Sunday, December 1, 2013

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.

This scientist be knowin' :



Sunday, October 13, 2013

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 livingeverything 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 previous post in this series is here.

Saturday, September 28, 2013

The U.S. Government Report & The IPCC Fifth Report Are In Agreement

In 1988 in the United Nations (UN), based on the scientific climate change consensus around the world, formed the United Nations Intergovernmental Panel on Climate Change (IPCC).

The IPCC was established and designed with a requirement that it produce periodic reports on the status of the global climate system.

Soon afterward, in 1990, the U.S. Congress passed and President G.W. Bush signed into law a bill that formed a similar U.S.A. group to study civilization's ongoing damage to the global climate system.

Like the IPCC, the American group was required to do a similar report every few years.

On Friday the IPCC released portions of its Fifth Assessment Report.

Likewise, some months back the U.S. Government group released its periodic report:
Climate Change and the American People

Climate change, once considered an issue for a distant future, has moved firmly into the present. This report of the National Climate Assessment and Development Advisory Committee concludes that the evidence for a changing climate has strengthened considerably since the last National Climate Assessment report, written in 2009. Many more impacts of human-caused climate change have now been observed. Corn producers in Iowa, oyster growers in Washington State, and maple syrup producers in Vermont have observed changes in their local climate that are outside of their experience. So, too, have coastal planners from Florida to Maine, water managers in the arid Southwest and parts of the Southeast, and Native Americans on tribal lands across the nation.

Americans are noticing changes all around them. Summers are longer and hotter, and periods of extreme heat last longer than any living American has ever experienced. Winters are generally shorter and warmer. Rain comes in heavier downpours, though in many regions there are longer dry spells in between.

Other changes are even more dramatic. Residents of some coastal cities see their streets flood more regularly during storms and high tides. Inland cities near large rivers also experience more flooding, especially in the Midwest and Northeast. Hotter and drier weather and earlier snow melt mean that wildfires in the West start earlier in the year, last later into the fall, threaten more homes, cause more evacuations, and burn more acreage. In Alaska, the summer sea ice that once protected the coasts has receded, and fall storms now cause more erosion and damage that is severe enough that some communities are already facing relocation.

Scientists studying climate change confirm that these observations are consistent with Earth’s climatic trends. Long-term, independent records from weather stations, satellites, ocean buoys, tide gauges, and many other data sources all confirm the fact that our nation, like the rest of the world, is warming, precipitation patterns are changing, sea level is rising, and some types of extreme weather events are increasing. These and other observed climatic changes are having wide-ranging impacts in every region of our country and most sectors of our economy.

(Government Climate Change Report). The IPCC report is in accord with the U.S. Government report:

The true take-home message of the latest IPCC report is crystal clear:
Climate change is real and caused by humans, and it continues unabated. We will see far more dangerous and potentially irreversible impacts in the decades ahead if we do not choose to reduce global carbon emissions. There has never been a greater urgency to act than there is now.

The latest IPCC report is simply an exclamation mark on that already-clear conclusion.

(The IPCC, Climate Change and Bad Faith Attacks on Science). Keep up resistance to Oil-Qaeda.

"Wild Life" - by Paul McCartney

Thursday, July 25, 2013

A Savvy Ecocosmological Earth Calendar - 2

Click on Sun to Enlarge
In this series so far we have looked at the extremely close similarity (in terms of the ~26,000 year cycle) of the Long Count Calendar and the Earth's axial precession (see A Savvy Ecocosmological Earth Calendar).

In today's post we look at the cycle of the axial precession in terms of current calendar months.

We offer a hypothesis that this is a built-in cosmic global climate system dynamic (a ~26,000 year cycle).

The graphic above shows one complete cycle of the Earth's axial precession, i.e. one "rotation" of the axial tilt.

At each 30 degrees on the graphic there is a date, beginning with 10,948 B.C. @ 0 degrees, then continuing to the present time (2012 A.D. @ 180 degrees), then proceeding on around to 14,972 A.D. @ 360 degrees.

Which comprises and completes one axial precession cycle of the Earth's axial tilt (which is one global climate system axial precession cycle).

