Adaptation is a natural phenomenon, a visible pattern of the living world we can see. We can see, for instance, that evergreen plants are adapted — in this pattern sense of the word — to cold winter weather. Pines, firs, and spruce have needles instead of broad flat leaves. Broadleaved evergreens such as holly and live oak have relatively small leaves with thick waxy coverings on them. We can see these distinctive features and so we know it’s likely those features have something to do with these plants’ abilities to remain green even through cold winters. So even without any other knowledge, we can see a good fit between these plants and the habitats they live in. That good fit is the pattern of adaptation.
We can more fully understand the “what” of these particular adaptive traits by observing them more closely, using mostly Intellectual ways of knowing. Science can document the relationship between cold air and low absolute humidity, evaporative water loss from plant leaves, and the way the small surface area to volume ratio of needles or waxy coverings of holly leaves prevents water loss. But understanding that these structural patterns are adaptions doesn’t tell us anything about the process of how these plants came to have these traits. The thing that trips people up is that the process of change (a verb), that produces the visible pattern (noun) we call adaptation, is also called adaptation. But whereas the pattern can be observed and sometimes even measured, the process cannot be seen taking place. It can only be inferred (Gould 1994, Simpson 1953).1
There are several different ideas about how adaptive patterns came to be, most of them having to do with evolutionary changes of specific structures (such as leaves) in response to environmental changes (such as lower temperatures and humidities). “Evolution” is the general term for the larger natural phenomenon of which the process of adaptation is a major part. Exactly how big (or small) a part adaptation plays in evolution is a rather hotly contested issue between organismal, systems, and molecular biologists (see, for example, Travisano and Shaw 2013, Gould 1985). But people who study both the pattern and process of adaptation have come to see the process of adaptation in such a dramatically differently way over the past 50 years that it’s carried our understanding of adaptation across a major paradigm shift.
Yet somehow this change has not made its way into textbooks or media. So educated non-biologists, science journalists, and the general public still think of adaptation the way people thought of it in 1920 or 1955. This is not a problem that affects only people in ivory towers or research labs. Because of the impact of this change on ecology, the critical state of many ecosystems, and the interrelationships between humans and these ecosystems, I would argue that this particular failure to communicate literally threatens us with needless death and destruction we have learned enough to at least potentially avoid — were it not for the fact that policy-makers are using ecological science that’s 50 years out of date! That’s why coastal ecologist Deborah Brosnan (2021:1) says we desperately need “clear communication on resilience as a scientific principle and as a solution” in order to respond appropriately to the natural dynamics of resilient ecosystems, and decries the fact that “the [natural disaster] planning, response, recovery and mitigation framework that has proven so effective in addressing direct human needs does not incorporate ecosystems or ecosystem resilience.”
Perhaps the more telling, frustrating, and even terrifying issue here is that nothing about the problem is new. More than 25 years ago, Harvard paleontologist Stephen Jay Gould, a key participant in evolutionary theory’s paradigm shift and a scientist of international renown, was frustrated to a point of helpless rage over the complete absence of the dramatically different paradigm of evolutionary adaptation in textbooks and publications written for the larger audience of educated professionals who might have expected such materials to at least introduce ideas that had turned several major disciplines on their heads. It’s important to understand that these ideas had been in wide circulation within the field, and become widely accepted, starting more than twenty years earlier. So the invisibility of this information in textbooks and media was not a minor matter. What frustrated Gould the most was that not only were none of the new ideas reported or represented, old ideas the research community had come to realize were literally incorrect were still being included as “fact” in biology textbooks.2 As a scientist who paid very close attention to the difference between pattern and process, he restricted his anguish about how and why this had happened to the more answerable questions of “what,” describing the infuriating situation without attempting to explain it. “. . . [I]nvalid statements in professional publications,” he observed, “often follow an unfortunate path towards inclusion in basic textbooks — and errors in this particular medium are almost immune to natural selection, as extinction-proof as a living fossil in the deep ocean” (Gould 1994:6765).
