Friday, 8 January 2016

Help us to Help You

GB/3D results page for Didymograptus murchisoni geminus (Hisinger)

The GB/3D team are busy exploring various ways of financing the next stage of the project – the inclusion of figured and cited specimens and the British Geological Survey “Type & Stratigraphic Fossil Collection” – a collection of a quarter of a million macrofossils that illustrates most of the invertebrate and plant species and subspecies found in the UK, plus a good selection of vertebrates. To build the case for funding, we need to document the impact that the project is already having, and to do this, we need your help.

Didymograptus murchisoni geminus (Hisinger)

If you have used any of the GB/3D resources, please consider writing your project up as a guest blog for this site. It is a good opportunity to include links to your own sites, plus any papers or articles you may have written. If you would like to volunteer a guest blog, or simply offer an email of support, please use the Email Dr Michael Howe facility on my BGS web page: . I look forward to hearing from you.

Wednesday, 23 December 2015

Resurrecting of the Unfortunate Dragon - a plesiosaur fossil destroyed in WW2

FIGURE 1. Historical photograph of the skeleton of the holotype (BRSMG Cb 2335) of Atychodracon megacephalus (Stutchbury, 1846). Photograph taken from glass plate negative in the Bristol City Museum & Art Gallery, originally published by Swinton (1948). Bristol City Museum & Art Gallery, reproduced with permission. Length of skeleton = 4960 mm
Plesiosaurs are an extinct group of Mesozoic marine reptiles. Their fossil record ranges from the latest Triassic (approx. 200 million years ago) to the latest Cretaceous (approx. 65 million years ago), and they have a short body with four flippers, a long neck, and a head full of sharp teeth. They are unlike any modern day animal and were once described as looking like a snake threaded through the body of a turtle.

The five metre-long holotype specimen of Plesiosaurus megacephalus, from the Jurassic of Street-on-the-Fosse, Somerset, was one of several plesiosaur specimens once displayed in the Bristol City Museum and Art Gallery during the first half of the 20th Century. As one of the earliest plesiosaurs to evolve it is an important species for understanding the early history of the group. Sadly, the fossil skeleton was destroyed along with many other specimens, when the museum was struck by a bomb during the Second World War. This destroyed fossil material is sometimes referred to as the ghost collection.

All was not lost, however. Moulds of some of the fossils had been taken before the war. In the case of Plesiosaurus megacephalus, multiple casts of its skull and forelimb were produced prior to its destruction, and these had been deposited in the collections of several other museums (British Geological Survey, Keyworth; Natural History Museum, London; Trinity College, Dublin).

These casts recently provided a valuable resource for Dr Adam Smith, Curator of Natural Sciences and a palaeontologist at the Nottingham Natural History Museum, Wollaton Hall. Smith used the casts to conduct a research project on the Plesiosaurus megacephalus, published this April in the open access journal Palaeontologia Electronica (18.1.20A p.1-19). The study was facilitated by The Bristol Museum and Art Gallery, who provided historical photographs of the ghost collection from their archives. These show how the fossil skeletons appeared before they were destroyed (Figure 1). To assist with the project, the British Geological Survey produced three-dimensional digital laser scans of the casts as part of their JISC-funded GB3D fossil types online project. The resulting virtual models can be rotated and studied on a computer screen, and even printed with a 3D printer (Figure 2, 3).
FIGURE 2. Plaster cast (BGS GSM 118410) of the holotype (BRSMG Cb 2335) skull of Atychodracon megacephalus (Stutchbury, 1846) in ventral (palatal) view. Three dimensional scan with texture (colour) removed. Scale bar = 100 mm.

The scientific study shows that ‘Plesiosaurus’ megacephalus is distinct from all other plesiosaurs, including Plesiosaurus, and so it is given a new name, Atychodracon, meaning ’Unfortunate Dragon’. This is in recognition of the unfortunate destruction of the original fossil, as well as the colloquial name ‘Sea Dragon’, sometimes applied to extinct swimming reptiles. The project also shows that fossil casts, and 3D laser scans, provide valuable data for palaeontologists - they can be described, measured, and coded into analyses. When the original fossil material has been lost, damaged or destroyed, the scientific value of casts increases even further. This study is the first publication to make use of the publicly available repository of 3D laser scans provided by the BGS. The Bristol Museum and Art Gallery is now investigating the possibility of using physical representations of their ‘ghost collection’ in future exhibitions, to bring long lost fossils such as Atychodracon ‘back to life’.

