Friday, January 25, 2013

Weekend Rebel Science Excursion - 13

In this Dredd Blog series I have tried to bring up scientific realities that are so radical, new, or mysterious that I have had to use the word "rebel" in the title so as to give readers a heads up.

After reading a few of these posts regular readers know that being a science rebel is not always a bad thing.

That is true, for one reason, because this series also shows that from time to time and often enough, but not always, today's rebel science becomes tomorrow's main stream science, even though at any given moment a new discovery that has surfaced may seem to be anti-scientific, because perhaps it departs from current textbook knowledge (see for example Weekend Rebel Science ExcursionThe Appendix of Vestigial Textbooks - 4 and/or Textbooks Take Another Hit - 2).

An example for illustrating that, as will be seen later in this post, can be seen in a post of this series that will substantially relate to today's post:
In the previous excursion I broached the subject of human-microbe symbiosis, a promising yet unexpected new direction in microbial research and science.

I say "unexpected" because it has the impact of redefining what the nature of our physical being is, redefining what it is "to be human" physically, and, as I will point out in this post, mentally as well.
(Weekend Rebel Science Excursion - 10). Today's post, as I said, is akin to that reality because this new rebel science renders substantial libraries of current textbooks obsolete:
Today, we are at the edge of a main turning point in understanding biological processes. The prevailing central dogma of molecular biology of the last 50 years is no more than a subordinate clause, relevant only to a small fraction of reality.
Now, the new renaissance of viruses is taking centre stage. Research data from the last decade indicate the important roles of viruses, both in the evolution of all life and as symbionts or co-evolutionary partners of host organisms. There is increasing evidence that all cellular life is colonized by exogenous and/or endogenous viruses in a non-lytic but persistent lifestyle. Viruses and viral parts form the most numerous genetic matter on this planet.
To understand their competence in natural genome editing, we have to look not only at their linguistic competence in editing and regulating correct nucleotide sequences, but also at their communicative competence, that is, how they interact with each other, how they compete within host organisms, how they symbiotically interact with host organisms to ward off competing parasites, how they generate de novo sequences and what life strategies they share. Exactly these features are presented in this volume. Persistent infection lifestyles that do not harm hosts, and symbiotic, cooperating viral swarms, may be more successful in evolutionary terms for integrating advantageous phenotypes into host organisms than are “selfish” agents. Increasing empirical data about the abundance of viruses and virus-derived parts in the ecosphere of this planet, and their roles in the evolution and developmental processes of cellular life forms at the level of the microscopic processes of replication, transcription, translation, alternative splicing, RNA-editing, epigenetics and repair, raise a fundamental question concerning a crucial decision about how to define and explain life ...
(Viruses: Essential Agents of Life, at viii-ix; see also this). Uh oh, the big picture we have been textbook taught for the past half century is only attached a tiny bit to reality?

Where have you heard that on Dredd Blog -- perhaps The Ways of Bernays?

Hey gang, how's that for a weekend rebel science excursion?!

Anyway, let's get on with this post:
The agent-based perspective is evident in the observation that every coordination process between cells, tissues, organs and organisms depends on signs that function as signals between signalling agents. Signalling and communication does not occur by signals alone, but by living agents that are competent to use signs. In all cases, the participating agents share a competence to generate signs, to receive appropriate messages and to interpret their content.
(ibid, at x). Oh my, some regular readers are going to be reminded of a recent Dredd Blog post:
The general statement in the quote above ("cancer is caused by damage to DNA that leads to uncontrolled cellular growth and spread throughout the body, either by increasing chemical signals that cause growth or by interrupting chemical signals that control growth") indicates that clear signals are required for healthy cell performance.
Regulatory conflicts occur when two signals that individually trigger opposite cellular responses are present simultaneously. Here, we investigate regulatory conflicts in the bacterial response to antibiotic combinations.
Quorum sensing bacteria produce and release chemical signal molecules ... bacteria use quorum sensing communication circuits to regulate a diverse array of physiological activities ... Although the nature of the chemical signals, the signal relay mechanisms, and the target genes controlled by bacterial quorum sensing systems differ, in every case the ability to communicate with one another allows bacteria to coordinate the gene expression, and therefore the behavior, of the entire community ... signal integration abilities are critical to survival.
We are in constant communication with our microbes, and the messages are broadcast throughout the human body.
(Childhood Leukemia Linked To Government Carelessness, emphasis in original). Oh what science rebels we posters, commenters, and readers of Dredd Blog are!

Note also, another Dredd Blog System post about the importance of one particular virus symbiont:
If not for a virus, none of us would ever be born.
(Are Toxins of Power Machines or Organisms?). Another virologist asked "Can Viruses Make Us Human?":
"THIS QUESTION WILL SEEM preposterous to most. Viruses are molecular genetic parasites and are mostly recognized for their ability to induce disease in their host. Their effect on host evolution has long been thought to be like that of a predator on its prey, eliminating the host with weakened defenses. How can we propose any constructive role for viruses? Many viruses, however, can infect their host in a stable and persisting manner, generally with no disease, often for the life of the host. Such viruses can bring to bear onto their host the viral seeds of genetic creation.
Based on this premise, this essay will examine the possible role of viruses in the evolution of complexity, including the evolution of human-specific attributes. This view of human evolution is part of a larger idea, that stable persisting viruses (genetic parasites) can allow the host to acquire complicated functions (complex phenotype) in one punctuated event of colonization. Such a process can now be considered as a possible explanation for several major dilemmas in evolutionary biology. All these dilemmas involve the origin of various host lineages that have acquired a complex and interacting set of functions in a relatively short time frame. Such acquisitions of complexity have always been difficult to explain by a simple Darwinian process."
(Proceedings of the American Philosophical Society, Vol. 148, NO. 3, Sept. 2004, by Luis P. Villarreal, p. 296). Dr. Villarreal was Director (2000-2010) of the Center for Virus Research, University of California, at Irvine (cf. Have We Solved Darwin’s Dilemma?American Scientist).

I further encourage you to read a "less rebellious" review of the book quoted from above at one of my favorite wee little people blogs, Small Things Considered.

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

The great rock group ... Amygdaloids:

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