Conservation in the Genomic Era

HAVE DNA TECHNOLOGIES REPLACED THE NEED FOR MUSEUMS?


By Sotiria Boutsi, Intern

I am PhD student at Harper Adams University with MSc in Conservation Biology, currently doing a professional internship at the Museum of Natural History in the Public Engagement office. My PhD uses genomic data to study speciation in figs and fig wasps.


The year 1995 marked the first whole-genome sequencing for a free-living organism, the infectious bacterium Haemophilus influenza. Almost three decades later, biotechnological advances have made whole-genome sequencing possible for thousands of species across the tree of life, from ferns and roses, to insects, and – of course – humans. Ambitious projects, like the Earth BioGenome Project, aim to sequence the genomes of even more species, eventually building the complete genomic library of life. But do these advancements help us with conservation efforts? Or are the benefits of biotechnology limited to industrial and biomedical settings?

The value of genetic information is becoming increasingly apparent: from paternity tests and DNA traces in forensic investigations, to the characterization of genes related to common diseases, like cancer, we are becoming familiar with the idea that DNA can reveal more than meets the eye. This is especially the case for environmental DNA, or eDNA — DNA molecules found outside living organisms. Such DNA is often left behind in organic traces like tissue fragments and secretions. Practically, this means that water or air can host DNA from organisms that might be really hard to observe in nature for a variety of reasons — like being too small, too rare, or just too shy.

So, how do we determine which species left behind a sample of eDNA? The method of identifying a species based on its genomic sequence is called barcoding. A barcode is a short genomic sequence unique to a species of organism. Therefore, every time we encounter a barcode sequence, whether it is taken from a living animal or eDNA, we can associate it to the species which it belongs to.

When we have a mix of different species to identify, things become a bit more complicated. Sometimes we will pick up samples which represent an entire ecological community, and must sort through these using a process called meta-barcoding.

How does meta-barcoding work? Well, we want to be able to identify species based on the shortest possible species-specific sequence. Traditional laboratory methods for DNA amplification (PCR) are combined with DNA sequencing to read the DNA sequences found in any given water or air sample. Then, having a database of reference genomes for different species can serve as the identification key to link the sample sequences to the species they originated from.

Pinned insects can be found in the Upper Gallery of the Museum. There are currently 5 million insect specimens at the Museum, serving as a record of biodiversity at the time and space of collection. Museum collections are invaluable ways of monitoring biodiversity but rely on capturing live animals.

So, what does this mean for the future of ecology and conservation? Traditional monitoring of biodiversity can involve capturing and killing live animals. This is the case with insect specimens found in museums across the world. Although museum collections are irreplaceable as a record of the history of wild populations, regular monitoring of endangered species should rely on non-invasive methods, such as meta-barcoding of eDNA. Indeed, eDNA has been used to monitor biodiversity in aquatic systems for almost a decade. Monitoring terrestrial ecosystems through air samples is now also becoming possible, opening new possibilities for the future of conservation.

During March, the Museum delivered practical molecular workshops in our laboratory, reaching more than 200 Key Stage 5 students. Students have had the opportunity to learn about the use of eDNA in ecology, as well as get some hands-on experience in other molecular techniques. These include DNA extraction, PCR, the use of restriction enzymes, and gel electrophoresis.  The workshops were delivered by early-career researchers with practical experience in working in the laboratory, as well as Museum staff with a lot of experience in delivering teaching. Through the Museum’s workshops, which run regularly, the next generation of scientists is introduced not only to both human genetics, but also molecular tools used in ecological research, which without a doubt will become increasingly relevant for future conservationists.

Since 2009, the Museum runs practical workshops for Key Stage 5 students in the molecular laboratory at the Museum’s main facilities. Workshops started again this March, after the mandatory 2-year covid-19 break. Students can learn about and discuss the use of molecular techniques in biology by extracting their own DNA.  

We cannot conserve what we do not know. Monitoring biodiversity is the cornerstone of any conservation practice. Doing it efficiently, by making use of both traditional as well as molecular tools, can allow more accurate predictions for the future of biodiversity under the lens of anthropogenic change.


