October 10, 2022 | David F. Coppedge

Epigenetics: Adaptation Without Darwinism

Regulating existing genetic information is a way life
gains heritable change without blind natural selection


 — What if much of the alleged evidence for evolutionary adaptation is not Darwinian? —

The fit of organisms to their environment, called adaptation, has fascinated biologists since ancient times. To Charles Darwin, it became a fundamental part of his theory of natural selection. Darwinian theory, and then later Neo-Darwinism (which attributed variability to random mutations) pictured the environment as a “driver” of adaptation. There’s another way of understanding the fit of organisms to their environment, however, that ascribes adaptation to intelligent causes. That way is the newer science of epigenetics, in which internal factors “tune” the genome to its surroundings quickly, without waiting for some “beneficial random mutation” to show up.

One Sequence, Many Variations (The Scientist, 5 Oct 2022). At the Van Andel Institute, researchers have a new take on what makes animals and plants adapt to their environment. It’s called epigenetics, “above the genes.” Andrew Pospisilik is a founding member of the VAI’s Metabolic and Nutritional Programming group. “Pospisilik explores the epigenetic changes that give organisms the plasticity to change in response to their environments.”

Is this a big change in thinking?

For years, scientists have been fascinated with how DNA mutations impart phenotypic changes. However, epigeneticists including Andrew Pospisilik think mutations are responsible for only a portion of the variation present in all organisms. Epigenetic changes from molecules attaching to DNA and histones—proteins that compact DNA into chromatin—and other factors that modulate gene expression allow organisms the flexibility to change according to their environment. These changes can be inherited, altering the phenotypes of future generations in the absence of mutations.

DNA is tightly wound around chromatin, affecting access to genes by transcription factors and polymerases. (Credit: Illustra Media)

To the extent this happens, it represents a very different picture from classic Neo-Darwinism. Neo-Darwinism places all phenotypic change in random mutations—mistakes in the genes, whether from cosmic rays, copying errors or other undirected sources—and claims that only those that are mildly “beneficial” will be inherited, while the vast majority are deleterious or neutral.

But if Pospisilik is right, organisms can get many variations from one sequence, applying epigenetic factors built into the cell’s internal operations (e.g., regulatory elements). He explains why the study of epigenetics is important:

Ever since scientists discovered DNA, figured out what genes were, and started making mutations and sequencing genes, they saw how reproducible the consequences of strong mutations were and got lost in the default notion that everything must be genetics. As scientists map all the genetic differences between humans, we are finding that we are on course to understand, at most, one-third of the puzzle.

Mutations cannot tell the whole story, he continues. “For example, identical twins are not always identical.”

The missing piece is developmental plasticity, which is a major determinant of who and what we are. In organisms that originate from the same DNA template, factors have evolved to compress their variability and mediate their plasticity.

Whether these “factors” have “evolved” in a Darwinian sense, they are not external, but internal to the organism. They exist within the epigenome to give flexibility to organisms placed in new environments. His claim that “factors have evolved to compress their variability” might be a holdover from decades of Neo-Darwinian dogma. It is just as possible to assert that epigenetic factors were built into the organism from the start. If variations are resulting from within the organism, they are not the consequence of mutations.

A designing intelligence, for instance, might pre-program variability for robustness, similar to how the immune system generates millions of antibodies in a targeted search for an antigen. A targeted search for a match is different from a random search (or blind search), because the outcome has been specified beforehand. This implies the pre-existence of information that specifies the target and recognizes a successful outcome. The environment, oblivious as it is to an organism’s needs, cannot be the source of information.

Usually, we think that DNA mutations drive this, but epigenetics allows the same DNA template to generate additional outcomes. For organisms that produce many offspring, such as fruit flies, it does not make evolutionary sense to have hundreds of truly identical offspring. If their DNA sequence makes them sensitive to an environmental perturbation, then they could all die. It is best to have variability in that system so that some of them can live.

Histone tags on chromatin constitute a code separate from DNA. This “histone code” is one method cells regulate gene transcription and alternative splicing, yielding many variations from one sequence.

“Variability in that system” sounds like something that requires foresight. A designer of programmed robots, for instance, might build in modules that drive variability such that some of the products would flourish in a given situation. This would be very different from traditional Neo-Darwinism, where the environment is thought to “drive” adaptation via random mutations.

Pospisilik gives examples of how the same genome can generate completely different phenotypes, depending on the epigenetic regulatory factors. One dramatic example is honeybees: from the same genome, the hive produces a queen, workers, drones and other members of the caste system. What if varieties of bee, wasp, termite and ant colonies had adapted differently based on epigenetic factors? This could explain why similar species within a family have caste systems and others do not, and why the caste systems are highly organized and successful.

Sometimes epigenetically-driven phenotypic plasticity can go awry. He gives an example:

In humans, the Dutch Hunger Winter is a famous example. It was a prolonged famine period during the Second World War. Scientists have found that offspring of people who lived through that period are more susceptible to cardiometabolic diseases a half-century later. Like the queen bee example, these seem to be direct early consequences of the fetus being reprogrammed.

In the remainder of the interview, Andrew Pospisilik shares ideas about how knowledge of epigenetics can help treat diseases like cancer. Based on his experience to this point, he thinks that

Epigenetics is probably one-third of the puzzle that causes a person’s specific disease, but is relatively understudied. Understanding this black-box is important; it could open the door to new epigenetic therapies. By enabling precision diagnosis, we will know why one person with type 2 diabetes will respond to one medication but the next person might not. Also, because many epigenetic processes are believed to be generated very early in life, scientists could measure biomarkers at birth to see what epigenetic risk a person has for a disease.

With his colleague Peter Jones, Pospisilik shares his opinion that the Van Andel Institute has a “world-class, forward-thinking faculty and scientific cores who are most interested in publishing great science.” Will the great science of the 21st century abandon Neo-Darwinism and focus on epigenetics?

This article is exciting because it appears to support ICR’s current research program on Continuous Environmental Tracking (CET) as a model for adaptation (see this lead article from ICR with links to detailed explanations). Epigenetic matching of the genome to environmental constraints is very different from Neo-Darwinism, because it locates adaptation internally instead of externally. ICR’s “engineering-based biological model” rids biology of the mystical notion of a personified natural “Selector” that picks winners and losers by chance, and puts the design into the foresight and programming skill of the designing intelligence.

This is a good introduction into the significance of epigenetics.

Another advocate of epigenetics as a purpose-driven alternative to Darwinism is Dr Thomas Woodward, founder of the C.S. Lewis Society at Trinity College of Tampa, Florida. His book with Dr James P Gills, The Mysterious Epigenome: What Lies Beyond DNA (2011) introduced readers to the factors that tune the genome for the organism’s health and success. This new article at The Scientist by secular geneticists supports the contention of the book that epigenomics would overtake genomics as a flourishing avenue toward understanding biology in the coming years.

No one yet knows the extent to which epigenetics can account for adaptation. I suspect, though, that this “engineering-based approach” to phenotypic plasticity and variability within species up to the family taxonomic level will prove fruitful, much more so than the current reliance on the Stuff Happens Law of natural selection, which relies on sheer dumb luck.




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