Tuesday, July 23, 2013

2nd/3rd line inheritors of the civil rights movement gotta find a new hustle...,

hoover | Today's black leadership pretty much lives off the fumes of moral authority that linger from its glory days in the 1950s and '60s. The Zimmerman verdict lets us see this and feel a little embarrassed for them. Consider the pathos of a leadership that once transformed the nation now lusting for the conviction of the contrite and mortified George Zimmerman, as if a stint in prison for him would somehow assure more peace and security for black teenagers everywhere. This, despite the fact that nearly one black teenager a day is shot dead on the South Side of Chicago—to name only one city—by another black teenager.

This would not be the first time that a movement begun in profound moral clarity, and that achieved greatness, waned away into a parody of itself—not because it was wrong but because it was successful. Today's civil-rights leaders have missed the obvious: The success of their forbearers in achieving social transformation denied to them the heroism that was inescapable for a Martin Luther King Jr. or a James Farmer or a Nelson Mandela. Jesse Jackson and Al Sharpton cannot write a timeless letter to us from a Birmingham jail or walk, as John Lewis did in 1965, across the Edmund Pettus Bridge in Selma, Ala., into a maelstrom of police dogs and billy clubs. That America is no longer here (which is not to say that every trace of it is gone).

The Revs. Jackson and Sharpton have been consigned to a hard fate: They can never be more than redundancies, echoes of the great men they emulate because America has changed. Hard to be a King or Mandela today when your monstrous enemy is no more than the cherubic George Zimmerman.

Why did the civil-rights leadership use its greatly depleted moral authority to support Trayvon Martin? This young man was, after all, no Rosa Parks—a figure of indisputable human dignity set upon by the rank evil of white supremacy. Trayvon threw the first punch and then continued pummeling the much smaller Zimmerman. Yes, Trayvon was a kid, but he was also something of a menace. The larger tragedy is that his death will come to very little. There was no important principle or coherent protest implied in that first nose-breaking punch. It was just dumb bravado, a tough-guy punch.

The civil-rights leadership rallied to Trayvon's cause (and not to the cause of those hundreds of black kids slain in America's inner cities this very year) to keep alive a certain cultural "truth" that is the sole source of the leadership's dwindling power. Put bluntly, this leadership rather easily tolerates black kids killing other black kids. But it cannot abide a white person (and Mr. Zimmerman, with his Hispanic background, was pushed into a white identity by the media over his objections) getting away with killing a black person without undermining the leadership's very reason for being.

The purpose of today's civil-rights establishment is not to seek justice, but to seek power for blacks in American life based on the presumption that they are still, in a thousand subtle ways, victimized by white racism. This idea of victimization is an example of what I call a "poetic truth." Like poetic license, it bends the actual truth in order to put forward a larger and more essential truth—one that, of course, serves one's cause. Poetic truths succeed by casting themselves as perfectly obvious: "America is a racist nation"; "the immigration debate is driven by racism"; "Zimmerman racially stereotyped Trayvon." And we say, "Yes, of course," lest we seem to be racist. Poetic truths work by moral intimidation, not reason.

In the Zimmerman/Martin case the civil-rights establishment is fighting for the poetic truth that white animus toward blacks is still such that a black teenager—Skittles and ice tea in hand—can be shot dead simply for walking home. But actually this establishment is fighting to maintain its authority to wield poetic truth—the authority to tell the larger society how it must think about blacks, how it must respond to them, what it owes them and, then, to brook no argument.

yet another admonition against the hair-trigger male ego...,

WSJ | Two tragedies are apparent in the Trayvon Martin case. The first is obvious: A teenager—unarmed and committing no crime—was shot dead. Dressed in a "hoodie," a costume of menace, he crossed paths with a man on the hunt for precisely such clichés of menace. Added to this—and here is the rub—was the fact of his dark skin.

Maybe it was more the hood than the dark skin, but who could argue that the skin did not enhance the menace of the hood at night and in the eyes of someone watching for crime. (Fifty-five percent of all federal prisoners are black though we are only 12% of the population.) Would Trayvon be alive today had he been walking home—Skittles and ice tea in hand—wearing a polo shirt with an alligator logo? Possibly. And does this make the ugly point that dark skin late at night needs to have its menace softened by some show of Waspy Americana? Possibly. 

What is fundamentally tragic here is that these two young males first encountered each other as provocations. Males are males, and threat often evokes a narcissistic anger that skips right past reason and into a will to annihilate: "I will take you out!" There was a terrible fight. Trayvon apparently got the drop on George Zimmerman, but ultimately the man with the gun prevailed. Annihilation was achieved.

