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PART 1
Introduction

1
What Is a
Bioprocess Engineer?

1.1. INTRODUCTORY REMARKS

We can now manipulate life at its most basic level—the genetic. For thousands of years
people have practiced genetic engineering at the level of selection and breeding. But now
it can be done in a purposeful, predetermined manner with the molecular-level manipula-
tion of DNA. We now have a tool to probe the mysteries of life in a way unimaginable 25
years ago.
With this intellectual revolution emerge new visions and new hopes: new medicines,
semisynthetic organs grown in large vats, abundant and nutritious foods, computers based
on biological molecules rather than silicon chips, superorganisms to degrade pollutants,
and a wide array of consumer products and industrial processes.
These dreams will remain dreams without hard work. Engineers will play an essen-
tial role in converting these visions into reality. Biological systems are very complex and
beautifully constructed, but they obey the rules of chemistry and physics and they are sus-
ceptible to engineering analysis. Living cells are predictable, and the processes to use
them can be rationally constructed on commercial scales. Doing this is the job of the bio-
process engineer.
Probably the reason you are reading this book is your desire to participate in this in-
tellectual revolution and to make an important contribution to society. You can do it, but it

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is not easy to combine the skills of the engineer with those of the biologist. Our intent is
to help you begin to develop these skills. This book and a one-term course are not enough
to make you a complete bioprocess engineer, but we intend to help you form the neces-
sary foundation.

1.2. BIOTECHNOLOGY AND BIOPROCESS ENGINEERING

When new fields emerge from new ideas, old words are usually not adequate to describe
these fields. Biotechnology and what constitutes engineering in this field are best de-
scribed with examples rather than single words or short phrases.
Biotechnology usually implies the use or development of methods of direct genetic
manipulation for a socially desirable goal. Such goals might be the production of a partic-
ular chemical, but they may also involve the production of better plants or seeds, or gene
therapy, or the use of specially designed organisms to degrade wastes. The key element
for many workers is the use of sophisticated techniques outside the cell for genetic manip-
ulation. Others interpret biotechnology in a much broader sense and equate it with applied
biology; they may include engineering as a subcomponent of biotechnology.
Many words have been used to describe engineers working with biotechnology.
Bioengineering is a broad title and would include work on medical and agricultural sys-
tems; its practitioners include agricultural, electrical, mechanical, industrial, environmen-
tal and chemical engineers, and others. Biological engineering is similar but emphasizes
applications to plants and animals. Biochemical engineering has usually meant the exten-
sion of chemical engineering principles to systems using a biological catalyst to bring
about desired chemical transformations. It is often subdivided into bioreaction engineer-
ing and bioseparations. Biomedical engineering has been considered to be totally separate
from biochemical engineering, although the boundary between the two is increasingly
vague, particularly in the areas of cell surface receptors and animal cell culture. Another
relevant term is biomolecular engineering, which has been defined by the National Insti-
tutes of Health as “. . . research at the interface of biology and chemical engineering and is
focused at the molecular level.”
There is a difference between bioprocess engineering and biochemical engineering.
In addition to chemical engineering, bioprocess engineering would include the work of
mechanical, electrical, and industrial engineers to apply the principles of their disciplines
to processes based on using living cells or subcomponents of such cells. The problems of
detailed equipment design, sensor development, control algorithms, and manufacturing
strategies can utilize principles from these disciplines. Biochemical engineering is more
limited in the sense that it draws primarily from chemical engineering principles and
broader in the sense that it is not restricted to well-defined artificially constructed
processes, but can be applied to natural systems.
We will focus primarily on the application of chemical engineering principles to
systems containing biological catalysts, but with an emphasis on those systems making
use of biotechnology. The rapidly increasing ability to determine the complete sequence
of genes in an organism offers new opportunities for bioprocess engineers in the design
and monitoring of bioprocesses. The cell, itself, is now a designable component of the
overall process.

