Friday, October 4, 2013

Weekend Rebel Science Excursion - 24

Proton Tunneling in Genes
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).

We focused on this dynamic both in DNA and RNA, and in both the coding and non-coding sections (a.k.a. "junk DNA" and "non-junk DNA") of genomes.

The specific purpose for looking at proton tunneling is that it is utterly independent of biological functions, because it is an abiotic dynamic explained by quantum mechanics and cosmology rather than by biology.

We are in reference to proton dynamics that evolved during abiotic evolution, billions of years prior to biotic evolution, and before carbon atoms existed --carbon atoms that became part of carbon based life forms (Putting A Face On Machine Mutation - 3).

As you can see in the graphic above (click to enlarge), there are a lot of hydrogen ("H") locations in the individual molecules that make up RNA and DNA (cytosine, guanine, adenine in each; uracil only in RNA, and thymine only in DNA).

Anyway, those "H" locations might seem to be potential sites for the quantum proton tunneling which we are specifically in reference to in this post, however, it is a bit more involved than simply having hydrogen atoms in those molecules:
The reason why A [adenine] pairs with T [thymine] and G [guanine] pairs with C [cytosine] all comes down to matching electron lone pairs.
DNA is not alive

 In essence the hydrogen bond is a single proton shared between two lone electrons (two separate atoms, each containing an extra unpaired electron in their outer orbital shell compete for possession of the single proton).
In addition to the normal forms, the tautomeric forms of the nucleotide base pairs must also be considered. Tautomeric forms are obtained by moving a proton from its original (or normal) lone pair into another position. This changes the inherent complementarity between the bases and as such the tautomeric bases pair differently.
These changes from the normal to the tautomeric forms introduce errors into the DNA replication process–creating point mutations–and can irreparably effect the genetic code. These point mutations, if not checked after initial replication, can be amplified through continued replications, ultimately leading to severe mutations in the cell.
(Quantum Tunneling in DNA, by Megan Wolfe; PDF). We see, then, that the highly random event of proton tunneling can generate a random mutation in DNA -- an abiotic mutation free of any need for any teleological intrusions or notions (such as intelligent design or natural selection) enhancements to the data.

The phenomenon is simply abiotic evolution through quantum mutation, which, in our world today eventually impacts carbon based life forms by doing what protons were already doing (quantum "tunneling") long before genes or carbon based life forms existed.

When the organism dies the DNA will eventually degenerate into molecules and atoms with the same protons and electrons being recycled somewhere else in the land, air, water, or in other organisms within the ecosystem.

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

Thursday, October 3, 2013

The Uncertain Gene - 4

Molecular Machine Work
I began this series with a look at human genetic mutation through the abiotic quantum mechanical dynamic called "proton tunneling" (The Uncertain Gene).

I used the word abiotic because proton tunneling is machine-like, rather that being life-like.

In short, this type of mutation in DNA is not an organic event at the onset.

In other words, the result of proton tunneling is not life, it is molecular, i.e. a mutation of molecules rather than being a direct mutation into a carbon based life form.

To be very clear, recall that in the second post of this series (The Uncertain Gene - 2) we looked once again at the history of evolution, finding that what is quite notable in that regard is that the great bulk of evolution, in terms of time, has been abiotic evolution (i.e. the evolution of molecular machines) rather than having been biotic evolution (the evolution of carbon based life forms).

That being the case, molecular machine evolution and/or mutation, a.k.a. abiotic evolution, needs more attention than it gets, thus, the focus in this series is on a purely abiotic dynamic, which is proton tunneling induced mutation.

In the previous post I indicated that we would look at how "150,000 initiation machines" in the "non-gene" or "non-coding" portion of DNA could be utilized by various types of RNA and their operations promoted by the "molecular machine" known as a ribosome:
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).
(Wikipedia, emphasis added). That protein synthesis or translation is where the ribosomes perform the critical task of bridging the gap from abiotic to biotic, by processing the proton tunneling mutation.

The ribosomes, using RNA, do so by perpetuating that mutation into molecules containing carbon atoms --into molecular arrangements called amino acids from which proteins are then made.

Both amino acids and proteins are organic compounds:
An organic compound is any member of a large class of gaseous, liquid, or solid chemical compounds whose molecules contain carbon.
(Wikipedia, "Organic Compound", emphasis added). But until recently that translation has been known to take place only in the area of genes, not in the area of "junk DNA" or "dark matter."

