Adaptation Without Darwinism

Copying and pasting genetic
information contradicts
mutation and selection

 

The core of Darwinism (whether old-style or neo-Darwinism) is that progress up the “tree of life” is driven by unguided natural processes. Neo-Darwinism linked the progress to genetic mutations: chance mistakes in alleles, like typos in text, some of which might be beneficial among the millions of harmful errors. Darwin’s core thesis was “selection” of these beneficial mistakes by a mindless Selector. Since both mutation and selection reduce to chance, we call it the Stuff Happens Law. Every beautiful thing in nature, every wonder, every harmonious interaction, every complex molecular machine, just happened. This has become enshrined as the consensus fogma of Big Science. Bucking the consensus is grounds for persecution. All scientists must swear allegiance to the Stuff Happens Law or else!

But what if genetic information can be shared or even duplicated? What if there are mechanisms built into organisms for information sharing? That would be a far cry from Darwinism. Two recent papers in the Proceedings of the National Academy of Sciences (PNAS) presented ways that organisms have adapted to new environments by copying and pasting existing information.

A horizontally transferred bacterial gene aids the freezing tolerance of Antarctic bdelloid rotifers (PNAS, 4 March 2025). In this paper, James A. Raymond of the University of Nevada identified an adaptive trait that rotifers gained through horizontal transfer of genetic information: the ability to survive freezing.

Bdelloid rotifers have attracted a lot of interest in recent years for their extraordinary ability to survive extreme conditions, including long periods of freezing. They are also known for a remarkable ability to incorporate foreign genes into their genomes. However, little is known about the mechanisms underlying their freezing tolerance. Here, I show that bdelloid rotifers from an Antarctic algal community have acquired bacterial genes that encode a well-known family of ice-binding proteins called DUF3494 proteins that are found in a variety of ice-associated microorganisms, including bacteria, fungi, and algae. These genes and the ice-binding activity of their encoded proteins provide important clues to the freezing tolerance of bdelloid rotifers.

Dr Raymond notes that rotifers often reproduce asexually, which is considered “an evolutionary dead end” among evolutionary biologists. If they are able to get adaptive genes from the local library, however, they can thrive. [Note: “bdelloid” means “leech-like.”]

The success of bdelloid rotifers in hostile environments despite the loss of sexuality is at least partly due to their remarkable ability to acquire foreign genes [or retain those acquired] from a variety of sources, including bacteria, fungi, and plants. For example, they have hundreds of horizontally acquired genes against fungal pathogens. These findings have led to the idea that exogenous genes have played an important role in bdelloid evolution.

He calls this evolution, but it is a far cry from neo-Darwinism. A better analogy might be plagiarizing someone else’s software instead of expecting it to emerge from scratch through a random letter generator.

Copy number variation contributes to parallel local adaptation in an invasive plant (PNAS, 3 March 2025). Four authors mostly from Melbourne, Australia found an instance of an invasive plant that adapted by making additional copies of some of its genes. “Copy number variation” has usually been considered a type of random mutation, but in the plant they studied, something unusual seems to be going on. It suggests the existence of an adaptation-generating mechanism that takes advantage of existing genetic information.

Using a population-genomic approach, we identified copy number variants (CNVs)—stretches of DNA that can be either present, absent, or in multiple copies—displaying parallel signatures of local adaptation across the native and introduced ranges of the invasive weed Ambrosia artemisiifolia. We further identified 16 large CNVs, some associated with ecologically important traits including sex allocation and height, that show strong signatures of selection over space, along with dramatic temporal changes over the past several decades. These results highlight the importance of an often-overlooked form of genomic variation for both local adaptation and rapid adaptation of invasive species.