If this was all there was to it, the Trayvon/Zimmerman story would be no more than a cautionary tale, yet another admonition against the hair-trigger male ego.

steele got the "bound man" part right...,

WaPo | It was disarming to hear the most powerful man in the world speak of powerlessness.

“You know, when Trayvon Martin was first shot I said that this could have been my son,” the president said. “Another way of saying that is Trayvon Martin could have been me 35 years ago.”

Obama noted that “the African American community is looking at this issue through a set of experiences and a history that doesn’t go away,” then narrowed his focus once again to the personal. I quote the next passage at length because, for me, it is the heart of the speech:

“There are very few African American men in this country who haven’t had the experience of being followed when they were shopping in a department store. That includes me. There are very few African American men who haven’t had the experience of walking across the street and hearing the locks click on the doors of cars. That happens to me — at least before I was a senator. There are very few African Americans who haven’t had the experience of getting on an elevator and a woman clutching her purse nervously and holding her breath until she had a chance to get off.”

I’m not sure I know an African American man who hasn’t had these experiences. What’s new is the idea that the president of the United States knows what it feels like to be eyed warily, to be presumed guilty of malicious intent. That gets your attention.

Obama went on to explain why, in his view, Martin’s death and Zimmerman’s acquittal had such tremendous impact for black Americans. African Americans are not naive, he said; we know that young black men are “disproportionately both victims and perpetrators of violence.” But it is not making excuses for bad conduct to recognize that the pathology seen in many poor black communities has a historical context. Refusing to acknowledge this context, Obama noted, “adds to the frustration” that many African Americans feel.

“There is a history of racial disparities in the application of our criminal laws,” Obama said. He might have gone further and noted that nowhere will you find citizens more supportive of tough law-and-order policies than in poor, high-crime neighborhoods. But law-abiding citizens want those policies applied fairly — and know that often they are not.

There is “a sense that if a white male teen was involved in the same kind of scenario, that, from top to bottom, both the outcome and the aftermath might have been different.” Here the president was guilty of understatement; most of us don’t have “a sense” that things would be different, we’d bet the ranch on it.

the wild west mentality...,

WaPo | Zimmerman would not have followed Martin if Zimmerman weren’t carrying a gun. If Martin were perceived as dangerous, wouldn’t an unarmed individual keep his distance until police arrived? 

Thus, we conclude that Zimmerman’s actions led to the confrontation that ultimately resulted in a fight that ended with the fatal shooting. 

It never should have happened. And it didn’t have to.

The jury obviously felt that Zimmerman acted in self-defense, or, at least, that the state failed to prove otherwise. It must have been a terrible conclusion to reach because, no matter the legal definitions that guided them, it seems impossible that someone’s young son, guilty of nothing, should die while his killer walks. Adages become such for a reason: The law is an ass.

As soon as passions cool, assuming we let them, the discussion that needs to take place surrounds a question: What was George Zimmerman doing walking around his neighborhood armed and loaded? In what world is this normal behavior? 

The answer: Not a world most of us want to live in. Let’s start there.

Monday, July 22, 2013

james earl carter: the u.s. has no functioning democracy...,

jonathanturley | We have been discussing the collapse of the American civil liberties movement and the attacks on the free press and privacy under the Obama Administration. As discussed in prior columns, we continue to refer to the United States as the “land of the free” despite a comprehensive reduction of civil liberties and due process in this country. The Snowden affair has put that record in sharp relief as the White House and Congress has joined together in barring the prosecution of perjury by high ranking officials and pursuing Snowden with close to unhinged rage. As previously discussed, our governing class has created a new American Animal farm. Long ago, American politicians adopted a type of dismissive paternalism toward the public as shepherds to so many sheep. Then one sheep goes and spooks the flock. The response has been bipartisan rage that has included demands to cut off aid to entire nations if they grant sanctuary to this whistleblower and even boycott the Olympics. The shepherds want Snowden made into mutton for stampeding the flock and no measure appears too extreme. Now Jimmy Carter has entered the fray and said what many citizens are saying in denouncing our duopoly. Carter told Spiegel “America has no functioning democracy.” Of course, you have to live in Germany to read such views. 

Carter has rightfully pointed to the dramatic reduction of the United States as a moral authority in the world after Bush and Obama. He clearly views Edward Snowden as a whistleblower. Yet, the media has yielded to the demand of the White House that Snowden not be called a whistleblower. This is follows media allies who have attacked Snowden and even mocked his concern about coming back home. As for the refusal to call him a whistleblower, it seems part of the full court press to demonize Snowden or prevent favorable references to him.

math behind leak crackdown

NYTimes | Soon after President Obama appointed him director of national intelligence in 2009, Dennis C. Blair called for a tally of the number of government officials or employees who had been prosecuted for leaking national security secrets. He was dismayed by what he found. 

