Using computers to study mushrooms (1 of 2)
Nathan J. Wilson
nathan at cse.ucsc.edu
Fri Sep 3 15:33:19 EST 1993
This is the first of two documents related to my efforts to create computer
programs that will be helpful for studying mycology. The one below is a
newsletter article aimed at knowledgable yet amature mycologists (i.e.
mushroom enthusiasts) with minimal knowledge of computers. The second
article, posted separately, is aimed at computer scientists with little
or no knowledge of fungi.
Although neither of these articles are aimed at people who are
knowledgable about both computers and fungus taxonomy, I am especially
interested in contacting such people at the moment to talk over the
architecture and implementation of my next generation of software. The
software I have created to date include a synoptic key style identification
system (the principle subject of the two articles) and small utilities
for creating species lists and name labels.
--- Begin article ---
The Future of Mushroom Identification
Like many of you my favorite hobby is mycology. I've been studying
mushrooms on and off for over 15 years. Most of what I've learned comes
from field guides, supplemented by what I can pick up from others at
forays and meetings. This learning process has been slow and at times
frustrating and tedious. For example, I believe I just found my
first Leucocoprinus luteus, a beautiful brilliant yellow Lepiota-like species.
Most of the books I have give short descriptions of one or maybe two
species in this genus and one gives a description of the genus, but I
want to know more. How many described species are there in this group?
How often does it occur in my area? What is its world wide distribution?
To find out more I would have to try to find someone who knows more
about the genus or at least tell me a few references. If that doesn't
work I would have to arrange access to the library collection in San
Francisco and then find the time to make the hour and a half drive to San
Francisco and spend a day hunting down the answers to my questions.
It also bothers me that if I did go to the effort to track this information
down, that my only way to share it with others is by talking to them at
forays or, if I where really ambitious, by someday including it in a book.
Professionally, I'm a computer scientist, and this part of me rebels at
the inefficiency of these methods. I should be able to sit down
at my computer, and quickly find descriptions of all the relevent species.
Furthermore, I should be able to use my computer to help me identify the
species and to record my observations. Finally, I should be able to make my
observations available to others who might be interested in the species in
the future. Here is a short story demonstrating the use of some future
Stardate 22938.1. Planet Earth. Yosemite Valley.
Student 1: Great field trip! What did you see?
Student 2: I'm not sure, but I collected a few samples for identification.
Student 1: Wow! Those are neat. Let's see what we can find out with your
Student 2: OK, let's see...Yosemite Valley...Wildlife...Identification. It's
requesting features of the organism.
Student 1: Well, they're sort of like a brown plant.
Student 2: Yes, and 5 to 9.4 cm high and 3.6 to 5.4 cm wide, dark brown,
made of a soft but slightly brittle substance.
Student 1: and sort of like a sponge or a pine cone.
Student 2: The tablet is asking if the surface is wrinkled or pitted.
Student 1: I'd say pitted.
Student 2: Hmm, now it wants to know which picture better describes the
Student 1: Let me cut one in half.
Student 2: The more hollow one. There it's come up with an identification:
Morchella elata (M).
Student 1: What does the "M" mean?
Student 2: Here it is. "A species name followed by (M) indicates a `macro-
species' or a group of species that are macroscopically
indistinguishable. To more precisely identify your specimen it
would be necessary to examine either the microscopic or chemical
characteristics. The nearest facility with such equiptment is the
Lower Yosemite Valley Ranger Station."
Student 1: Does it say any more about what we found?
Student 2: Yes. It is a fungus or mushroom common this time of year in this
part of the planet. It is also known as the Black Morel There are
124 recognized micro-races forming 25 reproductively isolated
species. It is one of a number of macro-species known as Morels all
of which are in the genus Morchella. Several of these species are
cultivated as a delicacy.
Student 1: Mmmm, delicacy.