But new research tells us that in fact is precisely what takes place in what is becoming known as an area of treasure, not of junk:
The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation.
(ENCODE Project Consortium, "An integrated encyclopedia of DNA elements in the human genome," Nature, Vol. 489:57-74, September 6, 2012, emphasis added). Those operations by RNA etc. in that region were totally unexpected by pop science writers who unfortunately expressed themselves in undesirable teleological terms:
"It stretches even their creative ingenuity to make a convincing reason why an intelligent designer should have created a pseudogene -- a gene that does absolutely nothing and gives every appearance of being a superannuated version of a gene that used to do something -- unless he was deliberately setting out to fool us ...

Leaving pseudogenes aside, it is a remarkable fact that the greater part (95 percent in the case of humans) of the genome might as well not be there, for all the difference it makes."
(The Greatest Show on Earth, by Richard Dawkins, pp. 332-33). That area in the human genome and/or microbiome is the target for today's post, because in the previous post I said:
Thus, even if she is correct that proton tunneling induced mutant DNA is placed in the non-coding section, along with the other 98% of the human genome, that does not mean that RNA of various sorts will not later utilize it or that it will not be passed on to future iterations of that DNA molecule (to be covered exhaustively in next post of this series).
(The Uncertain Gene - 3). If a quantum proton tunneling induced mutation took place, and the results of that mutation are placed, for any reason, into the "junk DNA" or "dark matter" section of the human genome and/or microbiome, it is clear that it could still be included in subsequent biological protein synthesis or translation.

In conclusion for today, the results of purely quantum-mechanical proton tunneling could cross the bridge spanning the gap from abiotic to biotic at the time of translation --a non-carbon-based-machine-component could thereby become part of a biological component --part and parcel of the DNA of some carbon based life form.

In the next post of this series, we will look into the operation of microbes in and on both sections of the human genome and/or microbiome, in terms of inducing mutations or other genetic related events.

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

Wednesday, October 2, 2013

She's Come Undone

Roman Empire Legislators
The disjointed spasms of the neoCon gang of the-too-few-crew in the current dystopia called the U.S. House of Representatives raises the eyebrows of other governing bodies around the world.

It raises the eyebrows of the American people too.

Americans are people who by-and-large do not like to see dysfunctional antics that are on par with childish temper tantrums in places where professional behavior is properly expected.

These garish displays of "me like me take" social conduct in a supposedly respectable public body are signs of a lack of social conscience:
The reality of these wars is a story of the shame of the warmongers among us:
Every gun that is made, every warship launched, every rocket fired signifies in the final sense, a theft from those who hunger and are not fed, those who are cold and are not clothed. This world in arms is not spending money alone.

It is spending the sweat of its laborers, the genius of its scientists, the hopes of its children.

This is not a way of life at all in any true sense. Under the clouds of war, it is humanity hanging on a cross of iron.
(President & General Eisenhower, emphasis added). MOMCOM has sold herself via the main stream media as the saviour, yet she is actually the crucifier.
(The Policy "Me Like Me Take" Declines). The House's current neoCon-induced temper tantrum infused by a few sociopaths and/or psychopaths (who have scared its Speaker into a Stockholm-Syndrome-type trance) alarms mature nations who are watching:
As the United States approached a budget crisis that will shut down many federal services and affect more than 700,000 workers, other countries looked on with a mixture of puzzlement and dread.

For most of the world, a government shutdown is very bad news - the result of revolution, invasion or disaster. Even in the middle of its ongoing civil war, the Syrian government has continued to pay its bills and workers' wages.
Elsewhere in the world, such shutdowns are practically impossible. The parliamentary system used by most European democracies ensures that the executive and legislature are controlled by the same party or coalition. Conceivably, a parliament could refuse to pass a budget proposed by the prime minister, but such an action would likely trigger a failure of the government and a new election - witness the current situation in the Netherlands, where Prime Minister Mark Rutte's government faced a no-confidence vote at the start of debate over his 2014 budget proposal. And even when there is a gap prior to a new government taking office, national services continue to operate.
(The World's Eyebrows Raised, emphasis added). The grins and giggles of those too-few-crew neoCons (intoxicated by wannabe Wahhabism) are having too costly an impact on the U.S. reputation in the world (ObamaCare: Good Foreign Policy).

