Do Epigenetic Changes Become Hard-Coded?

On April 22 2017, Jonathan McLatchie was kind enough to host me on his Apologetics Academy video livecast. We enjoyed a lively discussion about Evolution 2.0.

Generally, Jonathan and his audience were skeptical of macro-evolution and common descent. We discussed what Intelligent Design is, and what it is not; and how ID relates to evolution. I insisted that macro-evolution demands a higher view of God… a God that does not have to keep coming back and introducing new life forms on earth.

As I say in Evolution 2.0: “Darwinists underestimate nature. Creationists underestimate God.”

Midway through the show, a caller asked about epigenetics.

Layman’s explanation of epigenetics from Evolution 2.0:

In the Dutch famine of 1944 during World War II, thousands of unborn children experienced harsh deprivation, which resulted in unexpected changes. Not only were the children who were in utero during the famine smaller; when these children grew up and had children, their children were also smaller than average. Over their lifetime, the children of the famine experienced far-above-average rates of obesity, type 2 diabetes, cardiovascular problems, and other diseases related to an unhealthy body weight.

This data suggests that the famine experienced by the mothers triggered epigenetic changes that were inherited by the next generation.

Epigenetics doesn’t just alter the metabolism of children conceived in times of famine, though. It controls the expression of every cell in your body. The reason you have hair on the top of your head and not your forehead is because epigenetic factors control the expression of hair differently in different areas of your skin. It’s also the reason identical twins with identical DNA can still have different allergies, intelligence, aptitudes, and even different inherited diseases.

Epigenetics is blade #3 of the Evolution 2.0 Swiss Army Knife. It’s a switch that “grays out” genes, altering DNA’s function without changing the DNA sequence itself. It produces different cell types in fetal development; it alters tissues based on the external environment, and passes learned traits to offspring.

I suggested to her that it may be possible for epigenetic changes to become hard-coded into the genome over time, so that temporary adaptations become permanent. She challenged me on this. I promised to get back to her. Here’s what I found.

First, some further explanation of epigenetics, from Evolution 2.0:

I can take a sentence and make it say the opposite of what it said before, just by selectively “graying out” words and phrases:

Flight 6429 was delayed from Chicago to Winnipeg so it will not be departing before 6:45 P.M.

Flight 6429 was delayed from Chicago to Winnipeg so it will not be departing before 6:45 P.M.

(“Flight 6429 was from Winnipeg.”)
Flight 6429 was delayed from Chicago to Winnipeg so it will not be

departing before 6:45 P.M. 
(“Flight 29 to Winnipeg will depart before 6.”)

This illustrates how Epigenetics works—by “graying out” DNA sequences and making them silent. The mechanism that grays out the code is called methylation.

So… can this temporary graying-out of genes (which happens all the time, in response to external threats – things like callouses, temperature swings and a thousand other things) become hard-coded and permanent? Is epigenetics a powerful force for long-term evolution?

From correspondence with James Shapiro of the University of Chicago:

You are describing the fascinating but mysterious phenomenon discovered by Waddington known as “genetic assimilation.” Waddington treated Drosophila embryos to induce epigenetic changes producing flies with two pairs of wings (Bithorax).

After doing this for a few generations and mating the phenotypically altered flies, he discovered he no longer needed to treat the embryos. They had acquired Bithorax mutations in their genomes!

I’m not sure this has been replicated, and I’m not aware whether the mutations were ever subjected to detailed analysis. Nonetheless, Waddington’s observations have been widely cited and gained broad credibility from his status as the father of modern epigenetics.

Epigenetics is the interface between the organism and its environment.

See Shapiro’s 2011 book Evolution: A View from the 21st Century for a broader explanation of how cells rewrite their genomes in response to a dynamically changing environment.

From Epigenetic Inheritance: A Contributor to Species Differentiation?

…how extensive, and how stable, is the information carried in the germline by the epigenome? Several known examples of epigenetic inheritance demonstrate that it has the ability to create selectable traits, and thus to mediate Darwinian evolution. Here we discuss the possibility that epigenetic inheritance is responsible for some stable characteristics of species…

From Transgenerational Epigenetics by Trygve Tollefsbol:

Differentially expressed versions of a single allele have the potential to create an undetermined assortment of phenotypic novelties. Moreover, this increased phenotypic variation, observed within only a few generations, has the potential to play an important role in long-term evolutionary change, accelerating population divergence and driving speciation.