Student 2: In addition, they are still collected in the
wild for recreation and consumption. However, it warns that the
species is poisonous unless properly prepared and that
inexperienced collectors should be sure to precisely identify the
species before trying them. Further information includes a list of
the species and their descriptions, as well as references dating
back almost 300 years.
Student 1: Well that's enough for me. I want to go on that hike up the falls
Student 2: I'll be at the ranger station. I want to find out more.
Student 1: Well if you decide to eat them, let me know. I'd like to try them!
Student 2: OK.
I am currently working on creating a computer based system that would be capable
of performing the role of the 'tablet' in this fable. I would like it to
include a way to perform taxinomic identification, to record field
observations, and to easily extend the underlying database of species.
I am working on a masters degree in computer science and hope to
make this project my thesis. I already have a simple prototype up and running
that principally addresses the identification problem. I am currently
other people who are interested in these ideas and would like to help make
them a reality.
My ultimate goal is to create a system that can carry all the current
knowledge of fungi and which can be extended and updated as new things
are learned. I believe that it is critically important for the results
of this project to be freely available to anyone to encourage use,
interchange, and development. The current idea is that all data in the
system would indicate both who developed it and who entered it into the
system. Data that becomes `obsolete' would remain accessible in a
There are several other important issues pointed out by this fable that I
hope my project will handle. One is another take on the latin versus
common name issue. I see names as the way we connect something to
previous knowledge. As we extend our knowledge names necessarily
change. At the same time the old knowledge and old names remain
important and often capture important connections. For example, in the
fable the concept of a macro-species remains important since it describes
a set of species which are related simply because they cannot be
differentiated by the human eye. Obviously both common names and latin
names carry important information. By including all of this information
in the computer system, it would be easy for two people to make sure that
the names they are using refer to the same thing.
A second point of the fable is to acknowledge an important tension
between so called 'lumpers' and 'splitters'. The issue as I see it is
between what we know and what we don't know. Lumpers are trying to organize the
information that we know into a coherent order that is reliable, easily learned,
and accessible. Splitters are trying to extend our knowledge of fungi and
understand more precisely the relationships between species and their roles in
the natural world. Both of these endeavours are important, but they should be
done together in an organized way. I see my proposed project connecting
these two endeavours, by providing a complete, though easily used,
reference which gives the user as much information as they want.
In general, I try very hard not to use what I have gathered to be the most
accurate scientific name for the species I identify. However, given the
current accessibility of accurate information, the names I end up using
are often inaccurate. Often the closest description I have to a species
I collect is from a guide that is several years old and I have no way of
knowing if it is still correct information. This is because at best a
book is a snapshot of the knowledge of at most a few people at a
particular point in time. A computer system, on the other hand, could be
dynamically updated through the various computer networks that are
currently available throughout the world.
This points out another important issue which we must not lose sight of.
A species name is a pigeon-hole that we humans have created to help us
categorize the world around us. These pigeon-holes will never be a
completely correct description of the relationships between the individual
organisms. Mushrooms will always be evolving and changing. New strains
will arise, and new species will develop. Our task as enthusiastic
fungophiles is to develop the knowledge and share it with others so we
can better understand and appreciate these fascinating creations.
As for helping with the project, anyone can help. The only requirements for
helping are willingness, and a computer. Tasks include data entry, program
testing, discussion of design issues, programming new features, and
making it work on different types of computers. You do not have to feel
you are an expert to help. Simply getting the knowledge that can be
learned from the most common guide books into the system is a daunting
task, and it can be a wonderful way to learn new things about the species
you work on.
I look forward to hearing from you,
Co-Science Advisor and Minister of Local Forays
Fungus Federation of Santa Cruz
1620 Bay St.
Santa Cruz, Ca 95060
Internet: nathan at cse.ucsc.edu
Nathan Wilson <_________>
nathan at taurus.apple.com |_| It is no dream!
velosa at apple.com /___\ Matsutake are growing
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