Remember that loss of reputation damages foreign policy efforts:
What if the sole superpower on the planet makes its will known -- repeatedly -- and finds that no one is listening?  Barely a decade ago, that would have seemed like a conundrum from some fantasy Earth in an alternate dimension.  Now, it is increasingly a plain description of political life on our globe, especially in the Greater Middle East.
These are among the many examples of America’s slumping authority in the Greater Middle East, a process well underway even before Obama entered the Oval Office in January 2009.  It had, for years, been increasingly apparent that Washington’s wars in Afghanistan and Iraq, along with several lesser campaigns in the Global War on Terror, were doomed.
President Obama had failed to form a “coalition of the willing” on the Syrian issue at the G20 summit in St. Petersburg, managing to rally only 10 members. Those who opposed military strikes against Syria without a U.N. Security Council mandate included the five-strong BRICS powers -- Brazil, Russia, India, China, and South Africa -- along with Indonesia, the world’s most populous Muslim nation, and Argentina.

A week earlier, the British parliament defeated a motion to join a U.S.-led operation against Syria. With the British “poodle” slipping Washington’s leash -- an unprecedented act in recent memory
(The Mystery of Washington's Waning Global Influence). Respect has to be earned in the greater world at large, which has more adults per square yard than the entire neoCon section of the House of Representatives Reprehensibles (A Decline Of The American Republic - 2).

MOMCOM has come undone (lyrics here):

Tuesday, October 1, 2013

Epigovernment: The New Model - 4

The word "epigovernment" means "above government" in the same way that "epigenetics" means "above genetics".

The word "above" means having superior control, influence, or power.

In the behavioral sciences it is known that human behavior can determine, alter,  and/or trump genetic activity (Ways of Grandparents).

In the context of political science, in this series Dredd Blog has posted information showing that forces outside of government can "determine, alter,  and/or trump genetic government activity".

Those with curious minds who research this issue have long known about epigovernment because it has been openly declared by those who have been, at one time or another, government officials, employees, and/or contractors:
THE conscious and intelligent manipulation of the organized habits and opinions of the masses is an important element in democratic society. Those who manipulate this unseen mechanism of society constitute an invisible government which is the true ruling power of our country. We are governed, our minds are molded, our tastes formed, our ideas suggested, largely by men we have never heard of. This is a logical result of the way in which our democratic society is organized. Vast numbers of human beings must cooperate in this manner if they are to live together as a smoothly functioning society.
(A Closer Look At MOMCOM's DNA - 4). That is a quote of Edward L. Bernays from his book entitled Propaganda, of whom it is said:
Today, few people outside the public relations profession recognize the name of Edward L. Bernays. As the year 2000 approaches, however, his name deserves to figure on historians' lists of the most influential figures of the 20th century.

It is impossible to fundamentally grasp the social, political, economic and cultural developments of the past 100 years without some understanding of Bernays and his professional heirs in the public relations industry. PR is a 20th century phenomenon, and Bernays -- widely eulogized as the "father of public relations" at the time of his death in 1995 -- played a major role in defining the industry's philosophy and methods.
"Bernays' papers . . . provide illuminating and sometimes disturbing background on some of the most interesting episodes of twentieth-century history, from the way American tobacco tycoons made it socially acceptable for women to smoke to the way other titans of industry persuaded us to pave over our landscape and switch to beer as the 'beverage of moderation.' The companies involved aren't likely to release their records of those campaigns, assuming they still exist. But Bernays saved every scrap of paper he sent out or took in . . . In so doing, he let us see just how policies were made and how, in many cases, they were founded on deception."

In an industry that is notable for its mastery of evasions and euphemisms, Bernays stood out for his remarkable frankness. He was a propagandist and proud of it.
(The Matriarch of the Matrix - 3). What I want to focus on today is not the people involved in the Epigovernment, because they eventually die of old age, rather I want to focus on the
ideology of the Epigovernment, which persists over time to slowly morph, mutate, and change what the visible government does and is.

The graphic to the right shows what we generally consider to be "the government" of the people, by the people, and for the people.

Compare that to the graphic at the top of this post and you see that epigovernment supplants the U.S. Constitution, which we who took Civics 101 understand to be the supreme law of the land under our system of government by laws, not a system of government by individuals:
"This Constitution, and the Laws of the United States which shall be made in Pursuance thereof; and all Treaties made, or which shall be made, under the Authority of the United States, shall be the supreme Law of the Land ..."
(U.S. Constitution, Article 6, Clause 2). The writings of Bernays, quoted up-thread in this post, reveal that a coup was at work long ago (e.g. Committee on Public Information, The Engineering of Consent, and Manufacturing Consent).

