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155 Posts authored by: John Jackson
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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/

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Adrian GloverDeep-Sea Systematics and Ecology Group, Department of Life Sciences

Wednesday 28 January 11:00

Sir Neil Chalmers seminar room, Darwin Centre LG16 (below Attenborough studio)


The deep oceans contain a vast and untapped wealth of minerals useful to humans. In geological terms, there is much known with regard the distribution of these minerals at different types of deep-sea environment. The first polymetallic (or manganese) nodules were recovered by the Challenger expedition in 1873, in the deep Atlantic. In the 1960s, the first estimates were made of the total mineral wealth of the oceans, and the first surveys undertaken. In 1978, the first fully integrated mining trials recovered several hundred tonnes of nodules from the central abyssal Pacific at depths of 5500m; in the preceding year, hydrothermal vents were discovered on the Galapagos rift. Since then, an average of 5 hydrothermal vent fields have been discovered every year, and 19 exploration licences for deep-sea minerals in both abyssal nodule and deep-sea vent environments have been issued by the United Naitons International Seabed Authority, 5 of these in 2014 alone. The United Kingdom government is sponsor to 2 exploration licence claims in the central Pacifc covering 267,000 square km, an area larger thant the UK itself.

Despite our accumulated knowledge of the mineral wealth of deep-sea ecosystems, our biological data remains extremely patchy. The central Pacific nodule regions have been well-sampled for nodules, but the majority of species are undescribed and fundamental questions such as the biogeographic distributions of animals unstudied. The diversity and ecological resilience of species to disturbance regimes are largely untested. At hydrothermal vents, critical data such as degrees of endemicity and gene-flow between vent fields is lacking.

The NHM is in a unique position to provide advice to industry and government, as well as academic research, in deep-sea mining from both the geological and environmental point of view. This has potential to be a key area in our Sustainable Futures strategy. In my research group, we have been working with an industrial contractor on the UK-1 deep-sea mining claim in the central Pacific for the last 18 months and are part of an EU FP7 deep-sea mining project. In this talk I will outline some of the history of deep-sea mining, the fundamental science at stake, our role in current projects, the importance of taxonomy, open data and bioinformatics and some of our plans for our forthcoming fieldwork (we sail for a 2-month trip on Feb 12).

 

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

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Large centipedes and larger datasets

 

Dr Greg Edgecombe, Department of Earth Sciences, NHM

 

27th January - 4.00 pm

 

Earth Sciences Seminar Room (Basement, WEB 05, formerly Mineralogy Seminar Room)

                                         

Scolopendromorpha includes the largest and most fiercely predatory centipedes, totalling more than 700 species.  Subjected to phylogenetic analysis since the late 1990s, early studies drew on small sets of external morphological characters, mostly those used in classical taxonomic works.

 

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Scolopendra gigantea

 

In order to bolster the character sample, new anatomical data were worked up by systematically sampling the group’s diversity in order to formulate new characters from understudied structures/organ systems. Simultaneously, targeted sequencing of a few markers for a small (but growing) number of species provided the first molecular estimates of phylogeny.  These have resulted in stable higher-level relationships that predict a single origin of blindness in three lineages that share this trait, and are now backed up by transcriptomic datasets with high gene occupancy. Explicit matrices of morphological characters and fossils coded as terminal taxa remain vital to “total evidence” dating/tip dating of the tree.

 

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

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We introduced our new digital herbarium project in a previous post: with the herbarium of the Royal Botanic Gardens, Kew, we are moving 70,000 plant specimens temporarily to Picturae, a specialist company in the Netherlands, so that the herbarium sheets can be imaged in the most speedy and effective way. 

 

The images will then be sent to Suriname for transcription of the typed and hand-written information on the sheets into electronic form.  The information includes the species identification, the place and date of collection and often the collector, that can link to field notebooks and other resources. The images and data will then be accessible via online databases to scientists and conservation biologists and others for research and better understanding of plant distribution and biogeography.

 

This is what it all looked like as we packed up and got ready to go - not many people see this, so worth showing:

 

NHM_JAJ_DSC_7974.jpgThe NHM herbarium compactors

 

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and the grey cupboards on the compactors

 

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Jacek Wajer removing specimens of Dioscoreaceae (yams and related plants)

 

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And wheeling them away on a trolley

 

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Steve Cafferty preparing the transport boxes for the specimens

 

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Jacek putting the specimens into the boxes

 

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with colleague Jonathan Gregson

 

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And Jonathan fitting the boxes onto the trolleys on which they will travel to Picturae in the Netherlands

 

 

More blogs to follow as the project progresses!  #DigitalHerbarium #NHM #Kew

 

 

@KewScience @NHM_Science

 


 


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Kew and the Natural History Museum are working together on large scale digitisation of their plant collections - #digitalherbarium #Kew #NHM

 

 

Trolleys containing green boxes.

