Daily Archives: November 21, 2022

October 10, 2022 | David F. Coppedge

Regulating existing genetic information is a way lifegains 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. Theres 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. Its called epigenetics, above the genes. Andrew Pospisilik is a founding member of the VAIs 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 histonesproteins that compact DNA into chromatinand 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 mutationsmistakes in the genes, whether from cosmic rays, copying errors or other undirected sourcesand 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 cells 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 organisms 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 persons 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 ICRs 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. ICRs 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 organisms 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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Epigenetics: Adaptation Without Darwinism CEH

Photo: Galpagos marine iguana, by Datune at English Wikipedia, Public domain, via Wikimedia Commons.

Editors note:We are delighted to present a new series by biologist Jonathan Wells asking, Is Darwinism a Theory in Crisis? This is the first post in the series, which is adapted from the recent book,The Comprehensive Guide to Science and Faith.Find the full series here.

What does it mean to say that a theory is in crisis? Its not enough to point out that a theory is inconsistent with evidence. Critics have been pointing out for decades that Darwinism doesnt fit the evidence from nature. Biologist Michael Denton publishedEvolution: A Theory is Crisis in1986.1Thirty years later, he drove the point home withEvolution: Still a Theory in Crisis.2

But Darwinism is still with us, for two reasons. First, Darwinism is not just a scientific hypothesis about specific phenomena in nature, like Newtons theory that the gravitational force between two bodies is inversely proportional to the square of the distance between them (17th century), Lavoisiers theory that things burn by combining with oxygen (18th century), or Maxwells theory that light is an electromagnetic wave (19th century). Darwin calledOn the Origin of Speciesone long argument, and a central part of it was atheologicalargument against the idea that species were specially created.3

Second, established scientific research programs such as Darwinism are never abandoned just because of some problems with the evidence. The idea that all species are descendants of one or a few common ancestors that have been modified by mutation and natural selection will maintain its dominance until large numbers of scientists embrace a competing idea. Currently, the major competing idea is intelligent design (ID), which maintains (contra Darwin) that some features of living things are better explained by an intelligent cause than by unguided natural processes. The shift, if and when it happens, will be a major scientific revolution. One way to approach this phenomenon is through philosopher of science Thomas Kuhns 1962 bookThe Structure of Scientific Revolutions.4

I will begin by summarizing some of Kuhns key insights. I will then apply those insights to the present conflict between Darwinism and intelligent design. As I do so, I point out some problematic aspects of Kuhns work, but I conclude that recent events fully justify calling Darwinism a theory in crisis.

According to Kuhn, normal science is research firmly based upon one or more past scientific achievements, achievements that some particular scientific community acknowledges for a time as supplying the foundation for its further practice. Those achievements were sufficiently unprecedented to attract an enduring group of adherents away from competing modes of scientific activity. They were also sufficiently open-ended to leave all sorts of problems to be solved. Kuhn called achievements that share these two characteristics paradigms.5

Once a paradigm becomes dominant, the normal practice of science is simply to solve problems within that paradigm. In the process, an institutional constellation forms that includes the formation of specialized journals, the foundation of specialist societies, and the claim for a special place in the curriculum.6The last is very important, because one characteristic of the professional scientific community [is] the nature of its educational initiation. In the contemporary natural sciencesthe student relies mainly on textbooks until the third or fourth year of graduate work, at which point the student begins to do independent research. It is a narrow and rigid education, probably more so than any other except perhaps in orthodox theology.7

Kuhn wrote,

No part of the aim of normal science is to call forth new sorts of phenomena; indeed, those that will not fit the box are often not seen at all. Nor do scientists normally aim to invent new theories, and they are often intolerant of those invented by others.8

Yet no paradigm that provides a basis for scientific research ever completely resolves all its problems. When anomalous evidence emerges, however, scientists first line of defense is usually to devise numerous articulations andad hoc modifications of their theory in order to eliminate any apparent conflict. They never simply renounce the paradigm unless another is available to take its place. Thus the decision to reject one paradigm is always simultaneously the decision to accept another, and the judgment leading to that decision involves the comparison of both paradigms with natureandwith each other.9

The most effective claim that proponents of a new paradigm can make is that they can solve the problems that have led the old one to a crisis.10Even then, Kuhn wrote,

The defenders of traditional theory and procedure can almost always point to problems that its new rival has not solved but that for their view are no problems at allInstead, the issue is which paradigm should in the future guide research on problems many of which neither competitor can yet claim to resolve completely. A decision between alternate ways of practicing science is called for, and in the circumstances that decision must be based less on past achievement than on future promise.11

How does a new paradigm originate? Kuhn wrote,

Any new interpretation of nature, whether a discovery or a theory, emerges first in the mind of one or a few individuals. It is they who first learn to see science and the world differently, and their ability to make the transition is facilitated by two circumstances that are not common to most other members of their profession.12

First, Kuhn wrote, their attention has been concentrated upon the crisis-provoking problems. Second, these individuals are usually so young or so new to the crisis-ridden field that practice has committed them less deeply than most of their contemporaries to the world view and rules determined by the old paradigm.13

According to Kuhn,

Paradigms differ in more than substance, for they are directed not only to nature but also back upon the science that produced them. They are the source of the methods, problem-field, and standards of solution accepted by any mature scientific community at any given time. As a result, the reception of a new paradigm often necessitates a redefinition of the corresponding science.14

Next, Theory in Crisis? Redefining Science.

See the original post here:

Is Darwinism a Theory in Crisis? | Evolution News