Sunday, October 30, 2011

Are Toxins of Power Machines or Organisms?

Bacteriophage T4
In the ongoing discussion concerning microbes, specifically human - microbe symbiosis, we have considered the part that symbiosis might play in the concept of "toxins of power".

Now seems like a good time to pause to go into a deeper focus, down beyond microbes, down into a deeper look into the universe of tiny things smaller than microbes.

So, today we will focus on "microbial viruses", the "virus" world that impacts only microbes.

"Viruses" are "viruses" except where microbes are concerned, in which case we encounter instead the words "prions" and "phages", which can equate to microbe infectors.

Even though these are tiny entities that are much, much smaller than the unseen world of the much larger microbe, they have a major impact on microbes, because they infect microbes in various ways.

The drawing shown in this post is of a "Bacteriophage T4" virus particle, an entity discussed in principle and more at length below.

Another valid reason to do this pause, so as to consider phages and prions instead of microbes exclusively, is because we know that the great bulk and majority of microbes are helpful, even essential to life, rather than being a danger to life.

That includes human life.

But since prions and phages are not of the same ilk, in that they are primarily mischievous, let's insert them into the hypothesis we are formulating to consider the origin of the toxins of power.

But first, let's briefly focus on the theory of the evolution of elements, called Big Bang Nucleosynthesis, a span of time when the first elements are said to have been formed.

Following that short period of time, the first "machines", which are more complicated compositions of various basic elements, called molecules, are said to have been formed.

Then cells are said to have developed from those molecular machines:
"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.
(Putting A Face On Machine Mutation, emphasis added). But perhaps even before that, prions and phages developed, because there is ongoing debate as to whether or not they are living or non-living (i.e. machine or organism):
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.
(Microbe World). The controversy over viruses has stark contrasts which can be applied to prions and phages too:
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.
(Astrobiology). So, some scientists believe that viruses, which are more machine like, came before organic cellular life, which makes more sense to me, in terms of a logical sequence.

That theoretical sequence would then be:
1) neutrons & protons, 2) elements (atoms), 3) molecules, 4) complex molecules ("molecular machines") like the prion, 5) phages, 6) more complex viruses, then 7) single cell organisms.
That sequence would move from the very simple, to slightly more complex, then on to very complex, so it would appear to be a more logical sequence.

Our "Bacteriophage T4", shown in the drawing at the top of the post, which does sorta look machine-like anyway, would fit into sequence #4 or sequence #5.

Microbes would fit into sequence #7, thus the answer to the question, in the title of this post, depends on whether phages generate the toxins or whether microbes do so.

Whether or not viruses, phages, or toxins of power are considered to be machine or organism, in the upcoming development of the hypothesis, we will also consider prions and phages when we consider ideas about the toxins of power.

A scientific paper published in Science contains this abstract:
The processes responsible for the evolution of key innovations, whereby lineages acquire qualitatively new functions that expand their ecological opportunities, remain poorly understood. We examined how a virus, bacteriophage λ, evolved to infect its host, Escherichia coli, through a novel pathway. Natural selection promoted the fixation of mutations in the virus’s host-recognition protein, J, that improved fitness on the original receptor, LamB, and set the stage for other mutations that allowed infection through a new receptor, OmpF. These viral mutations arose after the host evolved reduced expression of LamB, whereas certain other host mutations prevented the phage from evolving the new function. This study shows the complex interplay between genomic processes and ecological conditions that favor the emergence of evolutionary innovations.
(Repeatability and Contingency, Science, Jan. 2012, italics added). There is an entire unknown world out there upon which to base our belief system.

Various non-life machines like prions, phages, and viruses can also be symbiont to humans and other species to help them survive:
If not for a virus, none of us would ever be born.

In 2000, a team of Boston scientists discovered a peculiar gene in the human genome. It encoded a protein made only by cells in the placenta. They called it syncytin.
...
What made syncytin peculiar was that it was not a human gene. It bore all the hallmarks of a gene from a virus.

Viruses have insinuated themselves into the genome of our ancestors for hundreds of millions of years.
...
It turned out that syncytin was not unique to humans. Chimpanzees had the same virus gene at the same spot in their genome. So did gorillas. So did monkeys. What’s more, the gene was strikingly similar from one species to the next.
(Discover). While that may complicate things, in the sense that it is more controversial to contemplate non-living machines doing things critical for living things, nevertheless, it emphasizes the importance of microbes and even smaller entities in terms of what we need for survival on this planet.