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1.3. BIOLOGISTS AND ENGINEERS DIFFER IN THEIR APPROACH

TO RESEARCH

The fundamental trainings of biologists and engineers are distinctly different. In the devel-
opment of knowledge in the life sciences, unlike chemistry and physics, mathematical theo-
ries and quantitative methods (except statistics) have played a secondary role. Most progress
has been due to improvements in experimental tools. Results are qualitative and descriptive
models are formulated and tested. Consequently, biologists often have incomplete back-
grounds in mathematics but are very strong with respect to laboratory tools and, more im-
portantly, with respect to the interpretation of laboratory data from complex systems.
Engineers usually possess a very good background in the physical and mathematical
sciences. Often a theory leads to mathematical formulations, and the validity of the theory
is tested by comparing predicted responses to those in experiments. Quantitative models
and approaches, even to complex systems, are strengths. Biologists are usually better at
the formation of testable hypotheses, experimental design, and data interpretation from
complex systems. Engineers are typically unfamiliar with the experimental techniques
and strategies used by life scientists.
The skills of the engineer and life scientist are complementary. To convert the
promises of molecular biology into new processes to make new products requires the inte-
gration of these skills. To function at this level, the engineer needs a solid understanding
of biology and its experimental tools. In this book we provide sufficient biological back-
ground for you to understand the chapters on applying engineering principles to biosys-
tems. However, if you are serious about becoming a bioprocess engineer, you will need to
take further courses in microbiology, biochemistry, and cell biology, as well as more ad-
vanced work in biochemical engineering. If you already have these courses, these chapters
can be used for review.

1.4. THE STORY OF PENICILLIN: HOW BIOLOGISTS

AND ENGINEERS WORK TOGETHER

In September 1928, Alexander Fleming at St. Mary’s Hospital in London was trying to
isolate the bacterium, Staphylococcus aureus, which causes boils. The technique in use
was to grow the bacterium on the surface of a nutrient solution. One of the dishes had
been contaminated inadvertently with a foreign particle. Normally, such a contaminated
plate would be tossed out. However, Fleming noticed that no bacteria grew near the invad-
ing substance (see Fig. 1.1).
Fleming’s genius was to realize that this observation was meaningful and not a
“failed” experiment. Fleming recognized that the cell killing must be due to an antibacter-
ial agent. He recovered the foreign particle and found that it was a common mold of the
Penicillium genus (later identified as Penicillium notatum). Fleming nurtured the mold to
grow and, using the crude extraction methods then available, managed to obtain a tiny
quantity of secreted material. He then demonstrated that this material had powerful an-
timicrobial properties and named the product penicillin. Fleming carefully preserved the
culture, but the discovery lay essentially dormant for over a decade.

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Figure 1.1. Photograph of Alexander

Fleming’s original plate showing the growth
of the mold Penicillium notatum and its in-
hibitory action on bacterial growth. (With
permission, from Corbis Corporation.)

World War II provided the impetus to resurrect the discovery. Sulfa drugs have a
rather restricted range of activity, and an antibiotic with minimal side effects and
broader applicability was desperately needed. Howard Florey and Ernst Chain of Ox-
ford decided to build on Fleming’s observations. Norman Heatley played the key role
in producing sufficient material for Chain and Florey to test the effectiveness of peni-
cillin. Heatley, trained as a biochemist, performed as a bioprocess engineer. He devel-
oped an assay to monitor the amount of penicillin made so as to determine the kinetics
of the fermentation, developed a culture technique that could be implemented easily,
and devised a novel back-extraction process to recover the very delicate product. After
months of immense effort, they produced enough penicillin to treat some laboratory
animals.
Eighteen months after starting on the project, they began to treat a London bobby
for a blood infection. The penicillin worked wonders initially and brought the patient to
the point of recovery. Most unfortunately, the supply of penicillin was exhausted and the
man relapsed and died. Nonetheless, Florey and Chain had demonstrated the great poten-
tial for penicillin, if it could be made in sufficient amount. To make large amounts of peni-
cillin would require a process, and for such a process development, engineers would be
needed, in addition to microbial physiologists and other life scientists.
The war further complicated the situation. Great Britain’s industrial facilities were
already totally devoted to the war. Florey and his associates approached pharmaceutical
firms in the United States to persuade them to develop the capacity to produce penicillin,
since the United States was not at war at that time.

