Overview of Biology + Engineering

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If you are new to the issues associated with biology+engineering, then a quick browse through the following may be of interest:

Cornell Report on Research Initiatives (Excerpts)

The increasingly sophisticated tools of molecular biology have taken us to the threshold of a new era in biology. For many years the ability to accumulate data was rate-limiting for biologists. Now large scale DNA sequencing will soon reveal all the genes required to encode most major life forms, including humans, microbes, plants and animals, leading us into an unprecedented era of discovery.

Underlying the birth of this "new biology" will be a major shift in the paradigm of biological research from a reductionist approach, which focuses on individual phenomena, to a high level approach that integrates the molecular information for whole organisms, physiological systems, and behavior. The major tasks for the "new biology" over the next 30-100 years will be: 1) to associate DNA sequence data with biological function and to determine how sequences have changed through evolutionary time to create the diversity of life forms that now inhabit this planet, and 2) to understand the flow and control of information from the genome and the interaction of that information with information from the environment. The ensuing discoveries will revolutionize our understandings of the origins of life and the molecular processes that underlie life. They will also lead to many revolutionary discoveries in engineering, medicine, the environment and agriculture.

Cornell can combine its expertise in plant, animal, microbial, and human biology/genetics to address issues that could not be approached by studying a single organism. For example, unlike human systems, plant and animals have been bred for specific multigene traits, and this process is well-documented -- especially in Cornell's agricultural disciplines. These systems provide an exceptional resource from which to discover underlying principles that govern complex genetic systems. Further, researchers studying these systems should join forces with engineers, computer scientists and researchers skilled in systems integration and systems dynamics. Work pursued on this horizon in Ithaca should, moreover, complement work in the strategic areas (Genetics and Genetic Medicine, Structural Biology and Neurobiology) identified by Cornell University Medical College. The impact of the research of each campus would be enhanced through research exchanges. This approach would integrate knowledge (and therefore discovery) horizontally across species by using a functional perspective as a common unifying theme.

Another exciting aspect of integrative biology is the possibility of chemical prospecting--research that integrates chemical ecology with molecular biology and chemistry to discover potential pharmaceutical or agrochemical agents in natural occurring compounds. Biological data are accumulating at a rate that exceeds the ability of biologists to digest it. Bioinformatics, "data base mining" and computational biology will be critical in the "new biology." It is likely that new and very fast algorithms will be required for comparing and culling interpretations from vast amounts of data. Cornell, with its top-rated Computer Science Department, Theory Center, Applied Mathematics and Statistics Center, is ideally positioned to lead the field of computational biology and bioinformatics.

Perhaps less obvious, but no less important, is the human impact that will result from a better understanding of genomics. Ethical and legal issues are apparent. A more fundamental understanding of genomics and what it means for both the origin and nature of humankind will have repercussions throughout the humanities and social sciences. We will ultimately perceive ourselves differently because of this biological revolution. We need to be prepared to deal with the consequence of our increased understanding of the mechanics of life.

Initiatives such as those outlined here require significant intellectual flexibility on the part of the participating faculty, as many biologists adjust to a systems approach and as non-biological scientists and engineers learn both biological concepts and vocabulary. If Cornell students are to be leaders in the upcoming biological revolution, they must have an opportunity to learn in this integrative mode of thought.

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Excerpts from the CCGB

Is Biology useful in the overall curriculum? M. Shuler feels that biology is important for all educated persons. Biology has changed from 20 -25 years ago. Biology is going from an information poor to an information rich subject. People are accumulating information regarding biology faster that they can digest it. Synthetic and theoretical biology is now integrated,. Engineers encounter two areas where knowledge of biology is helpful: health and safety and environment. It would be useful for students to know biology, but the course should be different from that for biologists. The big barrier to biology is the language; an introductory course in biology would eliminate that.

Genomics and the Future Soon we will know the sequence of the human genome as well as those for other plants and animals.

