Friday, August 8, 2014

On the Origin of the Genes of Viruses - 10

The DNA molecule is NOT alive.
In this series we contemplate the spectre of viruses being the first carbon based life forms to evolve billions of years after molecular machines had already evolved.

People have a difficult time wondering about how machines could evolve.

Which is not logical because machines are not as complex as organic life forms are.

If evolution proceeds from non-life to life, from simple to complex, then it should be obvious that machines composed of atomic parts, which later became molecules, would have to evolve first.

Those controversial issues have been discussed in the previous posts in this series as well as the following complimentary series (The Uncertain Gene, 2, 3, 4, 5, 6, 7, 8, 9, 10) and (Putting A Face On Machine Mutation, 2, 3, 4).

Those issues were also writ large in the posts (The New Paradigm: The Physical Universe Is Mostly Machine, Autopoiesis: It's Not Just For Machines Anymore).

With that background in mind, let's consider a recent paper:
The MSU-led research provides the first detailed blueprint of a multi-subunit "molecular machinery" that bacteria use to detect and destroy invading viruses.

"We generally think of bacteria as making us sick, but rarely do we consider what happens when the bacteria themselves get sick. Viruses that infect bacteria are the most abundant biological agents on the planet, outnumbering their bacterial hosts 10 to 1," said Blake Wiedenheft, senior author of the paper and assistant professor in MSU's Department of Microbiology and Immunology.

"Bacteria have evolved sophisticated immune systems to fend off viruses. We now have a precise molecular blueprint of a surveillance machine that is critical for viral defense," Wiedenheft said.
Abiotic Came 1st
"This surveillance machine consists of 12 different parts and each part of the machine has a distinct job. If we're missing one part of the machine, it doesn't work."

Understanding how these machines work is leading to unanticipated new innovations in medicine and biotechnology and agriculture. These CRISPR-associated machines are programmable nucleases (molecular scissors) that are now being exploited for precisely altering the DNA sequence of almost any cell type of interest.

"In nature, these immune systems evolved to protect bacteria from viruses, but we are now repurposing these systems to cut viral DNA out of human cells infected with HIV. You can think of this as a form of DNA surgery. Therapies that were unimaginable may be possible in the future," Wiedenheft said.
(Molecular Machine Dynamics Identified, emphasis added). In other words, this is not science fiction, rather, it is applied science now.

The microbial world has molecular machine tools at its disposal which are used to do phenomenal brain surgery:
"... this is a protozoan parasite that knows more about the neurobiology of anxiety and fear than 25,000 neuroscientists standing on each other's shoulders ..."
(Hypothesis: Microbes Generate Toxins of Power - 6, quoting Dr. Sapolsky). In future posts we will look at genetic tools of viruses.

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


  1. This is amazing Dredd. My youngest would be interested in this, so i'm going to send it in an e-mail link.


  2. Like was mentioned last week, the better way is communication via simple molecules rather than the complexity of nano-surgery.

    The natural language communication beats frontal lobotomy in human and other organisms.


    Tom is correct that the complexity of life and machines interacting together is amazing.

    We are only beginning to see it.

  3. Dredd, Randy: have you seen this?


    According to the researchers' newly proposed theory, however, our universe was never inside a singularity. Rather, it arose outside the event horizon of a black hole — a black hole from another, higher-dimensional universe. It was thus protected from the singularity.

    Though it's a difficult concept to wrap the mind around, this new idea is just one level up from our current understanding of how black holes operate. In our three-dimensional universe, black holes have two-dimensional event horizons; that is, they are surrounded by a two-dimensional boundary that marks the "point of no return" for any object plummeting toward the black hole's center.

    In a theoretical four-dimensional universe, however, black holes would instead possess three-dimensional event horizons. So the researchers' new theory suggests that our three-dimensional universe is nothing more than a "mirage" caused by a star collapsing into a black hole in such a four-dimensional universe.

    [read it if interested, comments appreciated]


    1. Dr. Roger Penrose and the gang are not satisfied with the plain vanilla Big Bang model, as are the theorists you link to.

      I mentioned that in Autopoiesis: It's Not Just For Machines Anymore.

      Near the end of the post is this quote: "According to conformal cyclic cosmology (CCC) ... what would normally be regarded as a probable entire history of our universe, starting with its Big Bang and ending with its accelerating de Sitter-like expansion (assuming a positive cosmological constant Λ ...), is taken to be but one aeon in a (perhaps unending) succession of such aeons, where the conformal 3-surface B representing the big bang of each aeon is regarded as the conformal continuation of the remote future (i.e. conformal infinity I ...) of the previous one. CCC takes there to be no inflationary phase in any aeon, the observational support that inflation enjoys being supposed to be equally supported by the existence of the final exponential expansion occurring in the previous aeon ..."

      There is a lot of dissatisfaction with some of our fundamental cosmology concerning the Big Bang theory.

      That rebellion has not traditionally been mentioned much in polite company.