CASABIO

The Beginners Guide to Contributing to Citizen Science Using the CASABIO.org Web Platform

noreply@blogger.com (Anonymous) — Sun, 10 Dec 2017 03:19:00 +0000

So you want to contribute your beautiful pictures of plants and animals to a citizen science platform? Perhaps you want identifications of something you saw?

Using the CASABIO platform is quick and easy once you've got the hang of it. There are several ways to ease you into it. There is a "shepherd" that walks you through it when you first contribute images. There are also help and keyboard shortcuts at every stage that look like this

and then there's this...

The Absolute Beginners Guide On Contributing Images To The casabio.org Website.

I find the workflow of CASABIO pretty great. On my fibre connection I can get through several hundred pictures and observations in an hour or so. Here's my suggestion for how to do so basically and efficiently. Please try contributing images using this as a guide if you get stuck.

Right now...

Open up a picture directory on your hard drive with plants or animals...

done that?

Now click here ---> casabio.org

Okay - you're on your way. I'd really appreciate the feedback and the contributions. You can always delete your contributions later if you make a mistake. Just keep going through this.

You'll need:

images of plants or animals (preferably geotagged, see my post on how to do so if you have a GPS using Geosetter).
access to a desktop computer or a laptop with an internet connection

Step 1) Before uploading the images - if you can, name at least one of the files associated with an observation. i.e. to family, genus or species level. Here you can see I've selected the file '_9093970', presssed F2 to rename, pressed the right arrow to go to the end of the file, and appended 'Moraea' to the filename. Moraea will be matched against the database and the full set of pictures will acquire the name within CASABIO. If you don't know any names, don't worry about it. Just skip this stage.

Step 2) Register / login to CASABIO.org. I suggest a username that is memorable and suits your character.

Are you ready?! Deep breath and...

STAGE 1: ADDING PICTURES

Step 3) Go to Add | Observations near the top left hand corner of the screen.

Step 4) Name your collection. I like to use the same date and name as the folder I put it into - and then I append "uploaded" to the folder on the hard drive (select it and press F2).

Step 5) Now drag and drop your images from your folder to the dialogue.

(Do this by selecting the images you want uploaded. Once you've selected them, hold the left mouse button down to drag them onto the dialogue, then release the mouse button). If you cannot see the target dialogue, drag the images onto the browser icon on the taskbar, when the browser opens up, continue to drag it onto browser tabs that has the CASABIO upload page, and then the dialogue will show).

Optional Step 5.1) Once uploaded the images will be available below the drag dialogue as thumbnails. One or more of these thumbnails can be selected at a time and rotated using the dialogue in the top left (or l for left/counter clock-wise and r for right/clockwise). If 'edit' is selected (or e to edit), then you can choose what attributes those pictures have.

Optional Step 5.2) Subject can then be selected from the dialogue.

Clicking the fields bar will allow you to see the attributes of the photographs. eg. Subject.

Once you're satisfied with tagging, click continue to go to the next stage.

STAGE 2: GROUPING THE PICTURES

Step 6) After loading a dialogue will ask you if you want to group the pictures. Most of the time you will want to do this unless your pictures are disconnected from each other and do not represent multiple images of the same observation. It is based on the time that the image was taken with the assumption that you take multiple images of the same species within a certain timeframe, then move onto the next species with a gap between observations.

As can be seen in the example above - there are two different species - shown by the arrow. The simplest solution is to select these photos from the first or second group, and click regroup (or r key). If all you pictures are separate observations (for instance herbarium specimen scans), then use "group as individuals". If you don't want an image to show - leave it ungrouped.

Another option that is useful for helping you to group is to display date and time (in seconds) or the filename.This is where it helps if you've named the files.

A newly added feature is the handy star at the top of each thumbnail. Click it and if it is one of several pictures in a group, that thumbnail will go to the front and be the representative picture for that group. Handy to showcase your very best pictures. I do it as a final step before going onto Step 7.

Step 7 - click continue at the top of the page to go to stage 3.

Stage 3 - Working with observations

If you have named your files, click Auto-identify on the dialogue. This will compare the database to the filenames and if there is a match it will identify the observation as such. You can see if this worked by clicking on the identifications tab. As you can see, the three left-hand observations worked, whereas the one on the right did not.

Step 8) Select the observation that needs to be identified. By clicking on filenames (second button from the left) I can see that the filename is Callatropha procera. The third button from the left is identification - or you can press 'i'. This will generate an identify dialogue.

As can be seen, Callatropha wasn't found. By clicking 'add the species' we can add this to the database to be selected. However it was not found on GBIF, so a quick search revealed I had mis-remembered the name - the actual name being Calotropis, which as can be seen is in the database.

I now type in the correct name, and select the species name and the likelihood. I like to be conservative to make it easy for subsequent experts to improve the identification. And my identification is done.

Step 9) I can also select one, more or even all (ctrl+a) of my observations and edit ('e', position 1, below) the information associated with the collections. This will bring up the general information including the observer name which is by default the person logged in. If I am contributing someone else's pictures, I will put that person's name at position 2. If the subject is not an organism and cannot usefully be identified with a scientific name (like a landscape or a person), then change the classification to "not an organism" at position 3.

The description tab simply allows one to add a species description to the observation.

The location tab is where any georeferenced observations will be shown automatically on the map. Here the selected observations are in red, and the unselected observations in blue. The map can be zoomed (controls at position 1, below), scrolled (left click on the map and move the mouse around) and points can be added (left click on the map). To choose a location, select from the box at position 2. To contribute a new locality - select position 3.

Optional Step 9.1)

If I select 'contribute new locality', then the name of the location must be entered and a description (I typically compile this from a variety of internet resources). If it is a private location and is only meaningful to yourself (like 'my back garden') , select Private at position 1, below. This then will not be visible to anyone but yourself and admin. Now centre the map so that the entire region that you wish to demarcate is within the view. Click on the polygon tool at position 2 and start clicking around the boundary. Double click to compleete and close the polygon. Press the 'x' button in the tools to remove a polygon if you made a mistake.

Ignore the 'weight', but under parents select the country and parental positions as best as possible (in this case the province Eastern Cape is selected) then click 'save'.

Select your new locality under and save the page.

Step 10) Once you're all done. Check that the images have the information you can give by scrolling through the buttons particularly 'observer', 'coordinates', 'locality', 'specimen number' and 'identifications' fields.

Step 10.1) If you have collected specimens and wish to add a 'life number'/collection number to the specimens, this can be done by selecting observations and selecting the 'number specimens' (position 1, below). This will open up the dialogue in which a seeding number can be entered (position 2), with all selected observations obtaining a subsequent number. This numbering system should be improved and made more customisable in the near future.

These numbers can be manually edited if needed (i.e. to change the order) under edit | basic observations | specimen ID.

Step 11) Now click Finish at the top of the page, and your full set of observations are saved.

After this your observations will be identifiable by fellow contributors. You can also start to build up collections and create field guides to areas. We're also working on an app for use with smart phones. Thanks for taking the time to work your way through this. If you have any questions or suggestions, please email me (David) on capebio@gmail.com.

Epic Update! CASABIO pre-launch and app progress

noreply@blogger.com (Anonymous) — Thu, 14 Sep 2017 10:43:00 +0000

It's been a long time since I've updated the CASABIO blog. That's because I've been so ridiculously busy preparing the CASABIO Next Generation Citizen Science Platform for launch. For several months I have been working closely with Dane Rossenrode of Touchdreams to improve the web platform. This has shown steady improvement and the website is now fairly operational though not entirely intuitive yet. That being said we've implemented Shepherd to guide users through the upload process and started making walk-through videos.

Firstly we've had a logo makeover... hope you like it?!

It is not just a smiley face, it's: a C and a B; a seed germinating in the ground; a combination of the marine (the C is a wave) and terrestrial (plant) components, but it also tells a delightful love story. The sea-bean is Entada gigas, the world's largest bean. It's pod, also known as the sea-heart washes up in beaches around the world and thus connects the continents. It is the African Dream-herb, and CASABIO is a dream that needs all the magic it can get to realize to its fullest potential. Finally it is the Zulu Love Bean and a discoverer of a bean is said to be irresistable to admirers. That's potent stuff integrated into a beautiful friendly logo designed by Chantal Swiegers of Spika.

Talking of exciting developments, Aiden Graumann has been developing the BioSnapp iOS and Android app. Together with the work of Neural Net specialist Alex Karpul Neural Net implementation for automatic identification should prove a massive step up for African citizen science.

The front page of BioSnapp

The live feed

A neural net needs a basis for identification though. Botanist Cameron McMaster gave me nearly 22000 images totalling 41Gb of mostly named images. I've begun to upload these to the CASABIO website though my time is obviously limited. He is an expert on bulbs, so here is just one selected image of the tens of thousands!

We've also photographed a representative herbarium specimen of every species within the Cape Town area with a high resolution 40MP camera. Nearly half these images have now been cropped to highlight features and to fit in with the field guide layout. Once this project is finished every species in Cape Town should have a representative image by which a plant occurring within the city can be identified.

A crop of a Tritoniopsis unguiculatus showing the detail obtained from a larger image of the specimen

Project Bety (Biological Etymologies) is about to be initiated though we currently have etymologies for 7960 taxa. This is a crowdsourcing attempt to get every plant species within South Africa with the origins of the name associated. This is a very accessible citizen science programme open to everyone because all it needs is a connection to the internet. Potentially it will take a matter of weeks for this task to be accomplished.

