TECHNOLOGY FOCUS - BIOTECHNOLOGY - Preferred Method: Altering the phenotype of a cell further comprises determining the phenotype of the altered cell. The method further comprises repeating the mutation of the nucleic acid to produce an nt1 generation altered cell. The method further comprises determining the phenotype of the nth generation altered cell. The step of repeating the mutation of the global transcription machinery comprises isolating a nucleic acid encoding the mutated global transcription machinery and optionally, its promoter, from the altered cell, mutating the nucleic acid, and introducing the mutated nucleic acid into another cell. The cell is a prokaryotic cell. The prokaryotic cell is a bacterial cell or an archaeal cell. The global transcription machinery is a sigma factor or an anti-sigma factor. The nucleic acid encoding the sigma factor is an rpoD (sigma70) gene, an rpoF (sigma28) gene, an rpoS (sigma38) gene, an rpoH (sigma32) gene, an rpoN (sigma54) gene, an rpoE (sigma24) gene or a fecI (sigma19) gene. 10. The method of claim 8, where the sigma factor or anti-sigma factor is expressed from an expression vector. The cell is a eukaryotic cell, a yeast cell, a mammalian cell, a plant cell, an insect cell, a stem cell or a fungus cell. The eukaryotic cell is contained in a multicellular organism. The nucleic acid is expressed in the cell from a tissue-specific promoter, a cell-specific promoter, or an organelle-specific promoter. The global transcription machinery binds to an RNA polymerase I, an RNA polymerase II or an RNA polymerase III, or a promoter of an RNA polymerase I, an RNA polymerase II or an RNA polymerase III. The global transcription machinery is TFIID or its subunit. The subunit is TATA-binding protein (TBP) or a TBP-associated factor (TAP), such as TAF25. The nucleic acid encoding the global transcription machinery is a GAL11 gene, a SIN4 gene, a RGR1 gene, a HRS1 gene, a PAFI gene, a MED2 gene, a SNF6 gene, a SNF2 gene, or a SWII gene. The global transcription machinery is a nucleic acid methyltransferase, a histone methyltransferase, a histone acetylase or a histone deacetylase. The global transcription machinery is expressed from an expression vector. The nucleic acid is a nucleic acid of an organelle of the eukaryotic cell. The organelle is a mitochondrion or a chloroplast. The nucleic acid is part of an expression vector. The nucleic acid is a member of a collection of nucleic acids. The method further comprises introducing the collection into the cell. Expressing the nucleic acid comprises integrating the nucleic acid into the genome or replacing a nucleic acid that encodes the endogenous global transcription machinery. The mutation of the nucleic acid comprises directed evolution of the nucleic acid. The directed evolution comprises mutation by error prone PCR. The directed evolution comprises mutation by gene shuffling. The mutation of the nucleic acid comprises synthesizing the nucleic acid with one or more mutations. The nucleic acid mutations is/are one or more point mutations. The nucleic acid mutations is/are one or more truncations or deletions. A promoter binding region of the global transcription machinery is not disrupted or removed by the one or more truncations or deletions. The mutated global transcription machinery exhibits increased transcription of genes relative to the unmutated global transcription machinery. The mutated global transcription machinery exhibits decreased transcription of genes relative to the unmutated global transcription machinery. The mutated global transcription machinery exhibits increased repression of gene transcription relative to the unmutated global transcription machinery. The mutated global transcription machinery exhibits decreased repression of gene transcription relative to the unmutated global transcription machinery. The method further comprises selecting the altered cell for a predetermined phenotype. The step of selecting comprises culturing the altered cell under selective conditions. The step of selecting comprises high-throughput assays of individual cells for the phenotype. The phenotype is increased tolerance of deleterious culture conditions. The phenotype is solvent tolerance or hazardous waste tolerance. The solvent is ethanol, hexane or cyclohexane. The phenotype is tolerance of industrial media. The phenotype is tolerance of high sugar concentration. The phenotype is tolerance of high salt concentration or osmotic stress. The phenotype is tolerance of high temperatures. The phenotype is tolerance of extreme pH. The phenotype is tolerance of surfactants. The phenotype is tolerance of deleterious conditions, such as tolerance of high sugar and ethanol concentrations. The phenotype is increased metabolite production. The metabolite is lycopene or ethanol. The metabolite is polyhydroxybutyrate (PHB). The metabolite is a therapeutic protein. The therapeutic protein is an antibody or an antibody fragment. The phenotype is tolerance to a toxic substrate, metabolic intermediate or product. The toxic metabolite is an organic solvent. The