Friday, August 8, 2014

On the Origin of the Genes of Viruses - 10

The DNA molecule is NOT alive.
In this series we contemplate the spectre of viruses being the first carbon based life forms to evolve billions of years after molecular machines had already evolved.

People have a difficult time wondering about how machines could evolve.

Which is not logical because machines are not as complex as organic life forms are.

If evolution proceeds from non-life to life, from simple to complex, then it should be obvious that machines composed of atomic parts, which later became molecules, would have to evolve first.

Those controversial issues have been discussed in the previous posts in this series as well as the following complimentary series (The Uncertain Gene, 2, 3, 4, 5, 6, 7, 8, 9, 10) and (Putting A Face On Machine Mutation, 2, 3, 4).

Those issues were also writ large in the posts (The New Paradigm: The Physical Universe Is Mostly Machine, Autopoiesis: It's Not Just For Machines Anymore).

With that background in mind, let's consider a recent paper:
The MSU-led research provides the first detailed blueprint of a multi-subunit "molecular machinery" that bacteria use to detect and destroy invading viruses.

"We generally think of bacteria as making us sick, but rarely do we consider what happens when the bacteria themselves get sick. Viruses that infect bacteria are the most abundant biological agents on the planet, outnumbering their bacterial hosts 10 to 1," said Blake Wiedenheft, senior author of the paper and assistant professor in MSU's Department of Microbiology and Immunology.

"Bacteria have evolved sophisticated immune systems to fend off viruses. We now have a precise molecular blueprint of a surveillance machine that is critical for viral defense," Wiedenheft said.
Abiotic Came 1st
"This surveillance machine consists of 12 different parts and each part of the machine has a distinct job. If we're missing one part of the machine, it doesn't work."

Understanding how these machines work is leading to unanticipated new innovations in medicine and biotechnology and agriculture. These CRISPR-associated machines are programmable nucleases (molecular scissors) that are now being exploited for precisely altering the DNA sequence of almost any cell type of interest.

"In nature, these immune systems evolved to protect bacteria from viruses, but we are now repurposing these systems to cut viral DNA out of human cells infected with HIV. You can think of this as a form of DNA surgery. Therapies that were unimaginable may be possible in the future," Wiedenheft said.
(Molecular Machine Dynamics Identified, emphasis added). In other words, this is not science fiction, rather, it is applied science now.

The microbial world has molecular machine tools at its disposal which are used to do phenomenal brain surgery:
"... this is a protozoan parasite that knows more about the neurobiology of anxiety and fear than 25,000 neuroscientists standing on each other's shoulders ..."
(Hypothesis: Microbes Generate Toxins of Power - 6, quoting Dr. Sapolsky). In future posts we will look at genetic tools of viruses.

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

Thursday, August 7, 2014

Civilization Is Now On Suicide Watch - 3

Serious as a heart attack comes to mind.
Regular readers of Daily Kos know that it is a moderate site when it comes to global warming and conspiracy theories because those regular readers know Daily Kos tends to be highly cautious about such matters.

So, I was a bit taken aback with a post there by Meteor Blades, who read some information on another moderate site that was alarming.

The subject was methane release in the Arctic, specifically in the sense of a "tipping point" being reached, a point of no return to business as usual.

It is not "radical" to consider what is real and what is happening now, nor is it "radical" to contemplate the consequences of the government ignoring Oil-Qaeda madness that seems to be designed to kill a lot of people.

The Time Magazine cover, above, from some years back, conveys the feeling generated by the post at Daily Kos:
This week, scientists made a disturbing discovery in the Arctic Ocean: They saw "vast methane plumes escaping from the seafloor," as the Stockholm University put it in a release disclosing the observations. The plume of methane—a potent greenhouse gas that traps heat more powerfully than carbon dioxide, the chief driver of climate change—was unsettling to the scientists.

