end goal. As it is Friday afternoon and next week I need to turn my attention to other projects for a while I thought I’d visualise one of the clearer images and check I’m still on course. The images are fascinating so I wanted to share them.

You may have seen a recent article in the Guardian “How green is your city? UK’s top 10 mapped and ranked”. Edinburgh came out top with 49% “green”. These maps were produced by ESRI based on Normalised Difference Vegetation Index and are very simplified in comparison with what I hope to do. I’d recommend taking a look at that article as I don’t think I can reproduce the images here for copyright reasons. (I also think Edinburgh cheats a bit in the ranking by including a chunk of the Pentland Hills within its boundary which one wouldn’t do in a serious analysis!).

Close up of EVI for the botanics and surrounding area. Note how bright green the playing fields are compared to the botanics. Also note the mosaic of gardens and buildings.

Landsat 8 data has a resolution of 30m. Each pixel is about 100 foot across. I’m hoping that at this resolution we’ll be able to produce a proxy metric for how green and area “feels” to people living and working there especially when using Google Street View analysis to paint a fuller picture. It is not going to be simple. As you can see large blocks of green represent the biodiversity deserts that are playing fields. I’d also consider these aesthetic deserts. The mosaics of different greens seen in the botanics, the allotments, Warriston Cemetery and St Marks Park tell a different story as do the built up areas of the new town. I’m excited to see where we can take this analysis.

Jan 112017
 

We instinctively know that a walk in the garden or somewhere else filled with natural beauty is good for us but it is difficult to justify expensive or restrictive planning decisions on the basis of instinct alone. This is why scientists have been trying for years to quantify just how exposure to green space improves our mental and physical health. They have managed to show that what we see out of the window or walk past on the street really does matters for our stress levels and it is particularly good if what we see is plants. But how do we extend these results beyond small studies based on a few volunteers?

As I’ve posted before there is an emerging field (Biophilomatics) which is using big data resources to look at these problems. This latest study from RBGE takes a new approach to the subject by plugging together some of the latest Google technologies in a novel way.

Computers are getting better at assessing the contents of our photos. If you use photo sharing sites you may have noticed that they use this technology to sort your photos by subject. Google has now given developers access to the algorithms behind their image classification systems through the Google Vision API. By combining this image recognition technology with Google Street View images from around Edinburgh we have demonstrated the possibility of assessing our cities streets for their perceived naturalness and potential restorative value using automatically sampled images.

Map of Edinburgh showing sample area and points. Greener dots are more natural. Redder halos are more deprived according to the Scottish Index of Multiple Deprivation. Where Street View panoramas are offset they are joined to sample points by lines.

It is very early days yet and before we can draw strong conclusions we need to develop it further but this could be an addition to the tool box for building more liveable cities.

The work was done as part of the Edinburgh Living Landscape (ELL) project which involves a number of partner organisations with interest and skill in our shared environment. ELL promotes improving, expanding and connecting up the green space in the city and encourages innovation in greening up built structures recognising that the local natural environment is a health asset. There are key questions about how best to achieve this for all sectors of the population and the methodology described in this paper contributes to building the evidence base for decision making.

Below is a slide show of the randomly sampled Street View images. Is this the Edinburgh you know?



Note: There are privacy and other issues around street view images and Google therefore remove any areas they are requested to. In the slide show above images are loaded directly from Google and so any that have been removed or replaced since the experiment was originally carried out in early 2016 will appear as unavailable.

Nov 292016
 
Three Landsat 8 Scenes covering central Scotland

Three Landsat 8 Scenes covering central Scotland

I’ve been looking at producing a good quality Normalized Difference Vegetation Index (NDVI) dataset for central Scotland so that I can investigate correlation between green space, biodiversity and well-being indicators. To do this I need access to satellite imagery.

Fortunately every sixteen days the Landsat 8 satellite passes over every part of the earth photographing at a resolution of 30 metres in eleven spectral bands. The U.S. Geological Survey generously make this data available for free and Amazon kindly distribute it as one of their public datasets. NDVI can be calculated by simply comparing the red and near infra-red bands of these images. It sounds very simple until we get into the detail.

