Thursday, April 3, 2014

On the Origin of the Genes of Viruses - 3

RNA & DNA: post-carbon
This series is an unusual one in the sense of daily sequential posts.

Usually, I mix different subjects from day to day, one day it is politics, another day it is climate change, another day some evolution, and so on.

Anyway, in today's post I have to present my hypothesis again.

It has to do with why there is confusion among scientific researchers and teachers about which came first viruses or cells, which came first RNA or DNA, and which came first abiotic evolution or biotic evolution (The Uncertain Gene - 9).

These and related matters incessantly come up when discussing "the evolution of life" --especially when there is no consensus as to what "life" is.

I attribute seven sources to this confusion, which will be discussed today, to wit:
1) interdisciplinary walls
2) teleology
3) carbon ignorance
4) quantum uncertainty
5) evolution from simple to complex
6) virus ignorance
7) propaganda via evangelism
So, let's go through the list as we look at some examples in papers and in Dredd Blog System posts to show how egregious and ubiquitous the problem is.

I. Interdisciplinary Walls

This is an old and persistent problem within the biological sciences as shown by what is called the great synthesis (and a few other names I won't mention):
The modern synthesis solved difficulties and confusions caused by the specialisation and poor communication between biologists in the early years of the 20th century.
(Wikipedia, "Modern evolutionary synthesis", emphasis added). I have pointed out that particular problem time and again (The Uncertain Gene - 2).

Any wall between disciplines is also a problem in the struggle to fabricate a scientific subject-matter nomenclature that is stable enough to cross over boundaries, for example, boundaries between quantum physics and evolutionary biology (If Cosmology Is "Off," How Can Biology Be "On?").

II. Teleology

The teleology discipline is a study of the use of magic language in scientific papers and discourse (The Uncertain Gene - 3).

The use of the word "selfish" when applied to scientific discussions of machinery, i.e. genes, is an example of teleological language which is not professional, because it is not useful (machines are not selfish or unselfish - duh!).

Nevertheless, this magic language continues unabated even with competent scientists (see propaganda via evangelism below), and is also used even in otherwise competent papers:
Under this concept, the principal lineages of viruses and related selfish agents emerged from the primordial pool of primitive genetic elements, the ancestors of both cellular and viral genes. Thus, notwithstanding the numerous gene exchanges and acquisitions attributed to later stages of evolution, most, if not all, modern viruses and other selfish agents are inferred to descend from elements that belonged to the primordial genetic pool.
(Koonin 2006, emphasis added). No, genes are not alive, not selfish, they are molecular machine parts, that is, they are parts in RNA and DNA molecular machines, which are not alive (The Uncertain Gene - 8).

Regular readers know that Dredd Blog provides an example of a more professional use of nomenclature by using the phrase "the uncertain gene."

That is an exacting nomenclature in the context of quantum mechanical proton tunneling as well as its direct impact on genes (see The Uncertain Gene).

III. Carbon Ignorance

By "ignorance" I mean ignoring the established scientific consensus that carbon evolved within stars after stars evolved then went nova, or otherwise ejected their carbon into space.

After carbon was ejected into space it eventually, in some locations in the cosmos, became parts of the molecules of carbon-based life forms.

Until carbon arrived, the chemical structure of pre-RNA would not have contained carbon, so in future posts that will be discussed, because pre-carbon-RNA would be different from post-carbon-RNA.

IV. Quantum Uncertainty

The RNA molecule, with its many genes, can evolve through mutation without any carbon existing, i.e. without the existence of carbon-based life forms.

One way that could take place was pointed out in the first post of the series:
"In this paper we have pointed out that, since the protons are not classical particles but "wave packets" obeying the laws of modern quantum theory, the genetic code cannot --in spite of all precautions-- be 100% stable. Due to the quantum-mechanical "tunnel effect," there is always a small but finite probability that the protons will change place, alter the genetic code, and give rise to mutations.
(The Uncertain Gene). This can happen to DNA or to RNA, however, RNA was exposed to quantum proton tunneling before DNA was, assuming RNA evolved first of course.

V. Evolution From Simple To Complex

Notice again the graphic of RNA and DNA at the top of the post.

Look at the RNA genetic molecular machine system, and then look at the DNA genetic molecular machine system, and it is readily apparent that the RNA molecule is less complex and simpler than the DNA.

This is another reason to expect or assume that RNA was going through genetic evolution prior to DNA.

VI. Virus Ignorance

Again, what I mean by "ignorance" is our ignoring of viruses because they were defined as not alive, not living, and not a carbon-based life form.