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Many companies and government laboratories, assisted by many universities, took

up the challenge. Particularly prominent were Merck, Pfizer, Squibb, and the USDA
Northern Regional Research Laboratory in Peoria, Illinois.
The first efforts with fermentation were modest. A large effort went into attempts to
chemically synthesize penicillin. This effort involved hundreds of chemists. Conse-
quently, many companies were at first reluctant to commit to the fermentation process, be-
yond the pilot-plant stage. It was thought that the pilot-plant fermentation system could
produce sufficient penicillin to meet the needs of clinical testing, but large-scale produc-
tion would soon be done by chemical synthesis. At that time, U.S. companies had
achieved a great deal of success with chemical synthesis of other drugs, which gave the
companies a great deal of control over the drug’s production. The chemical synthesis of
penicillin proved to be exceedingly difficult. (It was accomplished in the 1950s, and the
synthesis route is still not competitive with fermentation.) However, in 1940 fermentation
for the production of a pharmaceutical was an unproved approach, and most companies
were betting on chemical synthesis to ultimately dominate.
The early clinical successes were so dramatic that in 1943 the War Production
Board appointed A. L. Elder to coordinate the activities of producers to greatly increase
the supply of penicillin. The fermentation route was chosen. As Elder recalls, “I was
ridiculed by some of my closest scientific friends for allowing myself to become associ-
ated with what obviously was to be a flop—namely, the commercial production of peni-
cillin by a fermentation process” (from Elder, 1970). The problems facing the
fermentation process were indeed very formidable.
The problem was typical of most new fermentation processes: a valuable product
made at very low levels. The low rate of production per unit volume would necessitate
very large and inefficient reactors, and the low concentration (titer) made product recov-
ery and purification very difficult. In 1939 the final concentration in a typical penicillin
fermentation broth was one part per million (ca. 0.001 g/l); gold is more plentiful in sea
water. Furthermore, penicillin is a fragile and unstable product, which places significant
constraints on the approaches used for recovery and purification.
Life scientists at the Northern Regional Research Laboratory made many major
contributions to the penicillin program. One was the development of a corn steep
liquor–lactose based medium. This medium increased productivity about tenfold. A
worldwide search by the laboratory for better producer strains of Penicillium led to the
isolation of a Penicillium chrysogenum strain. This strain, isolated from a moldy can-
taloupe at a Peoria fruit market, proved superior to hundreds of other isolates tested. Its
progeny have been used in almost all commercial penicillin fermentations.
The other hurdle was to decide on a manufacturing process. One method involved
the growth of the mold on the surface of moist bran. This bran method was discarded be-
cause of difficulties in temperature control, sterilization, and equipment size. The surface
method involved growth of the mold on top of a quiescent medium. The surface method
used a variety of containers, including milk bottles, and the term “bottle plant” indicated
such a manufacturing technique. The surface method gave relatively high yields, but had a
long growing cycle and was very labor intensive. The first manufacturing plants were bot-
tle plants because the method worked and could be implemented quickly.
However, it was clear that the surface method would not meet the full need for peni-
cillin. If the goal of the War Production Board was met by bottle plants, it was estimated

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that the necessary bottles would fill a row stretching from New York City to San Fran-
cisco. Engineers generally favored a submerged tank process. The submerged process pre-
sented challenges in terms of both mold physiology and in tank design and operation.
Large volumes of absolutely clean, oil- and dirt-free sterile air were required. What were
then very large agitators were required, and the mechanical seal for the agitator shaft had
to be designed to prevent the entry of organisms. Even today, problems of oxygen supply
and heat removal are important constraints on antibiotic fermenter design. Contamination
by foreign organisms could degrade the product as fast as it was formed, consume nutri-
ents before they were converted to penicillin, or produce toxins.