In the previous four years, the record showed, 153 cases had been referred to the Justice Department. Not one had led to an indictment. 

That scorecard “was pretty shocking to all of us,” Mr. Blair said. So in a series of phone calls and meetings, he and Attorney General Eric H. Holder Jr. fashioned a more aggressive strategy to punish anyone who leaked national security information that endangered intelligence-gathering methods and sources. 

“My background is in the Navy, and it is good to hang an admiral once in a while as an example to the others,” said Mr. Blair, who left the administration in 2010. “We were hoping to get somebody and make people realize that there are consequences to this and it needed to stop.” 

The Obama administration has done its best to define those consequences, with an aggressive focus on leaks and leakers that has led to more than twice as many prosecutions as there were in all previous administrations combined. It also led to a significant legal victory on Friday when a federal appeals court accepted the Justice Department’s argument that the First Amendment does not protect reporters from having to reveal the sources suspected of leaking information to them. 

In tracing the origins of this effort, present and former government officials said the focus on leaks began at the administration’s highest levels and was driven by pressure from the intelligence agencies and members of Congress.

ayn rand killed sears...,

salon | Eddie Lampert, the legendary hedge fund manager, was once hailed as the “Steve Jobs of the investment world” and the second coming of Warren Buffett. These days, he claims the number 2 spot on Forbes’ list of America’s worst CEOs. He has destroyed Sears, the iconic retail giant founded in 1886, which used to be known as the place “Where America Shops.”

America now avoids Sears at all costs, thanks largely to Mr. Lampert and his love of twisted economic logic.

So when you walk into a Sears store today, you find a sad, dingy scene with scuffed floors and chipped paint. Tense-looking workers hover over merchandise scattered onto ugly display tables. Hardly makes you want to buy a microwave.

Conclusion:  The lessons of Crazy Eddie seem so obvious that a bunch kids running a lemonade stand could understand them. You have to know something about the business you’re running, especially a big one. Success requires cooperation rather than constant competition. Greed is ultimately destructive.

The invisible hand of the market appears to have attempted to slap Lampert upside the head to teach him these things. But he remains committed to his nonsense, and the real losers are all the hard-working people who have lost their jobs, and the potential loss to the American economy of two revered brands.

It’s probably a good thing Ayn Rand never tried to run a business.

Sunday, July 21, 2013

establishment "peace and social activism" opposes escalation of violent self-defense..,

WaPo | A useful moment in President Obama’s thoughtful and thought-provoking remarks Friday on crime, race and Trayvon Martin — one of several such useful moments — came when Mr. Obama questioned the thinking behind “stand your ground” laws:

“If we’re sending a message as a society in our communities that someone who is armed potentially has the right to use those firearms even if there’s a way for them to exit from a situation, is that really going to be contributing to the kind of peace and security and order that we’d like to see?” 

The president’s question resonated with the words of Eric H. Holder Jr., his attorney general, who addressed the NAACP early last week. These laws “senselessly expand the concept of self defense,” Mr. Holder argued. “By allowing — and perhaps encouraging — violent situations to escalate in public,” he continued, “such laws undermine public safety.” 

Critics slammed both men for their remarks. But Mr. Obama and Mr. Holder were right to address the issue, and they are right on its substance.

Florida was the first to adopt a stand-your-ground statute, in 2005; about half the states have followed. Instead of requiring potential victims of crime to retreat if they have a safe escape route, these laws allow people to use deadly force without attempting to avoid a potentially lethal confrontation. They also often contain other generous protections for killers claiming self-defense.

George Zimmerman, who shot Trayvon Martin, didn’t invoke Florida’s stand-your-ground statute in an attempt to avoid trial. But the law could have contributed to the police decision not to charge him for more than a month after he killed Mr. Martin. At trial, the judge informed the Zimmerman jury explicitly of the stand-your-ground law, and the statute came up in closing arguments. 

There is a reason that the duty to retreat is a concept respected by centuries of legal application. Setting a laxer standard encourages tragic mistakes, poor judgment and perhaps even vigilantism. A recent study from two Texas A&M University researchers found that “lowering the expected cost of lethal force causes there to be more of it.” Stand-your-ground states saw more homicides than their peers — about 600 more a year over the period they studied. One possible explanation is that stand-your-ground laws encourage people to escalate conflicts rather than withdraw.

duty to retreat?

wikipedia | In the criminal law, the duty to retreat is a specific component which sometimes appears in the defense of self-defense, and which must be addressed if the defendant is to prove that his or her conduct was justified. In those jurisdictions where the requirement exists, the burden of proof is on the defense to show that the defendant was acting reasonably. This is often taken to mean that the defendant had first avoided conflict and secondly, had taken reasonable steps to retreat and so demonstrated an intention not to fight before eventually using force.

