Distinguishing ecological engineering from environmental engineering

This paper uses complex system thinking to identify key peculiarities of ecological engineering. In particular it focuses on the distinction between the purpose-driven design of structures in environmental engineering and the natural process of self-organization characteristic of life, which needs to be integrated into ecological engineering.Conventional engineering addresses the problem of fabrication of an organized structure, say a road, which reflects a goal at the outset, as well as considerations external to the road. At the outset there is an essence of which the organized structure is a realization. This realization belongs to a certain type (apartment building, suspension bridge). The type is in relation to: (a) the expected contexts (e.g. housing in Manhattan, a bridge in rural Africa) and (b) location-specific socio-economic constraints (low/high economic budget). Conventional engineering does not question the goals of the selected plan and can only object to the feasibility of a proposed typology in a given context. Engineers deal with the challenge of the realization of a plan at a given point in space and time.The central dogma of biology identifies organisms as informationally-closed and this makes possible their use as machines. Ecological systems, on the contrary, are informationally-open. They cannot be used as machines to create functional structures, because they are becoming in time. For engineered structures to work it is usually required that there is (1) stability of system components; (2) admissibility of a workable context; (3) validity of purpose and concept. Ecologically-engineered structures challenge these requirements because of specificity of required environments and lability of system parts over the time the engineered structure functions. Other engineering is better if it achieves flexibility, but ecological engineering must be so flexible as to take on a looping character that updates the system to meet changing requirements. Accordingly, the original goals cannot be taken for granted later in the process of ecological engineering. Ecological engineering has to be a flexible iterative process of design, in which the designer must continually update goals, essences, typologies and processes of realization.     

Antibody engineering

Monoclonal antibodies (Mabs) have been used as diagnostic and analytical reagents since hybridoma technology was invented in 1975. In recent years, antibodies have become increasingly accepted as therapeutics for human diseases, particularly for cancer, viral infection and autoimmune disorders. An indication of the emerging significance of antibody-based therapeutics is that over a third of the proteins currently undergoing clinical trials in the United States are antibodies. Until the late 1980's, antibody technology relied primarily on animal immunization and the expression of engineered antibodies. However, the development of methods for the expression of antibody fragments in bacteria and powerful techniques for screening combinatorial libraries, together with the accumulating structure-function data base of antibodies, have opened unlimited opportunities for the engineering of antibodies with tailor-made properties for specific applications. Antibodies of low immunogenicity, suitable for human therapy andin vivo diagnosis, can now be developed with relative ease. Here, antibody structure-function and antibody engineering technologies are described.     

Metabolic engineering

Metabolic engineering has developed as a very powerful approach to optimising industrial fermentation processes through the introduction of directed genetic changes using recombinant DNA technology. Successful metabolic engineering starts with a careful analysis of cellular function; based on the results of this analysis, an improved strain is designed and subsequently constructed by genetic engineering. In recent years some very powerful tools have been developed, both for analysing cellular function and for introducing directed genetic changes. In this paper, some of these tools are reviewed and many examples of metabolic engineering are presented to illustrate the power of the technology. The examples are categorised according to the approach taken or the aim: (1) heterologous protein production, (2) extension of substrate range, (3) pathways leading to new products, (4) pathways for degradation of xenobiotics, (5) improvement of overall cellular physiology, (6) elimination or reduction of by-product formation, and (7) improvement of yield or productivity.     

Antibody engineering

The antibody molecule is a therapeutic agent, designed by nature to bind to a wide range of antigen molecules and to trigger effector functions, such as complement lysis and cell-mediated killing. The genes encoding antibodies can be manipulated in vitro, allowing the binding sites for antigen and effector molecules to be dissected, and new properties to be engineered. The future for the application of engineered antibodies in medicine is reviewed in the context of the past century.     

Anti-apoptosis engineering

An increased understanding of apoptosis makes anti-apoptosis engineering possible, which is an approach used to inhibit apoptosis for the purpose of therapeutic, or industrial applications in the treatment of the diseases associated with increased apoptosis, or to improve the productivity of animal cell cultures, respectively. Some known anti-apoptotic proteins are the Bcl-2 family, IAP (inhibitor of apoptosis) and Hsps (heat shock proteins), with which anti-apoptosis engineering has progressed. This article reviews anti-apoptosis engineering using known anti-apoptotic compounds, and introduces a 30 K protein, isolated from silkworm hemolymph, as a novel anti-apoptotic protein, that shows no homology with other known anti-apoptotic proteins. The regulation of apoptosis, using anti-apoptotic proteins and genes originating from the silkworm,Bombyx mori, may provide a new strategy in this field.     

Chromosomal engineering

Artificial chromosomes (ACs) are engineered chromosomes with defined genetic contents that can function as non-integrating vectors with large carrying capacity and stability. The large carrying capacity allows the engineering of ACs with multiple copies of the same transgene, gene complexes, and to include regulatory elements necessary for the regulated expression of transgene(s). Artificial chromosome based systems are composed of AC engineered to harbor and express gene(s) of interest and an appropriate recombination system for 'custom' engineering of ACs. These systems have the potential to become an efficient tool in diverse gene technology applications such as cellular protein manufacturing, transgenic animal production, and ultimately gene therapy. Recent advances in artificial chromosome technologies outline the value of these systems and justify the future research efforts to overcome the obstacles in exploring their full capabilities.     

Protein engineering

The techniques of protein engineering are proving to be a revolutionary experimental tool for understanding protein structure-function relationships. Even at this early stage, proteins of improved characteristics for specific industrial and therapeutic uses have already been produced. Tailoring enzymatic properties for non-physiological substrate conditions, altering pH optima, changing substrate specificity, and improving stability have already been demonstrated to be feasible. Nevertheless, the ability to make useful proteins which radically differ from a natural structure or designing altogether new structures exceeds present understanding.