This is the ultimate triumph of the reductionist approach; it's accomplishment will necessitate a dramatic shift in biological through and education.

The primary problem will be relating genes to biological function. A systems integration approach will become essential.

The study of modern biology is primarily on the flow and control of information. There are many parallels with information science.

Computational biology and bioinformatics will be central.

As we understand biology, textbooks will become smaller.

Engineers/computer scientists will need more biology; biologists will need training in systems approach.

Cornell's breadth will provide unique opportunities in relating genomics to biological function.

Bioengineering can play an important role in this endeavor.

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President of Rice University

[On the new department of Bioengineering started by Whitaker Foundation.] "I am especially happy that this award will enable us to offer undergraduates a new major in a field of such significance for science and medicine in the 21st Century.'' (Malcolm Gillis, University President). Six new faculty positions. Future bioengineers will need to build on recent advances in molecular and cell biology in order to translate scientific aspects of biotechnology into new cost effective products and processes. To be succesful in this effort, however, bioengineers will need interdisciplinary skills that reach from the biological sciences to modern materials science, systems modeling,computer science, and bioprocess design.

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What is Bioengineering? 

Bioengineering combines the analytical and experimental methods of the engineering profession with the biological and medical sciences to achieve a more detailed understanding of biological phenomena and to develop new techniques and devices. The engineer's quantitative and analytical approach; traditional competence in the processing and control of information, energy, and materials; and ability to design and analyze systems are powerful tools when applied to biology, medicine; and quantitative studies of relationships between biological systems and their environments.

Bioengineers deal with a wide variety of problems. Graduates may work as biomedical engineers with medical practitioners to develop new medical techniques, medical devices, and instrumentation for manufacturing companies. Clinical engineers work in hospitals and clinics to maintain and improve the vast amount of technological support required in modern medicine. With advanced degrees in the various fields of bioengineering, some graduates perform basic research related to biology and medicine in the research laboratories of educational and governmental institutions or in the medical industries.

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What is Biomedical Engineering?

Biomedical engineering combines engineering expertise with medical needs for the enhancement of health care. It is a branch of engineering in which knowledge and skills are developed and applied to define and solve problems in biology and medicine. Students choose the biomedical engineering field to be of service to people; for the excitement of working with living systems; and to apply advanced technology to the complex problems of medical care. The biomedical engineer is a health care professional, a group which includes physicians, nurses, and technicians. Biomedical engineers may be called upon to design instruments and devices, to bring together knowledge from many sources to develop new procedures, or to carry out research to acquire knowledge needed to solve new problems.

Specific Activities

Examples of work done by biomedical engineers include:

•designing and constructing cardiac pacemakers, defibrillators, artificial kidneys, blood oxygenators, hearts, blood vessels, joints, arms, and legs.

•designing computer systems to monitor patients during surgery or in intensive care, or to monitor healthy persons in unusual environments, such as astronauts in space or underwater divers at great depth. •designing and building sensors to measure blood chemistry, such as potassium, sodium, 02, CO2, and pH.

•designing instruments and devices for therapeutic uses, such as a laser system for eye surgery or a device for automated delivery of insulin.

•developing strategies for clinical decision making based on expert systems and artificial intelligence, such as a computer-based system for selecting seat cushions for paralyzed patients or for, managing the care of patients with severe burns or for diagnosing diseases.

•designing clinical laboratories and other units within the hospital and health care delivery system that utilize advanced technology. Examples would be a computerized analyzer for blood samples, ambulances for use in rural areas, or a cardiac catheterization laboratory.

•designing, building and investigating medical imaging systems based on X-rays (computer assisted tomography), isotopes (position emission tomography), magnetic fields (magnetic resonance imaging), ultrasound, or newer modalities.

•constructing and implementing mathematical/computer models of physiological systems.

•designing and constructing biomaterials and determining the mechanical, transport, and biocompatibility properties of implantable artificial materials.

