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February 2015
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As part of International Open Data Day, the Natural History Museum is opening up its digital collections and research data through its new Data Portal. An increasing number of governments and publicly-funded organisations are committed to making data available for unrestricted use - Open Data.  NHM supports this principle and its data are of particular value to scientific research on biodiversity, looking at changes of species over time and in geographical distributions, and predicting future trends. This is something of particular interest in the face of human pressures on the natural environment and the need for effective policy responses for a sustainable future.


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The Portal provides a digital access point to over 2.7 million specimens in the Museum’s collection, as well as thousands of other records and datasets that enthusiasts can browse, download and reuse.  The Data Portal also holds a growing and varied collection of research datasets, including the Museum's wildlife sound archives, checklists of British species, and even assembly instructions for a Lego device to manipulate pinned insects.

 

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The Museum’s Vince Smith and Ben Scott created the system. Vince Smith said,  “Data on the collection is one of our greatest assets. We wanted to expose the Museum’s data to our peers in a way that allows them to easily discover and reuse it.”

 

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“The Data Portal will provide an archive for the hundreds of research datasets generated by museum scientists each year”, said Vince. “It also allows the Museum to contribute to global science initiatives, such as the Global Biodiversity Information Facility, who are aggregating all known data on the occurrence of species worldwide.”

 

The collection could once only be accessed when academics took the opportunity to visit the Museum in person.  It is now accessible to anyone with an internet connection, anywhere in the world. Ben Scott said: "There is huge value in exposing this data to the world - we are excited to see what people use it for."

 

The Museum has over 300 Science staff, generating almost 1,000 scientific papers every year - these papers are now being presented as dynamic lists on the new staff biographies, which will link in coming months to a new NHM Open Repository for published materials.  The new Data Portal will provide a platform for scientists to share the datasets that have been created alongside their studies.

 

Vince Smith said: “We hope that the Museum's open approach will further understanding of the natural world, and foster innovation allowing other scientists to test and build upon existing Museum research.” 

 

Open Data Day brings people together around the world to  use open public data in innovative ways: creating new approaches to visual presentation; doing analysis and research; and exploring new data products.  It is part of efforts to  support and encourage open data policies all around the world to open up access and increase benefits to all.  As part of Open Data Day on 21 February 2015, Ben Scott will be attending the London outpost, and helping people use Museum data in their hackathons.

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What does the future hold for the Pangolin?  They are rapidly earning the reputation of being the mammal with the world’s highest level of illegal trade, yet many people have never heard of them.

 

Louise Tomsett, Mammal Curator at the NHM, is giving two Nature Live events on Saturday 21st February 2015 - World Pangolin Day - in order to raise awareness of these lesser-known animals, and to highlight the threat of extinction due to the illegal wildlife trade. She will be showing specimens from the NHM’s scientific collections, not normally on display to the public.

 

What are pangolins?


Pangolins are nicknamed "scaly anteaters" but they are not the same animal we generally think of as an anteater. Despite their distinctive appearance, making them hard to confuse with any other mammal, relatively few people know about them. The scales cover most of their body, giving them the appearance of a "living pine cone" or artichoke. They live in a variety of habitats such as grassland, rainforest and agricultural areas such as plantations. There are four species in Africa and four in Asia.

 

Sunda or Malyan pangolin ii.JPGThe Sunda or Malayan Pangolin


Pangolins are well adapted to their ecological niche. They feed primarily on ants and termites, using large, powerful claws to break open nests and mounds, and very long, sticky tongues to lick up the insects. Their specialised ears and eyelids can be closed to prevent attack by ants. The scales are an aid for digging burrows, and help some species climb trees in addition to acting as armour against ants and larger attackers such as lions.

 

pangolin_scales.JPGPangolin scales

 

When threatened pangolins curl up into a tight ball, rendering them virtually impenetrable, even to a lion’s teeth. Their common name ‘pangolin’ even comes from a Malay term generally meaning ‘rolled up’. Unfortunately it is this defence mechanism that also makes them rather easy for poachers to pick up and carry.


