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Lieber,
M.M. (2009), Biotechnology
and the Dynamic of Completion
[Back] Keywords. Biotechnology, dynamic, force, complementarity, completion, probe, hybridized, specific, universal Abstract. The methods of biotechnology ultimately require a complementation process, which is in effect a completion dynamic. This process is a drive for complementary structures, such as those composing DNA, to complete one another’s specific force configurations. Were it not for this universal, though specifically operating dynamic, the practice of biotechnology would be impossible. Biotechnology is subsumed by the dynamic of completion.
1.
Introduction On one level, the methods of biotechnology rely on molecular techniques. Yet, these very techniques have a deeper, more unifying basis. Such techniques could not be performed were it not for a process of dynamical complementation or completion. Every method of biotechnology ultimately depends on a dynamic of completion for the methods to be enabled or effected. Thought of in terms of molecular behavior, the methods must ultimately be thought of in terms of force behavior. If it were not for such force behavior, namely, the thrust for dynamical completion, biotechnology could not be practiced; it could not exist. Examples of this will be given. In describing the particular methodologies or technologies, an illustration will be given of how each relies on a dynamic completion process. 2. Techniques That Rely on Dynamical Completion or ComplementationBy means of recombinant-DNA technology, transgenic plants can be created through the introduction of beneficial, foreign genes into a plant genome. Also, this technology has enabled the cloning of medically relevant, beneficial genes, such as the gene for the insulin protein. Both applications require that those beneficial genes be first integrated into plasmids carried by bacteria. Regarding insulin, large amounts of the insulin protein have been produced in the bacteria through the agency of the insulin gene within the bacterial plasmids. Diabetics have long used insulin synthesized in this manner. With regard to plants, the beneficial genes were integrated into the plasmids present within agrobacteria. Since agrobacteria naturally infect plant cells and introduce their plasmids into plant cells, such agrobacteria have become excellent vectors for the introduction of beneficial genes into a plant. As a subsequent step to creating transgenic plants, these agrobacterial vectors were used to infect plant tissue in vitro. Within the plant cells, the foreign or beneficial genes transferred from the plasmid and integrated into the genomes of those cells. Under prescribed, in vitro culture conditions, such transformed cells developed into transgenic plants. The methods by which the foreign genes were incorporated into the plasmid of a bacterium were through the process of creating “sticky ends”. These sticky ends were respectively open, complementary single-strand sequences of DNA residing respectively on the plasmid and on the genetic material to be integrated. These complementary single strands were drawn to together by virtue of their complementarity, hence their stickiness. This drawing together and fitting together was through forces whose configuration was implicitly due to the complementary geometry of the DNA strands. The subsequent integration was enabled by such dynamics. Only through the complementarity of these DNA ends, their stickiness, would integration occur. The complementarity of the DNA bases, it can be inferred, engendered the stickiness, the complementary configuration of attractive, electrostatic forces so involved in hydrogen bonding of complementary DNA sequences, and grounded on the complementary geometry of the sequences of DNA bases. “ [The] appropriate geometrical correspondence of hydrogen bond donors and acceptors allows only the ‘right’ [DNA base] pairs to form stably” (“Base Pairs”, article in Wikipedia Encyclopedia, online), and thereby the stabilization of complementing or completing DNA sequences. As Mange and Mange (1990) state, “Double-stranded DNA molecules with protruding single-stranded tips…are said to have sticky or cohesive ends…which tend to spontaneously pair with any complementary end that is available…A key point is that DNA molecules that join together [in this manner] need not be from the same organism or even from the same species.” The dynamic, though specific, occurs independently of species and individual. In this connection, what enabled the integrated, recombinant-foreign DNA carried by the plasmid to enter into the genome of the plant? This was through a process of aberrant recombination, whereby the introduced DNA becomes transferred to the plant chromosome. Such recombination ultimately depends on two dynamic processes: First, it depends on complementary, single-stranded DNA molecules being created on regions of the plant genome and within the DNA of the beneficial gene obtained via the plasmid; and second, it depends on such complementary DNAs being specifically drawn to one another and fitting together, giving rise to a completed, foreign gene integrated within the plant genome. To confirm the integration of such