Tag: Plant databases

No shit Sherlock! finding your plant using databases and without smoking opium.

This is the outline for a talk I was due to give to the Bath Natural History Society, and which had to be postponed due to unexpected death of the President, Rob Randall

This is Coltsfoot; Tussilago farfara It’s got a number of other names but apart from English tobacco – which I’ll come back to, none are really common. its name comes from the similarity of the leaf shape to the footprint of a small horse, hence colt. The tobacco bit comes from its inclusion in smoking mixtures which until recently were commonly offered as a herbal medicine for asthma and other chest complaints. However some recent research has revealed that the plant also contains some pretty dangerous chemical compounds called hepatotoxic pyrrolizidine alkaloids (liver toxins) which could cause more harm than good – plants and fungi are terrifically effective synthesisers; that’s why drug companies spend so much time and money investigating them. I did once try to smoke a herbal cigarette containing coltsfoot but it was truly horrible and I never went back for more.

But beyond the health warnings it’s a favourite of mine because it offers a ray of sunshine in the spring; often in the ugliest of environments; and also it’s a plant that taught me a huge lesson in plant hunting. My first awareness of it came when I was working as a groundsman on a school playing field. The second find came, years later, on a bike ride around the villages where I worked as a parish priest. It had been snowing but the snow was melting quickly and where it lay on the verge it was stained and brown with mud thrown up by cars and lorries. Suddenly, in the midst of this gloopy, brown stained, melting snow I spotted a little group of bright yellow dandelion-like flowers poking through. As an avid but very inexperienced botanist I knew that they were Coltsfoot from watercolours I’d seen in my battered field guide and on a grim day they cheered me up. I was also pleased to have seen them because I knew that they were often associated with healing properties. Then they disappeared for a decade – well actually they didn’t disappear at all but I never looked in the right places.

It’s a pound for the stone and ninety nine pounds for knowing what to do with it.

Local drystone wall builder in conversation with customer

The quotation – the reply to a silly question – arose from a chat with a local stonemason who told me how he was once asked by a prospective customer how he had the nerve to charge so much for a cheap raw material like stone. It was a wonderfully tart response and I never knew whether he lost the job as a result of it.

Don’t get despondent get organised

If there’s any primrose path to finding your quarry in field botany it’s the ability to tap into all the information you can find for free in books and on the internet. After many field trips with some real experts I began to notice the secret they never revealed. They weren’t just wandering around hoping to bump into something interesting, they had all done reconnaissance trips in advance, and they had all researched the area we were visiting in extreme detail. It wasn’t the case at all that they had encyclopaedic knowledge of every UK plant. All they needed to do – and here’s where the experience comes in – was to search the chosen area on one or another of the huge databases available – I particularly like the BSBI Ddb plant distribution atlas (Google it and you’ll find it immediately) and specify the 2X2 Km square you’re visiting – there’s a bit of a learning curve here but a little patience will soon be rewarded with a neatly laid out printable list of plants that have been recorded inside what’s known in the jargon as a Tetrad. The 1800 wildflowers that grow in Great Britain and Ireland will immediately be cut down to three or four hundred which is much more manageable. If you’re a birder or fascinated by beetles and spiders, or if larger mammals are your thing, the NBN Atlas might suit you better. It’s like the BSBI database but for all species, and you can drill down to individual records. Another alternative is to print off the plant lists for the Vice County you’re in – these are already formatted on the BSBI website when you click on the “explore and record” pull down menu tab and click on “recording cards” and print the result off. The downside is it’s Latin names only, but if you get serious about plant hunting you’re going to have to use them anyway. Most modern field guides also have thumbnail distribution maps which won’t give you the grid reference, but will at least tell you that your plant only grows in Snowdonia.