Conservation issues


The main threats to pangolins are the illegal wildlife trade and habitat destruction. Trade in pangolins (live and dead) is on an international scale, with confiscated shipments often amounting to tonnes. Quantities found in seized shipments represent only a fraction of the real numbers traded and estimates of the trade indicate as much as tens of thousands of individuals each year. The main drive for trade is the falsely attributed health benefits of pangolin meat and other body parts such as scales. Alleged benefits range from curing acne to curing cancer. In some countries, the sheer cost of the meat and being able to afford it is used as a status symbol. Pangolins are also used as bush meat, for indigenous folk-law rituals and for leather goods.

 

The traditional source for pangolins for the illegal trade is southeast Asia but this is now appearing to change, with African pangolins now a target as Asian pangolins run out.  The consequence is that all species of pangolins are now threated with extinction.


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Tree or African White-Bellied Pangolin

 

Pangolins are easily stressed and many die during the hunting and trafficking process, or even once rescued. They are extremely difficult to keep in captivity due to the fact that very little is known about their biology and care. In addition to this a continuous food supply of live ants and termites is very difficult to source. They have rarely been bred successfully and usually only have one offspring at a time so with current hunting levels, populations are not sustainable.

 

giant African pangolin scale.JPGScale of the Giant African Pangolin

 

The NHM’s collections are used by scientific researchers from all over the world. Like many of our collections, the pangolin specimens we hold contain a wealth of information, much of it waiting to be unlocked. For example, the geographical information can provide historical species ranges, specimen tissue samples for DNA analysis shows the genetics of different populations and isotope analysis of samples indicates geographical sources and movements during an individual’s life. All of this information is extremely valuable for conservation.

 

Louise Tomsett

 

#worldpangolinday

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Museum collections are being transformed into a radical new resource for science through digitisation: creating image resources and immense databases that allow advanced research for the future of the planet. Professor Ian Owens, the NHM Director of Science, gave a symposium on this subject in collaboration with Dr Jonathan Coddington and Dr Kirk Johnston of the Smithsonian National Museum of Natural History at the American Association for the Advancement of Science in San Jose, California, on 14 February 2015.

 

Ecosystems and human needs

 

All humans depend on biodiversity in a wide variety of ways. Clean water, food crop production, sea fisheries, tourism, timber and many more human needs rely on the functions of ecosystems to a significant degree. Over the last twenty years we have seen much greater development of the idea of ecosystem services - a concept that thinks of the economic and other values of the natural world to humans and integrates those values into policy, education, natural resource management and other activities. This supports better decision making and aims to ensure sustainability - the continued use of ecosystem services by people over time and by generations in the future.  Biodiversity is central to ecosystem services - the variety and complexity of species and populations is immensely valuable to us all, but we know that we do not properly understand how ecosystems work, or the real value of biodiversity.

 

Data: 4.5 billion specimens, 1.9 million species, 300 years, and now DNA

 

Sustainable ecosystems management depends upon the availability of information about the variation of biodiversity. Natural history collections are a vital source of these data, holding billions of specimens collected over three centuries, each witness to past ecological conditions and historic distributions. This presentation showed how collection organizations are using digitization to unlock the vaults of their collections and develop tools to map, monitor and understand the natural world.


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The scale of the world's collections is immense, representing billions of datapoints. The Smithsonian NMNH in Washington is the largest collection with the NHM in London and the MNHN in Paris following. The data from these and many other colections together are a resource recording distribution, species and dates from which changes in biodiversity over time can be analysed.  However, most of these data from the last 350 years is on labels, cards and in books, meaning that they are not readily available to modern science or computing.  The challenge for collaboration is to transform the information into electronic data for modern biosphere science.

 

Collections  transforming science

 

Museum collections have always changed the way that we think about the world by enabling scientific comparison and research: the discovery of the dinosaurs; the origins of humans; and the processes of evolution.

 

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Charles Darwin's Galapagos finches in the NHM: a key to understanding evolution

 

As science and techniques change, so does the potential of museum collections - the recent revolutions in DNA and genomics enable collections to be seen in a completely new light as resources for researching evolution and relationships; the development of computing and data analysis allows rapid analysis of big patterns in space and time to be explored in ways that could only be imagined twenty years ago.  NHM uses CT scanning to create digital replicas of delicate specimens for complex modelling; advanced analytical techniques with electron beam instruments to understand the detail of mineral structure and economic potential; and new applications of electron microscopy to give insights into the smallest detail of anatomy and development.