The aforesaid coup was/is obviously designed to overthrow the U.S. Constitution and replace it with an "unseen mechanism of society" which is "an invisible government ... the true ruling power of our country" by which "our minds are molded, our tastes formed, our ideas suggested, largely by men we have never heard of" (ibid, quoting Bernays).

In the series A Tale of Coup Cities we explore, among other things, statements by officials who declare in public that a coup has taken place in America.

That coup is replacing or has replaced the freedoms and rights in our Constitution's Bill of Rights, and other constitutional norms (see e.g. ACLU vs. Clapper, Alexander, Hagel, Holder, and Mueller and American Feudalism - 3).

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

More about the Epigovernment:

Monday, September 30, 2013

The Uncertain Gene - 3

Genetic Transcription Mysteries Solved?
In this series we are exploring the old concept of "junk DNA", which is beginning to now be called "dark matter" by evolutionary biologists.

That is because daily discoveries in research are showing that the 98% of the human genome that has been very erroneously called "junk DNA" is anything but that.

The use of the term "dark matter" by biologists is interesting, because for one thing, here at Dredd Blog we feel that so far "dark matter" is a prime example of scientific teleology which is affecting the cosmology discipline whereby imagination gets way ahead of scientific data, then goes off into places where competent science would not go.

It is Freudian that evolutionary biologists would grab that phrase which cosmologists have been using to dogmatically tell us that some 96% of the universe is "dark matter/energy":
Let's remember that the subject is not only "dark matter", but is also the Dredd Blog scientifically rebellious binding of that subject with "faith," because this dark matter is more "scientific faith" than it is provable science.

The big deal in cosmology at the moment is "dark matter", so let's cut to the chase, and let one of the foremost experts explain why this dark matter subject is so hot to trot:
‘We are on the verge of finding out what dark matter is’, Professor Carlos Frenk told the British Science Festival in Bradford. Frenk, director of Durham University’s Institute for Computational Cosmology, predicts that within the next few months, ‘Either dark matter will be discovered, or our model of the universe is not quite right.’
(Subsequent Paper: Dark Matter). The professor said we will soon be "finding out what dark matter is", "dark matter will be discovered", "or our model of the universe is not quite right"?

What the hell, we don't know what 96% of the universe is, nor have we discovered it yet, but he hope to discover it soon?
(Heretics Deny The Dark Matter of Faith - 3). In that vein, let's get ready to zero in on the
Proton Tunneling Into Dark Matter?
specific purpose of today's post, which was explicitly stated in the last post of this series:
Thus, even if she is correct that proton tunneling induced mutant DNA is placed in the non-coding section, along with the other 98% of the human genome, that does not mean that RNA of various sorts will not later utilize it or that it will not be passed on to future iterations of that DNA molecule (to be covered exhaustively in next post of this series).
(The Uncertain Gene - 2). Let's quickly gather our thoughts before we move on, and reflect once again on where the wrong headed notion of "junk DNA" came from, not to mention the years of damage done to science by that faulty scholarship and faulty research:
The 1960s discovery that much nuclear DNA in eukaryotic cells does not code for proteins was quickly interpreted as evidence for the evolution of eukaryotic genomes. Papers were published suggesting a nomenclature reflecting evolutionary assumptions about this “junk DNA.” Noncoding DNA was also used as evidence for the selfish gene theory popularized by Richard Dawkins and others. As many important functions played by noncoding DNA have come to light, the assumption can no longer be made that it represents DNA potsherds of evolution. Now the assumption of functionality in what was once called junk DNA is widespread, but its interpretation within a Darwinian framework remains. Thus, what was once touted as evidence of life’s evolutionary history because of its lack of function is now interpreted as evidence of the same thing because it is functional. This experience calls into question how much data actually unambiguously support Darwinian evolution, what evolutionary theory actually predicts, and how data can be used to check its predictive power.
(Tel Aviv University, "Rushing To Judgment", PDF, emphasis added). Once researchers looked into the packages and all the traffic in the "junk" pile, they began to realize that the bed time stories about junk DNA were teleological imaginings outside of competent scientific reasoning:
Snippets of information contained in dark matter, or “junk DNA,” can alter the way a gene gets put together, according to new research.