Some U.S. jurisdictions require that a person retreat from an attack, and allow the use of deadly force in self-defense only when retreat is not possible or when retreat poses a danger to the person under attack. The duty to retreat is not universal, however. For example, police officers are not required to retreat when acting in the line of duty. Similarly, some courts have found no duty to retreat exists when a victim is assaulted in a place where the victim has a right to be, such as within one's own home.[1] The Model Penal Code[2] suggests statutory language that also recognizes an exception to the usual duty to retreat when the victim of the attack is in his or her own dwelling or place of work. It is common to exempt a person's home or car from the duty to retreat, known as the castle doctrine.

Many states employ stand your ground laws that do not require an individual to retreat and allow one to match force for force, deadly force for deadly force. The Washington State Supreme Court, for example, has ruled "that there is no duty to retreat when a person is assaulted in a place where he or she has a right to be."[3][4]

stand your ground law...,

wikipedia | A stand-your-ground law is a type of self-defense law that gives individuals the right to use reasonable force to defend themselves without any requirement to evade or retreat from a dangerous situation. It is law in certain jurisdictions within the United States. The basis may lie in either statutory law and or common law precedents. One key distinction is whether the concept only applies to defending a home or vehicle, or whether it applies to all lawfully occupied locations. Under these legal concepts, a person is justified in using deadly force in certain situations and the "stand your ground" law would be a defense or immunity to criminal charges and civil suit. The difference between immunity and a defense is that an immunity bars suit, charges, detention and arrest. A defense, such as an affirmative defense, permits a plaintiff or the state to seek civil damages or a criminal conviction but may offer mitigating circumstances that justify the accused's conduct.

More than half of the states in the United States have adopted the Castle doctrine, that a person has no duty to retreat when their home is attacked. Some states go a step further, removing the duty of retreat from other locations. "Stand Your Ground", "Line in the Sand" or "No Duty to Retreat" laws thus state that a person has no duty or other requirement to abandon a place in which he has a right to be, or to give up ground to an assailant. Under such laws, there is no duty to retreat from anywhere the defender may legally be.[1] Other restrictions may still exist; such as when in public, a person must be carrying firearms in a legal manner, whether concealed or openly.

"Stand your ground" governs U.S. federal case law in which right of self-defense is asserted against a charge of criminal homicide. The Supreme Court of the United States ruled in Beard v. U.S. (158 U.S. 550 (1895)) that a man who was "on his premises" when he came under attack and "...did not provoke the assault, and had at the time reasonable grounds to believe, and in good faith believed, that the deceased intended to take his life, or do him great bodily harm...was not obliged to retreat, nor to consider whether he could safely retreat, but was entitled to stand his ground."[2][3]

Justice Oliver Wendell Holmes, Jr. declared in Brown v. United States (1921) (256 U.S. 335, 343 (16 May 1921)), a case that upheld the "no duty to retreat" maxim, that "detached reflection cannot be demanded in the presence of an uplifted knife".[4]

castle doctrine...,

wikipedia | A Castle Doctrine (also known as a Castle Law or a Defense of Habitation Law) is an American legal doctrine that designates a person's abode (or, in some states, any legally-occupied place [e.g., a vehicle or workplace]) as a place in which that person has certain protections and immunities permitting him, in certain circumstances, to use force (up to and including deadly force) to defend against an intruder -- free from legal responsibility/prosecution for the consequences of the force used.[1] Typically deadly force is considered justified, and a defense of justifiable homicide applicable, in cases "when the actor reasonably fears imminent peril of death or serious bodily harm to himself or another".[1] The doctrine is not a defined law that can be invoked, but a set of principles which is incorporated in some form in the law of most states.

The legal concept of the inviolability of the home has been known in Western Civilization since the age of the Roman Republic.[2] The term derives from the historic English common law dictum that "an Englishman's home is his castle." This concept was established as English law by 17th century jurist Sir Edward Coke, in his The Institutes of the Laws of England, 1628.[3] The dictum was carried by colonists to the New World, who later removed "English" from the phrase, making it "a man's home is his castle", which thereby became simply the Castle Doctrine.[3] The term has been used in England to imply a person's absolute right to exclude anyone from his home, although this has always had restrictions, and since the late twentieth century bailiffs have also had increasing powers of entry.[4]

Saturday, July 20, 2013

yeah, let's examine them joints...,

Visit NBCNews.com for breaking news, world news, and news about the economy

Along the same lines, I think it would be useful for us to examine some state and local laws to see if it -- if they are designed in such a way that they may encourage the kinds of altercations and confrontations and tragedies that we saw in the Florida case, rather than defuse potential altercations.

