Natural genetic engineering: intelligence & design in evolution?

In this review, I will have a look at four topics: 1.) why I think genomics is not the whole story; 2.) my own perspective of E. coli genomics, and how I think it relates to this book; 3.) a brief discussion on "Intelligence, Design, and Evolution"; and finally, 4.) a section "in defense of the central dogma".Merely knowing the DNA sequence of the genome does not give the full picture; knowledge of biological systems can provide a more robust explanation. The emergence of novel functions often comes from the 'retention, duplication, and diversification of evolutionary inventions' (page 133 [1]). For example, the evolution of a novel system of motility has been found in Myxococcus xanthus, apparently resulting from an ancient duplication and then diversification of genes originally involved in sporulation [2]. As Shapiro warns the reader, there are many parts of the book that are technical. The case is built up for an analogy between the genome and a read/write storage system, which can, in a sense, program itself. This is in contrast to the traditional view that DNA is for storage only, with occasional change through small incremental mutations. The technical details are meant to present the current views of the subject, and in some ways this section feels a bit like browsing through some of the recent publications in a journal such as Genome Research, with details about genome rearrangements and genomic islands and large regions coming and going from chromosomes. At the time of writing, I read an editorial in Science magazine (7 October, 2011), with the title "Genomics is not enough", about how "Genes and their products almost never act alone, but in networks with other genes and proteins and in context of the environment." This is what is meant by Systems Biology - the subject of evolution as addressed in Shapiro's book. Although Shapiro seems to have difficulty in describing the exact function of a gene, from a bacterial perspective, the concept of a 'gene' is bo