At the time Gould wrote the passage I cited, he was just beginning to perceive the larger pattern of this new understanding of adaptive evolution: complexity theory. That same year (1994) he participated in a project with other leading evolutionists, to meet and to produce a joint book in honor of the 50 year anniversary of Erwin Schrödinger’s seminal book “What Is Life?” That commemorative volume, “What is Life? The Next Fifty Years: Speculations on the Future of Biology,” published by Cambridge University Press (Murphy and O’Neill 1995), covered the range of areas in which biology was being shaken to its foundations by paradigmatic storms that weren’t yet fully understood. But a third of the twelve papers addressed complexity theory in some way. By the time Gould penned the last book before his death, “The Structure of Evolutionary Theory” (2002:1263-1266), he had realized that punctuated evolution is an emergent process and that complexity itself was the larger context for the paradigm shift in evolutionary theory he’d begun to refer to as quantum evolution.
Gould had co-authored the first ground-breaking paper on punctuated speciation with Niles Eldredge in 1972 (with a follow-up publication in 1977), pointing out the “emperor has no clothes” problem Darwin himself had realized presented a serious problem to his model of evolution as the summative product of eons of gradually accumulating small-scale changes. That problem is, very simply, that the fossil record does not show any record at all of gradual change. What we see, instead, is that species persist unchanged for millions of years, and then a new species suddenly appears almost instantaneously and goes on to persist unchanged for a very long time just like its predecessor did. Subsequent work by a white-hot group of evolutionary scientists over the next 20 years documented more, and then still more, significant information that violated the fundamental principles of classic evolutionary theory in equally astonishing ways. These included the random pattern of almost all extinctions which meant extinction had nothing to do with adaptive failure (Raup et al 1985), the role of catastrophic (as opposed to gradualistic) events such as meteor impacts in earth history (Alvarez et al 1980), and the disconnect — at multiple levels and of multiple types — between genotype and phenotype. That last point is so important, and it’s so statistically likely that you’re mired in that outdated model of evolution and that it still impacts your thoughts about adaptive ecology in very dangerous ways if you do environmental evaluation work, that I want to take a moment to give you two specific examples of what this means and why it matters.
About 99.6% of the genes of chimpanzees and human beings are identical (Gibbons 2012). If genotype determines phenotype then at least some chimpanzees should be writing best-selling novels and at least some humans should be actually furry (to mention just two of many differences). How is it possible for these two species to be so different, in so many ways, when so few of their genes are different? Obviously there’s a lot of research going on to answer that question. The point, however, is that classical evolution posits a tight correlation between genotype and phenotype as being the thing that permits the environment to impact the genotype when it selects against or for a certain phenotype. That IS the process of classic adaptive evolution. If phenotype doesn’t map against genotype any tighter than 0.4%, we’re in a serious “Houston, we have a problem” situation.
One more example is Hox genes. Here you see scanning electron micrographs of “regular” or wild-type fruit fly on the left (a) and a fruit fly that has a mutation in a special type of gene called a Hox gene on the right (b). Expression of this particular Hox gene causes the fly’s antenna to develop as a [not terribly functional] leg instead. There are actually many different types of genes that have this kind of “all or nothing” control over the development of entire suites of characteristics, some structural and others functional (regulating things such as digestive processes). Again, this sort of disconnect between a one-to-one mapping between genotype and phenotype causes problems for the idea that adaptation (the pattern) happens due to gradual accumulation of tiny incremental changes in phenotype (and therefore genotype) selected by the environment (adaptation the process).
So. Adaptation, which had been defined for literally more than a hundred years as the ability of a single species to retain fitness in a slowly changing environment, due to natural selection of beneficial traits, suddenly could no longer be defined this way. For a while, the whole idea of adaptation went out the window as a largely unanswerable “why” question (Gould and Lewontin 1979). But ecologists working with living ecosystems experiencing increasingly serious stressors in real time were able to field the ball that paleontologists couldn’t. In particular, resilience ecologists began to realize that complexity theory had the paradigmatic power to make sense of the things they could see happening in the real world (Holling 1973). As a result, adaptation has a new definition.