Each degree, of the 360 degrees total, represents 72 years so each 30 degrees represents 2,160 years, thus, an axial precession cycle takes about 26,000 years (25,920 yrs. to be more exact).

The reason the 30 degree segments of 2,160 years is used is because we hypothesize that this is the amount of time it takes the climate to change in terms of a one-month morph of that month's seasonal characteristics (see Government Climate Change Report - 5 and Government Climate Change Report - 4).

The following list of months and their seasonal characteristics, in terms of being a Winter, Spring, Summer, or Autumn month, is shown for each date marked at every 30 degrees on the graphic at the top of this post:

10,948 B.C. (0 degrees)
(Winter) June, July, August
(Spring) September, October, November
(Summer) December, January, February
(Autumn) March, April, May

8,788 B.C. (30 degrees)
(Winter) May, June, July
(Spring) August, September, October
(Summer) November, December, January
(Autumn) February, March, April

6,628 B.C. (60 degrees)
(Winter) April, May, June
(Spring) July, August, September
(Summer) October, November, December
(Autumn) January, February, March

4,468 B.C. (90 degrees)
(Winter) March, April, May
(Spring) June, July, August
(Summer) September, October, November
(Autumn) December, January, February

2,308 B.C. (120 degrees)
(Winter) February, March, April
(Spring) May, June, July
(Summer) August, September, October
(Autumn) November, December, January

148 B.C. (150 degrees)
(Winter) January, February, March
(Spring) April, May, June
(Summer) July, August, September
(Autumn) October, November, December

==========================
2012 A.D. (180 degrees)
(Winter) December, January, February
(Spring) March, April, May
(Summer) June, July, August
(Autumn) September, October, November
==========================

4,172 A.D. (210 degrees)
(Winter) January, February, March
(Spring) April, May, June
(Summer) July, August, September
(Autumn) October, November, December

6,332 A.D. (240 degrees)
(Winter) February, March, April
(Spring) May, June, July
(Summer) August, September, October
(Autumn) November, December, January

8,492 A.D. (270 degrees)
(Winter) March, April, May
(Spring) June, July, August
(Summer) September, October, November
(Autumn) December, January, February

10,652 A.D. (300 degrees)
(Winter) April, May, June
(Spring) July, August, September
(Summer) October, November, December
(Autumn) January, February, March

12,812 A.D. (330 degrees)
(Winter) May, June, July
(Spring) August, September, October
(Summer) November, December, January
(Autumn) February, March, April

14,972 A.D. (360 degrees)
(Winter) June, July, August
(Spring) September, October, November
(Summer) December, January, February
(Autumn) March, April, May

The gist of this is that about each 13,000 years (each 12,960 yrs. --at the time they developed it, to be more exact), the months of Winter in Washington, D.C. in the U.S.A. now (December, January, February) become the months of Summer (June, July, August) in terms of their seasonal type-of-weather orientation.

This happens because the axial precession reaches the maximum 180 degree
Axial Tilt @ Main Degrees of Precession
opposite tilt (either tilting toward the Sun, or the opposite, tilting away from the Sun) then returns to 0/360 degrees to begin another axial precession cycle anew.

It is not that the months change, no, they still have their 30, 31, 28/29. number of days per month, are still spelled the same, and January is still the first month while December is still the 12th month (etc.).

It is just that the axial tilt of the Earth toward or away from the Sun impacts upon the global climate system (in terms of which hemisphere is impacted with more solar energy), and this is an easy way to symbolically represent that change in the global climate system, in terms of the impact on weather at that geographical location.

The quantity of the impact on weather in the northern hemisphere (temperature change, rainfall, ice melt, sea-level, etc.), as well as on the global climate system itself, will be considered in later posts in this series.

The previous post in this series is here.

The following video shows an axial procession cycle:



Wednesday, May 22, 2013

Microbial Languages: Rehabilitation of the Unseen

Some of my best friends are Germs
The Fourth Tenet of The Tenets of Ecocosmology urges us to recognize that microbial and other small life forms are useful as well as mandatory for our own existence and betterment.

