Environmental biotechnology is a vital component of the scientific and engineering tool kit needed to address environmental problems. Environmental biotechnology usually explain biological principles underlying environmental engineering but environmental biotechnology embodies so much more than this. Environmental biotechnology depends on a systematic view of the myriad factors involved when organisms are used to solve society’s problems. Thus, both the title and subtitle of this book are important.
A systems approach to biotechnology requires a modicum of understanding of a number of disciplines, especially environmental engineering, systems biology, environmental microbiology, and ecology. This book introduces all of these fields from the perspective of how to apply them to achieve desired environmental outcomes and how to recognize and avoid problems in such applications. This approach means that the treatment of these four disciplines is predominantly focused on biotechnology and is not meant to be an exhaustive treatise on any of the four. This book’ s principal value lies at the intersection of the four disciplines. However, engineering requires specifics, so my intention is that the reader gain a sufficient grasp of each so as to know when more details are needed and when to consult the references at the end of each chapter to seek out these important details.
BIOTECHNOLOGY AT THE INTERSECTION OF DISCIPLINES
Environmental engineering is a broad field, including both abiotic and biotic solutions to pollution and environmental problems. This book’s primary environmental engineering focus is on the biotic solutions, so the reader should consult general environmental engineering texts and specific chemical and physical treatment resources to find abiotic treatment methods to match the biotic approaches discussed here. For example, after reading a discussion of a particular biotechnology, e.g., Chapter 7’s exposition of a biofilter used to treat a specific organic pollutant, the reader may be inclined to look up that pollutant to see what other non-biotechnological methods, e.g., pumping and air sparging, have been used in its treatment. This book certainly includes discussions on abiotic techniques in Chapters 7 and 10, but limits the discussion to the treating of those pollutants that may result from biotechnologies (e.g., if a hazardous byproduct is produced, it may need to undergo thermal treatment).
Systems biology and molecular biology are addressed insofar as genetic engineering is an important part of environmental biotechnology. An understanding of genetic material and how it can be manipulated either intentionally or unintentionally is crucial to both applications and implications. As in environmental engineering, the discussion is focused less on a theoretical and comprehensive understanding of DNA and RNA for their own sake than would be found in a systems biology text. Again, if the reader needs more information, the references should be consulted and should lead to more specific information. In addition, the book addresses a number of emerging technologies used in environmental assessment, particularly drawing on systems biology, such as the computational methods associated with genomics, proteomics, and the other “omics” systems.
I recall how one of my many mentors, Ross McKinney at the University of Kansas, contrasted the world view of microbiologists from that of engineers. Microbiologists are interested in intrinsic aspects of the “bugs,” whereas engineers are interested in what the “bugs” can do [1]. I have been careful with the taxonomy of the organisms, but it is not the book’s intent to exhaustively list every microbe of value to environmental biotechnology. When the reader needs more detail on a particular organism and when trying to find other microbes that may work in a biotechnology, the references and notes should help to initiate the quest.
More than a few of my ecologist colleagues may cringe when I say that microbes have instrumental value, not intrinsic value, in many environmental biotechnologies. Engineers, including environmental engineers, are focused on outcomes. They design systems to achieve target outcomes within specified ranges of tolerance and acceptability. As such, they say a bacterium is a means, not an end in itself. In my opinion, ecologists in general have a comparatively more skeptical view of “ecological services” [2] than do practicing engineers. Ecologists tend to be more interested in the whole system, i.e., the ecosystem. Thus, the microbes, especially those that have been supercharged genetically, must be seen for how they fit within the whole system, not just the part of the system that needs to be remediated. This book, therefore, includes this ecological perspective, especially when addressing potential implications, such as gene flow and biodiversity. In fact, one of the themes of this book is that engineers must approach biotechnologies that seem to be completely acceptable with whole systems in mind, with considerations of impact in space and time, i.e., a systems approach to biotechnology. It may be that after such a systems review, the technology may indeed not be the panacea that it at first appears.