Someone humorously pointed out that distribution maps are really maps of recorders and all of the large databases contain the possibility that the plant in front of you has just never been recorded before. I just checked for our present location on the NBN Atlas and none of the four ferns within twenty yards of me have ever been recorded. Some big databases haven’t quite kept up with the momentous changes brought about by DNA analysis, and so – again today – I was surprised to see that BRERC – the Bristol Regional Environmental Records Centre still has the Harts Tongue fern as Phyllitis scolopendrium when it’s been in Asplenium for some time. But don’t be hard on the compilers, there are millions of records to be checked and processed. Sometimes plants just seem to be entirely in the wrong place. Having spent hours on the Cornish coast searching for Sea Spleenwort, Asplenium marinum; I mentioned the unsuccessful search to our Vice County Recorder and she pointed out several specimens in the centre of Bath.

If, on the other hand you think you’ve found a Ghost Orchid in the garden, you can access the BSBI Plant Atlas 2020 and type in “ghost” and the orchid will surely arise as the only option. Click on it and you will be given a map of the UK with just four little black spots in it. If your garden is not marked by the black spot you can be quite sure that it’s something else – not certain, mind you unless you’re out for a walk with a man called Peter Stroh and he’ll soon put you right in the nice way that really good botanists always do.

Slumping cliff without Coltsfoot – yet – in Aberdaron.

So if you’re looking for a particular plant, or group of plants, these databases can give you a huge advantage. Then you can find out everything possible about the preferred habitat for your plant. This is exactly where I went wrong with the humble Coltsfoot whose black dots seem to cover the entire country until you enlarge the map and see the gaps. Somewhere in your research you will read that the Coltsfoot is something of a pioneer plant because it loves disturbed ground, is salt tolerant, and grows particularly well on what are known as slumping cliffs. Muddy cliffs with an inclination to break down and collapse on to the beach below. So first, check the maps in the databases for the black dots, and second, look at the flowering dates. Although Coltsfoot can be identified by its leaves (which grow when flowering has finished) that’s a bit trickier because there are at least two other plants with very similar looking leaves – so Coltsfoot, smallest; Winter Heliotrope, middle sized and purple flowers from December onwards anyway; and then Butterburr which has the largest leaves of all. If you want to see the Coltsfoot flowers it has to be around March. In my book that’s learning three plants – three for one offers are good.

99% of the effort goes in before you leave home

What you should be taking from all this is the fact that 99% of the effort in finding less common plants is in the research. You probably wouldn’t do it if you were looking for Dandelions, Celandines or Primroses because they tend to turn up anywhere – they’re generalists, but perhaps most happy in springtime hedgerows, so maybe start there. But I found the Coltsfoot in abundance as soon as I started to apply the “right place, right time” approach, one day when we were walking along the beach called Porthor or known in English as Whistling Sands, here on the Lleyn peninsula.

Most of us begin naming plants by flicking through a book. That’s about as effective as standing on a bus stop and asking people if they know John Smith. With the advent of AI there are a wealth of phone apps available to help identify plants you don’t know. HOWEVER they’re not infallible and there are both more and less reputable contenders in the market. Even Google Lens can usually give you a family name with reasonable accuracy, but never trust it down to species because it seems to want to help so much that when it’s stumped it starts throwing in silly answers. With all phone apps – I’ve got loads on my phone – try another and then, when you’ve found some consistency always turn to the books.

Just a word of warning here. I left the Apple religious community three years ago and moved over to Android, and so my photos are taken on a Pixel 6a and this is being written on a Pixelbook. I gave up on Windows when I retired. Everything is stored in three places on the Cloud. The information I’m giving should work with minor variations on iPhones and most Android phones.