I know that there’s been commentary about the fact that the stand your ground laws in Florida were not used as a defense in the case.

On the other hand, if we’re sending a message as a society in our communities that someone who is armed potentially has the right to use those firearms even if there’s a way for them to exit from a situation, is that really going to be contributing to the kind of peace and security and order that we’d like to see?

And for those who resist that idea that we should think about something like these “stand your ground” laws, I just ask people to consider if Trayvon Martin was of age and armed, could he have stood his ground on that sidewalk? And do we actually think that he would have been justified in shooting Mr. Zimmerman, who had followed him in a car, because he felt threatened?

And if the answer to that question is at least ambiguous, it seems to me that we might want to examine those kinds of laws.

two-gun pete...,

chicagotribune | Two-Gun started as an anonymous bluecoat walking a beat, but he ended up as a ghetto superstar — a flamboyant, crooked, braggadocious, womanizing, hard-drinking, foul-mouthed police detective.

He was tasked with clearing out bad elements from every nightclub, flophouse and pool hall in what was then called Black Metropolis, a South Side community mired in poverty and violence, yet bouncing to a jazzy beat.

Washington spent most of his career working out of the old Wabash Avenue police station at 48th Street and Wabash Avenue. By the mid-1940s, his 5th District, with a population of 200,000, led the city in slayings, robberies and rapes, and was nicknamed the "Bucket of Blood." But the mention of Two-Gun Pete's name could clear a street corner in seconds.

"Everybody knew Sylvester Washington," said Rudy Nimocks, a former deputy police superintendent. "They knew his car. And the prostitutes would go hide someplace when they saw him. He was something else."
Facing criticism that police were failing to protect black residents, Chicago's top brass looked to Washington and other tough black cops to get ahold of crime. But the bosses may have made a pact with the devil, entrusting citizens' safety to a profoundly violent man.

"He was the meanest, cruelest person that I have ever seen in my entire life," said his third wife, Roslyn Washington Banks.

Pete augmented his fierce reputation with the tools of his trade: a nightstick and meaty hands that he used to slap grown men to the ground like small children.

And there were his sidearms — pearl-handled .357 Magnum revolvers. One had a long barrel, the other a short barrel. Each pistol was holstered in its own belt around his hips, both pearl handles pointing right for the right-handed gunslinger.

"I seldom miss the mark with them," Washington bragged to Ebony magazine. "I can put 14 bullseyes into a target out of 15 shots, and have made a marksmanship record of 147 out of a possible 150."  Fist tap BTx