A crop from Project Bety. Dropdowns can be used to only show taxa with etymologies or without. They can also be used for looking up an existing etymology. There are several look ups to help one find out the etymology if it exists elsewhere.

Lynda de Wet kindly provided a full collection of over 900 species of beautifully illustrated artworks from the Darling Area of the Western Cape, representing three years of work. The collection has been integrated into the database and may be perused as collection 1 and collection 2:

Gladiolus orchidiflorus from the Lynda de Wet art collection

Most excitingly - the field guide is shaping up well. This allows one to submit an area and have a field guide created for that area which includes images of the taxon (family, genus or species), distribution map (courtesy of GBIF), IUCN threatened status (international only - the South African criterion has not been received yet), a short etymology, and the description of the plant (so far only if it falls within the Cape Floristic Region).

Example of the field guide. I like that it gives a global perspective on the distribution at family, genus and species level

Additionally the herbarium label feature has been made incredibly useful. Essentially with no effort beyond the prerequisite submissions of images, the observations can be used to produce herbarium labels. On the first page observations can be selected or deselected. On the subsequent page the labels can be resized to print on a page (select narrow margins if it doesn't fit onto A4). This should drastically speed up the workflow of a biologist.

Our "supporters" page has been implemented and redesigned to allow funders and contributers to be readily recognised. We're starting to look for funding to take CASABIO to the next level, particularly in getting fresh information and in undertaking bioblitzes, so please get hold of me on capebio@gmail.com if you'd like to contribute to these causes.

Recent developments include:

- basis for gamification now producing stats

- herbarium labels now working and selectable

- Project Bety available

- BioSnapp development underway

- neural net integration being tested

User stats for myself. While it may not look like much, this has been generated from the user history so forms the basis for gamification of both the web platform and app

Necessary development before full launch includes:

- the taxonomic work of Cyrille Chatelain of Villeneuve needs to be integrated

- field guide needs to be tweaked to remove duplication

- tags needs to be working with multiple items

- photo selection for a taxon needs to be improved

- we need to resolve how to deal with accurate localities. Currently they are automatically fudged to quarter-degree square level.

- a new zoomable lightbox needs to be implemented

If you have photos of African flora, sign up and get contributing today. Although it won't show immediately, every first and second representative picture of the species that is received will forever have your name emblazened across that species. The top contributors will also be rewarded at the launch of CASABIO.

So sign up and send your feedback. This is your chance to tailor CASABIO to your needs.

Dave over and out!

First Ever Dual-Camera Test on WWF's Flagship Renosterveld Reserve: Haarwegskloof

noreply@blogger.com (Anonymous) — Sat, 29 Oct 2016 07:51:00 +0000

During a recent trip to Haarwegksloof, the world's largest Renosterveld Reserve owned by WWF and managed by Jannie Groenewald and director Odette Curtis of the Overberg Lowlands Conservation Trust. Situated in the Southern Cape, it and nearby fragments harbor a suite of red-listed species, six species only occurring on the farm and with many species threatened with extinction.

Swedish tourist group at Haarwegskloof - Zoë Poulsen a botanical blogger (far left), and Jannie Groenawald (light blue on left), manager of Haarwegskloof

Jannie Groenawald and Rachel Browning with a new undescribed species, Hermannia sperata

On the 26th of October I decided to conduct a live test of the process. Software developer Dane Rossenrode of Touchdreams has been putting some serious graft in the past few weeks, so I thought it was time to put the CASABIO Biodiversity Engine through its paces.

The premise of this post is that this is the first system that allows the pictures and information from two cameras to be amalgamated. Why two cameras? My Olympus TG-870 has a GPS and wide-angle, but the macro images are of poor sharpness. The Olympus OM-D EM-5 Mk II on the other hand has no GPS, and it is a mission to put on the wide-angle. Paired with the Olympus 35mm lens, macro images are crisp and sharp, but frustratingly slow at finding focus. So I use it sparingly to obtain great macro images. Because I have synchronised the two cameras, I am hoping that the automatic grouping feature of CASABIO will allow the images of each species at a locality to be grouped into an observation automagically. Let's see!

At 6:45 I dragged and dropped a selection of 474 files. By 08:00 it had finished uploading.
At 08:10 I added a further 501 pictures from the OM-D bringing the total to 975.

By 08:11 these were uploading and generating thumbnails at a rate of one image every six seconds. Scrolling through the entire set of 500 images is seamless with no visible lag!

By 08:30 and 75% progress, two non-fatal errors and had occurred:

I suspect they are the internet dropping intermittently - but may simply be exiftool not extracting the exif information correctly.

While waiting for the pictures to upload, I added two localities to be used in the upcoming pictures. It's currently a bit of a painful process to add them as I have to scroll from the world map into my position, and scrolling side-to-side is not working properly so I have to zoom out/in to get it to refresh. I've suggested that one can type in a co-ordinate to jump to.

At 9:20 while waiting for my omelette to cook, I attempted to tag images. A feature that has always worked. Not a single click worked :(

I clicked "continue".
At 9:26 the pictures started uploading on the next page, and by 9:27 all 927 images were displayed and were scrolling smoothly. A quick test showed that all functionality was working. I was able to click individual pictures, select a bunch with a swish of the mouse, ctrl+A to select all pictures, and 'c' to clear all selections. As the clock struck 9:30 I pressed the autogroup button - a feature that has bugged out in the past. I accepted the 30 second autogroup, and waited with breath held... 9:31 and no update. I retrieved my omelette. At 9:33 still no progress, so I clicked auto-group again. A blue sign popped up saying "auto grouping pictures" and then disappeared. No sign of change. At 9:42, still no progress, so I decided to do the dishes...

Autogrouping not working :(

At 9:53 when still nothing had happened I decided to take matters into my own hands. I closed the dialogue - still hanging and proceeded to group things manually.

By 10:45, after 5 minutes of work I had grouped all the ungrouped images. Running late for my massage I dashed off,

Returning at 3:30 from helping out a friend, I returned and after two minutes of grouping, realized that it had worked! The two cameras were integrated! At 4:15 I spent I went through the grouping and at 4:35 I had finished grouping.

At 4:43 I clicked the next button. Almost immediately I was able to see that either I had missed a few, or it had botched up slightly with the grouping - but not bad. After a few minutes of loading the baby thumbnails. By 4:46 it looked like everything had finished loading, but the progress wheel was still churning.

I returned later to find that everything had worked. Only a known issue prevented it from greatness - it was only obtaining a species name from the first file in an observation so not every picture was observation had an identification.

The final stage: Most observations but not all succesfully identified

So why am I writing a post of our system beset by issues? Because I think this is really exciting! The system is working but buggy. Dane says he'll put in hard graft this weekend, so I'll be able to post tomorrow showing the difference between them. This is cutting-edge development, and you're privy to it!

Also we'll try to get our system integrated with our potential partners, Ubercloud, to deliver a far more seamless and safer upload and browse experience wherever you are in the world. Not only that, but the Ubercloud is a carbon-neutral 'green' server, so something I support in principal.

I'm off to Kenya tomorrow to document plants for a month, but when I get back I'll put the system through it's paces once again, and I'm hoping it'll be ready for public testing!

Landmark CASABIO Upload Achieved with Gerhard Kirsten's Slide Collection of Ericas

noreply@blogger.com (Anonymous) — Sat, 29 Oct 2016 07:10:00 +0000

A landmark for online botany and CASABIO was made yesterday when 1120 images were uploaded to the CASABIO website. These were grouped into 592 species observations. To put this achievement in perspective, iSpot, a government/SANBI backed citizen science site at their peak in 2014 were averaging about 3000 observations of plants per month across South Africa (http://bit.ly/2etFpTx). This is the last time South Africans moderators were able to access statistics for iSpot as the South African node was subsumed into a global framework. This works out to 100 observations per day across South Africa. But elsewhere I've read figures of an average of 200 observations per day being submitted for iSpot - this is probably for all organisms, so let's take that figure.

So in one day using the public CASABIO system, I was able to upload more than twice the number of observations that iSpot receives from tens (hundreds) of contributors across South Africa. But bearing this in mind: with the iSpot system each observation needs to be submitted individually, the photos specified and the information added. The CASABIO system is fundamentally different, with images being uploaded just once - pictures are then grouped into observations of a species at a locality before information on locality, observer/collector details and plant attributes are added. So what is implemented is not just a website, but a considered system for efficiently uploading organisms. Although the uploading took about three hours (and the images were reduced for this test to full-screen size), the entire process of grouping pictures and adding information took about two hours. Sorry for flogging a dying horse, but at an average of five minutes per observation for iSpot, this would have taken 50 hours - and there would have been less information associated.

The Gerhard Kirsten historical Erica collection
This Erica collection (available now on the CASABIO website) comprises many of the slides that went into the book Ericas of South Africa, by Dolf Schumann and Gerhard Kirsten, Fernwood Press.