But it was even more unnerving to Dr. Jason Box, a widely published climatologist who had been following the expedition. As I was digging into the new development, I stumbled upon his tweet, which, coming from a scientist, was downright chilling:
If even a small fraction of Arctic sea floor carbon is released to the atmosphere, we're f'd.
Box, who is currently a professor of glaciology at the Geological Survey of Denmark and Greenland, has been studying the Arctic for decades. His accolade-packed Wikipedia page notes that he's made some 20 expeditions to the Arctic since 1994, and served as the lead author on the Greenland section of NOAA's State of the Climate report from 2008-2012. He also runs the Dark Snow project and writes about the latest findings in the field at his blog, Meltfactor. In other words, Box knows the Arctic, and he knows climate change—and the methane plumes had him blitzed enough to bring out the F bombs.

Now, the scientists in the Arctic didn't fully understand why the plumes were occurring. But they speculated that a warmer "tongue" of ocean current was destabilizing methane hydrates on the Arctic slope.

I called the scientist at his office in Copenhagen, and he talked frankly and emphatically about the new threat, and about the specter of climate change in general. He also swore like a sailor, which I've often wondered how climatologists refrain from doing, given the urgency of the problem—it's certainly an entirely accurate way to communicate the climate plight. […]
(Meteor Blades, cf. Motherboard, Salon, Stockholm Univ.). Regular readers here at Dredd Blog know that "radical" is not a word we shy away from, so long as it is the reality going on around us.

From posts in this series, one will quickly discern that Dredd Blog wants you to know what is going on, whether that knowledge is disturbing or not, such as in Civilization Is Now On Suicide Watch where I speculated that the recent, mysterious Siberian Craters were methane related.

As it turns out, Dredd Blog suspicions are, more often than not, confirmed (Nature: Siberian Craters Methane Related).

Regular readers know that together we have been watching the methane plumes for years:
Dramatic and unprecedented plumes of methane - a greenhouse gas 20 times more potent than carbon dioxide - have been seen bubbling to the surface of the Arctic Ocean by scientists undertaking an extensive survey of the region. The scale and volume of the methane release has astonished the head of the Russian research team who has been surveying the seabed of the East Siberian Arctic Shelf off northern Russia for nearly 20 years. In an exclusive interview with The Independent, Igor Semiletov of the International Arctic Research Centre at the University of Alaska Fairbanks, who led the 8th joint US-Russia cruise of the East Siberian Arctic seas, said that he has never before witnessed the scale and force of the methane being released from beneath the Arctic seabed.
(New Climate Catastrophe Policy: Triage - 5, cf. Perfect Storm ...). On the other hand, those who want to water reality down (so people don't "panic") are not doing a service, they are deceiving others.

They are doing the bidding of Oil-Qaeda.

In this context, the governments of the world that are not serious about saving civilization are serious about destroying it (MOMCOM's Mass Suicide & Murder Pact, 2, 3, 4, 5).

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

Wednesday, August 6, 2014

Origin of the Classic Nuclear Bully - 3

Will the "good nuke" please stand up
Some 69 years ago, today, a terrible virus was planted in the minds of Earthlings.

A virus that is still within our culture, but a virus that we try to forget and ignore.

Like the currently active Ebola virus indiscriminately attacking civilians as well as doctors, the Ebola Enola Gay dropped Little Boy on an unsuspecting civilian population in Hiroshima, Japan.

Like the Enola Ebola virus which indiscriminately kills those who give aid to both the dying and the infirmed, the nuclear bomb exploded over Hiroshima, killing doctors along with anyone else it could:
On this day in 1945, at 8:16 a.m. Japanese time, an American B-29 bomber, the Enola Gay, drops the world's first atom bomb, over the city of Hiroshima. Approximately 80,000 people are killed as a direct result of the blast, and another 35,000 are injured. At least another 60,000 would be dead by the end of the year from the effects of the fallout.
Of the city's 200 doctors before the explosion; only 20 were left alive or capable of working. There were 1,780 nurses before—only 150 remained who were able to tend to the sick and dying.

According to John Hersey's classic work Hiroshima, the Hiroshima city government had put hundreds of schoolgirls to work clearing fire lanes in the event of [conventional] incendiary bomb attacks. They were out in the open when the Enola Gay dropped its load.
(History Channel, "Aug 6, 1945: Atomic bomb is dropped on Hiroshima"). The Gaza Strip terrorism, where Israel committed the indiscriminate killing of civilians, has been condemned recently.

What makes a far worse killing that took place in Hiroshima a "good" thing?

