Talk Beliefs Interview II

Intro

This is an audio-visual version of my blog about what I consider to be slam-dunk evidence for common descent,









and the fact that you, me and Charlie the chimp are all cousins.










This is not an attack on God.






I don't care whether you believe in God or not, but I think we should all live in the real world, and evolution is as real as anything.

How do I know? There are markers, a bit like digital watermarks embedded in computer files, authenticating the fact that species descend from common ancestors.

These "watermarks" have been put in the genomes of our common ancestors by viruses.

But let's step back for a moment and look at the history of the discovery of viruses.

First off, how do we know there are viruses?

Let's start with cell theory.

Cell theory is the theory that all living organisms are either single cells or are composed of multiple cells. *  The discovery of cells is largely attributed to Robert Hooke in the 17th century, and came about with the development of microscopes powerful enough to image cells. This is is Hooke's microscope.

Before the discovery of viruses, it was believed that bacteria or other cellular organisms were the only disease causing agents. In the late 19th century, microscopes were still not able to resolve what came to be known as viral agents, but two researchers, Ivanovski and Beijerinck, showed that certain diseases could not be caused by cellular pathogens. They proved this by filtering infected material through ceramic filters - too fine to allow cells to pass through, and showing that it still contained an infectious agent. Beijerinck called the agent a "virus". 

(Electron micrograph of the rod-shaped particles of tobacco mosaic virus that are too small to be seen using a light microscope.) Are viruses alive? Much discussion goes on about whether viruses are living entities or not. Some say not, because they depend on living organisms. That doesn’t interest me. Too academic. After all, all animals and fungi are ultimately dependent on plant life. Viruses mutate and replicate, and aretherefore what Dawkins would call “evolvers”. Some of them actually prove (in the legal sense of “establish beyond any reasonable doubt”) that common descent and evolution are true. We will be coming to that soon. So what is a retrovirus? The co-called, (tongue-in-cheek) “Central Dogma” of molecular biology is that DNA makes RNA which then makes proteins. This means that the “recipe” for living creatures is written in DNA, which gets transcribed into RNA, and then translated into proteins, which make up most of the bodies of living organisms. The discovery of this is a wonderful example of the fact that science is not dogmatic. It adjusts itself (sometimes grudgingly, but always eventually) to accommodate new discoveries. It is not pushing an agenda, but merely trying to describe and explain reality. The discovery of _retro_viruses begins with the discovery of “reverse transcriptase”. This a substance (an enzyme) that “reads” RNA and produces DNA. Retroviruses have RNA genomes. They need to convert these genomes into DNA before inserting (integrating, in the jargon) their genomes into host cell DNA. The entire rationale of reverse transcriptase (and integrase and other retroviral genes that we will be coming to) is to enable viruses to induce host cells to replicate them. This is one of the key facts that anti-evolutionists who try to deny ERVs as evidence for common descent fail to explain. What else could they be for? What is an endogenous retrovirus? When a retrovirus integrates the DNA version of its genome into a germ-line cell (egg or sperm) it becomes heritable. Offspring produced by such cells, if the retroviral DNA is not lost in crossover, will appear in every single nuclear cell of the offspring, in exactly the same DNA locus every time. Such retroviral integrations are called endogenous - they have become part of the genome, and can be passed on down the generations. ERVs very rarely produce virions (viral particles) though. An organism with a fully functioning retroviral integration in every one of its cells would not survive, even if it could form in the first place. But reverse transcription (making DNA versions of RNA genomes) is a very error-prone process. The retroviral genomes of ERVs are overwhelmingly inactivated by reverse transcription errors, allowing the organisms that inherit them to form, survive and reproduce themselves. Although some components of some ERVs serve some useful, and sometimes even essential functions for their hosts, they cannot replicate themselves, and are thus not viable as retroviral insertions. What function they may have has been scavenged by evolution. Nobody knows at what stage in the evolution of life retroviruses started to come about. Their origins may go back to the RNA world and the emergence of DNA, but a retrovirus needs at least a single DNA-based host cell in order to induce it to replicate it. It doesn't need complex multi-cellular hosts. How was HIV identified as being a retrovirus? Endogenization - what is it? Integration “targeting” studied for chances of finding therapies. Integrase inhibitors. Endogenization as an explanation for common ERVs Do you think that ERVs are an example of “junk” DNA? Function in ERVs