In modern times this tenet has been considered to be an alien concept in Western Culture, especially in the Western medical sciences, so, in today's post let's discuss an emerging revolution in those general concepts of Western Civilization concerning perceptions of what it means to be "a human" and what it means to be "a germ."

Yes, let's reconsider the general concepts which without reservation tell us that the anti-biotic wars without any reservation have been a good thing, that consider microbes to be something to exterminate, and that are ignorant of what it actually means to be human in the biological reality of the planet Earth.

The text of the Fourth Tenet currently reads as follows:
The seeds of intelligence (genetic and memetic clues) required to successfully perform The Test are distributed into all species, races, religions, sciences, creeds, and genders. Thus, all individuals should be respected as carriers of some quanta of the seed of intelligence required to pass The Test, lest a fundamental quantum of necessary intelligence be lost.
(The Tenets of Ecocosmology, emphasis in original). The meaning of the word "intelligence" as it is first used in that text is enhanced by the later use of that word in the section of the text that reads "intelligence required to pass The Test" (compare: What Kind of Intelligence Is A Lethal Mutation?).

Which begs the question, what is "The Test"?

That question that is answered by the first three tenets to be the survival of species on planets near central stars.

Stars which eventually change in ways that mandate travel to another star system.

That is to say (taking our star the Sun as an example) that species on planets orbiting near the Sun are naturally destined for utter extinction and obliteration when the Sun enters its final phase.

Our star, early in that final phase, expands out to, or near to, the orbit of Mars, vaporizing or otherwise destroying those inner planets in the process (see Tenet One Basics).

There are other intermediate threats to species on habitable planets in our solar system, which we call "extinction events" (Asteroid Killed off The Dinosaurs, Sixth Mass Extinction?).

The sixth mass extinction is currently underway.

It is being caused by current human civilization.

The first five mass extinctions were primarily cosmological and other non-human events.

This brings us to the recent scientific discoveries in the microbiological sciences which focus on our new understanding of what it means to be human:
... the fields of medical and environmental microbiology have begun to merge. The resulting hybrid discipline embraces the complexity of a larger system; it’s integrative rather than reductive, and it supports the gathering view that our bodies, and the bodies of other animals, are ecosystems, and that health and disease may depend on complex changes in the ecology of host and microbes.
...
“We’ve all been trained to think of ourselves as human,” he says. Bacteria have been considered only as the source of infections, or as something benign living in the body. But now, he says, it appears that “we are so interconnected with our microbes that anything studied before could have a microbial component that we hadn’t thought about.” It will take a major cultural shift, says Karasov, for nonmicrobiologists who study the human body to begin to take microorganisms seriously as a part of the system.
...
Equally challenging, though in a different respect, will be changing long-held ideas about ourselves as independent individuals. How do we make sense of this suddenly crowded self? David Relman suggests that how well you come to terms with symbiosis “depends on how comfortable you are with not being alone.” A body that is a habitat and a continuously evolving system is not something most of us consider; the sense of a singular, continuous self is a prerequisite for sanity, at least in Western psychology.
(On The New Meaning of "Human" - 2, see also On The New Meaning of "Human"). Those two posts are a couple of years old, so let's look at a couple of more recent writings which show that this new science is moving along rapidly:
Justin Sonnenburg, a microbiologist at Stanford, suggests that we would do well to begin regarding the human body as “an elaborate vessel optimized for the growth and spread of our microbial inhabitants.” This humbling new way of thinking about the self has large implications for human and microbial health, which turn out to be inextricably linked.
...
Our resident microbes also appear to play a critical role in training and modulating our immune system, helping it to accurately distinguish between friend and foe and not go nuts on, well, nuts and all sorts of other potential allergens. Some researchers believe that the alarming increase in autoimmune diseases in the West may owe to a disruption in the ancient relationship between our bodies and their “old friends” — the microbial symbionts with whom we coevolved.
...
Human health should now “be thought of as a collective property of the human-associated microbiota,” as one group of researchers recently concluded in a landmark review article on microbial ecology — that is, as a function of the community, not the individual. Such a paradigm shift comes not a moment too soon, because as a civilization, we’ve just spent the better part of a century doing our unwitting best to wreck the human-associated microbiota with a multifronted war on bacteria and a diet notably detrimental to its well-being. Researchers now speak of an impoverished “Westernized microbiome” and ask whether the time has come to embark on a project of “restoration ecology” — not in the rain forest or on the prairie but right here at home, in the human gut.
(Some of My Best Friends are Germs, see also Smithsonian - Microbial Revolution). The Fourth Tenet has to do with the survival of human civilization long enough to develop the behaviors and skills necessary for space travel away from this solar system before the Sun extinguishes all life on Earth.

