Evolution without accidents
Despite advances in molecular genetics, too many biologists think that natural selection is driven by random mutations

Since 1859, when Charles Darwin’s On the Origin of Species was first published, the theory of natural selection has dominated our conceptions of evolution. As Darwin understood it, natural selection is a slow and gradual process that takes place across multiple generations through successive random hereditary variations.
...A lot has changed since 1859. We now know that Darwin’s ‘gradualist’ view of evolution, exclusively driven by natural selection, is no longer compatible with contemporary science.
...Today, we know in exquisite detail how these larger-scale ‘spontaneous’ variations come about without the intervention of random mutations.
...One of the most significant of these alternatives is symbiogenesis, the idea that evolution can operate through symbiotic relationships rather than through gradual, successive changes.
...According to molecular geneticists in 1965, mutations were supposed to take place only in two ways: through errors in DNA replication limited to just one or two base pairs, or by deletions of longer stretches of the genome. I eventually showed that the puzzling mutations I found in E coli were caused by the insertion of long segments of genetic material, typically more than 1,000 base pairs.
...This discovery revealed an entirely new mechanism of genetic regulation and variability: maize plants were rapidly changing their own genomes through transposable controlling elements (TEs). And moreover, TE changes were nonrandom in two ways. Firstly, the same DNA element could insert repeatedly at new target sites; and, secondly, TE mobility and mutagenic activity was activated by specific organismal stress conditions.
...For example, herbivorous beetles and nematode worms weren’t always able to digest complex plant polysaccharides. They acquired the enzymes allowing them to digest plants in a fully evolved state through horizontal DNA transfer from various bacteria and fungi. Horizontal DNA transfer occurs across all taxonomic boundaries in Earth’s biosphere and in both directions between complex and simpler organisms.
...Like horizontal DNA transfer, ‘domain shuffling’ involves inserting extended segments of protein-coding DNA in various locations in the genome. This means that cells can cut and splice their own DNA molecules, a capability that I call ‘natural genetic engineering’.
...By turning evolutionary variation from random accidents to biological responses, 21st-century molecular genetics and genomics have revealed that living organisms possess tremendous potential for adaptive genome reconfiguration. For evolution scientists, this revelation poses an important set of obligations. Those obligations include reorienting our studies of adaptive variation towards learning how deeply genome change is integrated with biocognitive sensory responses. This new evolutionary paradigm will require a more organic mode of research that combines genomics, physiology and cognitive science. For some philosophers of science, 21st-century evolutionary biology will require rethinking all the purely mechanical physics-based assumptions they have held about life. Biologists will have to incorporate as foundational a recognition that rapid genome reorganisation is not only a feature of all organisms but, evidently, has proved essential for the survival of life on an ecologically diverse and dynamic planet.