CMN Acquisitions

It is interesting to see what the Canadian Museum of Nature (CMN) has been accomplishing over the years, by investigating the museum’s collaborations with organisations worldwide. The museum is in partnerships with over 600 universities and research organisations in 52 countries. We could not achieve our mission alone!

There were more than 3000 acquisitions over the past 25 years, and they can be grouped under:

  • Botany      1348
  • Mineralogy   584
  • Palaeontology 55
  • Zoology     1072

Acquisitions can be in the form of donations, exchanges, purchases, or staff field trips.

Sometimes a donation is large. For example, in 2007 a donation of beetles, Coleoptera: Scarabaeidae included 64392 specimens!  In 2018, a donation from Université de Montréal of “Collection exhaustive des invertébrés (et poissons)de fond du St-Laurent maritime.” was almost as large.

The Canadian Museum of Nature’s CSIM department maintains a spreadsheet with a row for each acquisition. Information was entered into this spreadsheet by museum staff over the course of 25 years. The museum is much older than 25 years, but the spreadsheet only goes back that far. Some examples from the spreadsheet from six continents are:

  • Smithsonian Institution, Department of Paleobiology, Collections, Washington D.C., Section: Palaeontology, Collection: Fossil Vertebrate, Description: Plaster cast of holotype of Enaliarctic emlongi including skull and both mandibles, Transaction type: exchange,  Feb 2014,
  • Herbario Nacional de Bolivia, La Paz, Bolivia, Collection: Lichen (CANL), Description: Lichens of Bolivia,  Transaction type: donation, 1993
  • Herbarium (CHR), Landcare Research – Manaaki Whenua, Lincoln New Zealand, Collection: Vascular Plant (CAN), Section: Botany, Description: Pseudognaphalium duplicates of CHR 582880 & CHR 582881, Transaction type: exchange,   2013
  • National Herbarium, South African National Biodiversity Institute, Pretoria, South Africa, Section: Botany, Collection: Vascular Plant (CAN), Description: Vascular plants (list provided),  Transaction type: donation, 2013
  • Instituut voor Systematische Plantkunde, Rijksuniversiteit Utrecht, Utrecht, Netherlands, Section: Botany, Collection: Bryophyte (CANM)  Description: Bryophyta Neotropica Exsiccata, Fasc. VI, No. 251 – 300,  Transaction type: exchange, 1992
  • Department of Biology, Sri Venkateswara University, Tirupati, An.Pra, India, Section: Zoology, Collection: General Invertebrate, Description: Poecilobdella granulosa (Savigny), 1988

How did we investigate the information in this spreadsheet? It is large, over 3000 rows, so it is not something you can read directly. The information is easier to visualise with the help of the interactive map  HERE to get a better feel for the extent of the worldwide collaboration. We created the map using custom computer programs which were written for this purpose over the past few weeks. The programs read in the spreadsheet and tabulate the rows and fields. 

The spreadsheet was created by wetware (a computer geek term for humans), so as expected there are normal variations in spelling. For example, ‘Ontario’ was sometimes entered as ‘Ont’, ‘ON’, with or without the capitalisation, (that is 6 variations so far). Add an incorrect spelling or two for a total of 7 or so variations. The variations are only a problem when we need to use a software program to process the information: the program thinks there are 7 different provinces where there is in fact just one Ontario. The problems were not just in ‘Ontario’, the words University and Department have a few abbreviations and variations, not to mention some Quebec names with accented characters. Did I mention typo’s? So we needed to do some ‘cleanup’ by hand before the programs could be used.

We ‘cleaned’ the data using OpenRefine, an open source program which makes the task easy. OpenRefine presents the information for view like a spreadsheet, but it does not work like a spreadsheet. It allows you to facet a column so you see something like this for the Province/State column:

  • Oklahoma 5
  • Ontario 600 
  • Ontartio 1
  • Ont  400 
  • ont 2
  • ON 45
  • Oregon 15

Looking at this, the variations stand out. Then OpenRefine allows you to correct typo’s. When a problem appears in several rows (like ‘ON’ appearing in 45 rows), they can all be corrected in one action.

Then we wrote a simple Python program to find the Latitude and Longitude coordinates for each city, by invoking a Google web service. The program stores the location data in a file. The program also reformats the pertinent spreadsheet information into a file that our interactive map program can read. 

The interactive map program presents a world map showing the locations of the organizations which we collaborated with. You can zoom and pan the map, and click on a location to see the name of the organization. The interactive map shows coastline and border mapping information from OpenStreetMap.

In some locations, we collaborated with several organizations so when you click on the icon in the map you see a list of them. At this point we encountered more variations’ such as ‘Biology Department’ vs ‘Department of Biology’, which results in two list entries where there should only be one. We went back to step one to remove duplication from the names.

Now, looking at the map, you can see where in the world we have been collaborating with scientific organizations! Our next step is to look at the partnerships over the years, and present this in charts. We also plan to go back further than 25 years, as the museum has been active since the 1850’s. It will be interesting to see the archives, I am looking forward to it.

Bio: Rick Leir is a volunteer who worked many years in IT but regrets not being a scientist!