Living in harmony with the nature around us and in us is a fundamental prerequisite --because if we make critical life forms extinct, we thereby make our species extinct at the same time.

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?

The next post in this series is here.


The following video illustrates how we are beginning to understand the tiny language of the unseen world where most living things dwell.




Sunday, April 28, 2013

New Hypothesis Says Life Began Before The Earth

Old Atlas, Young Atlas feel alright ...
Many have asked "What Is Pseudo Science?"

It has been said that: “The application of Scientific Method is universal. … there is nothing too lowly, repulsive, obscure, contentious, or deceptive to come within its scope. Neither is there anything too ‘sacred,’ which generally means a fear that the things so denominated cannot bear investigation.” — F. C. S. Schiller, Logic for Use (1930)

It has also been said that subjecting “religion,” like any other subject, to Scientific Method quickly reveals its fundamentally ludicrous supposition: namely, that the world works not according to discoverable laws working everywhere the same but through the whim of obscure, fickle personalities whose “powerful” appetites and prejudices one can assuage or conciliate through stereotypical ritual practices such that the world will work otherwise than predictably, and to one’s own personal advantage.

Oh, if only reality was that simple!

A scientist many have heard of once said "make things as simple as possible, but no simpler than that." Another champion with many trophies, and currently a world renowned scientist, said:

Quantum mechanics is an incredible theory that explains all sorts of things that couldn’t be explained before, starting with the stability of atoms. But when you accept the weirdness of quantum mechanics [in the macro world], you have to give up the idea of space-time as we know it from Einstein. The greatest weirdness here is that it [quantum mechanics] doesn’t make sense. If you follow the rules, you come up with something that just isn’t right.

(The Memes of Penrose, quoting Dr. Sir Roger Penrose, emphasis added). What ... the venerable Penrose dissing the venerable Einstein (inspiring many orthodox scientists and their laity, wielding pitchforks, to advance upon the labs and classrooms of Penrose for talking out of school like that)?

A very recent paper (March 2013) has indicated that biological life is older than previously hypothesized:

An extrapolation of the genetic complexity of organisms to earlier times suggests that life began before the Earth was formed. Life may have started from systems with single heritable elements that are functionally equivalent to a nucleotide. The genetic complexity, roughly measured by the number of non-redundant functional nucleotides, is expected to have grown exponentially due to several positive feedback factors: gene cooperation, duplication of genes with their subsequent specialization, and emergence of novel functional niches associated with existing genes. Linear regression of genetic complexity on a log scale extrapolated back to just one base pair suggests the time of the origin of life 9.7 billion years ago. This cosmic time scale for the evolution of life has important consequences: life took ca. 5 billion years to reach the complexity of bacteria; the environments in which life originated and evolved to the prokaryote stage may have been quite different from those envisaged on Earth; there was no intelligent life in our universe prior to the origin of Earth, thus Earth could not have been deliberately seeded with life by intelligent aliens; Earth was seeded by panspermia; experimental replication of the origin of life from scratch may have to emulate many cumulative rare events; and the Drake equation for guesstimating the number of civilizations in the universe is likely wrong, as intelligent life has just begun appearing in our universe. Evolution of advanced organisms has accelerated via development of additional information-processing systems: epigenetic memory, primitive mind, multicellular brain, language, books, computers, and Internet. As a result the doubling time of complexity has reached ca. 20 years. Finally, we discuss the issue of the predicted technological singularity and give a biosemiotics perspective on the increase of complexity.

(Cornell Archives, emphasis added). What is wrong with hypothesizing like that?

