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.
T4 in "living" color

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.

Friday, October 7, 2011

Hypothesis: Microbes Generate Toxins of Power - 2

Regular readers of Toxins of Power blog probably also read other websites or blogs that deal with the issue of "corrupting power".

We note that Psychology Today, no piker by any means, purported to answer the question about how what we call "power" corrupts leaders in office.

But that article, which we reference and link to below, never attempts to even define "power", rather, it only goes through a reasoning process that bifurcates "power" into "social" power contrasted with "personal" power.

That Psychology Today article goes on to state that even though the answer to the question "why and how does power corrupt leaders?" is complex, it is nevertheless "fairly clear":
The answer is complex, but fairly clear. Leadership is at its core all about power and influence. Leaders use their power to get things done. A simple distinction is between two forms of power. Socialized power is power used to benefit others. We hope that our elected officials have this sort of power in mind and are primarily concerned with the best interests of their constituents.

The other form of power is called personalized power, and it is using power for personal gain.
(Psychology Today, emphasis added). That article goes on to say that leaders can also become "intoxicated" by power, which implies a toxic element, a toxin of power, without further explaining the notion of a toxin that "intoxicates".

Meanwhile, the Toxins of Power blog has continually attempted to answer the question: "why does power corrupt and absolute power corrupt absolutely?", and we have tried to do so in multiple ways.

We have even alluded to a possible "mystical" aspect of the notion of "power", as well as toxins of power, but we never stopped there just because sometimes the type of "power" that corrupts humans may sometimes seem to be a "mysterious" notion.

No, we plod along, and we recently began a series where we postulate that, in light of recent microbiology research, perhaps microbes are players in forming those "hard to figure" toxins of power.

In the previous post of this series, it was determined that:
In the next post of this series we will review the impact that pollution has on the environment, specifically on microbes, then tie that data into the hypothesis.

From there we can follow the domino effect that pollution could have on microbial performance.

Moving on from there, in light of these recent discoveries set forth above, we can follow the impact on symbiont microbes on to potential impact on our human cognition.

That is, we will move from potential impact in general on toward the impact on specific symbiont microbes that could cause, in turn, specific behavior impacting the generation of toxins of power.
(Hypothesis: Microbes Generate Toxins of Power). It doesn't take long to determine that anthropogenic pollution, at least in terms of environmental pollution outside of the human-microbe symbiotic community, is difficult to isolate as a participant in the development of toxins of power.

If we look back into human history, back to the first empires such as Egypt or Akkad, we can clearly see what we could identify as corruption by power caused by the toxins of power, but we can't find the massive, destructive episodes of environmental pollution that endangers civilization on a massive scale like we have in today's world.

So, at a macro level it would seem, at least at first blush, that any microbial participation in the production of the toxins of power is innate to the symbiotic relationship itself, whether generated primarily by human cells, by microbial cells, or by both in concert.

This general conclusion is supported by recent experimental evidence:
We therefore studied the expression of these genes in the frontal cortex, striatum, amygdala, and hippocampus of GF and SPF mice, by means of in situ hybridization technique. In GF mice, NGFI-A mRNA expression was significantly lower in various subregions of the prefrontal cortex, including the orbital frontal cortex (Fig. 4 A and A′); as well as in the striatum (GF vs. SPF: 329 ± 33 vs. 586 ± 18, P < 0.0001), hippocampus (CA1 region, GF vs. SPF: 258 ± 15 vs. 499 ± 22, P < 0.0001; CA3 region, GF vs. SPF: 166 ± 13 vs. 236 ± 6, P < 0.001; dentate gyrus, GF vs. SPF: 76 ± 4 vs. 113 ± 5, P < 0.0001) and amygdala (GF vs. SPF: 126 ± 17 vs. 212 ± 19, P < 0.01) compared with SPF mice. Similarly, GF mice had significantly lower BDNF mRNA expression in the hippocampus, amygdala (Fig. 4 B and B′), and cingulate cortex (GF vs. SPF: 162 ± 6 vs. 193 ± 10, P < 0.05), which are key components of the neural circuitry underlying anxiety and fear ... Our results suggest that during evolution, the colonization of gut microbiota has become integrated into the programming of brain development, affecting motor control and anxiety-like behavior.
(National Academy of Sciences, emphasis added). These data show that when microbe free (GF) subjects are compared to the other subjects that are not microbe free, almost a doubling of relevant factors, in certain areas, occurs in the Amygdala.

That is significant to the hypothesis, because previous posts on this blog have shown the Amygdala to be a critical potential factor in the corruption by power.

Thus, we can conclude this post by noting that we have moved ever closer to identifying potential mechanisms, systems, or environments wherein toxins of power can emerge.

We can also conclude that, while massive, environmental, modern pollution could still be a factor in contributing to toxins that lead to corruption by power, that environmental pollution can not be a sole source of toxins of power, nor can it be the original source of the toxins of power on this planet, because corruption by power has been around longer than massive modern pollution has been around.

Thus, in upcoming posts, Toxins of Power blog intends to explore the issue further, keeping those conclusions in mind.

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

Thursday, October 6, 2011

What Is Pseudo Science?

There are times in history when science has become a political tool.

In such times the participants become more interested in supporting the ruling elite than in establishing independent and unbiased practices and methods with which to discern physical reality around us.

Sometimes it is the common people who practice pseudoscience but at other times, surprisingly, it is the scientific community itself that practices pseudoscience.

The development of "germ theory" is one stark example.

If you could ask Ignaz Semmelweis he just might say pseudoscience is "the kind of science that rejects the obvious, then has a violent reaction towards those who don't reject the obvious":
Semmelweis's observations conflicted with the established scientific and medical opinions of the time and his ideas were rejected by the medical community. Some doctors were offended at the suggestion that they should wash their hands and Semmelweis could offer no acceptable scientific explanation for his findings. Semmelweis's practice earned widespread acceptance only years after his death, when Louis Pasteur confirmed the germ theory. In 1865, Semmelweis was committed to an asylum, where he died of septicemia, at age 47.
(Ignaz Semmelweis, emphasis added). Galileo or Copernicus would have similar notions, as would modern scientists who also experienced blinding bias during their scientific careers.

Some people today think that climate scientists who declare that global warming is happening are hoaxers, that is, pseudo scientists, thus the problem:
The demarcation problem between science and pseudoscience has ethical political implications as well as philosphical and scientific issues. Differentiating science from pseudoscience has practical implications in the case of health care, expert testimony, environmental policies, and science education.
(Wikipedia). It is further illustrated by the notion of jury trials, where scientific experts will testify about their credentials, then have opposite conclusions on the same set of facts.

There are actually science police who may try to enforce absolutism, but sometimes run into problems since one man's pseudoscience is another man's science.

Most of the time the issue can be decided clearly, but not always, as with so many human endeavors.

The toxins of power do not stop at the laboratory door.

The scientist in the video below was considered, by establishment scientists, to be a heretic when she first postulated what is now considered to be basic:

Dr. Lynn Margulis:

Part I:

Part II:

Part III:

Dr. Lynn Margulis passed away in November of 2011 (Washington Post). She wanted a new 9/11 investigation conducted using forensic scientific methods (Architects).