Methods for incorporating the parameterization of epiallelic instability in order to accurately reflect the variability of germline epigenetic modifications have no been established. These theoretical models have revealed how transgenerational epigenetic inheritance has the potential to profoundly affect usual evolutionary trajectories and result in elevated levels of phenotypic variation that would otherwise be unaccounted for under a standard population-genetic model. It has therefore been proposed that the Mendelian model requires amending in order to accommodate the transmission of “soft inheritance” alongside traditional genetic inheritance.

Although DNA methylation has been the focus of most of this research, many stably inherited epigenetic variants are believed to be caused by small RNAs, or perhaps a combination of different interacting epigenetic mechanisms. These data suggest that the composition or level of RNA in germ cells or associated cells could lead to a partial retention of epigenetic states down generations – through a combination of transmission stability and maternal effects…

From Epigenetics and Evolution by Mendizabal, Keller, Zeng and Soojin

The epigenome constitutes the interface between an organisms’ genome and its environment. Environmental factors such as chemicals, nutritional factors, or pathogens can alter the epigenetic landscape. A well-known example is how nutrition can determine the caste system in honey bees (Kucharski et al. 2008)

From: Friend or Foe: Epigenetic Regulation of Retrotransposons in Mammalian Oogenesis and Early Development by Alexei Evsikov, Caralina Marín de Evsikova

Bridging the realms of genetics and epigenetics, transposons are genetic elements regulated by epigenetic factors at biochemical and molecular levels.

TEs [Transposable Elements, discovered by Barbara McClintock] bridge genetic and epigenetic landscapes because TEs are genetic elements whose silencing and de-repression are regulated by epigenetic mechanisms that are sensitive to environmental factors. Ultimately, transposition events can change size, content, and function of mammalian genomes. Thus, TEs act beyond mutagenic agents reshuffling the genomes, and epigenetic regulation of TEs may act as a proximate mechanism by which evolutionary forces increase a species’ hidden reserve of epigenetic and phenotypic variability facilitating the adaptation of genomes to their environment.

…in mammalian genomes, experimental evidence supports epigenetic regulation of transposons as being critical to initiate synchronous, temporal expression of genes in germline, early embryos, and stem cells…

…living organisms developed and continue reinventing mechanisms for TE silencing, mostly via epigenetic mechanisms, which spares removal of TE loci from their genome…

TRANSLATION: Epigenetics gives an organism an ability to switch on a reserve of hidden programmed responses. Transposable Elements change the expression of genes and closely interact with epigenetic changes to coordinate adaptations to a constantly changing environment. Epigenetic switches can silence TEs and alter gene expression.

From Epigenetic Inheritance and Its Role in Evolutionary Biology: Re-Evaluation and New Perspectives by Warren Burggren:

In a few more extreme, yet illustrative examples, epigenetically-inherited phenotypes caused by RNA interference persist across as many as 50 generations in Caenorhabditis elegans [34,58,110,111]. In the plant toadflax, epigenetically-inherited phenotypes are said to persist across possibly hundreds of generations [59]. Thus, the mere persistence of a modified phenotype across as many generations as most investigators have the patience to wait for is in and of itself insufficient evidence for the fixation of epigenetically-modified traits into the genome. Yet, there is evidence and theoretical arguments for both the direct and indirect involvement of epigenetics altering the genome, as will now be considered.

Confounding the determination of the role of epigenetics in evolution and speciation is the key question of whether epigenetically-acquired phenotypic traits themselves can actually become fixed intact, i.e. permanently added to the genome, as opposed to having the markers that generate them have indirect influence on the subsequent genome through genome destabilization, mutation, natural selection or other mechanisms. Mechanisms by which this might occur are emerging, but evidence remains somewhat circumstantial [4,19,27,119].

Importantly, it is not required for the epigenetically-inherited phenotype to become fixed into the genotype to affect the evolution of traits.