Now, we find out that they are by very, very far the greatest population of entities that contain RNA or DNA:
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.
(On the Origin of the Genes of Viruses). It is a no-brainer to realize that it is about a hundred years late that we now begin to study them in earnest:
Now, with the recent discovery of a truly monstrous virus, scientists are again casting about for how best to characterize these spectral life-forms. The new virus, officially known as Mimivirus (because it mimics a bacterium), is a creature "so bizarre," as The London Telegraph described it, "and unlike anything else seen by scientists . . . that . . . it could qualify for a new domain in the tree of life." Indeed, Mimivirus is so much more genetically complex than all previously known viruses, not to mention a number of bacteria,that it seems to call for a dramatic redrawing of the tree of life.

"This thing shows that some viruses are organisms that have an ancestor that was much more complex than they are now," says Didier Raoult, one of the leaders of the research team at the Mediterranean University in Marseille, France, that identified the virus. "We have a lot of evidence with Mimivirus that the virus phylum is at least as old as the other branches of life and that viruses were involved very early on in the evolutionary emergence of life."

That represents a radical change in thinking about life's origins: Viruses, long thought to be biology's hitchhikers, turn out to have been biology's formative force.

This is striking news, especially at a moment when the basic facts of origins and evolution seem to have fallen under a shroud. In the discussions of intelligent design, one hears a yearning for an old-fashioned creation story, in which some singular, inchoate entity stepped in to give rise to complex life-forms—humans in particular. Now the viruses appear to present a creation story of their own: a stirring, topsy-turvy, and decidedly unintelligent design wherein life arose more by reckless accident than original intent, through an accumulation of genetic accounting errors committed by hordes of mindless, microscopic replication machines. Our descent from apes is the least of it. With the discovery of Mimi, scientists are close to ascribing to viruses the last role that anyone would have conceived for them: that of life's prime mover.
(Unintelligent Design, Discover). Yes, we have formulated our theories of genetic mutation and other evolutionary concepts without seriously considering what is  by very far the greatest population of entities that contain genes.

VII. Propaganda via Evangelism

Bloviating about "selfish genes" for decade upon decade, as if genes were not molecular abiotic entities, as if genes were alive, is not at all laudable.

What is shameful is the hateful rhetoric and propaganda spewed by teleological evangelists who have now made it into several books about the origin of assholes (On The Origin of Assholes).


So, I move on in this series, noting that there is some debate as to whether or not the RNA world preceded the DNA world, and whether the form of the first genetic evolution took place because of viruses or instead because of cells.

For example, consider:
The “RNA world” hypothesis, first promoted in 1986 in a paper in the journal Nature and defended and elaborated on for more than 25 years, posits that the first stages of molecular evolution involved RNA and not proteins, and that proteins (and DNA) emerged later ... “I’m convinced that the RNA world (hypothesis) is not correct,” Caetano-Anollés said. “That world of nucleic acids could not have existed if not tethered to proteins.”
“This is a very engaging and provocative article by one of the most innovative and productive researchers in the field of protein evolution,” said University of California at San Diego research professor Russell Doolittle, who was not involved in the study. Doolittle remains puzzled, however, by “the notion that some early proteins were made before the evolution of the ribosome as a protein-manufacturing system.” He wondered how – if proteins were more ancient than the ribosomal machinery that today produces most of them –“the amino acid sequences of those early proteins were ‘remembered’ and incorporated into the new system.”

Caetano-Anollés agreed that this is “a central, foundational question” that must be answered.

“It requires understanding the boundaries of emergent biological functions during the very early stages of protein evolution,” he said. However, he said, “the proteins that catalyze non-ribosomal protein synthesis – a complex and apparently universal assembly-line process of the cell that does not involve RNA molecules and can still retain high levels of specificity – are more ancient than ribosomal proteins. It is therefore likely that the ribosomes were not the first biological machines to synthesize proteins.”
(Study of ribosome evolution challenges RNA world hypothesis). Caetano-Anollés does not seem to realize that ribosomes, like everything else,  evolved from simple to complex.

Which means that ribosomes which today process molecules with carbon in them (DNA) had to evolve after carbon had evolved.

Thus, pre-ribosomes that process pre-carbon RNA and had no carbon molecules to work with, are the likely candidate ribosomes to have evolved first, and to have been more simple.

Finally, ribosomes that process both RNA and DNA are still that way today ("Ribosomes from bacteria, archaea and eukaryotes ... differ in their size, sequence, structure, and the ratio of protein to RNA") as was mentioned in the previous post of this series (On the Origin of the Genes of Viruses - 2).

That will be the focus of the next post in this series: the evolution of ribosomes.

The next post in this series is here, the previous post in this series is here.

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