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Recasting Darwin Stories into Engineering Models

Image: Three-spine stickleback, by Alexander Francis Lydon, Public domain, via Wikimedia Commons.

Not all change is “evolution” in the Darwinian sense. Darwin theorized that every change was the result of unguided variations somehow “selected” by the environment for reproductive success and survival. But what if organisms were engineered to survive in changing environments? What if a designer had the foresight to install mechanisms in the genetic code that would switch on under stressful circumstances? Stickleback fish offer an opportunity to test those alternatives.

The three-spine stickleback has been Michael Bell’s evolutionary pet since he retired from Stony Brook University. News from U.C. Berkeley tells how he became intrigued by these 2.5” fish that swim up Alaskan streams to spawn. They are his version of Darwin’s finches, “evolving” in short enough timeframes to shed light on the mechanisms of adaptation. They have lately been among evolutionists’ favorite icons demonstrating the truth of Darwinian evolution.

Michael Bell, currently a research associate in the University of California Museum of Paleontology at UC Berkeley, stumbled across one such natural experiment in 1990 in Alaska, and ever since has been studying the physical changes these fish undergo as they evolve and the genetic basis for these changes. He has even created his own experiments, seeding three Alaskan lakes with oceanic sticklebacks in 2009, 2011 and 2019 in order to track their evolution from oceanic fish to freshwater lake fish. This process appears to occur within decades — very unlike the slow evolution that Charles Darwin imagined — providing scientists a unique opportunity to actually observe vertebrate adaptation in nature. [Emphasis added.]

Writers at Evolution News have commented on stickleback “evolution” for years, arguing that the changes are microevolutionary at best, simply oscillating back and forth with no net fitness gains. The CELS event last month, though, provided an opportunity to look at the empirical data from an engineering perspective. Were these marine fish equipped with mechanisms to adapt when trapped in freshwater lakes, finding themselves surrounded by different ecological conditions? 

Puzzling Observations for Darwinists 

Before analyzing the scientific paper, note that the news mentions some observations that Darwinian biologists should find puzzling. For one, the “evolution” was very rapid: within a decade or less, the offspring of the trapped fish had adjusted to their new surroundings. For another, similar genetic changes were found in populations that had “evolved” independently. Additionally, the code for adaptation seems to be imbedded in the fish before they adapt.

The title of the paper in Science Advances, by Garrett A. Roberts Kingman et al., also looks curiously out of sync with traditional Darwinism: “Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution.” Isn’t Darwinian evolution unguided and therefore unpredictable? Eighteen authors, besides Michael Bell, hailing from 11 institutions in 8 states and one from Germany, participated in this heroic attempt to document evolution and to elevate stickleback fish to the iconic stature of Darwin’s finches. Those birds, in fact, figure prominently in the paper. The team believes that their findings will help explain the adaptive success of Darwin’s finches and other species that show rapid adaptation to a changed environment.

Similar forms often evolve repeatedly in nature, raising long-standing questions about the underlying mechanisms. Here, we use repeated evolution in stickleback to identify a large set of genomic loci that change recurrently during colonization of freshwater habitats by marine fish. The same loci used repeatedly in extant populations also show rapid allele frequency changes when new freshwater populations are experimentally established from marine ancestors. Marked genotypic and phenotypic changes arise within 5 years, facilitated by standing genetic variation and linkage between adaptive regions. Both the speed and location of changes can be predicted using empirical observations of recurrence in natural populations or fundamental genomic features like allelic age, recombination rates, density of divergent loci, and overlap with mapped traits. A composite model trained on these stickleback features can also predict the location of key evolutionary loci in Darwin’s finches, suggesting that similar features are important for evolution across diverse taxa.

Standing Genetic Variations 

A key element of the new model is Standing Genetic Variations (SGV), mentioned a dozen times in the paper. As opposed to de novo mutations, which arise randomly over time in traditional neo-Darwinism, standing genetic variations are already present within a population. Moreover, these “ancient adaptive alleles” can be linked to other alleles in what they call EcoPeaks that confer adaptive success to the organism. Is this beginning to sound more like internal programming indicative of foresight? Perhaps that is why there is no operative mention of Darwinian evolution, neo-Darwinism or random variation/mutation in the paper. It’s not that the authors disbelieve or discredit old neo-Darwinism. They just find a short-term process that is observable and predictable:

Although the predictability of evolution may appear to be in conflict with the unpredictability of historical contingency, understanding the past can yield important insights into future evolution. For example, vertebrate populations frequently harbor large reservoirs of standing genetic variation (SGV) that give independent populations access to similar raw genetic material to respond to environmental challenges, as observed in diverse species including songbirds, cichlid fishes, and the threespine stickleback (Gasterosteus aculeatus). SGV is often apparent in divergent species or populations where it is pretested by natural selection and then distributed by hybridization to related populations. Thus filtered and capable of leaping up fitness landscapes, SGV can also drive rapid evolution, helping address a very real practical challenge to testing evolutionary predictions: time.

