Bringing nature online – all 13 million samples of it

In downtown Helsinki, the remains of millions of animals and plants rest in cabinets in the long hallways of the Finnish Museum of Natural History. They've been collected over 300 years, and in the era of climate change and biodiversity loss they are more important than ever. But how will one transfer more than 13 million specimens from the cabinets to the Internet?

The wasp's stare is piercing.  Each hair on its head shows clearly, the yellow and black patterns criss-crossing its face. The colours are so bright they pop. It looks perfectly alive.

Yet it is not. The female wasp in the photo died on October 2, 2012 when Marja-Liisa Seväkivi collected it in the Leppiniemi village of Muhos, near the city Oulu in Northern Finland. Now its remains rest in downtown Helsinki, in one of the grey cabinets that fill the hallways of the Finnish Museum of Natural History, along with nine million other insect specimens. A small paper label records the collector’s name and the date and place of collection.

The wasp belongs to the collections of the Finnish Museum of Natural History that comprise 13.3 million animal, plant, fungal, mineral and fossil samples and specimens. Its photograph, on the other hand, represents a recent effort in a massive undertaking that seeks to photograph each specimen and store it and the accompanying data in a database, thus allowing people anywhere in the world to examine and analyse the information online.  

Carrying out this undertaking is a complex process that will take years to complete, but the work is of vital importance. Quite literally: the future of our planet may depend on it.

 

One of the largest collections in the world

The report by the UN Intergovernmental Panel on Climate Change (IPCC) this autumn was a grim read. In order to escape the most catastrophic consequences of changing climate, we must limit global warming to 1.5°C. To achieve this, we must reduce carbon dioxide emissions to zero by 2050.

The World Wide Fund for Nature (WWF) did not provide much relief. According to its report, the average population sizes of vertebrate species have already dropped by more than half in just four decades.

Humankind was blissfully ignorant of such developments in March 1678, when the Royal Academy of Turku granted Professor Elias Tillandz permission to fence in a herb garden to establish a botanical garden. Tillandz’s garden launched the work that this year culminates in the 340th anniversary celebration of the national collections fostered by the Finnish Museum of Natural History, an independent research institution that functions under the University of Helsinki.

Most Finns know the natural history collections thanks to the museum’s three public attractions showcasing them: the Natural History Museum, Kaisaniemi Botanic Garden and Kumpula Botanic Garden. Last year, the three venues attracted almost 250,000 visitors in total. The Natural History Museum is one of Finland’s most popular museums, and school and daycare groups visit it regularly.

Although public exhibitions are the most visible part of the museum’s activities, its most important and extensive task is to gather and preserve the collections and make them available for researchers.

The museum’s storage rooms hold millions of pressed plants, mammal skins, pinned butterflies, dried fungi, swan wings, mineral crystals, deer antlers, whole fish, cave bear fossils, stuffed birds, meteorite pieces, bird’s eggs – practically anything one can imagine finding in nature.

Most specimens are from Finland, but the collections also include a wide variety of foreign samples that Finns have brought back from their expeditions in the course of history. The samples have been preserved by drying, freezing or immersion in alcohol. The collections make up one of the fifty largest natural science collections in the world.

In addition to the collection samples, Luomus maintains several databases, including systematically collected data on bird distribution.

Ordinary people have always contributed to the collections as well. The bird movements database, for example, is based on the observations of thousands of volunteer birdwatchers. People also continually add to the vertebrate collections by sending dead animals to the museum. Every year, the collections grow by more than 50,000 samples.

Birds have moved northward by 1.5 kilometres per year

The specimens were originally collected to identify and classify species – to better understand biodiversity, or the variety of plant and animal life in the world. However, today the collections also offer a direct view into the population sizes and distribution of different species over a span of several centuries. For researchers studying climate change, species loss, and other environmental changes natural history collections are a treasure trove.

“The information stored in these collections is unique because we cannot go back to the 18th or 19th century to gather new information. Information from the past lives on only in collections like these,” explains professor Leif Schulman, director of the Finnish Museum of Natural History.

“In recent decades, we have come to realise how incredibly quickly we humans are changing the world. All comparative data from the past has become invaluable because it allows us to understand just how much and how quickly we have already changed the environment.”

By examining the past of species, we can also try to predict the future.

Researcher Aleksi Lehikoinen coordinates the museum's bird monitoring schemes. Based on the museum's collections and databases, he has estimated that bird species nesting in Finland have been shifting northward by 1.5 kilometres per year for the past three decades. This means that northern species will soon reach the Arctic Ocean and no longer be able to adapt by continuing to move north. If climate change continues, these species are facing extinction.

To make full use of the sample data, the information must be digitized so that researches can access the information online and take full advantage of tools to analyse big data. Yet to do so is not a simple task.

Production lines and 3D scanners

Next door to the Natural History Museum in downtown Helsinki a square construction vaguely resembling a model railway set fills a small room. A black conveyor belt transports a little box on a journey around the room. Midway, the box stops under a set of bright lights. A camera photographs its contents: a butterfly and its label. After the image is taken, the box continues to chug along until it returns to the desk of Jere Kahanpää.