the kind of peace, and security, and order I'd like to see

Friday, July 19, 2013

of course cancer is caused by bacteria..., told you so years ago

bytesizebio | Cancer and microbiology have been closely linked for over 100 years. Cancer patients are usually immunosuppressed due to chemotherapy, requiring special treatment and conditions to prevent bacterial infection. Bladder cancer is typically treated with inactivated tuberculosis bacteria to induce an inflammatory response which turns against remaining cancer cells, with remarkably effective results.  Also, viruses are known to cause cancer, including  papillomavirus (cervical cancer), Hepatitis B (liver cancer), and  HTLV (human T-lymphocyte virus, causing lymphoma). In 1982, the bacterium  Helicobacter pylori was discovered to be the main cause of gastric ulcers, and the first direct link between bacteria and cancer — stomach cancer — was established. The link between chronic ulcers and stomach cancer was already well known: what was not knows is that bacteria were the initial cause of stomach ulcers. Since then, several other suspects have been named, including links between Chlamydia and lung cancer, and  Salmonella and gallbladder cancer.
Inflammation changes the gut ecosystem 
There are two fields in which are not  generally thought of as being linked: microbial ecology and cancer research.  When we think of microbial ecology, we think of agricultural soil enrichment, marine ecology, air quality, nutrient recycling, species interaction,  diversity and all that jazz. Not of cancer though. But in the past five years we have amassed more genomic DNA data than we have in the 50 years preceding them, including data from cancer tissue and associated bacteria. These data are beginning to show us that that the links between microbial populations and cancer are more prevalent, complex and intimate than we thought. Bacteria, as microbiologists keep repeating ad nauseam, make up 90% of the cellular population of our bodies (the extra 10% are, well, us).  Following metagenomic sequencing, human microbial flora have been shown to affect conditions as varied as obesity, metabolic disease (including diabetes)  infant growth and colorectal cancer — all of which we have not associated with bacteria until recently. As a result the people who study bacteria, and the people who study cancer are working together more than ever before. Last year, a study in Science  led by a group from the University of North Carolina Chapel Hill, has shown a clear mechanistic link between microbial communities, inflammation, and colorectal cancer. In a nutshell, their study suggests that the following sequence of events takes place: 1) inflammation disturbs gut ecosystems; 2) this disturbance to conditions that allow pathogens to invade the gut; 3) the pathogens damage the host cells increasing the risk of the development of colorectal cancer. The study used mice that lacked the gene that makes Interleukin-10 (IL-10). IL-10 suppresses the inflammatory response, and IL10-deficient mice (IL10-/-) are genetically prone to gut inflammation.  The team compared bacterial communities in the inflamed guts of IL10-/- mice with those in healthy normal (“wild type”) mice. They found that the diversity of different kinds of bacteria was significantly lower in the IL10-/- mice. But the team found little difference in microbial diversity between mice that simply had inflammation and those that had inflammation and cancer, indicating that the inflammation was the critical factor affecting bacterial populations, reducing the diversity of bacteria in the colon. In fact, one major species to shoot up and dominate the inflamed gut was E. coli, another was Enterobacter faecalis. But IL10-/- mice that were inoculated with E. faecalis only rarely developed cancer, while 80% of the group with E. coli did. Specifically, E. coli strain NC101 was foind to be the culprit. The NC101 strain has a cluster of genes under the name of “pks island”. In 2010 a group from Toulouse found that pks island genes cause cellular replication and DNA damage in the host: the harbingers of cancer.  The UNC researchers colonized a mouse gut cell-line with E. coli that had the pks genes, and with E. coli lacking the pks genes. The inflammation remained, but the cells inoculated with E. coli without the pks developed fewer tumors. While mice take longer to develop tumors, the researchers saw 80% more DNA damaged cells in gut cells of IL10-/- mice inoculated with E. coli that had pks genes, versus those that were associated with E. coli without the pks genes.
Bacterial DNA in Cancer Cells
But the link between bacteria and cancer may run deeper than a changing microbial community. A recent study by a group at the University of Maryland School of Medicine shows that bacteria DNA gets transferred to human cells, in a process known as lateral gene transfer, or LGT.  LGT is known to occur quite commonly between bacteria, including bacteria of different species. In fact, that is how antibiotic resistance is transferred so quickly. But findings of bacterial LGT to humans are generally treated as possible experimental artifacts, rather than true events. The UMSM team scanned data from from the 1,000 Genomes Project and found more than 7,000 instances of LGT from bacteria to human cells. When they analyzed sequences from the Cancer Genome Atlas, they discovered 691,000 more cases  of LGT, and an overwhelming majority of LGT findings came from tumor samples, not from healthy cells. They found that DNA from Acinetobacter , was integrated into the genome of acute myeloid leukemia cells, especially in the mitochondrial genome. Acinetobacter is a soil bacterium but some species are known to be oppotunitic pathogens. For unknown reasons, this bacterium’s DNA was found more frequently in the genome of myeloid leukemia cells. Fist tap Dale.

isn't smegma believed to cause cervical cancer?

thescientist | In what appears to be a novel form of bacterial gene transfer, or conjugation, the microbe Mycobacterium smegmatis can share multiple segments of DNA at once to fellow members of its species, according to a study published today (July 9) in PLOS Biology. The result: the generation of genetic diversity at a pace once believed to be reserved for sexual organisms.

“It is a very nice study providing clear evidence that, in Mycobacterium smegmatis at least, conjugation underlies much of species diversity,” said Richard Meyer, who studies conjugation at The University of Texas at Austin, in an email to The Scientist.

Traditionally, transfer of genetic material through conjugation has been considered an incremental process. Plasmids mediate the transfer of short segments of DNA, one at a time, between pairs of touching bacterial cells, often conferring such traits as antibiotic resistance.

But M. smegmatis, a harmless bacterium related to the pathogen M. tuberculosis, appears to use a more extensive method of gene shuffling, endowing each recipient cell with a different combination of new genes. The researchers dubbed this form of conjugation “distributive conjugal transfer.” “We can generate a million [hybrid bacteria] overnight, and each of those million will be different than each other,” said coauthor Todd Gray, a geneticist at the New York State Department of Health’s Wadsworth Center.