CMN Loans

It is interesting to see what the Canadian Museum of Nature (CMN) has been accomplishing over the years, by investigating the museum’s collaborations with organizations worldwide. The museum is in partnerships with over 600 universities and research organisations in 52 countries. We could not achieve our mission alone!

The Canadian Museum of Nature’s CSIM department maintains a spreadsheet with a row for each loan. Information was entered into this spreadsheet by museum staff over the course of 25 years. The museum is much older than 25 years, but the spreadsheet only goes back that far.

The map above shows loans during a five year period. Click ‘next’ to see the next five years. You can zoom and pan. Loans from the CMN are shown with short-dashed lines and loans to the CMN are shown with long-dashed lines. When there are both to and from loans in a five year period, they are shown with a solid line. Hover over a marker to see loans details.

Marine Fishes of Arctic Canada

A Spotted Wolffish on the cover of Marine Fishes of Arctic Canada. 
© Candaian Scientific Submersible Facility/DFO, 2014

Coad, Brian W. and Reist, James B. (Edited and authored) with contributions by Peter Rask Møller, Claude B. Renaud, Noel R. Alfonso, Karen Dunmall, Michael Power, Chantelle D. Sawatzky, Fikret Berkes, J. Brian Dempson, Les N. Harris, and Heidi K. Swanson. 2018. Marine Fishes of Arctic Canada. Canadian Museum of Nature, Ottawa and University of Toronto Press, Toronto, Buffalo, London. xiv + 618 + pp., 521 figures, 219 maps, 182 colour figures.

This large format book will tell you everything you want to know about Arctic fishes. Up until now, information on Arctic fishes was relatively difficult to find because the Arctic is remote and scientific studies on fishes were more likely to be done closer to home. Museum of Nature researchers have been changing that and documenting new species in the north. Here is their announcement of the book

It was awarded the Dartmouth Medal.

A few years ago while the book was being written, a blog post (link to nature.ca) gave us some background.

Now you can read the book at OPL. Their description and summary of the book:
“Because of its wide geographic scope and harsh conditions, Canada’s Arctic presents many challenges for researchers and biologists. In this book, scientists from the Canadian Museum of Nature and Fisheries and Oceans Canada present a guide to the marine fishes found in Arctic Canadian waters and featuring up-to-date research on 222 species. Each of the 58 families is described in a general account followed by species accounts comprising common name, taxonomy, physical description and identification, habitat data, biology, distribution, commercial importance, and traditional knowledge. Many of the species are known only to scientists and come from the deeper waters of the Davis Strait while others have been important food sources for Indigenous peoples for millennia. A wide-ranging general introduction looks at the history of research, fish habitats, climate, fisheries, fish structure, and the collection and preservation of fishes while an essay on traditional ecological knowledge provides an important perspective. Exquisite black-and-white drawings of each species complement colour photos and illustrations. Finally, new range maps showing distributions across Arctic Canada were created for this volume. The book will be a welcome reference work for Northern residents, biologists and ecologists, environmental groups, and resource extraction companies operating in the North, as well as commercial and amateur fishers in Canada and in other circumpolar countries.”

A review by Betty Galbraith, Washington State University:
“Marine Fishes of Arctic Canada is a beautiful book. It is the first encyclopedia dedicated exclusively to the Arctic fishes of Canada and contains 222 species organized by 58 families. Each family of fishes is introduced with an overarching description of the biology, life cycle, behavior, and specific habitat. This family section is followed by accounts of each species within the family, including common name, taxonomy, physical description, biology, life history, distribution, commercial and cultural importance, and a short bibliography of sources. Each species also has a map of its range and beautiful line drawings. An introduction to the subject covers the history of research, fish habitats, climate, environment, and more. The book also contains a glossary of terms and a bibliography. Coad (emer., Canadian Museum of Nature) and Reist (Fisheries and Oceans Canada) both bring considerable expertise to this subject, having written several articles and bibliographies on Arctic fishes. A must-have book. Summing Up: Highly recommended. All readers.”

Backyard Wilderness 3d Movie

An image from the Backyard Wilderness 3d movie

The Nature Museum in Ottawa is playing an amazing movie showing wildlife in the north america forests. Backyard Wilderness has a feel-good family oriented theme.

It is amazing how close-up the photography is. The foxes, wood ducks, mice and salamanders are at times just inches from the camera. Clearly the photographer would be using a sensor to trigger the camera, but still, how could she set up the equipment in such a perfect position?

The theatre’s 3d vision is much better than what you see in the Cineplex with their disposable polarised glasses. Nature.ca has non-disposable glasses which give a bright, clear 3d view. The glasses use active shutter technology.  The left lens ‘opens’ for a fraction of a second, and the projector/screen shows the left view. Then the right lens ‘opens’ and the projector/screen shows the right view, and the cycle repeats. You cannot see any flickering or hear any mechanism. The 3D effect is more striking that what you get with polarised glasses, because they do not perfectly block your left eye from seeing the right image and vice versa.

There are some human actors in the movie, but they are upstaged by the wild animals. The human family lives in a rather nice two storey house, which is in a forested setting and harmonious with nature. Any neighbouring house seems to be out of sight. Any vehicles or roads are almost out of sight. This is an ideal living arrangement that would be difficult to attain for most of us!

The cost is $4 in addition to the regular museum entrance fee.