On The Origin of Propaganda - 2

It is not just for the human species

In the first post of this series we considered some of the ways of deception and propaganda.

Specifically we looked at cases where microbes and other creatures exhibit deceptive behaviors.

Since then, one journal has gone all out by dedicating an entire edition to the subject of those types of microbial manipulations.

On the other hand, there is also a recent paper which shows communicative examples where some microbes issue factual or accurate signals in communication with other species to help other species to navigate to a suitable location where metamorphosis can be initiated (Settlement Signal).

An entire edition of one journal, for an example of primitive propaganda, concerns how some parasitic species can develop processes for the manipulation of the brains of their host species:

The ability of parasites to alter the behaviour of their hosts fascinates both scientists and non-scientists alike. One reason that this topic resonates with so many is that it touches on core philosophical issues such as the existence of free will. If the mind is merely a machine, then it can be controlled by any entity that understands the code and has access to the machinery. This special issue of The Journal of Experimental Biology highlights some of the best-understood examples of parasite-induced changes in host brain and behaviour, encompassing both invertebrate and vertebrate hosts and micro- and macro-parasites. The observation that parasitic infection can modify specific host behaviours is an old one (see Moore, 2002). The general consensus has been that these parasites have evolved the ability to manipulate host behaviour in order to advance their own reproductive success (Moore, 2002). Unfortunately, there has been a lack of information on two key points of this hypothesis. Firstly, it has proved difficult to unequivocally demonstrate that changes in host behaviour benefit the parasite (i.e. enhance parasitic fitness). Secondly, the mechanisms that parasites use to change host behaviour were completely unknown for many years, particularly in the case of vertebrate host systems.

(Neural Parasitology). Regular readers will remember that in other Ecocosmology Blog posts we have looked at how that pathogenic behavior can and has been changed whereby the pathogenic and/or parasitic behavior can become mutualistic once again to benefit both host and symbiont (Microbial Languages: Rehabilitation of the Unseen--2).

This concept of wanting to understand interspecies and intra-species communication for better or worse is a long and winding road:

Many parasite taxa are able to alter a wide range of phenotypic traits of their hosts in ways that seem to improve the parasite’s chance of completing its life cycle. Host behavioural alterations are classically seen as compelling illustrations of the ‘extended phenotype’ concept, which suggests that parasite genes have phenotype effects on the host. The molecular mechanisms and the host–parasite cross-talk involved during the manipulative process of a host by its parasite are still poorly understood. In this Review, the current knowledge on proximate mechanisms related to the ‘parasite manipulation hypothesis’ is presented. Parasite genome sequences do not themselves provide a full explanation of parasite biology nor of the molecular cross-talk involved in host–parasite associations. Recently, first-generation proteomics tools have been employed to unravel some aspects of the parasite manipulation process (i.e. proximate mechanisms and evolutionary convergence) using certain model arthropod-host–parasite associations. The pioneer proteomics results obtained on the manipulative process are here highlighted, along with the many gaps in our knowledge.

(Host–parasite Molecular Cross-talk). Signaling and messaging is common within, between, and among species, and that cross-talk is composed of both propaganda messaging and truthful messaging.

It would seem that our approach to other species sends them a scary message which may affect their behaviors (Are Microbes The Origin of PTSD?).

We attack small and large life on Earth incessantly with pollution, antibiotics, and just about anything else we can throw at them (On The Memorial Daze, Mammals May Be Nearly Half Way Toward Mass Extinction).

In the sense that we live off the bounty of the Earth, yet are destroying it, we are a parasitic species.

But like those pathogens and parasites that have changed their behaviors into benefiting others, we can and must do so as well (Change Is Not An Option - It Is A Must).

The previous post in this series is here

Microbial Languages: Rehabilitation of the Unseen--2

Are They Friend or Foe?

In the first post of this series (Microbial Languages: Rehabilitation of the Unseen) I postulated that perhaps there was a way to communicate with those microbes which are leading a pathogenic lifestyle, so as to induce modifications to their behavior.

Those modifications to their behavior would result in a change from a pathogen into a symbiotic microbe.

The result of their becoming a symbiont, a mutualistic microbe (which by definition means that it offers some benefit to its host --rather than being a damaging pathogen or parasite) would be a benefit to both.

A benefit to the host and to the new symbiont, which had previously been a pathogen or parasite endangering the host and perhaps even the used-to-be pathogen as well.

