Environmental Computer Programming

“I was one of the first ecologists to use computers, beginning in 1965 when I was a graduate student working on a PhD at Rutgers University.

Another graduate student in ecology was also interested in computers, and he persuaded the Engineering Professors to put one of the first external (wired, no Wi-Fi back then) computer stations in his building. We sat down and tried to figure out what all this meant, including the use of FORTRAN. During my graduate work at Rutgers, I was also the caretaker of Hutcheson Memorial Forest, the last known never cut and never burned oak-hickory forest in New Jersey. Furthermore, I was the teaching assistant for a field course taught by my major professor. In those roles, I often went for walks in forests with my major professor, Murray Buell.

Sometimes we went to check field sites for the next field course session; sometimes we went for walks in Hutcheson Forest.  Often on these walks, Murray would stop, look at a tree and say, “Dan, now why do you think that tree is growing right there?” We would discuss it and persuade ourselves that we understood the causes.  But having a major in physics as an undergraduate, I always felt that, in those situations, there had to be a way to develop a mathematical model that would test our ideas to see if they worked. I did considerable review of scientific literature about the physiology, taxonomy, and geography of these tree species, and worked out in my mind how this knowledge could be turned into a mathematical model.

After I graduated, my first academic appointment was as a faculty member of the Yale School of Forestry, now recognized as the Yale School of Forestry and Environmental Studies. One day, IBM contacted the Dean and said the corporation was sponsoring seven summer projects in which modern computers would be applied to help societal and environmental problems. The Dean asked all the faculty if they had any ideas, and I spoke up about my plan to make a mathematical- therefore a computer- model of forests. IBM invited me to the Thomas J. Watson IBM Research Center, where I presented my ideas to interested PhDs working there. Two were very interested in my ideas: James Wallis, a statistician and forester, and James Janak, a theoretical physicist.  By the end of the summer, we had created a working computer model of forests, and had tested it in preliminary ways against the growth of real trees and real forests.

​We called the computer program JABOWA, which was the first two letters of each of our names, and a play on Jabberwocky from Lewis Carroll’s Alice in Wonderland. This became a multi-year project. One of my graduate students was employed as well and he created a video display version of the computer model. At that time, IBM already had touch screen TVs, so we had the program shown on the individual trees in a small area.  If you wanted to cut down a tree, you touched its image on the screen, and the computer cut that tree from the mathematical model.

This model has been, and continues to be, used widely, with at least 50 versions of it rewritten in other names, but having all of our original mathematics. It has been carefully validated, and, to my knowledge, is recognized as the best validated environmental computer model, much better validated that the global climate models. My colleague, Professor Don DeAngeles of the University of Miami, tells his colleagues in public discourses, that my invention of this computer model also created an entirely new field within the science of ecology.

JABOWA was used in the early 1970s and onward to today to test of possible effects of climate change as forecast by the global climate models that get so much attention. There are many papers we have published on the use of this model for a variety of purposes.”

 

OTHER COMPUTER MODELING RESEARCH

         Elephant populations

         Moose and wildlife

         Lake ecosystems

         Stability in ecosystems

 

– Dan Botkin

environmental computer
Using computer in the 1980s, programming it to grow forests. You can see the simulated trees on the screen, and I could cut down a tree by pointing at it with the computer mouse, and the program would remove that tree and continue to grow that forest with the opening created by that cut down tree. The model continues to be used widely, in many versions, around the world.
jabowa
Early computer display of trees in a simulated forest, using our JABOWA computer program
One of the applications we made of our JABOWA forest model was to try to determine whether the Kirtland’s warbler, the colorful bird shown here, Would go extinct from global warming, based on 1980s climate model forecasts. This warbler only nests in young jack pine forests that at the time grew to the south Of the Great Lakes. The question was whether the trees could move north and the warbler persist. (Note: photograph of Kirtland’s warbler is from https://www.fws.gov/midwest/endangered/birds/Kirtland/index.html U.S. Fish and Wildlife)

ARTICLES 

(​Books published are listed separately)

​Botkin, D.B., 1993, JABOWA-II: A Computer Model of Forest Growth, Oxford University Press. (Software and manual)
 
Botkin, D.B., 1969, Prediction of net photosynthesis of trees from light intensity and temperature, Ecology 50: 854– 858.