This book, now out of print, is an incredible testament to the botanizing that went into finding all these Ericas. Featured in the collection are a number of slides of botanists alive and no longer associated with Gerhard in his endevours, like Ted Oliver, Dolf Schumann and Thys de Villiers. There are also triumphant scenes like the finding of the Critically Endangered (Meaning of IUCN Red List Categories used to measure the risk of extinction: http://bit.ly/2eRl0s6) Erica alexandri by Clive McDowell and Ted Oliver. The slides were lovingly dusted off, placed in the carousel and then scanned using the incredible Braun Multimag Slidescan 6000 (review here). Despite beautiful construction, it's a pity that when I was using it, the firmware and software was archaic and inefficient, seemingly from the era of slides itself!

Our scanner that takes 100 slides at a time - the Braun Multimag. Photo from ScanDig website.

Clive McDowell with Erica alexandri (CE)

Ted Oliver with Erica alexandri (CE)

Or a young Thys next to the vulnerable Erica insolitanthera, known only from a single population that is threatened by a pine invasion.

Thys de Villiers with Erica insolitanthera

Talking of pines, Erica caledonica is a vulnerable species known from just three localities in the mountain region of Caledon with probably the worst pine infestation I have ever encountered.

And while we're on about pines, here's a picture of someone with E. lageniformis, an endangered species with a serious invasion of pines in the background. This is only known from a single population on the Onrusrivier mountains.

What you may have noticed is that the pictures are not of optimal quality. Fungus has beset many of the pictures. Despite each slide getting a dust-off with a oil-free air compressor, I've had to throw out many pictures that are totally unusable. So here I show one of the worst hit of those I've chosen to keep: This one of the Vulnerable and decreasing Paranomus longicaulis, a Langeberg endemic.

Paranomus longicaulis (VU)

And my favourite pictures? Those of Erica vallis-aranearum (a strange name - could it be from the latin vallis, a valley and aranearum, to do with spiders or a spiders web - maybe from a place I've never heard of called Spider Valley?) a critically endangered species known from only one population of 15 species in the Kogelberg.

Erica vallis-aranearum (CE)

Next is the red-flowered Erica saxigena, a beautiful species of status Least Concern, and Erica cygnea (cygnea meaning swan), a Rare species.

Erica saxigena

Erica cygnea (R)

And finally, not the best picture due to the mould, but special nonetheless. Erica lageniformis, an endemic known from less than 250 plants from the tiny Onrusrivier mountains and threatened by vineyard expansion. This picture depicts a wonderful interaction between it and a long-tongued fly - almost certainly the pollinator.

Erica lageniformis (CE) and a long-tongued fly

Penultimate consideration
And this rather heartwarming nostalgic yet haunting shot of the last century shot in the Cedarberg or Beaverlac area. Haunting, because like these two people with lives and a history, and who's images were only by chance saved and scanned. The majority of the hundreds of thousands of local slides will be thrown away because people do not know what to do with them. Entire eras wasted, if not reluctantly discarded, then consumed by mould and neglect.

Nostalgic Cedarberg

Going through just a few of these pictures I was struck by how, with the exception of Erica saxigena, nearly every species I decided to showcase was on the red-list of threatened species. This is poignant because a recent study by William Ripple of Oregon State University found that there are over 300 mammal species on the brink of extinction. It really hits home at what a tremendous contribution Gerhard Kirsten made by documenting these plants, and how critical it is to scan in old collections, especially by taxonomists, or in this case a keen ericophile.

Epitaph

The slide-scanning programme has been beset by problems. Firstly SANBI, after messing me around for literally six-months reneged on their contract with CASABIO to sponsor R100 000 for the digitization of 20 000 slides (a bargain!). Then my hard-drive crashed with the contents of thousands of slides - and will be retrieved when I can get the money to have it restored. Finally the Braun slidescanner critically broke. I sent it for repairs at a local shop that charged R700 and never properly fixed it. I then hand-delivered it to Germany where it was taken to Braun. They wanted to charge me further, and upon my appeal based on having paid already and it being a defective unit, they failed to comment further. I believe I will never get the scanner back from Braun. A sad indictment on an company of past renown that should be supporting conservation - not holding it back.

It feels like I'm ending off this post, that should have been a tremendous achievement and contribution to our botanical community - on a negative note. So two positives, I'm going to contact Braun again, show them the post and what has been achieved with their scanner, and try and get them to sponsor another scanner or fix the old one. Secondly, I'm going to try to raise the funds to retrieve the images of thousands of slides on the damaged hard drive. For now browse the Erica collection, then email me on capebio@gmail.com if you want to contribute as I'm off to explore Kenyan mountains tomorrow for a month.

Auf Wiedersehen!

Making Sense of the Golder/Shell EMP Comment Submissions

noreply@blogger.com (Anonymous) — Fri, 12 Feb 2016 13:53:00 +0000

The Golder comment email was sent on the 22nd of January.
Their deadline for submission of comments is 22nd of February. Don't go a day over. I did last time and they wouldn't accept it, despite an hour long phone-call to them. You would think they didn't actually want the comments or reasons why not to frack - it's almost as if they want Shell to go ahead with fracking.

Anyhow - here they are in as practical-a-form as possible.

1) The comment sheet in English due the 22nd of February: http://bit.ly/1QYX9kR
2) Download and view the following set of documents.
These are all from 2011 and the Western Precinct that Shell is planning to frack.
The EMP Exploration Application - Vol 1: http://bit.ly/1Rub3NK
The Soil Report: http://bit.ly/1RuaJ1N
The Groundwater Report: http://bit.ly/20Yl9t2
The Surfacewater Report: http://bit.ly/20Yl9t2
The SW Basin Gas Exploration Project: http://bit.ly/20rpQcB
The Terrestial Ecology Report - Appendix 5: http://bit.ly/23ZWyGE
Noise Technical Report: http://bit.ly/1TbvsXP
Cultural Heritage Technical Report: http://bit.ly/1KezA88
Social Technical Asssessment: http://bit.ly/1WgSeNk
Technical Additions and Changes to the EMP: http://bit.ly/20Yl9t2
Additives/chemicals (Material Safety Data Sheets - MSDS) for use in fracking: http://bit.ly/1ovFPKX

All other documents can be retrieved directly from here: http://bit.ly/1XmkMX5

Including comments and response reports.
I suggest skimming through them as there are some pretty potent comments.
Here is an example of a great report by Bekker Consultants: http://bit.ly/1QaiYe1

For a remarkably informative video on fracking and the hazards associated with it, look at this video by Dr. Colborn called "What You Need to Know About Natural Gas Production": http://bit.ly/1WgX2SQ

For petitions:
An AVAAZ Frack-free petition for Matatiele: http://bit.ly/1TkOMSA

Urgent Anti-Fracking Meeting and Workshop

noreply@blogger.com (Anonymous) — Sun, 31 Jan 2016 01:09:00 +0000

The Karoo

is a beautiful and soulful arid area occupying a vast space in the heart of South Africa. On miraculous summer evenings the clean air rises and aggregates into thunderous clouds that rains down with evocative petrichory, water gathers into streams and rivers and seeps into cracks in the earth to recharge ancient aquifers. The water and rain spreads the dust of koppies and plains that have intermingled since time immemorial with karoo bushes, domestic and wild beasts and a symphony of insects.

A view from near Sutherland looking out over the Moordenaars Karoo, the SW boundary of Shell's claim on our land.

Shell

is the largest of an increasing number of companies that are currently staking claim to enormous tracts of land they plan to transform into a fracked and dystopian landscape. These companies are backed by a corrupt and myopic self-serving president Zuma ^[7]; a colonial legal system that lends rights to companies; and a naive and susceptible government organ, the Department of Mineral Resources that ironically now implements environmental impact assessments AND grants rights to companies over the very soil beneath our feet. Pro-fracking lobbyists poured $726M into the U.S. campaign candidate's coffers between 2001 and 2011 ^[9]. Do not think that our ministers are beyond being enticed.

A juggernaut

is defined as "a literal or metaphorical force or object regarded as unstoppable, that will crush all in its path". These fuel companies are a series of money-centric juggernauts hell-bent on unleashing the climate-changing hydrocarbons that lie dormant and safely locked away beneath the earth. Six of the top ten largest companies of the world are occupied by oil and gas companies ^[2]. At the fourth largest company in the world, Royal Dutch Shell made $421 B (R6 752 235 000 000) in 2015 ^[2] . This is more than South Africa's entire GDP for a year.

Let us not beat around our remaining karoo bushes:

despite what they claim, Shell have not made this money by caring for the earth, the people, or the creatures that inhabit it. Neither have other fossil fuel companies laying stake to other segments of our land that aspire to Shell's lofty profits.

Despite what Shell claims

at fracking meetings and in their website, they have extracted profit at the cost of the earth and the people and are not about to change their business-as-usual model.

Their website states:

"Shell provides energy responsibly, helping the world move towards a future where the energy used causes minimal impact on the planet."; "We are committed to protect [sic] the environment, respect our neighbours, cause no harm to people, and help the world move towards a lower-carbon future"; with similar rhetoric and snake oil under the headings of climate change,

air quality ["Air pollution has been blamed for the presence of toluene and xylene (which can cause central nervous system damage among a host of other ill effects) in the bodies of the majority of residents living near certain shale gas wells in Texas" ^[9]]

and water ("The extra road traffic from fracking is harder to dispute. One Texas study found that each well required almost 600 one-way truck journeys during its construction and operation. A typical drilling site could have up to 1,000 wells) ^[9].

