Friday, March 20, 2015

On the Origin of the Genes of Viruses - 13

Emergence all at once?
All my carping about the dearth of scientific papers concerning evolutionary abiology may have paid off.

A paper recently published, in a peer reviewed setting, addresses some of the issues I have wondered about.

But, as I explain below, it does not do so in a way I would have preferred.

Basically, I have considered the hypotheses and theories of evolution to contemplate a dynamic proceeding from simple to complex, as have others (From Simple To Complex, The Scientist).

But this paper I mentioned, and quote from below, urges a spontaneity whereby several steps are taken at the same time, in different places, and ostensibly in different species:
A minimal cell can be thought of as comprising informational, compartment-forming and metabolic subsystems. To imagine the abiotic assembly of such an overall system, however, places great demands on hypothetical prebiotic chemistry. The perceived differences and incompatibilities between these subsystems have led to the widely held assumption that one or other subsystem must have preceded the others. [from simple to complex] Here we experimentally investigate the validity of this assumption by examining the assembly of various biomolecular building blocks from prebiotically plausible intermediates and one-carbon feedstock molecules. We show that precursors of ribonucleotides, amino acids and lipids can all be derived by the reductive homologation of ​hydrogen cyanide and some of its derivatives, and thus that all the cellular subsystems could have arisen simultaneously through common chemistry. The key reaction steps are driven by ultraviolet light, use ​hydrogen sulfide as the reductant and can be accelerated by Cu(I)–Cu(II) photoredox cycling.
(Phys Org, cf Nature - Chemistry, emphasis added). Why these researchers avoided the discussion of viruses is another diversion from simple to complex.

Ignorance of the microbial realm, and even more so of the realm of abiotic viruses ("viruses are not alive") has previously been pointed out in this series:
Recent advances in genomics of viruses and cellular life forms have greatly stimulated interest in the origins and evolution of viruses and, for the first time, offer an opportunity for a data-driven exploration of the deepest roots of viruses. Here we briefly review the current views of virus evolution and propose a new, coherent scenario that appears to be best compatible with comparative-genomic data and is naturally linked to models of cellular evolution that, from independent considerations, seem to be the most parsimonious among the existing ones.
The existence of several genes that are central to virus replication and structure, are shared by a broad variety of viruses but are missing from cellular genomes (virus hallmark genes) suggests the model of an ancient virus world, a flow of virus-specific genes ... existence of a complex, precellular, compartmentalized but extensively mixing and recombining pool of genes ...
(On the Origin of the Genes of Viruses - 2, quoting Koonin, et al.). In that same post I pointed out that the molecular machines, at work in the genetic realm, are so complex together, that instant karma emergence is less likely than simple to complex emergence is:
"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.
(ibid, emphasis in original). I am constantly amazed at the reluctance of some scientists, and some scientific writers, to go with the flow.

For example, let's review the Dredd Blog post about the mythical primordial soup:
For 80 years it has been accepted that early life began in a 'primordial soup' of organic molecules before evolving out of the oceans millions of
Souper Salesman
years later. Today the 'soup' theory has been over turned in a pioneering paper in BioEssays which claims it was the Earth's chemical energy, from hydrothermal vents on the ocean floor, which kick-started early life.

"Textbooks have it that life arose from organic soup and that the first cells grew by fermenting these organics to generate energy in the form of ATP. We provide a new perspective on why that old and familiar view won't work at all," said team leader Dr Nick lane from University College London.
(Soupy Sales & Evolutionary Tales, emphasis added). Yet, two papers commenting on "complex emergence" and/or abiotic evolution, from simple to complex, still use the "primordial soup" concept (GEN, cf Origins of Life "@ Clermont College").

Search for "primordial" in that text.

Here are some additional posts that touch upon the subject matter of today's post: (Weekend Rebel Science Excursion - 27, On the Origin of the Genes of Viruses - 11, The Uncertain Gene - 9, On the Origin of the Genes of Viruses - 8).

Have a good weekend.

The previous post in this series is here.

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