Virginia Institute of Marine Science
Patterson Home

Mark R. Patterson

Professor of Marine Science

Email : [[mrp]]
Phone : (804) 684-7374
Office : Andrews Hall 338
Department : Biological Sciences
Address : P.O. Box 1346 Gloucester Point, VA 23062-1346, USA

  • A.B., magna cum laude with highest honors in biology, Harvard College, 1979
  • A.M., Harvard University, 1982
  • Ph.D., Harvard University, 1985
Research Interests

I direct the Autonomous Systems Laboratory (ASL). We design and build free-swimming robots.

I have always loved marine ecology and biomechanics, because they are so interdisciplinary. Inspired by Ken Sebens and Steven Vogel, I like asking questions that require new technology to find the answer. Serious students of the history of science know that this is usually how science advances: new instruments lead to new insights that often spawn whole disciplines, rather than vice versa. For the last decade, I have been developing Autonomous Underwater Vehicles (AUVs), free-swimming robots that survey the bottom and water column in ways superior to previous approaches like towed bodies or lowering an instrument over the side of a ship. I am convinced that AUVs are oceanography’s most important recent technological advance. The ASL has used AUVs to make new discoveries such as coherent structuresr of lowered oxygen over coral reefs, how krill swarms in the Antarctic appear on high frequency side scan sonar, and how to identify fishes from their side scan sonar images using neural network processing. This last area is poised to become a new tool for fisheries stock surveys.

AUVs are the mobile components that will be vital to filling in the gaps between the fixed nodes of Ocean Observing Systems. The ASL is currently working on expanding our ability to recognize everything an AUV sees with its sensors, to detect anomalies and respond to them (for it is the anomalies that often herald interesting things the ocean is doing), and to develop efficient methods for AUV sampling of pressing environmental problems like coastal hypoxia, the growth of gelatinous zooplankton populations, and coral reef degradation.

Current initiatives of the ASL include 1) developing a deep-sea autonomous vehicle swarm that can persist on-station for months, and return thousands of miles back to shore with physical samples, using a radical new approach to AUV design, 2) biologically-inspired autonomy whereby behaviors and structures by evolved organisms as diverse as salps, squids, sponges, fishes, marine mammals, and marine reptiles can increase the robust intelligence of AUVs, 3) new software for coordinating AUV swarms (CARNIVORE), and 4) developing methods to thwart the misuse of unmanned systems by terrorists.

The physical biology of invertebrates (sponges, cnidarians, squid), plants (macroalgae, sunflowers, seagrasses), and fishes is another area in which I am broadly interested. The allometry of metabolism is an area where I apply chemical engineering theory to lower aquatic invertebrates and algae. Contrary to the predictions of “universal scaling laws” that have appeared in the literature, e.g., the West, Brown, Enquist (WBE) theory, these taxa do not follow 3/4 power scaling of metabolic rate with body mass. Instead they exhibit a diversity of scaling exponents for which I have developed a predictive theory based on first principles from fluid transport and mass transfer. This “flow modulated allometry” model is now being tested in my laboratory and in the field using the NOAA underwater habitat Aquarius. Since 1984, I have used saturation underwater habitats to conduct research in situ on corals and their allies. Recent work using Aquarius has examined how reef corals respond to water motion during bleaching episodes by altering their photobiology and expression of stress proteins. Our lab has recently developed a predictive electrical network model of the gastrovascular system of corals of the two types of coral bauplan, perforate (where an extensive plumbing connects the polyps) and imperforate (where polyps are not connected directly). This model will help us understand how corals respond to environmental stress including that posed by global warming and ocean acidification.

During 2008, I spent my sabbatical in Iceland working with Jörundur Svavarsson (University of Iceland) and Daniel Jones (National Oceanography Centre, UK) on a new kind of shallow-water hydrothermal vent (high pH and temperature, low salinity, precipitating smectite), only found (so far) in one fjord on planet Earth. We demonstrated that we can detect vents efficiently using an AUV, and gathered preliminary data on the biological and chemical environment around the vents, including biodiversity and trophodynamics. We hope to continue work on this system that requires an interdisciplinary approach between marine robotics, benthic ecology, geology and physical oceanography.