More Information:


British Insect Collections: HOPE for the Future is an ambitious project to protect and share the Museum of Natural History’s unique and irreplaceable British insect collection. Containing over one million specimens – including dozens of iconic species now considered extinct in the UK – it offers us an extraordinary window into the natural world and the ways it has changed over the last 200 years. The HOPE for the Future project is funded by the National Lottery Heritage Fund, thanks to National Lottery players.

Sisters of Science

THE PIONEERING LEGACIES OF KATHLEEN LONSDALE AND DOROTHY CROWFOOT HODGKIN


By Leonie Biggenden, Volunteer


As Women’s History Month comes to a close, this blog post looks at two ‘sisters of science’, friends and contemporaries Dorothy Crowfoot Hodgkin (1910 – 1994) and Kathleen Lonsdale (1903-1971), and considers some links between these remarkable women.

Dorothy Crowfoot Hodgkin is the only female bust in the Oxford Museum of Natural History and is the only British woman to have been awarded the Nobel Prize for science.  When she was awarded the Prize in 1964 – for her ground-breaking discovery of the structures of vitamin B12 and penicillin – there was much scepticism about whether women belonged in the field of science. One newspaper commemorated her achievement with the headline “Nobel prize for a wife from Oxford”.

Hodgkin was assisted and supported in her endeavours by fellow scientist Kathleen Lonsdale, who worked in London while Hodgkin was based in Oxford.  Both women were pioneers who advanced the x-ray crystallography technique, in which x-rays are fired at crystals of molecules to determine their chemical structure. Lonsdale applied the technique to diamonds, benzene, and later kidney stones.  For her efforts, she had a type of diamond named after her: Lonsdaleite.  It was not just any diamond, but one formed in meteorites, as a result of the heat and pressure of impact into the Earth’s atmosphere.

Both had similar difficulties as girls wanting to study science.  Hodgkin was initially not allowed to take chemistry at her grammar school as it was considered a ‘boy’s subject’, but she thankfully managed to reverse the school’s decision, allowing her to pursue her scientific career.  Lonsdale had to transfer to a boys’ school to be able to study maths and science, as these were subjects not offered at her girls’ school. She later described how her love of maths was inspired by learning to count at school using yellow balls.

Both women were supported by strong male advocates and mentors, such as the scientist William Bragg. Bragg first met Lonsdale when he was assigned as one of her examiners, and subsequently asked her to join his research school at University College London (UCL).  Lonsdale would later follow Bragg when he moved his laboratory to the Royal Institution.  Bragg was also responsible for inspiring Hodgkin’s interest in the properties of atoms, giving her a copy of ‘Concerning the Nature of Things’ when she was 15 years old.

Lonsdale and Hodgkin worked hard to show that science was a viable option for girls.  Lonsdale’s essay, ‘Women in Science – why so few?’, argued that social expectations placed on women discouraged them from pursuing science [1]. In fact, she was so determined to encourage girls’ interest in the subject that, while ill in hospital, she received special permission to be able to leave to award prizes for science at a local girls’ school. Hodgkin advocated for female scientists and directly mentored several who went on to become important crystallographers in their own right.

Both women eventually became professors, and Lonsdale was one of the first two women elected as Fellows of the Royal Society (FRS) in 1945. In 1947, Hodgkin was one of the youngest people to be elected FRS. 

Both Hodgkin and Lonsdale were extremely concerned about the threat of nuclear war, and in 1976 Hodgkin became president of the Pugwash Conference which advocated for nuclear disarmament.  Lonsdale was also involved with Pugwash and was president of the Women’s International League of Peace and Freedom.  A lifelong pacifist, she went to Holloway prison in London for a month for failing to register for war service and not paying her £2 fine.  She became a dedicated advocate for prison reform after seeing the conditions of the women first-hand.

My favourite facts about both Lonsdale and Hodgkin are those that give us a glimpse of their ingenuity.  Lonsdale made her own hat to meet the Queen and have her Damehood conferred upon her.  It was constructed with lace, cardboard and 9d worth of ribbon.  Similarly, when awarded her first honorary degree, Lonsdale pinned a strip of beautiful material inside her gown as a substitute for buying a whole new dress.  Hodgkin was also very creative. As a child, she created her own personal laboratory in the attic and acquired acids from the local chemist to experiment with.

