An exploration of convergent evolution in academia:
Why ecosystem ecologists and
biogeochemists should think about the
tools of software engineering
Robert A. Payn, Dept. of Land Res. & Environmental Sci.
Clemente Izurieta, Computer Science Department
Geoffrey C. Poole, Dept. of Land Res. & Environmental Sci.
Montana State University and
Montana University System Institute on Ecosystems
2015 Annual Meeting of the Society for Freshwater Science
Milwaukee, Wisconsin, USA
Thursday, 21 May, 10:45 – Room 102C
An exploration of convergent evolution in academia:
Why ecosystem ecologists and
biogeochemists should think about the
tools of software engineering
Robert A. Payn, Dept. of Land Res. & Environmental Sci.
Clemente Izurieta, Computer Science Department
Geoffrey C. Poole, Dept. of Land Res. & Environmental Sci.
Montana State University and
Montana University System Institute on Ecosystems
2015 Annual Meeting of the Society for Freshwater Science
Milwaukee, Wisconsin, USA
Thursday, 21 May, 10:45 – Room 102C
An exploration of convergent evolution in academia:
Why ecosystem ecologists and
biogeochemists should think about the
tools of software engineering
Robert A. Payn, Dept. of Land Res. & Environmental Sci.
Clemente Izurieta, Computer Science Department
Geoffrey C. Poole, Dept. of Land Res. & Environmental Sci.
Montana State University and
Montana University System Institute on Ecosystems
National Science Foundation EPSCoR Track-1
program under grant # EPS-1101342.
2015 Annual Meeting of the Society for Freshwater Science
Milwaukee, Wisconsin, USA
Thursday, 21 May, 10:45 – Room 102C
Software Engineering Lab
Fluvial Landscape Lab
Timberlake Observatory Wetland
National Science Foundation grant # DEB-1021001
Convergence in ecosystem and information sciences:
Same ontology... different semantics...
Ecosystem ecology
System component
Structure
Function
Tansley 1935
Integrate abiotic and biotic
controls on plant succession
Software engineering
UML
Class
Attributes
Methods
Dahl and Nygaard ca. 1965
“In silico” simulation of
complex systems
Two kinds of ontological hierarchies in UML
Inheritance
More abstract class
Structure
Function
More specific class
UML example of inheritance in benthos
Inheritance
Diptera
“Tipula is a
Dipteran”
Tipula
UML example of inheritance in benthos
Diptera
“Tipula is a
Dipteran”
Amphipoda
“Gammarus is an
Amphipod”
Tipula
Gammarus
UML example of inheritance in benthos
“Tipula is an
Arthropod”
Diptera
“Tipula is a
Dipteran”
Arthropoda
“Gammarus is an
Arthropod”
<<interface>>
Shredder
<<interface>>
Collector
Shred method
Collect method
Tipula
“Tipula is a Shredder”
“Gammarus is a Shredder”
“Gammarus is a Collector”
Amphipoda
“Gammarus is an
Amphipod”
Gammarus
UML example of inheritance in biogeochemistry
Microbe
Heterotroph
<<interface>>
Aerobe
reduceO2()
Obligate
Aerobe
Facultative
Denitrifier
<<interface>>
Nitrate Reducer
Autotroph
reduceNO3()
Nitrifier
Two kinds of ontological hierarchies in UML
Inheritance
More abstract class
Composition
Composite class
Component class
Structure
Function
“... is a ...”
More specific class
“... has a ...”
Component class
Biosphere
UML example of
composition in biology
Ecosystem
Biological composite
Organism
Biological component
Organ
Tissue
Cell
UML example of
composition in biology
BioComponent
BioLeaf
BioComposite
Biosphere
Ecosystem
Organism
Organ
Tissue
Cell
UML example of composition
in cross-disciplinary models
Computer file system
folder
folder
file
folder
file
Biosphere
Ecosystem
Composite “pattern”
Component
Leaf
Composite
Organism
Organ
Tissue
Cell
Examples in literature
BioSystems 2005
Briefings in
Bioinformatics 2009
Take home messages (even if you never write code)
Inheritance
Clearer definitions of
structural or functional
hierarchies
Composition
Composite class
More abstract class
Component class
Structure
Function
“... has a ...”
“... is a ...”
More specific class
Component class
Composite pattern
Clearer abstractions of
repeated pattern
across nature
Component
Leaf
Composite
Biosphere
Ecosystem
Organism
Organ
Tissue
Cell