TRANSLATION: Epigenetic changes can extend 50-100+ generations without becoming hard-coded into the genome! This doesn’t mean the hard coding doesn’t ever happen, and there are both anecdotal indications and mathematical models to suggest it does. In any case, epigenetic factors undoubtedly affect long-term evolution.

I very commonly find that Intelligent Design advocates have a knee-jerk reaction against the power of epigenetics, transposition, symbiogenesis etc to produce large scale changes.

This opposition puzzles me. Why? Because the capabilities of such mechanisms do not, per se, undercut the general ID proposition that there is ultimate intelligence involved. But intelligence is found in the cells themselves and this makes the entire question vastly more interesting. It makes it possible for natural forms of id (lower case i, lower case d) to offer testable hypotheses that can be scientifically verified.

It seems ID people are looking for the hand of God in differences between species. But the ability for organisms to engineer new species in response to their environment is far more impressive than a God who has to repeatedly inject new forms of life into the earth.

So… given how limited our models of these systems presently are, we can only benefit by giving each adaptive process the benefit of the doubt and studying how it works – as evidenced by the fact that this very question stands at the bleeding edge of current scientific knowledge. Seeing how it took me many hours to compile just the information you see here, there is much productive work to be done.

Instead of opposing evolution scientists, why not join in and help?

ID advocates, I invite you to stop standing skeptically with your arms crossed. Instead, delve into these fascinating topics of research. In them you will find the mysteries of life.

7 Responses

  1. Jon Perry says:

    Perry, along those lines, check out this overview of “genetic capacitance” by Joanna Masel. She is an excellent teacher of a very complex concept:

    FYI, I will eventually get our podcast up. I’ve been overwhelmed with other projects.

  2. Kim Otten says:

    This information is very interesting. Thank you for sharing it! And from a purely scientific viewpoint it easily explains the Biblical account of an evolution of each species into the enormous varieties of each species we see today over a relatively short time period.

    However on that same scientific front, I fail to see any evidence pointing to an evolution between species. What am I missing from your perspective?

    On a more Biblical perspective, one thing I think you might be missing is the rationale God had for requiring a male AND female of each species be put on the ark? Why do that if all of life could simply start over without anything more than Noah himself, (and why involve a man at all if some simple, single life form that could possibly even have survived the world-wide flood?)

    And why did Christ Himself refer to the same when He said…
    “Haven’t you read,” He replied, “that at the beginning the Creator ‘made them male and female,'” Matthew 19:5

    Again, I don’t see a conflict between what science is discovering and what the Bible has already told us. And I’m not sure why you’re prone to stretching it beyond that?

    • Tom Godfrey says:

      While healthy skepticism can be a good thing, I like Perry’s call “[to] delve into these fascinating topics of research.” He also said, “It seems ID people are looking for the hand of God in differences between species. But the ability for organisms to engineer new species in response to their environment is far more impressive than a God who has to repeatedly inject new forms of life into the earth.” Whether ID people are actually “looking for the hand of God” or just evidence of intelligent design in nature, people who answer Perry’ call to further study may be wise to ignore his suggestion (or maybe even straw man) that ID people believe in “a God who has to repeatedly inject new forms of life into the earth.” Whatever the mechanical details of “the ability for organisms to engineer new species” may be, it can still be an excellent candidate for an ID (capital letters) argument. Cells have no legitimate claim to credit for their own intelligence any more than a human genius does.

      Some of us believe that the intelligence behind the original designs in this case is ultimately God’s. We also believe that his work of creation was finished in just six days, but changes within each kind remained possible. It might be helpful in later discussion of this topic to clarify what this means. Near the beginning of this article, Perry said, “Generally, Jonathan and his audience were skeptical of macro-evolution and common descent.” Some readers may gather that evidence from a study of epigenetics ought to justify eliminating the skepticism. While observation of “organisms engineering new species” may be helpful in building a case for macro-evolution and common descent, it is certainly far from sufficient. I dare say that most creationists understand macro-evolution to refer to kinds of evolution never observed in nature, for example, a dinosaur evolving into a bird, while any other kind of evolution is generally uncontroversial. Common descent goes far beyond macro-evolution to posit a single life form ancestral to every fossil or observed life form that ever existed. Considering how poorly common descent is documented in the fossil record and how slowly some life forms evolve according to evolutionists, the idea that epigenetic evidence ought to eliminate skepticism about common descent seems particularly unwarranted.

