OF SCHOOL SCIENCE AND TECHNOLOGY AND FACULTY OF GRADUATE STUDIES BULLETIN BIOLOGYM.S. and Ph.D. Programs ROBERT A. CUSHMAN, JR., Ph.D., Program Coordinator The Department of Earth and Biological Sciences offers the Biology Program, leading to the Master of Science and Doctor of Philosophy degrees. These curricula provide a broad and unified approach to the life sciences, and also specialization, as evidenced by the conduct of significant, original research and in the selection of courses related to the area of research interest. Study in various areas, from molecular biology to natural history, is available to the student seeking preparation for teaching or for research in modern biology. Some areas of specialization are: animal behavior, animal physiology, molecular systematics, ecological physiology, behavioral ecology, conservation biology, marine biology, and paleontology. OBJECTIVES The Biology Program strives to: 1. Instill in students the values of honesty, scientific integrity, careful research, and critical, independent thinking. 2. Provide the tools and intellectual environment in which biologists can attain their highest potential in scholarship, research, and teaching. 3. Challenge graduate students to consider the relationships among science, faith, and societal responsibility. FACULTY LEONARD R. BRAND, Ph.D. Cornell University 1970 Professor of Biology and Paleontology Vertebrate paleontology, taphonomy, and philosophy of science H. PAUL BUCHHEIM, Ph.D. University of Wyoming 1978 Professor of Geology Sedimentology, stratigraphy, and limnogeology RONALD L. CARTER, Ph.D. Loma Linda University1977 Professor of Biology Molecular ecology and systematics ROBERT A. CUSHMAN, JR., Ph.D. Colorado School of Mines 1994 Chair; Program Coordinator; Assistant Professor of Geology Biostratigraphy, paleopalynology, and terrestrial paleoecology STEPHEN G. DUNBAR, Ph.D. Central Queensland University 2002 Assistant Professor of Biology Tropical marine and intertidal ecology and marine invertebrate ecophysiology, comparative physiology, behavior and distribution ROBERT FORD, M.P.H. Loma Linda University 1973; Ph.D. University of California, Riverside 1982 Professor of International Sustainable Development Earth systems and sustainability science
WILLIAM K. HAYES, Ph.D. University of Wyoming 1991 Professor of Biology Behavioral ecology, herpetology, ornithology, and conservation biology KEVIN E. NICK, Ph.D. University of Oklahoma 1990 Assistant Professor of Geology Sedimentology and paleomagnetics ASSOCIATE FACULTY HANSEL M. FLETCHER, Ph.D. Temple University 1990 Associate Professor of Microbiology and Molecular Genetics Bacterial pathogenesis and antibiotic resistance DAVID A. HESSINGER, Ph.D. University of Miami 1970 Professor of Physiology and Pharmacology Cell biology, sensory transduction, and marine toxicology MICHAEL A. KIRBY, Ph.D. University of California at Riverside 1984 Associate Professor of Pathology & Human Anatomy and of Pediatrics Developmental neurobiology JUNICHI RYU, Ph.D. Tokyo Metropolitan University 1978 Associate Professor of Microbiology and Molecular Genetics Gene regulation and restriction-modification enzymes of enteric bacteria ADJUNCT FACULTY GORDON J. ATKINS, Ph.D. McGill University 1987 Adjunct Associate Professor of Biology Neurophysiology RAUL ESPERANTE, Ph.D. Loma Linda University 2002 Adjunct Assistant Professor of Paleontology Vertebrate paleontology and taphonomy H. THOMAS GOODWIN, Ph.D. University of Kansas 1990 Adjunct Professor of Biology Vertebrate paleontology and biogeography JOHN F. STOUT, Ph.D. University of Maryland 1963 Adjunct Professor of Biology Behavioral physiology
DEPARTMENTAL PROGRAMS The Department of Earth and Biological Sciences administers the Biology Program. The department also administers programs leading to the following degrees or combined-degrees: M.S. and Ph.D. in biology M.S. in natural sciences Ph.D. in earth science M.S. in geology B.S. in geology MASTER OF SCIENCE Admission Applicants must meet the general admission requirements of the School of Science and Technology, as outlined in the current School of Science and Technology bulletin. Expected undergraduate preparation includes a bachelors degree from an accredited college or university, with a biology major or equivalent; statistics, Pre-calculus (required), calculus (recommended), one year of general chemistry, one year of organic chemistry, one year of general physics and biochemistry (recommended). Students pursuing the M.S. degree are urged to select a research project with a primary faculty member from the department. Student aid Research and teaching assistantships are available from the department on a competitive basis. Further information can be obtained from the chair of the department. Qualified students are also encouraged to seek fellowships from federal and private agencies such as the National Science Foundation and the National Institute of Health. General requirements For information about requirements and practices to which all graduate students are subject, the student should consult the Policies and General Regulations section of the School of Science and Technology bulletin. CURRICULUM The following constitutes the curriculum for the Master of Science degree in biology. A minimum of 48 quarter units of academic credit is required. Of the 48 units, 30 must be in biology and cognate science subjects (as approved by the guidance committee), with 40 at or above the 500 level (exclusive of research), including: BIOL 545 BIOL 558 BIOL 607 BIOL 616 BIOL 617 Genetics and Speciation Philosophy of Science and Origins Seminar in Biology (1 unit each quarter in residence) Research and Experimental Design Proposal Writing and Grantsmanship (4) (4) (3+) (2) (2)