THE SYSTEMS APPROACH
One way to address environmental biotechnology is to ask whether it is “good” or “bad.” Of course, the correct answer is that “it depends.” According to my colleague at Duke, Jeff Peirce, this is one of the few universally correct statements in engineering. The tough part of such a statement, of course, is deciding to some degree of satisfaction on just what “it depends.”
The same biotechnology can be good or bad. It just depends. It depends on risks versus rewards. It depends on what is valued. It depends on reliability and uncertainty of outcome. It depends on short-term versus long-term perspectives. It depends on the degree of precaution needed in a given situation. Mostly, it depends on whether the outcome is ideal, or, at a minimum, acceptable, based on the consideration of the myriad relationships of all of the factors. Such factors include not only the physical, chemical, and biological aspects of a biotechnology, but also those related to sociological and economic considerations. That is, the same technology is good or bad, depending on the results of a systematic perspective [3].
I would recommend that the question about the dependencies driving the acceptability of a given environmental biotechnology be asked at the beginning of any environmental biotechnology course. I recognize just how tempting it is in teaching an environmental biotechnology course to jump into how to use living things to treat pollution, with little thought as to whether to use a biotechnology. Perhaps this is because we expect that other perspectives, such as abiotic treatment, will be addressed in courses specifically addressing these technologies, and after having completed courses in every major treatment category, the student will then be able to select the appropriate method for the contaminant at hand. This is much like the need for a really good course in concrete and another excellent course in steel, as a foundation (literally and figuratively) in structural engineering. Such reductionism has served engineering well. In environmental sciences and engineering, the newer views do not lessen the need for similar specific knowledge in the foundational sciences, but in light of the importance of the connections between living things and their surroundings, newer pedagogies are calling for a more systematic view to put these basics into systems that account for variations in complexity and scale.
Biotechnologists are justifiably tempted to keep doing that which has worked in the past. For those in the fields of biological wastewater treatment and hazardous waste biotechnologies, the art of engineering is to move thoughtfully, with some trepidation, from what is known to the realm of the unknown. This microbe was effective in treating contaminant A, so why not acclimate the microbe to a structurally similar compound, e.g., the same molecule with a methyl group or one with an additional ring? Often this works well under laboratory conditions and even in the field, so long as conditions do not change dramatically. Such acclimation was the precursor to more dramatic and invasive forms of genetic modification, especially recombinant DNA techniques. This book explores some of the knowns and unknowns of what happens systematically when we manipulate the genetic material of an organism. Perhaps, the system is no more influenced by a genetically modified organism than by those that bioengineers have manipulated by letting the organism adapt on its own to the new food source. But, perhaps not.
When I originally proposed the concept for this book, I thought that I would dedicate it almost exclusively to potential implications of environmental biotechnologies. I thought that others had done admirable jobs of writing about the applications. After delving into the topic in earnest, I came to the conclusion that I was only half right. Indeed, the previous texts in environmental biotechnologies were thorough and expansive. Some did a really good job of laying out the theory and the techniques of environmental biotechnology. However, most were not all that interested in what may go wrong or what happens outside of the specific application. This is not meant to be a criticism, because the authors state up front that their goal is to enhance the reader’s understanding of these applications. The implication, to me at least, is that their work starts after the decision has been made to destroy a certain chemical compound using the most suitable technique. In this instance, “suitable” may be translated to mean “efficient.” How rapidly will microbe X degrade contaminant A? How complete is the degradation (e.g., all the way to carbon dioxide and water)? How does microbe X compare in degradation rates to microbes Y and Z? How efficiently will microbe X degrade contaminant A if we tweak its DNA? How broadly can microbe X’ s degradation be applied to similar compounds? These are all extremely important questions. Efficiency is an integral but not an exclusive component of effectiveness. Thus, my original contention was half wrong. I could not discuss implications without also discussing applications. I liken this to the sage advice of a former Duke colleague, Senol Utku. He has been a leader in designing adaptive structures that often follow intricate, nonlinear relationships between energy and matter. His students were therefore often eager to jump into nonlinear mathematical solutions, but he had to pull them back to a more complete understanding of linear solutions. He would tell them that it is much like a banana. How can one understand a “non-banana” without first understanding the “banana”? Thus, my systematic treatment of environmental biotechnology requires the explanation of both applications (bananas) and implications (non-bananas).
