The whole cell is considerably more than the sum of the working parts. The same can also be said about the genome, where the identifi cation of the blueprint for individual molecular components of the cell is undertaken in the expectation that a rigorous characterization of all of the parts separately will lead to an understanding of the whole. This is a system of investigation called reductionism, which has been a dominant philosophy in biological investigation for decades. However, just to identify the molecular parts of the puzzle is not going to tell us how the whole works if we do not understand the rules for their assembly. This requires the development of approaches to investigate ‘systems biology’ or ‘biocomplexity’, and represents a paradigm shift (i.e. ‘thinking outside the box’) in biological research, wherein the challenge is to understand the collective interactions of multiple molecular processes, not only within the cell itself, but also at the tissue, organ, and organism level. The bottom line is ‘do the molecules drive the cell to drive the organism, or does the organism drive the cell and its molecules? In reality, such interactions lie somewhere between the cell responding to its immediate environment, balanced against the controls of gene expression.
There are many new exciting areas of research into cells. Some involve the understanding of how cellular behaviour can change so dramatically after subtle changes at the level of genes and proteins. Other approaches use cells to cure a disease, for extraction of metals, the breakdown of petroleum products, or to harness light to produce biofuels. Equally fascinating are our efforts to create synthetic life and understand the biology behind ageing. In this chapter we briefly examine some of these future directions and how they might evolve.
Systems biology
We now know the complete DNA sequence of just a few humans. We also have a rapidly increasing understanding of the biochemical mechanisms involved in the day-to-day existence of the cell and how it divides and differentiates. In the past ten years, advances in molecular technology have allowed us to induce and monitor changes in thousands of genes, their accompanying RNA signals, and protein production. These changes can now be measured more or less at the same time and even within a single cell. The knowledge coming out of this collection of technologies has developed into its own subject, known as systems biology. It has allowed us to see millions of more subtle interactions between the different components of the cell. Early experiments monitored the changes that occur within a cell when it is subjected to a known pharmaceutical drug. For example, in the simplest case, a drug interacts with its target enzyme protein and stops it working. What is apparent now through our ability to analyse thousands of individual genes and their products simultaneously is that a drug also triggers changes in the levels of many other proteins, often seemingly unconnected to the original target enzyme, which may be increased or reduced, often at differing rates. This may account for some drug side effects but also allows the development of ‘cleaner’ more specific pharmaceuticals. By further applying this methodology to various biological systems, we are starting to discover the alterations in gene expression and protein levels that take place during various biological processes such as cell division and differentiation. While these experiments themselves take relatively little time to perform, understanding what they mean will take longer as the vast amount of data generated needs to interpreted. Fortunately, analysis of this information has been made possible by powerful computing. Increasingly, cell and molecular biology relies on this in silico biology, which is known as bioinformatics, to solve the difficult questions of biological behaviour in terms of DNA and protein sequence.