Multiple copies of a gene can effect the dosage of a protein in a cell. If the dosage of a protein needs adjustment for sex allocation or height, the organism can exhibit better adaptation in a strange environment—not by chance—but by regulation of existing genetic information. The authors speak of “selection pressure” for adaptation (the old neo-Darwinian lingo) but the sheer number of CNVs in this case hint at a mechanism allowing rapid adaptation by adjusting the dosage of existing functional proteins. Their example, they say, points to a “previously unrecognized component” of adaptation that may be widespread in nature:

Our study highlights the importance of copy number variation (CNV) in the evolution of a widely distributed and rapidly adapting invasive weed. While CNVs have previously been implicated in adaptation in response to specific selection pressures in other species, our genome-wide discovery approach was able to identify candidate genomic regions that are more broadly representative of the contribution of CNVs to local adaptation. We have linked several of these candidates with traits ranging from flowering time to pathogen resistance. Along with previous studies showing that SNPs [single nucleotide polymorphisms] and chromosomal inversions underlie local adaptation during A. artemisiifolia’s expansion across vast environmental gradients, these new findings make it clear that CNVs account for a significant and previously unrecognized component of this plant’s past success and are consequential for its invasive capacity wherever it may be introduced in the future.

These scientists most likely adhere to neo-Darwinism, and we have no reason to doubt it. In their opening paragraph, though, they ask some pointed questions about how creatures adapt. They seem open to mechanisms apart from traditional Darwinian mutation and selection:

Understanding how populations adapt and persist in the face of rapid environmental change is one of the most pressing challenges of our time. Fundamental to this goal is determining the genetic basis of adaptive evolution. But despite considerable empirical and theoretical work in this area, many questions remain unresolved.

Hold on a second: haven’t we been told that Darwinian evolution is a proven fact, for which no further evidence is needed? Continue reading:

For example, does adaptation typically rely on new and beneficial mutations or on standing genetic variation? Does adaptation generally result in the removal or maintenance of genetic variation affecting fitness? Do mutations contributing to adaptation have uniformly small phenotypic effects, or are large-effect mutations important as well? Do populations exposed to similar environments evolve using the same or different genetic variants?

Yikes! These questions border on undermining everything we have been taught about evolution. “Standing genetic variation” is like having more tools in your toolkit than you need for the present, but that might come in handy in the future. That speaks of foresight—a hallmark of intelligent design. “Removal or maintenance” of that standing genetic information speaks of intelligent planning for robustness, like a racing driver having a well-trained pit crew on the sidelines. They call CNV a form of “large-effect mutation” but it’s really adjusting the effect of existing genetic information. The larger the mutation, the more the chance of breaking something, unless it is regulated. And needless to say, removal of genetic information is devolution, not evolution. And “maintenance of genetic variation” sounds downright purposeful.

The evolution of quantitative traits was traditionally thought to almost exclusively depend on evolutionary changes at many polymorphic loci with individually small phenotypic effects.

That’s traditional Darwinian gradualism. That’s what evolutionary biologists “traditionally thought.”

But now these scientists are asking questions:

However, comparatively recent theoretical and empirical studies demonstrate that large-effect variants can also play important roles in adaptation. Large-effect mutations are particularly likely to contribute to the initial stages of a population’s evolutionary response to a sudden shift in the environment and to facilitate stable adaptive genetic differentiation among populations connected by migration. Such large-effect variants promote local adaptation by resisting the swamping effects of gene flow, including cases in which the alleles carry substantial pleiotropic costs.

Translated into lay terms, the old-school random variations carry a big cost: the risk of breaking other genes. Pleiotropy is a risk when mutating a gene that affects other genes. You can’t expect a random change to one gene to act alone. If a car engine starts running faster, that’s not good if the engine overheats because the radiator can’t handle it, leaving the car smoking on the side of the road.

CNVs of important genes can “resist the swamping effects of gene flow” (random variations) just like having backup copies of your computer files or extra ketchup in the fridge. It’s noteworthy that the CNVs they studied showed parallelism in their signatures between different populations. What’s the probability of such changes becoming adaptive by chance? If, on the other hand, they occurred via designed mechanisms, that would make sense when observing their success in a new environment.