The term “systems” has become an adjective. For decades, design professionals, failure engineers, and engineering managers have employed systems engineering. Scientists, engineers, and technologists now have systems biology, systems medicine, and even systems chemistry. Early on, systems simply meant a comprehensive approach, such as a life cycle or critical path view. Later, another connotation was that it provided a distinction from compartmental or reductionist perspectives. Now, the systems moniker conveys a computational approach. Lately, subdivisions of the basic sciences have also become systematic in perspective. For example, systems microbiology approaches microorganisms or microbial communities comprehensively by integrating fundamental biological knowledge with genomics and other data to give an integrated representation of how a microbial cell or community operates. This text attempts to address all of these perspectives and more, but all through the lens of the environment.
Along the way, I became aware that there was not a good term that included all of these perspectives. Pioneers in environmental modeling, such as Donald MacKay and Panos Georgopoulos, advanced the field of chemodynamics. In fact, I have drawn heavily from their work. The challenge is how to insert biology into such chemodynamic frameworks.
For many in the environmental sciences and engineering fields, environmental biotechnologies that most readily come to mind are various waste treatment processes, those that often begin with the suffix “bio.” Thus, I decided to use the term biochemodynamics to refer to the myriad bio-chemo-physical processes and mechanisms at work in environmental biotechnologies. At one point, I even suggested calling this book Environmental Biochemodynamics. However, although such a title would distinguish the focus away from abiotic processes, it would leave out some of the important topics covered, such as the societal and feasibility considerations needed in biotechnological decisions.
Environmental biotechnology is all about optimization, so it requires a systematic perspective, at least in its thermodynamic and comprehensive connotations. In particular, biotechnologists are keenly interested in bioremediation of existing contaminants, as well as those that may enter the environment in the future.
To optimize, we must get the most benefit and the least risk by using biology to solve an important problem or fill a vital need. In my research, I discovered a very interesting workshop that took place in 1986 [3]. The workshop was interesting for many reasons. It was held by a regulatory agency, the U.S. Environmental Protection Agency, but predominantly addressed ways to advance environmental biotechnology. In other words, the entity that was chastising polluters was simultaneously looking for ways to support these same polluters financially and scientifically so as to become nonpolluters!
Such an approach is not uncommon in its own right, because in the previous decade the same agency had funded research and paid to build wastewater treatment plants to help the same facilities being fined and otherwise reproved for not meeting water quality guidelines and limits. This is a case of the “stick” being followed by the “carrot.” The 1986 workshop was actually refreshing, because it was an effort to help scientists come up with ways to push the envelope of technology to complement the growing arsenal of rules and standards for toxic chemicals in the environment.
One of the challenges posed in the mid-1980s was that the National Academy of Sciences had just sketched a schematic to address risks posed by chemicals. It followed a sequence that consisted of identifying chemical hazards and seeing how people may come into contact with these hazards, i.e., exposure. The combination of these factors led to what the academy called risk assessment. This seemed to work adequately for chemical hazards to one species (Homo sapiens), but did not fit quite well with hazards that behave differently than pharmaceuticals, pesticides, or other chemical agents, i.e., physical (e.g., UV light) or biological (e.g., microorganisms) hazards. The Academy recently has proposed new schema that may better fit biotechnological risks.
So, indeed, it was good that experts were getting together in 1986 to find new applications of biotechnology to treat and control pollution. However, it appears that even after almost a quarter century some of the challenges have not been addressed, at least not fully. Some of the concerns expressed in 1986 are no longer being widely expressed. The proceedings of the meeting state:
Federal, State and local regulatory policies pose barriers to field-testing and thereby the development of commercial genetically
engineered biotechnology products. Permitting and reporting requirements and the uncertain regulatory climate were identified
as additional barriers to the development of the biotechnology control technology [4].
