Proposal and Outline

David A. Vaccari, Ph.D., P.E.

Dept. of Civil, Environmental and Ocean Engineering
Stevens Instititute of Technology
Hoboken, NJ 07030
201/216-5570, Fax: 201/216-5352 Email:

James E. Alleman

Environmental Engineering
Purdue University
West Lafayette, IN 47907-1284
317/494-7705, Fax: 317/496-1107, Email:

When one of us (D.V.) first came to teach environmental engineering from a science undergraduate background, it was some surprise to discover that engineers typically do not have a single biology course in their programs. Even environmental engineering students are often exposed only to sanitary microbiology. However, the growth of the environmental sciences has greatly expanded the scope of biological disciplines with which engineers need to deal. With the possible exceptions of biomedical and biochemical engineering, environmental engineering is the engineering discipline which has the closest connection with biology. Certainly it is the only engineering discipline which connects with such a wide range of biological fields.

As a result of the need to make engineers literate in biological concepts and terminology a new graduate-level course was developed. The first half of the semester was devoted to an introduction to general biology. The students were required to purchase a used college-level general biology textbook -- a useful addition to anyone's library. One week was spent on each of the general biology topics which are summarized in outline form in the appendix. However, no single text covered the range of topics presented in the second half, which is the focus of and motivation for this book. This book would also be useful, of course, to other non-biologists involved with the environmental field, such as chemists and geologists.

Specialists in every field have learned not to expect their collegues trained in other areas to have certain basic knowledge in their own. The aim of this book is to break one of the barriers of overspecialization. I often tell my students the following: the objectives of this course will have been met if they are meeting with a biologist to discuss a situation of environmental concern, and the biologist at some point turns to the them and says: "How'd you know that?". It should not be a surprise that any well-educated person possesses some specialized knowledge outside their own profession.

A secondary need which this subject meets is the necessity for any technically literate person to be familiar with biology. Exposing engineers and other professionals to this field broadens their knowledge of the living world around them, and even of their own bodies. The biologically literate engineer will better understand and cope with the impacts of technologically-driven changes in the world. This understanding should encompass not only environmental issues such as pollution effects, ecosystem destruction and species extinction, but also genetic engineering in agriculture and medicine, other medical technology, and bioethics.


This will be the only book specifically devoted to covering all of the specialized fields of biology related to the environment. Several excellent books exist on environmental science which include all of these topics, but the need to cover other environmental aspects (chemistry, engineering, management, legal, etc.) necessarily makes the coverage of the biological topics more superficial than would be useful for a semester course.

The book will be organized into two parts. Part I will be a consise outline of general biology. This is intended for use as a study guide and a summary of prerequisite information. It is necessary since the intended audience presumably does not have exposure to college-level biology.

Part II will contain the chapters which are specific to environmental applications. In broad terms, the important areas are sanitary microbiology, ecology and toxicology. Two chapters cover the traditional areas of microbiology taught to environmental engineers, adding the public health aspects. Ecology is divided into four chapters, each focussing on one type of ecosystem of interest to engineers. Practical matters should be included such as wetlands delineation and restoration and methods for assessing ecosystem health. Four chapters relate to toxicology. The chapters on aquatic nad mammalian toxicology could be somewhat smaller than the others, since the general toxicology chapter will cover many of the relevant concepts. A significant amount of toxicity data should be included for common classes of pollutants to increase the reference value of the book.


The book will be a two-author volume. Each chapter will attempt to cover the "core knowledge" from each sub-discipline. This knowledge should include an overview of the most important concepts in the field. It should cover a wide range of terminology. Any questions and problems included after each chapter will emphasize practical uses of the information, rather than testing aquisition of information. A short annotated bibliography will be included for each chapter, for further reading. For example, reference could be given to one or two of the most comprehensive books on the subject, as well as some which are simpler and more accessible to the nonspecialist. A brief comparative description for each will guide the reader in selecting the most appropriate source of more information. Instead of a glossary, each important term will be highlighted in boldface the first time it is used, and a clear "stand-alone" definition will follow immediately.

Important field and laboratory methods will be described with enough detail to give an appreciation for errors and interferences which may occur, yet not so much as to be a protocol for performing the test. Illustrations should be carefully selected to help the reader understand some point which is too difficult to describe clearly in words.

In order to play to the strengths of the engineers, mathematical techniques should be emphasized, where appropriate. Examples include population dynamics, microbial growth kinetics (focusing on batch systems, and stopping at the chemostat, short of treatment process models), pharmacokinetic models of toxicity, ecosystem modeling, statistical approaches to epidemiology, and probabilistic modeling of bioassays.

A textbook should have more depth than could actually be covered in a course, so a student can make his own choices in moving beyond lecture material. Assuming six hours of reading material per week for a 14-week course, and a reading speed of five pages per hour, then the book should have at least 420 pages. Adding space for illustrations and additional material would increase the size to about 500 to 550 pages. Part I will be about 200 pages, with the balance for Part II. Each chapter will average about 30 pages. Some chapters which may be longer include those dealing with microbiology, which has a dominant role in environmental engineering. Others which may be shorter are those on Public Health, Epidemiology, and Risk Assessment.


The book is aimed at professionals in the environmental field, especially engineers, who have had only a cursory introduction to general biology, and little specialized biological training beyond that given in introductory environmental engineering courses. Familiarity with basic environmental chemistry concepts will be assumed, including understanding of alkalinity, oxygen demand, etc.

The book will be designed as a textbook for a course in environmental biology. A secondary market, which may be larger than the primary, will be as a primer/reference for environmental professionals without biological training, including engineers, chemists, and geologists. Inclusion of a significant amount of data on biological effects of numerous pollutants should increase the reference value of the book.