FIGURE 3. Plaster cast (BGS GSM 118410) of the ventral surface of the right forelimb of Atychodracon megacephalus (Stutchbury, 1846) (BRSMG Cb 2335).
Guest blog written by Adam Smith

GB/3D Type Fossils Online – Highlights of 2015

The International Data Rescue Award in the Geosciences trophy 
awarded to the GB/3D British Type Macrofossils online project, April 2015

As 2015 draws towards its close, it is a time for reflection on progress and highlights for the year. Work continues on adding and updating entries. We have, for example, a number of new images to add to existing entries. We are also keen to discuss with the curators of collections not yet included how we can add their material. Provided the data is in the correct format, adding it is fairly simple and quick. We are also looking at ways to finance extending the database to include figured and cited specimens and other good representative material to make the database more comprehensive. Crowdfunding is one method under consideration. 

Graph showing monthly visits to the GB/3D website for the last two years

One highlight has been the growth through the year in visits to the GB/3D website. After a high of 72,000 visits during September 2013, immediately after the launch, monthly visits declined to 2,500 a year ago – but they have been rising steadily through 2015 and have now been over 4,000 for several months. Such behaviour is well documented in project cycles – we have been through the peak of “euphoria” and the trough of “despondency” and are hopefully entering a prolonged period of “optimism”.

Another highlight has been the coining of the first GB/3D DOIs for three casts of sections of 'Plesiosaurus' megacephalus in a recent Palaeontologica Electronica paper by Adam S. Smith - see . Adam has prepared a guest blog on the subject.

The main highlight of the year was the receipt of the International Data Rescue Award in the Geosciences, presented at EGU in Vienna, in April. 

The award was created to improve the prospects for preservation and access of research data, particularly of dark data, and to share the varied ways that these data are being processed, stored, and used. Lack of access may be due to the nature of the formatting (e.g., analogue data, magnetic tapes that lack format description) or the nature of the data curation and/or organization (e.g., no formal database repository, no backup), such that those data cannot be shared. Consequently, the progress of research suffers unless extra steps are taken to recover the data or transform them to a dependable electronic media. 

In our case, the award marked the provision of a single database to locate type material in numerous museum collections, and to facilitate access by providing high resolution images and stereo-anaglyphs, and in many cases, 3d digital models. 

Mike  Howe (National Geological Repository, British Geological Survey) – centre -   receiving the award from  Kerstin Lehnert, (Director, IEDA) and Dan Lovegrove, ( Elsevier).

GB3D winner.tif

Thursday, 30 April 2015

Exhibition of GB/3D Type Fossils project images in Athens, Greece (4-5 April 2015)

Guest blog by Panagiotis Latsoudis, Forester-High school teacher, The Moraitis School, Athens, Greece

A selection of stereoscopic GB/3D Type Fossils project fossil images were displayed in a special exhibition organized during the 2 days’ annual school fair “Panigiri Scholis Moraiti” in Greece.

The fair was held on 4-5 April 2015 at the Moraitis’ School buildings in Psychiko, a suburb north of the Greek capital, Athens. The event is organized by its high-school students once a year and hosts activities and events in order to raise money for charity. The specific exhibition was prepared by the high school “Nature observation and interpretation Group”.

The aim of the exhibition was to portray the possible landscape, flora and fauna of the wider school area during different geological periods and to feature the importance of the fossils in understanding about how life evolved on earth.

Due to GB/3D Type Fossils project help, the visitors had the opportunity to examine typical fossils of animals that lived during the long distant past, using special red-cyan glasses prepared by the students. The project also inspired the students to make their own stereoscopic images using pairs of photographs and relevant free software.