Landsat 8 Panchromatic sample captured on 3rd June 2016 (note incomplete new Forth crossing)

Landsat 8 Panchromatic sample captured on 3rd June 2016 (note incomplete new Forth crossing)

NDVI is a measure of light absorbed by chlorophyll but much of the vegetation in Edinburgh and Glasgow that I am interested in is only actively growing for half the year. It is therefore important to compare images from different times of year. For consistency I’d like to restrict the data to the Landsat 8 satellite which entered into service in 2013 which further restricts the number of potential images. The Google Earth snapshot above shows the extent of the three Landsat scenes that cover the area of interest. Because we are so far North they overlap and so most of our area of interest is covered by at least two of the scenes and therefore imaged on average every eight days.  From mid 2013 until today this adds up to 187 images. More are being added all the time. This all seems good but we then run into the next problem.

If you are in central Scotland and look straight up the chances are you will see clouds. This isn’t just a stereotype of Scottish weather (or character?) but is supported by the data. The graph below shows the percentage of cloud cover in each of the 187 available images. The average cloud cover is 55%. For a crude analysis I may be able to select individual images from different years to represent winter and summer but if I want to have a more granular understanding of seasonal change, some indication of change through the years and some redundancy to correct for errors I’ll need to do something more sophisticated.

cloud_cover_2013-16To build my dataset I will therefore have to write scripts that examine all images created for these scenes, remove clouded areas and calculate NDVI for the remaining parts. These parts will then form a jigsaw puzzle that can be assembled in different ways to give seasonal or temporal change for different sub areas. The system should update automatically or semi-automatically as new scenes are released onto the Amazon hosting platform. Well that is plan anyway.

This all makes me very appreciative of the Google Earth data which, apparently effortlessly, does this process at higher resolution for visual satellite imagery, merging it with aerial photography as you zoom in.

Update: I just discovered the USGS service for surface reflectance corrected NDVI and EVI products – this may save some work and cut Amazon out of the loop.

Nov 012016
 

resilience_-midlothian-science-festival-2016

At the end of last month I spent a Thursday evening at IKEA Edinburgh, not for the usual reason of eating chips in the café with my daughter but to contribute to an event called Untangling Resilience to Depression as part of Midlothian Science Festival.

Recently we have been working with Stella Chan, a clinical psychologist from the Edinburgh University, as part of the Edinburgh Living Landscape project. Our discussions are around the effect connection with nature has on people’s well-being and the role that botanic gardens have in mediating those relationships.

The evening of talks at IKEA was part of the public outreach for the STRADL project lead by Prof Andrew McIntosh in which Stella is involved. STRADL is a multimillion pound, five year, Welcome Trust funded project that tries to understand the different ways in which people are resilient to depressive illnesses. There are many factors effecting depression ranging from genes through support networks out to the wider environment. The talks were arranged along this spectrum with me speaking last on green space and its affect on well-being. Speakers included Prof McIntosh, Prof Andrew Gumley from University of Glasgow, Prof Matthew Smith from University of Strathclyde and myself. Stella and Prof Stephen Lawrie acted as compères.

Stella asked me to speak because I had been describing some of my work in this area. I have been developing a mobile phone app called the Ten Breaths Map which aims to measure people’s engagement with natural spaces and been working on a paper that uses automated image categorisation to predict how restorative an image of a place is. This somewhat overlaps with Stella’s Project Soothe. (We’ve also been talking with Sarah Payne at Heriot Watt University about running experiments on the restorative value of the gardens.)

Stating that a walk in beautiful, natural surroundings might be good for mental and physical well-being seems so obvious as to not be worth investigating but in the context of rapid urbanisation where over half the world’s population and 80% plus of those in the developed countries  live in towns and cities the question of why a walk in the garden is better than a walk on a treadmill becomes more urgent. Coming from the other direction the expansion of urbanisation and associated agricultural intensification means there is less room for the biodiversity and those same urban green spaces become important as nature reserves. There is also evidence that exposure to green space makes people more pro-environmental and therefore more likely to support the lifestyle changes necessary to protect the planet in the face of threats like global warming. Research that leads to policy that helps us get our urban green spaces right is likely to have a big impact on future well-being of both humans and nature.

urban_population_graph

In fact there is good empirical evidence dating back to the 1960s that exposure to nature is beneficial for dealing with psycho-physiological effects of stress.  Just viewing images of nature has been shown to have a restorative effect. The two main theoretical models for why this happens are Stress Recovery Theory (SRT) and Attention Restoration Theory (ART). These theories are complementary. SRT is more concerned with physiological and negative affect whilst ART is concerned with attentional fatigue. Major questions that remain to be answered are: What is it about natural environments that produce these benefits and is this compatible with those same spaces acting as biodiversity refugia that nudge people to be more pro-environmental? Is it enough to just expose people to green space or is education, background and cultural meaning important? Is it equally beneficial for all or are there genetic, personality, gender or age factors?

