Category Archives: Curators and researchers

The WHO global partners meeting in Geneva and launch of the 4th WHO NTD report | Sustainability

Starting the Neglected Tropical Disease summit in Geneva this week gone, the World Health Organisation brought together its global partners for a meeting to launch the 4th WHO report on Neglected Tropical Diseases (NTDs). As an important player in the global effort to control and eliminate these debilitating diseases, the Museum has been following the meeting closely.

Photograph with a number of jars of preserved worms, and two dishes with worms within them in the centre. A pair of forceps lies on the table beside them for scale.

Soil-transmitted helminths in the Museum’s collection

The Museum has had a long history of researching NTDs, particularly those caused by worm infections and/or transmitted by insects. Today the Museum hosts DeWorm3, funded by the Bill and Melinda Gates Foundation, a major project researching the control and elimination of soil-transmitted helminths, aka intestinal worms. Intestinal worms are the most common of NTDs. DeWorm3 and Museum NTD experts travelled to Geneva for the NTD summit and report on the meeting.

Continue reading

Bioleaching cobalt from sulfide ores| COG3 Consortium

Recently, members of the Acidophile Research Team at Bangor University carried out some bioleaching experiments which aimed to leach cobalt from the Captain sulfide ore (from New Brunswick, Canada). Sarah Smith, a geomicrobiologist at Bangor University and one of the collaborators in the COG3 project reports.

bioleaching-blog-image-1

a) Mixed bacterial cultures used to inoculate the bioreactor experiments. b) A bioreactor before the addition of the culture and the ore. c) Adding the culture to the bioreactor experiment. d) The bioreactor at the end of the bioleaching experiment carried out at 45°C.”

Continue reading

Endorsing the Science International Open Data Accord | Digital Collections Programme

A growing number of museums are joining open data initiatives to publish their collection databases and digital reproductions online. The Museum has operated a policy of open by-default on our digital scientific collections.

Photograph of Vince Smith, Head of Informatics reading the Science International Data Accord

Vince Smith, Head of Informatics reading the Science International Data Accord

By signing the International Open Data Accord, the Museum recognises the opportunities and challenges of the data revolution and adopts a set of internationally recognised principles as our response to these.

Continue reading

Using the “Natural History Large Hadron Collider” to tell us about plant diversity

by Sandy Knapp, NHM Department of Life Sciences

The world’s herbaria hold millions of samples of plants, and until recently they have been largely the domain of taxonomists – those scientists who describe diversity. Herbarium taxonomists compare specimens collected in different parts of the world, assess variation and then come to conclusions about what to name as new, and what to call the same. Our ability to talk about plant diversity depends upon this activity – without names, we would be unable to tell each other about distribution – and as so alarmingly today, decline – of the some half a million plant species with which we share the planet.

Herbaria though are often depicted as dry, dusty out-of-date places, not really connected to the dynamic world of today’s societal needs. But actually, a herbarium can be considered a physical database – each plant specimen is a data point – something that occurred somewhere, sometime, with a particular combination of traits. In a study recently published in BMC Biology, Marc Sosef and colleagues show how powerful a resource these herbarium collections can really be, even in the underexplored tropical rainforests.

The data

Using the RAINBIO dataset  – a collaborative, curated (more about that later) database of herbarium specimens from many institutions all collected in tropical Africa – they perform a number of analyses exploring African plant diversity. Heterogenous datasets like these assembled from herbarium specimens – whose collection is by its very nature ad hoc – are sometimes considered to be less than useful for generating solid estimates of things like species richness, rarity, or turnover (but see commentary in BMC Biology). But for many environments, these are all the data we have.

Specimens in the RAINBIO dataset date from 1782 to the present – almost 250 years of data collection. Figure 5 in the paper graphically shows how exploration of Africa unfolded, along the rivers, tragically along the west coast in association with the iniquitous trade in enslaved people, and patchily through colonial activity in the early part of the 20th century. The history of European engagement with Africa unfolding along with the plants sent to collections, first in European and later also African institutions, is a reminder that science is part of society and does not develop outside of it.

Fig5-1024x683Time lapse of botanical collecting history across tropical Africa. Figure 5.

