Monday, September 29, 2014

The New Paradigm: The Physical Universe Is Mostly Machine - 2

DNA is not biological
This series has been pointing out that the DNA, pictured in the graphic to the left, is the same as the DNA in you or me, viruses, and everything else that contains DNA.

That is, DNA is not alive, it is a molecular machine.

The same goes for RNA, it too is a molecular machine, as was pointed out in the first post of this series  (The New Paradigm: The Physical Universe Is Mostly Machine).

Why that would seem strange to us is revealing, in the sense that we tend not to know where we are or who we are (You Are Here).

Nevertheless, this knowledge of the basic cosmic nature is quite a normal concept, since carbon based life is said to have evolved very recently (by comparison to ancient stars) in our section of the universe, so, what is not a normal concept is our misunderstanding of the nature of RNA and DNA.

Why we deny the logical deduction, under the deductive reasoning compelled by Big Bang Cosmology, that abiotic machines evolved long before biotic organisms evolved.

Then those molecular machines morphed, mutated, or whatever evolutionary term you choose, into biotic organisms:
(see also The Uncertain Gene, 2, 3, 4, 5, 6, 7, 8, 9, 10). Regular readers know that Dredd Blog has pointed out this conundrum several times, and that the reason for it boils down to faith and trust rather than boiling down to knowledge (The Pillars of Knowledge: Faith and Trust?).

A new paper is getting around to discussing the dynamics of how machines became organisms:
Because RNA can be a carrier of genetic information and a biocatalyst, there is a consensus that it emerged before DNA and proteins, which eventually assumed these roles and relegated RNA to intermediate functions. If such a scenario—the so-called RNA world—existed, we might hope to find its relics in our present world. The properties of viroids that make them candidates for being survivors of the RNA world include those expected for primitive RNA replicons: (a) small size imposed by error-prone replication, (b) high G + C content to increase replication fidelity, (c) circular structure for assuring complete replication without genomic tags, (d) structural periodicity for modular assembly into enlarged genomes, (e) lack of protein-coding ability consistent with a ribosome-free habitat, and (f) replication mediated in some by ribozymes, the fingerprint of the RNA world. With the advent of DNA and proteins, those protoviroids lost some abilities and became the plant parasites we now know.
(Viroids: Survivors from the RNA World?, emphasis added). If the scientific jargon sometimes is not as pleasing to you as the layman's jargon, read about it in this piece:
New research suggests that [viroids already] existed at the earliest stages of life on Earth, enduring in their primitive state for billions of years. These are the pterodactyls of the microbial world — except that they are still very much with us. We just didn’t realize it.

Machinelike Bacteriophage T4
And [viroids] contain RNA, a single-stranded molecule similar to DNA. Among many other jobs, RNA carries the information for building proteins from a cell’s genes to its protein factories.

Many scientists have argued that before this kind of life emerged, life was based solely on RNA. RNA can store genetic information, but scientists have discovered that some RNA molecules also carry out chemical reactions. In other words, this single molecule might have been able to handle all the basic tasks required for life. Only later did DNA and proteins evolve.

At first, the proponents of the so-called RNA-world theory assumed that RNA-based life had become extinct long ago, driven to extinction with the arrival of superior DNA-based life. Researchers have relied only on indirect hints to infer what RNA-based life was like.

But in the current issue of Annual Reviews of Microbiology, a team of Spanish scientists argues that these primitive life forms share the planet with us today. “Viroids are probably relics of the RNA world,” said Santiago F. Elena, an evolutionary biologist at Spain’s National Research Council in València.
(NY Times, emphasis added). What makes the logic here more compelling is that scientists have struggled with the question "Are viruses alive?" for many, many years:
When is a life form not a life form? When it's a virus.

Viruses are strange things that straddle the fence between living and non-living. On the one hand, if they're floating around in the air or sitting on a doorknob, they're inert. They're about as alive as a rock. But if they come into contact with a suitable plant, animal or bacterial cell, they spring into action. They infect and take over the cell like pirates hijacking a ship.
Viruses are a curious lot. The standard drawing of the tree of life, the one you find on the inside back cover of biology textbooks, is divided into three branches: Archaea, Bacteria and Eukarya. Viruses don’t make it onto the page.

That makes sense, some scientists argue, because they’re not alive. They can’t reproduce on their own; they require the cozy environment of living cells for their survival. Others disagree. Not only are viruses alive, they say, but genetic evidence indicates that they may have been the first forms of life on Earth, predating cellular life.
(Are Toxins of Power Machines or Organisms?). Viroids are all the more suspect as not being alive compared to viruses.

Something had to jump the gap from abiotic molecular machine to biotic organism, so RNA viruses and viroids are prime suspects.

Yes, "the plot thickeneth" as we begin to notice the most prolific dynamic on Earth - microbes, viruses, and virus-like entities.

Science and Religion ... gotta luv 'em.

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

We are the Bored of Education ...


  1. Black-hole cosmology is also being questioned: link

  2. wow - that kind of kicks the whole concept of "god" out of the picture, no?


    1. "Ixtab (Mayan pronunciation: [iʃˈtaɓ]) or Rope Woman was the Yucatec Mayan goddess of suicide according to Diego de Landa. In Yucatec society, under certain circumstances, suicide, especially suicide by hanging, was considered an honorable way to die. Ixtab would accompany such suicides to paradise (thus playing the role of a psychopomp). Here, joined by people who died as soldiers or as sacrificial victims, by women who died in childbirth and by members of the priesthood, they enjoyed a delectable existence rewarded with delicious food and drink and resting under the shade of a pleasant tree, Yaxche, free from all want." - Wikipedia ("the god of suicide")