I like to walk in the garden and intrinsically feel that my training in mindfulness techniques helps me connect with nature but what excites me professionally is that, in this age of big data, some of these questions are going to become much more computable. This is best illustrated with an example. A recent paper by James et al (2016) looked at how exposure to greenness around where you live may be linked to your chances of dying early. They combined two sources. The first dataset came from the Nurses’ Health Study, a project that has been tracking the health of nurses in the United States for the last forty years. These women fill in regular questionnaires about their health and lifestyle. The second dataset was Normalized Difference Vegetation Index (NDVI) calculated from satellite imagery. The study tracked 108,630 women over eight years during which 8,604 of them died. It looked at how much greenness there was within 250m and 1,250m of their homes and, because the study design was longitudinal and the health data is so comprehensive, it could confidently say: “Higher levels of green vegetation were associated with decreased mortality.”

The James et al study was only possible because two large, disparate datasets could be combined in ways their original authors probably never envisaged yet the results are good, highly relevant and potentially impactful. In a far, far less major way my recent studies have been using automated sampling and mapping techniques to try and infer human-nature connections. I’m reading similar studies and there is scope to do much more. My problem is how to describe what this is in less than the eight hundred words I’ve taken here. In conversation with a long suffering colleague we half jokingly came up with Biophilomatics. But many a good neologism is created in jest and this one is worth documenting.

There is a field called Bioinformatics  from bio- (Greek), information (Latin) and -matic (Greek) which has come to be associated with the computationally complex tasks associated with DNA and protein structure. The smaller scale bits of biology.

The field we generally work at the Botanics is more Biodiversity Informatics than bioinformatics. This is information at the taxonomic and systematic levels, the names of organisms, how they are related, where they occur and in what combinations. Whole organism stuff.

Biophilia is a term coined by E.O. Wilson in his 1984 book of the same name to mean ”love of life or living systems” or “the connections that human beings subconsciously seek with the rest of life”. It is the notion that we need connections with nature to thrive. It has spawned several movements notably Biophilic Design, bring a love of nature into architecture, and Biophilic Cities, integrating nature into urban planning.

The new field of Biophilomatics is a specialisation of Biodiversity Informatics in that it includes much of the same data used in describing the natural world but then combines it with data about human well-being. It is cross domain as it requires collaboration between the biodiversity and health worlds.

  • Formally: Measurement of the effects on human well-being and pro-environmental behaviour of the quality and quantity of connection with nature.
  • Informally: Describing the human love affair with nature.
  • Literally:  The willingness to perform (-matics) life (bio-) loving (philo).

Whether or not biophilomatics takes off as a new term the process of thinking it up has helped clarify, at least in my mind, what I’m working on. Thanks are due to Midlothian Science Festival and IKEA for hosting an evening that helped me through this process.

Aug 222016
 

meg1A group of dedicate activists lead by Meg Beresford and her dog Pollaidh are setting off from the Botanics to walk to Wiston Lodge in the Scottish Borders to raise awareness of the decline in bees.

They will start from the Botanics at 10:30 on Tuesday 30th August with stops at Neidpath Hotel in Peebles round 8.30pm on Friday 2nd September then  Atkinson Pryce Books in Biggar for a talk by Andrew Whitley at 7.30pm on 5th September.

You can sponsor them or come along for all or part of the walk. For more details see the Let’s Make a Bee Line website.

 

Aug 122016
 
William_McNab_by_Hill_&_Adamson,_1843-47

William McNab 1780-1848

This is the first professional photographic portrait of a professional horticulturist, the last horticulturist to live in the Botanic Cottage and the man who left the cottage behind.

In 1843 the painter David Octavius Hill and engineer/chemist Robert Adamson formed a partnership to professionally exploit the newly invented positive/negative photographic process introduced by Fox Talbot in 1841. Their base was Rock House on Calton Hill. Edinburgh residents are most likely to know it as  the white building opposite John Lewis.

The Hill & Adamson portraits are amongst the most famous and significant photographs ever taken – partly because they are so early in the development of the positive/negative process but also because they were the first to combine the eye of the artist with the skill of the technician. The pair were prolific, photographing many of the great and the good in early 19th Century Scotland but also the less celebrated Newhaven fishers – perhaps producing the first social documentary photographs.