A systems approach to biotechnology requires a modicum of understanding of a number of disciplines, especially environmental engineering, systems biology, environmental microbiology, and ecology. This book introduces all of these fields from the perspective of how to apply them to achieve desired environmental outcomes and how to recognize and avoid problems in such applications. This approach means that the treatment of these four disciplines is predominantly focused on biotechnology and is not meant to be an exhaustive treatise on any of the four. This book’ s principal value lies at the intersection of the four disciplines. However, engineering requires specifics, so my intention is that the reader gain a sufficient grasp of each so as to know when more details are needed and when to consult the references at the end of each chapter to seek out these important details.
BIOTECHNOLOGY AT THE INTERSECTION OF DISCIPLINES
Environmental engineering is a broad field, including both abiotic and biotic solutions to pollution and environmental problems. This book’s primary environmental engineering focus is on the biotic solutions, so the reader should consult general environmental engineering texts and specific chemical and physical treatment resources to find abiotic treatment methods to match the biotic approaches discussed here. For example, after reading a discussion of a particular biotechnology, e.g., Chapter 7’s exposition of a biofilter used to treat a specific organic pollutant, the reader may be inclined to look up that pollutant to see what other non-biotechnological methods, e.g., pumping and air sparging, have been used in its treatment. This book certainly includes discussions on abiotic techniques in Chapters 7 and 10, but limits the discussion to the treating of those pollutants that may result from biotechnologies (e.g., if a hazardous byproduct is produced, it may need to undergo thermal treatment).
Systems biology and molecular biology are addressed insofar as genetic engineering is an important part of environmental biotechnology. An understanding of genetic material and how it can be manipulated either intentionally or unintentionally is crucial to both applications and implications. As in environmental engineering, the discussion is focused less on a theoretical and comprehensive understanding of DNA and RNA for their own sake than would be found in a systems biology text. Again, if the reader needs more information, the references should be consulted and should lead to more specific information. In addition, the book addresses a number of emerging technologies used in environmental assessment, particularly drawing on systems biology, such as the computational methods associated with genomics, proteomics, and the other “omics” systems.
I recall how one of my many mentors, Ross McKinney at the University of Kansas, contrasted the world view of microbiologists from that of engineers. Microbiologists are interested in intrinsic aspects of the “bugs,” whereas engineers are interested in what the “bugs” can do [1]. I have been careful with the taxonomy of the organisms, but it is not the book’s intent to exhaustively list every microbe of value to environmental biotechnology. When the reader needs more detail on a particular organism and when trying to find other microbes that may work in a biotechnology, the references and notes should help to initiate the quest.
More than a few of my ecologist colleagues may cringe when I say that microbes have instrumental value, not intrinsic value, in many environmental biotechnologies. Engineers, including environmental engineers, are focused on outcomes. They design systems to achieve target outcomes within specified ranges of tolerance and acceptability. As such, they say a bacterium is a means, not an end in itself. In my opinion, ecologists in general have a comparatively more skeptical view of “ecological services” [2] than do practicing engineers. Ecologists tend to be more interested in the whole system, i.e., the ecosystem. Thus, the microbes, especially those that have been supercharged genetically, must be seen for how they fit within the whole system, not just the part of the system that needs to be remediated. This book, therefore, includes this ecological perspective, especially when addressing potential implications, such as gene flow and biodiversity. In fact, one of the themes of this book is that engineers must approach biotechnologies that seem to be completely acceptable with whole systems in mind, with considerations of impact in space and time, i.e., a systems approach to biotechnology. It may be that after such a systems review, the technology may indeed not be the panacea that it at first appears.
THE SYSTEMS APPROACH
One way to address environmental biotechnology is to ask whether it is “good” or “bad.” Of course, the correct answer is that “it depends.” According to my colleague at Duke, Jeff Peirce, this is one of the few universally correct statements in engineering. The tough part of such a statement, of course, is deciding to some degree of satisfaction on just what “it depends.”