What Is a Species Anyway?

Darwin’s book was titled On the Origin of Species, but what is a species? Another paper in PNAS discussed the philosophy of taxonomy, arguing that the amount of variation allowed for an organism to be considered a “species” varies between prokaryotes and eukaryotes:

Genomic divergence across the tree of life (PNAS, 23 Feb 2025). “Nucleotide sequence data are being harnessed to identify species, even in cases in which organisms themselves are neither in hand nor witnessed,” say three authors from the University of Texas at Austin. “But how genome-wide sequence divergence maps to species status is far from clear.”

While gene sequence divergence is commonly used to delineate bacterial species, its correspondence to established species boundaries has yet to be explored across eukaryotic taxa. Because the processes underlying gene flow differ fundamentally between prokaryotes and eukaryotes, these domains are likely to differ in the relationship between reproductive isolation and genome-wide sequence divergence. In prokaryotes, homologous recombination, the basis of gene flow, depends directly on the degree of genomic sequence divergence, whereas in sexually reproducing eukaryotes, reproductive incompatibility can stem from changes in very few genes.

Based on historical trends, their delineation of a species at the 1% sequence divergence level between prokaryotes and eukaryotes is subject to revision by other scientists. The paper illustrates that taxonomy is not an exact science. Terms devised by natural philosophers like Linnaeus may be useful for human needs, depending on context, but do not necessarily carve nature at its joints. Moreover, the fairly recent discovery of widespread horizontal gene flow across species (see this article at Evolution News) scrambles definitions even further. This is one reason why many Biblical creationists allow for substantial “standing variation” and adaptation up to the family level.

Adaptation—the fit of an organism to its environment, and adaptability—the ability of an organism to adjust and thrive in a new environment—are not the same as evolution. Here we have seen two examples of non-Darwinian adaptation that might best be explained by intelligent design. It’s a mark of super intelligence to be able to design a system capable of adapting its instructions to cope with unforeseen circumstances. That takes foresight, a hallmark of intelligence. I would hasten to explain, however, that this is not the same thing as “front-loading” believed by some theistic evolutionists. They try to argue that God front-loaded all the adaptability from big bang to man, but they side with the Darwinians by believing that everything evolved by unguided natural processes.

The CET model of adaptation (Continuous Environmental Tracking) being researched at ICR  is different from neo-Darwinism and from theistic evolutionary front-loading. For one thing, it denies that organisms can cross family barriers, because the Bible limits things to reproducing “after their kind.” For another thing, CET criticizes natural selection as a mystical idea. Finally, the CET model is built on intelligent design and on Genesis. Adaptation was part of God’s plan in Genesis for organisms to “fill the earth” (Gen 1:22, 28). Organisms unable to adapt would have gone extinct.

Originally, each organism was perfectly adapted to its created environment, but a rotating globe under the sun would be subject to major changes. For organisms to fulfill their created roles, they needed the ability to adapt to new environments rapidly, such as when a bird migrates to another continent or island, or a climatic swing occurs (the Flood, the Ice Age). ICR predicted that “engineered adaptability” would lead to the discovery of built-in mechanisms permitting rapid adjustments. ICR president Randy Guliuzza wrote,

We find that for most of the documented adaptations, creatures used elements that match well with those underlying the self-adjustable properties of human-designed tracking systems. These are 1) input sensors to gather data on external conditions; 2) internal programming specifying reference values and “logic segments” that compares input data to a reference and selects a suitable response; and 3) output actuators to execute responses. The route from detected condition to specific adaptation runs through these components. The systems exhibit the engineering principle of functional coherence. This means that key elements must be available at the right time, place, and amount to attain function.

ICR is running experiments to test these expectations on blind cave fish. We encourage our readers to investigate the CET model with regard to the PNAS papers discussed above. For more, click here and here.