The Epigenetics of Viruses

Does That Mean a "Living" Origin?

I. Introduction

Epigenetics is about doing things to genes (on/off) rather than about what genes do.

It can be more complicated than that when the subject of epigenetics includes genes in living entities compared with genes in non-living entities.

For example, if I ask you if DNA and/or RNA are alive your reaction illustrates the issue:

"We are involved in a project to incorporate innovative assessments within a reform-based large-lecture biochemistry course for nonmajors. We not only assessed misconceptions but purposefully changed instruction throughout the semester to confront student ideas. Our research questions targeted student conceptions of deoxyribonucleic acid (DNA) along with understanding in what ways classroom discussions/activities influence student conceptions. Data sources included pre-/post-assessments, semi-structured interviews, and student work on exams/assessments. We found that students held misconceptions about the chemical nature of DNA, with 63 % of students claiming that DNA is alive prior to instruction. The chemical nature of DNA is an important fundamental concept in science fields. We confronted this misconception throughout the semester collecting data from several instructional interventions. Case studies of individual students revealed how various instructional strategies/assessments allowed students to construct and demonstrate the scientifically accepted understanding of the chemical nature of DNA. However, the post-assessment exposed that 40 % of students still held misconceptions about DNA, indicating the persistent nature of this misconception. Implications for teaching and learning are discussed."

(Is DNA Alive?, Research in Science Education, Volume 43, Issue 4, Aug. 2013, pp.1361-1375, emphasis added; cf. Living things). Epigenetics in humans is a subject that includes acquired and/or learned behavior (see video below, and this).

II. Background

About a decade ago when Dredd Blog began to consider epigenetics, I wrote:

"Epigenetics is a main-stream scientific concept now (One Man's Junk Gene Is Another Man's Treasure Gene?, On The Origin of Genieology).

Historical epigenetic evidence is being sought and found in ancient specimens now..."

(On the Origin of Cultural Epigenetics). Studies at that time focused primarily on DNA, but "Recently, epigenetic modifications of RNA ... have gained increasing attention" (Epigenetics in Neurodevelopment). 

Epigenetics is becoming viral because, among other things the epigenetics of viruses is hosted in microbes:

"Viruses are not living things. Viruses are complicated assemblies of molecules, including proteins, nucleic acids, lipids, and carbohydrates, but on their own they can do nothing until they enter a living cell. Without cells, viruses would not be able to multiply. Therefore, viruses are not living things."

(Omicron (OMC!) - 2). The few genes in viruses, compared to their hosts, is worth considering, because unlike biotic creatures, abiotic viruses do not reproduce themselves or their RNA.

The concept of epigenetics is even better suited to RNA viruses because they are part of the pure epigenetic reality ("above genes").

The "epigenetics R us" applies to virus RNA more per capita (compared to human cells) because human cells do their own DNA replication, but RNA virus events of that sort are conducted by host microbes, not by the viruses themselves.

Epigenetic events that turn genes on and off are external to genes, and are done to us, not by us (The "It's In Your Genes" Myth, 2, 3). 

III. Appendices

In previous posts on Dredd Blog the SARS-CoV-2 genetic database material in GenBank has been featured (Omicron (OMC!), 2, 3).

It is not always easy to present that vast expanse of data in blog posts, so today I am trying again by presenting additional appendices.

See them in the following links: Countries With SARS-CoV-2 and/or Omicron Virus Patterns (AC, DF, GI, JL, MO, PR, ST, UZ),  Patterns of SARS-Cov-2 and/or Omicron explained (0-76, 77-153, 154-230, 231-307, 308-383), and Pattern Change Percentages.

In the Dredd Blog epigenetic database there are 337,154 rows of SARS-CoV-2 data, including 'patterns' of epigeneic and/or damage-caused changes to the SARS-CoV-2 virus genomes (as of early December 2021).

These data are from a very, very narrow span of time because that is the span of time since SARS-CoV-2 was discovered (December 30, 2019 to December 9, 2021).

I mean "very, very narrow" in the sense that millions of years of virus change has taken place:

"The modern ribosome was largely formed at the time of the last common ancestor, LUCA. Hence its earliest origins likely lie in the RNA world. "

(On the Origin of the Genes of Viruses - 2). Ribosomes are molecular machines inside single celled microbes which take part in the replication of SARS-CoV-2 viruses.

Anyway, the appendices include: 1) virus pattern information by country of origin, 2) a list of 483 virus patterns and a list of what those individual pattern characters ('=', '>', and '<') mean in each virus.

The way to use the appendices is to look up a country in the alphabetized list (AC ... UZ) based on the country's name, then look up the virus change documentation in the numerical appendix list based on the virus number (0-76 ... 308-383).

For example, if the country name starts with a 'B' (look in the 'AC' appendix) and has a virus number '207', look up the virus detail in the '154-230' appendix.

IV. Closing Comments

Will virologists try to explain the haphazard genetic changes in those appendices with 'magic words' or will they consider that the microbes hosting these viruses around the world are being damaged and destroyed with antibiotic chemicals? 

(Yes to magic words: "For a virus to evolve, it needs to develop a strategy to fuse itself with the cell membrane of the host and/or to induce host cell–cell fusion." link;  WTF ... "it NEEDS to ... DEVELOP A STRATEGY" ... without a brain, eyes, ears, laboratory ... how does that explain the haphazard percents of change?)

'Questions' in science are tools, not toys:

"And I've been making this argument forever and it doesn't seem to penetrate to some people that science is not a fantasy story. It's not a Harry Potter story about magical things that might be true. Science is about what you can verify—hypotheses that you can test and verify."

(Think About Nature). Accord: On The Origin of Genieology.

The video below features comments of professors from various universities and organizations that deal with the reality and impact of epigenetics.

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