Current and Recent Projects
  • Counterterrorism from unmanned systems: threats to ports and harbors.
  • Landscape-level habitat assessment at Conch Reef: high frequency sidescan sonar and video survey from an Autonomous Underwater Vehicle (NOAA Coral Reef Conservation Program).
  • pH dynamics on coral reefs: from single polyps to reefs (Aquarius Reef Base, NOAA).
  • How does the gastrovascular system in perforate and imperforate corals affect physiological response to environmental stress? Proposal in review.
  • A new way to explore the deep sea: low-cost persistent robotic swarms. Proposal in review.
  • Neural networks and the identification of underwater targets, including fishes and gelatinous zooplankton in the Chesapeake Bay, krill in the Antarctic, and mines in shallow water, using Autonomous Underwater Vehicles. Past funding by NOAA Sea Grant and the National Science Foundation. Seeking new support.
  • Bonaire 2008: Exploring Coral Reef Sustainability with New Technologies. AUV mapping and SCUBA surveys compared to a survey 25 years ago by Dr. Fleur van Duyl. Past funding by NOAA Office of Ocean Exploration. The team is now working on a full-color atlas describing the results of this signature expedition.
  • Project SeaCAMEL sponsored by the Living Oceans Foundation, a unique experiment in college-level teaching from the world's only underwater habitat, Aquarius.
  • Outstanding Faculty Award, Commonwealth of Virginia, 2010
  • Lockheed Martin Award for Excellence in Ocean Science & Engineering, 2008 
  • Antarctic Service Medal, National Science Foundation, 2006
  • Phi Beta Kappa Award for the Advancement of Scholarship, Alpha Chapter, College of William & Mary, 1996
  • Magnar Ronning Award for Teaching Excellence, University of California, Davis, 1987

Autonomous Underwater Vehicles:

  • Patterson, M.R., and S.J. Patterson. (in press). Unmanned systems: an emerging threat to waterside security. In IEEE Proceedings of the 2nd International Waterside Security Conference, 3-5 November, 2010, Marina di Carrara, Italy, IEEE/Oceanic Engineering Society. Sponsored by the Office of Naval Research and ECA, 8 pp.
  • Relles, N.J., and M.R. Patterson*. 2011. AUVs (ROVs). Encyclopedia of Modern Coral Reefs (Editor, David Hopley), Encyclopedia of Earth Sciences, Springer-Verlag, Heidelberg. *corresponding author.
  • Patterson, M., T. Hiller, and A. Trembanis. 2008. Exploring coral reef sustainability. Hydro International 12(7): 10-15.
  • Patterson, M.R., and N.J. Relles. 2008. Autonomous Underwater Vehicles resurvey Bonaire: a new tool for coral reef management. Proceedings of the 11th International Coral Reef Symposium, Ft. Lauderdale, Florida, 7-11 July 2008, 5 pp.
  • Hayes, D., T. Boyd, and M.R. Patterson. 2007. Sensors and instrument requirements for Autonomous Underwater Vehicles. Proceedings of the Masterclass in AUV Technology for Polar Science at the National Oceanography Centre, Southampton, 28-30 March 2006, London, Society for Underwater Technology, pp. 39-48.
  • Patterson, M.R., D.F. Doolittle, Z-u. Rahman, and R.S. Mann. 2007. Method for identification and quantification of biological sonar targets in liquid medium. US Patent 7,221,621. 20 Claims, 13 Drawing Sheets.
  • Patterson, M.R., J.H. Sias, and D.V. Gouge. 2001. AUVs and scientific diving: a looming conflict? Journal of the Marine Technology Society 34: 75-81.
  • Bartol, I.K., and M.R. Patterson. 2000. Swimming mechanics of squid and its applicability to the design of highly maneuverable autonomous underwater vehicles. Proceedings of the First International Symposium on Aqua Bio-Mechanisms, Vol. 1, ISAMBEC 2000, Honolulu, Tokai University, 6 pp.
  • Patterson, M.R., and J.H. Sias. 1999. Modular Autonomous Underwater Vehicle System. U.S. Patent No. 5,995,882. 8 Claims, 17 Drawing Sheets.
  • Patterson, M.R., and J.H. Sias. 1998. Fetch!® commercial autonomous underwater vehicle: a modular, platform-independent architecture using desktop personal computer technology. Ocean Community Conference '98 Proceedings, Volume 2, Marine Technology Society Annual Conference, November 16-19, 1998, Baltimore, MD, pp. 891-897.
  • Patterson, M.R. 1998. A finite state machine approach to layered command and control of autonomous underwater vehicles implemented in G, a graphical programming language. Ocean Community Conference '98 Proceedings, Volume 2, Marine Technology Society Annual Conference, November 16-19, 1998, Baltimore, MD, pp. 745-751.