toxic metabolite is acetate or parahydroxybenzoic acid (pHBA). The toxic metabolite is an overexpressed protein. The phenotype is antibiotic resistance. The phenotype is increased resistance to apoptosis. The cell is contained in a multicellular organism. The phenotype is one or more growth characteristics, generation time, resistance to one or more pests or diseases, production of fruit or other parts of a plant, one or more developmental changes, one or more lifespan alterations, gain or loss of function and/or increased robustness. The cell used in the method is optimized for the phenotype prior to mutating the global transcription machinery. The method further comprises identifying the changes in gene expression in the altered cell. The changes in gene expression are determined using a nucleic acid microarray. The method comprises altering the expression of one or more gene products in a first cell that are identified by detecting changes in gene expression in a second cell, where the changes in gene expression in the second cell are produced by mutating global transcription machinery of the second cell. Altering the expression of the one or more gene products in the first cell comprises increasing expression of one or more gene products that were increased in the second cell. The expression of the one or more gene products is increased by introducing into the first cell one or more expression vectors that express the one or more gene products. The expression of the one or more gene products is increased by increasing the transcription of one or more endogenous genes that encode the one or more gene products. Increasing the transcription of the one or more endogenous genes comprises mutating a transcriptional control sequence of the one or more genes. Altering the expression of the one or more gene products in the first cell comprises decreasing expression of one or more gene products that were decreased in the altered cell. The expression of the one or more gene products is decreased by introducing into the first cell nucleic acid molecules that reduce the expression of the one or more gene products. The nucleic acid molecules are, or express, siRNA molecules. The expression of the one or more gene products is decreased by mutating one or more genes that encode the one or more gene products or a transcriptional control sequence of the one or more genes. The changes in gene expression in the second cell are determined using a nucleic acid micro array. The changes in gene expression in the second cell are used to construct a model of a gene or protein network. The model is used to select which of the one or more gene products in the network to alter. The global transcription machinery comprises more than one nucleic acid and/or polypeptide or is encoded by more than one nucleic acid. Altering the production of a metabolite comprises mutating, global transcription machinery of a cell that produces a selected metabolite to produce an altered cell, and isolating altered cells that produce increased or decreased amounts of the selected metabolite. The method further comprises culturing the isolated cells, and recovering the metabolite from the cells or the cell culture. The metabolite is lycopene or ethanol. The metabolite is polyhydroxybutyrate (PHB). The metabolite is a therapeutic protein. The therapeutic protein is a recombinant protein. The therapeutic protein is an antibody or an antibody fragment. The method for bioremediation of a selected waste product comprises:(1) mutating global transcription machinery of a cell to produce an altered cell;(2) isolating altered cells that metabolize an increased amount of the selected waste product relative to unaltered cells;(3) culturing the isolated cells; and(4) exposing the altered cells to the selected waste product, thereby providing bioremediation of the selected waste product.Preferred Collection: In the collection of nucleic acid species, the directed evolution is performed using gene shuffling. The mutations in the global transcription machinery are one or more point mutations. The mutations in the global transcription machinery are one or more truncations or deletions. The truncation does not include the promoter binding region of the global transcription machinery. The global transcription machinery of a cell is mutated. The collection of cells comprises cells, each of the cells comprising one or more of the nucleic acid molecules. The nucleic acid molecules are integrated into the genome of the cells or replace nucleic acids that encode the endogenous global transcription machinery. Preferred Nucleic Acid: The nucleic acid encodes global transcription machinery produced by rounds of mutation. The rounds of mutation comprise directed evolution. The directed evolution comprises mutation by error prone PCR. The directed evolution comprises mutation by gene shuffling. The nucleic acid encodes different global transcription machinery species. The nucleic acid encodes different versions of the same type of global transcription machinery species. EXAMPLE - No suitable example given.