I want to discuss an interesting theme that runs through James A. Shapiro's brilliant book, Evolution: A View from the 21st Century. Because the work is so dense, it's easy to miss it on the first read. Indeed, I only caught the theme on my fourth read. It is this: Massive ecological changes will force the genomes of organisms to generate innovations. Shapiro brings it up in passage after passage, section after section, until at the end of the book, he comes close to fully expressing the concept in a section called "Can Genomic Changes Be Linked to Ecological Disruptions?"
If we think about the kind of ecological disruption that will lead to mass extinctions, it is readily apparent that many organisms will suffer severe physiological and nutritional distress and that populations will be greatly depleted, thereby altering customary mating patterns and host-symbiont relationships (commensal, pathogenic, parasitic, and mutualistic). The population depletion effect can reasonably be expected to lead to a marked increase in abnormal matings between organisms previously subject to reproductive isolation mechanisms and also to unusual associations between hosts and novel infective agents (symbionts and pathogens).
What he is saying here is that a genome under tremendous environmental stress will, by a process of genomic innovations, search for ways to adapt the organism to the new and difficult conditions. This process permits a profusion of monsters by switching or altering the cell's regulatory architecture. This ramped-up process, Shapiro suspects, might help explain the accelerated mass “originations” that follow "mass extinctions." He points to the fossil record and brings up the explosion of new organisms that soon followed the extinction of dinosaurs, a catastrophe caused by a meteorite that hit earth 66 million years ago.
Now let's think about this for a moment. We are, as you well know, in the middle of a mass extinction event. What has hit earth, however, is not a meteorite but a 300-year-old human cultural innovation called comet capitalism.
It must be explained that Shapiro's book is not about mass extinctions. It is something he only brings up in passing. And sometimes this passing is so fast, it is missed. The main concern of the book is to challenge the neo-Darwinist concept of genetic innovation. For this school—which synthesized in the 1930s and 1940s, and still dominates the biological sciences—organisms evolve (or change over time) because of random genetic accidents (mutations). All the environment does is select the accidents that work and reject the ones that do not. This is called natural selection. Shapiro instead sees genetic novelties as largely the result of what he calls "natural genetic engineering" (he also includes lateral gene transfer, symbiosis, and viral infections). And in this way, he turns the role of selection on its head. It does not pick the best accidents. It picks the best innovations, which were developed by sentient molecular beings within organisms.
Yes, for Shapiro, molecules like the messenger RNA, or the Ribosome, or the systems that monitor and repair and delete errors that occur during DNA replication and recombination, are not mechanical but mindful. They see, they think. He had to arrive at this conclusion because the facts are impossible to avoid. He also knows very well that proponents of the intelligent design (ID) program (a Christian pseudo science) will eagerly pounce on this conclusion. There is a designer, a greater being, an ultimate mover that is unmoved, and so on and so on.
But Shapiro believes mindfulness or aboutness or sentience is completely natural. Our mistake, and a mistake from which the rubbish of ID emerges, is to think that thinking is somehow special, when it's apparently ordinary and widespread. If we see "the molecules dedicated to executing the basic biochemical and biomechanical events" within cells as what they truly are, conscious, we should also conclude that mindfulness is not all that. The human error has been to imagine a super-ghost brain in the clouds. And the root of this error is that soulful qualia that associates the human imagination not with other animals, like bats, but with incredible beings like angels. But if we view the real, material micro-systems of genetic processes as if they were as thoughtful as anything we find in the fatty big heads of humans, then we certainly do not need a supernatural being that's all about the universe.
And now for the point of this post: Once we accept that "living organisms actively change themselves," and that "environmental influences, and specific biological activities" are "at the [root] of novel genetic structures and altered DNA sequences," then we can begin to appreciate that information from a stressful environment can be read by some of the deepest sentient systems in our being. The function of these thinking and reading processes is "survival, growth, and reproduction." If these functions are severely challenged by a radically changed environment, then natural genetic engineering will switch gears and begin genomic experiments.
It is precisely the conditions that stimulate natural genetic engineering functions. Hybrid dysgenesis, interspecific mating, infection, and prolonged stress conditions in the laboratory can all serve as experimental proxies for the genome-destabilizing events that would logically follow major ecological disruption.
Although high-level changes in the biosphere have been considered, little attention has been paid to the relationship between ecological disruption and genetic change. The influence that stimulus-sensitive regulatory processes and changes in population structure may have on the processes of genome restructuring requires greater scrutiny.
The conceptual consequence of Shapiro's natural genetic engineering—bio-systems that connected at every level of life—is that genomes must not be seen as isolated entities. They are genetic processes embedded in networks to other genetic processes that process living and non-living information. What this means is a mass-extinction event will not only be recognized by the organism but an organism's molecular "regulatory processes." We are not individuals, we are always other living things, inside and outside.
As Scott F. Gilbert, Jan Sapp, and Alfred I. Tauber state in the important 2014 paper "A Symbiotic View of Life: We Have Never Been Individuals," the present definition of individuality cannot be trusted. It is misleading. One organism is not one genome. It is a dense mixture of genomes (hence the new field of metagenomics), each interacting with other genomes. We are not a thing (or substance) but a process of things, which is why when an animal, like a type of rhinoceros, goes extinct, it is the extinction not of one species, but the form of a community that has been together for millions upon millions years.
If the boundaries "that heretofore had characterized the biological individual" are impossible to determine, and the evidence points to what Gilbert, Sapp, and Tauber describe as an "all-pervading symbiosis" (animals, trees, microorganisms as interconnected micro and macro ecosystems) and accept the facts of Shapiro's natural genetic engineering, it is hard to believe that widespread extinctions and climate change will somehow leave us untouched. The individual is a religion, not a scientific fact. We do not know the information processing systems of life very well. Our culture in this respect is primitive. It is possible that we will enter the current mass extinction—caused by comet capitalism—as humans, but exit it as completely different animals.