One course from each of the following areas: Biological Systems Cell or Molecular Biology Physiology Advanced Genetics
Microbiology Biochemistry Ecology Marine Biology Biogeography Behavioral Ecology Biodiversity and Conservation Techniques in Vertebrate Ecology Plant Ecology Organismal Biology Behavioral Ecology Marine Invertebrates Mammalogy Advances in Sociobiology Paleontology The remaining 18+ units must include: Additional courses required by the students guidance committee Research, 4-12 units Thesis, 2 units, including final oral examination and defense Religion, 3 units Seminar attendance requirements Attendance at all departmental seminars is required of the student while in residence at Loma Linda University. Research proposal A written research proposal and an oral defense of the students proposed research should be completed by the end of the 3rd quarter of study. Questions will typically focus on the students research area, but may expand to other areas as appropriate. Advancement to candidacy Students may apply for advancement to candidacy after: 1. completing all deficiencies and prerequisites, 2. selecting a research committee, 3. having an approved written research proposal, 4. passing the oral defense of the research proposal, and 5. being recommended by the dept. faculty (should be completed by the end of the 3rd quarter of study). Thesis The written thesis must demonstrate the completion of significant, original research. Defense of thesis An oral presentation and defense of the thesis is required.
DOCTOR OF PHILOSOPHY Admission The successful applicant must meet the general admission requirements of the School of Science and Technology. Undergraduate preparation should include a biology bachelors degree (MS recommended), statistics, pre-calculus (required), calculus (recommended), one year of general physics, one year of general chemistry, one year of organic chemistry and Biochemistry (recommended). CURRICULUM The following constitutes the curriculum for the Doctor of Philosophy degree in biology. A minimum of 72 quarter units of academic credit for courses, seminars, and research beyond the masters degree is required; i.e., a minimum of 120 units beyond the baccalaureate degree, including the following required courses: BIOL 545 BIOL 558 BIOL 607 BIOL 616 BIOL 617 Genetics and Speciation Philosophy of Science and Origins Seminar in Biology (1 unit each quarter in residence) Research and Experimental Design Proposal Writing and Grantsmanship (4) (4) (6+) (2) (2)
Two courses in each of the following areas: Biological Systems Cell or Molecular Biology Physiology Advanced Genetics Microbiology Biochemistry Ecology Marine Biology Biogeography Behavioral Ecology Biodiversity and Conservation Techniques in Vertebrate Ecology Plant Ecology Organismal Biology Behavioral Ecology Marine Invertebrates Mammalogy Advances in Sociobiology Paleontology The required 72+ units must also include: Additional courses required by the students committee: Research, 10-25 units Dissertation, 2 units Religion, 3-unit course beyond masters degree level Graduate level statistics
Seminar attendance requirements Attendance at all departmental seminars is required of the student in residence at Loma Linda University. Recommended Teaching is recommended during at least one quarter. This experience may be obtained in the laboratory or it may include presenting several lectures for a course. Research proposal A written research proposal and an oral defense of the proposed research should be completed by the end of the 3rd quarter of study. Questions will typically focus on the students research area, but may expand to other areas as appropriate. Comprehensive examinations An oral and a written comprehensive examination are given near completion of the formal course work. The purpose is to measure the students knowledge of the various fields of biology, philosophy of science, and preparation for research. These examinations should be completed by the beginning of the 3rd year of study. Advancement to candidacy The student may apply for advancement to doctoral candidacy after: 1. completing all deficiencies and prerequisites, 2. passing the comprehensive examinations, 3. selecting a research committee, 4. having an approved written research proposal, 5. passing the oral defense of the research proposal, and 6. being recommended by the department faculty. Dissertation The written dissertation must demonstrate the completion of significant, original research. Defense of dissertation An oral dissertation presentation and defense are required.