 

Packing specimens at Kew. Kew is sending 41,000 specimens.

 

Plants preserved as herbarium specimens provide the evidence of what plants there are, where they grow and when they were collected. They provide the basis for modelling plant distribution over time, act as evidence that ensures plants are named consistently, and are a source of material for analyses of anatomy, disease and disease control, biochemistry and evolutionary relationships. Together, the herbaria at Kew and the Natural History Museum, London, contain more than 12 million specimens and are consulted by many visitors from around the world. Much of the information that these researchers need is stored away in cupboards, and is therefore not discoverable until a scientist visits the institution and looks inside. By providing images and data from these specimens online, anyone interested in plant diversity, for research or just for interest, can discover what our institutions hold and then access the information they need.

 

Recently some large European herbaria such as the Muséum National D’Histoire Naturelle in Paris and Naturalis in The Netherlands have had digital images made of their entire collections in order to make both specimen images and data about each collection available. Kew and the Natural History Museum have been working closely with Picturae, the company involved in the digitisation of the Naturalis herbarium, to develop cooperative workflows to make digital images and capture data from part of the two institutions’ collections.


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Jacek Wajer and Jonathan Gregson selecting specimens for packing at the Natural History Museum

 

We are embarking on the first stage of this adventure starting the last week of January. This first stage is a pilot to refine workflows and to gather information so we can plan larger scale projects in the future. We are focusing our efforts on several groups of economic plants, the genus Solanum (potatoes, tomatoes and aubergines), the St. John’s Worts (Hypericum) and the family Dioscoreaceae (yams). In all, approximately 70,000 specimens will be digitised using Picturae’s ‘digistreet’ methods. A ‘digistreet’ is essentially a purpose-built conveyor belt system that minimises manual handling of fragile herbarium specimens and captures high resolution images of each. After quality control and checking at both Picturae and the respective institutions, detailed information on where and when each plant was collected will be transcribed from the labels on the specimens by a team in Suriname.


Our objectives for this pilot phase are:


  • Image all Kew’s and NHM’s selected pilot herbarium specimens to an agreed common standard
  • Transcribe all the label collection data from these specimens to an agreed standard.
  • Incorporate all of the images and data into the institutions’ specimen catalogues to make them discoverable on-line.
  • Work together to refine accurate costing of mass digitisation using Picturae’s methods and develop joint workflows that will facilitate future work involving more partners across the UK.

 

This important pilot will lay the foundation for future collaborative work, with the eventual goal of providing access to the rich botanical collections held in UK institutions. We will share the results of our pilot with other institutions to help increase access to the wealth of information on global plant diversity held within the UK and to maximise the scientific and conservation impact of data held in plant collections worldwide. We hope that others will want to join in on this adventure!


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The Picturae conveyor belt imaging system in Amsterdam.

 

 

The pilot began on the 19th of January with material being sent to Picturae in the Netherlands. We will be tweeting and blogging on the progress of the project as the specimens are shipped, imaged and transcribed - follow us on Twitter using the hashtags  #digitalherbarium #Kew #NHM

 

 

Find out more:

Picturae Digistreet

Natural History Museum: Digital Museum

Kew Herbarium

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Deep Diving, New Species Discovery and the Greatest Library on Earth

 

Special Science Seminar on communicating how biodiversity is the Earth's most valuable asset

 

Richard L. Pyle

Bishop Museum, Honolulu, Hawaii

   

Wednesday 14 January, 4pm Flett Theatre, NHM London

 

Preceded by coffee & tea in Flett Foyer from 3:15pm

    

The number of species on planet Earth that remain unknown to science exceeds (perhaps vastly) the number of species that have so far been discovered, let alone formally documented. Earth's biodiversity, which represents a library of accumulated information shaped by nearly four billion years of evolution, is arguably the most valuable asset on the planet for the long-term survival of humanity. Within the global biodiversity library, we are at this point in human history like toddlers running through the halls of the Library of Congress, largely unaware of the true value of the information that surrounds us. At the current pace of species discovery and documentation, in the context of what appears to be the dawn of the sixth great extinction, we are losing the race to document this enormous wealth of information before it is lost forever. Taxonomists are the librarians, developing new tools to build the card catalog for the Greatest Library on Earth. The tools include new research and means to access and integrate information. What we accomplish within the next twenty years will impact the quality of life for humans over the next twenty thousand years. 