So finally, there’s no finer instrument than the modern mobile phone for keeping records. Most phones store what’s called EXIF data (Exchangeable Image File Format) which sounds very technical but just means that as well as exposure etc. the phone records stuff like lat and long information for the exact place the photo was taken; date and time and is often editable so that you can add the name of the plant and any other information you think is important. This allows you to create a simple searchable database of your own photos. Google tells me I can’t do this, but as long as I separate the data with commas it works pretty well because the search facility is based on a very simplified comma delimited database . No need for endless hours designing your own. Phones also offer basic GPS but for proper accuracy it’s better to use a handheld. I’ve had photos given locations ten miles from where the photo was taken. The only problem with handheld GPS is that you have to carry a notebook and make sure you link the photo to the location in case the phone GPS turns out to be unreliable. But then, as an incorrigible compiler of lists I do that anyway. The latitude and longitude data can be loaded into the OS Maps application which will obligingly give you the national grid reference equivalent without any complicated calculations and pencil chewing.

Finally, but by no means least, there are applications which allow you to submit photographs of plants with provisional id’s and get them checked by panels of experts. Among these programmes one of the best is iNaturalist where, once you’ve signed up for free, you can submit photos and other details and – if you’re lucky – an expert somewhere in the world will verify the name. I only say if you’re lucky because there are so many records, most referees don’t have time to verify really well known things. I tried familiarising myself with the app at the beginning by posting some extremely common plants and they languished unloved and unnoticed until I took them down. The best and fastest responses seem to come from groups like mycologists (fungi) or pteridologists (ferns) but if you’re posting a less well known plant the support is good. Another virtue of iNaturalist is that verified records find their way onto the national and international databases and can be used for research. Vice County Recorders mostly use a Windows programme called MapMate which was state of the art when it was designed, but hasn’t been supported and has apparently become a bit clunky.

Flora incognita, another freebie uses AI and gives a useful percentage figure for certainty; and there are more coming on to the market all the time and may suit your needs completely.Finally, for birders I can’t resist recommending Merlin. I was out on a trip with the Three Musketeers in the autumn and we all heard an unrecognised bird song coming from a dense hedge. We all pulled our phones out and then discovered that we were all using Merlin.; an American app that comes with add-on national databases.

But saving the best until last, often the very best support and advice comes from your (in the UK) local Vice County Recorder. If you join a natural history society you’re bound to meet them very quickly. They’re all volunteers and many of them act as referees for iNaturalist as well. Ultimately every record comes down, in the end, to human judgement. AI is good and getting better, but rather like Satnav it can let you down spectacularly if you don’t use your own judgement or tap into someone else’s.

So I seem to have slipped into writing about records. You may, of course, spend a lifetime finding beautiful plants, fungi, mosses and ferns purely for your own pleasure, but in this epoch of ecological crisis every single record – even of daisies and dandelions contributes to the global picture. Natural history is a field where volunteers make a huge contribution. We can’t all afford our own scanning electron microscopes and perform DNA analyses on the dining room table but we can observe and record so that the scientists with all that expensive kit can pore over the trends and direct their research towards the most pressing challenges. As Joni Mitchell has it – “You don’t know what you’ve got ’till it’s gone.”

Google Photos as a natural history resource.

Most of these photographs were taken on what turned out to be a life changing trip to Dartmoor in March 2016. The Potwell Inn didn’t exist; we’d been through retirement and a major family crisis when our second grandchild was born with a still undiagnosed genetic disorder; we’d moved from a large vicarage to a small flat in Bath and the allotment was yet to come. Christmas had been a write-off and we had taken ourselves off to St Ives in the campervan in search of some respite – in the dog days of the old year just as a major Atlantic storm reached the south west.

January 1st 2016 – a stupidly hubristic resolution

The key photograph here is the one of the (at the time) unidentified little seagull. We were leaning on the railings above the harbour just down from St Ives lifeboat station and watching the gulls when I realized that this gull was very different from some of the other gulls and I had no idea what species it was. I remember feeling faintly annoyed with myself and later that day we went into the bookshop and bought the first bird guide we’d ever owned. It was about then that quite the stupidest resolution I’ve ever made began to form in my head. I would not – I resolved – pass by any plant or animal, without naming it. The picture I took that day was completely hopeless in terms of identification, even with an 80mm lens there was no detail that had any significance so far as I could see. Just for the record I now know perfectly well that the dark smudge behind the bird’s ear is all that remains of the Black Headed Gulls’ distinctive summer plumage on December 29th.