Kahanpää spends two hours a day in this room, using a pair of tweezers to carefully pick insects from their trays and arrange them in the conveyor box. After the sample has been photographed, he places it back on the tray. The work is slow and meticulous. It requires so much concentration that the digitising team decided to cut the shifts from three hours to two, because the quality of work began to suffer when the person handling the samples started to tire. The team members would forget to photograph the sample's data label or make typing errors in the database descriptions.

Kahanpää’s title is digitisation coordinator, but senior museum technicians, collections coordinators and trainees also photograph the samples. It’s all hands on deck.

For the work, Luomus has acquired production lines for digitisation, flatbed scanners, photo microscopes and a 3D scanner. The 3D scanner is used to create three-dimensional images of bones, especially of mammal sculls. Researchers can take computerised measurements of these images and study how genes affect skull shape or tooth structure.

So far, a tenth of the collections – 1.3 million samples – have been fully digitised, meaning that all their data is available electronically. Only half of these have been photographed.

Photographing the samples is important because pictures allow people on the other side of the world to examine the specimens without having physical access to them. Until now, Brazilian or Japanese researchers have had to travel to Helsinki to study a specific sample – or request the museum to send the sample by post. Now a sharp close-up photograph and the data are often enough to identify species and examine their distinctive characteristics. This saves researchers’ valuable time, reduces unnecessary travelling, and protects the samples against the strains of shipment.

Database already boasts 200,000 users from 51 countries

In 2017, the museum digitised more than 350,000 specimens, whereas just a few years ago the annual number was only a few tens of thousands. Full digitisation includes photographing the specimen and entering its label data into the database. This is no simple feat because the information is usually written by hand on a small piece of paper and can be in Finnish, Swedish, Latin or even Russian in the Cyrillic alphabet. The handwriting on the labels varies greatly, and some insect specimen labels use codes that are explained in the accompanying entomological collection notebook, a kladikirja in Finnish. Without the accompanying data, the specimen is worthless to science.

But the technical handling of the specimens is not exactly easy either: How do you photograph specimens immersed in alcohol and stored in glass jars? Or large bones? Entomological samples can also cause the team additional work because their tiny labels often lie under the insects, and the specimens must be unpinned to access the label. Researchers are hoping that in the future, the X-ray inspection technology used in airports will allow labels to be photographed through the insect, without having to remove it first.

The photographs and their accompanying data are recorded in an open database developed by the museum that encompasses all natural science collections in Finland. The data is accessible to the public through the Laji.fi portal launched last year, which gives everyone access to the information. In a year and a half, the portal has attracted over 200,000 users from 51 countries.

Luomus also hopes to be able to open the digitisation process of its collections to the public. The purpose is to create a website on which anyone could access the photographs of specimen labels on their own device and enter the relevant data in a digital format.

In addition, Luomus coordinates an EU-funded project that is developing methods to digitise Europe’s 1.5 billion natural science specimens within one generation.

Once fully digitised, the samples are likely to produce surprising findings.

From imaging ant brains to DNA barcoding butterflies

By analysing the chemical composition of a Colorado potato beetle, a notorious potato crop pest, researchers can find out how each beetle arrived in Finland. By examining mammoths’ teeth, scientists can reveal the environment mammoths lived in. By imaging an ant’s brain, researchers have been able to witness how a parasitic brain worm turns the ant into a zombie. An international research team found out how koala viruses have spread by examining 120-year-old koala skins. Researchers can even look at old eggshells to determine how the insecticide DDT has spread.

Modern techniques indeed allow researchers to glean new information from ancient samples. DNA analyses, X-rays, MRIs, CT scans and various chemical analyses can show how environmental toxins, viruses, and diseases have spread over centuries. 

The Finnis Museum of Natural History has already started to build a DNA barcode library of Finnish species in cooperation with the University of Oulu.

“Studies show that a specific segment of DNA can be used as the distinctive characteristic of that species. This works very well in insects, for example,” explains Director Schulman.

“We first analyse this DNA segment of a sample whose species has already been identified. For example, we can choose a swallowtail from our collections. We then run the same DNA analysis on a few different individuals of the same species to ensure that what we have is really the typical DNA barcode for the species in question.”

Once the names and DNA barcodes of species have been compiled in the library, researchers can investigate the occurrence of a given species in nature without actually seeing any individuals.

“We can take a soil sample and analyse the DNA it contains. The DNA of a specific species may have ended up in the soil from eggs, excrement, needles, feathers or any other part of an organism that may have fallen on the soil.”

Researchers can use these environmental samples to determine which species have existed where. As incredible as it seems, researchers can, for example, still discover the DNA of mammoths in Siberia’s permafrost. This would be impossible without the collection samples that researchers have used to determine mammoth DNA and extract the DNA barcode bearing the distinctive characteristic of mammoths.

With some techniques and findings, we immediately know how to put them to use. With others, we are not yet sure how they will be useful. But that is science: first you study something, then you scrutinise it further, and later you find that the information might be of utmost importance in a completely different context.

As has happened with the natural history collections.

Read more:

The Finnish Museum of Natural History
Photos and collection information of all the digitized samples at Laji.fi
European Union Icedig program for digitizing natural history collections