In addition, representative digital models, scanned and provided online by the GB/3D Type Fossils project, were  3d printed in the main entrance hall in order to attract the visitors’ attention, and to promote the new technology potentials and the pioneer initiatives!

Panagiotis Latsoudis

Friday, 27 February 2015

What's the point (on the map)?

In a previous post, we talked about the value of geo-locating some of the 20,000 or so fossil specimens we have processed in the 3D Fossils database. In this post, I want to explain a little more why it is useful, and also how we do it.

Visitors to the 3D Fossils site can at the moment choose to search by a number of criteria, for example, if I search for fossils from the Carboniferous I will return specimens around 300-360 million years old. However if I search for “Lyme Regis” I will only get those specimens where the location field contains at least those words. I won't see specimens from Charmouth, or Pinhay, both only a couple of miles away. At the moment, our system is not aware of any geospatial relations between the text in the locality field.

To fix this, we need to know where all our places are on the British National Grid. In the modern world where even your mobile phone knows exactly where it is within just a few metres, it is easy to forget that it was not always this easy :

  • A lot of our specimens were collected before the grid was standardised to the OSGB 1936 format currently in place
  • Distances were measured in miles or yards (sometimes even furlongs, rods and chains), rather than metres and kilometres.
  • Many of the localities are recorded in the style “small quarry (disused) on south side of lane, around 250 yards east of Dog and Duck public house, name of small village, etc”
  • There are plenty of places in the UK which share the same name, but are in completely different places. Examples might include Gillingham, Kent/Gillingham, Dorset, or Rainham, Kent/Rainham, Essex.
  • If two places sharing the same name is not confusing enough, some places like to move around. Dudley, in the two hundred or so years since it was recognised as a source of prime geological material, has been part of Worcestershire, Staffordshire and the West Midlands.
  • Sometimes, fossil dealers would not be keen to disclose the sources of their stock for fear of losing out on a sale. Hence we often see wonderful fossils with only scant location information, for example “Whitby” or “Lyme Regis”
Finally, sometimes the locality information can be so precise that there might be a risk of exposing the exact location of sites that may be on private land. In this case we obfuscate the locality slightly, whilst retaining full details on file should they ever be required for bona fide research.

Despite these challenges, we can use our resources to make our best estimate of the right place on the map, and we are being helped by a number of volunteers who can carry out a few minutes of investigation work for each one. Some of the resources we like to use are:

Ordnance Survey maps, old and new. We are lucky to have a comprehensive back catalogue of these, and in digital format too. We use GIS packages such as ArcGIS to examine them.
Geological maps, usually based on an OS map underneath, but the geology listed in the specimen data might be a valuable extra clue. You can have a look at some of our maps using the new Maps Portal
Gazeteers (such as the OS Open Data 50k version, or GeoNames, a crowdsourced alternative). These are simply lists of place names and their grid references. They can be very useful to simply get you to the right area to start looking, or where the locality information is so vague that there is no way to get any more accuracy. 
Web searches – sometimes old quarries will have become SSSI or RIGS sites and accompanying paperwork on these will often yield a grid reference. Similarly the original published descriptions of the specimens may provide location details
Friends and colleagues – sometimes, if a description is particularly ambiguous, contains colloquial references, or is spelled incorrectly, no amount of web searching will help. However, someone who is familiar with the area might instantly say “I know exactly where that is”!

When we find a point that we believe represents as accurately as possible where the fossil was found, it is just a matter of reading off a 12 digit reference (which represents the position, in metres, east and north of a datum point off the Isles of Scilly). We are compiling all these points into a database, which we can use to quality check the final results. I'll explain how we do that in a future post. 

We are a little more than half way through a list of around 4,000 points from the 3d Fossils database, but if you think this sounds like an interesting task then there are plenty more parts of our collection that would benefit from the same treatment. You can volunteer from home too, but if you're ever near Keyworth we'd be happy to show you around. Contact in the first instance. 