We are told that "WW II was a good war" ... so evidently the way a particular war is characterized, by Propaganda Central, makes the killing of civilians either good killing or bad killing?

Evidently everyone thinks "that kind of killing" is ok, because everyone wants a nuke or two.

Which has now brought us to the Doomsday Clock:
If some extraterrestrial species were compiling a history of Homo sapiens, they might well break their calendar into two eras: BNW (before nuclear weapons) and NWE (the nuclear weapons era). The latter era, of course, opened on August 6, 1945, the first day of the countdown to what may be the inglorious end of this strange species, which attained the intelligence to discover the effective means to destroy itself, but -- so the evidence suggests -- not the moral and intellectual capacity to control its worst instincts.

Day one of the NWE was marked by the “success” of Little Boy, a simple atomic bomb. On day four, Nagasaki experienced the technological triumph of Fat Man, a more sophisticated design. Five days later came what the official Air Force history calls the “grand finale,” a 1,000-plane raid -- no mean logistical achievement -- attacking Japan’s cities and killing many thousands of people, with leaflets falling among the bombs reading “Japan has surrendered.” Truman announced that surrender before the last B-29 returned to its base.

Those were the auspicious opening days of the NWE. As we now enter its 70th year, we should be contemplating with wonder that we have survived. We can only guess how many years remain.

Some reflections on these grim prospects were offered by General Lee Butler, former head of the U.S. Strategic Command (STRATCOM), which controls nuclear weapons and strategy. Twenty years ago, he wrote that we had so far survived the NWE “by some combination of skill, luck, and divine intervention, and I suspect the latter in greatest proportion.”
(Tomgram, Noam Chomsky, emphasis added). Not many are willing to say that human extinction is good, so will nuclear killing begin or end?

And even if nukes were to be banned and removed from the planet, would that remove the spectre of human extinction from before our eyes?

Regular readers know that Dredd Blog posts about civilization being on suicide watch (Civilization Is Now On Suicide Watch, 2), and a recent paper by a well known ecologist used different words to say the same thing:
It is prudent not to dismiss the possibility that the Earth System – the biosphere – could die if critical thresholds are crossed … Humanity’s well-being depends upon complex ecosystems that support life on our planet, yet we are consuming the biophysical foundation of civilization … Scientists need to take greater latitude in proposing solutions that lie outside the current political paradigms and sovereign powers …
(Collapse of the Global Biosphere, quoting a scientific journal, emphasis added). The war on our environment is not primarily nuclear, but it too can bring human extinction.

There are no good nuclear wars, so WW II was a bad war.

It is way past the time for us to grasp that reality before we become extinct.

The previous post in this series is here.

Tuesday, August 5, 2014

Agnotology: The Surge - 11

"War on whites" research staff of Rep. Mo Brooks (R-AL)
In this series we have noticed and noted several things while taking a look at Agnotology, the study of ignorance generators in American culture.

Ignorance generators within U.S. culture have been around for a century or so.

Their potency and realm of influence sharply increased as communication technology developed, improved, and then spread far and wide via radio, television, and the Internet.

Governments at times grabbed control of media, and ignorance via propaganda prospered and spread along with science, industry, and education (Mocking America, The Deceit Business).

In today's post let's take another look at how brazen the Ignorati have become.

Once ignorance generators establish control over the thinking of a meme complex, one suspects everything that those in that meme complex say is a quote from The Onion:
Representative Mo Brooks [R-AL] , appearing on Laura Ingraham’s radio program, diagnoses the Republican Party’s so-called difficulty attracting nonwhite voters. “This is a part of the war on whites that’s being launched by
Rep. Mo Brooks (R-AL) deep in thought.
the Democratic Party,” explains Brooks, “and the way in which they’re launching this war is by claiming that whites hate everybody else.”

White racial victimization is a [mythical] concept as old as racism itself. White reactionaries in the 19th century imagined that abolishing slavery would turn white people themselves into slaves, and the concept of white subjugation was transferred into such things as black suffrage, civil rights, and so on. The war on whites has raged continuously in the right-wing mind for more than two centuries.
Likewise, the operative mechanism of the War on Whites is in dire need of refinement. Brooks defines it as “claiming that whites hate everybody else."
(NY Magazine, by Jonathan Chait, emphasis added). Ignorance generators have been around for a long time.