There could be peace and health to both that way, rather than war and disease.

Well, as it turns out there is a scientific paper which was published after that Ecocosmology Blog post, which indicates --whether in part or in whole-- that this dynamic has now been shown to have not only taken place, but shown to have taken place more often than what was expected:

Like pretty much all multi-cellular organisms, humans enjoy the benefits of helpful bacteria. (As you may have heard, there are more [bacterial cells] in the human body than [human cells].) These mutualistic microbes live within the body of a larger organism, and, like any good long-term houseguest, help out their hosts, while making a successful life for themselves. It’s a win-win situation for both parties.

Scientists still don’t understand exactly how these relationships began, however. To find out, a team of researchers from the University of California, Riverside, used protein markers to create a detailed phylogenic tree of life for 405 taxa from the Proteobacteria phylum—a diverse group that includes pathogens such as salmonella as well as both mutualistic and free-living species.

Those analyses revealed that mutualism in Proteobacteria independently evolved between 34 to 39 times, the researchers report in the journal Proceedings of the Royal Society B.  The team was a bit surprised to find that this happened so frequently, inferring that evolution apparently views this lifestyle quite favorably.

Their results also show that mutualism most often arises in species that were originally parasites and pathogens.

(Smithsonian, emphasis added, links removed; paper is here). The statement "evolution apparently views this lifestyle quite favorably" should come as no surprise, assuming that a better chance at survival is a value of evolution.

This is a validation of the concept set forth in the first post of this series:

Living in harmony may also require us to do "remedial rehabilitation of the unseen", as the title of today's post suggests.

By that I mean to rehabilitate the microbes that have experienced past mass extinction events that utterly upended their world.

Which may have caused some of them to thereby end up going rogue and to then eventually become ill behaved parasites (Are Microbes The Origin of PTSD?).

Perhaps by learning to communicate with the rogues among them we will thereby be able to talk sense into some of the microbes that have become killers, maimers, or otherwise harmful?

(Microbial Languages: Rehabilitation of the Unseen). Who knows, perhaps "talking" to the pathogens as has been hypothesized will one day be the most efficient way to deal with diseases?

The previous post in this series is here.

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This scientist be knowin' :

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Putting A Face On Machine Mutation - 4

First Came the Machines

One statement gets our attention anytime we talk about machine mutation and/or machine evolution.

That statement is: DNA is not alive, is not life, it is a molecule, it is not living - it is a molecular machine.

Add to that peculiarity the narrative pointed out in this series, a narrative not always considered in discussions concerning evolution, which is that machine evolution has taken up the vast majority of evolutionary dynamics, especially in terms of the percentage of the span of the evolutionary timescale (Putting A Face On Machine Mutation - 3).

Thus, we come to the focus of today's post, which is the observation that one of the candidates for the apex of machine evolution, reached during the epoch of exclusive machine evolution (prior to biological evolution) is DNA.

Some students, when they begin to study college courses that focus on DNA, know that any DNA molecule is itself not alive:

... DNA is chemical compound ... DNA is non-living, because it is a molecule not an organism ... DNA is not living. It is a chemical - a large fragile molecule ... there is no debate in the biological community about this ...

(Is DNA living or non-living thing?, emphasis added). In other cases, however, students not only harbor the misconception that DNA is alive, they even have to be specially educated to "undo" that misconception:

We are involved in a project to incorporate innovative assessments within a reform-based large-lecture biochemistry course for nonmajors. We not only assessed misconceptions but purposefully

DNA molecule is not alive

changed instruction throughout the semester to confront student ideas. Our research questions targeted student conceptions of deoxyribonucleic acid (DNA) along with understanding in what ways classroom discussions/activities influence student conceptions. Data sources included pre-/post-assessments, semi-structured interviews, and student work on exams/assessments. We found that students held misconceptions about the chemical nature of DNA, with 63 % of students claiming that DNA is alive prior to instruction. The chemical nature of DNA is an important fundamental concept in science fields. We confronted this misconception throughout the semester collecting data from several instructional interventions. Case studies of individual students revealed how various instructional strategies/assessments allowed students to construct and demonstrate the scientifically accepted understanding of the chemical nature of DNA. However, the post-assessment exposed that 40 % of students still held misconceptions about DNA, indicating the persistent nature of this misconception. Implications for teaching and learning are discussed.