The two women held each other in great respect, as testified to by the fact that Hodgkin wrote a biographical memoir of Lonsdale.  She said of her friend: “There is a sense in which she appeared to own the whole of crystallography in her time.”  Let’s agree that both women can claim that crown. Looking back, we can remember these women for their remarkable stories, featuring precious gems, prisons, penicillin and peace. But, most importantly, we should remember Hodgkin and Lonsdale as pioneers who paved the way for future women scientists.


References

[1] Hodgkin D (1975) Kathleen Lonsdale 28 January–1 April 1971. Biogr Mems Fell R Soc 21:447–484

Reading Archival Silences

MAUD HEALEY AND HER GEOLOGICAL LEGACY


By Chloe Williams, History Finalist at Oxford University and Museum Volunteer

Email: chloegrace1000@gmail.com


“The professor regrets to have to record the loss of the invaluable services of Miss Healey, who as a result of overwork has been recommended to rest for an indefinite period. This will prove a serious check to the rate of progress which has for some time been maintained in the work of rearrangement, and it is hoped that her retirement may be only temporary.” So ends the Oxford University Museum of Natural History’s 1906 Annual Report, marking the near-complete departure of Maud Healey from the archival record.

Despite how little of her history has been preserved, it is clear that Maud Healey made significant contributions to the field of geology. After studying Natural Sciences at Lady Margaret Hall in 1900, Healey worked at the Museum as an assistant to Professor William Sollas from 1902–1906. Here, she catalogued thousands of specimens and produced three publications. These publications were at the centre of debates about standardising the geological nomenclature, and turning geology into a practical academic discipline that could sustain links across continents. However, Healey was continually marginalized on the basis of her gender. Closing the Geological Society of London’s discussion of one of her papers, “Prof. Sollas remarked that he had listened with great pleasure to the complimentary remarks on the work of the Authoress, and regretted that she was not present to defend before the Society her own position in the disputed matter of nomenclature.”[1] Predating the Society’s 1904 decision to admit women to meetings if introduced by fellows, Healey had been unable to attend the reading of her own paper.

Photo of the Geological Society of London centenary dinner in 1907, at which Maud Healey was present. Healey can be seen seated in the fourth row from the front, three chairs to the left. Of the 263 guests, 34 were women, 20 of whom were the wives or daughters of academics, and only 9, including Healey, were present ‘in their own right’. [2] Source: Burek, Cynthia V. “The first female Fellows and the status of women in the Geological Society of London.” Geological Society, London, Special Publications 317, no. 1 (2009): 373-407.

Healey later worked with specimens collected by Henry Digges La Touche in colonial Burma (now Myanmar). While Healey worked with the identification of species, acknowledged by La Touche himself as ‘a more difficult lot to work at’ than similar specimens assigned to her male contemporaries, the physical collection and therefore its name and record is attributed to a male geologist. [3] She continued her work identifying La Touche’s collection of Burmese fossils after retiring from the Museum in 1906 and published a report about them in 1908. What happened to her afterwards is unclear. Tantalizing snippets like a 1910 marriage record might suggest that she turned to a life of domesticity, but whether Healey continued to engage with geology as a hobby remains uncertain.

It is almost unbelievable that a professional of Healey’s calibre could abandon the work in which she excelled. However, Healey lacked any familial connections to geology, and apparently did not marry into money, which would have made it difficult for her to retain access to organizations like the Geological Society of London. The diagnosis of ‘overwork’ mentioned in the Annual Report makes it possible that a medical professional could have discouraged her from engaging further in academia. Unfortunately, any diaries or letters which might have provided us with further clues were not deemed worthy of preservation.

Maud Healey on a dig site (location unknown). Image from the Archives at Oxford University Museum of Natural History.

Tracing Maud Healey’s history to 1910, it might seem as though we hit a depressing dead end. Healey is one of many nineteenth-century female geologists who participated in an international community in a range of roles including collecting, preserving samples, and actively producing knowledge. However, like many of her colleagues, her contributions are largely absent from the historical record. My research doesn’t aim to simply ‘rediscover’ these exemplary women after previously being ‘hidden’ from history, but instead considers how history itself is constructed from a material archive created along lines of gender and class. A subjectivity which surfaces only rarely in appended discussions to academic papers, and in spidery cursive on ancient fossils, Maud Healey ultimately suggests the need for women’s history to read archival silences as their own stories.


