GigaScience at SPNHC 2022
The meeting of the Society for the Preservation of Natural History Collections (SPNHC), International Partner – BHL (Biodiversity Heritage Library) and National Partner – NatSCA (Natural Sciences Collections Association) took place in Edinburgh from June 5th-10th 2022. This was the first time GigaScience attended this conference, and it complemented well our growing expertise in publishing biodiversity data (see our new disease vectors series in GigaByte journal alongside previous work digitising botanic gardens and typed specimens). Chris Hunter and Chris Armit of GigaScience Press both attended this meeting and report on key highlights of this conference.
Confronting the loss of Biodiversity
“Nature is noisy. It walks, it crawls, it swims, it swoops, it buzzes. But extinction is silent. It has no voice except our own.”
-Paul Hawken
A major theme of the SPNHC 2022 conference was the loss of biodiversity. Plenary speaker Mark Maslin (UCL) highlighted that the Holocene – the current geological era that has lasted since the Last Glacial Period ended approximately 11,650 years ago – is different to the other interglacials, and Mark uses the term ‘Anthropocene’ to define the latter part of the Holocene where humanity increasingly controls the environment of the Earth. Deforestation is a major indicator of the impact of humanity, and human behaviour has increased extinction rates >100 fold over background. To emphasise our role in the loss of biodiversity, Mark made us consider the biomass of land mammals, where 67% of this biomass are livestock and pets, 30% are humans, but only 3% are wild mammals.
So how should we confront the biodiversity collapse. Keynote speaker Gilles Doignon, who is Team Leader for Biodiversity and nature-based solutions at the European Commission Directorate-General for Research and Innovation, highlighted that, with one million species at risk of extinction (see media release by IPBES), researchers and museum curators are encouraged to “speak up for Nature”. Towards this end, Gilles highlighted the critical role of museums in public engagement, and illustrated this with a poignant exhibition at the Bristol Museum & Art Gllaery entitled “Extinction Voices”, where a black veil was placed over 32 museum specimens that were on the IUCN Red List of Threatened Species. This is a powerful visual message, and encourages us all to act now rather than later.
Gilles further invited us to join the Global coalition ‘United for Biodiversity’ organised by the European Commission (EC) and for which he is the coordinator. The United for Biodiversity website has the following detail:
- “The Commission is turning to all national parks, aquariums, botanic gardens, zoos, science and natural history museums, research centers to join forces and raise their voice about the nature crisis.”
- “With their collections, education and conservation programmes, these institutions are the best ambassadors to inform the public about the dramatic effects of the biodiversity crisis.”
For a recent interview with Gilles Doignon on the importance of ‘United for Biodiversity’, please see the ‘Global Warming’ article in Zooquaria.
Museums and Civic Engagement
A core concept of the ‘United for Biodiversity’ initiative is the exchange of ideas and best practices between museums and research centres. On this note, there was an interesting discussion in the session “Civically engaged natural history museums: transforming public programmes to address societal challenges” where Liz Hide (Sedgwick Museum of Earth Sciences, University of Cambridge) highlighted the key role of museums in our society. Liz explained that museums can target schools to address societal changes, and that there is a need for civically engaged natural history museums where events should be seen as conversations, and visitors to the museum participate in the event. This is a shift from the more traditional focus where the expectation was that visitors to a museum would be there primarily to listen and to learn from museum curators. Through such civic engagement, Liz presented museums as a vehicle for social change, and was swift to emphasise the power of advocacy that a museum or research institution can achieve through public engagement and interaction with the local community.
As another example of civic engagement, Miranda Lowe (Natural History Museum, London) – who was recently awarded a CBE for her role in diversity, inclusion, and public engagement – offered the enticing example of botanical illustrations. Whereas many botanical illustrations were originally created for the purpose of taxonomy, the artwork that was generated as part of these scientific studies is a great inspiration to many. Miranda further highlighted that, by observing the inspiration that came from museum collections of botanical illustrations, museums now organise workshops for the community to create botanical illustrations.
As curators of the GigaScience Database, we were additionally interested in the civic-engagement role of digital libraries in our communities. On this note, Liz Hide highlighted that digital libraries are an incredibly powerful tool and resource that represent important partnership opportunities for public engagement. As Liz explained, one of the fruits of digital media is that ‘citizen scientists’, who are interested in following up on a subject that caught their attention at an event in a museum, can be directed by museum curators to additional digital resources which can be utilised in their own research.
As a further example of civic engagement, we were impressed by the work of the Global Biodiversity Information Facility (GBIF), who had an exhibitor stand at the conference, and of which Arnald Marcer gave a talk entitled “Spatial uncertainty in data from Natural History Collections as mediated by GBIF. Implications for ecological research”. GBIF have been exploring the utility of citizen science in creating occurrence records as evidence of the occurrence of a species, or other taxa, at a particular place on a specified date. At GigaScience Press, we have been working closely with GBIF in publishing data papers describing datasets of Vectors of Human Disease. In this series, there has been a great focus on Europe and the Americas, and the data papers report on occurrence data of sand flies in the Brazilian Amazon and 21 American countries, triatomine species (conenose bugs) in the Americas, arbovirus vectors (mosquitoes) in Southwestern Colombia, and citizen science approaches that utilise observations from the public to create a pan-European mosquito occurrence dataset. We hope to further promote these data mobilisation efforts to share occurrence data in Asia and Africa.