 

Our partial knowledge - species and diversity as a key to understanding ecosystem value and function

 

When it comes to the Biosphere and understanding how ecosystems work, the last 350 years have seen the discovery and description of around a quarter of the species that exist (excluding bacteria and similar microbes). 400,000 beetle species have been discovered, but this almost certainly represents a minority of those that exist.  New technologies with DNA look likely to revolutionise the nature of discovery - and give access to greater knowledge of the link between diversity and our needs from ecosystems.  Around 1.9 million Eukaryote species have been described out of a probable 8-9 million.  If we consider bacteria, there could be tens of millions more species.  We are currently, worldwide, describing around 15,000 species a year so the rate of discovery with current techniques is not going to close the knowledge gap: we need more rapid approaches to description and characterisation of biodiversity, and more sophisticated thinking on the importance of biodiversity in ecosystem function.

 

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How do we understand biodiversity in a different way, and how can we speed up the development of our knowledge, particularly for the huge diversity of minute soil organisms, fungi and microbes? The effort of our science is at the moment focused on larger, more charismatic species such as birds and mammals, and the work of scientists on big processes and patterns in biodiversity - macroecology - is a small proportion of total activity.

 

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A key area of strategic development is focused on acceleration of biodiversity description and discovery, using forest insects as a pilot group: Breaking the Taxonomic Barrier, an important complement to the digital initiatives.

 

Digitisation - the beginning of the surge

 

We need to unlock the potential of our collections through digitisation to speed up this science -  transforming the labels and individual records into large datasets.  However, this is a major task that requires extensive collaboration and significant resources. Our efforts so far have digitised around 3% of our collection of 80 million specimens - and of this, only some is in suitable form for scientific analysis.

 

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Our response is the development of the Digital Museum: Collections. Over the last year, we have successfully transformed our approach from individual research projects to an efficient processing line with our iCollections project: we've digitised 500,000 UK butterflies and moths with an expert team who have taken images and transformed data for scientific use, taking 2 minutes per specimen and costing £1 per specimen.

 

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Our current project is the rapid digitisation of 70,000 plant specimens on a conveyor-belt digitiser, followed by transcription and database development, as a pilot towards the creation of a Digital Herbarium to allow wider and much more ambitious scientific use.

 

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And we have already put millions of printed pages into digital form as part of the collaborative Biodiversity Heritage Library -  NHM's efforts are part of a global network of digitisation - iDigBio in the US has digitised 25 million specimens from a network of institutions, just as one example.  These efforts amount to the development of big data for biosphere science in coming years.

 

The need for citizen science

 

However, there is a significant challenge in transcribing the label data from older scripts - it cannot be done automatically and until we have transcriptions, these older collections are inaccessible to science

 

15903365787_67d188e362_o copy.jpgAnd this is where the involvement of thousands of volunteers can be essential in transforming collections into a scientific data resource: citizen science and transcription.  Some of this is through online crowdsourcing portals, such as Zooniverse, where we are experimenting with the transcription of our digitised collections.  However, we are also looking at how we can make crowdsourcing a live event: at our annual Science Uncovered event in September 2014 we welcomed 10,000 members of the public into the NHM to see science at first hand and one of the activities on offer was citizen science transcription of beetle specimens.

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Results and data use

 

New science is emerging from these growing digital resources: the beginning of a new type of science possible from this investment.  Steve Brooks, Angela Self and Flavia Toloni from the NHM, with Tony Sparks from Coventry University, have used the digitisation of butterflies and moths to look at how UK butterflies are responding to climate change.  There are good observation data for the UK from the 1970s, but collections hold the key to looking further into the past. They analysed data from 2,630 specimens of four species of British butterflies (Anthocharis cardamines, Hamearis lucina, Polyommatus bellargus and Pyrgus malvae), collected from 1876 to 1999. The data on collection dates gives a record of the first emergence of these species each year and the research shows a good relationship between higher early spring temperature and early emergence dates.

