Review: Darwin in the Genome
Work under Review
What if mutations are not random? A mechanism that curtails mutation in critical housekeeping genes while allowing exploratory mutations in certain contingency genes would be a boon to a population of organisms. In a highly variable or changing environment, directed mutations could provide an ideal survival strategy; a species could in a sense regulate its own evolution, not leaving its fate entirely to chance. Is this possible? Molecular biologist Lynn Helena Caporale, in her book Darwin in the Genome: Molecular Strategies in Biological Evolution, argues that the mechanisms by which genetic variation occur are themselves subject to natural selection. The result, she contends, is that genomes have evolved mechanisms that enhance the possibilities for beneficial mutations and genomic changes, while limiting changes that are likely to be detrimental. In other words, organisms have evolved mechanisms to harness genetic change to their advantage.
Nearly one hundred and fifty years ago, Charles Darwin laid the foundation for a scientific understanding of biological evolution. Darwin built a strong case for the common ancestry of living organisms and gave biologists a mechanism to explain the vast diversity of life; the process of natural selection is his legacy.
Evolutionary theory has not remained static, however. In the first half of the twentieth century, new insights about mutation and the genetics of variation revitalized Darwinism, leading to the development of powerful mathematical approaches to study evolution. Neo-Darwinism, as the synthesis of genetics and natural selection came to be labeled, possessed great explanatory power and continues to dominate much of evolutionary thought. In this view, heritable variations, the raw material for evolution, result from random mutations in a population. Biotic and physical constraints, acting through natural selection, then shape the evolution of a population in a non-random way.
During the past twenty or more years, we have seen an explosion of molecular and biochemical investigations into the nature of genetic systems. Our understanding of how information is stored, maintained,retrieved,and transmitted has changed considerably as a result of genome exploration. Biologists are now more hesitant to talk about "junk DNA", for there are clear examples of non-protein-coding, repetitive DNA sequences that modulate gene expression. We now recognize a variety of small RNA molecules that affect genomic interpretation. We have documented genomic reorganizations by retroviruses and transposons. We now know that the structure of DNA is not uniform throughout a genome, and we have learned that the rate, type, extent, and location of DNA mutations can vary within a given genome.
These new understandings have led some biologists to suggest that the traditional gradualism of neo-Darwinism may not be the only pattern of biological evolution, and that speciation might in some instances have occurred quickly and dramatically through processes such as endosymbiosis, horizontal gene flow, or genomic reorganization by retroviruses.
Caporale presents examples of both non-random and large-scale genomic changes. She describes, for example, how mutational hot spots in genes for vertebrate antibodies can enhance the capabilities of our immune system and how similar hot spots in cone snail toxin genes expand their arsenal of toxic weaponry. Caporale argues that some DNA sequences are more prone to mutational events because of their chemical nature and the biochemistry of DNA replication machinery. She points out that blocks of genetic information can be shuffled within a genome and even passed to the genome of another species. The strength of her book is in collecting and detailing relevant examples from the literature. She maintains throughout that not all mutations are random and that "focused, regulated variation is biochemically possible."
Caporale's idea of "variation-targeting mechanisms" has been criticized for implying foresight in the selection process. She argues,however, that naturalistic mechanisms can explain what appears to be directed purposeful mutation. Caporale offers an approach to working out the molecular and biochemical details, and challenges us to consider the idea that the mechanisms for generating genetic diversity can themselves evolve.
Of course, creationists will attempt to portray such theorizing by biologists as a crisis in neo- Darwinian thought. They will be wrong, as usual. "Survival of the fittest" via natural selection remains the cornerstone of evolutionary theory. Now under discussion are the mechanisms for generating genetic variation; that is, the "arrival of the fittest", with molecular biology demonstrating that genetic change is not limited to an accumulation of random point mutations.
Although written for a lay audience, Caporale's prose is clumsy and cloudy at times, and unfortunately small errors crept into the text, as, for example, when she gives the size of the human genome as three billion base pairs distributed in forty-six chromosomes instead of the haploid number of twenty-three (twenty-four if we make allowance for two different sex chromosomes).
She uses informal language, attributing "anticipation" or "strategy" to genomes. Although it should be clear to biologists that these are rhetorical devices, this distinction may be lost to others, and could provide fertile ground for that creationist specialty, quotation out of context. To talk of genomes as having "worldviews", or to say that "information can flow back from survival to the places in the genome that affect the generation of diversity," will leave some readers uncomfortable.
Despite these weaknesses, I recommend this book to anyone interested in learning more about the molecular complexities of genomes and current discussions on genetic variation.
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Finn Pond is Professor of Biology at Whitworth College.