The same biotechnology can be good or bad. It just depends. It depends on risks versus rewards. It depends on what is valued. It depends on reliability and uncertainty of outcome. It depends on short-term versus long-term perspectives. It depends on the degree of precaution needed in a given situation. Mostly, it depends on whether the outcome is ideal, or, at a minimum, acceptable, based on the consideration of the myriad relationships of all of the factors. Such factors include not only the physical, chemical, and biological aspects of a biotechnology, but also those related to sociological and economic considerations. That is, the same technology is good or bad, depending on the results of a systematic perspective [3].
I would recommend that the question about the dependencies driving the acceptability of a given environmental biotechnology be asked at the beginning of any environmental biotechnology course. I recognize just how tempting it is in teaching an environmental biotechnology course to jump into how to use living things to treat pollution, with little thought as to whether to use a biotechnology. Perhaps this is because we expect that other perspectives, such as abiotic treatment, will be addressed in courses specifically addressing these technologies, and after having completed courses in every major treatment category, the student will then be able to select the appropriate method for the contaminant at hand. This is much like the need for a really good course in concrete and another excellent course in steel, as a foundation (literally and figuratively) in structural engineering. Such reductionism has served engineering well. In environmental sciences and engineering, the newer views do not lessen the need for similar specific knowledge in the foundational sciences, but in light of the importance of the connections between living things and their surroundings, newer pedagogies are calling for a more systematic view to put these basics into systems that account for variations in complexity and scale.
Biotechnologists are justifiably tempted to keep doing that which has worked in the past. For those in the fields of biological wastewater treatment and hazardous waste biotechnologies, the art of engineering is to move thoughtfully, with some trepidation, from what is known to the realm of the unknown. This microbe was effective in treating contaminant A, so why not acclimate the microbe to a structurally similar compound, e.g., the same molecule with a methyl group or one with an additional ring? Often this works well under laboratory conditions and even in the field, so long as conditions do not change dramatically. Such acclimation was the precursor to more dramatic and invasive forms of genetic modification, especially recombinant DNA techniques. This book explores some of the knowns and unknowns of what happens systematically when we manipulate the genetic material of an organism. Perhaps, the system is no more influenced by a genetically modified organism than by those that bioengineers have manipulated by letting the organism adapt on its own to the new food source. But, perhaps not.
When I originally proposed the concept for this book, I thought that I would dedicate it almost exclusively to potential implications of environmental biotechnologies. I thought that others had done admirable jobs of writing about the applications. After delving into the topic in earnest, I came to the conclusion that I was only half right. Indeed, the previous texts in environmental biotechnologies were thorough and expansive. Some did a really good job of laying out the theory and the techniques of environmental biotechnology. However, most were not all that interested in what may go wrong or what happens outside of the specific application. This is not meant to be a criticism, because the authors state up front that their goal is to enhance the reader’s understanding of these applications. The implication, to me at least, is that their work starts after the decision has been made to destroy a certain chemical compound using the most suitable technique. In this instance, “suitable” may be translated to mean “efficient.” How rapidly will microbe X degrade contaminant A? How complete is the degradation (e.g., all the way to carbon dioxide and water)? How does microbe X compare in degradation rates to microbes Y and Z? How efficiently will microbe X degrade contaminant A if we tweak its DNA? How broadly can microbe X’ s degradation be applied to similar compounds? These are all extremely important questions. Efficiency is an integral but not an exclusive component of effectiveness. Thus, my original contention was half wrong. I could not discuss implications without also discussing applications. I liken this to the sage advice of a former Duke colleague, Senol Utku. He has been a leader in designing adaptive structures that often follow intricate, nonlinear relationships between energy and matter. His students were therefore often eager to jump into nonlinear mathematical solutions, but he had to pull them back to a more complete understanding of linear solutions. He would tell them that it is much like a banana. How can one understand a “non-banana” without first understanding the “banana”? Thus, my systematic treatment of environmental biotechnology requires the explanation of both applications (bananas) and implications (non-bananas).
