Using computers to study mushrooms (1 of 2)

[Nathan J. Wilson]

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.

-Nathan Wilson

--- 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 
version.

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 
        tablet.
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 
        cross section.
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 
        this afternoon.
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
searching for 
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 
historical record.

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,

Nathan Wilson
Co-Science Advisor and Minister of Local Forays
Fungus Federation of Santa Cruz
1620 Bay St.
Santa Cruz, Ca 95060
(408)423-3773
Internet: nathan at cse.ucsc.edu
-- 
 ---------------------        _________
     Nathan Wilson           <_________>
nathan at taurus.apple.com          |_|         It is no dream!
   velosa at apple.com             /___\     Matsutake are growing