Basics of Taxonomy: Describing, Illustrating
and Writing biodiversity
A course in the Edit Modern Taxonomy course programme 2010-2011, as a four module course: 1Learning the computer program DELTA (DEscription Language for TAxonomy), 2Vectorbased digital illustration technique, 3Scientific writing and communication, 4Different methods to make a scientific illustration (equivalent to 5 ECTS).
Report to EDIT/DEST 2010-11-25
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Instructors and participants at the Edit course “Basics of Taxonomy”. Standing from left: Gabor Lövei, Biju Abraham, Oliver Coleman, Marko Proust, Margret Packer, Charlotte Havermans, Thomas Kunze (standing behind), Ascensão Ravara, Kerry Hadfield, Verena Kutschera (standing behind), Camilla Hatton‐Brown, Anton Lyakh (kneeling in front), Yves Braet, Diana Penna, Ankita Gupta, Tomas Cedhagen, Sancia Van der Meij, Matz Berggren (standing behind), Milka Elshishka, Ivo de Sena.
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Introduction Exploration of biodiversity is one of the big challenges of this century. In many areas there is ongoing loss of species and the biodiversity is decreasing. There is increasing demand for taxonomic expertise and increased need for more efficient data handling by the taxonomists. There is therefore a dire need for courses dealing with different aspects of taxonomy. To meet this need and to increase the interest, knowledge and skills in taxonomy, it was decided to offer PhD-students and early postdoc’s the opportunity of learning DELTA (DEscription Language for TAxonomy), which is the state of the art tool in taxonomy. Together with illustration, writing and presenting lectures we thought this would be a good help for the future taxonomists! Funding Funding for the course was provided by the Edit Modern Taxonomy course programme 2010-2011. Venue The venue of the course was at the Sven Lovén Centre for Marine Sciences, Kristineberg, Sweden. 8 – 19 November 2010. Participants The course was attended by 13 Ph.D. and M.Sc. students and three post doc.; of which , two were Belgian, two were British, two were German, two were Indian and the other eight was divided as being one person from Estonia, South Africa, Ukraine, Netherlands, Bulgaria, Portugal, Brazil and Colombia respectively. A list of participants and teachers is enclosed in Appendix 1. Organizers The course was set up by Dr. Isabella Van de Velde (Royal Belgian Institute of Natural Sciences, Brussel, Belgium) together with Dr. Matz Berggren (Inst. Marine Ecology, Gothenburg University, at the Sven Lovén Centre for Marine Sciences, Kristineberg, in Fiskebäckskil, Sweden) that also was the organizer on-site. Teachers The teachers consisted of (listed for the different modules): DELTA: Dr Matz Berggren, Institution of Marine Ecology, Göteborg University, Sweden and Dr Charles Oliver Coleman, Museum für Naturkunde, Berlin, Germany. Digital drawing: Dr Charles Oliver Coleman, Museum für Naturkunde, Berlin, Germany. Scientific illustration: Prof. Tomas Cedhagen, Department of Marine Ecology, University of Aarhus, Denmark. Scientific writing and communication: Dr Gabor Lövei, Department of Plant Protection, Danish Institute of Agricultural Sciences, Slagelse, Denmark.
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Content The course focused on describing taxonomy in different ways. The first part was the software package DELTA (DEscription Language for TAxonomy) used for description of both species and higher taxa of organisms. The course also gave some general introductions to databases and construction of databases in general, and to biological databases available at the internet. Another part was aiming to how to write and present scientific studies, explaining extensively the details of writing scientific publications. Also an important part was how to prepare figures and tables for publications and presentations. The two remaining parts of the course were how to illustrate the material one wants to describe. The first part concentrated on the technical issues on how to use the software program Adobe Illustrator to make vector based illustration, from a photo or a sketch from a camera lucida. The program makes it possible to edit the illustration continuously until a publishable result has been reached! The last (and second illustration module) part, aimed at to understand the human perception of illustrations as well as to be informed about a variety of methods and illustration methods and techniques. For day to day schedule see Appendix 2.
The first day various types of databases were introduced and some taxonomy sources on the internet were also shown and discussed. Then the DELTA-lectures started with an overview of the system
with the highlights and drawbacks and ending with how it can be published on the internet. After the general structure of the program has been demonstrated, and the software was installed on the student’s laptop they could start building their own interactive keys. All students were given the new published “Beginners guide of DELTA” in both printed as pdf-format.