foreign DNA into a plant genome, the methodology of Southern Blot is used. First, DNA is isolated from the plant genome of the presumed transgenic plant; the DNA is denatured into single strands, and these are added to the end of a gel in wells. Through electrophoresis, the DNA spreads or migrates through the gel. The single-stranded DNA in the gel is then absorbed onto a sheet of nitrocellulose filter paper to which the single-stranded DNA sticks. This paper is then placed in a bath containing radioactive-labeled DNA, complementary to the presumed integrated DNA in the plant genome. This is referred to as a radioactive probe. The radioactive probe is only drawn to and hybridizes with its complementary DNA attached to the filter paper. It is drawn to and hybridizes or attaches with such DNA by virtue of such specific complementarity. The paper with the hybridized DNA is placed on photographic film. The radioactive, hybridized DNA of the joined complements generates radiation, and this shows on the film as a black region, a process referred to as autoradiography. This confirms that the foreign DNA, complementary to the probe, resides in the plant genome. This method thus confirms that the desired foreign gene or genes has integrated into the plant genome, creating a transgenic plant. Yet, were it not for the degree of specific attraction through which complementary, single-stranded DNA regions or sequences are specifically drawn to each other, and to no other, non-complementary DNA regions, this confirmation method of the Southern Blot would not have occurred. It could not have occurred. The specific dynamic of complementation is required. Through the Northern Blot method, it can be tested whether or not the foreign DNA or beneficial gene(s) is being expressed in the plant; that is, is it producing mRNA through complementary transcription. If such mRNA is being produced in the plant nucleus, this RNA, after extraction and being subject to gel electrophoresis, and then placed on the filter paper, would be detected through the addition of a radioactive probe of DNA specifically complementary to the mRNA produced by the integrated gene(s). A radioactive hybrid of complementary DNA/RNA chains would be created and in turn detected on a photographic plate or film as a dark region. Such a hybrid, which confirms the expression of the specific, integrated gene(s), would not have been created if the complementary DNA were not specifically drawn to the mRNA to which it is complementary. Again, they were drawn together and hybridized by virtue of such complementarity, that is, through the specific dynamics created by or through such complementarity. This specific drawing together is through a specific array of attractive forces, and the array is due to the geometry of a specific complementarity. This specific methodology, which tests for gene expression, could not have been exercised if it were not for the process of specific complementation and the specific dynamics formed or generated through such. The very replication of genes, of DNA, and their expression through the production of mRNA, ultimately rests on the specific dynamics of complementation. Polymerase Chain Reaction (PCR) is a technique that enables one to recursively synthesize large amounts of DNA from initially an extremely small amount or sample. The method relies on a repeating, cascading replication of DNA. This is a process that ultimately derives from or is based on the repeated replication of specific complementary chains of DNA from complementary templates. This repeated replication could not occur if a specific dynamic defined or determined by complementation did not exist. Thus, the methodology of PCR would be impossible without the dynamic of complementation, as would the genetic tests that rely on it. Microarray technology, which sometimes uses PCR, is a complex method that enables one to observe in vitro the expression pattern of a group of genes that were expressed in a cell. It is especially useful in studying the expression patterns of genes in cells isolated from diseased tissue, such as cancerous tissue, or from persons with given diseases. By observing the pattern of such gene expression in diseased cells and the pattern of gene expression that had occurred in normal cells, the control, scientists can arrive at insights into those patterns of gene expression, or lack thereof, that could lead to various diseases such as carcinogenesis. In cells, expressed genes produce mRNA through a dynamic process of complementation, the transcription process. Such transcription-products of expressed genes are isolated from the cells of the diseased tissue, such as cancerous tissue, to be studied and used as templates to make, also through the complementation, single-stranded DNA, referred to as cDNA, which is labeled with a special dye, a fluorophore. Single-stranded DNAs from respectively thousands of specific genes in the human genome, whose expression is to be studied, are isolated, and, if necessary, the amounts from the specific genes are increased with PCR. These DNAs become probes. On a special slide, containing many extremely small pockets arranged in a grid or array, these probes of DNA from the thousands of known human genes