What does all this have to do with the Botanics you may ask?

20160607-DSCF5351This year has seen the opening of the Botanic Cottage. This is the original entrance to the Leith Walk site of the Botanics that has been moved stone by stone to a new location within the garden. It was left behind when the garden moved to its current Inverleith site in the 1820s and has only just caught up. The man who physically moved the garden and left the cottage behind was William McNab. He was the last head gardener to live in the cottage on Leith Walk. He was still alive and running the Inverleith garden in the 1840’s when Hill & Adamson were practicing and so appears as one of their subjects. The actual date of the photograph isn’t known but the partnership ended in 1848 with the untimely death of Adamson who had been ailing for several years. The majority of their three thousand photographs were therefore made at the beginning of their collaboration. McNab died in 1848 as well and was buried next to his wife – coincidently on Calton Hill.

It isn’t a flattering portrait or one of Hill & Adamson’s best. McNab looks stern with closed eyes (probably because he had to sit still for so long for the image to register) when by all accounts he was very nice and liked by all. There is another exposure with eyes open that has been rather unfairly captioned “the mad horticulturist” on the internet. Only the above image appears to be available at high resolution in the public domain.

IMG_20160622_191305I have a fascination with photographing people and my major project for last year was to photograph those involved in moving the cottage. You can read about the project and see some of the images on my personal blog. Thumbnails were used in the new guidebook and we may produce a self print book of the complete set to leave in the cottage. For the time being there is a small exhibition of portraits in the Botanic Cottage.

Of course I was familiar with Hill & Adamson but hadn’t known they had photographed McNab until I found a National Portrait Gallery catalogue of their work in a second hand book shop. I was reminded of my photograph of David Rae, the Director of Horticulture and McNab’s equivalent during the instigation of cottage project. I’ve managed to make a jovial member of staff look stern and authoritarian – just like Hill & Adamson did to McNab.

DSCF2352

David Rae

And so we come to the real reason for this blog post. A tenuous excuse for me to get my amateur snaps associated with Hill & Adamson!

Mar 032016
 

Botanics_Pano

We know that spending time in beautiful green spaces is good for our mental and physical well-being but there are things we can do to make the most of this precious time and spread the effects into the rest of our lives.

This year I’m running a series of two hour workshops to introduce techniques for mindfully engaging with the environment. Each is held ‘on the hoof’ in the botanics after closing time and is suitable for absolute beginners or people with some experience of meditation. The workshops are designed to be free-standing but with the intention that some people may like to do them multiple times.

Roger Hyam_2013-05-21-1Although I trained as a botanist and currently focus on digital information at the Botanics for the last twenty years I have been a mindfulness meditation practitioner. I have a postgraduate certificate in secular mindfulness based techniques from Bangor University and have been ordained as a lay member of the Order of Interbeing – the order founded by Vietnamese Zen master Thich Nhat Hanh.

The workshops will run on Tuesdays between 6pm and 8pm on 12th & 26th April, 10th & 24th May 2016 and cost £15.

If you are interested you can book through the Education office on 0131 248 2937. If you would like more information please drop me an email. You can download a Two Feet, One Mind flier if you would like to share this with friends.

Dec 222015
 

map_750_1334This week the Water of Leith Walkway Audio Tour app went live in the Apple iOS app store and the Google Play store. We have produced this in partnership with our friends at the Water of Leith Conservation trust.

The walkway was established in 2002 and runs from Balerno all the way to Leith passing near to the foot of our garden in Inverleith. The most popular section of the walkway is between the botanics and the Scottish National Gallery of Modern Art.

The trust created an audio tour of the route several years ago but it was only available on-line. You needed a data connection on your phone to listen to the tour. You only discovered the points as you got to them.

The new app uses the same technology as our Dawyck Scottish Trees app. There are twenty audio points to listen to, a sketch map and a GPS positioning system to show where you are along the route. It was relatively little work to accommodate the larger scale of the walkway map. Importantly from the point of view of the botanics a series of bug fixes and improvements were incorporated into the core code and a new version of Dawyck Scottish Trees app released. These improvements will also roll forward into the planned Inverleith audio tour next year. Each time we produce one of these audio tour the quality goes up and the work involved goes down.

This is a soft launch at a quiet time of year to check everything is working and get some feedback. We will advertise it more widely in the spring. If you would like to try it out just search for “Water of Leith” in the app store on your device. Please let us know how you get on and if you like the app rate it in the store.