Works cited

[1] Healey, M. ‘Notes on Upper Jurassic Ammonites, with Special Reference to Specimens in the University Museum, Oxford: No. I’, Quarterly Journal of the Geological Society of London 60, (1904), p.1-4.

[2] Burek, Cynthia V. “The first female Fellows and the status of women in the Geological Society of London.” Geological Society, London, Special Publications 317, no. 1 (2009): 373-407.

[3] La Touche, H.D. Letter to Anna La Touche, 1 August 1907. La Touche Collection. MSS.Eur.C.258/77. Asian and African Studies Archive, The British Library, London, UK.


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Open Doors

OXFORD UNIVERSITY MUSEUMS AT THE INTERFACE OF ‘TOWN’ AND ‘GOWN’


By Rawz, Sound Artist in Residence for 2022, St John’s College, Oxford


Oxford is a curious place and, for me, it’s getting curiouser and curiouser. 

I love this city; I’ve called it my home for more than three decades. I couldn’t picture myself living anywhere else. But recently, I realised I’d only ever really seen half of my fair city, that there was a world beneath the dreaming spires that I had never even considered that I would be permitted to explore. I realised that I had never really walked through Oxford city centre; I had always been guided around it by 10 foot high fortifications and locked doors.

I grew up very much on the town side of Oxford’s notorious ‘town versus gown’ divide. I left school with no qualifications, and since then have spent much of my working life supporting the most marginalised people in the city, particularly young people struggling with formal education as I did. Doing this in a city whose very name is a buzzword for elitism and privilege means that I’m no stranger to juxtaposition. It continues to influence my art to this day.

I’m a hip hop artist, primarily focused on lyric writing and poetry. In 2009 I set up my own business, the Urban Music Foundation, with the hope that I could pass on some of the art skills that helped me get through tough times growing up, and that have enabled me to express myself fluently as an adult, and build a career around my art. I’ve found music and lyrics to be a uniquely useful tool in communicating ideas that are hard to transmit in any other way. Someone once said to me that music is what emotions sound like, and I’ve found that to be true.

After a video call with one of GLAM’s community engagement team during the lockdowns of 2020, I had an idea for a project that became Digging Crates — a decolonisation project using hip hop music to reinterpret the musical instrument collection at the Pitt Rivers Museum, next door to the Museum of Natural History. I immediately saw the project’s value as a way to analyse and address some of the divisions and imbalances I see in Oxford, and in wider society. Just over a year after I sat down and wrote the original proposal for this project, I was offered the position of Resident Sound Artist for 2022 at St John’s College. Even as I write this I feel a surreal mix of pride and disbelief — not many people from my community in Blackbird Leys would have considered the idea of being offered such a post in their wildest dreams!

The front doors of the Museum are open every day from 10:00 to 17:00.

The past 18 months have seen doors open – both literally and figuratively – that I had never even considered walking through. I hope they continue to do so, and that they remain at least a little ajar for those following my path. Many of you, dear readers, will be glad to know that one place I have enjoyed exploring, both as a “townie” and, more recently, in my newer self-proclaimed title as “Town Ambassador to the Land of Gown”, is the Museum of Natural History. Of all Oxford’s museums, the Museum of Natural History has the biggest impact as soon as you walk through the doors (which are usually wide open). I’ve taken many “disengaged” and “hard to reach” young people to visit, and the heady cocktail of stuffed animals, dino bones, and cool rocks almost always proves irresistible to all but the most sceptical children, young and old. I would love an opportunity to get creative in this amazing space and am often trying to think of an excuse. Any ideas – you know where to find me! 

Whatever happens next, stepping through the looking glass into this strange new world of the gown with its quirky, bizarre traditions, and its fascinating, inspiring, and problematic histories, is an experience I will never forget. I’m honoured to be the person taking this step on behalf of my community, and grateful for all those who worked hard and made sacrifices for me to be able to do so.


Want to find out more?