Coauthor Keith Derbyshire, also a geneticist at the Wadsworth Center, and colleagues had previously published data indicating that M. smegmatis used a novel form of conjugation, but the new study confirms and expands on their suspicions using genetic data. The researchers compared the whole genome sequences of donor and recipient bacteria before and after the massive gene transfers.

The researchers found that, after the transfers, up to a quarter of the recipient bacteria’s genomes were made up of donated DNA, scattered through the chromosomes in segments of varying lengths.

According to the authors, the diversity resulting from distributive conjugal transfer approaches that achieved by meiosis, the process of cell division that underlies sexual reproduction. “The progeny were like meiotic blends,” said Derbyshire. “The genomes are totally mosaic.”

the doe has a "joint genome institute" exploring uncharted reaches of the microcosmos...,

thescientist | The tree of life is dominated by microbes, but many large branches remain uncharted because scientists have been historically restricted to studying the small fraction of species that will grow in a lab. An international team of scientists has now begun to redress this bias, sequencing full genomes from single cells to bring the “uncultured majority” into view.

In total, the team identified more than 200 new microbial species belonging to 29 underrepresented or unknown lineages. And the results, published today (July 14) in Nature, were full of new metabolic abilities and genetic surprises.

“[There has been a] strong imperative to fill in the microbial tree of life,” said Philip Hugenholtz from the University of Queensland, one of the study’s leaders. “If you have an incomplete view of evolution—vastly incomplete in the case of microorganisms—you have a vastly incomplete understanding of biology.”

By sequencing DNA directly from environmental samples, geneticists have suggested that the two microbial domains of life—bacteria and archaea—include at least 60 major lineages (phyla), but just four of these account for more than 88 percent of cultivated microbes. Of the others, around half are “candidate phyla,” whose members have never been grown in lab cultures.

To fill these gaps, the team collected samples from nine diverse habitats, including industrial reactors, hot springs, and a gold mine. The researchers gravitated towards places that were low in oxygen since these tend to harbor a greater and more interesting spread of microbes than familiar sites like our bodies. 

From these samples, Tanja Woyke from the Department of Energy’s Joint Genome Institute in California isolated 9,600 individual cells and amplified the genomes of around a third of these. If any of these genomes looked like they came from new lineages, the team sequenced them completely.

They ended up with 201 full genomes representing 21 bacterial lineages and 8 archaeal ones. Some of these were candidate phyla known only by abstract codes, but the team has now given them descriptive names based on the biology of their members. For example, EM19 is now Calescamantes (“heat lovers”) because they hail from an extremely hot environment, and OD1 is now Parcubacteria (“thrifty bacteria”) for its streamlined metabolism. 

pandoraviruses hint at fourth domain of life...,

fauxnews | The discovery of two new jumbo-sized viruses is blurring the lines between viral and cellular life and could point to the existence of a new type of life, scientists suggest. 

The two large viruses, detailed in this week's issue of the journal Science, have been dubbed "Pandoraviruses" because of the surprises they may hold for biologists, in reference to the mythical Greek figure who opened a box and released evil into the world.

The discovery of Pandoraviruses is an indication that our knowledge of Earth's microbial biodiversity is still incomplete, explained study coauthor Jean-Michel Claverie, a virologist at the French National Research Agency at Aix-Marseille University.

"Huge discoveries remain to be made at the most fundamental level that may change our present conception about the origin of life and its evolution," Claverie said.

Eugene Koonin, a computational evolutionary biologist at the National Center for Biotechnology Information in Bethesda, Md., who was not involved in the study, called the Pandoraviruses a "wonderful discovery," but not a complete surprise.

"In a certain sense, it's something that we saw coming, and it's wonderful that it has come," Koonin said.

Thursday, July 18, 2013

the human eusocial prime directive - cybernetic civilization

paulchefurka | Humanity appears to be in the grip of a global system - one that we originally created, but which is now shaping our lives independently of our wishes.

I've recently begun to suspect that humanity is at a point of endosymbiosis with our electronic communications and control technology, especially through the Internet. In a sense, we humans have incorporated ourselves as essential control elements of a planet-wide cybernetic super-organism. The precedent for something like this is the way that mitochondria migrated as bacteria into ancient prokaryotic cells to become essential components of the new eukaryotic cells that make up all modern organisms, including us.

To expand on the "super-organism" concept a bit, it looks to me as though what humanity has done over the last few centuries is built ourselves a global cybernetic exoskeleton. Although its development started back with the emergence of language and the taming of fire, it's most visible in the modern world, and especially in the last two decades.