Before we retired (i.e when we had a bit more money), I bought an iPhone and a Macbook. Madame had already settled into the Apple ecosystem because she was teaching photography at the time and it made sense for us to share resources. For the first time I owned a mobile that would add location data to the EXIF file. At roughly the same time I started keeping a private journal using Day One software and this integrated seamlessly between the iPhone, the Macbook and a big desktop. But it wasn’t so long before we came up against Apple’s policy of abandoning their products by making it impossible to upgrade the software. Day One suddenly stopped talking to my Macbook and when I complained I was told that it was my fault for not upgrading. We struggled on for several years, but applications like Photoshop and Lightroom were less and less easy to run on our aging machines and in any case their memory hogging features were far beyond my own needs. I was using Microsoft Windows for work and so we landed up in the worst of all worlds, moving photographs between incompatible software. Heaven knows how much data was lost; but in the end I began a long process of ditching Apple and moved as much data as I could find into Dropbox as a security for the future.

It was our oldest son who broke the impasse by giving me an old Pixel 3 phone after an upgrade and I started using Google Photos. To be honest there was nothing about the iPhone that I particularly missed, and when – a couple of years later – he gave me a basic HP Chromebook that he’d acquired during another upgrade, and after he helped me with a fast and pretty seamless setup and data transfer, I put my agonisingly slow Macbook on a shelf and started enjoying an entirely new and fast cloud-based ecosystem.

Anyway, to get back to the photographs at the top of this post, they represent something of a sea change. My ludicrous resolution to try to name things brought about a move towards much more purposeful photography. As my interest in plants moved up a step, I discovered that well composed photographs of plants I didn’t recognise, meant I didn’t have to dig them up and take them home which is at best inconsiderate and at worst illegal. It’s taken ever since to refine the technique so that I remember to photograph the sometimes apparently insignificant details that make the difference between a correct and a wrong identification.

None of this particularly mattered, of course, as long as I was the only person ever to see the record. But then, as I wrote in a post last week, I began sending them for verification by the local BSBI East Cornwall recorder – which is when it dawned on me that my photographs were more akin to archaeological compost than a filing system. Looking for old photos meant trawling through thousands of them in the hope of alighting upon the right one.

By now I’d got myself a powerful little Pixelbook and I was beginning to understand that the originally utilitarian Google Photos has a few new tricks up its sleeve. One of Google’s most useful – although much feared – attributes is its formidable artificial intelligence software. If you’ve ever used Google Lens on the phone you’ll know that. It can be a curse as well as a blessing – this morning I had an email from someone asking what was the launching fee at Percuil. We were on holiday for the last two weeks and I mentioned Percuil several times in the blog and the odd request must have flowed from a bit of AI that was too clever for its own good.

Google Photos uses AI to do a lot of basic sorting and indexing of photos behind the scenes; so I can search on months and years, faces and places. But last week I wanted to start indexing keywords like genera, species, English and Latin names and various other bits of searchable data. I’d contemplated using some third party software but after hours of searching I couldn’t find anything I liked better. Any records I’d submitted or had accepted would be somewhere in one of a number of vast external databases, but I wouldn’t be able to access them in a simple personal list.

So here’s the exciting thing. After a bit of experimentation it seems that contrary to what I read on the internet, I can do keyword searches on terms that I type into the “details” column at the head of all the EXIF data. The only downside is that the AI facilities remain in play, so a keyword search on primrose might yield a few lookalikes as well – not the end of the world in my view. My guess is that some of the AI used in Google Lens is already being built into Google Photos. The software connects seamlessly to WordPress, so I can use my photographs in this blog; and I can easily forward diagnostic photographs to the referees for acceptance.