This link will connect you to some of the projects I am working on and some of my past works: https://linktr.ee/rawz_official I’d love to connect with you on social media or via any other means, I’m always up for discussing this important work.

If you’d like to attend my next workshop at St John’s on March 10th, we will be watching the documentary made during Digging Crates and I’ll be sharing some behind the scenes photos and stories, you can sign up via this link: https://www.sjc.ox.ac.uk/discover/events/workshop-digging-crates-project-and-film-screening/

Beyond Buckland

DISCOVERING YORKSHIRE’S ANCIENT BEASTS


By Susan Newell

Susan Newell is a doctoral student researching the teaching collections of William Buckland, the first Professor of Geology at Oxford who taught from 1813 to 1849. She reminds us here about Buckland’s role 200 years ago in interpreting the important Pleistocene discoveries being celebrated this year, and the way that Mary Morland, a talented local naturalist, and many others, contributed to making this new knowledge.


This year marks the 200th anniversary of a great advance in our understanding of the geological past… a story which begins in the nineteenth century, with the discovery of a bone-filled cave in Kirkdale, Yorkshire. 

Uncovered by local quarrymen in 1821, the discovery of the Kirkdale cave and its contents of mysterious bone was the source of much intrigue. When news of the discovery reached William Buckland, Professor of Geology at Oxford University, he decided to travel up North to visit the site. However, by the time Buckland arrived at the cave, local collectors had scooped up most of its contents. Nonetheless, he was able to retrieve and examine some of the cave’s remaining material, which led him to an astonishing conclusion — Yorkshire must once have been home to hyaenas, elephants, hippopotamus and rhinoceros, and what was now known as the Kirkdale cave was once a hyaenas’ den.

W. B. Conybeare, lithograph, ‘The Hyaena’s Den at Kirkdale near Kirby Moorside in Yorkshire, discovered A.D. 1821’. Reproduced by kind permission of Christ Church, Oxford.
This light-hearted reconstruction of the hyaenas’ den shows Buckland illuminating the scene, in every sense. It is thought to be the first visual reconstruction of the pre-human past.

Central to Buckland’s theories were some small white balls that he had found amongst the debris in the cave. Buckland sent these balls to William Wollaston, a celebrated chemist based in London, for analysis.  He also asked Wollaston to visit the zoo at Exeter Exchange in London and show the balls to the hyaena’s keeper there.  Together with the results from Wollaston’s chemical analyses, the keeper confirmed Buckland’s hypothesis — the balls were droppings from animals very similar to modern hyaenas. Meanwhile, the anatomist William Clift was able to identify the bones from the Kirkdale cave as belonging to other extinct species related to those found living in tropical countries today. Buckland concluded that the cave must have been a den for ancient hyaenas, who would drag parts of the dead animals they had found (or killed) inside and, after feeding on them, leave piles of bones and droppings behind.

In order to strengthen his theory, Buckland discussed the behaviour of hyaenas in the wild with army officers connected to Britain’s colonial expansion in India. These officers also sent Buckland fresh specimens captured by local people. When a travelling menagerie visited Oxford in 1822, Buckland took the opportunity to experiment; feeding bones to a hyaena and noting that the teeth marks matched those on the fossilised bones from the cave.

Buckland’s findings were something of a shock to his contemporaries. When lecturing, he employed several different methods to try and convince his audiences that his theories were true. This included presenting fossil specimens and bones from living species for comparison, and showing maps, diagrams and drawings. Mary Morland contributed some of these illustrations, including large drawings of living animals, and technical drawings of bones that were later engraved for use in Buckland’s publications. Mary’s Kirkdale drawings seem to have been the first that she produced for William before the couple married in 1825.

Fossil hyaena jaw in the Museum’s collection, possibly the one featured in the engraving alongside it. Engraving is by James Basire after a drawing by Mary Morland. Published in William Buckland’s article in the Royal Society’s journal (1822) on the Kirkdale cave discoveries. [1]

Buckland’s work on the Kirkdale cave was revolutionary, not least because he was the first to make a scientific study of a cache of bones of this type.  Although similar bones from ‘tropical’ species had previously been found in Northern Europe, people thought that they had been washed up by a catastrophic flood, believed by many to be the biblical Noah’s Flood.  Modern analysis has now allowed us to deduce that the bones date to an Interglacial period when Britain was joined to Europe and had a hot climate, about 120,000 years ago.  