Botkin, D.B., J.F. Janak and J.R. Wallis. 1970, A simulator for  northeastern forest growth: a contribution of the Hubbard Brook Ecosystem Study and IBM Research, IBM Research Report  3140, Yorktown Heights, NY. 21 pp.

Botkin, D.B., J.R. Janak and J.R. Wallis, 1971, A simulation of  forest growth, pp. 812 – 819, In: Proceedings of the Summer  Computer Simulation Conference, Board of Simulation Conferences, Denver, CO.

Botkin, D.B., J.R. Janak and J.R. Wallis, 1972A, Rationale, limitations and assumptions of a northeast forest growth simulator, IBM J. of Research and Development 16: 101 – 116.

Miller, R.S., G.S. Hochbaum and D. B. Botkin, 1972, A simulation model for management of sandhill cranes, Yale Univ. School of Forestry and Environmental Studies Bull. No. 80. 49 pp.

Botkin, D.B., J.F. Janak and J.R. Wallis, 1972B, Some ecological consequences of a computer model of forest growth, J. Ecology 60: 849 – 872.

Botkin, D.B., J.F. Janak and J.R. Wallis, 1973, Estimating the effects of carbon fertilization on forest composition by ecosystem simulation, pp. 328 – 344, In: G.M. Woodwell and E.V. Pecan, eds., Carbon and the Biosphere, Brookhaven National Laboratory Symposium No. 24, Technical Information Center, U.S.A.E.C., Oak Ridge, TN.

Botkin, D.B. and R.S. Miller, 1974, Mortality rates and survival of birds, American Nat. 108: 181 – 192.

Miller, R.S. and D.B. Botkin, 1974, Endangered species: models and predictions, Amer. Sci. 62: 172 – 181.

Botkin, D.B. and R.S. Miller, 1974, Complex ecosystems: models and predictions, Amer. Sci. 62: 448 – 453.

Miller, R.S., D.B. Botkin and R. Mendelssohn, 1974, The whooping crane (Grus americana) population of North America, Biol. Conservation 6: 106 – 111.

Lehman, J.T., D.B. Botkin and G.E. Likens, 1975, The assumptions and rationale of a computer model of phytoplankton population dynamics, Limnology and Oceanography 20: 343 – 364.

Botkin, D.B. and M.J. Sobel, 1975, Stability in time-varying ecosystems, Amer. Nat. 109: 625 – 646.

Lehman, J.T., D.B. Botkin and G.E. Likens, 1975, Lake eutrophication and the limiting CO2 concept: a simulation study, pp. 300 – 307, in V. Sladecek (ed.) Proceedings of the International Congress of Theoretical and Applied Limnology, Nagele and Obermiller, Stuttgart.

Botkin, D.B. 1975, A functional approach to the niche concept in forest communities, pp. 149 – 158, In: G.S. Innes, eds., New  Directions in the Analysis of Ecological Systems, Simulation  Council Proceedings: Society of Computer Simulation, La Jolla, CA.

Botkin, D.B. and M.J. Sobel, 1976, Stability in ecosystems: semantics, models and reality, pp. 239 – 250. In: R.J. Sharma, J.D. 

Buffington and J.T. McFadden, eds., Proceedings: The Biological Significance of Environmental Impacts. Argonne National Lab.

Botkin, D.B., 1976, The role of species interactions in the response of a forest ecosystem to environmental perturbation, pp. 147 – 171. In: B.C. Patten, (ed.), System Analysis and Simulation in Ecology, vol. IV. Academic Press, NY.

Botkin, D.B., 1977. Life and death in a forest community: the computer as an aid to understanding, pp. 213 – 234. In: C. Hall and J. Day, eds., Models as Ecological Tools: Theory and Case Histories. Wiley, NY.

Botkin, D.B., 1977, Bits, bytes, and IBP, Editorial in BioScience 27: 385.

Botkin, D.B. and M.J. Sobel, 1977, Optimum sustainable marine mammal populations, Report to the U.S. Federal Marine Mammal Commission, 126 pp.

Botkin, D.B. and R.E. Levitan, 1977, Wolves, moose and trees: an age specific trophic-level model of Isle Royale National Park, IBM Research Report in Life-Sciences RC 6834, 64 pp.