Figure 1.2(a). Series of large-scale antibiotic fermenters. (With permission, from T.D.
Brock, K.M. Brock, and D.M. Ward. Basic Microbiology with Applications, 3d ed., Pear-
son Education, Upper Saddle River, NJ, 1986, p. 507.)

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In addition to these challenges in reactor design, there were similar hurdles in prod-
uct recovery and purification. The very fragile nature of penicillin required the develop-
ment of special techniques. A combination of pH shifts and rapid liquid-liquid extraction
proved useful.
Soon processes using tanks of about 10,000 gal were built. Pfizer completed in less
than six months the first plant for commercial production of penicillin by submerged fer-
mentation (Hobby, 1985). The plant had 14 tanks each of 7000-gal capacity. By a combi-
nation of good luck and hard work, the United States had the capacity by the end of World
War II to produce enough penicillin for almost 100,000 patients per year (see Figs. 1.2
and 1.3).
This accomplishment required a high level of multidisciplinary work. For example,
Merck realized that men who understood both engineering and biology were not avail-
able. Merck assigned a chemical engineer and microbiologist together to each aspect of
the problem. They planned, executed, and analyzed the experimental program jointly, “al-
most as if they were one man” (see the chapter by Silcox in Elder, 1970).
Progress with penicillin fermentation has continued, as has the need for the interac-
tion of biologists and engineers. From 1939 to now, the yield of penicillin has gone from
0.001 g/l to over 50 g/l of fermentation broth. Progress has involved better understanding
of mold physiology, metabolic pathways, penicillin structure, methods of mutation and se-
lection of mold genetics, process control, and reactor design.

Figure 1.2(b). Inside view of a large antibiotic fermenter. (From Trends in Biotechnol-
ogy 3 (6), 1985. Used with permission of Elsevier Science Publishers.)

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Figure 1.3. Schematic of penicillin production process.

Before the penicillin process, almost no chemical engineers sought specialized

training in the life sciences. With the advent of modern antibiotics, the concept of a bio-
process engineer was born. The penicillin process also established a paradigm for bio-
process development and biochemical engineering. This paradigm still guides much of
our profession’s thinking. The mind set of bioprocess engineers was cast with the peni-
cillin experience. It is for this reason that we have focused on the penicillin story, rather
than on an example for production of a protein from a genetically engineered organism.
Although many parallels can be made between the penicillin process and our efforts to use
recombinant DNA, no similar paradigm has yet emerged from our experience with geneti-
cally engineered cells. We must continually reexamine the prejudices the field has inher-
ited from the penicillin experience.
It is you, the student, who will best be able to challenge these prejudices.

1.5. BIOPROCESSES: REGULATORY CONSTRAINTS

To understand the mind set of a bioprocess engineer you must understand the regulatory
climate in which many bioprocess engineers work. The U.S. FDA (Food and Drug Ad-
ministration) and its equivalents in other countries must insure the safety and efficacy of

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medicines. For bioprocess engineers working in the pharmaceutical or biotechnology in-