Nothing.

But one of the fundamental assumptions of the paper is problematic, i.e., that certain things have remained the same during a period of split second Big Bang changes going way faster than the speed of light.

Additionally they may have overly associated their rear view mirror analysis with Moore's Law, which concerns the technological evolution of computers within human society when they write "The increase of genetic complexity follows Moore’s law" (PDF, page 1).

Additionally, they do not adequately overturn a basic tenet of the Big Bang Theory, which is that carbon formed in stars as those stars eventually declined and went Nova, releasing that carbon into space to later make its way to planets.

From there biological evolution is said to have resulted in carbon based life we see on Earth today.

The additional assertion in the paper that "Earth was seeded by panspermia" reminds me of what S.E. Cupp said on The Cycle (MSNBC) recently ("There are too many penises in Washington, D.C.") ... so isn't it fair to ask "what about panseggia?" (which came first, sperm or eggs?)

Seriously, let's face it, there are denominations in science just as there are in religion.

To take the pose of some mechanistic purity of scientific thinking or doctrine, or to take the pose of some mechanistic purity of religious thinking or doctrine, is to overly simplify reality.



Tuesday, January 1, 2013

What Kind of Intelligence Is A Lethal Mutation?

Lethal Mutation?
Regular readers know that several recent series on Ecocosmology Blog have dealt with various concepts of intelligence as well as variations within several "types of intelligence."

For example, in What Kind of Intelligence Is Prescience? and What Kind of Intelligence Is Prescience? - 2 we looked at ancient writings of two well known religions to contemplate intelligent ancient views of environmentalism which seem to be prescient.

In Did Abiotic Intelligence Precede Biotic Intelligence? we contemplated whether or not there are two types of intelligence as well as which type came first.

In the series Putting A Face On Machine Mutation we lament the dearth of peer reviewed papers (compared with those on biological evolution) concerning molecular-machine evolution in the context of the evolution of intelligence.

Today, we are going to indulge the notion of noted American biologist Ernst Mayr, who unabashedly hypothesized that human intelligence is a lethal mutation which is likely to lead to the extinction of the human species, as well as most other species on the planet Earth.

Let's begin with a debate between astrophysicist Carl Sagan and the American biologist Ernst Mayr; two scientists who saw human intelligence in a different light:
I'LL BEGIN with an interesting debate that took place some years ago between Carl Sagan, the well-known astrophysicist, and Ernst Mayr, the grand old man of American biology. They were debating the possibility of finding intelligent life elsewhere in the universe. And Sagan, speaking from the point of view of an astrophysicist, pointed out that there are innumerable planets just like ours. There is no reason they shouldn't have developed intelligent life. Mayr, from the point of view of a biologist, argued that it's very unlikely that we'll find any. And his reason was, he said, we have exactly one example: Earth. So let's take a look at Earth. And what he basically argued is that intelligence is a kind of lethal mutation ... you're just not going to find intelligent life elsewhere, and you probably won't find it here for very long either because it's just a lethal mutation ... With the environmental crisis, we're now in a situation where we can decide whether Mayr was right or not. If nothing significant is done about it, and pretty quickly, then he will have been correct: human intelligence is indeed a lethal mutation. Maybe some humans will survive, but it will be scattered and nothing like a decent existence, and we'll take a lot of the rest of the living world along with us.
(Human Intelligence and The Environment, Dr. Noam Chomsky, 9/30/10). Dr. Chomsky argues that Dr. Mayr had a good point if we take into consideration our "intelligent" use of the Earth's resources, including producing weapons of mass destruction, like hydrogen bombs and other nuclear weapons that threaten the existence of life on Earth.

Which brings to mind the photo of Dr. Einstein at the top of the post, in as much as it was his intelligence in large part that made weapons of mass destruction and human extinction possible.

The Tenets of Ecocosmology counsel against the improper use of the Earth's environment in any way, urging instead that all species contain some germane bit of information which humanity is likely to need in order to continue to exist.

The Toxins of Power Blog cautions that the source of toxins that do damage to intelligence so as to render it lethal, arise only in the presence of a certain type of power.