 

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Big Data and Open Data

 

The data produced from our digitisation work is being released through a new Data Portal, enabling scientists to find information of interest and to download datasets for research on Open Data principles - the NHM has adopted a policy of being Open by Default.

 

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The broad challenge of global biodiversity

 

New work is using much broader datasets to understand big changes across multiple ecosystems: Andy Purvis and his team in the PREDICTS project which is taking data from multiple sources, including collections, to look at patterns of how local biodiversity typically responds to human pressures such as land-use change, pollution, invasive species and infrastructure, and aims to ultimately improve our ability to predict future biodiversity changes.  Data is being assembled from a wide range of biomes.

 

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The future of the Digital Museum for the Biosphere: Open Data; Big Data; Community Data

 

The future for the Digital Museum of the Natural History Museum is based on a new model for the development and use of collections data through digitisation:

 

  • Open Data that are available to scientists all around the world for collaboration and research.  We need to involve as wide a range of expertise in thinking about science for the future.  Museums will continue to be a key resource as a focus for evidence and extended collaboration;


  • Big Data that cover whole ecosystems over long periods of time, based on the solid evidence base of collections and extending from population and species to molecules and DNA.  Internationally, there are 4.5 billion specimens of 1.9 million species from 300 years of collecting. We need to use these data effectively but also work out new ways of gathering data on the millions of other species that will allow  understanding to help humanity to  tackle the challenges of the future in terms of environmental change and sustainable use; and


  • Community Data that are based on the involvement of a wide spectrum of public participation, from schoolchildren to students to communities: online, in museums and in the field. This is science for everybody, from basic curiosity, to observation and recording, to data development and interpretation, from appreciation to understanding practical application for the future.

 


 



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One of the most prestigious international gatherings of scientists, policy specialists, journalists, science communications professionals and the US public is the annual meeting of the American Association for the Advancement of Science.  It attracts several thousand participants every year: in 2015 it is in San Jose, California from 12-16 February.

 

The NHM is represented this year by Professor Ian Owens, Director of Science, who is co-organiser and speaker at a session Unlocking Natural History Collections to Model the Biosphere in collaboration with NHM's sister institution the Smithsonian National Museum of Natural History (NMNH) from Washington D.C.

 

Session information


Unlocking the Vault: Digitizing Collections To Understand Global Biodiversity
Saturday, 14 February 2015: 3:00 PM-4:30 PM, Room LL21C (San Jose Convention Center)
https://aaas.confex.com/aaas/2015/webprogram/Session9604.html


Ian and Jonathan Coddington (from the NMNH) will be speaking on the potential of collections data in addressing global environmental challenges. 4.5 billion specimens in natural history collections are a key resource for science supporting our future on Earth.  Unlocking this valuable data source through digitisation will support sustainable use of biodiversity, better understanding of parasite threats to human health, and essential insights for the development of new crops to feed a growing population.

 

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Both NHM and NMNH have ambitious programmes of digitising collections - creating images, data and DNA evidence - to enable much wider scientific use by researchers around the world.   The future of this bold enterprise will be mapped out in the session on at AAAS on Saturday 14 February, showing how  major institutions are creating genomic collections and digitizing biological data to make it openly available, often with the help of thousands of online citizen scientists. Researchers are harnessing the potential of collections as an immense dataset on the planet’s past and present, used for modelling the future for better-informed policy. 

 

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Digitization, genomics and citizen science are enabling scientists to work across multiple collections and millions of specimens. The collections highlight geographic, temporal, morphological, and genomic patterns of diversity across a vast range of species. By combining collections data with new modeling and data visualization tools, analyses of biodiversity are possible on a scale never before seen. 

 

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Society needs systems that deliver the best possible estimate of the abundance, distribution and functional role of all species, from the recent past to projecting into the future. Delivering this requires an unprecedented level of cooperation by natural history organizations and the wider community.