dustry the primary concern is not reduction of manufacturing cost (although that is still a
very desirable goal), but the production of a product of consistently high quality in
amounts to satisfy the medical needs of the population.
Consider briefly the process by which a drug obtains FDA approval. A typical drug
undergoes 6.5 years of development from the discovery stage through preclinical testing
in animals. Human clinical trials are conducted in three phases. Phase 1 clinical trials
(about 1 year) are used to test safety; typically 20 to 80 volunteers are used. Phase II clini-
cal trials (about 2 years) use 100 to 300 patients and the emphasis is on efficacy (i.e., does
it help the patient) as well as further determining which side effects exist. Compounds that
are still promising enter phase III clinical trials (about 3 years) with 1000 to 3000 patients.
Since individuals vary in body chemistry, it is important to test the range of responses in
terms of both side effects and efficacy by using a representative cross section of the popu-
lation. Data from clinical trials is presented to the FDA for review (about 18 months). If
the clinical trials are well designed and demonstrate statistically significant improvements
in health with acceptable side effects, the drug is likely to be approved. Even after this
point there is continued monitoring of the drug for adverse effects. The whole drug
discovery-through-approval process takes 15 years on the average and costs about $400
million (in 1996). Only one in ten drugs that enter human clinical trials receives approval.
Recent FDA reforms have decreased the time to obtain approval for life-saving drugs in
treatment of diseases such as cancer and AIDS, but the overall process is still lengthy.
This process greatly affects a bioprocess engineer. FDA approval is for the product
and the process together. There have been tragic examples where a small process change
has allowed a toxic trace compound to form or become incorporated in the final product,
resulting in severe side effects, including death. Thus, process changes may require new
clinical trials to test the safety of the resulting product. Since clinical trials are very expen-
sive, process improvements are made under a limited set of circumstances. Even during
clinical trials it is difficult to make major process changes.
Drugs sold on the market or used in clinical trials must come from facilities that are
certified as GMP. GMP stands for good manufacturing practice. GMP concerns the actual
manufacturing facility design and layout, the equipment and procedures, training of pro-
duction personnel, control of process inputs (e.g., raw materials and cultures), and han-
dling of product. The plant layout and design must prevent contamination of the product
and dictates the flow of material, personnel, and air. Equipment and procedures must be
validated. Procedures include not only operation of a piece of equipment, but also clean-
ing and sterilization. Computer software used to monitor and control the process must be
validated. Off-line assays done in laboratories must satisfy good laboratory practices
(GLP). Procedures are documented by SOPs (standard operating procedures).
The GMP guidelines stress the need for documented procedures to validate perfor-
mance. “Process validation is establishing documented evidence which provides a high
degree of assurance that a specific process will consistently produce a product meeting its
predetermined specifications and quality characteristics” and “There shall be written pro-
cedures for production and process-control to assure that products have the identity,
strength, quality, and purity they purport or are represented to possess.”
The actual process of doing validation is often complex, particularly when a whole
facility design is considered. The FDA provides extensive information and guidelines

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which are updated regularly. If students become involved in biomanufacturing for phar-
maceuticals, they will need to consult these sources. However, certain key concepts do not
change. These concepts are written documentation, consistency of procedures, consis-
tency of product, and demonstrable measures of product quality, particularly purity and
safety. These tasks are demanding and require careful attention to detail. Bioprocess
engineers will often find that much of their effort will be to satisfy these regulatory
requirements.
The key point is that process changes cannot be made without considering their
considerable regulatory impact.

SUGGESTIONS FOR FURTHER READING

A. History of Penicillin
ELDER, A. L., ed., The History of Penicillin Production, Chem. Eng. Prog. Symp. Ser. 66 (#100),
American Institute of Chemical Engineers, New York, 1970.
HOBBY, G. L., Penicillin. Meeting the Challenge, Yale University Press, New Haven, CT, 1985.
MOBERG, C. L., Penicillin’s Forgotten Man: Norman Heatley, Science 253: 734–735, 1991.
MATELES, R. I., ed., Penicillin: A Paradigm for Biotechnology, Candida Corp., Chicago, IL, 1998.
(This contains the work by Elder which is no longer in print plus two additional chapters on cur-
rent pratice.)
SHEEHAN, J. C., The Enchanted Ring. The Untold Story of Penicillin, MIT Press, Cambridge, MA,
1982.

B. Regulatory Issues
DURFOR, C. N., AND SCRIBNER, C. L., An FDA perspective of manufacturing changes for products in
human use, Ann. NY Acad. Sci. 665:356–363, 1992.
NAGLAK, T. J., KEITH, M. G. AND OMSTEAD, D. R., Validation of fermentation processes, Biopharm
(July/Aug.):28–36, 1994.
REISMAN, H. B., Problems in scale-up of biotechnology production processes, Crit. Rev. Biotechnol.
13 :195–253, 1993.

PROBLEMS

1.1. What is GMP and how does it relate to the regulatory process for pharmaceuticals?
1.2. When the FDA approves a process, it requires validation of the process. Explain what valida-
tion means in the FDA context.
1.3. Why does the FDA approve the process and product together?

10 What Is a Bioprocess Engineer? Chap. 1