Aha! This Is Rich

They basically say, “We can’t watch natural selection work in real time, but we can observe mutations that were pre-selected to leap up fitness peaks. Whether in species of fish or birds, individuals can just borrow the pre-adapted alleles by hybridization and get through hard times. See? Evolution is predictable after all!” This is how dogmatic Darwinists can have their cake and eat it, too. Mutations are still random, but they occurred in the invisible past. What we have now are pools of pre-selected genes able to help organisms evolve quickly and predictably. Evolution is still a fact!

Stickleback fish provide an outstanding system for further study of the genomic basis of recurrent evolution. At the end of the last Ice Age, threespine stickleback, including anadromous populations that migrate from the ocean to freshwater environments to breed, colonized and adapted to countless newly exposed freshwater environments created in the wake of retreating glaciers around the northern hemisphere. This massively parallel adaptive radiation was facilitated by natural selection acting on extensive ancient SGV. Under the “transporter” hypothesis, these variants are maintained at low frequencies in the marine populations by low levels of gene flow from freshwater populations. Reuse of ancient standing variants has enabled identification of genomewide sets of loci that are repeatedly differentiated among long-established stickleback populations. In addition, SGV enables new freshwater stickleback populations to evolve markedly within decades, including conspicuous phenotypic changes in armor plates and body shape.

What if those adaptive alleles instead were engineered? A designing intelligence would have the foresight to provide organisms with a toolkit for adapting to changed environments. If so, one would expect organisms to already possess the tools (standing genetic variation) or a means to get them (hybridization). One would expect populations to adapt quickly and independently, not gradually. Consequently, the fossil record would be characterized by systematic gaps. Which model fits the evidence?

Pretested Adaptive Information

Evolutionists have been complaining about gaps in the fossil record long before Stephen Jay Gould spoke of them as the “trade secret of paleontology.” The gaps were explained away by punctuated equilibria and other rescue devices, arguing that evolution occurred too fast to leave fossils but too slow to observe. Well, these 19 authors are now saying that adaptation can be observed, but what happens is not natural selection of random mutations. It’s genetic sharing of pretested adaptive information. That is why Darwin’s finches quickly adapt to droughts and availability of food sources. That is why stickleback fish can gain and lose armor, depending on the predation ecology. The authors insist that their model improves old evolutionary theory:

The importance of SGV for evolution is becoming increasingly apparent, especially in species with large genome sizes, including humans. At first glance, the dependence of threespine stickleback on SGV for freshwater adaptation may appear to be a peculiarity in terms of repeatability and speed and their particular natural history. However, by more comprehensively understanding the dynamics of this highly optimized process, we have extracted general features of genome architecture and evolution that successfully translate to species on distant branches of the tree of life, thus demonstrating the tremendous power of the stickleback system to identify unifying principles that underlie evolutionary change.

But if this is a “highly optimized process” around the tree of life (or, better, network of life), how is it Darwinian? The paper says precious little about the fitness, survival, and speciation — terms that used to be centerpieces of evolutionary theory. The idea of progressive evolution is also merely assumed, not demonstrated:

This suggests that individual regions may grow over time, with alleles originally based on an initial beneficial mutation accumulating additional linked favorable mutations, snowballing over time to form a finely tuned haplotype with multiple adaptive changes. This is consistent with work in other species identifying examples of evolution through multiple linked mutations that together modify function of a gene (50–52) and implies that progressive allelic improvement may be common.

Their three examples in the references, however, only refer to regulatory effects on existing genes — not the origin of species that Darwin wished to explain. Their new model actually sounds designed: organisms can borrow existing know-how supplied to them in a vast library of SGV.

No Need for Excuses

Today’s engineering-conversant biologists have no need of the old excuses for rescuing neo-Darwinism’s gradualism, which contradicts the fossil evidence. Adaptive alleles can be viewed not as a haphazard pool of pre-filtered random mistakes that just happen to work. They are sets of tools for surviving in a dynamic world. This new paper, which does not provide any evidence for randomness or gradualism, proposes a distributed network strategy that looks like good design. Just as each car does not need to carry every tool if it can be obtained from a warehouse, each organism does not need to carry all possible adaptive alleles if it can obtain what it needs from the population’s library. That’s a design strategy that engineering-aware biologists may wish to develop, using this paper (sans its neo-Darwinist assumptions) as evidence.