The next and following three days the participants had mixed lectures and demonstrations. After each new introduced part of the computer program the participants used their own data to build a simple database in the Delta-program. These activities allowed the students to add on more and more
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details into their dataset after each new parts of the program was explained and exemplified. A small section was dedicated to images and illustration handling inside the Delta program as more of making images and illustrations would be covered in forthcoming modules in the course. This was explained in the form of a demonstration using the photo/illustration editing program Adobe Photoshop, editing an image using different layers in order to emphasize the character of interest using layer techniques and then resize the image to a usable size in DELTA. The further step of making the illustrations interactive using clickable areas in the DELTA program, e.g. Intkey, was demonstrated, and later tried out by the students through hands-on.
During the four first days the evenings were designated to student presentations, where the students were presenting their current (or intended) research and thereby indicating the need for this course (titles in appendix 3).
Friday morning started with a short talk by Prof. Mike Thorndyke (The Swedish Royal Academy of Science) about some programs aiming to give access to marine stations in Europe (Assamble) and the European marine network (Mars) and some future programs. The rest of Friday the Delta module ended with the last lectures and hands-on. In the afternoon did Matz Berggren gave a short talk
about the “Swedish Taxonomy Initiative (STI)” and showed some of the books that are already published.
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The next module, starting on Saturday, was one and a half day of digital drawing, introducing a new method to make publishable illustrations using the Adobe illustrator together with a digitizer. It was first described during a lecture and also shown in detail by a series of small movies focusing on the different steps. Thereafter the students were grouped into two and two and had successively an intensive lecture and hands-on testing/training of the method.
On mid-Sunday, the module of “Scientific writing and communication” started. It covered how to make a scientific text understandable and how to communicate with the potential reader to make the message as clear and interesting as possible. Also the use of tables and figures was extensively discussed and how they should be designed
to enhance the understanding of the text. Examples from the library were used to exemplify how the writer should think when deciding to which journal a certain manuscript should first be sent to. Also the important aspects of participating at international conferences (posters, talks, personal interactions) were covered.This course module was running from midday to Sunday evening and then continued whole following day.
The last module “Scientific illustration” started on Tuesday 16 November. This module dealt with the theories behind the use of illustrations for various scientific purposes, human perception of illustrations and the composition, colour theory, choice of illustration method. The lectures also included a short history of scientific illustrations. Both demonstrations and hands-on of different techniques were covered including aids
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like camera lucida, black and white methods like copper graphics, charcoal, pencil and black ink and also colour methods like water-colour (aquarelle), crayons, coloured pencils, pastel, computer graphics and airbrush. Beside illustrations of biological specimens, aspects on diagrams, tables, typography and posters were discussed.
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Course material The course material consisted of the DELTA program package, including a new user guide “Delta for beginners”. A number of printed text, explaining special parts of the program more in detail, was distributed. In Digital drawing, Scientific writing as well as in Scientific illustration, different instruction texts were given to the participants both in print as in pdf-format. Also many examples of recommended textbooks for the more interested to buy from the internet were given. Evaluation The course was evaluated by a questionnaire (Appendix 4). (Information compiled by one of the participants, Thomas Kunze). The certificate given to the participants:
Appendix 1 – list of participants.
Belgium Yves Braet - Institut National de Criminalistic et Criminologie, Brussels, Belgium Charlotte Havermans - Royal Belgian Institute of Natural Sciences, Brussels, Belgium United Kingdom Camilla Hatton-Brown - SAHFOS, Plymouth, UK Margaret Packer - NHM London, UK Germany Thomas Kunze - Ludwig-Maximilians-Universität München, Germany Verena Kutschera - Univeristy of Ulm, Germany India Ankita Gupta - National Bureau of Agric. Important Insects, Bangalore, India Biju Abraham - National Institute of Oceanography, Kerala, India Estonia Marko Prous - University of Tartu, Estonia South Africa Kerry Ann Hadfield - University of Johannesburg, South Africa Ukraine Anton Lyakh - Institute of biology, Ukraine Netherlands Sancia Van der Meij - Netherlands Centre for Biodiversity, Naturalis, Nederland Bulgaria Milka Elshishka - Bulgarian Academy of Science, Bulgaria Portugal Ascensaõ Ravara - Univeristy of Aveiro, Portugal Brazil Ivo Oliveira de Sena - University Leipzig, Germay for Ph.D. studies (Univ. Minas Gerais, Brazil) Colombia, Diana Arias Penna - University of Illinois at Urbana-Champaign, USA
Instructors: DELTA:
Dr Matz Berggren, Institution of Marine Ecology, Göteborg University, Sweden Dr Charles Oliver Coleman, Museum für Naturkunde, Berlin, Germany
Digital drawing: Dr Charles Oliver Coleman, Museum für Naturkunde, Berlin, Germany
Scientific illustration: Prof. Tomas Cedhagen, Department of Marine Ecology, University of Aarhus, Denmark
Scientific writing and communication: Dr Gabor Lövei, Department of Plant Protection, Danish Institute of Agricultural Sciences, Slagelse, Denmark
Appendix 2 – Schedule.