Flow-modulated metabolism:

  • Carpenter, L.W., M.R. Patterson, and E.S. Bromage. 2010. Water flow influences the spatiotemporal distribution of heat shock protein 70 within colonies of the scleractinian coral Montastrea annularis following heat stress (Ellis and Solander, 1786): implications for coral bleaching. Journal of Experimental Marine Biology and Ecology 387: 52-59.
  • Bromage, E., L. Carpenter, S. Kaattari, and M. Patterson. 2009. Quantification of coral heat shock proteins from individual coral polyps. Marine Ecology Progress Series 376: 123-132.
  • Carpenter, L.W., and M.R. Patterson*. 2007. Water flow influences the distribution of photosynthetic efficiency within colonies of the scleractinian Montastrea annularis (Ellis and Solander 1786): implications for coral bleaching. Journal of Experimental Marine Biology and Ecology 351: 10-26. *corresponding author
  • Shashar, N., S. Kinane, P.L. Jokiel, and M.R. Patterson. 1996. Hydromechanical boundary layers over a coral reef. Journal of Experimental Marine Biology and Ecology 199(1): 17-28.
  • Lesser, M.P., V.M. Weis, M.R. Patterson, and P.L. Jokiel. 1994. Effects of water motion on carbon delivery and productivity in the reef coral, Pocillopora damicornis: diffusion barriers, inorganic carbon limitation, and biochemical plasticity. Journal of Experimental Marine Biology and Ecology 178: 153-179.
  • Patterson, M.R. 1992. A mass transfer explanation of metabolic scaling relations in some aquatic invertebrates and algae. Science 255: 1421-1423.
  • Patterson, M.R. 1992. A chemical engineering view of cnidarian symbioses. American Zoologist 32(4): 566-582.
  • Patterson, M.R., K.P. Sebens, and R.R. Olson. 1991. In situ measurements of flow effects on primary production and dark respiration in reef corals. Limnology and Oceanography 36(5): 936-948.
  • Patterson, M.R., and K.P. Sebens. 1989. Forced convection modulates gas exchange in cnidarians. Proceedings of the National Academy of Sciences (USA) 86: 8833-8836.

Benthic-pelagic coupling:

  • Trussell, G.C., M.P. Lesser, M.R. Patterson, and S.J. Genovese. 2006. Depth-specific differences in the growth of the reef sponge Callyspongia vaginalis: the role of bottom-up effects. Marine Ecology Progress Series 323: 149-158.
  • Witman, J.D., M.R. Patterson, and S.J. Genovese. 2004. Benthic-pelagic linkages in subtidal communities: influence of food subsidy by internal waves. In: Food Webs at the Landscape Level (G.A. Polis, M.E. Power, and G.R. Huxel, Eds.) pp. 133-153. University of Chicago Press.
  • Pile, A.J., M.R. Patterson, M. Savarese, V.I. Chernykh, and V.A. Fialkov. 1997. Trophic effects of sponge feeding within Lake Baikal's littoral zone: 2. Sponge abundance, diet, feeding efficiency, and carbon flux. Limnology and Oceanography 42(1): 178-184.
  • Savarese, M., M.R. Patterson, V.I. Chernykh, and V.A. Fialkov. 1997. Trophic effects of sponge feeding within Lake Baikal's littoral zone: 1. In situ pumping rates. Limnology and Oceanography 42(1): 171-178.
  • Pile, A.J., M.R. Patterson, and J.D. Witman. 1996. In situ grazing on plankton < 10 µm by the boreal sponge Mycale lingua. Marine Ecology Progress Series 141: 95-102.