      People who like Perry’s take on this topic should also think seriously about his claim, “Creationists underestimate God,” evidently based at least partly on his opinion that God’s work would be “far more impressive” if he gave primordial cells an ability to engineer the entire tree of life, given billions of years to evolve, than if he finished creation of lots of kinds of plants and animals in only six days, giving them an ability to adapt only within their kinds. At least for some of us, opinions about how impressive some feat may be are entirely irrelevant. What matters to us is what God claims he actually did, so we are far more concerned about underestimating the importance of God’s word, including the history of our origins as reported in Genesis.

    • Perry Marshall says: Follow the various links. You can reliably generate new species if you know what to do.

  3. Abed Peerally says:

    Very interesting scientific and philosophical input about evolution in relation to supernatural creation. This viewpoint is the very essence of my recently published book “In search of consciousness and the Theory of Everything” as ebook, soft and hardcover. I have deliberately published this first part of my trilogy to explain precisely the kind of philosophy and science insinuated in the above input on epigenetics. However my trilogy will focus on the same philosophy but based on cosmology and the theory of everything. The whole context is of enormous importance, intellectually, to humanity and needs to be progressively presented. Clearly ID is an oversimplification of a supernatural science that does not present God as a supernatural human administrator.

  4. Tomi Aalto says:

    ‘Evolution’ has a direction – Inevitable Degradation

    Changes in organisms are based on epigenetic mechanisms or loss of biological information

    Textbooks say that evolution is an inevitable natural process that has no direction. According to the theory of evolution, small random changes are naturally selected in a population for better survival fitness. Does this theory have anything to do with observed science? Absolutely not. Let’s find out the most significant reasons, why the theory of evolution is a pseudoscientific theory.

    1. Human genome is rapidly deteriorating. There are 203,885 disease-causing genomic mutations in the human genome at population level. The number is rapidly getting higher. About 10% of people are living with a genetic disease. One in five ‘healthy’ adults may carry disease-related genetic mutations. Scientists are in a hurry to develop gene editing architectures, like CRISPR etc. Human Y-chromosome is rapidly losing genetic material. The number of SNPs is correlated with a loss of genes. For example, the Icelanders have lost 1,171 genes. There are over 20 million SNPs in their genome. Modern science is not aware of beneficial random mutations.

    2. Rapid genetic degradation is a scientific fact within other mammals too. A good example is the Canidae lineage. The more adaptation and variation, the more organisms experience genetic degradation. The Red Fox has 1,500 protein coding genes less than the Bat Eared Fox or a dog. The lifespan of the Red Fox is only 2-4 years in the wild. It’s susceptible to several diseases. The decreasing number of chromosomes within mammals is associated with faulty and lost genes.

    Bat-eared fox 72 chromosomes lifespan 13-15 years
    Gray Fox 66 chromosomes lifespan 6-8 years
    Fennec Fox 64 chromosomes lifespan 8-10 years
    Bengal Fox 60 chromosomes lifespan 6-8 years
    Kit Fox 50 chromosomes lifespan 5.5 years
    Tibetan sand fox 36 chromosomes lifespan 6-10 years
    Red Fox 34 chromosomes lifespan 2-4 years

    3. Bacteria are also rapidly losing genetic material despite their ability to transfer genes between each other. Gene loss results in robust parasitic or pathogenic bacteria or highly specialized harmful bacteria. This same phenomenon can be observed all over nature. Loss of biological information leads to negative consequences within organisms.

    4. Changes in organisms are based on epigenetic mechanisms directed by diet type, climate, stress, toxicants etc. Traits are not determined by gene sequences. Genes are no drivers or controllers. Alterations in epigenetic information patterns typically result in genetic errors. Aberrant methylation patterns are the most significant reason for genetic degradation. We can slow down the genetic degradation but we can’t stop it from happening. It’s an inevitable fact that there is only one direction in nature. A dead end. Evolution has never been observed because there are no mechanisms that could increase biological information leading to increase in functional or structural complexity. That’s why creation and design. Don’t get lost.

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