Botkin, D.B., D.S. Schimel, L.S. Wu and W.S. Little, 1978, Some comments on the density dependent factors in sperm whale populations, pp. 83 – 88. In: Annual Proceedings of the International Whaling Commission, Rep. Int. Whale Commission  (special issue 2), 1980.

Botkin, D.B, 1979, A grandfather clock down the staircase: stability and disturbance in natural ecosystems, pp. 1 – 10.  In: R.H. Waring, ed., Forests: Fresh Perspectives from Ecosystem Analysis. Proceedings of the 40th Annual Biology Colloquium, Oregon State University Press, Corvallis, OR, 1980.

Botkin, D.B, 1979, Status of ecological theory, pp. 101 – 102, In: M,N, Dastoor, L, Margulis, and K,H, Nealson, eds., Interaction of the Biota with the Atmosphere and Sediments,  Final Report of NASA Workshop on Global Ecology, held October 18 – 20, 1979.

Wu,  L. S. and D.B. Botkin, 1980, Of elephants and men: a discrete, stochastic model for long-lived species with complex life histories, American Nat. 116: 831 – 849.

Beddington, J., D.B. Botkin and S.A. Levin, 1980, Mathematical models and resource management, In: T.L. Vincent and J.M. Skowronski, eds., Renewable Resource Management, Springer – Verlag, Lecture Notes in Biomathematics.

West, D., H.H. Shugart and D.B. Botkin, 1981, Introduction, Chapter 1, pp. 1 – 6. In: West, Shugart and Botkin, eds., Forest Succession: Concepts and Applications. Springer-Verlag, NY.

Botkin, D.B., 1981, Causality and Succession, Chapter 5, pp. 36 – 55, In: West, Shugart and Botkin, eds., Forest Succession: Concepts and Applications, Springer-Verlag, NY.

Davis, M. B. and D. B. Botkin, 1985, Sensitivity of the Cool–Temperate Forests and Their Fossil Pollen to Rapid Climatic Change, Quaternary Research  23:327-340.

Botkin, D. B., T. E. Reynales and K. D. Woods, 1985, Adding Spatial Considerations to the JABOWA Model of Forest Growth, Machine Processing of Remotely Sensed Data Symposium, pp. 141-148.

Botkin, D. B., R. A. Nisbet, and T. E. Reynales, 1989, “Effects of Climate Change on Forests of the Great Lake States, pp.2-1 to 2-31 in The Potential Effects of Global Climate Change on the United States, J. B. Smith and D. A. Tirpak (eds.) U. S. Environmental Protection Agency, Washington, D. C., EPA -203-05-89-0.

Rosenfeld, A. H., and D. B. Botkin, 1990, Trees Can Sequester Carbon, Or Die, Decay, and Amplify Global Warming: Possible Positive Feedback Between Rising Temperature, Stressed Forests, and CO2, Physics and Society 19:4pp.

Wilson, M. V. and D. B. Botkin, 1990, Models of Simple Microcosms: Emergent Properties and the Effect of Complexity on Stability, Amer. Nat. 135:414-434.

Botkin, D. B. and R. A. Nisbet, 1990, Response of Forests to Global Warming and CO2 Fertilization, Report to EPA.

Botkin, D. B., 1990 (August) Minimum Standard and Criteria For Models of Forest Stands, B. Stout, (ed.) National Council of the Paper Industry for Air and Stream Improvement, Inc. Tech. Bull. 583, 28pp.

Botkin, D. B., D. A. Woodby, and R. A. Nisbet, 1991, Kirtland’s Warbler Habitats: A Possible Early Indicator of Climatic Warming, Biological Conservation 56 (1): 63-78.

Botkin, D. B. 1991, Global Warming and Forests of the Great Lakes States: An example of the use of Quantitative Projections in Policy Analysis.  An Essay Submitted for the George and Cynthia Mitchell International Prize Competition, 1991, which won first prize and was published by the Mitchell Foundation, Houston, TX.

Botkin, D. B., and R. A. Nisbet, 1992, Forest response to climatic change: effects of parameter estimation and choice of weather patterns on the reliability of projections, Climatic Change 20: 87-111.

Botkin, D. B., R. A. Nisbet and L. G. Simpson, 1992, Forests and Global Climate Change, Chapter 19, pp. 274- 290 in S. K. Majumdar, L. S. Kalkstein, B. M. Yarnal, E. W. Miller, and L. M. Rosenfeld (eds.)  Global Climate Change: Implications, Challenges and Mitigation Measures, Pennsylvania Academy of Sciences, Philadelphia.