Aquatic locomotion:

  • Grusha, D.S., and M.R. Patterson. 2005. Quantification of drag and lift imposed by pop-up satellite archival tags and estimation of the metabolic cost to cownose rays (Rhinoptera bonasus). Fishery Bulletin 101(3): 63-70.
  • Bartol, I.K., R. Mann, and M. R. Patterson. 2001. Aerobic respiratory costs of swimming in the negatively buoyant brief squid Lolliguncula brevis. Journal of Experimental Biology 204: 3639-3653.
  • Bartol, I.K., M. R. Patterson, and R. Mann. 2001. Swimming mechanics and behavior of the shallow-water brief squid Lolliguncula brevis. Journal of Experimental Biology 204: 3655-3682.

Suspension feeding:

  • Sanderson, S.L., J.J. Cech, Jr., and M.R. Patterson. 1991. Fluid dynamics in suspension-feeding blackfish. Science 251: 1346-1348.
  • Patterson, M.R. 1991. The effects of flow on polyp-level prey capture in an octocoral, Alcyonium siderium. The Biological Bulletin 180: 93-102.
  • Patterson, M.R. 1991. Passive suspension feeding by an octocoral in plankton patches: empirical test of a mathematical model. The Biological Bulletin 180: 81-92.
  • Patterson, M.R. 1984. Patterns of whole colony prey capture in the octocoral Alcyonium siderium. The Biological Bulletin 167: 613-629.
  • Patterson, M.R. 1980. Hydromechanical adaptations in Alcyonium sidereum (Octocorallia). In: Biofluid Mechanics 2 (D.J. Schneck, ed.) Plenum, New York, pp. 183-201.

Plant biomechanics:

  • Patterson, M.R., M.D. Harwell, L.J. Orth, and R.J. Orth. 2001. Biomechanical properties of the reproductive shoots of eelgrass. Aquatic Botany 69: 27-40.
  • Wing, S.R., and M.R. Patterson. 1993. Effects of wave-induced lightflecks in the intertidal zone on photosynthetic efficiency in the macroalgae Postelsia palmaeformis and Hedophyllum sessile (Phaeophyceae). Marine Biology 116: 519-525.
  • Patterson, M.R. 1992. Role of the mechanical microenvironment in growth of sunflower (Helianthus annuus) seedlings. Journal of Experimental Botany 43: 933-939.

Sensory biology:

  • Patterson, M.R., A.Z. Horodysky, B.W. Deffenbaugh, and R.W. Brill. 2010. Using active echo cancellation to minimize stimulus reverberations during hearing studies conducted with the auditory brain response (ABR) technique. Journal of Biomedical Science and Engineering 3: 861-867. doi:10.4236/jbise.2010.39116

K-12 education:

  • Patterson, M.R., S. Haynes and L. Carpenter. 2004. Activity: Designing an Autonomous Underwater Vehicle (AUV): Concepts in Lift, Drag, Thrust, Energy, Power, Mass, and Buoyancy. Journal of Marine Education 20: 28-35.
  • Patterson, M. R., S. Haynes, and L. Carpenter. 2003. A classroom flume to study boundary layers and flow over coral reefs – a lesson plan. University of South Florida/NOAA CD.
  • JASON XI Curriculum. 2000. Going to Extremes. JASON Foundation for Education, 248 pp. + 2 prolog videos (1 hour each)(+ co-host of 55 live 1 hour satellite video shows from the Aquarius underwater habitat).
Current and Past Students
  • Jennifer Elliott, 2010 - present. The coral reefs of Mauritius: resurvey using Autonomous Underwater Vehicles.
  • Noelle Relles, 2007 - present. Resurvey of the coral reefs of Bonaire and Curaçao: have Marine Protected Areas worked?
  • Lawrence W. Carpenter, Ph.D. 2006. Physiological consequences of high water flow on the coral Montastrea annularis (Ellis and Solander, 1786), (Marine environmental consultant)
  • Daniel Doolittle, M.S. 2003. Automated fish species classification using artificial neural networks and autonomous underwater vehicles (Ph.D. student, Geology, University of Kansas, Lawrence)
  • Wm. Stephen Price, Ph.D. 2000. The influence of tentacle shape, soft-tissue polyp, and corallite morphology, on microscale currents over corals, and implications for particle feeding: a physical model approach. (Custom flume fabricator and wildlife telemetry consultant)
  • Ian K. Bartol, Ph.D. 1999. Distribution, swimming, physiology, and swimming mechanics of brief squid, Lolliguncula brevis. (Associate Professor, Department of Biological Sciences, Old Dominion University)
  • David H. Niebuhr, Ph.D. 1999. Environmental stress in hard coral : evaluating lipid as an indicator of sub-lethal stress on short time scales. (Director, Watermen's Museum/Man and the Sea Project, Inc., Yorktown, Virginia)
  • Geoffrey C. Trussell, Ph.D. 1998. Phenotypic clines in the intertidal snail Littorina obtusata: the role of water temperature and predator effluent as inducers of phenotypic plasticity and associated trade-offs in shell form. (Associate Professor and Director, Marine Science Center, Northeastern University)
  • Kim H. Driver, Ph.D. 1998. Hydrodynamic properties and ecomorphology of the hammerhead shark (family Sphyrnidae) cephalofoil (Environmental scientist, MicroClean Services, LLC)
  • Rochelle M. Seitz, Ph.D. 1997. The role of epibenthic predators in structuring marine soft-bottom communities along an estuarine gradient. (Research Associate Professor, Virginia Institute of Marine Science, College of William & Mary)
  • Adele J. Pile, Ph.D. 1996. The role of microbial food webs in benthic-pelagic coupling in freshwater and marine ecosystems. (Senior Lecturer, School of Biological Sciences, University of Sydney, Australia)
  • Shani Kleinhaus, Ph.D. 1994. Ecophysiology of mutualism in a unique stream symbiosis between a polymorphic cyanobacterium, Nostoc parmeliodes, and the larvae of the midge, Cricotopus nostocicola. (Environmental advocate, Santa Clara Valley Audobon Society)
  • Stephen R. Wing, Ph.D., 1993.  Physical-biological coupling mechanisms in the near-shore ocean. (Associate Professor & Deputy Director, Ecology Programme, Department of Marine Science, University of Otago, New Zealand)
  • Carolyn H. Declerck, Ph.D. 1991. Evolution and comparative functional morphology in suspension feeding in prosobranch gastropods. (Associate Professor, Faculty of Economics and Applied Economics, University of Antwerp)
Courses Taught
  • MSCI/BIOL/GEOL 330 Introduction to Marine Science. Co-instructor: Kam Tang.
  • MSCI 577 Biomechanics of Marine Organisms.
  • MSCI 578 Ocean Observing Systems: Technology and Applications.
Collaborative and Interdisciplinary Efforts
  • Host Researcher on JASON XI, a $3 Million K-12 Outreach Program, from June 1999 – April 2000. Performed 55 live 1 hour shows over a 16 day period from the Aquarius underwater habitat, reaching 1.5 million students. JASON Web site hits peaked at 50,000 per day. Effort is arguably the largest (numbers and impact) sustained education outreach achieved to date by College of William & Mary. Dozens of national newspaper and magazine articles, and many TV programs reported on the mission. 23 days in field in 2000 (5 in 1999), plus 21 days science preparation, plus 3 days of script editing and revision, plus 7 days of time to pre-mission chats and 2 local school presentations, and 3 days devoted to various media interviews: 61 days donated to cause of K-12 science education
  • Economic development expert: As a faculty member, I regularly advise private industry on deep sea biology, chemistry, geology, and physics, port and harbor security, and AUV technology. I'm a member of the VIMS/Industry partnership, and the Hampton Roads chapter of the Association of Unmanned Vehicle Systems International (AUVSI). My lab helps support the international Roboboat competition in Virginia Beach, sponsored by AUVSI and the Office of Naval Research. I am also a mentor to the NASA Knights, a FIRST Robotics Team, which helps ensure a supply of engineers for the country's future.
  • Flock of Dodos: the Evolution/Intelligent Design Circus, a film by Randy Olson, a genius at communicating science to the public. I participated in this documentary on-screen, and helped the filmmaker with appearances at screenings as a panelist. This film is an insightful, humorous, but ultimately serious examination of how scientists are failing to communicate with the public on this important subject.