As a botanist,

I am parcticularly concerned by Shell's audacious claim that, "Our projects can affect local natural habitats but we apply stringent mitigation standards."

In their fracking EMP report, they claim that they will take into consideration when selecting sites "Areas with high densities of Red Data or Protected Plant species". Mostly red data species are low in density and scarce in the environment which is frequently why they are on the list in the first place. Secondly they write "SITE NOT to be within any untransformed area of protected habitat". However, in their conclusion, all of the vegetation types are listed as least threatened. And it would need the site to be untransformed AND protected for the rig not to be placed there!

After all this candy-coated greenwashing, they put one final crispy caramel topping: "Red data species encountered during well site preparation are to be removed... and replanted on the site during rehabilitation". Have they any idea how difficult it is to recreate a functioning habitat using red data species. A habitat that represents the culmination of millions of years of habitat structuring, evolutionary sorting and soil development?! Functioning communities of microbes, lichens, mosses and mother plants cannot just be recreated by sticking a few trees back in the soil or spreading a few seed over a wrecked area and watering liberally.

So how trustworthy are Shell

as potential custodians of our land? Shell's website ^[6]is worth a gander: "We are committed to[...] help the world move towards a lower-carbon future". Yet there is a palpable contradiction in their actions as Shell are signatories to a coalition of businesses opposed to greenhouse gas regulations ^[3].

"Shell has one of the worst safety records of any company operating in either the United States or the United Kingdom. A review of 2007 data found that Shell had the highest mortality rate of any large western oil company in the U.S. The company’s North Sea operations have one of the worst safety records of any oil company operating in the UK, violating safety rules 25 times from 2005 to 2011 and spending at least £1 million ($1.5 million) in fines and legal costs". ^[4]

Clearly it's easier and much cheaper to pay reparations and legal costs than to take responsibility. Furthermore:

"Shell has a long history of egregious environmental violations … In 2008 and 2009, the company’s trans-Niger pipeline in Ogoniland, Nigeria, had two breaks that caused approximately 10 million gallons of oil to be spilled – an environmental disaster equivalent to the Exxon Valdez oil spill in 1989. In 2011, Shell’s drilling operation was responsible for the worst underwater oil spill in the UK in a decade, spilling as much as 4,380 barrels of oil into the North Sea over 10 days. Shell failed to report the spill to regulators until two days after it began." ^[4]

I echo the sentiment of a report on drilling in the Arctic that unveils a "disturbing history around the world that ultimately shows that Shell cannot and must not be trusted with our one and only Arctic Ocean" ^[5]. We cannot and must not trust Shell or other petroleum companies to be benefactors of our one and only precious Karoo.

Under fracking

Animals will be displaced by a latticework of metal towers. Plants will be replaced by a network of concrete, roads and pipelines. The symphony of insects drowned out by the rumble of thousands of water bearing trucks and the industrial thud and whine of drilling. Mother earth will be forced open and injected with a cocktail of toxic fluids that will illicit screams of gases and spittle. Eager engineers will claim and bottle her ejected gases and convert it into vitri-oil that will continue to power our infernal combustion engines and consumer lifestyle. This will happen unless we the people of South Africa stand together, united into a glorious chorus of Liliputians against the juggernauts of this world, and demand clean energy generation within South Africa.

The juggernauts are not unstoppable.

In Denmark where "from start to finish the Danish authorities in fact put the facilitation of the corporate fracking venture above democratic and environmental concerns". And "shortly after test drilling had begun in the spring of 2015, a State agency chose to rubber-stamp Total’s illegal use of drilling chemicals instead of shutting down the operation on the grounds of failure to comply with the Environmental Impact Assessment". With challenges similar to that of South Africa, "it was popular resistance that forced Total to scrap its fracking plans in Denmark" ^[9].
In Poland public and political concern was sufficient to prevent Chevron from further fracking operations ^[9].
In Australia in 2010, a 50-day Lock The Gate Alliance blockade by locals cost the fracking firm Metagasco tens of millions of dollars, and precipitated their withdrawal from the region ^[9].
In France, vocal protests forced the government to declare first a moratorium and then a national ban on shale gas extraction ^[9].
In Balcombe, UK, after a series of blockades by activists and numerous arrests, Cuadrilla has, at least temporarily, withdrawn its fracking application ^[9].
In Canada, strong resistance from the Tahltan First Nation and other environmental campaigners has led to the banning of fracking in the Sacred Headwaters area, while Quebec has imposed a moratorium on the fracking ^[9].
In Bulgaria in 2011, a series of unofficial protests, online petitions and large demonstrations, eventually drove home public opinion and an overwhelming parliamentary vote of 166:6 led to a ban on fracking ^[9].

It is time for us as South Africans, proud of our land, our heritage and our people to combine our efforts and self-organise. Come to CASABIO's first public anti-fracking meeting.

About the meeting

Shell have given us just under a month to respond to their Environmental Management Plan . The deadline for comments closes on the 22nd of February. This is our last stand, thus to spread awareness and inform the public we'll be holding our very own public meeting!

As scheduled above, We'll be kicking off at 4 pm with some short anti-fracking documentaries, followed by an overview of fracking by myself and Jonathan Deal of Treasure the Karoo Action Group. At 5.30 pm we'll do a quick introduction followed by talks by our expert panel (see below). This will include a poetic break by Cape Town's own bard, Simric Yarrow, and possibly some music. At 7 pm we'll break up into action groups or work as a group on the comment form. From 8 pm we'll give thanks and then allow an open session for questions, networking and planning of campaigns.

Guest speakers will be:

- Dr. David Fig - published energy activist and is chair of the board of Biowatch South Africa, an NGO concerned with agro-ecology, food sovereignty and biosafety.

- David le Page is leader of both Fossil Free UCT and the fossil fuel divestment movement in South Africa. He'll be focusing on the climate change aspects of fracking.

- Saliem Fakir, head of the Living Planet Unit of WWF has agreed to speak at the meeting and will be on the Q&A panel. Saliem held the position of Associate Director for the Centre for Renewable and Sustainable Energy Studies (University of Stellenbosch).

- Karel Lewy-Philips, an environmental consultant. Karel is intimately versed with fracking having an honours degree focused on shale-gas air quality. He will be co-facilitating the evening's events.

- and myself, Dr. David Gwynne-Evans, botanist, activist, and adventurer.

Funding:

CASABIO is hiring the hall and sound equipment and I'm spending my time co-ordinating and organising the event. We'd also like to print out posters. Please donate on the day in cash and if you can't make it, please donate generously to:

Bank: Capitec
Acc Name: CASABIO
Acc No: 1411486402
Br. No: 470010
Swift code: CABLZAJJ

Reference: Your name and the word NoFrack

or donate Bitcoin to 1JtqmEgQmtvjo8UKWwt2wG8hR1jH5nxYFY

Bitcoin QRCode:

[2] http://bit.ly/23xbRGC
[3] https://www.wikiwand.com/en/Royal_Dutch_Shell
[4] http://www.adn.com/article/20120612/shells-international-record-slammed-opponents-arctic-oil-drilling
[5] http://www.alaskawild.org/wp-content/uploads/shell_final_report.pdf
[6] http://www.shell.com/sustainability/environment.html
[7] http://ewn.co.za/2015/05/29/Nkandla-Nhleko-worried-Zumas-security-at-risk
[8] http://www.commondreams.org/views/2015/11/07/danish-anti-fracking-success-makes-case-constructive-resistance
[9] http://www.utne.com/environment/anti-fracking-protests-zm0z14mazros.aspx

The Deadly Consequences of South Africa's Energy Policy

noreply@blogger.com (Anonymous) — Sun, 23 Feb 2014 10:01:00 +0000

By 2017, it is estimated that 94% of South Africa's energy requirements will come from coal. With a suite of the largest coal-fired plants in the world, South Africa will be contributing to global warming faster than ever before. What is CASABIO's interest in this? Not only is this concerning for the long-term impacts of climate-change on our vegetation, but there are very serious health implications as well. Read about the findings of CASABIO's CEO, The Naked Bloganist (http://bit.ly/OpgwIJ).

Zuma's State of the Nation Speech Concerning

noreply@blogger.com (Anonymous) — Fri, 14 Feb 2014 07:58:00 +0000

Today I posted a critique of Zuma's State of the Nation Speech. At an hour and 27 minutes, you might be forgiven for thinking he was trying to numb his viewers into overlooking the bits of his speech that would negatively affect them. My main concerns are around greasing of the wheels of industry for the mass roll-out of fracking. CASABIO is absolutely against any form of fracking taking place, be it exploration or gas abstraction (http://bit.ly/LZf25Y).
David Gwynne-Evans

Our food security would certainly be threatened by fracking

CASABIO's Environmental Stance Against Fracking

noreply@blogger.com (Anonymous) — Mon, 10 Feb 2014 08:34:00 +0000

I spent the night working on a representative model of what Cape Town would look like if the fracking that is taking place in Dakota, took place in our own city. This has been done to allow you to visualise the scale of a fracking operation in a familiar context. There is another rationale for superimposing well sites over Cape Town. Fracking in rural areas of South Africa won't simply affect the local environment, but as cities are reliant on produce from rural areas, it will affect city-zens too. That Karoo lamb you are so fond of, may just contain a whole lot more endocrine disruptors to the detriment of your health (http://bit.ly/1ffi7X4). And what you save on energy bills thanks to fracking, may just be offset by the termination of farming operations that lead to swollen food prices.