The term “systems” has become an adjective. For decades, design professionals, failure engineers, and engineering managers have employed systems engineering. Scientists, engineers, and technologists now have systems biology, systems medicine, and even systems chemistry. Early on, systems simply meant a comprehensive approach, such as a life cycle or critical path view. Later, another connotation was that it provided a distinction from compartmental or reductionist perspectives. Now, the systems moniker conveys a computational approach. Lately, subdivisions of the basic sciences have also become systematic in perspective. For example, systems microbiology approaches microorganisms or microbial communities comprehensively by integrating fundamental biological knowledge with genomics and other data to give an integrated representation of how a microbial cell or community operates. This text attempts to address all of these perspectives and more, but all through the lens of the environment.
Along the way, I became aware that there was not a good term that included all of these perspectives. Pioneers in environmental modeling, such as Donald MacKay and Panos Georgopoulos, advanced the field of chemodynamics. In fact, I have drawn heavily from their work. The challenge is how to insert biology into such chemodynamic frameworks.
For many in the environmental sciences and engineering fields, environmental biotechnologies that most readily come to mind are various waste treatment processes, those that often begin with the suffix “bio.” Thus, I decided to use the term biochemodynamics to refer to the myriad bio-chemo-physical processes and mechanisms at work in environmental biotechnologies. At one point, I even suggested calling this book Environmental Biochemodynamics. However, although such a title would distinguish the focus away from abiotic processes, it would leave out some of the important topics covered, such as the societal and feasibility considerations needed in biotechnological decisions.
Environmental biotechnology is all about optimization, so it requires a systematic perspective, at least in its thermodynamic and comprehensive connotations. In particular, biotechnologists are keenly interested in bioremediation of existing contaminants, as well as those that may enter the environment in the future.
To optimize, we must get the most benefit and the least risk by using biology to solve an important problem or fill a vital need. In my research, I discovered a very interesting workshop that took place in 1986 [3]. The workshop was interesting for many reasons. It was held by a regulatory agency, the U.S. Environmental Protection Agency, but predominantly addressed ways to advance environmental biotechnology. In other words, the entity that was chastising polluters was simultaneously looking for ways to support these same polluters financially and scientifically so as to become nonpolluters!
Such an approach is not uncommon in its own right, because in the previous decade the same agency had funded research and paid to build wastewater treatment plants to help the same facilities being fined and otherwise reproved for not meeting water quality guidelines and limits. This is a case of the “stick” being followed by the “carrot.” The 1986 workshop was actually refreshing, because it was an effort to help scientists come up with ways to push the envelope of technology to complement the growing arsenal of rules and standards for toxic chemicals in the environment.
One of the challenges posed in the mid-1980s was that the National Academy of Sciences had just sketched a schematic to address risks posed by chemicals. It followed a sequence that consisted of identifying chemical hazards and seeing how people may come into contact with these hazards, i.e., exposure. The combination of these factors led to what the academy called risk assessment. This seemed to work adequately for chemical hazards to one species (Homo sapiens), but did not fit quite well with hazards that behave differently than pharmaceuticals, pesticides, or other chemical agents, i.e., physical (e.g., UV light) or biological (e.g., microorganisms) hazards. The Academy recently has proposed new schema that may better fit biotechnological risks.
So, indeed, it was good that experts were getting together in 1986 to find new applications of biotechnology to treat and control pollution. However, it appears that even after almost a quarter century some of the challenges have not been addressed, at least not fully. Some of the concerns expressed in 1986 are no longer being widely expressed. The proceedings of the meeting state:
Federal, State and local regulatory policies pose barriers to field-testing and thereby the development of commercial genetically
engineered biotechnology products. Permitting and reporting requirements and the uncertain regulatory climate were identified
as additional barriers to the development of the biotechnology control technology [4].
[EBOOK] Environmental-Biotechnology (A Biosystems Approach), Daniel A. Vallero, Published by AP
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