 

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https://aaas.confex.com/aaas/2015/webprogram/Session9604.html


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NHM EARTH SCIENCES SEMINAR

 

Unravelling global warming through soil mineralogy: A case study from a proglacial valley in the Swiss Alps

 

Dr Christian Mavris, Marie Curie Fellow (ES, NHM)

 

Tuesday 10th February - 4.00 pm

 

Earth Sciences Seminar Room (Basement, WEB 05, the previous Mineralogy Seminar Room)

 

Investigations in Alpine soils indicate that mineral weathering is much faster in ‘young’ soils (<1000 yr) than in ‘old’ soils (10,000 yr). However, little is known about the initial stages of weathering and soil formation, i.e. during the first decades of soil genesis. Due to the continuous retreat of the Morteratsch glacier (Upper Engadine, Swiss Alps), the proglacial area offers a full time sequence from 0 to 150 yr old surfaces. The area is well documented regarding vegetation and soils.

 

The glacial till has an acidic character (granitoid parent rock). Mineralogical measurements were carried out using a broad range of analytical approaches, from XRD to wet chemistry to cathodoluminescence and Nomarski DIC microscopy. Specifically, cathodoluminescence and Nomarski DIC microscopy were used for the first time on minerals involved into an early pedogenic process.

 

This work clearly demonstrates that in cryic, ice-free environments, chemical weathering rates are high, leading to the formation and transformation of minerals. This clearly influences pedogenic processes to a remarkable extent – and thus, is linked to the settlement of life in previously deglaciated (and extreme) areas.

 

 

More information on attending seminars at http://www.nhm.ac.uk/research-curation/news-events/seminars/

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Polymerization in hydrothermal conditions: Darwin's prescient idea.

Dave Deamer, Department of Bimolecular Engineering, University of California, Santa Cruz CA

 

In an often quoted note to Joseph Hooker in 1871, Darwin speculated that life may have begun in a "warm little pond." We have tested this idea in simulations of fluctuating hydrothermal fields associated with volcanism. We found that the chemical energy available in such conditions can drive polymerization of ordinary mononucleotides into surprisingly long oligonucleotides resembling ribonucleic acid (RNA). The polymerization occurs in lipid environments so that the RNA-like polymers become encapsulated in membranous compartments to form protocells, the first milestone on the evolutionary path toward primitive cellular life. 


Energy and Matter at the Origin of Life

Nick Lane, Department of Genetics, Evolution and Environment, UCL

 

There is a paradox at the base of life. Membrane bioenergetics - the use of ion gradients across membranes to drive carbon and energy metabolism - are universal, but membranes are not. Radical differences between bacteria and archaea in membrane chemistry and active ion pumping suggest that LUCA, the last universal common ancestor, may have used natural proton gradients in alkaline hydrothermal vents to drive growth. I will outline a possible scenario for the origin of life in this environment, and present some experimental and modelling results which suggest that proton gradients could have driven the transition from geochemistry to biochemistry, and the deep divergence of archaea and bacteria.

Location:

Flett Lecture Theatre, Natural History Museum, Cromwell Road, London - Map

Poster:

Download a copy of the poster here - Poster

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Palaeo-ecosystems in Pleistocene Europe: Insights from stable isotopes of large mammal fossils

 

Prof. Hervé Bocherens, University of Tübingen, Germany

 

Tuesday 3rd February - 4.00 pm

 

Earth Sciences Seminar Room (Basement, WEB 05, the previous Mineralogy Seminar Room)

 

The climatic fluctuations of the Pleistocene have caused dramatic changes in the ecosystems of Europe during the last million years. These ecosystems, cold or warm, included a high diversity of megafauna, in contrast to recent ecosystems under similar climatic conditions.

 

NaturalHistoryMuseum_PictureLibrary_024715_preview.jpgTooth of a woolly mammoth (Mammuthus primigenius)

 

To gain a better understanding of the functioning of these ecosystems with no modern analogue, the isotopic composition in carbon, nitrogen and oxygen of the large mammal fossil bones and teeth were used to document key aspects of their ecology, such as habitat, diet preference, niche partitioning, and predator-prey interactions. In addition, isotopic analysis of fossil hominids and their prey allows the reconstruction of subsistence patterns and inferences on the possible anthropogenic impact on the environment.

 

More information on attending seminars at http://www.nhm.ac.uk/research-curation/news-events/seminars/