 

Rich Pyle is globally recognised as an ichthyologist exploring extreme deep reef habitats, a bioinformatician and an ICZN Commissioner, a SCUBA re-breather engineer and and a two-time, two-topic TED Speaker. Here’s his TED blurb:

  • Ichthyologist Richard Pyle is a fish nerd. In his quest to discover and document new species of fish, he has also become a trailblazing exploratory diver and a pioneer of database technology.  A pioneer of the dive world, Richard Pyle discovers new biodiversity on the cliffs of coral reefs. He was among the first to use rebreather technology to explore depths between 200 and 500 feet, an area often called the "Twilight Zone." During his dives, he has identified and documented hundreds of new species. Author of scientific, technical and popular articles, his expeditions have also been featured in the IMAX film Coral Reef Adventure, the BBC series Pacific Abyss and many more. In 2005, he received the NOGI Award, the most prestigious distinction of the diving world.
  • Currently, he is continuing his research at the Bernice P. Bishop Museum, outside Honolulu, Hawai'i, and is affiliated with the museum's comprehensive Hawaii Biological Survey. He also serves on the Board of Directors for the Association for Marine Exploration, of which he is a founding member. He continues to explore the sea and spearhead re-breather technology, and is a major contributor to the Encyclopedia of Life.
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Clay minerals on Mars: updated views on distribution, mineralogy and geologic context

 

Joe Michalski, Earth Sciences Department, NHM

 

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

 

Tuesday 13th January, 1600h

 

While some Martian meteorites contain minor abundances of clays formed on Mars, most of our understanding of the clay mineralogy of Mars comes from orbital infrared remote sensing measurements. The European Space Agency’s Mars Express spacecraft was, in 2004, the first mission to detect clay minerals on Mars. Since that time, both Mars Express and NASA’s Mars Reconnaissance Orbiter have detected >10,000 deposits spanning a range of geologic contexts and mineralogies. These deposits are extremely interesting for many reasons, not the least of which is that they seemingly date to an era not preserved on Earth (>3.7 Ga). 

 

In this talk, Joe will describe an updated perspective on the mineralogy of Martian clays, and their implications for ancient aqueous geological processes on and habitability of Mars.

 

mars.JPG

 

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

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Prof. Mel Greaves FRS, Institute of Cancer Research

 

Friday 5 December 12 noon,  Sir Neil Chalmers seminar room, Darwin Centre LG16 (below Attenborough studio)

 

All cancers share the common feature of being clonal expansions of mutant cells that, over years or decades, disseminate within and between tissues, hijacking essential normal functions. But cancers differ widely in their tissue of origin, underlying mutational spectra, time frame of progression, pathological impact and clinical course. The systematics or classification of cancer subtypes therefore poses a considerable challenge with biologists, histopathologists and oncologists applying differing criteria.

 

Over recent years, a new conceptual framework has emerged that makes biological sense of all the diversity. This views cancer as a process of somatic cell evolution driven by mutational diversification and natural selection or adaptation within the specialised ecosystem habitats of the body. The implications of this new vision for diagnosis, prognostication and control of disease are very substantial.

 

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

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What are the benefits of natural history museums working with local record centres?

 

Thursday 4 December 1430-1600 Flett Theatre, NHM.

 

Steve Hewitt, Curator of Natural Sciences, Tullie House Museum and Gallery

Teresa Frost, Manager Cumbria Biodiversity Data Centre

 

The relationship between natural history museums and local records centres was once strong, complementing and supporting each other. The pooling of historical museum collections with contemporary data provided a valuable perspective on the country’s changing biodiversity. But in recent decades this important link has diminished.

 

Join this session to hear about the relationship between Tullie House Museum, Carlisle Natural History Society and the Cumbria Biodiversity Data Centre (CBDC). Together they support each other to create a momentum for biodiversity study. As well as the management and dissemination of collections data through CBDC, the museum gains from relationships with external organisations engaging with the centre. What can we at the Natural History Museum learn from these and other benefits of a now rare arrangement?

 

Open to all.  The seminar is open to all Museum staff.  We welcome colleagues from other institutions.

 

If you would like to attend please email: julie.reynolds@nhm.ac.uk.

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