Transportation systems act as its gut and bloodstream, carrying raw materials (the food of civilization) to the digestive organs of factories, and carrying the finished goods (the nutrients) to wherever they are needed. Engines and motors of all kinds are its muscles. The global electronic communication network is its nervous system. Electronic sensors of a million kinds are its organs of taste, touch, smell and sight. Legal systems, police and military make up its immune system.

Human beings have evolved culturally to the point where we now act largely as hyper-functional decision-making neurons within this super-organism, with endpoint devices like smart phones, PCs and their descendants acting as synapses, and network connections being analogous to nerve fibers.

Just as neurons cannot live outside the body, we have evolved a system that doesn't permit humans to live outside its boundaries. Not only is there very little "outside" left, but access to the necessities of life is now only possible though the auspices of the cybernetic system itself. (For example, consider living without a socially-approved job. It's barely possible for a few people, but essentially impossible for most of us.) As we have developed this system around us, we have had to relinquish more and more of our autonomy in favor of helping the machine continue functioning and growing.

While we can no longer survive outside our cybernetic exoskeleton, in return it can't exist without our input. I realized over the last month or so that this means the symbiosis has already occurred. If I had to put a "closure date" on it, the period where it transitioned to its current form was around 1990 (plus or minus a decade or so). We didn't even notice it happening - to us it just looked like our daily lives going on as usual.

I realize that I'm re-visiting an old, familiar science-fiction idea. In reality it seems to have happened through a quiet, "natural" process of coevolution driven by the mutual amplification effects of human ingenuity, electronic technology and large amounts of available energy - rather than through the drama of a Borg-like assimilation of humans into a hive mind, or Ray Kurzweil's eschatological vision of a Technological Singularity.

vatican inc.

tdf | Pope Benedict’s resignation shocked the Catholic Church and left the Vatican in disarray. His successor will face many challenges, from recurrent sexual scandals to concerns about financial impropriety at the Vatican’s own bank, the IOR or Institute of Religious Works.

In 2011, Al Jazeera investigated allegations that the IOR had been involved in money laundering and examined Pope Benedict’s plans for cleaning up the secretive system. With many of those reforms having fallen short and the Vatican’s finances still under a cloud, the next Pope might benefit from watching this report once again.

Every Sunday worshipers crowd the Saint Peter’s colonnades in square and from its balcony the Pope imparts a sacrament and the latest behavioral guidelines. Over one billion Catholics look to the pontiff for guidance and donate their money to the Catholic Church. A large portion of this money makes its way to the Vatican and into the vaults of the IOR, the Institute for Religious Works, the Vatican’s Bank.

The IOR is the vehicle through which thousands of charitable and religious initiatives around the globe are financed. In the recent past, Italian state prosecutors placed the bank under investigation for suspected money laundering. Twenty three million Euros in Vatican funds were seized representing only a fraction of suspect transactions now being scrutinized. IOR president, Ettore Gotti Tedeschi, was also placed under investigation and a huge financial scandal now threatens to envelop the church. For many Catholics, it has the disturbing echoes of another scandal of 30 years ago, the infamous “Banco Ambrosiano affair” and some now fear that history may be repeating itself.

President Ettore Gotti Tedeschi was questioned in order to clarify the situation, but after the questioning the prosecution thought that they had not received satisfactory answers. It is surprising that even the president of the IOR could not find a way to clarify the circumstances.

The Institute for Religious Works is located behind the walls of the Vatican City state and inside the massive tower build by Niccolo V. The bank was founded in 1942 by Pope Pius XII with the purpose of safe keeping the Vatican’s vast assets in capital and real estate. The IOR doesn’t allow everyone to open accounts. There are specific regulations allowing only religious organizations or members of clergy to do so.
The IOR is administered by industry professionals under the supervision of the Council of Cardinals, but because the IOR has only one central branch inside the Vatican, it has to use other banks outside the city state to move its funds around. However, the names of its accounts holders are kept secret and transactions bare no other identification than that of the IOR. This means the origins of any deposit coming into an IOR account are wiped from the record before the funds are moved out to the international banking system and that, say critics, makes money laundering all too easy.

Generally, the profits that the IOR makes during a year’s worth of financial operations and from the deposits made, are given to the Pope for charitable works that are carried out worldwide. The amount corresponds roughly to 70 or 80 million Euros every year.

Inevitably, this huge flow of cash, much of it untraceable, has attracted the attention of investigators. The latest probe began in the hills around Rome in late 2008 when Father Evaldo Biasini, treasurer of the Congregation of the Missionaries of the precious blood, answered his mobile phone.