•implementing new diagnostic procedures, especially those requiring engineering analyses to determine parameters that are not directly accessible to measurements, such as in the lungs or heart. •investigating the biomechanics of injury and wound healing.



What are the Specialty Areas?

Some of the well established specialty areas within the field of biomedical engineering are bioinstrumentation, biomechanics, biomaterials, systems physiology, clinical engineering, and rehabilitation engineering.

Bioinstrumentation is the application of electronics and measurement principles and techniques to develop devices used in diagnosis and treatment of disease. Computers are becoming increasingly important in bioinstrumentation, from the microprocessor used to do a variety of small tasks in a single purpose instrument to the extensive computing power needed to process the large amount of information in a medical imaging system.

Biomechanics is mechanics applied to biological or medical problems. It includes the study of motion, of material deformation, of flow within the body and in devices, and transport of chemical constituents across biological and synthetic media and membranes. Efforts in biomechanics have developed the artificial heart and replacement heart valves, the artificial kidney, the artificial hip, as well as built a better understanding of the function of organs and musculoskeletal systems.

Biomaterials describes both living tissue and materials used for implantation. Understanding the properties of the living material is vital in the design of implant materials. The selection of an appropriate material to place in the human body may be one of the most difficult tasks faced by the biomedical engineer. Certain metal alloys, ceramics, polymers, and composites have been used as implantable materials. Biomaterials must be nontoxic, noncarcinogenic, chemically inert, stable, and mechanically strong enough to withstand the repeated forces of a lifetime.

Systems physiology is the term used to describe that aspect of biomedical engineering in which engineering strategies, techniques and tools are used to gain a comprehensive and integrated understanding of the function of living organisms ranging from bacteria to humans. Modeling is used in the analysis of experimental data and in formulating mathematical descriptions of physiological events. In research, models are used predictively in designing new experiments to refine our knowledge. Living systems have highly regulated feedback control systems which can be examined in this way. Examples are the biochemistry of metabolism and the control of limb movements.

Clinical engineering is the application of technology for health care in hospitals. The clinical engineer is a member of the health care team along with physicians, nurses and other hospital staff. Clinical engineers are responsible for developing and maintaining computer databases of medical instrumentation and equipment records and for the purchase and use of sophisticated medical instruments. They may also work with physicians on projects to adapt instrumentation to the specific needs of the physician and the hospital. This often involves the interface of instruments with computer systems and customized software for instrument control and data analysis. Clinical engineers feel the excitement of applying the latest technology to health care.

Rehabilitation engineering is a new and growing specialty area of biomedical engineering. Rehabilitation engineers expand capabilities and improve the quality of life for individuals with physical impairments. Because the products of their labor are so personal, often developed for particular individuals or small groups, the rehabilitation engineer often works directly with the disabled individual.

These specialty areas frequently depend on each other. Often the biomedical engineer who works in an applied field will use knowledge gathered by biomedical engineers working in more basic areas. For example, the design of an artificial hip is greatly aided by a biomechanical study of the hip. The forces which are applied to the hip can be considered in the design and material selection for the prosthesis. Similarly, the design of systems to electrically stimulate paralyzed muscle to move in a controlled way uses knowledge of the behavior of the human musculoskeletal system. The selection of appropriate materials used in these devices falls within the realm of the biomaterials engineer. These are examples of the interactions among the specialty areas of biomedical engineering.

Where do they Work?

Biomedical engineers are employed in industry, in hospitals, in research facilities of educational and medical institutions, in teaching, and in government regulatory agencies. They often serve a coordinating or interfacing function, using their background in both the engineering and medical fields. In industry, they may create designs where an in-depth understanding of living systems and of technology is essential. They may be involved in performance testing of new or proposed products. Government positions often involve product testing and safety, as well as establishing safety standards for devices. In the hospital, the biomedical engineer may provide advice on the selection and use of medical equipment, as well as supervising its performance testing and maintenance. They may also build customized devices for special health care or research needs. In research institutions, biomedical engineers supervise laboratories and equipment, and participate in or direct research activities in collaboration with other researchers with such backgrounds as medicine, physiology, and nursing.