Simon Harris
GB\3D Team

Tuesday, 17 February 2015

Georeferencing/Geolocating, GeoIndex and the BGS Maps Portal

It may be 18 months since the end of  official Jisc funding for the GB/3D Type Fossils Online Project, but development of this important resource has continued apace. Some of our volunteers have been georeferencing (or geolocating) many of the fossil localities. Georeferencing is the addition of a grid reference, or latitude and longitude, to a location, and it will be described in more detail in a forthcoming post. The aim of georeferencing is to allow localities to be plotted more easily on a map, or in a GIS (Geographical Information System), and then subjected to more rigorous analysis. As a geological survey, our traditional business has always been the production of geological maps, and not surprisingly, we are heavily involved in GIS. We have an online GIS known as “GeoIndex”, which provides access to many of our datasets and is available at:  .

BGS “GeoIndex” GIS: . Screen shot showing SW Scotland, the English Lake District and parts of the Isle of Man and Northern Ireland. Colours correspond to the BGS 1:625,000 scale Bedrock geology, and the triangles represent rock samples in the BGS Collections. Black triangles indicate online images of thin sections – both plane and cross polars. 
The BGS has recently made over 6000 geological maps and sections available through its online Maps Portal. The 1:50,000 (and previously 1:63,360) maps established a standard which many other geological surveys around the world have endeavoured to copy. Typical map sheets now include not only the basic map and key, but generally several cross-sections and a “generalised vertical section”. Some maps also include geophysical, metamorphic & biostratigraphic data, and a summary geological history.
Key “marginalia” on the Sidmouth Sheet (below) include:
  • Two horizontal cross sections, showing the general relations of the rocks along the two lines drawn on the map. The vertical scale is x2
  • Generalised vertical section. This acts as a key, drawn roughly to scale, indicating thickness variations, and the relationships between the solid geology lithostratigraphic units. Dominant lithologies are also described
  • Key to symbols and other units
  • Various location maps showing adjacent map sheets, component maps and survey dates
  • Surveying history and bibliographic reference
  • 2000/2005 –in the bottom left corner – indicates 2000 copies were printed in 2005

British Geological Survey 1:50,000 solid & drift geological map sheet 326 & part of 340 – Sidmouth. Published in 2005.

The online maps portal is available at: . It allows you to select from the latest versions of the 1:50,000 geological maps, or many of the older versions, plus many other small scale maps and sections. For each map or section there is a detailed record of the metadata and links to view or buy the map. The link to view the map open a high resolution JPEG2000 image within the IIPMooViewer (IIPImage HTML5 Ajax High Resolution Image Viewer), which allows you to zoom in and move around the screen. At full magnification (typically around x3), you can see more on the image that you can on the original – at least without a magnifying glass.

    The BGS online maps portal, available at: 

    The inclusion of all the historical maps allows the user to appreciate the understanding of the geology and the stratigraphical nomenclature that would have been current at any point in time, for example when a particular fossil was collected. One of the key localities in the GB3D database is Lyme Regis, and I have included extracts from the 2005 and 1846 maps. I will leave the reader to compare the two.

    Close-up of the area around Lyme Regis. BGS 1:50,000 geological map sheet 326 & part of 340 – Sidmouth. Published in 2005.

    Close-up of the area around Lyme Regis. Geological Survey of England and Wales 1:63,360 solid geological map, Sheet 22  – Coast from Lyme Regis to Torbay, Exeter, Newton Abbot, Totnes. Published in 1846.

    Thursday, 10 April 2014

    Jisc Technology Garden - Update #1

    The GB3D Fossil Types Online stand in the  Technology Garden at the Jisc Digital Festival 2014 in Birmingham raised significant interest in 3d-printing and the power of digital models for sharing objects and ideas.

    MeshLab representation of 3d digital model of Iguanadon thumb spike, NEWHM G36-63  

    Lawrie Phipps of Jisc was so intrigued by the digital model of an Iguanodon thumb spike in the Great North Museum, Newcastle  that he blogged about it - 

    You can download the digital model for yourself from the GB3D Type Fossils online website at:

    If you don't have access to a 3d printer, you can still appreciate the fossil in three dimensions by viewing the 3d stereo anaglyphs - all you need is a pair of red-cyan glasses that you can buy online for around a pound...

    Red-Cyan Stereo Anaglyph of the Iguanadon thumb spike