COURSES UNDERGRADUATE BIOL 116 Introduction to Human Biology (3) Introductory course in human biology. This course will explore basic principles of human anatomy and physiology and their relationships to social functioning. It is designed to fulfill the Human Biology prerequisite for the Masters program in Social Work. BIOL 314 Genetics and Speciation (4) Introduction to genetic mechanisms of biological change. Processes of inheritance through time evaluated in their ecological context. BIOL 315 Ecology (4) Principles of terrestrial, aquatic, and marine ecology, with a focus on individual, population, community, and ecosystem levels of organization. Laboratory work includes field studies designed to examine ecological principles. Three class hours and one three-hour laboratory per week.
BIOL 475 Philosophy of Science and Origins (3) Concepts in the history and philosophy of science, and the application of these principles in analyzing current scientific trends. Cross-listing: GEOL 475 BIOL 495 Undergraduate Research (1-4) Original investigation and/or literature study pursued under the direction of a faculty member. May be repeated for additional credit. Prerequisite: Consent of the instructor. ESSC 401 Earth Systems Science and Global Change I (4) This is part I of a 2 quarter sequence course. Both courses explore the dynamic biogeophysical processes in the geosphere, hydrosphere, atmosphere, biosphere, and sociosphere, with part I covering the geosphere and hydrosphere. The focus is on acquiring an interdisciplinary understanding of the basic principles and concepts of Earth Systems Science (ESS) and the Human Dimensions of Global Environmental Change (HDGC). ESSC 402 Earth Systems Science and Global Change II (4) This is part II of a 2 quarter sequence course. Both courses explore the dynamic biogeophysical processes in the geosphere, hydrosphere, atmosphere, biosphere, and sociosphere, with part II covering the atmosphere, biosphere, and sociosphere. The focus is on acquiring an interdisciplinary understanding of basic the principles and concepts of Earth Systems Science (ESS) and the Human Dimensions of Global Environmental Change (HDGC). Prerequisite: ESSC 401
GRADUATE BIOL 504 Biology of Marine Invertebrates (4) Behavior, physiology, ecology, morphology, and systematics of marine invertebrates, with emphasis on morphology and systematics. Three class hours per week, one-day field trip alternate weeks, or the equivalent. BIOL 505 Marine Biology (4) Survey of the marine species of the world, and of the oceanographic processes and ecological interactions that affect them. Emphasis on tropical and coral ecosystems. Includes an independent project. Four class hours per week, plus all-day field trips (usually on Sundays). BIOL 509 Mammalogy (4) Study of the mammals of the world, with emphasis on North America. Includes classroom and field study of systematics, distribution, behavior, and ecology. Three class hours, one three-hour laboratory per week. BIOL 515 Biogeography (3) Present and past distribution and migrations of the natural populations of organisms. Prerequisite: Biology or systematics of at least two plant or animal taxa desirable. BIOL 517 Ecological Physiology (4) Study of the interface between the individual and the environment, with emphasis on unusual environments, to explore the limits of physiological systems. Four class hours per week.
BIOL 518 Readings in Ecology (2) Study, analysis, and discussion of current and classic papers. Prerequisite: A course in ecology or consent of the instructor. BIOL 524 Paleobotany (4) Fossil plants; their morphology, paleoecology, taphonomy, classification, and stratigraphic distribution. Analysis of floral trends in the fossil record. Three class hours plus one three-hour laboratory or field trip per week. Cross-listing: GEOL 524 Prerequisite: Consent of the instructor. BIOL 525 Paleopalynology (4) Morphology, paleoecology, classification, & stratigraphic distribution of plant microfossils. Includes introduction to biostratigraphic and paleoecologic analytical methods. Three class hours and one three-hour laboratory or field trip per week. Cross-listing: GEOL 525 Prerequisite: Consent of the instructor BIOL 526 Principles and Methods of Systematics (3) Study of the principles and methods of modern systematic biology, with focus on the assumptions, concepts, and computerized methods of phylogeny reconstruction. BIOL 534 Invertebrate Paleontology (4) Structure, classification, ecology, and distribution of selected fossil invertebrate groups. Principles and methods involved in the study and analysis of invertebrate fossils considered. Three class hours and one three-hour laboratory per week. Cross-listing: GEOL 534 Prerequisite: Consent of the instructor. BIOL 535 Animal Behavior (4) Behavioral mechanisms of animals and their role in survival. Lectures and projects. BIOL 536 Readings in Animal Behavior (2) Critical analysis of research literature on animal behavior. Prerequisite: A course in animal behavior or consent of the instructor. BIOL 537 Advances in Sociobiology (3) Current concepts and ideas relating to the origin & structure of social behavior of animals. Special attention to the adaptive significance of species-specific behavior in a wide variety of environments. BIOL 538 Behavior Genetics (4) Study of interactions of genotype and phenotype as it relates to animal behavior. Primary focus at the molecular and physiological levels of behavior. Modern understanding of the nature/nurture debate extended to topics that include biological determinism and ethics. BIOL 539 Behavioral Ecology (4) An in-depth examination of how behavior contributes to the survival of animals, with an emphasis on behavioral strategies that reflect adaptation to the animals environment.