Of course it wouldn't take place in Cape Town, not because it is a populated area mind you, but because we are on deep sands not shale. In America, not even schools and universities (http://bit.ly/1ePn3Hl) have been spared fracking.

CASABIO is strongly opposed to fracking and the thin edge of the wedge - fracking exploration.
Here is the blog: http://bit.ly/1kuRnJr

BOSBABY - Robotic Concept to Save Forests from Illegal Activities

noreply@blogger.com (Anonymous) — Sat, 21 Dec 2013 09:49:00 +0000

CASABIO is seeking collaborators to help save our forests from illegal activities. One of the largest threats to forests across the world is illegal harvesting of timber. Of local concern is the harvesting of bark that slowly starves trees, and allows the ingress of pathogens. Rainforest Connection came up with the concept of using old smartphones to monitor for illicit activity. A great idea, but of limited functionality beyond the loud and characteristic sound of chainsaws. What about people being where they shouldn't or bark stripping?

I believe that the technology is ripe for the distribution of sensors in crime hotspots that detect illegal activity. These sensors are connected to solar-powered wirelessly connected processors that then alert citizens of a potentially illegal signal. If found to be positive, the source can be tracked using a variety of cameras and directional Microflown microphones. The authorities alerted immediately, and the exact position of the crime given to the authorities. Once apprehended, the footage and recorded sounds can be used in court evidence against the perpetrators.

Several technological advances have recently become available that make the BOSBABY concept a possibility. These are highlighted in this document below. Are you good at robotics. Do you care about forest destruction?? How about helping start a kickstarter campaign? Get hold of me at capebio@gmail.com
David Gwynne-Evans

Project SATRN - Public Announcement of Africa's Largest, Most Diverse Nature Reserve

noreply@blogger.com (Anonymous) — Tue, 22 Oct 2013 15:12:00 +0000

Project SATRN is the code-name for Africa's most ambitious, most connected, most diverse and importantly publicly available reserve network to date. Spanning over 362 000km, South Africa has the 18th largest road network in the world. Nearly every road has a strip of land between the roadside and the adjacent property known as a road reserve. This reserve varies from a few metres to over 30m wide, but has been considered on average to exceed 20m on either side of the road (http://bit.ly/1eGrOzW). This makes for a considerable body of potentially conservation worthy vegetation.

How impressive is this road reserve?

South Africa is around 1 600km east to west and the same from the southern most tip of Africa, Cape Agulhas, to the northern-most point of South Africa, with a coastline of 2 798km. Roads skirt most of the coastline, and criss-cross the country up to 2 874m elevation on Sani Pass in the Drakensberg range. This pass continues to an elevation of 3200m, making it the highest road in Africa, and the third highest in the world (http://bit.ly/H86d7P). Major roads and highways alone - those roads connecting cities have been calculated at 15 607km. So if we assume a conservative estimate of 10m on either side of the road, this makes for a total reserve size of 312km². This makes it fifty percent larger than Table Mountain National Park, a World Heritage Site.

New Arctotis species found in road reserve near Bredasdorp during the latest field trip.

A scan of the new Arctotis species

How much diversity can be expected within the reserve?
Its impossible to say, but in spring of 2008, Greg Nicolson, then a botany student at the University of Cape Town, walked the length of the N7 from the Namibian border to Cape Town, a total distance of 684km. He documented some 670 plant species, 62 of these species being of conservation concern. At a visual swath of 5m, that amounts to a total area surveyed of just 3.42km². Plotting this with other Cape reserves, reveals that the N7 road reserve is on a par with the richest of nature reserves, and higher than anything else of its size.

Comparative species diversity - Greg Nicolson's walk down the N7 versus other nature reserves.

So why is this so revealing? Because it shows that road reserves have a considerable diversity, and this is just a single north-south trending road of less than 700km length, surveyed just once, at one time of year, and there are over 300 000km of roads out there. Nicolson's study traversed 24 vegetation types, yet South Africa has over 435 types, most of which are traversed by road reserves. The potential for species diversity in a nationwide road reserve is astounding!

“At a time when worldwide an enormous effort is being made to beautify road verges for locals and tourists, and to improve their nature conservation value by replanting roadsides with indigenous vegetation, it is strange and tragic that natural vegetation should be cleared from road sides in this very arid part of South Africa.” Sue Milton, 2005.

Roadsides are already road reserves, so what more do we need to do?
Unfortunately, road reserves are named as such because they are reserved for the future expansion of the road. They are currently managed with a very heavy hand by the government, municipalities, and SANRAL, the South African National Road Agency. The tools of management currently include spades, brushcutters, tractors, bulldozers, grazers. Lately herbicide is becoming increasingly popular, which has led to a total scorched earth policy. It is said that nature abhors a vacuum, and the immediate response is to fill the void with weeds. Weeds that then lead to an endless cycle of further mismanagement. It is imperative that this mindset is changed at all levels from policy to local municipal level, and this is one of the goals of Project SATRN. We need to start considering how we can conserve the existing biodiversity, and rehabilitate recently destroyed ground.

A team clearing the roadside at Niewoudtville, Bulb Capital of the World

Kilometres of pristine protea-veld cleared and stacked at Niewoudtville

A bulldozer and team clearing natural vegetation at Darling, wildflower show of the Cape.

Dead plants along the road in the Swartland, Caledon, due to herbicide application

What about safety? Don't we need to clear the roadsides to prevent accidents?
As far as I am aware, there has been no study on the link between roadside vegetation and accidents due to wild animals wandering onto the road. Certainly domestic animals wandering onto the road is a considerable issue. Turning abroad for evidence, a study commissioned by the state of Delaware (http://on.fb.me/16sOw9j - warning large file) found that there were a number of advantages to maintaining a more natural state. Besides the obvious, such as the vegetation acting as a buffer in the case of an accident, and screening oncoming headlights, there were two surprising findings. The first is that natural vegetation was seen as at least as desirable as green grass, and more desirable than cleared land. Secondly, that natural vegetation reduces the roadside monotony, and thus keeps drivers alert for longer. As South Africa has the dubious ranking of eighth most fatalities in the world per 100 000 inhabitants (http://bit.ly/1gBt9MG), this is no insignificant factor!

Where to from here? A ten step programme.
1) Publish a paper on the value of road reserves.
2) Create a logo, a campaign, and rally the public to champion the cause.
3) Create a documentary on the issue (currently in negotiation with Sally Smith of Savannah Pictures).
4) Have (another) public workshop inviting relevant and affected parties to discuss the issues.
5) Negotiate and create a master document to manage road reserves.
6) Obtain funding from schools through CASABIO's Bucks 4 Biodiversity programme to fund the project.
7) Go on a UK and Eurotour to raise funds for buying, creating and managing reserves.
8) Change the legislation to conserve road reserves, and setup nature reserves where need the most.
9) Do a national bioblitz weekend in which the public submit pictures of species collected in road reserves to the CASABIO Biodiversity Engine. We can then start to get an idea of how many species are in the road reserves.
10) Initiate research into road reserves, best management practices, and their relation to safety.

What can you do?
Simple, contact me, David Gwynne-Evans on capebio (at) gmail.com, and let's work out how to make this happen.

My Totally Secret Workflow For Dealing with Specimens

noreply@blogger.com (Anonymous) — Wed, 02 Oct 2013 21:44:00 +0000

I'm always searching for the most efficient way to collate data and create labels. Although I aim to produce the most efficient form in the way of the CASABIO Biodiversity Engine, for now I wish to show you my current approach. I have tried many methods in the past, including the excellent, though complex BRAHMS. BRAHMS is however not a system for the technologically challenged.

Todays approach is very straightforward, and totally free. Though there are many steps, these steps are but tools to dealing with your data. Many useful practices could come out of trying these steps.

It rides on several premises:
1) A photo of the subject is desirable, as is providing a link between the photo and the voucher/collection.
1) Digital photos inherently have embedded information that may prove useful: i.e. date, time, associated plants and habitat information.
2) A GPS of the site is not imperative, but its more accurate and efficient than any other readily available form of mapping.
3) That the GPS and the photos can be linked to form georeferenced images.

Step 1, copy files:
You have your photos in a folder on your camera / flash stick. Don't move, but copy them to your hard drive (this creates a temporary backup).

Step 2, download GPS co-ordinates:
Plug your GPS into your computer (using the attached cable), and download the points using EASYGPS freeware. Once it has downloaded, go to File > Save As, and save your points as a GPX file. It should look something like the screenshot below.

EASYGPS screenshot

Step 3, synchronise GPS co-ordinates and images: (If you don't have or intend using a GPS, you can skip to step 4).
Open GeoSetter, and navigate to your photographic folder. Go into the folder and highlight the relevant images so that they turn blue. You can probably use Ctrl+a to select the entire folders contents. Once one or more photos are highlighted, a mapping icon will become available in the toolbar. Click this mapping icon, and a dialog will magically appear.

Geosetter in action

Step 3b: Click synchronise with data file, and select the file you created in EASYGPS. Click either assign directly (ideal) or if your batteries ran out or you forgot to mark a point, select interpolate time.