The robustness of the conclusions drawn by Sosef and colleagues is highly dependent upon the curational state of the data themselves. Taxonomic verification of the identities of samples held in RAINBIO dataset is key to this – this requires taxonomists. One of the things that most impressed me about this study was the degree to which data were validated by taxonomic experts – those scientists whose knowledge of whether or not two names in a list represent the same thing or different species, or whether a species described as a tree on a specimen label really is a tree. There have been criticisms of data served through the GBIF network, for example, but such data are only as good as the curation effort expended; to make use of these rich data sources, first catch some taxonomists and have them on the team!

The findings

The functional data analyzed from the RAINBIO dataset is novel and reveals really interesting patterns. The authors show that the proportion of herbaceous to woody plants is at the upper suggested limit (just under half, 44%). This says to me that tropical botanists need to focus on this vegetation layer as well as on those sexy big trees. An interesting comparison would be of rarity of herbaceous versus woody components of tropical vegetation. If Begonia species are anything to go by, herbs can be extremely rare and range restricted indeed!

Shockingly, the average number of collections per 0.5° square in Africa is 1.84 – that is fewer than two plant records in a square 55 kilometers on each side. Some places, of course, are better collected than others, but let’s get out there! The authors use the patterns revealed by their analysis to suggest collecting priorities for tropical Africa – they identify Tanzania, Atlantic Central Africa and West Africa as priority areas for further collecting to increase our knowledge of plant diversity.

But I might argue that looking at Figure 5, we should seriously think about increasing collecting effort at the northern edge of the African tropics – after all, that is the leading edge of climate change and the area where effects will be felt soon as the environment degrades. These aren’t the big rainforests, but these habitats and areas can be canaries for climate change.

Herbaria (and other natural history collections) represent big science – they are the CERN of natural history. These resources represent an unparalleled infrastructure for looking at how plant diversity is distributed, and are our best hope for documenting how it is changing at a global scale. Imagine if governments or private foundations invested in the digitization of all these invaluable resources, pretty straightforward for flat 2D objects like herbarium sheets, more difficult for 3D objects like insects or worms. The infrastructure thus created, especially if investment is also made in its careful curation and verification, would be the most powerful picture, however flawed it might be, of the Earth’s diversity before it is lost forever. We are crazy not to pull together to create this infrastructure to help us predict our plant’s fate.

This blog post was originally published in the On Biology blog

 

 

The story behind putting Geography into our collections | Digital Collections Programme

Guest blog by Liz Duffel, Georeferencing Digitiser

Most specimens within the Museum collection have locality information, showing where the specimen was found, on the accompanying label(s). When we are digitising our specimens, we can use that locality information for georeferencing – the process used to give the locality of a specimen geographical coordinates, so that it can be plotted on a map.

Data map with hotspots

A data portal visualisation showing the global distribution of the Museum’s zoological specimens with digital records

This is important because it allows for mapping and modelling, which underpins research on anything from species distributions and relationships, to environmental changes or targeting conservation practices.

Continue reading

The importance of being an unglamorous collection | Curator of Micropalaeontology

Most geological collections we hear about in the news are the prettiest, oldest, youngest, largest, smallest, rarest, most expensive or have some exciting story related to them that ties them to the evolution of our planet. Dinosaurs, human remains and meteorites are particularly popular. Over the last year we’ve embarked on a major curatorial project rehousing something that is the opposite – an unglamorous collection of bags of crushed rock.

Protective equipment

Curators Becky Smith, Helena Toman and Robin Hansen in protective equipment.

I’ll be explaining why the samples needed to be re-housed and most importantly why they are strategically important to the work of the Museum and needed to be kept for future reference. And also why we are all dressed up in protective equipment and why I had to learn to drive a fork lift truck! Continue reading

Hacking the Museum – the Informatics Team at #SMHack

On 21-22 February, four members of the Informatics team spent two days at our neighbour, the Science Museum, exploring their online collections with the invitation to build something “digital or physical, practical or whimsical, scholarly or punk rock”.

Photo showing pens and paper, laptop, sweets and coffee cups on a desk with sketches of ideas on the paper

Taking part in the #SMHack

The event was the first in a series of Hackathons to be put on by the Science Museum’s Digital Lab, and the goal was to think creatively about what “Museum+Tech” can mean. Some of the participants were pre-formed teams from organisations such as the Imperial War Museum, the Wellcome Collection, Penguin Books, the V&A, RedWeb, the Institute of Physics, and Night ZooKeeper. And some participants were freelancers or solo attendees who collaborated with others or formed teams of their own.

Continue reading