are placed respectively at known locations within the grid, where they adhere as microdots to the specially prepared surface of the slide. This makes them stationary probes. The cDNA, the mobile target, sometimes referred to as the mobile probe, and whose source, via mRNA, is the genome of the cancerous tissue, is added to the respective microdots of stationary probe DNA obtained or copied from the thousands of genes that have been maintained in a “library” of human genes. If and when any cDNA in any microdot complements and hybridizes with a stationary gene-probe by being specifically drawn to or moving to its complement, and binding to it, which indicates that the gene was originally expressed in vivo and produced mRNA, the hybridized-complexes fluoresces after exposure to a laser beam, and a scanner detects this for visual observation. Non-hybridized cDNA will have been removed from the array or grid through a special washing of the slide before scanning with the laser beam. If complementary cDNA to the stationary gene probe was not present in any microdot within the array, and hence no mRNA had been produced, before, due to non-expression of that particular gene, there would have been no subsequent hybridization of complements and no detected fluorescence due to the lack of a dye-labeled hybrid in the microdot. The visual pattern of fluorescence/non-fluorescence of the microdots represents or is a function of the pattern of gene expression-non-expression that had occurred in cells from the diseased tissue. That pattern is compared to the visual fluorescent pattern of microdots on another slide, the control, which represents the genetic-expression products of cells obtained from normal tissue. These microdots are prepared with the dye-labeled cDNA derived from the cellular genomes of normal tissue and with the complementary, stationary probes of single-stranded DNA obtained from the same known human genes. The positions of these probes of known human genes on the control array would be the same as those on the experimental array or grid. If the pattern of gene expression in diseased cells differs from that pattern in non-diseased cells, the respective, visual-grid patterns of fluorescent/non-fluorescent microdots will be different on the respective slides or grids. Different patterns of gene expression/non-expression of known genes in respectively different types of tissue become detected. There are variations of this method, where, for example, two different color dyes are used in each microdot to tag respectively cDNA (or mRNA) from diseased and normal tissue. Yet, all the variations of microarray technology depend on the thrust of probes to complement or complete. “The whole process is based on hybridization probing, a technique that uses fluorescent labeled nucleic acid molecules as [labeled] ‘mobile probes’ to identify complementary molecules … [the expressed genes.] When two complementary sequences find each other, such as the…[stationary gene] DNA and the mobile probe, such as cDNA or mRNA, they will lock together, or hybridize” (“Microarrays: Chipping Away at The Mysteries of Science and Medicine”, in NCBI, online; also see, “DNA Microarray”, in Wikipedia). They find each other through the dynamic of specific complementation, the act of guided completion. This detection method is similar to the Northern Blot method, but far more refined, sophisticated, and complex, and ultimately rests on a dynamic more inclusive than the methodology. The mapping of important genes on the molecular level, thought to be involved in a disease process or those genes determining desired traits in agriculture, also rests on the use of radioactive probes of the gene being complementary to specific complementary regions of a DNA segment of a specific length, whose position on a chromosome can be arrived at through another technology, Restriction Fragment Length Polymorphism (RFLP). The latter is a technology whose very methodology is based upon creating single, DNA segments of various lengths through the induction of specific DNA breaks by enzymes being drawn to specific DNA sequences, most likely through a complementation dynamic. After being spread in a gel, through electrophoresis, to various positions as a function of their lengths, these segments are treated to become single-stranded DNA. The positions of various DNA segments originating from different persons or species can then be compared or screened through autoradiography by using radioactive probes of DNA respectively complementary and drawn to the respective, single-stranded segments. In this way, by means of the visualized, joined complements, genetic differences between organisms can be determined or visualized at the molecular level as well as the location of new mutant genes or regions that may be either beneficial or disease related. Based on these visualized, positional differences, genetic maps on the molecular level can be constructed for various species that include the locations of genetic regions of particular interest. RFLP is included in another methodology known as “DNA Finger Printing”. This method is used to determine the source of DNA present at a crime scene and also rests on a complementation dynamic that makes the analysis, using