As you are a good dog you have no doubt synchronised your camera with your GPS. If not the time adjustment dialog is just for you. Take a photo of your GPS time, and then you can compare the time on the GPS and the camera, and dial in the appropriate adjustment. Important note: I spent ages trying to get the time right, thinking that I was edging closer to the correct time. However, with 'Add offset values to date taken' option, I was incrementally adding to my previous adjustment, and my frustration was incrementally rising.

Step 3c: Once synchronised, plot your photos using the "map to google earth" button, using the thumbnails to give you an idea of what was taken where. If its out, consider adjusting the synchronisation time.

Step 3d: Final step with Geosetter - click the save button. This commits the georeferencing changes to the files. It takes a few minutes if you have several hundred images.

Step X (the mystery step):
Now that you have your files georeferenced. Its time to rename them with a unique reference number. This means that if someone sees a picture of yours, or a reference to a picture, you can find it immediately using SEARCH EVERYTHING without scratching around to find which IMG0034 it is. Search everything is INCREDIBLE for finding files, and beats the pants off anything else I've found. It can even search external hard drives within seconds so long as they are NTFS formatted. In the screenshot below, it found 17,000 objects within 2 seconds!

Step 4, rename files:
To do this naming I use the daunting looking Rename Master. You may have to google to find a download link. Although i usually use Flash Renamer to search and replace the previous file number with a new unique number, while keeping any plant names in place, as it is not free I shall be foregoing the replacement option, and using Rename Master.

Step 4, Rename Master:
Open Rename Master, navigate using the central frame to your image folder. Below the right panel, select *.jpg to only renumber the image files. Click on the files tab at the bottom of the right hand window, as you probably don't want to rename the folders as well. Now, as the screenshot shows, click on the folder tools button, and select 'subfolder scan' (Ctrl+F5). This will generate a list of all files in your image directory.

Step 4b: Set your counter to your last number using the counter tab.

Step 4c: Now go to the renaming script tab, and select "Add to beginning / ending". Add your personal identifier, in my case DGE for David Gwynne-Evans, add a zero for good measure (for when you get in your millions ;-P), and then ?02? or ?06?. These are variable identifiers, and relate to the counter number.
Now you're ready to click the RENAME button! Remember to use the undo button next to it if you mess up.

Step 5, append a name to each plant you want to make a label for:
Either: Use windows explorer, highlight the one representative picture of each species and give it a name and or collecting number by pressing F2.
or: Browse through the pictures using Irfanview or Faststone Image Viewer, and repeat the process using F2.
Note, you probably don't ever want to re-use the Windows multi-rename feature, as it removes your unique photo identifier. I will give other options at the end.

Step 5, copy file names and exif info to excel:
Use BR's Exif Extractor: Tick the options: Date, Time, Latitude, Longitude, Altitude, and then click on the EXTRACT button. Save it (maybe in the photo directory).
or open Total Commander and Mark > Copy the selected names to the clipboard, as shown in the screenshot below. This is the inferior option as it leaves out the latidude, longitude and altitude.

Step 6, create labels in Excel:
Now open the saved BR Exif Extractor .CSV file in Excel (or use Open Office as we're going freeware).
You will be confronted by something like this:

Step 6b: What are those hashes?? Fear not, this shows that the contents are fuller than the cell. Moved to the line between the column headers (between column A and B in this case), and the cursor changes. Double click, and the column width will match the width of the contents.

But now we have a problem, the photo number and plant name are in one column.
We are going to use the text to columns tool and the data tab to solve this. This splits up the contents of the cell across adjacent cells. However it replaces adjacent cells, so we want this to be a terminal column for this process. Highlight the entire column by clicking on the column name. Right click and select 'cut' or ctrl+x. Highlight the entire fresh end column, and now right click and select 'paste' or ctrl+v.

Step 6c: Now again highlight the offending end column, and click on Text to Columns. Select delimited, and then tick space. Now click finish.
Now you should have your beautiful cell spread across a whole bunch of cells. What a mess!

Step 6d: But this is where we take advantage of the mess. We only want to see named cells, not every photo represented. So highlight the column, and click on the filter button. Now shimmy to the end of the list, and unselect 'blanks'. This will remove from view all blank cells, in other files that haven't been named.
You may have to at this point select all cells (click on the top-left corner cell), and copy and paste to a new sheet. This will remove all the rows hidden by the filter but are still lurking in the background.

Step 6e: Cell trickery time!
Go to the top of an empty column and type in the following: =G3&" "&H3&a" "&I3&" "&J3
Where G3 refers to the cell reference, the ampersand (&) allows you to append the next section, either another cell or text. In my case I am inserting a space between the text by enclosing a space between inverted commas. Don't forget it will throw up an error unless there is an ampersand between each term.
When you press enter your cells will magically be merged into one. Two problems. It is only in one cell and it is still a formula, not actual text. So if you move it around the contents will change.

Step 6f: Click on the cell with the formula in, hover over the bottom right corner of the box. It will turn to a cross. Now holding down the left button, drag it down to the bottom of your contents, and the formula will suitably replicate itself across the length of the page.

Step 6g: But it is still a formula. Now select the column with the formula. Copy, select the first cell of a new clean column > right click > paste as > values (a 123 button in excel). Voila, it is now no longer a formula but the actual text.

Final step! Neatening our labels.
Step 7: We don't want long thin labels, we want them thick and stubby, yes?
So now you're going to repeat Step 6e, but this time selecting the lat, long, alt, cells, putting in a "E; ", "S; " and "m. ". Note the space after each punctiation for neatness so they are not on top of each other.
Similarly you can do "Image no. " followed by '&' and the cell reference. But what if you want long words on separate lines?? In place of a cell reference write char(10). char(10) is a carriage return that tells the cell to put the words on subsequent lines. However you have to ensure that "wrap text" is enabled. To do this, right click on the column header > Format Cells and in the alignment tab tick "wrap text". We also don't want .jpg or other extensions so select the entire spreadsheet (click on top left corner box), press ctrl+h, and in the replace box type ".jpg" (without inverted commas) and leave the "with" box blank.
Also, you may wish to space out your rows. Select the entire spreadsheet, click and hold between the row identifiers till the desired width is attained.
Ta daah!

Please let me know if you've learned any tips, or if you have any better methods or useful tools. I'm always keen to try new things. This is just what currently works for me. My apologies if its poorly written, but its late and I've still gotto pack for Walking The Daisies followed by a week long Donkey Trail in the Karoo.
Email me, David on capebio at gmail.com

Auction of New Species Ends at 5PM GMT and New Analysis of Biodiversity Reveals Astounding Biodiversity in Road Reserves!

noreply@blogger.com (Anonymous) — Sat, 07 Sep 2013 05:34:00 +0000

Today is the last day of the auction of the right to name a new species of dolls rose: http://bit.ly/154fq9B. Billed as being the most romantic doll's rose on account of its heavenly perfume, flame-coloured petals and heart shaped leaves. The name of an iris from the another part of South Africa raised £29,200 on the same auction site last year.

I would be delighted if it reaches £10,000. That is the sort of money I can do something with. I am auctioning the species, along with a unique pendant cast by acclaimed craftsmen, Nic Bladen, to raise funds to conserve South Africa's unique natural heritage.

One of the greatest threats to biodiversity is the senseless and ongoing destruction of road reserves. Today I present the finished analysis of biodiversity, and the results are astounding! The graph below, depicting area compared with species diversity, shows that road reserves are at least as diverse as the richest of South Africa's nature reserves. Given that they also sample mainly lowland flora, that same flora that is greatly threatened by agriculture and development, conserving this extensive habitat is incredibly important.

The blue dots are species area plots extracted from Cowling & Lombard (2002). The green and red dots are the values of species diversities within nature reserves, around South Africa, and within the Cape Metropolitan Area (Jennings and Branch, 2010) respectively. The black dot is the result of a study by Greg Nicolson (Nicolson, 2010). In 2008 Nicolson walked from Namibia to Cape Town along the road reserve, photographing every species he felt he could identify. He found 670 species in 650km. The total he surveyed is a mere 3.6 km², yet he found 60 species of conservation concern. Considering that Greg surveyed this road only once, compared with the thorough sampling of the other studies plotted on the graph, the actual road reserve species count should really be far higher.

The most extraordinary fact though, is that at the 18th longest road network in the world, South Africa has more than 320,000 km of roads. Just the paved roads alone, accounting for 73,000km, translate to a conservative estimate of more than 1,400 km² of road reserve. If you add up all sixteen nature reserves of Cape Town and its surrounds, including the richest reserves in South Africa, and multiply that area by four, you still haven't reached the area to be found in road reserves!

Despite being the richest, most diverse, and most extensive of our biological assets, they remain unprotected. If the road reserve were declared a nature reserve, it would be the third biggest nature reserve in South Africa, the most diverse in the world by a long way, and the most accessible reserve in the world!