Adaptation is defined as an emergent property of ecosystems that generates change in response to long-term environmental variation in parameters such as climate (Bousquet et al 2016). Because it is an emergent property, adapative change is not incremental and cumulative. Adaptive change is not a “complicated” tangle of many smaller linear changes that can be “figured out” by reducing patterns and processes to bits small enough for humans to conceptualize, or to many thousands of tiny bits that can be analyzed by supercomputers and AI. Because it is an emergent property of ecosystems, adaptive change is a holistic process that involves an entire ecosystem responding as a whole living entity in the same kind of harmonic way that’s been observed in human brain neurons engaged in the much simpler complex process of perception. You cannot ask which of all these neurons is essential to perception, and you cannot ask which of all the elements of an ecosystem is essential to adaptation. This has enormous, and at this point in our world’s history, terrifying implications for the tremendous loss of biodiversity in most ecosystems. These ecosystems are like brains in which the neurons are dying here and there and all over. It means the whole system is at great risk of dropping below threshold, at which point it would cease to function at that emergent level any more and the emergent property — in this case adaptive capacity rather than perceptive capacity — would suddenly vanish. Adaptive capacity is defined as “the capacity of actors in a system to influence resilience” (Folke et al 2010), and it’s generally seen as the process through which human populations achieve resilience (Colombi and Smith 2012).
Perhaps you can see why this change in our understanding of adaptation and resilience is so vitally important that I’ve explained it as carefully as I can given the constraints that bind us — time constraints being a nearly obscene consideration, however practical, given the urgency of finding some way to get this knowledge to policy-makers who work with the environment. It’s the root of Brosnan’s anguished 2021 editorial and was the source of Gould’s angry frustration nearly 30 years ago. But it’s essential here to point out the fact that the change in our understanding of adaptation happened as it shifted into a complex paradigmatic understanding of the natural world.
Remember, in this context, Cash Ahenakew’s canny observation (2016) about professional publications, textbooks, and information that is outside a linear, mechanistic paradigm. These forms and formats of communication that we all rely on cannot help but marginalize ways of knowing — and the knowledge acquired in those ways — as well as peoples and whole cultures. The relationship between form and function, and the different ways that human brains perceive and understand, play out right here in the very arena where we find ourselves being crippled by our communication system’s functional inability to transmit knowledge of a paradigm different from its own. The new paradigm of adaptation we’ve been talking about is deeply informed by complexity theory, and there seems to be a real pedagogic and epistemic barrier in communicating the non-linear knowledge of complexity and the non-linear Knowledge of Indigenous worldview via the very linear structural system that is print publication. We must take it seriously that selective, culturally-based, paradigmatic filtering is creating a very serious problem we need to deal with.
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 In passing, I will observe that sometimes people outside of the sciences ask “how” questions as questions of “why” instead. So whereas an evolutionary scientist or ecologist might ask “How does the process of adaptation produce the pattern of adaptation that fits an organism to its environment?” they frame their inquiry along the lines of “Why does a pine tree have needles instead of flat leaves?” “Why” questions collapse pattern and process. Since the pattern and the process are called by the same name in adaptation research, “why” questions are particularly lethal in that field. For instance, we can explain “why” pines have needles instead of flat leaves (“answering” the why question this paragraph opened with) by simply describing and measuring leaf and needle surface-to-volume ratios and evaporative water loss rates and then comparing these to absolute humidity values in winter forests of various habitats. But this tells us only about the pattern of adaptation, and nothing at all about how it came to be there (the process). Framing questions about adaptive processes as “why” questions makes it that much harder to approach process questions about adaptation in a way that’s intellectually responsible or rigorous. This serious problem exists for all “why” questions in science, but is apparently not part of basic science education curricula. So “why” questions are the absolute bane of science fair judges who happen to be actual scientists, and they are red flags of major proportions when we see people who claim to be scientists or philosophers of science ask them about living systems at all.
 This is still enough of a problem that I quit giving “dinosaur talks” in public more than 20 years ago because it caused so much distress to children who correctly responded to questions on standardized tests based on what they had learned in my talk, but were scored incorrectly by the system because the tests were so far out of date even then.