BIOL 544 Vertebrate Paleontology (4) Fossil vertebrates, with emphasis on the origins of major groups. Systematics, biology, and biogeography of ancient vertebrates. Three class hours, one three-hour laboratory per week. Cross-listing: GEOL 544 Prerequisite: General Biology or consent of the instructor. BIOL 545 Genetics and Speciation (4) Comparative analysis of species concepts, mechanisms of speciation, and analysis of micro- and macroevolution. Prerequisite: A course in genetics and Philosophy of Science. BIOL 546 Techniques in Vertebrate Ecology (3) Theory and practice of vertebrate ecology research , including marking methods, population estimation, home range and habitat analysis, radiotelemetry. Software will be used extensively for analysis of data, some of which will be collected during field trips. BIOL 547 Molecular Biosystematics (4) Analysis at the molecular level of genetic events that underlie speciation. Laboratory work integrated with lecture, demonstrating basic molecular genetic research tools applicable to molecular biosystematics studies. Prerequisite: Genetics and Speciation or molecular genetics, and Philosophy of Science. BIOL 548 Molecular Ecology (4) Application of molecular markers to the study of ecology and natural history of populations. Special emphasis placed on molecular techniques that uniquely contribute to resolving major problems in phylobiogeography and measures of adaptiveness. Prerequisite: Genetics and Speciation plus a course in either ecology or biogeography. BIOL 549 Biodiversity and Conservation (3) This course examines contemporary issues related to diminishing biodiversity on regional and global scales and the need to conserve both biodiversity and the critical habitats that support threatened flora and fauna. BIOL 558 Philosophy of Science and Origins (4) Study of selected topics in the history and philosophy of science, and the application of these principles in analyzing contemporary scientific trends. Cross-listing: GEOL 558 BIOL 588 Current Topics in Biology (1-5) Review of cutting edge literature in the biological sciences. Different sections of the course may be repeated for additional credit. Prerequisite: Consent of the instructor. BIOL 589 Readings in Biology (1-4) Study, analysis, and discussion of current and classic papers. BIOL 607 Seminar in Biology (1) Presentations by guest scientists on recent research and developments in biological science. Student attends seminar; no student presentation required. BIOL 616 Research and Experimental Design (2) Concepts, methods and tools of research, including experimental design and data analysis.
BIOL 617 Proposal Writing and Grantsmanship (2) Skills and practice of effective proposal writing and strategies for locating and obtaining research grants. BIOL 695 Special Projects in Biology (1-4) Responsibility for a special research project in the field, laboratory, museum, or library. May be repeated for additional credit. BIOL 697 Research (1-8) See department checklist for recommended number of units. BIOL 698 Thesis (2) Credit for writing the masters thesis. BIOL 699 Dissertation (2) Credit for writing the doctoral dissertation.