All road reserves are subject to protection from the Biodiversity Act (No. 10 of 2004) which supports the conservation of plant and animal biodiversity, including the soil and water upon which it depends. Much of the road reserve additionally falls within the Cape Floristic Region, a region declared a UNESCO World Heritage Site due to its unique and threatened biodiversity. Even the constitution, section 24 states that everyone has the right to have the environment protected for the benefit of present and future generations, through reasonable legislative and other measures that prevent pollution and ecological degradation. Yet despite this, archaic road maintenance legislation and colonial mindsets continue to thoughtlessly eradicate vegetation, and destroy habitats in our roadside. Habitats not only for plants, but animals including birds. This makes the road reserves a national asset, and a tourism drawcard. Yet roads authorities are treating them like an English country meadow.

Its time to conserve our national natural heritage. I, David Gwynne-Evans, CEO of CASABIO.org am committed to that cause. Please empower me to make a protect our flora and fauna by bidding on todays auction: http://bit.ly/154fq9B or donating directly to the NGO: http://bit.ly/175oVpC.

References:

Cowling, R.M. and Lombard, A.T. 2002. Heterogeneity, speciation/extinction history and climate: explaining regional plant diversity patterns in the Cape Floristic Region. Diversity and Distributions, 8, 163-179.

Jennings, G and Branch, M. 2010. City of Cape Town Nature Reserves. 2nd edition. City of Cape Town Report. ISBN 978-0-9802784-4-6.

Nicolson, G. 2010. Road reserves as conservation assets: exploring the species of conservation concern and the ecological condition of the N7 road reserve. Masters thesis, University of Cape Town.

Spring fundraising drive announced - Auction of new species and new roadshow.

noreply@blogger.com (Anonymous) — Tue, 20 Aug 2013 07:48:00 +0000

Preparations are underway for a grand spring fundraising drive to fund CASABIO. First we have an online auction of a new species, the rights to name the species going to the highest bidder. Flowers of the species were cast using acclaimed artist and silversmith, Nic Bladen’s unique process. This is one of his most delicate pieces ever made, and around 100 flowers were cast in order to obtain just this one flower. This is the first time a new species has been cast in silver. Bid online at http://bit.ly/154fq9B.

View more information and pictures of this new species at http://thenakedbloganist.blogspot.com/
Or donate directly into the NGO bank account on: http://bit.ly/175oVpC

Secondly, we announce a new roadshow by botanist and director of CASABIO, David Gwynne Evans. Tonight (6th Sept) is the final lecture and showcase of astounding plants that he has encountered in his 17 years as a botanist. These lectures have taken place around Cape Town, and coincide with the first week of spring. Tickets for this fundraiser are free but seats are limited.

University of Cape Town, Zoology LT1: Friday 6th, 7-8.30pm. Book at http://bit.ly/147MHgG

Or contact David on capebio@gmail.com or 072 368 9244

Finally we have an Avaaz Petition that will be handed to Parliament on Monday the 9th of September. It currently (06 Sept) stands at 430 signatories. Please speak up for those millions of plants without a voice who are getting mown for no good reason thoughout the country. http://bit.ly/16QQVJt

New invasive for Newlands Forest, the cherry guava, discovered and mapped

noreply@blogger.com (Anonymous) — Wed, 19 Jun 2013 06:38:00 +0000

A bright and tasty invasive has remained under the radar alongside the most commonly used route at Newlands Forest. A population of Psidium cattleianum, the cherry guava, has been allowed to proliferate at the expense of indigenous flora. Weighing in at number 76 on 100 of the World's Worst Invasive Alien Species, the cherry guava is a formidable opponent of our indigenous counterparts. Growing up to 6m tall, its tasty fruit are spread by birds, pigs, and possibly our very own resident porcupines. Once established, it poisons surrounding plants, and then sends out underground runners which emerge a short distance away to totally inundate an area. Numerous areas have been devastated by this invasive, particularly Mauritius and Hawaii.

James Deacon tagging a cherry guava by night.

An unripe fruit

Scouring the site of the invasion, James Deacon and I mapped over 600 plants with a high-cover GPS unit. We found that the population covers over 84 000 square metres, mainly under pine plantations. Three major stands were found within this population, with some thick trees being in excess of 6m tall. This species poses a major threat to the forest, especially if it gets into the indigenous parts.

James Deacon mapping a large population of over 20 mature plants.

Map showing all known points of P. cattleianum within Newlands Forest, Cape Town.

What can you do? If you find any trees without a pink tag, remember the locality, and email me on capebio@gmail.com.

Here is our preliminary report on the invasion.

My Big Fat Bookscanning Ordeal!

noreply@blogger.com (Anonymous) — Sun, 09 Jun 2013 08:40:00 +0000

Here is a continuation of my previous blogpost, Virgin DIYBookscanner Gets His First Handson Experience.

Well, I had all the tools at my disposal: Irfanview, Faststone; Scan Tailor, Abbyy Finereader 11. So why did it take me a whole afternoon to setup the cameras, and three flipping hours to process a 47 page book?

Having tested CHDK on my first Canon Powershot A4000IS camera, yesterday I purchased my second. It was a remarkable deal for R1000, as it came with an 8Gb card. However, it turns out it is too new! Its firmware is ver. 102a, and thus is not supported by CHDK yet :(

So next I borrowed a friends Powershot A550. Before I could even get started though, my card-reader broke as I pulled out the USB cable. Uploading a copy of CHDK firmware to the camera without it proved a herculean task. STICK is great for determining the correct CHDK version, and downloading it onto your flash stick. STICK worked fine on my desktop, but I now had no way to get STICK to pick up my SD card. Connecting the USB to the camera (after having to charge the battery) didn't work, as it seems almost impossible to copy the files TO these cameras. Why can't they just have an option to show them as a drive instead of a camera?? Anyhow, I put STICK onto my laptop that has a flashcard reader, but the stickx.cmd file just kept recursively opening up the STICK jar file. Grrr! Eventually, I just copied the CHDK files downloaded by STICK (into a subdirectory within stick) directly onto the flash stick, and from there to my SD card. I pressed the play button on the camera followed by a few buttons that culminated in the print button being the magic one. Miraculously the CHDK alt menu appeared. The alt menu shows that CHDK is running, so woohoo!! After selecting the correct script for a remote trigger, and setting the remote trigger to one push and normal mode, I was ready to proceed.

I lopped off the USB end of a micro-usb cable, selected the red and black wires, and connected up the trigger and battery to both cameras. The trigger worked perfectly, first time. After taking a series of pictures, I endeavored to process the pictures into a single PDF.

Herewith follows MY BIG FAT SOFTWARE ORDEAL!

Firstly, this is what the raw Jpeg (if that makes sense) output looks like from the A4000IS:

Output from A4000IS.

As you can tell, the picture is firstly offset. Its probably fine for A4 sized book, but I need to be able to adjust the angle for A5 sized books. Its also a little too close to cutting off the margin for my liking. The photo is slightly overexposed and lacking in contrast. This may well be the result of my 6mm thick safety glass. Recommendations suggest 3 or 4mm. There's also a bit of reflection above, which may require the duplication and offset of the lightsource.

Irfanview has always been my first line of photographic recourse. I played with the settings, managing to quickly figure out the batch rename console. I've never needed to batch crop before, so I figured that I would leave that up to Scantailor.

I opened up Scantailor, that soon greeted me with a 'fix DPI' dialog. I put in some numbers which resulted in my pages getting all vertically compressed. Next attempt with 300x300dpi at least kept the pages in proportion. Rotating the pages worked perfectly. Deskew automatically skewed my pages, so I unskewed those pages. Select content did some horrible stuff. Finally margins worked really well, but then the rest did such a hash job, that I abandoned Scan Tailor altogether.

I then tried colour corrections. Faststone has a change levels function which did a great job making the blacks blacker. But Faststone does not allow for applying change levels to batches. I therefore returned to Irfanview which doesn't do change levels but does allow one to batch contrast and to change gamma. The latter I found gave a passable result when adjusted to 0.5. I then explored the use of batch crop which proved simple:

Page adjusted by Irfanview with a gamma setting of 0.5.

How to batch crop in Irfanview (skip paragraph if this is not pertinent to you).
Select a photo (press enter to get out of full-screen mode, as that mode won't allow you to edit the picture), drag a border around your page using the mouse cursor. Then write down the values it gives you above: something like 123,456;1234x5678. The first two numbers are the co-ordinates for the top corner, and the second two numbers the dimensions to be cropped to. Go to File > batch-conversion. Add files from the one camera only (as the page will be positioned differently on the other camera), and make sure you select a different output directory. Now select Advanced, and put those values into the Crop dialog at the top. You can rotate the pages and apply corrections at the same time if you like.

Irfanview batch crop settings. Newbies! Note the use location of the advanced button and the use current directory button.

After combining the files into a single directory, I then opened up the files in Abbyy Finereader. Be patient as it imports the files, analyses them, and reads them. It never picked up the text captions in the pictures, so I had to manually select these, eventually figuring out I had to re-read each page I had reannotated. I then spent some time re-ordering the pages, clunkily dragging thumbnails around in Abbyy - a horrible process. Penultimately, I exported the result as a PDF, five times! Each time it would chop off a picture and resize the pages. Finally, I begrudgingly accepted an output with the PDF settings use original source that at least showed me the full pictures. However it made the pictures all different sizes, more than two times the dimensions of the text pages. WTF??

So I concede defeat for now. I'll have to work on my processing workflow before squeezing an agreeable product from this suite of fine software. Here's the final unsatisfactory result: Some South African Edible Fungi by Stephens and Kidd.

