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What Is the Key to a Realistic Theory of Evolution?

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In The Origin of Species by Means of Natural Selection, Charles Darwin proposed to explain how one life form gave rise to another. He subtitled the book, "The Preservation of Favoured Races in the Struggle for Life." He argued that a succession of small improvements in reproductive success would gradually lead to the major changes that distinguish one species from another. This gradualist hypothesis followed the Uniformitarian principle learned from his geology professor, Charles Lyell.

Since 1859, Darwin's followers have focused on optimizing reproductive success, now called "fitness." For them, natural selection increases fitness and, thus, generates new life forms, including their sophisticated and complex adaptations.

Darwin put it this way in Chapter 6: "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find no such case."

There has always been controversy about whether random variation and natural selection for improved fitness can truly explain biological evolution over time. Today we can apply genome sequence data to test Darwin's theory. It answers clearly about gradualism.

Many genome changes at key stages of evolution have been neither small nor gradual. For example, plant breeders are familiar with rapid speciation. When we wish to create new plant species artificially, we do not use selection. We generate hybrids by mating different species. In a fine 1951 (!) Scientific American article on this subject entitled "Cataclysmic Evolution," the distinguished 20th Century evolutionist, G. Ledyard Stebbins, explained how flour wheat evolved, suddenly, by hybridization.

Hybridization frequently leads to a process of "whole genome doubling." Doubling the genome takes one generation and potentially affects all hereditary traits. Note that the production of new species with novel characters by hybridization occurs too rapidly for natural selection to act creatively.

Perhaps the most important evolutionary step of all took place at least one billion years ago, when two or more cells fused to produce the first "eukaryotic" cell having a defined nucleus. This nucleated cell was apparently the progenitor of all "higher" forms of life, including plants and animals. Such cell mergers are known as "symbiogenesis," long championed as an evolutionary force by the recently deceased biologist, Lynn Margulis .

It's remarkable that even though processes like hybridization and symbiogenesis have been well-known for decades, many neo-Darwinists firmly insist on gradualism in evolutionary change. Their position notwithstanding, living organisms have many tools at their disposal for generating sudden change.

As I described in my previous HuffPost blog, "Evolutionary Lessons from Superbugs," bacteria get new DNA information from unrelated organisms. Microbes transform into superbugs in a few minutes by "horizontal DNA transfer." Similar events confer new traits to many microbial and eukaryotic recipients, often multiple characters in a single step.

Was Darwin simply mistaken about the gradual nature of hereditary variation? Such ignorance would be unavoidable before we knew about Mendelian genetics and DNA. Or was there a deeper flaw in the theory that he (and Alfred Russell Wallace) propounded? The answer may well be that it was a basic mistake to think that optimizing fitness is the source of biological diversity.

My recent book, Evolution: A View from the 21st Century, begins: "Innovation, not selection, is the critical issue in evolutionary change." This blog expands on that assertion.

The first problem with selection as the source of diversity is that selection by humans, the subject of Darwin's opening chapter, modifies existing traits but does not produce new traits or new species. Dogs may vary widely as a result of selective breeding, but they always remain dogs.

The second problem is that Darwin understood only "numerous, successive, slight modifications" as the sources of inherited change. His neo-Darwinian followers have modified this position to assert that all mutations occur randomly. They insist there is no biological input into the change process. For them, the genome determines organism characteristics. They think of it as a read-only memory (ROM), which only changes by accident.

However, the last 60 years of molecular biology and genome sequencing have established that genome change is very much an active cellular biochemical process. I call this "natural genetic engineering." In my book, I argue that DNA biochemistry has changed our 21st-century view of the genome. We now have to consider the genome a read-write (RW) memory system.

In other words, the genome is more like an iPod than a CD.

Moreover, cells can target genome changes controlled by cell regulation and sensory inputs. Cells and organisms with RW genomes can respond creatively to life-threatening challenges.

My claim of creativity in genome change clearly requires empirical support. Decades of molecular biology research show that organism traits result from action by protein-RNA-DNA networks, which also respond to multiple sensory inputs and signals.

The genome sequence record shows that these networks and their DNA recognition sites have evolved by well-documented natural genetic engineering processes. The examples include:

• How cells generate new proteins by combining parts of existing ones
• How families of proteins expand by copying segments of DNA & RNA
• How innovations spread from part of the genome to another
• How DNA "cassettes" move through the genome (with eerie similarity to familiar human technologies).

Given these well-documented examples of molecular innovation by natural genetic engineering, the new century may be an appropriate time to revisit our basic assumptions about the sources of biological diversity. Perhaps natural genetic engineering plays a more important role than natural selection.

As Barbara McClintock predicted three decades ago, the 21st Century brings us new insights about how cells adapt to challenges. Let us hope that we acquire nature's wisdom. Just as life has survived by repeated innovation, we humans can solve our own daunting problems by learning the lessons cells have to teach.