Life is a history of change over time. That change moves in the direction of complexity.
We can observe these truths plain enough in the course of our own lives. But we owe it to Charles Darwin and his Victorian colleague Alfred Wallace that we can trace them on timescales reaching back millions of years.
In classical evolutionary theory, "descent with modification" explains the origin of new species and ultimately the vast diversity of the biological world. Yet Darwin's was only the first step, Ken Weiss said. "He knew that this evolution required something to be inherited, but he didn't know what it was."
Weiss, who is Evan Pugh professor of anthropology and genetics at Penn State, delivered the third installment of "Change Happens: Understanding How Living Things Evolve," the 2006 edition of the Penn State Lectures on the Frontiers of Science. In the first few minutes of his talk, he traced a scientific lineage from The Origin of Species to the present day.
"In the 1930s," he said, "a field called population genetics was developed, and that showed how genes—whatever they were—evolve through history, that genetic variation arises, is transmitted from one generation to the next, and that populations evolve by a process of natural selection."
Then came the dramatic discovery of DNA's structure: The genes we inherit were modular units of amino-acid sequences, arranged in very long molecules called chromosomes which, added together, make up the genome, "the repository of evolutionary memory."
Together these theories made sense of evolution. "But none of them provided a phenogenetic understanding of life," Weiss said. None of them could describe in detail the relationship between genes and the traits they produce.
An image flashed on the screen above his head. On the left, an undifferentiated block of DNA code; on the right, a young woman intently bowing a violin in the middle of a lush wood. "How exactly does this"—he pointed to the block of A's, T's, G's, and C's—"become this?"—and he pointed to the violinist. "How does this string of billions of nucleotides translate into the diversity of life?
"To answer this question we can't just look at evolution," Weiss said. "We have to look at development"—at how an individual organism develops from a single 'general' cell into a coordinated unit of billions of specialized cells.
"Above all, organisms are differentiated entities," he said. "So making cells differentiate is the main job of development and, in a way, the main job of genes."
Complexity made simple?
It's because of recent technical advances in molecular genetics—including the publication of whole-genome sequences for a growing number of species—that understanding how genes do their job is beginning to be possible. "In essence," Weiss has written, "these methods have revealed the nature, use, and mechanisms of differential gene expression in cells, complex organisms, and systems."
A set of fundamental principles has emerged, elements of what Weiss calls "the logic of organisms." What's become clear, he said, "is that cells can change into more complex forms by undergoing some very simple processes."
In the long view, "genomes are the modular product of billions of years of duplication events," Weiss explained. Across the generations, the code is copied out again and again and again, and there are foul-ups in the process—mutations. "Pieces can be rearranged, break off, rejoin, be copied twice. This doesn't happen often," he said, "but it happens often enough for evolution to take place."
The eventual product is a string of modular units, "like a necklace with different colored beads on it. And these modules directly and indirectly correspond to structures and functions in organisms."
That's the part where the logic comes in. By and large, Weiss said, genes aren't independent functional units that translate directly into traits. Rather, traits are produced by combinations of genes interacting. "A fundamental aspect of development," he explained, "is that each of your cells has all of these genes, the full set of 3.1 billion nucleotides, but it only uses a subset of them. That's how a liver cell and a skin cell are different: They have the same genes, but they use different combinations of them."
"Most genes have general rather than specific functions," he added. "Of those we know, a large percentage have to do with regulating other genes, or signaling to other cells—not with making the stiff stuff in your skin or the pigment in your eye."
Much of the action of development, he went on, takes place not inside the cell nucleus where the chromosomes dwell, but outside the cell. There, signaling factors sent by other cells find the right receptor on the cell's surface, which allows them to communicate their message to proteins inside the cell, which in turn go to the nucleus and signal the expression of a particular gene. "The same signaling factors are used in many different contexts," Weiss noted. "It's the combination that counts."