Museomics and Preservation of DNA in Type Specimens
At GigaScience we have a huge interest in genomic studies and we were deeply impressed by the talk by Rina Morisawa of Harvard University on “Preserving the Genomes of Type Specimens: Lessons from the Museum of Comparative Zoology”. Rina cut the phrase ‘Museomics’ to refer to genomic studies using museum specimens, and specifically highlighted the need to preserve DNA from archaic and very often type specimens that are included in the Harvard University Museum of Comparative Zoology (MCZ). A ‘type specimen’ is the particular specimen, or series of specimens, upon which a new taxon group is based. Rina explained that the MCZ includes “50,705 catalogued types” and that “as one of the oldest natural history museums in the US, the MCZ houses a significant share of type specimens of the world.” With this in mind, the Cryogenic Collection at the MCZ was established in 2012 to house the genetic resources of the museum collections. It is known that, even in fixed specimens, DNA degrades over time, and the goal of this initiative is to minimise DNA degradation for as many primary types as possible by cryopreserving subsampled tissue.
Rina additionally highlighted that the MCZ ‘Museomics’ initiative aligns with the core premise of the Earth BioGenome Project, which has the ultimate goal of generating genomic data for all species on the planet. We look forward to hearing of collaborative findings from the MCZ and genomics researchers from the Earth BioGenome Project (for recent GigaBlog on Biodiversity Genomics and the Earth BioGenome Project).
Imaging: the Role of Digitisation and Virtual Access
There was a great focus on digitisation of museum specimens at this year’s conference. Ralph Kugler (Milwaukee Public Museum), in his talk entitled “Preserving and Sharing Museums and Collections Through Exhibit Hall and Collections Area Virtual Tours and 3D Specimen Photogrammetry”, explained how virtual tours, which really came to fruition in the early days of the COVID pandemic, have been extraordinarily successful and extended the reach of museums worldwide. Ralph additionally explained the principles of photogrammetry, which enables 3D models to be created for museum specimens. This approach involves multiple photographs being stitched together to form a 3D image. For small samples, the camera position can be stationary and the sample can be rotated on a turntable, and a light tent setup is used to obtain diffuse and even lighting of the specimen that is being imaged. Software tools are then used to generate 3D models from adjacent and overlapping photographs. Ralph was swift to point out that one of the key advantages of digitising museum specimens is that it helps to preserve specimens and allows sharing of irreplaceable holotypes.
The theme of digitisation was further explored by Pierre-Yves Gagnier (Muséum National d’Histoire Naturelle, Paris) in his talk entitled, “Diversifying virtual access: going for 3D”, compared surface scans generated by photogrammetry, laser scanning (FARO Edge Arm), and structured light scanning (Artec Spider). Each of these methods can generate a detailed 3D model with over 200,000 polygons. Laser scanning and structured light scanning were faster in terms of image acquisition (5 minutes) when compared to photogrammetry (20 minutes). Of note, post-processing of laser scans to generate the 3D model was exceptionally fast (2 minutes) when compared to structured light scanning (20 minutes) and photogrammetry (35 minutes). In his talk, Pierre-Yves reported on the the ANR-funded e-COL+ project that aims to provide infrastructure to generate 10,000 3D models per year. Pierre-Yves additionally stressed the importance of digitisation in circumventing the need to ship rare or type specimens.
Both Ralph and Pierre-Yves also touched on the significance of MicroCT, which uses X-rays to generate 3D models of the internal structure of biological specimens at microanatomical resolution. At GigaScience Press, we have a deep interest in MicroCT and we have published studies that utilise this technology to enable sharing of printable 3D models whilst preserving the original museum specimens and sharing of 3D models of fossilised planktonic foraminifera species (in addition, see GigaBlog on the Cyber Centipede).
I discussed with Ralph and Pierre-Yves the possibility of combining photogrammetry and MicroCT. The core concept here is that, whilst MicroCT is superior in terms of image resolution and visualisation of internal anatomy, X-rays are fundamentally unsuited for capturing surface texture such as the patterns of butterfly wings, snakes, or fishes, which are significant biological traits used for camouflage, mimicry, and of course taxonomic identification. It would be interesting to explore the process of spatially mapping texture, captured using photogrammetry, onto a 3D mesh generated from MicroCT. This ‘hybrid model’ approach would deliver both surface patterns needed for taxonomic identification, and internal anatomical structure required for a deeper understanding of the specimen, whilst still preserving the original museum specimens.
The Nature / Culture dichotomy: a flaw in the design of Museum Space?
Museums are usually thematically organised with, for example, Natural History collections housed in separate gallery spaces from Anthropology and Ethnology collections. But is this a good thing? Isla Gladstone (Bristol Museum & Art Gallery) in her talk entitled “Natural history collections and social impact in the context of the climate and ecological crises”, highlighted that the way we organise museum space tends to segregate environmental issues from social issues. Perhaps we should reconsider the organisation of museum space? It would be interesting to see this put into practice, with a re-design of museum space perhaps more similar to an artspace, with more bridges between the human world and the natural world. We look forward to hearing more about this.
The next SPNHC conference will be in San Francisco from May 28th – June 2nd 2023 where it will be hosted by the California Academy of Sciences. We look forward to seeing you there.