complementary radioactive DNA probes, highly specific and reliable. If there is originally available only a very small amount of DNA, and large amounts of DNA are needed for the essential test, the amount of this DNA can be greatly increased through the PCR process. The development of the DNA Finger Printing methodology is extremely important for the legal process of justice and has resulted in the freeing of many innocent persons from prison, who were wrongly incarcerated based on previous, imperfect tests. The necessity of complementarity involving forces also exhibits itself on the protein level. In medical research, the monoclonal antibody technology has proven very effective. This method rests on uniform antibodies being drawn to and attaching to specific antigens of the same kind, by virtue of regional complementarity of their respective shapes. Such shapes determine the complementary configurations of the attractive forces, and thereby, determine the drawing together of complementary regions and the joining of such, enabling a specific antibody to fit only into a specific antigen on a cell surface. In experimental cancer therapy, a toxic chemical or radioactive compound capable of killing cells is attached to monoclonal antibodies, all specific for a given type of antigen characteristically present on the surface of cancerous cells or tissue. Upon injection of these antibodies at the site of the cancerous tissue in the organism, these antibodies are drawn to the complementary antigens on the surface of the cancer cells, and, by virtue of such forces of specific complementarity, the antibodies bind only with those antigens on the surface of the cancer cells. The immunotoxin or radioactive compound, attached only to the respective antigen/antibody complexes that have become bound only to the cancerous tissue, destroys the cancerous tissue, but not the healthy tissue, thus acting like “magic bullets”. These are all methods that ultimately rest on a complementation dynamic. These and other related technologies are described in various textbooks in genetics and molecular biology. ((For example, see Manage & Mange, 1990). These various methods used in biological research, medicine and agriculture provide overwhelming evidence that their very application is grounded on the dynamic of specific complementation or completion.
3.
Concluding Remarks: Theoretical Implications The previous examples and illustrations have demonstrated that the various methods of biotechnology depend on a complementation dynamic, which is a drive for completion. This would be expected if such a dynamic were a universal feature of nature. The feasibility of this being the case has been described elsewhere (Lieber, 1996, 1998, 2006). And in the context of an immunological system, Neuman (2006) argues that specific complementation reflects a cognitive system operating creatively through all levels or scales of organization in an organism. Might this in turn be reflective of a universal dynamic operating through all scales of organization in nature, making biotechnology the powerful tool that it is? Biotechnology, the application of the concepts and observations of molecular biology, would hence have at its very basis a universal dynamic of completion, with cognitive features. Thus, it can be predicted that any further development of an improved biotechnology, through the human mind, would also require this universal dynamic that operates through all hierarchies of existence. Perhaps, if new biotechnologies were designed with that conceptual view in mind, such methods could be designed more effectively, comprehensively, and with more insight in the context of a global perspective. This should be especially the case for those methods designed for the level of nanotechnology. In this regard, the global dynamic of complementation or completion, occurring on all levels of organization in nature, from the quantum to the macroscopic, irrespective of species, is an invariant and universal dynamic, though it can act specifically. It demonstrates that biotechnology, long thought of and designed in terms of reductionist, molecular approaches, is ultimately and ironically explicable in a non-reductionist, globally dynamic mode. Biotechnology is subsumed by the dynamic of completion. Dynamical complementation/completion has served the life of man. It can be said to be a transcalar dynamic essential to a humanitarian process and can continue to be so, if man allows. It is predicted that it will continue, as this dynamic is of the very life of humankind.
Michael M. Lieber Genadyne Consulting
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A. P. and E. J. Mange [1990], Genetics: Human Aspects, Second
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Inc., Sunderland ( Neuman, Y. [2006], The Specificity Enigma: From Mechanics to Poiesis. Riv. Biol. / B. Forum 99: 327-342. “Base Pairs” Wikipedia Encyclopedia. http://en.wikipedia.org/wiki/Base_pair “Microarrays:
Chipping Away at the Mysteries of Science and Medicine” “DNA Microarray” Wikipedia Encyclopedia http://en.wikipedia.org/wiki/DNA_microarray Michael M. Liebeer Genadyne Consulting michaellieber@juno.com
July, 2009
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