From a hardware side, I'm reasonably happy with the output, especially considering that I was using two different cameras. The only thing I would change, is having two offset lights instead of the single central light that gave slight reflections. Also my 5mm safety glass is too thick. Otherwise I'm happy with the setup, and now just needing to work on my workflow. Will keep you posted!

Virgin DIYBookscanner Gets His First Handson Experience

noreply@blogger.com (Anonymous) — Sun, 09 Jun 2013 08:38:00 +0000

Finally, all the functional elements of the DIYBookscanner are in place, and at midnight I finally got to test out the scanner. It took me five minutes to photograph 47 pages which works out at 950 pages an hour! The trigger, focus, and capture was close to instantaneous, so the main hurdle was certainly the speed at which I could turn the pages. A few times the pages got stuck together costing me precious seconds, so I feel this was a very reasonable first attempt. Below are the pictures of Skelly in all her naked, wiry glory. Skelly is named after Sceletium, which is a local succulent plant that the aboriginal people, the San, use to provide stamina and speed. So I think its an appropriate name for the First African DIYBookscanner.

CASABIO DIYBookscanner front view

Side View showing the Edible Fungi book in place and camera on.

Here is the PDF result of the book I scanned: Some South African Edible Fungi by Stephens & Kidd. An appropriate choice given that its mushroom harvesting time in Cape Town!

Processing the books I found to be a ghastly affair! Theoretically, all I needed to do was
1) Copy the files to separate directories.
2) Batch rename the files with page numbers (odd and even pages alternately for the two directories).
3) Crop the images to the pages.
4) Rotate, OCR, and concatenate the pages in order of page number.
EASY PEASY LEMON SQUEEZY I hear you say?!

Read the details at MY BIG FAT BOOKSCANNING ORDEAL!

DIY Bookscanner framework complete, remote trigger tested.

noreply@blogger.com (Anonymous) — Wed, 05 Jun 2013 12:54:00 +0000

Last night was a milestone in the DIY Bookscanner creation. The completion and painting of the bookscanner framework. The remote trigger mechanism for the camera was also tested.
Four items remain before the bookscanner is complete and ready to image books and magazines:

1) Custom paint job.
1) A second A4000IS camera (R1200)
2) Lights (2xR300)
3) Scripting for rapid shooting of pages.

Contributors so far:
Callan Cohen of Birding Africa - materials and cutting;
Fran Siebrits and Nathalie Koenig of the ScottishRum Bar - A4000IS camera;
Bernard Lembeck and Sven Kroger of ProNature for the natural paints for customising the scanner.
If you wish to contribute or buy the camera or lights, please contact me on capebio (at) gmail.com

African DIY book scanner next to Canus africanus
ProNature paints used to depict first known human art,
artefact found at Blombos in Africa... humble beginnings

First test page from the book scanner.
No lighting installed yet.

Do The Math screening, Cape Town

noreply@blogger.com (Anonymous) — Thu, 30 May 2013 10:38:00 +0000

Robert Zipplies, volunteer coordinator for 350.org, hosted the screening of Do The Math in Cape Town last night. After an introduction to the ethos behind 350.org, Zipplies pointed out that we have now reached 400 ppm CO2 in the atmosphere for the first time in 3-5 million years. Despite recent attempts to ameliorate carbon emissions, our unimpeded "progress" of 2ppm increase per year have been increasing at the worst possible climate change scenario.

Do The Math Screening, Cape Town, 29 May 2013

Do The Math is in enlightening movie narrated by an engaging speaker, Bill McKibben. His prescient book "The End of Nature" written in 1989 reveals the perils of carbon dioxide emissions not be curtailed. His latest movie exposes the dire impacts that global warming is having around the world; the role of oil companies in promoting their agenda of making insane amounts of profit; and reveals that oil reserves stockpiled for the future amount to more than five times what the planet can handle.

We are absolutely being held hostage by the oil companies who have systematically undermined any attempt to free ourselves of the carbon-based economy. It is our imperative that we find solutions now for the future of our offspring, and for the survival of life as we know it. The acidity of our oceans has risen by 30%, leading to massive coral bleaching and the ice caps have shrunk by more than half since our forefathers walked this earth. What is really frightening is that the change in ice is reflecting less radiation back to space leading to increased insolation being converted into heat, and that the ice is effectively acting as a massive ice block, absorbing heat as it is transformed into water. We've been living on borrowed time, and when the caps go, the resulting heating to the rest of our planet is currently unimaginable! It is our responsibility, and the time is now to start making a concerted effort to spread awareness of the vast and grave impact climate change will, and is having on our planet.

Watch: http://www.youtube.com/watch?v=2stHuRMMxog to see how global temperatures have changed in a handful of years.

CASABIO is committed to documentating plants and animals from around South Africa. This will provide very necessary baseline localities for organisms which will allow for comparisons with future distributions. Documenting population sizes will allow us to identify dwindling species. Changing elevations of the boundaries of populations will allow us to assess the impacts of climatic warming.

Contact me on capebio (at) gmail.com to get involved with organising climate change action within Cape Town.

Scottish Rumbar raises R1000 for DIY Book Scanning camera

noreply@blogger.com (Anonymous) — Thu, 30 May 2013 09:39:00 +0000

I wish to thank the two queens of the Scottish Rumbar, Fran Siebrits and Natalie Koenig for their fundraising evening the other night. Their event raised R1000 “for a good cause”, the social events alternating between social and environmental causes. Their fundraising enabled CASABIO to buy a digital camera for their DIY book scanner.

Being a Canon camera, we can now test the CHDK functionality of the camera and its compatibility with the book scanning process. CHDK is a way of controlling most CANON cameras via a script and a simple and inexpensive USB trigger. The A4000IS was chosen for its DIGIC4 processor that enables rapid focus times, snappy processing, and lower noise. The results will be posted shortly.

Media and Africa's First DIY Bookscanner?

noreply@blogger.com (Anonymous) — Wed, 13 Mar 2013 14:44:00 +0000

This Friday at 12:10pm GMT +2 I will be doing an interview with Busisiwe Mtabane for local talk station, Bush Radio. This will be for her show, Sakhisizwe: Building The Nation, as part of the Arts, culture & Environment slot.

I recently condensed and revealed the innovation of CASABIO at the Pecha Kucha 10th anniversary. This is a fun and informative series in the 20x20 format, i.e. 20 slides, that change every 20 seconds. The talk was well-received, and several interesting and promising contacts were made.

In final news, construction has begun upon what could be Africa's first DIY book scanner?! After some four months of trying to get the plywood CNC milled, the job was finally completed... on one side. I had to take it to Ulli Mutzeck at the UCT workshop who did a phenomenal job, precisely drilling out the reverse side. Its gearing up to be a tremendously collaborative effort, with Callan Cohen of Birding Africa contributing the cameras, and Ryan Bass implementing an LED lighting solution. I will keep you posted on bookscanner progress.

CASABIO and Vogelgat NR Start Funding Campaign

noreply@blogger.com (Anonymous) — Wed, 13 Feb 2013 16:44:00 +0000

Today CASABIO launched a crowdsourcing campaign to get funds to document the flora and fauna at Vogelgat Nature Reserve. CASABIO CEO, David Gwynne-Evans arrived in January to find the place burnt down with stumps still smouldering. Inspired by the opportunity to document the post-fire regrowth and flowering he, together with reserve manager, Giorgio Lombardi, put the video together that they hope will garner enough funds to fund a student for at least a year.
This student will use the CASABIO Biodiversity Engine to document all flowering species and their localities. The student will also film interesting interactions.
Donors will receive a digital field guide to the flora of Vogelgat.
View the campaign, and fund it at http://igg.me/at/vogelgat-fire/x/2332447

CASABIO now recruiting!

noreply@blogger.com (Anonymous) — Wed, 06 Feb 2013 15:28:00 +0000

CASABIO has chosen Benevola to recruit volunteers. Benevola is a fledgling organisation that allows organisations to post requests for volunteers. The volunteers and organisation then connect and decide whether they want to work together. Once the transaction is done, volunteers then pay a nominal fee (R250 in South Africa) per quarter to remain a Benevola volunteer. Volunteering is a great way to gain experience in a chosen field, and for those just starting out from school, a really important and painless way to find out whether its what you really want to commit your life to. As many jobs require prior experience, in a congested field like biology, volunteering is an ideal means to learn and contribute to a cause at the same time.

Join our ranks via http://benevola.net/projects/172-explore-the-cape-and-document-biodiversity#.URJyih328Z-

CASABIO's Software Developer Speaks at TEDx

noreply@blogger.com (Anonymous) — Sat, 17 Nov 2012 06:06:00 +0000

Tresor Mvumbi spoke about the future role of CASABIO within Cape Town at TEDx City 2.0.
This is a special two minute, six slide bite-size chunk. Unfortunately the footage from the one camera was lost. So view it with eyes wide shut :)

Tresor Mvumbi speaking at TEDx 2012

Link: http://youtu.be/qdH_SEC1aDw

noreply@blogger.com (Anonymous) — Mon, 15 Oct 2012 23:24:00 +0000

UCT Monday Paper explains software
Thanks to Yusuf Omar for running this article at the University of Cape Town. It gives a reasonable overview of the software.
http://www.uct.ac.za/print/mondaypaper/?id=9330