Natural Genetic Engineering

Shapiro next turns his attention to the role of natural genetic engineering in evolution:

All the preceding whole-genome sequence discoveries implicate cut-and-paste type DNA rearrangements as basic evolutionary processes. What do we know about the capacity of cells to carry out such natural genetic engineering? An important clue is the discovery that our own genomes are at least 43% composed of DNA segments that can transpose from one location to another (International Human Genome Consortium, 2001). Two classes of transposable or mobile genetic elements have been recognized from the work of Barbara McClintock and her molecular followers (McClintock, 1987; Bukhari et al., 1977; Shapiro, 1983; Berg and Howe, 1989; Craig et al., 2002; Deininger et al., 2003): DNA transposons move exclusively at the level of DNA molecules while retrotransposons and other retroelements move by means of an RNA intermediate that can be reverse-transcribed into genomic DNA (Coffin et al., 1997; Kazazian, 2000).

And he also adds:

There appears to be something of a molecular division of labor: DNA elements mediate rearrangements of large segments (Fig. 1), while retroelements mobilize smaller segments, generally not larger than several kilobases in length (Fig. 2). The mechanisms underlying these rearrangements are just the kind of processes needed to explain the patterns of genome conservation and scrambling found by comparing whole genome sequences.


An especially illuminating example of natural genetic engineering is the mammalian immune system. This system evolved from DNA transposons and cellular repair functions (Agrawal et al., 1998; Bassing et al., 2002; Gellert, 2002). It ensures the rapid evolution in lymphocytes of a virtually infinite array of antigen-recognition protein domains starting with a finite set of germ line coding elements.

In this case, what guides the natural genetic engineering is the antigen itself, as it functions as the “bait” to fish out the correctly engineered antibody. As I explain in The Design Matrix, the processes of random reshuffling and tweaking can be guided by providing the bait.

Shapiro also notes:

Acquisition of new DNA regulatory regions and protein domains are examples of engineering a new system by arranging known components in new combinations. The rearrangement process can always be followed, as it often is in human engineering, by fine-tuning or modification of individual components (microevolution). Here again, the immune system is instructive. A similar “rearrangement-followed- by-fine-tuning” sequence of events occurs in targeted somatic hypermutation of joined exons encoding antigen-binding domains of immunoglobulins (Bassing et al., 2002; Kinoshita and Honjo, 2001).

Rearrangement-followed- by-fine-tuning, guided by the appropriate bait, is an intelligent use of chance. The method of rearrangement-followed- by-fine-tuning provides a logic to the evolutionary process and the bait provides guidance.

We are now ready to take in the recent research on FAST.

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