(Is DNA Alive?, Research in Science Education, Volume 43, Issue 4, Aug. 2013, pp.1361-1375, emphasis added). As that abstract points out, some students have a difficult time with the concept that a DNA molecule is composed of an arrangement of atoms which are not alive.

That difficulty continues into the concept of molecular machines, that is, it is difficult for us to conceive that atoms and molecules can be configured in such a way that they are actually machines:

The ribosome ... is a large and complex molecular machine, found within all living cells, that serves as the primary site of biological protein synthesis (translation)....

(The Uncertain Gene - 4). That "large and complex molecular machine" is only one among many thousands in cells:

"We took this approach because so many RNAs are rapidly destroyed soon after they are made, and this makes them hard to detect," Pugh said. "So rather than look for the RNA product of transcription we looked for the 'initiation machine' that makes the RNA. This machine assembles RNA polymerase, which goes on to make RNA, which goes on to make a protein." Pugh added that he and Venters were stunned to find 160,000 of these "initiation machines," because humans only have about 30,000 genes. "This finding is even more remarkable, given that fewer than 10,000 of these machines actually were found right at the site of genes. Since most genes are turned off in cells, it is understandable why they are typically devoid of the initiation machinery."

The remaining 150,000 initiation machines -- those Pugh and Venters did not find right at genes -- remained somewhat mysterious.

(The Uncertain Gene - 3). That the complex machinations of DNA and RNA are considered to be of the realm of machines is not new nomenclature.

For example, "machine" or "molecular machine" has been the nomenclature used to describe other non-living entities within cells:

Dr Clarke said: “There are a lot of fundamental questions about the origins of life and many people think they are questions about biology. But for life to have evolved, you have to have a moment when non-living things become living – everything up to that point is chemistry.”
...
“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.
...
Many cellular processes are carried out by molecular ‘machines’ — assemblies of multiple differentiated proteins that physically interact to execute biological functions ... Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.
...
The most complex molecular machines are found within cells.
...
Writing in the journal PLoS Pathogens, the team from Queen Mary's School of Biological and Chemical Sciences show how they studied the molecular machine known as the 'type II bacterial secretion system', which is responsible for delivering potent toxins from bacteria such as enterotoxigenic E. coli and Vibrio cholerae into an infected individual.

Professor Richard Pickersgill, who led the research, said: "Bacterial secretion systems deliver disease causing toxins into host tissue. If we can understand how these machines work, then we can work out how it they might be stopped."

(Do Molecular Machines Deliver Toxins of Power?, emphasis in original). Since RNA and DNA are required for carbon based life forms to exist and to continue to exist, we can argue that DNA is possibly the most evolved entity to have resulted during the epoch of machine evolution.

Before closing today's post, let's consider one of the causal factors leading to the inability of some students to fathom the concept of machine evolution:

Teleology in both science and religion appears in many forms, formats, and verbal expressions during many a dogmatic brainstorm.

Scientists complain that teleological  concepts exist at even the fundamental levels of our modern science (compare If Cosmology Is "Off," How Can Biology Be "On?" with The Uncertain Gene - 2).

In the series The Uncertain Gene, Dredd Blog posts attempt to discuss a pure, i.e. teleology free, account concerning issues about how abiotic machine-evolution intersects with biotic carbon-based-life-form evolution through the advent of the quantum tunneling dynamics of protons.

Specifically, I am referring to proton tunneling at the location of certain hydrogen bonds in gene related molecules (The Uncertain Gene).

(Weekend Rebel Science Excursion - 24). Teleological language is a problem because its users subconsciously or consciously use verbiage that connotes essences to machines or organisms which those machines or organisms do not have:

Since at least the 17th century (and mostly because of Newton), natural scientists have stopped using formal or final causes to explain natural phenomena ... except in biology. This was first pointed out by Colin Pittendrigh (Pittendrigh, C. S. Behavior and Evolution) (ed. by A. Rose and G. G. Simpson), Yale University Press, 1958), who coined the term "teleonomy" to refer to the kind of teleological phenomena observed in biological processes.
...
So, let's get back to the book (Quantum Aspects of Life) to further emphasize that physicists also can get loose with their discipline, i.e. can get off into the weeds of teleology, unless they are careful:

Expressed differently, how does a quantum superposition recognize that it has “discovered” life and initiate the said collapse? There seems to be an unavoidable teleological component involved: the system somehow “selects” life from the vastly greater number of states that are nonliving ... But this implies the environment somehow favours life—that life is “built into” nature in a preordained manner. So an element of teleology remains. (p. 11) ... an element of teleology is required; namely that the molecule must somehow know before hand what it is aiming for. (p. 42) There is no teleology needed here since we describe the measurement as a two-step process ... (p. 45) ... there’s the teleological point that, hey, we search for something ... (p. 357) ... As far as the teleological aspects are concerned (p. 360) ... Teleological aspects and the fast-track to life ... there is a teleological issue here ... (p. 392)

(ibid, Quantum Aspects of Life, emphasis added). The point being made is that "natural selection" discussions by either evolutionary biologists or physicists can become fundamentally teleological unless great care and focused technical language skills are employed ...

(The Uncertain Gene - 2). For those who want to go through that experiment, describe the machine epoch, beginning at the Big Bang then progressing through some ~10.21 billion years of machine evolution until finally molecules of DNA became part of the universe of machines, all of which transpired prior to the advent of any carbon based life forms.

Don't leave out some of E.O. Wilson's pleas for discourse and nomenclature on the evolution of morality, altruism, and ethics, especially as it has been considered on Ecocosmology Blog in the same vein that abiotic intelligence has been considered:

The stars like our Sun, at the center of all solar systems, will support life forms for an amount of time, but will then destroy life on the planets near them at an unknown time during each solar system's developmental life cycle.
...
This could be read to imply that abiotic evolution includes a process whereby undesirable carbon based biotic life forms that might later evolve will eventually be extinguished, will "automatically" become extinct, should they evolve/develop primarily "maladjusted behaviors."
...
It would seem to imply, then, the existence of some form of abiotic intelligence intent on preventing future undesirable biotic evolution from getting out of hand and populating the cosmos with undesirables

(Did Abiotic Intelligence Precede Biotic Intelligence?). How could any one describe "what is up with that", in terms of morality, ethics, and/or altruism, by using the nomenclature and theory of a "natural selection" apparatus which results in the mass murder extinction (Tenet One Basics) of innocent and/or helpless species?

Nevertheless, be sure to use the nomenclature of natural selection as your linguistic word source to describe machine evolution: beginning at energy evolving into subatomic particles like protons, then those subatomic particles evolving into atoms, the atoms into molecules, then molecules into compounds, then compounds into dust clouds which condense into planetoids, which eventually evolve into stars that create carbon within themselves, then release that carbon when those stars "go nova" or "go supernova."

You will find that you will encounter some teleological problems, just like the physicists in the book Quantum Aspects of Life who tried a similar teleological-language-free task (ibid).

For example consider the use of the word "behavior":

be·hav·ior

1. manner of behaving or acting.
2. Psychology, Animal Behavior.

a. observable activity in a human or animal.
b. the aggregate of responses to internal and external stimuli.
c. a stereotyped, species-specific activity, as a courtship dance or startle reflex.

3. Often, behaviors. a behavior pattern.
4. the action or reaction of any material under given circumstances: the behavior of tin under heat.

(Dictionary). The quanta (e.g. electrons, photons, protons, neutrons) will have "behavior" ... which carbon based life forms will also have ... so be careful that teleological language does not subvert your nomenclature:

On one planet — a most ordinary planet, orbiting a mediocre star, one speck on the spiral arm of a standard galaxy — surging continents and roiling oceans organized themselves, and out of the oceans an ooze of organic molecules reacted and built proteins, and life began.

(The God Particle, Lederman, p. 1, bold added). The assertions "organized themselves" and "reacted and built" are teleological slips (or are they inferences that abiotic intelligence existed?) that reflect a need for better nomenclature.

For another example, if you think "genes are selfish" you may tend to explain machine evolution in terms like "machines are selfish" (because genes are simply molecular machine entities which are not alive).

The language of that thought experiment could be extrapolated, if you are not careful, to a notion of "protons that became selfish" ... so those selfish genes protons gathered an electron to themselves to form a hydrogen atom.

Then later they became more selfish and therefore gathered a neutron to themselves too, so as to form other atoms.

Then atoms became selfish and gathered other atoms to themselves to form molecules, etc. etc.

With such contemplation you may expose more flaws in such teleological practices, which exposure may lead to some form of improvement over flawed historical teleological communications and misunderstandings (looking on the bright side that could lead to some remedy in the form of scientifically sound and improved nomenclature).

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