These small sequences of genetic information tell the gene how to splice, either by enhancing the splicing process or inhibiting it. The research opens the door for studying the dark matter of genes. And it helps us further understand how mutations or polymorphisms affect the functions of any gene,” says study senior author Zefeng Wang, assistant professor of pharmacology in the University of North Carolina School of Medicine.

Published in the current issue of Nature Structural & Molecular Biology, the findings may be viewed in terms of the film industry’s editorial process where snippets of celluloid are spliced, while others end up unused on the proverbial cutting room floor.

Taken from a DNA point of view, not every piece of it in each human gene encodes for a functional protein; only about 10 percent does, in coding regions called “exons.” The other 90 percent of the stuff that fills the intervening regions are longer stretches of dark matter known as “introns.”

But something mysterious happens to introns during the final processing of messenger RNA (mRNA), the genetic blueprint that’s sent from the cell’s nucleus to its protein factory. Only particular exons may be included within the final mRNA produced from that gene, whereas the introns are cut out and destroyed.

It’s therefore easier to understand why more scientific attention has been given to exons. “When people are looking at the genetics of a disease, most of the time they’re looking for the change in the coding sequence,” Wang says.

“But 90 percent of the sequence is hidden in the gene’s introns. So when you study gene variants or polymorphisms that cause human disease, you can only explain the part that’s in the exon. Yet the majority remains unexplainable because they’re in the introns.”
(Univ. South Carolina, ‘Junk’ DNA Assembly Instructions, emphasis added). The genetic movie starring you, me and everyone else, we now know, is being made by also using the information in "the junk DNA or dark matter" of the human genome and/or microbiome.

In the previous post of this series we discussed the book Quantum Aspects of Life, a science textbook, which calls some of this activity "quantum choreography", while at the same time cautioning against teleology.

So, how is all that cutting, pasting, and organizing done so that the genetic movie is a hit, and not a disaster?

The answer is thousands of specialized molecular machines, not made of junk, but made of various atoms which comprise a sophisticated genetic factory of such machines.

Here is what "junk DNA" or "dark matter" really is:
"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. "These initiation machines that were not associated with genes were clearly active since they were making RNA and aligned with fragments of RNA discovered by other scientists," Pugh said. "In the early days, these fragments of RNA were generally dismissed as irrelevant ["junk"] since they did not code for proteins." Pugh added that it was easy to dismiss these fragments because they lacked a feature called polyadenylation -- a long string of genetic material, adenosine bases -- that protect the RNA from being destroyed. Pugh and Venters further validated their surprising findings by determining that these non-coding initiation machines recognized the same DNA sequences as the ones at coding genes, indicating that they have a specific origin and that their production is regulated, just like it is at coding genes.
(Scientists Discover the Origins, emphasis added). One wonders why this was not contemplated prior to going off into junk science, especially since molecular machines are found elsewhere in cells.

Other molecular machines are doing other types of work necessary for cell existence (see e.g. Putting A Face on Machine Mutation, Do Molecular Machines Deliver Toxins of Power?, Weekend Rebel Science Excursion - 17,  and Did Abiotic Intelligence Precede Biotic Intelligence?).

In the next episode of this series we will take a look at the participation of microbes within the realm of the human genome and/or microbiome previously wrongly presumed to be just a junk yard (preview The Human Microbiome Congress for a taste of what is coming).

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

Sunday, September 29, 2013

Follow The Immunity - 2

New Meaning of "National Immunity"
In the first post of this series, we focused primarily on the immunity of individual political figures and corporations from prosecution for crimes.

So, in today's post we will focus on the immunity of nations ... national immunity from doing wrong things to America and Americans.

Specifically, today Dredd Blog will focus on the nation of Saudi Arabia and its immunity from having done wrong to America and Americans --its immunity granted to it by the Epigovernment --its immunity talked about and declared in public in the media, in the press.

Since this has been revealed in another Dredd Blog series,  let's review the information from that post (Fighting Terrorism For 200 Years - 4):

Lest we forget: a day or so ago Saudi Arabian Royals offered to pay us in full to invade Syria and bring down Assad (The War Whores Ride The War Horse).

Hardball, March 1, 2012:

Morning Joe, March 1, 2012:

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