Here at the Museum, Buckland’s collections and archives are as much of a treasure trove as the Kirkdale cave. It is through accessing these archives that we can learn about the surprising range of people who contributed to the emergence of new scientific knowledge from the Kirkland cave — quarrymen, collectors, zookeepers, chemists, anatomists, colonial officers in India, workers in India, and artists like Mary Morland. To find out more about the incredible legacy of the Kirkdale Cave, look out for ‘Kirkdale200 – Lost Beasts of the North’, a symposium organised by the Yorkshire Fossil Festival, 12th March 2022.

Mary Morland, watercolour and gouache, lecture illustration of a hippopotamus, signed ‘MM’.
Hippopotamus bones were found at Kirkdale cave in Yorkshire, but as there were no living hippos to be seen in Britain at the time, this drawing would have been a valuable teaching aid.

[1] William Buckland, ‘Account of an Assemblage of Fossil Teeth and Bones of Elephant, Rhinoceros, Hippopotamus, Bear, Tiger, and Hyaena, and Sixteen Other Animals; Discovered in a Cave at Kirkdale, Yorkshire, in the Year 1821: With a Comparative View of Five Similar Caverns in Various Parts of England, and others on the Continent’, Phil. Trans., 2 (1815-30), 165-167.

Thanks for the Myrmories

AMAZING ANTS AND THE LEGACY OF E.O. WILSON


By Jordan Wernyj – Deputy Visitor Services Manager


If you happen to encounter one of the 50+ ant types in Britain, observe their hurried activities and interactions with each other. One cannot help but compare the complex functioning of an ant society to our own, and consider its advanced societal structures in relation to humans. The way an ant colony organises itself is highly industrial and commanding, subdivided into castes including queens, males, and worker ants, the latter of which contribute to their colony through roles as diverse as tending to larvae, foraging, or attacking rival threats.

Having worked at the Museum of Natural History for a few months, my interactions with specimens and discussions with the entomology department have reignited an intrigue in myrmecology, the study of ants. This began with locating the ant case on the Upper Gallery on the south side of the Museum. You can find fantastic British insects on display, selected from our ginormous British Insect Collection. Specimens include Lasius fuliginosus (Jet Black Ant) and Formica saunguinea (Slave-Making Ant) —the latter aptly named given its tendency to attack ants from other colonies and force its victims to work for them.

Slave-making Ant and Jet Black Ant on display in the Museum

Outside of the Museum, a viral video of a group of ants following each other in a circle led me to the even more surprising discovery that ants can mistakenly cause their own demise. The name of this circular march is an ‘ant mill’ which, rather morbidly, is a circle of death. Ants use pheromones to communicate with and organise each other during normal behaviour. However, these chemical trails can be lost, which for worker or army ants that leave the colony to forage or attack, it is a prominent risk. Ants follow one another, and if the leading ant loses the trail and begins to follow an ant behind, a rotational spiral motion occurs. Sadly, an ant mill can cause tragic consequences, with either the ants picking up the trail back to the colony, or continuing in the rotation until they die of exhaustion.

Having expressed curiosity in myrmecology, an entomologist at the Museum provided me with a fascinating book Tales of the Ant World by Edward O. Wilson. Wilson’s enlightening work within myrmecology and ecology gave him the nickname ‘Dr. Ant’. Wilson, highlighting his scholarship on the ant species Camponotus femoratus – one of the most aggressive in the world.

These intriguing invertebrates are located within the depths of the Amazon rainforest and are largely arboreal, territorial, and scary! Nonetheless, the intrepid Wilson decided to test out the ants’ offensive tactics. A mere brush up against an inhabited tree would provoke swarming formations, snapping mandibles and, if the pain wasn’t already discomforting enough, a release of formic acid. Edward Osbourne Wilson sadly passed away on Boxing Day 2021, while I was halfway through reading this book. It is a fascinating work that not only informs the reader of ant facts, but tells the most interesting story of a myrmecologist’s life and his discovery of ant species.