When we go out plant hunting I take the phone with a macro lens so I can take the necessary photos. I’ve got stacks of useful apps on the phone as well, including OS mapping, accurate National Grid references, altitude, and shortcuts to the BSBI plant distribution database. I’ve also got iRecord, I Naturalist and a link to the local list of plants which I download as a PDF before leaving home. Google Lens is surprisingly helpful in steering me in the right direction but it’s not infallible. Of course I will take a book along with me but I always take photographs because I can use them with my library of plant books at leisure when I get home. It doesn’t always work, and I often have to go back, look more closely and take more photos in order to do a full ID.

The upshot is that the more of this kind of intense work I do, the more my plant ID skills improve. Typing details into the software drills the English and Latin names into my memory very effectively too. I think the take-home point is that while for some people, staggering across a bog with a large camera and tripod, an expensive GPS unit and a copy of Stace 4 weighing in at well over a kilogramme is the only way forward. But for my purposes I can get it all into a pocket without my trousers falling down. I take a 6″ ruler, I use my walking pole as a 1.5 metre measuring stick. I take a plastic zip bag, just in case; a Rite in the Rain waterproof notebook and a pen that writes on it underwater and upside down – who knows when that might be needed! a scalpel and a couple of hand lenses. Total weight around 500g.

Maybe I’ll be forced to eat my words one day, but this seems to me to be the simplest and cheapest way – it’s free – of creating a searchable, automatically backed up photographic database for plant recording. No good at all, of course for insects, mammals and birds because they all race around too far away for a phone camera. But my subjects stand still – unless it’s very windy – and best of all the photos escape the dangers of being lost forever in my fallible memory. What’s not to like?

Computer says no!

Having gone on – perhaps a little too lyrically – about the joys of big data in yesterday’s post; I came up against one of its limitations today. It was nothing; or it was something …… who knows, but it was a wonderful example of the way that – re-using the phrase I used yesterday – absence of evidence is not evidence of absence. Or to put it in more immediate terms – there is little to no evidence that the plant in the photo has ever been found in, or anywhere near, the Lost Gardens of Heligan – or even in East Cornwall. This may of course be because the gardens – being lost – cannot be invaded by this plant because it can’t find them. On the other hand, there it was in front of me on Wednesday, and all I knew for sure was that I’d never seen one before …… but it was almost certainly a form of comfrey.

So I spent quite a few painful hours checking and then double checking but, as an amateur, you have to hang your hat somewhere and so I decided it was probably but not certainly Symphytum bulbosa. The haunting possibility is that it’s something entirely different; so much so that any halfwit would have known its real name. Common as muck! Where have you been living, you botanical imposter. And there’s the crux of the problem. There are two possible outcomes to the conundrum and one of them is to submit the record to the scrutiny of someone who actually knows what they’re talking about, but who may dismiss me scornfully they may also be looking at the same maps, records and data as me and go on to say that tuberous comfrey simply doesn’t grow where I saw it and so, QED I was wrong.

Now this isn’t that big a deal – it would hardly be a hardly a paradigm shift if I turned out to be right; but the sheer inertia of the system resists change and for a learner like me, taking on a system is a really big deal. Nobody dies either way, whether I’m right or wrong; but if I don’t submit the record because I don’t want to rock the boat, everybody loses. I miss an important lesson, and the maps and data are just that little bit less accurate than they could be.

So I bit the bullet and filled in the online form; emphasising my lack of experience and humility (I wish!) in the company of experts and all that blah blah, and then spent twenty minutes trying to change a GPS reading from my phone to British National grid without realising that the programme accepted it either way. The only thing I forgot to fill in was the species name which by this time I had forgotten. So once I’d found the name again I filled in the form and immediately a red triangular warning sign appeared against the entry; I’d been flushed out before I’d even pressed the send button!

So there we are. My contribution to citizen science is out there, somewhere in cyberspace, awaiting final judgement by a recorder who may well be knackered and daunted by a stack of 10,000 records that they wished they’d never signed up for.

Today the sun shone. There was a stiff northwesterly wind and so we found a sheltered spot in full sun on the beach and I recorded some celandines and sea beet. At least I know what they are.