Monday 8 November 2010 08:00 – 13:30 Arrival 14:00 – 15:00 Welcome to the station by Matz Berggren – Lab-safety by Bengt
Lundve 15:30 – 17:00 Intro to databases, what is available and overview of DELTA Tuesday 9 November 2010 09:00 – 17:00 DELTA 19:00-20:00 4 Participant presentation of their research (10+5min each) Wednesday 10 November 2010 09:00 – 17:00 DELTA 19:00-20:00 4 Participant presentation of their research (10+5min each) Thursday 11 November 2010 09:00 – 17:00 DELTA 19:00-20:00 4 Participant presentation of their research (10+5min each) Friday 12 November 2010 08:30 – 09:30 Presentation on European marine networks Mike Thorndyke 09:30 – 17:00 DELTA – after lunch a short presentation of The Swedish
Taxonomy Initiative (STI) by Matz Berggren 19:00-20:00 4 Participant presentation of their research (10+5min each) Saturday 13 November 2010 09:00 – 17:00 Digital drawing Course dinner Shrimp (Pandalus borealis [Crustacea: Decapoda: Caridea])
dinner Sunday 14 November 2010 09:00 – 12:00 Digital drawing 13:00 – 17:00 Scientific writing & communication Evening Scientific writing & communication Monday 15 November 2010 09:00 – 12:30 Scientific writing & communication 13:30 – 17:00 Scientific writing & communication Evening test of the Swedish stinking specialty “Surströmming” Tuesday 16 November 2010 09:00 – 12:30 Intro to Scientific illustration – Just before lunch: A short walk
around on the research vessel “Skagerak” of Gothenburg university
13:30 – 17:00 Scientific illustration Wednesday 17 November 2010 09:00 – 17:00 Scientific illustration (testing to illustrate live specimens in the
aquaria hall) Thursday 18 November 2010 09:00 – 17:00 Scientific illustration Evening Farewell evening with Swedish “Glögg” Friday 19 November 2010 09:00 – 12:00 Summary and Departure
Appendix 3 – Participants presentations.
Biju Abraham - "Taxonomy and ecology of Crustacean mysids" Yves Braet - "INCC-NICC and the microtraces laboratory" Milka Elshishka - "Taxonomy, microhabitat and geographic
distribution of nematodes of order Dorylaimida from polar deserts"
Ankita Gupta - "Biodiversity of parasitic (Hymenoptera) of India" Kerry Ann Hadfield - "The biodiversity and systematics of marine
fish parasitic isopods of the family Cymothoidae from southern Africa"
Camilla Hatton-Brown – "SAHFOS – Sir Alister Hardy Foundation
of Ocean Science" Charlotte Havermans – "Antarctic amphipods: Lysianassoidea" Thomas Kunze - "What are Skeneimorph Gastropods? – How 3D
based anatomy can help to shed some light on the polyphyletic assemblage called Skeneidae"
Verena Kutschera - "The phylogenetic value of the malacostracan
pleon" Anton Lyakh - "On-line guides and expert systems for marine
organisms identification" Sancia Van der Meij - "The host-specificity approach: what
symbionts can teach us about taxonomy" Margaret Packer – "Philippine Polychaetes" Diana Arias Penna – "Exploring intraspecific diversity of
Glyptapanteles parasitoids wasps (Hymenoptera: Braconidae: Micogastrinae) from the Neotropics"
Marko Prous - "The genus Empria [Hymenoptera: Tenthredinidae]" Ascensão Ravara - "A revision of the polychaete family
Nephtyidae, based on morphological and molecular data" Ivo Oliveira de Sena - "Study of biogeography, taxonomy,
phylogeny and biodiversity of Onychophora (velvet worms): a contribution to research and conservation"
Appendix 4 – course evaluation.
COURSE EVALUATION
Name of course: Basics of Taxonomy: Describing, Illustrating and Writing biodiversity. Consisting of: 1Learning the computer program DELTA (DEscription Language for TAxonomy), 2Vectorbased digital illustration technique, 3Scientific writing and communication, 4Different methods to make a scientific illustration (equivalent to 5 ECTS).
Semester: Year Autumn 2010
NB! If the answer in the questions can’t be applied to all of the course modules, please make it more clearly in the comments!