The wrong-wingers like to hold on to ancient myths and become zealots of obvious nonsense.

Blacks in America did not go to Africa to kidnap then bring whites to this land to become slaves, nor did Blacks maintain Jim Crow laws and discrimination for decades after the Civil War (Blind Willie McTell News).

The "party of ignorance" came to the mind of Gov. Jindal when he heard idiotic statement
A book about ignorance
after idiotic statement from GOP candidates:
“It is no secret we had a number of Republicans damage our brand this year with offensive, bizarre comments — enough of that,” Jindal said. “It’s not going to be the last time anyone says something stupid within our party, but it can’t be tolerated within our party. We’ve also had enough of this dumbed-down conservatism. We need to stop being simplistic, we need to trust the intelligence of the American people and we need to stop insulting the intelligence of the voters.”
(Politico, quoting Gov. Jindal, R-LA). Agnotologists know that volumes of research has been done on racism --research which shows that symbolic racism is deeply embedded in the U.S. psyche and is perpetuated by racial ignorance now being promoted by Koch Brothers types of ignorance generating organizations (Symbolic Racism: A Look At The Science - 3, Hypothesis: The Cultural Amygdala, 2, 3, 4).

But as long as the Southern Strategy (see video below) is used to maintain darkness in the cultural amygdala of the Ignorati, Agnotology will continue to bear fruits like Mo Brooks, Curly Brooks, and Larry Brooks (shown in photos above).

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

Monday, August 4, 2014

If CSPAN is Not Afraid to Listen, Why is Anyone Afraid to Listen?

"The Beginning is near"
Fear to depart from the status quo happens when there is either an end or a beginning that would change things.

That a beginning or an ending is near is not in and of itself a bad thing.

The thing itself that is about to begin or to end is the good or bad thing.

"Time keeps on slippin' into the future" no matter what fears we do have or we do not have as the song points out ("Fly Like an Eagle, Steve Miller Band").

Here are some quotes about fear:
1) Abraham Maslow, psychologist: "I have learned the novice can often see things that the expert overlooks. All that is necessary is not to be afraid of making mistakes, or of appearing naive."

2) Bill Cosby, comedian: "Decide that you want it more than you are afraid of it."

3) Gandhi, spiritual/political leader: "The enemy is fear. We think it is hate; but, it is fear."

4) Winston Churchill, UK politician. statesman; former British Prime Minister: "When I look back on all these worries, I remember the story of the old man who said on his deathbed that he had had a lot of trouble in his life, most of which had never happened."

5) Judy Blume, author: “Each of us must confront our own fears, must come face to face with them. How we handle our fears will determine where we go with the rest of our lives. To experience adventure or to be limited by the fear of it.”

6) Don Miguel Ruiz, author, speaker, Shaman: "Death is not the biggest fear we have; our biggest fear is taking the risk to be alive—the risk to be alive and express what we really are."

7) Ralph Waldo Emerson, essayist, poet, philosopher: "When a resolute young fellow steps up to the great bully, the world, and takes him boldly by the beard, he is often surprised to find it comes off in his hand, and that it was only tied on to scare away the timid adventurers."

8) Dale Carnegie, speaker, writer: "Inaction breeds doubt and fear. Action breeds confidence and courage. If you want to conquer fear, do not sit home and think about it. Go out and get busy."

9) Oprah Winfrey, television pioneer, actress/producer: “The thing you fear most has no power. Your fear of it is what has the power. Facing the truth really will set you free.”

10) Henry Ford, US industrialist: "One of the greatest discoveries a man makes, one of his great surprises, is to find he can do what he was afraid he couldn't do."

11) Frank Sinatra, singer, actor: "Fear is the enemy of logic."

12) Colin Powell, US statesman; four-star general: "Don't take counsel of your fears or naysayers."

13) Franklin D. Roosevelt, 32nd US President: "The only thing we have to fear is fear itself."
(Psychology Today, "13 Quotes to Help You Face Your Fears", emphasis added). Now you are ready to listen to something some people think is too scary.

But first remember: “Never believe anything until it has been officially denied.” – Claud Cockburn

CSPAN (Link to CSPAN Video) listens to Architects & Engineers for 911 Truth.