Evolution, A View from the 21st Century: Shapiro

The Modern Synthesis is dead. Evolution doesn’t take place the way we thought it did, the way we make a building out of individual bricks—genetic mutations— added one at a time through the action of natural selection. Instead it happens more the way we build a bridge, out of long sections already fully functional and configured ready to plug into an existing structure and extend it. That's the clear message in Evolution: A View from the 21st Century from one who should know, James A. Shapiro, professor in the Department of Biochemistry and Molecular Biology at the University of Chicago, for the last twelve years of her life a confidant of Barbara McClintock.

"...Cells utilize many kinds of molecular interactions to process information and execute appropriate decisions... we are now in a systems biology era of research.... Gone is the atomistic view that molecules act independently and automatically." And we're only up to page 9. These claims are backed up succinctly in the rest of this compact book and in detail online. The trail of examples is astonishing rich. As a layman I was incredulous that the systems described could be elucidated by mere mortals. Periodically I wondered if the book was a joke and the author would admonish me for being so gullible. But no such notice appeared, and I came to accept the data as genuine.

Here are themes that caught my attention.

1. Retirement of the Modern Synthesis:
"...systems engineering is a better metaphor for the evolutionary process than the conventional view of evolution as a selection-biased random walk through the limitless space of possible DNA configurations." " Using transcription factors and chromatin binding proteins as examples... these classes of proteins did not evolve one amino acid at a time. Instead, the two classes of protein 'shuffled' and 'accreted' copies of functional protein segments called domains. . . the capacity of living cells to carry out the required natural genetic engineering operations for protein evolution by domain swapping is unequivocally established." "proteins evolve by accumulating and rearranging polypeptide domains rather than by undergoing a sequence of individual amino acid changes." "little evidence fits unequivocally with the theory that evolution occurs through the gradual accumulation of 'numerous successive slight modifications.' On the contrary, clear evidence exists for abrupt events of specific kinds at all levels of genome organization. These sudden changes range from horizontal transfers and the movement of transposable elements through chromosome rearrangements to whole genome duplications and cell fusions."

2. Volition (my term--Shapiro prefers "cognition") operates at all scales of life, both at different levels of complexity, and time.
Volition: "Living cells do not operate blindly. They continually acquire information about the external environment and monitor their internal operations. Then they use this information to guide the processes essential to survival, growth and reproduction."
Scale in levels of complexity: "Life requires cognition at all levels..."
Scale in time: " Cells operate at roughly three different biological time scales: within a single cell cycle; over a finite number of cell cycles (as in plant or animal morphogenesis); over the countless cell cycles of evolutionary time."

3. The same mechanisms underlie evolution as life's other primary functions, so need not be sought separately; continuing from above:
"At each of these three time scales, cells reorganize their genomes, thereby inscribing information that influences all aspects of genome function."

4. Evolution occurs not at the level of species but at the level of the genome considered as common to life as a whole:
"Prokaryotes and eukaryotes in a common environment freely share DNA.... No inviolable taxonomic banners exist for horizontally transferred DNA.... contemporary evolutionary theories have to incorporate horizontal transfer of multiple coding sequences from any realm of life as a basic mode of genome change."

5. Lamarckism*:
"The potential for life-history-based control over the occurrence of hereditary variation is one of the most trenchant and fundamental differences between the 21st century view of genome change resulting from a constellation of regulated cell functions (natural genetic engineering) and the traditional view that genome changes result from random and accidental events."

How are we now to think about evolution? "What characteristic do these [genetic engineering operators] display that fit them into the new systems perspective? The brief answer is they have the capacities needed for a process similar to the kind of engineering humans undertake when we want to develop novel products or carry out established functions in a more efficient or responsive manner. Accordingly, let us adopt systems engineering as a theoretical metaphor for evolutionary change."

For molecular biologists the appropriate metaphor may be systems engineering. But for a layperson such as me the appropriate theoretical metaphor is "volition," involving intelligence, free will and creativity. In many living creatures the genome is the most complex brain-like tissue. It may without contradicting logic be regarded as a brain, capable of supporting volition. (This is me speaking, Shaun Johnston, not Shapiro.) And without contradicting logic we may suppose that communities of genomes can pool their talents to further augment their capabilities as ants do by collaborating in colonies.

Where does this intelligent agent forge the novel products that other forms of life cobble together serve to their ends? Some molecular biologists, Shapiro says, have pointed out that viruses are not subject to the same constraints as cells, and have proposed that "viruses serve as sources of novelties that can later be adapted by cells."

Shapiro dutifully raises the specter of creationists turning his speculations to their ends (and by inference people like me turning them to ours), then reflects that the irreplaceable benefits the speculations promise to bring to the pursuit of biology make the risk worthwhile.

Let me see if I can shake his composure. First he says "Life requires cognition at all levels..." Then he credits cells with further aspects of volition: "They continually acquire information about the external environment [cognition] and monitor their internal operations. Then they use this information to guide the processes essential to survival, growth and reproduction." I take this as a license to conclude that life exercises volition, not cognition only, at all levels. We of course can exercise volition. And at the other extreme of scale, we find viruses identified as creative agents, also a characteristic of volition. Just one more step and we may say, "It's volition all the way down, from us down to the genome itself."

One more step: in the course of evolution the genome became capable of volition, and able to create increasingly complex creatures. Finally it creates us, into whom it builds conscious direction of volitional powers similar to its own. Once again we can conceive of a great chain of being, with living creatures ordered in chronological order of their creation, up to us. But above us in this chain is the genome, and between humans and genome, like a flock of angels, viruses celebrating their muse of creative genetic engineering.

Of contemporary evolutionary theories let's insist they can account for the origin and subsequent development of volition.

* Somewhere within the book Shapiro say his finding do not support Lamarckism, since Lamarck supplied no mechanism, but I feel Lamarck's distinctive contribution was supposing that the agent of evolution lay not in the environment but in creatures themselves, which the new findings appear to support.

Evolution: A View from the 21st Century