Sample size is 15 1. The correspondence between the objective and content of the course has been:
Very good Very bad
14 1 Comments:
The course met all the objectives outlined in the program
Course info was value, but I am very satisfied my personal objectives were met
All that was announced has been covered
Appropriate enough for beginners in taxonomy
2. How was the work load compared to the number of credits? Much too high Much too low
1 4 Comments:
N/A N/A N/A Not enough time for the part 4. But the first 4 parts are well covered and load
of work is OK. Not applicable Equal I am not used to this credits system, so I am not able to answer this question Don’t know, do not take this course for credits
3. Where there areas where you didn’t have the necessary previous knowledge? No Yes, in
13 3 Comments:
“no”: The DELTA element was explained from scratch so no prior knowledge was necessary
other than taxonomy
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“No”: I had no knowledge in DELTA and digital drawing, but the course starts from zero, so
there wasn’t any pre-knowledge necessary
“yes”: DELTA course, digital drawing
“yes and no”: yes in delta, no in illustration
“yes”: DELTA & digital illustration & different methods of scientific illustrations were new
and informative
4. How will you assess the lectures? Very useful Not at all useful
14 1 Comments (on the pedagogics, the standard, etc.):
Teachers all very well prepared, good pedagogics – first complementing then criticizing At times the lectures were – “trouble shooting” with individuals. This was very helpful.
Lectures were interacting and incorporated various learning styles. All teachers are passionate, and very competent. The lectures are interactive and answer well
to any question The most useful and most organized lecture was “scientific writing & communicating” We
should have more time for it. Very informative
5. How will you assess the field course/practicals (delete if does not apply)? Very useful Not at all useful
12 2 Comments (on the pedagogics, the standard, did you get the necessary help, etc.):
Practical Delta sessions, illustration, digital illustration were all extremely useful. Class size allowed 1-1 advice and class feedback (illustration).
We always get necessary help. All lecturers have a high skill on subjects they have presented. Great to work on own species in DELTA n/a 1
6. How will you assess the seminars/student presentation (delete if does not apply)? Very useful Not at all useful
10 3 1 1 Comments:
We all enjoyed giving and listening to each other’s talks. Evenings after DELTA though I would prefer to absorb the days lesson instead.
It was nice to get to know what everyone else is studying and to have the opportunity to present.
Seemed a bit more formal than necessary Very interesting to know what the others do in their fields of research. Several future
collaborations will be made!
7. How will you assess the syllabus (extent and contents)? Too big Too small Very good Very bad
8 5 1 Comments:
1 5 5
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More on illustrator programme some repetition on graphics/tables between tutors which could
have been omitted. Modern acquisition of maps would be good (GIS).
I have learnt so many useful things I think the content was excellent and covered a broad
range.
More time to practice was needed
Syllabus was ok but sometimes more information would have been helpful.
Extendable in a practical way, especially for the drawing part.
n/a 1
8. How do you assess the organizing and practical arrangements of the course? Very good Very bad
13 2 Comments:
Lab not suitable for lengthy tutorials. Additional info on traveling to the course was very welcome.
Great job – perhaps lecture hall better than lab. Organisation is the best Very comfortable Great lodging, beautiful area, all convenient good vibe Good rooms, meals, people, landscape good internet, facilities, library.
9. Your general impression of the course: Very good Very bad
15 Useful course with friendly teachers Very informative as some aspects were really new in all areas of the course.
10. Did this course readily combine with other courses that you took this term (e.g. in terms of work load and schedule)? Yes, very much so No, not at all
7 2 1 Comments: N/A: 3 11. How did you receive information about the course?
Via email from a friend
Personal communication
Via email from institution
Email from institution
Informed by professor
Email list
From my supervisor.
From my supervisor
Internet
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Email from supervisor
From supervisor through the crustacean group I think?
EDIT newsletter
From institute
Internet search
Taxacon
Internet search
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Any suggestions on how to advertise future courses?
Email museums if not already doing so.
More information for students from developing countries needed. Perhaps it
should be placed on regional websites.
Mailing lists and adverts in universities
More email mailing lists
Contact NGOs in developing countries for the people working there in the
field of taxonomy, environment, education.
……………………………………………………………………………………………………………
General comments / suggestions for improvement / criticism:
Very interesting course
More time spent on practicing techniques
I am very impressed with the quality and dedication of the teachers. The level
seemed exactly right for this group although the scientific writing element
started at too basic a level. Information on figure preparation was very
informative.
Maybe add a short module about the use of DELTA database from a
phylogenetic point of view. Possibly add a short (1/2 day – 1 day) course on
phylogenetic programme (ie Mesquite)
Arriving/ leaving day before. This course was outstanding, nothing
comparable in my own hometown/country. More learning about digital
drawing scientific writing maybe a little longer one day also grand proposals
should be included.