Botkin, D. B. and R. A. Nisbet, 1992, Projecting the effects of climate change on biological diversity in forests,  pp. 277 – 293 in R. Peters and T. Lovejoy, (Eds.) Consequences of the Greenhouse Effect for Biological Diversity, Yale University Press, New Haven.

Woodby, D. and D. B. Botkin (1993). “Stock sizes prior to commercial whaling. The Bowhead Whale.” in J. J. Burns, J. J. Montague, C. J. Cowles. Lawrence K. S., The Society for Marine Mammalogy. Special publication No. 2: 387-407.

Nisbet, R.A. and D. B. Botkin, 1993, Integrating a Forest Growth Model With a Geographic Information System, pp.265-269 in Goodchild, M.S. , B.O. Parks, L.T. Steyaert (eds.) Environmental Modeling with GIS, Oxford University Press, N.Y.

Hunsaker, C.T.,R. A. Nisbet, D. C. L. Lam, J. A. Browder, W. L. Baker, M. G. Turner, D. B. Botkin, 1993, pp.248-264 in Goodchild, M.S. B.O. Parks, L.T. Steyaert (eds.) Environmental Modeling with GIS, Oxford University Press, N.Y.

Guggenheim, D. and D. B. Botkin, 1996, CO2 Offset Opportunities in Siberian Forests, Report to the Electric Power Research Institute, Center for the Study of the Environment, Santa Barbara, CA, EPRI report # TR-106059.

Ngugi, M. R.  D. B. Botkin, J. Bronwen and A. Williams, 2005, “Needs and opportunities for using a forest dynamic model as a practical tool in biodiversity conservation and management,” IUFRO World Congress, Brisbane, Australia.

Botkin, D. B., Henrik Saxe, Miguel B. Araújo, Richard Betts, Richard H.W. Bradshaw, Tomas Cedhagen, Peter Chesson, Terry P. Dawson, Julie Etterson, Daniel P. Faith, Simon Ferrier, Antoine Guisan, Anja Skjoldborg Hansen, David W. Hilbert, Craig Loehle, Chris Margules, Mark New, Matthew J. Sobel, and David R.B. Stockwell. 2007 “Forecasting Effects of Global Warming on Biodiversity.” BioScience 57(3): 227-236.

Ngugi,  Michael R.  and Daniel B. Botkin, 2011, “Validation of a multispecies forest dynamics model using 50-year growth from Eucalyptus forests in eastern Australia,” Ecological Modelling. 222: 3261– 3270.

Ngugi, M.R., Daniel B. Botkin, David Doley, Mark Cant, and Jack Kelley.2013 “Restoration and Management of Callitris Forest Ecosystems in Eastern Australia: Simulation of Attributes of Growth Dynamics, Growth Increment and Biomass Accumulation.” Ecological Modelling 263 (2013) 152– 161.
 
Ngugi, M.R., D. Doley, and D.B. Botkin, 2013. “Application of a forest dynamics simulator to inform sustainable biodiversity conservation and grazing management in Australia”. 20th International Congress on Modelling and Simulation(MODSIM2013). 2013: Adelaide (December 1, 2013).
 
Botkin, D.B., M.R. Ngugi, and D. Doley. 2014. “Estimates and Forecasts of Forest Biomass and Carbon Sequestration in North America and Australia: A Forty-Five Year Quest.” Drewno 2014, Vol. 57, No. 192 DOI: 10.12841/wood.1644-3985.S05.01
 
Ngugi, Michael R.,  David Doley, Daniel B. Botkin, Mark Cant, Victor J. Neldner & Jack Kelley. 2014. Long-term estimates of live above-ground tree carbon stocks and net change in managed uneven-aged mixed species forests of sub-tropical Queensland, Australia  Australian Forestry  DOI:10.1080/00049158.2014.979979 Published online: 26 Nov 2014.
 
Ngugi, Michael R., David Doley, Mark Cant, Daniel B. Botkin, 2015. “Growth rates of Eucalyptus and other Australian native tree species derived from seven decades of growth monitoring.” Journal of Forestry Research, 26 (4) 811-826 ISSN 1007-662X,  DOI 10.1007/s11676-015-0095-z

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