Tuesday, April 1, 2014

On The Origin of the Genes of Viruses

Does That Mean a "Living" Origin?
Today, I begin a new series about the origin of genes of viruses.

Before anyone can track down the origin or source of something, there are fundamental prerequisites that should first be dealt with, for example, is what you are looking for dead, or to the contrary is it alive?

One would not get to the proper place if one was told that what they are looking for is not alive if in fact it is alive.

By the same token, one would not get to the proper place of origin if one was told that what they are looking for is alive if in fact it is not alive.

"Living" has criteria different from "non-living," so if we look into a very ancient grave while we are searching for a living person, in general we are off on a fool's errand, and consequently will reap a fool's reward.

So, before we begin the search for the origin of genes, we should ask "is a gene alive or is it a non-living entity?"

But, since this search also involves viruses, in the sense that when we ask "where will we find virus genes", we must also consider where we will find viruses.

That doesn't help much in the sense that the answer is "everywhere":
There are an estimated 1031 viruses on Earth. That is to say: there may be a hundred million times more viruses on Earth than there are stars in the universe. The majority of these viruses infect microbes, including bacteria, archaea, and microeukaryotes, all of which are vital players in the global fixation and cycling of key elements such as carbon, nitrogen, and phosphorus. These two facts combined—the sheer number of viruses and their intimate relationship with microbial life—suggest that viruses, too, play a critical role in the planet’s biosphere.
(Ecosystems & Microbes). Nor does it solve the initial inquiry if we ask "is a virus alive?" because in science that is still as controversial as "what is life?":
For about 100 years, the scientific community has repeatedly changed its collective mind over what viruses are. First seen as poisons, then as life-forms, then biological chemicals, viruses today are thought of as being in a gray area between living and nonliving: they cannot replicate on their own but can do so in truly living cells and can also affect the behavior of their hosts profoundly. The categorization of viruses as nonliving during much of the modern era of biological science has had an unintended consequence: it has led most researchers to ignore viruses in the study of evolution. Finally, however, scientists are beginning to appreciate viruses as fundamental players in the history of life.
(The Uncertain Gene - 9). We can, however, narrow the search by asking "are genes alive?" which would limit our search area:
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.
(The Uncertain Gene - 8, emphasis in original). Genetic material, including genes of course, is not alive (wait, wait, let me finish).

It is, instead, sophisticated molecular machinery which preceded carbon-based life forms:
“Our cells, and the cells of all organisms, are composed of molecular machines. These machines are built of component parts, each of which contributes a partial function or structural element to the machine. How such sophisticated, multi-component machines could evolve has been somewhat mysterious, and highly controversial.” Professor Lithgow said.
Many cellular processes are carried out by molecular ‘machines’ — assemblies of multiple differentiated proteins that physically interact to execute biological functions ... Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.
The most complex molecular machines are found within cells.
Writing in the journal PLoS Pathogens, the team from Queen Mary's School of Biological and Chemical Sciences show how they studied the molecular machine known as the 'type II bacterial secretion system', which is responsible for delivering potent toxins from bacteria such as enterotoxigenic E. coli and Vibrio cholerae into an infected individual.

Professor Richard Pickersgill, who led the research, said: "Bacterial secretion systems deliver disease causing toxins into host tissue. If we can understand how these machines work, then we can work out how it they might be stopped."
(Do Molecular Machines Deliver Toxins of Power?, emphasis in original). When those scientists mentioned that particular molecular machine nomenclature, I don't think that they were exactly ready for the verification which followed:
"We took this approach because so many RNAs are rapidly destroyed soon after they are made, and this makes them hard to detect," Pugh said. "So rather than look for the RNA product of transcription we looked for the 'initiation machine' that makes the RNA. This machine assembles RNA polymerase, which goes on to make RNA, which goes on to make a protein." Pugh added that he and Venters were stunned to find 160,000 of these "initiation machines," because humans only have about 30,000 genes. "This finding is even more remarkable, given that fewer than 10,000 of these machines actually were found right at the site of genes. Since most genes are turned off in cells, it is understandable why they are typically devoid of the initiation machinery."

The remaining 150,000 initiation machines -- those Pugh and Venters did not find right at genes -- remained somewhat mysterious. "These initiation machines that were not associated with genes were clearly active since they were making RNA and aligned with fragments of RNA discovered by other scientists," Pugh said. "In the early days, these fragments of RNA were generally dismissed as irrelevant ["junk"] since they did not code for proteins." Pugh added that it was easy to dismiss these fragments because they lacked a feature called polyadenylation -- a long string of genetic material, adenosine bases -- that protect the RNA from being destroyed. Pugh and Venters further validated their surprising findings by determining that these non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating that they have a specific origin and that their production is regulated, just like it is at coding genes.
(The Uncertain Gene - 3). So, in this search for the origin of the genes of viruses, we must look for "non-living viruses" which were active prior to the origin of carbon based life forms (see e.g. The Uncertain Gene - 9), that is, non-living viruses which were active subsequent to the origin of molecular machines.

That narrows it down some.

The next post in this series is here.

Evolutionists tell us, based on genetic analysis, that hominids in toto came from Africa ...

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