  1. INTRODUCTION -- Motivation for the Study of Environmental Biology. Present perspectives on environmental engineers and scientists. Past perspectives on environmental engineers and scientists. Guidelines for study. The ambiguity of biological definitions.Conservation and environmental ethics.


  1. GENERAL BIOLOGY -- Holistic views of biology. What is life? Overview of biological hierarchy: biochemistry and metabolism, cell theory, cell structure & function, cell division, procaryotes & eucaryotes, organelles; organs, systems, organisms, physiology, species, population, community, ecosystem; taxonomy. Evolution. Taxonomy. Interaction of the biosphere and the environment (Gaia hypothesis).
  2. BIOCHEMISTRY -- Basic organic chemistry, carbohydrates, proteins, nucleic acids, lipids, photosynthesis, respiration, nitrification, fermentation, methanogenesis; the cell membrane. Energetics and ATP. Energy and entropy. The origin of life.
  3. THE CELL -- Cell theory and cell structure & function, the cell membrane, cell division, procaryotes & eucaryotes.
  4. GENETICS -- Heredity, the chemical basis of heredity, genetic engineering, carcinogenesis. heterozygote advantage (sickle-cell anemia), genetic basis of evolution, mutations, single-gene mutation, gene duplication, exon shuffling, recombination, Hardy-Weinberg, genetic drift, bottleneck effect, founder effect, inbreeding, assortive mating, effective population. Genetics and evolution.
  5. BOTANY -- Summary of divisions, plant physiology & reproduction.
  6. ZOOLOGY -- Summary of phyla, animal and human physiology & reproduction.
  7. MICROBIOLOGY -- metabolic pathways, pure culture techniques and limitations, aerobes, anaerobes, autotrophs, heterotrophs, chemoautotrophs, Bergey's classification. Protista, Fungi. Sterility and the ubiquity of microorganisms.
  8. GENERAL ECOLOGY -- structure and types of ecosystems, habitats; energy flow & pyramid, food chains & webs, trophic levels, biological productivity, biogeochemical cycles, population dynamics, species interactions, species diversity.


  1. MICROBIAL ECOLOGY and POLLUTION MICROBIOLOGY -- BOD, Monod growth curve, effect of toxicity, competitive growth, nitrogen cycle, microbial transformation of toxic pollutants. Aquatic microbiology, soil microbiology. Indicator organisms. Genetic engineering in the environment.
  2. BIOLOGY OF POLLUTION CONTROL -- Discussion of microbiology of particular biological treatment processes: activated sludge, bulking and filamentous organisms, nitrogen and phosphorous removal, removal of toxics, anaerobic digestion, land application, composting, bioaugmentation. Disinfection biology. Bioremediation. Nonmicrobial treatment: macrophytes (hyacinth, reed beds, duckweed), phytoremediation, fungal processes (white rot fungi) earthworms.
  3. PUBLIC HEALTH -- pathogens, vectors, water and aerosol transmitted diseases (include a list with characteristics such as vector, symptoms, etc.).
  4. FRESHWATER ECOLOGY-- Limnology, stream sanitation, ecosystems (benthos, etc.) eutrophication, transport of nutrients, succession, acid rain impacts; food chain.
  5. MARINE AND ESTUARINE ECOLOGY -- ecosystems, water column communities, fisheries biology. Effects of thermal pollution.
  6. WETLANDS -- The value of wetlands, natural and disturbed ecosystems, wetland delineation and restoration, artificial wetlands.
  7. TERRESTRIAL ECOLOGY -- deforestation & habitat destruction, erosion, impact of acid rain on forests, wildlife management.
  8. GENERAL TOXICOLOGY -- target organs, dose-response extrapolation models, acute and chronic bioassays, LD50 and LC50, etc., biomagnification, bioconcentration.
  9. AQUATIC TOXICOLOGY -- bioassays, acute, chronic, etc.; effects of common pollutants; water quality criteria and effluent permitting.
  10. ECOLOGICAL RISK ASSESSMENT -- Hazard assessment.
  11. MAMMALIAN TOXICOLOGY -- health effects of common pollutants, methods of ingestion, pharmacokinetic models, biotransformation, teratogenesis, mutagenesis, carcinogenesis, in-vitro/in-vivo testing.
  12. ENVIRONMENTAL EPIDEMIOLOGY -- Measurements and observations, descriptive studies, case-control studies, cohort studies, experimental studies, clinical studies, statistical methods (description) - ANOVA, multilinear regression, polynomial regression, factor analysis, principal component analysis.
  13. HUMAN RISK ASSESSMENT -- risk assessment steps (hazard identification, exposure assessment, toxicity assessment, risk characterization) roles of engineer and toxicologist.

REFERENCES (Partial list):

Any college-level General Biology textbook.

"Fundamentals of Ecology", by Eugene P. Odum (W.B. Saunders Co.)

"Fund. of Aquatic Toxicology" by G.M. Rand and S.R. Petrocelli, Hemisphere Pub. (1985).

"Chemistry and Ecotoxicology of Pollution", by D.W. Connell & G.J. Miller, Hemisphere Pub (1984).

"Water Pollution Biology", R.A. Coler and J.P. Rockwood, Technomic Pub. (1989).

"Microbial Ecology", Atlas & Bartha, Addison-Wesley (1981).

"Control of Communicable Diseases in Man", Abram S. Benenson, ed., APHA (1970).

"Fundamentals of Aquatic Ecology", Barnes & Mann, Blackwell Scientific (1991).

"Bioremediation", Katherine H. Baker & Diane S. Herson

"Dynamics of Marine Ecosystems", Mann & Lazier, Blackwell Scientific (1991).

"Primer of Epidemiology", Friedman, McGraw-Hill (1987).

"Superfund Public Health Evaluation Manual", USEPA