EARTH SYSTEMS SCIENCE COURSES (Available as electives) ESSC 541 Remote Sensing and Systems Modeling I (4) Provide students fundamental knowledge and skills of modern remote sensing for environmental data acquisition and analysis as well as applications in related social, earth, health, and biosciences. Topics include GIS-based image interpretation and spatial data generation, satellite remote sensing applications, and case studies in sustainable development, social policy, health, and biosciences. Spatial analysis software tools used will include Clark labs IDRISI Kilimanjaro and Leica-Geosystems ERDAS Imagine as well as ArcPAD, ArcGIS, GPS/Garmin-Recon. ESSC 542 Remote Sensing and Systems Modeling II (4) Introduces students to the concepts and methods of systems science as a methodology within the social, health, earth, and biosciences. Specifically focus on use of dynamic modeling tools such as STELLA (from Isee Systems) as well as spatial and non-spatial tools and datasets such as Spatial Analyst-ArcGIS, GeoNetweaver, EMDS, Criterion PLUS, and other tools as needed. Learn to apply systems thinking and analysis frameworks to specific interdisciplinary policy issues within sustainable development, forensic science, earth systems science, social and health policy, and other applied sciences. Prerequisite: ESSC 541 or consent of the instructor. ESSC 575 Field Practicum: Applied Earth System Science (4) Students and teachers work together in the field to apply geospatial tools, Earth System Science methods and concepts, social policy analytical frameworks, and other conservation science methods to integrated placebased sustainability problems within a given ecosystem, community or region. The focus is on applying in practice the concepts and tools of sustainability science (see: http://sustsci.harvard.edu/index.html ). Practice using in the field modern field analytical tools such as GPS, ArcPAD (mobile GIS), varied ecological monitoring and assessment instruments (focused on ecosystems analysis, e.g. water, land, air, ecosystems), PRA (Participatory Rural Appraisal) as well as traditional ethnographic and socioeconomic qualitative research methods. Places studied will include both domestic and international such as Mesoamerica, the U.S. Southwest, Southern California, and elsewhere. Prerequisite: Consent of the instructor.
ROSARIO BEACH SUMMER COURSES In cooperation with the Walla Walla College Marine Station in Anacortes, Washington, facilities are available for marine courses and research by graduate students of this department. Some of the available courses are listed below. BIOL 455 Comparative Physiology (5) Comparative study of the physiology and life process of animals, with emphasis on invertebrates. Prerequisite: Cell biology. BIOL 458 Marine Biology (5) Study of marine life and its ecology, and of oceanography as it affects marine life. BIOL 459 Marine Invertebrates (5) Study of the biology of selected groups of marine invertebrates. BIOL 460 Marine Ecology (5) Study of interspecific, intraspecific, and community relationships demonstrated by marine organisms. BIOL 462 Ichthyology (5) Systematic study of fishes found in Puget Sound, with a survey of fishes of other waters. BIOL 463 Marine Botany (5) Systematic study of plants found in Puget Sound, with a survey of marine plants from other areas. BIOL 508 Physiology of Algae (5) Comparative study of the physiology of representative members of the major algal groups. Collection and growth of cultures of single-celled forms; related metabolic processes, nutritional factors, light requirements, synchronization, and growth emphasized. BIOL 516 Behavior of Marine Organisms (5) Study of inter-and intraspecific behaviors of marine animals and their behavioral responses to the physical environment. Laboratory experiences, field observations, and a research project. Prerequisite: A background in organismal biology and permission of the instructor.
GEOLOGY COURSES Course descriptions can be found in the Geology section of the School of Science and Technology bulletin.
OTHER COURSES Numerous courses offered by the basic medical sciences and other departments are available to graduate students. Some are listed here, and their course descriptions may be found elsewhere in the School of Science and Technology bulletin. ANAT 546 ANAT 548 ANAT 554 BCHM 508 Electron Microscopy Advanced and Molecular Cytology Techniques in Experimental Morphology Principles of Biochemistry (3) (3) (2) (6)
BCHM 523 BCHM 525 BCHM 534 ENVH 557 ENVH 566 ENVH 568 ENVH 569 MICR 536 MICR 539 MICR 545 MICR 546 MICR 565 MICR 566 PHSL 501 PHSL 535 PHSL 541 PSYC 501 PSYC 502 PSYC 503 STAT 521 STAT 522 STAT 523 STAT 525
Introduction of Physical Biochemistry Metabolic Interrelationships and Control Techniques of Biochemistry Geographical Techniques for Health and Environmental Analysis Outdoor Air Quality and Human Health Water-Quality Assurance Environmental Sampling and Analysis Laboratory in Gene Transfer and Gene Expression Molecular Biology of Prokaryotes and Eukaryotes Molecular Biology Techniques, Laboratory Advanced Immunology Virology Cell Culture Neurophysiology, DN Comparative Physiology Cell and Molecular Biology Advanced Statistics I Advanced Statistics II Advanced Multivariate Statistics I Biostatistics I Biostatistics II Biostatistics III Applied Multivariate Analysis
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