Some biomedical engineers are technical advisors for marketing departments of companies and some are in management positions. Some biomedical engineers also have advanced training in other fields. For example, many biomedical engineers also have an M.D. degree, thereby combining an understanding of advanced technology with direct patient care or clinical research.

Career Preparation

The biomedical engineer should plan first and foremost to be a good engineer. Beyond this, he or she should have a working understanding of life science systems and terminology. Good communications skills are also important, because the biomedical engineer provides a link among professionals with medical, technical, and other backgrounds.

The high school preparation for biomedical engineering is the same as for any other engineering discipline, except that some life science course work should also be included. At the college level, the student usually selects engineering as a field of study, then chooses a discipline concentration within engineering. Some students will major in biomedical engineering, while others may major in a traditional field such as electrical, mechanical, or chemical engineering, with a specialty in biomedical engineering.

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What is Biotechnology?

Check out our own Biotechnology center which focuses on five major areas of research and technology development:

biocontrol: biological alternatives to chemical methods of disease and pest control.

gene isolation and enhancement: identifying and altering particular genes to enhance the traits of plants and animals for disease resistance, crop yield, and nutritional quality

bioremediation: the use of biological systems for environmental stewardship

diagnostics: tests for health, safety, and other conditions, with applications in humans and animals, in food, and in the environment.

health care: structure based drug design; vaccines for human and animal health

Other resources include  http://www.bio.org/ , the Gateway to Biotechnology on the World Wide Web, and a ste maintained by the USDA.

There is also a website concerned with nanobiotechnology.  http://www.bio.cornell.edu/nanobiotech/nbt.htm

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What is Bioinformatics?

Bioinformatics, sometimes, is used interchangeably with the term Computational Biology. (See below). Bioinformatics is defined as the systematic development and application of computing systems and computational solution techniques analyzing data obtained by experiments, modeling, database search, and instrumentation regarding Biological aspect. George Mason University has a strong program in Computational Biology and Bioinformatics and their website is filled with interesting links and resources.

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What is Computational Biology?

Computational Biology is defined as the systematic development and application of computing systems and computational solution techniques to models of biological phenomena.

Another answer to  that question can be obtained by looking at the CS 438 website at Johns Hopkins University. Here is an abridged syllabus:

Week 0.   Introduction to the course and text. Overview of computational biology.
Week 1.   Introduction, biological background. Topic: Molecular biology for non-biologists. Restriction mapping and interval graphs.
Week 2.   Mapping probes and clones. Sequence-tagged site mapping and why it is computationally ``hard.'' 
Week 3.   The Linguistics of DNA.
Week 4.   Sequence alignment, part 1: global distance alignment, global similarity alignment, and local alignment.
Week 5.   Sequence alignment, part 2: heuristic alignment methods including BLAST.
Week 6.   Sequencing by hybridization.
Week 7.    Threading Approach to Inverse Protein Structure Prediction. Parallel Genetic Linkage Analysis.
Week 8.    Algorithms for constructing amino acid substitution matrices. Hidden Markov Models for sequence analysis.
Week 9.    Genetic sequence and map databases and the Human Genome Project. 
Week 10.  The Genome Data Base.  
Week 11.  Computational models of morphogenesis.
Week 12.   Comparative genomics.
Week 13.   Description of the gene finding problem. Computer systems for gene finding. DNA computing; molecular evolution.  

George Mason University has a strong program in Computational Biology and Bioinformatics and their website is filled with interesting links and resources.

There are two web sites with links to a lot of "computational biology" courses at other universities. They are   mainly grad-level, but they give a sense for what other people are doing   in the computer science direction: